From cf5d4174a76f32b164133a5158a47de18279b2be Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Sat, 30 Jul 2016 11:17:40 -0400 Subject: [PATCH 01/76] To help with debugging --- assets/js/jquery.min.map | 1 + 1 file changed, 1 insertion(+) create mode 100644 assets/js/jquery.min.map diff --git a/assets/js/jquery.min.map b/assets/js/jquery.min.map new file mode 100644 index 000000000..01f1f980d --- /dev/null +++ b/assets/js/jquery.min.map @@ -0,0 +1 @@ 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\ No newline at end of file From 6acf0b8d5cb93ea99abf1d7f82bac2f1296d5971 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?F=C3=A9lix-Antoine=20Fortin?= Date: Fri, 30 Sep 2016 17:11:28 -0400 Subject: [PATCH 02/76] Add missing tild before code of increment_me --- reference.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/reference.md b/reference.md index 63580acb5..20f1de2e0 100644 --- a/reference.md +++ b/reference.md @@ -84,7 +84,7 @@ In R, the last executed line of a function is automatically returned - Specifying a default value for a function argument -~~ +~~~ increment_me <- function(value_to_increment, value_to_increment_by = 1){ value_to_increment + value_to_increment_by } From f48c10c8dd5a82b5c680414cfd2b548aed08d2cc Mon Sep 17 00:00:00 2001 From: Marco Chiapello Date: Mon, 3 Oct 2016 10:22:49 +0100 Subject: [PATCH 03/76] Added SUMMARY function --- .swp | Bin 0 -> 12288 bytes _episodes_rmd/01-starting-with-data.Rmd | 10 ++++++++++ 2 files changed, 10 insertions(+) create mode 100644 .swp diff --git a/.swp b/.swp new file mode 100644 index 0000000000000000000000000000000000000000..1d20d4a5c74af9b9fd2d8ce044eb917560f3ea7d GIT binary patch literal 12288 zcmeI&y>8S%5C`xL6=?t^FEF_@L?l+eB;XzZiGl`{G$_)I?Y-P8yX#{=P82NoQL!tyD)Pl0H{%inAaG9t>nBHt2m9?}+oLVo+&H69gat0SG_<0uX=z1Rwwb2tWV= zk5GW+J%95|slO8K`~Ttj|K_<;*AiC}e##5SUsyQ)D13SIj9Z$2bl4(4RVs`Qk`*K7T+bUc6 zBt4G16lc6~+0%k;9_}(BCi;>&BxCz?PS=M0s;bk&zce$UzRe`|^{OU+9qOH%h4wVl zc0SFPYMt2FNL)5Kb*Yiv+)CpnreMn4Hd`n)nM_pQ@k`m$=iP(x@!5{rrcd2A%r{NL q*4o_f;fGQmiEV6X#!~+Fs;t3@R;7%N6k9d6!seW?3>dQNSp5UK+n0I( literal 0 HcmV?d00001 diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index 97611564a..16b3dccbf 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -327,6 +327,16 @@ median(dat[, 7]) sd(dat[, 7]) ``` +R also has a function that summaries the previous common calculations: + +```{r} +# Summarize function +summary(dat[,1:4]) +``` + +For every column in the data frame, the function "summary" calculates: the minimun value, the first quartile, the median, the mean, the third quartile and the max value, given helpful details about the sample distribution. + + What if we need the maximum inflammation for all patients, or the average for each day? As the diagram below shows, we want to perform the operation across a margin of the data frame: From 94ab5879fdfe58a3818f363542b696e23a20e968 Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Wed, 5 Oct 2016 15:09:16 -0400 Subject: [PATCH 04/76] Adding link to training survey to config --- bin/lesson_initialize.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index a3c478d5a..e0c2881bf 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -211,6 +211,7 @@ # Surveys. pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id=" post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id=" +training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training" # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am). start_time: 0 From 0a8b55cd9705b69d597bd468e9a8efd42c2b99dc Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Fri, 7 Oct 2016 10:38:42 -0400 Subject: [PATCH 05/76] Starting to incorporate Library Carpentry materials --- _includes/lesson_footer.html | 9 ++++- _includes/navbar.html | 8 ++++ _layouts/base.html | 5 ++- _layouts/workshop.html | 5 ++- assets/img/lc-icon-black.svg | 76 +++++++++++++++++++++++++++++++++++ bin/lesson_initialize.py | 2 +- favicon-lc.ico | Bin 0 -> 1267 bytes 7 files changed, 98 insertions(+), 7 deletions(-) create mode 100644 assets/img/lc-icon-black.svg create mode 100644 favicon-lc.ico diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index beef2cb38..e143daa64 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -3,8 +3,13 @@

Copyright © 2016 - {% if site.carpentry == "swc" %}Software Carpentry Foundation{% endif %} - {% if site.carpentry == "dc" %}Data Carpentry{% endif %} + {% if site.carpentry == "swc" %} + Software Carpentry Foundation + {% elsif site.carpentry == "dc" %} + Data Carpentry + {% elsif site.carpentry == "lc" %} + Library Carpentry + {% endif %}

diff --git a/_includes/navbar.html b/_includes/navbar.html index b0a2c3d83..8d4f1dd29 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -17,6 +17,10 @@ + {% elsif page.carpentry == "lc" %} + + + {% elsif site.carpentry == "swc" %} @@ -25,6 +29,10 @@ + {% elsif site.carpentry == "lc" %} + + + {% endif %} {% comment %} Always show link to home page. {% endcomment %} diff --git a/_layouts/base.html b/_layouts/base.html index 06f316df8..365d2e50f 100644 --- a/_layouts/base.html +++ b/_layouts/base.html @@ -14,9 +14,10 @@ {% if site.carpentry == "swc" %} - {% endif %} - {% if site.carpentry == "dc" %} + {% elsif site.carpentry == "dc" %} + {% elsif site.carpentry == "lc" %} + {% endif %} diff --git a/_layouts/workshop.html b/_layouts/workshop.html index f29e3ce11..2f4cd3040 100644 --- a/_layouts/workshop.html +++ b/_layouts/workshop.html @@ -30,9 +30,10 @@ {% if site.carpentry == "swc" %} - {% endif %} - {% if site.carpentry == "dc" %} + {% elsif site.carpentry == "dc" %} + {% elsif site.carpentry == "lc" %} + {% endif %} diff --git a/assets/img/lc-icon-black.svg b/assets/img/lc-icon-black.svg new file mode 100644 index 000000000..df711892a --- /dev/null +++ b/assets/img/lc-icon-black.svg @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index a3c478d5a..28b2f9075 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -175,7 +175,7 @@ # Values for this lesson. #------------------------------------------------------------ -# Which carpentry is this ("swc" or "dc")? +# Which carpentry is this ("swc", "dc", or "lc")? carpentry: "swc" # Overall title for pages. diff --git a/favicon-lc.ico b/favicon-lc.ico new file mode 100644 index 0000000000000000000000000000000000000000..f4f3c9356479843b967e8cd910a69aa3f81d7dd4 GIT binary patch literal 1267 zcmV4Tx062|}Ro!pfR1`mnZ(O7nKcKOW4i$^9Ra0BJ8yc;~21%2p=|UR0&DbiW z$#rfTQ`a`O(`{9s_5yDV_yd5l2Of}kLK+Oj_Ok5(v`JGz71bo9J#^YYXp{DWs&KBa zQ@dTpxRI}aIp=pi@6k0t$5)!;m`NF6-tt{FpOKHBn3g+MAqmexC-gw4rh87hTrL7G z#)U`L!(So6-Zux@>;H3gR;i~0B%VTSS3P|m@o9jRsXML@Al^p#@G0Lx-0?i(9WEw_ zSYddU<1E8793KxjQ|c&UmW!mTC>k>?{om1c9S zUx<6_jj_!T&^M{wWM#>IBbOSf*xP<^F{$j$aOQ5Y{cT zROCL1M7^NKKL z&(yA}mSw#iM0^;IB{ZO5!wl{^Sg-*ysE~&Yz8!E;Qv(A`lu*=Clo*MpVGd>OdF6n^ zam1Jntk;<}MrqIC5$=Q>n{*R}?8oOIDUw5En2dl--Xw34!z7E+5pr-OgyQ-soSab)C%saskMla`aQLVzg0+MZf20tJU&K{hZoBrUc+U4e9&3o zw|KmGEe4#xz17wBu{f`SS_4i66?j31EjY7n{zGfhONK~c+td!TS#B}JoR}5UAd7p& z5phTyXSkK0xCeD3xaYP^o&J~#Xp9xFb0C;HHml5fA<%h1eR|qw7wxF+oNL9T1Aits?sKNIwvGaN)^WO$I^cUV)HzL_| z1K?{9p!>B*)`xfEv!4N6IG{J&h49W#Bz^(#YWw%`e_a{8n{G9m5AeR~_yl0%<7V@p z`G6fhgftGDBAkmlt446R6 zHW-j-OaTT=pk*5jNHnGZ118Y24F)6{Q-A>zXxRn>5{)UqfC;p0g8_-g6qGkGJnpW5 zTX_hM)ZKY3E^mMhM2<%091LXAjnu|Kgi_`l3}n)c)W$%BQs$iDF0^wW$z0&9Hb-bi dC_682-~s1j4POiE#p(b6002ovPDHLkV1l;(W0?Q| literal 0 HcmV?d00001 From 7afa83e12388994ad5df501b83fe0098baa32717 Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Fri, 7 Oct 2016 10:58:59 -0400 Subject: [PATCH 06/76] Fixing typo in license file --- LICENSE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE.md b/LICENSE.md index 566ce5533..179758a7e 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -73,7 +73,7 @@ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ## Trademark -"Software Carpentry" an "Data Carpentry" and their respective logos +"Software Carpentry" and "Data Carpentry" and their respective logos are registered trademarks of [NumFOCUS][numfocus]. [cc-by-human]: https://creativecommons.org/licenses/by/4.0/ From 9fde967cab751535a1d3df6708fa3a5a82c82dee Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Fri, 7 Oct 2016 12:46:44 -0400 Subject: [PATCH 07/76] Contact address --- _includes/lesson_footer.html | 2 +- bin/lesson_initialize.py | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index e143daa64..0424e3309 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -18,7 +18,7 @@

/ Contributing / - Contact + Contact

diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index 28b2f9075..247b425fe 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -181,8 +181,10 @@ # Overall title for pages. title: "Lesson Title" -# Contact email address. -email: lessons@software-carpentry.org +# Contact. This *must* include the protocol: if it's an email +# address, it must look like "mailto:lessons@software-carpentry.org", +# or if it's a URL, "https://gitter.im/username/ProjectName". +contact: mailto:lessons@software-carpentry.org #------------------------------------------------------------ # Generic settings (should not need to change). From 177d441cf2243b247c5011514e1db8645be2ef2e Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Fri, 7 Oct 2016 13:20:16 -0400 Subject: [PATCH 08/76] Adding link to citation --- _includes/lesson_footer.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 0424e3309..d5c9ad9f4 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -18,6 +18,8 @@

/ Contributing / + Cite + / Contact

From 3293c26b485440c28a47ec10d2723d3f6af3ab0b Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Fri, 7 Oct 2016 13:23:18 -0400 Subject: [PATCH 09/76] Tidying up references to LC --- _includes/lesson_footer.html | 4 ++-- _includes/navbar.html | 4 ++-- bin/lesson_initialize.py | 3 ++- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index d5c9ad9f4..a37ba3ece 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -8,7 +8,7 @@

{% elsif site.carpentry == "dc" %} Data Carpentry {% elsif site.carpentry == "lc" %} - Library Carpentry + Library Carpentry {% endif %}

@@ -20,7 +20,7 @@

/ Cite / - Contact + Contact

diff --git a/_includes/navbar.html b/_includes/navbar.html index 8d4f1dd29..6a4df8a7c 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -18,7 +18,7 @@ {% elsif page.carpentry == "lc" %} - + {% elsif site.carpentry == "swc" %} @@ -30,7 +30,7 @@ {% elsif site.carpentry == "lc" %} - + {% endif %} diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index 247b425fe..71f508e3f 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -184,7 +184,7 @@ # Contact. This *must* include the protocol: if it's an email # address, it must look like "mailto:lessons@software-carpentry.org", # or if it's a URL, "https://gitter.im/username/ProjectName". -contact: mailto:lessons@software-carpentry.org +contact: "mailto:lessons@software-carpentry.org" #------------------------------------------------------------ # Generic settings (should not need to change). @@ -203,6 +203,7 @@ swc_github: "https://github.com/swcarpentry" swc_site: "https://software-carpentry.org" swc_pages: "https://swcarpentry.github.io" +lc_site: "http://datacarpentry.org" template_repo: "https://github.com/swcarpentry/styles" example_repo: "https://github.com/swcarpentry/lesson-example" example_site: "https://swcarpentry.github.com/lesson-example" From 2acc4f2234948d41ad6ea8513018f4745379bec1 Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Sat, 8 Oct 2016 15:38:11 -0400 Subject: [PATCH 10/76] Updating lesson checker to include Library Carpentry values --- bin/lesson_check.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/lesson_check.py b/bin/lesson_check.py index 311687e92..a594f2f47 100755 --- a/bin/lesson_check.py +++ b/bin/lesson_check.py @@ -151,9 +151,9 @@ def check_config(reporter, source_dir): config_file = os.path.join(source_dir, '_config.yml') config = load_yaml(config_file) reporter.check_field(config_file, 'configuration', config, 'kind', 'lesson') - reporter.check_field(config_file, 'configuration', config, 'carpentry', ('swc', 'dc')) + reporter.check_field(config_file, 'configuration', config, 'carpentry', ('swc', 'dc', 'lc')) reporter.check_field(config_file, 'configuration', config, 'title') - reporter.check_field(config_file, 'configuration', config, 'email') + reporter.check_field(config_file, 'configuration', config, 'contact') reporter.check({'values': {'root': '..'}} in config.get('defaults', []), 'configuration', From 4b90bb3858df92704b653ae852cd9559da0fc2ec Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Tue, 18 Oct 2016 16:44:48 +0100 Subject: [PATCH 11/76] Add link to setup from schedule --- _includes/syllabus.html | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/_includes/syllabus.html b/_includes/syllabus.html index bd520ed16..dfa7d51ec 100644 --- a/_includes/syllabus.html +++ b/_includes/syllabus.html @@ -13,6 +13,11 @@

Schedule

{% assign current = site.start_time %} + + + + + {% for episode in site.episodes %} {% if episode.start %} {% comment %} Starting a new day? {% endcomment %} {% assign day = day | plus: 1 %} From 11479078b9b84c85e532bb142a8bb288e03480cc Mon Sep 17 00:00:00 2001 From: Dean Attali Date: Fri, 28 Oct 2016 20:56:39 -0400 Subject: [PATCH 12/76] better whitespace in lesson: add space between comment character and comment --- _episodes_rmd/06-best-practices-R.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_episodes_rmd/06-best-practices-R.Rmd b/_episodes_rmd/06-best-practices-R.Rmd index dc7acbfd6..dd2781c95 100644 --- a/_episodes_rmd/06-best-practices-R.Rmd +++ b/_episodes_rmd/06-best-practices-R.Rmd @@ -32,8 +32,8 @@ source("../bin/chunk-options.R") 1. Start your code with an annotated description of what the code does when it is run: ```{r} -#This is code to replicate the analyses and figures from my 2014 Science paper. -#Code developed by Sarah Supp, Tracy Teal, and Jon Borelli +# This is code to replicate the analyses and figures from my 2014 Science paper. +# Code developed by Sarah Supp, Tracy Teal, and Jon Borelli ``` 2. Next, load all of the packages that will be necessary to run your code (using `library`): From 5c3dd3248f933c5606937cebf48a3e98e002a6a2 Mon Sep 17 00:00:00 2001 From: Dean Attali Date: Fri, 28 Oct 2016 20:57:13 -0400 Subject: [PATCH 13/76] better whitespace in lesson: add space between comment character and comment --- _episodes/06-best-practices-R.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_episodes/06-best-practices-R.md b/_episodes/06-best-practices-R.md index 1d4827369..96c2f36e3 100644 --- a/_episodes/06-best-practices-R.md +++ b/_episodes/06-best-practices-R.md @@ -31,8 +31,8 @@ keypoints: ~~~ -#This is code to replicate the analyses and figures from my 2014 Science paper. -#Code developed by Sarah Supp, Tracy Teal, and Jon Borelli +# This is code to replicate the analyses and figures from my 2014 Science paper. +# Code developed by Sarah Supp, Tracy Teal, and Jon Borelli ~~~ {: .r} From 70e79697c98bd8ea131c3021a79cb190aba7887c Mon Sep 17 00:00:00 2001 From: Ben Bolker Date: Thu, 3 Nov 2016 16:26:52 -0400 Subject: [PATCH 14/76] various tweaks to best practices episode --- _episodes_rmd/06-best-practices-R.Rmd | 34 ++++++++++++++------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/_episodes_rmd/06-best-practices-R.Rmd b/_episodes_rmd/06-best-practices-R.Rmd index dc7acbfd6..c6b91e7b9 100644 --- a/_episodes_rmd/06-best-practices-R.Rmd +++ b/_episodes_rmd/06-best-practices-R.Rmd @@ -7,7 +7,7 @@ questions: objectives: - "Define best formatting practices when writing code in R scripts." - "Synthesize a consistent personal coding style to increase code readability, consistency, and repeatability." -- "Apply this style to one's own code." +- "Apply this style to your own code." keypoints: - "Start each program with a description of what it does." - "Then load all required packages." @@ -25,33 +25,35 @@ keypoints: - "Use version control." --- -```{r, include = FALSE} +```{r source, include = FALSE} source("../bin/chunk-options.R") ``` -1. Start your code with an annotated description of what the code does when it is run: +1. Start your code with an annotated description of what the code does: -```{r} +```{r comment1} #This is code to replicate the analyses and figures from my 2014 Science paper. #Code developed by Sarah Supp, Tracy Teal, and Jon Borelli ``` -2. Next, load all of the packages that will be necessary to run your code (using `library`): +2. Next, load all of the packages needed to run your code (using `library()`): -```{r, eval=FALSE} +```{r loadpkgs, eval=FALSE} library(ggplot2) library(reshape) library(vegan) ``` +If you use only one or two functions from a package, it is sometimes useful to note that fact in a comment, e.g. `library(reshape2) ## for melt()` + 3. Set your working directory before `source()`ing a script, or start `R` inside your project folder: -One should exercise caution when using `setwd()`. Changing directories in a script file can limit reproducibility: +Exercise caution when using `setwd()`. Changing directories in a script file can limit reproducibility: -* `setwd()` will return an error if the directory to which you're trying to change doesn't exit or if the user doesn't have the correct permissions to access that directory. This becomes a problem when sharing scripts between users who have organized their directories differently. -* If/when your script terminates with an error, you might leave the user in a different directory than the one they started in, and if they then call the script again, this will cause further problems. If you must use `setwd()`, it is best to put it at the top of the script to avoid these problems. +* `setwd()` will return an error if the directory you're trying to change to doesn't exist or if the user doesn't have the correct permissions to access that directory. This becomes a problem when sharing scripts between users who have organized their directories differently. +* If/when your script terminates with an error, you might leave the user in a different directory than the one they started in, which will cause further problems if they then call the script again. If you must use `setwd()`, it is best to put it at the top of the script to avoid these problems. Putting a commented-out `setwd()` call at the top of your code can be a reasonable compromise: it reminds you where on your machine your material is living, is easy to copy-and-paste if necessary, but doesn't commit other users. -The following error message indicates that R has failed to set the working directory you specified: +This error message indicates that R has failed to set the working directory you specified: ``` Error in setwd("~/path/to/working/directory") : cannot change working directory @@ -61,13 +63,13 @@ It is best practice to have the user running the script begin in a consistent di 4. Annotate and mark your code using `#` or `#-` to set off sections of your code and to make finding specific parts of your code easier. -5. If you create only one or a few custom functions in your script, put them toward the top of your code so they are among the first objects created. If you have written many functions, put them all in their own .R file and then `source` those files. `source` will define all of these functions so that your code can make use of them as needed. For the reasons listed above, try to avoid using `setwd()` (or other functions that have side-effects in the user's workspace) in scripts you `source`. +5. If you create only a few custom functions in your script, put them toward the top of your code so they are among the first objects created. If you have written many functions, put them all in their own .R file and then `source()` those files. `source()` will define all of these functions so that your code can use them as needed. For the reasons listed above, avoid using `setwd()` (or other functions that have side-effects in the user's workspace) in scripts you `source()`. ```{r, eval=FALSE} source("my_genius_fxns.R") ``` -6. Use a consistent style within your code. For example, name all matrices something ending in `.mat`. Consistency makes code easier to read and problems easier to spot. +6. Use a consistent style within your code. For example, name all matrices something ending in `.mat`. Indent consistently and decide on a scheme for multi-word variable names (e.g. `resource.use`, `resource_use`, or `resourceUse`). Consistency makes code easier to read and problems easier to spot. 7. Keep your code in bite-sized chunks. If a single function or loop gets too long, consider looking for ways to break it into smaller pieces. @@ -85,20 +87,20 @@ rather than: dat <- read.csv(file = "/Users/Karthik/Documents/sannic-project/files/dataset-2013-01.csv", header = TRUE) ``` -10. R can run into memory issues. It is a common problem to run out of memory after running R scripts for a long time. To inspect the objects in your current R environment, you can list the objects, search current packages, and remove objects that are currently not in use. A good practice when running long lines of computationally intensive code is to remove temporary objects after they have served their purpose. However, sometimes, R will not clean up unused memory for a while after you delete objects. You can force R to tidy up its memory by using `gc()`. +10. R can run into memory issues. R scripts that run for a long time often run out of memory. To inspect the objects in your current R environment, you can list the objects, search current packages, and remove objects that are currently not in use. A good practice when running long chunks of computationally intensive code is to remove temporary objects after they have served their purpose. However, R will not always clean up unused memory immediately after you delete objects. You can force R to tidy up its memory by using `gc()`. ```{r, eval=FALSE} interim_object <- data.frame(rep(1:100,10),rep(101:200,10),rep(201:300,10)) # Sample dataset of 1000 rows object.size(interim_object) # Reports the memory size allocated to the object -rm(interim_object) # Removes only the object itself and not necessarily the memory allotted to it +rm("interim_object") # Removes only the object itself and not necessarily the memory allotted to it gc() # Force R to release memory it is no longer using ls() # Lists all the objects in your current workspace rm(list = ls()) # If you want to delete all the objects in the workspace and start with a clean slate ``` -11. Don't save a session history (the default option in R, when it asks if you want an `RData` file). Instead, start in a clean environment so that older objects don't remain in your environment any longer than they need to. If that happens, it can lead to unexpected results. +11. Don't save your workspace (the default option in R, when it asks if you want to "Save workspace image [y/n/c]?"). Instead, start in a clean workspace without old objects cluttering it. Leftover objects from previous sessions can lead to unexpected, hard-to-debug results. Do *not* put `rm(list=ls())` (which removes all objects in your current workspace, as shown in the previous code example) at the top of your code, as this is a trap for other users who might `source()` or copy-and-paste your code in the course of their R session. Instead, restart R when you want to start fresh. -12. Wherever possible, keep track of `sessionInfo()` somewhere in your project folder. Session information is invaluable because it captures all of the packages used in the current project. If a newer version of a package changes the way a function behaves, you can always go back and reinstall the version that worked (Note: At least on CRAN, all older versions of packages are permanently archived). +12. Wherever possible, keep track of `sessionInfo()` somewhere in your project folder. Session information is invaluable because it captures all of the packages used in the current project. If a newer version of a package changes the way a function behaves, you can always go back and reinstall the version that worked (Note: At least on CRAN, all older versions of packages are permanently archived). For more complex projects, you may want to use the [packrat](https://CRAN.R-project.org/package=packrat) package. 13. Collaborate. Grab a buddy and practice "code review". Review is used for preparing experiments and manuscripts; why not use it for code as well? Our code is also a major scientific achievement and the product of lots of hard work! From 8febcb66e704beb7ee3d875a0d9fff0b26b0bf28 Mon Sep 17 00:00:00 2001 From: Ben Bolker Date: Thu, 3 Nov 2016 16:29:44 -0400 Subject: [PATCH 15/76] missed a few chunk names --- _episodes_rmd/06-best-practices-R.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/_episodes_rmd/06-best-practices-R.Rmd b/_episodes_rmd/06-best-practices-R.Rmd index c6b91e7b9..807c5e44a 100644 --- a/_episodes_rmd/06-best-practices-R.Rmd +++ b/_episodes_rmd/06-best-practices-R.Rmd @@ -65,7 +65,7 @@ It is best practice to have the user running the script begin in a consistent di 5. If you create only a few custom functions in your script, put them toward the top of your code so they are among the first objects created. If you have written many functions, put them all in their own .R file and then `source()` those files. `source()` will define all of these functions so that your code can use them as needed. For the reasons listed above, avoid using `setwd()` (or other functions that have side-effects in the user's workspace) in scripts you `source()`. -```{r, eval=FALSE} +```{r source_ex, eval=FALSE} source("my_genius_fxns.R") ``` @@ -77,19 +77,19 @@ source("my_genius_fxns.R") 9. Keep all of your source files for a project in the same directory, then use relative paths as necessary to access them. For example, use -```{r, eval=FALSE} +```{r relpath, eval=FALSE} dat <- read.csv(file = "files/dataset-2013-01.csv", header = TRUE) ``` rather than: -```{r, eval=FALSE} +```{r abspath, eval=FALSE} dat <- read.csv(file = "/Users/Karthik/Documents/sannic-project/files/dataset-2013-01.csv", header = TRUE) ``` 10. R can run into memory issues. R scripts that run for a long time often run out of memory. To inspect the objects in your current R environment, you can list the objects, search current packages, and remove objects that are currently not in use. A good practice when running long chunks of computationally intensive code is to remove temporary objects after they have served their purpose. However, R will not always clean up unused memory immediately after you delete objects. You can force R to tidy up its memory by using `gc()`. -```{r, eval=FALSE} +```{r gc_ex, eval=FALSE} interim_object <- data.frame(rep(1:100,10),rep(101:200,10),rep(201:300,10)) # Sample dataset of 1000 rows object.size(interim_object) # Reports the memory size allocated to the object rm("interim_object") # Removes only the object itself and not necessarily the memory allotted to it From cfac06108b2721eba780f582c696c2cc5bae03d7 Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Tue, 8 Nov 2016 17:23:11 -0500 Subject: [PATCH 16/76] Web site for Library Carpentry --- bin/lesson_initialize.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index bce8323c2..b26bf2877 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -203,7 +203,7 @@ swc_github: "https://github.com/swcarpentry" swc_site: "https://software-carpentry.org" swc_pages: "https://swcarpentry.github.io" -lc_site: "http://datacarpentry.org" +lc_site: "http://librarycarpentry.github.io/" template_repo: "https://github.com/swcarpentry/styles" example_repo: "https://github.com/swcarpentry/lesson-example" example_site: "https://swcarpentry.github.com/lesson-example" From 616b50aeaf17fe4ea78f0a6e89b5024b8b36e348 Mon Sep 17 00:00:00 2001 From: Kenan Direk Date: Wed, 23 Nov 2016 01:19:21 +0000 Subject: [PATCH 17/76] useful_df_functions_sapply In keeping with the learning objectives of exploring data types and structures, I have added a simple yet effective way of checking the class of each column of a data frame. --- _episodes_rmd/13-supp-data-structures.Rmd | 1 + 1 file changed, 1 insertion(+) diff --git a/_episodes_rmd/13-supp-data-structures.Rmd b/_episodes_rmd/13-supp-data-structures.Rmd index ab3112cc6..8a441e247 100644 --- a/_episodes_rmd/13-supp-data-structures.Rmd +++ b/_episodes_rmd/13-supp-data-structures.Rmd @@ -381,6 +381,7 @@ dat > * `ncol()` - number of columns > * `str()` - structure of each column > * `names()` - shows the `names` attribute for a data frame, which gives the column names. +> * `sapply(dataframe, class)` - shows the class of each column in the data frame {: .callout} See that it is actually a special list: From 1a4cd683f6cb959a58bfc9cd2befb7aa939e2054 Mon Sep 17 00:00:00 2001 From: Dmytro Perepolkin Date: Fri, 25 Nov 2016 01:30:05 +0100 Subject: [PATCH 18/76] make changes to matrix, list and data.frame section --- _episodes_rmd/13-supp-data-structures.Rmd | 96 ++++++++++++++++------- 1 file changed, 66 insertions(+), 30 deletions(-) diff --git a/_episodes_rmd/13-supp-data-structures.Rmd b/_episodes_rmd/13-supp-data-structures.Rmd index ab3112cc6..a1fb92d11 100644 --- a/_episodes_rmd/13-supp-data-structures.Rmd +++ b/_episodes_rmd/13-supp-data-structures.Rmd @@ -1,21 +1,21 @@ --- title: "Data Types and Structures" +keypoints: +- R's basic data types are character, numeric, integer, complex, and logical. +- R's basic data structures include the vector, list, matrix, data frame, and factors. +- Objects may have attributes, such as name, dimension, and class. +objectives: +- Expose learners to the different data types in R. +- Learn how to create vectors of different types. +- Be able to check the type of vector. +- Learn about missing data and other special values. +- Getting familiar with the different data structures (lists, matrices, data frames). +questions: +- What are the different data types in R? +- What are the different data structures in R? +- How do I access data within the various data structures? teaching: 45 exercises: 0 -questions: -- "What are the different data types in R?" -- "What are the different data structures in R?" -- "How do I access data within the various data structures?" -objectives: -- "Expose learners to the different data types in R." -- "Learn how to create vectors of different types." -- "Be able to check the type of vector." -- "Learn about missing data and other special values." -- "Getting familiar with the different data structures (lists, matrices, data frames)." -keypoints: -- "R's basic data types are character, numeric, integer, complex, and logical." -- "R's basic data structures include the vector, list, matrix, data frame, and factors." -- "Objects may have attributes, such as name, dimension, and class." --- ```{r, include = FALSE} @@ -297,6 +297,12 @@ mdat <- matrix(c(1,2,3, 11,12,13), nrow = 2, ncol = 3, byrow = TRUE) mdat ``` +Elements of a matrix can be referenced by specifying the index along each dimension (e.g. "row" and "column") in single square brackets. + +```{r} +mdat[2,3] +``` + ### List In R lists act as containers. Unlike atomic vectors, the contents of a list are @@ -316,8 +322,17 @@ x x <- vector("list", length = 5) ## empty list length(x) +``` + +The content of elements of a list can be retrieved by using double square brackets. + +```{r} x[[1]] +``` +Vectors can be coerced to lists as follows: + +```{r} x <- 1:10 x <- as.list(x) length(x) @@ -326,21 +341,25 @@ length(x) 1. What is the class of `x[1]`? 2. What about `x[[1]]`? + +Elements of a list can be named (i.e. lists can have the `names` atttibute) + ```{r} xlist <- list(a = "Karthik Ram", b = 1:10, data = head(iris)) xlist +names(xlist) ``` 1. What is the length of this object? What about its structure? -Lists can be extremely useful inside functions. You can “staple” together lots +Lists can be extremely useful inside functions. Because the functions in R are able to return only a single object, you can "staple" together lots of different kinds of results into a single object that a function can return. A list does not print to the console like a vector. Instead, each element of the list starts on a new line. Elements are indexed by double brackets. Single brackets will still return -a(nother) list. +a(nother) list. If the elements of a list are named, they can be referenced by the `$` notation (i.e. `xlist$data`). ### Data Frame @@ -348,7 +367,7 @@ a(nother) list. A data frame is a very important data type in R. It's pretty much the *de facto* data structure for most tabular data and what we use for statistics. -A data frame is a special type of list where every element of the list has same length. +A data frame is a *special type of list* where every element of the list has same length (i.e. data frame is a "rectangular" list). Data frames can have additional attributes such as `rownames()`, which can be useful for annotating data, like `subject_id` or `sample_id`. But most of the @@ -356,12 +375,11 @@ time they are not used. Some additional information on data frames: -* Usually created by `read.csv()` and `read.table()`. -* Can convert to matrix with `data.matrix()` (preferred) or `as.matrix()` -* Coercion will be forced and not always what you expect. -* Can also create with `data.frame()` function. +* Usually created by `read.csv()` and `read.table()`, i.e. when importing the data into R. +* Assuming all columns in a data frame are of same type, data frame can be converted to a matrix with data.matrix() (preferred) or as.matrix(). Otherwise type coercion will be enforced and the results may not always be what you expect. +* Can also create a new data frame with `data.frame()` function. * Find the number of rows and columns with `nrow(dat)` and `ncol(dat)`, respectively. -* Rownames are usually 1, 2, ..., n. +* Rownames are often automatically generated and look like 1, 2, ..., n. Consistency in numbering of rownames may not be honored when rows are reshuffled or subset. ### Creating Data Frames by Hand @@ -374,33 +392,51 @@ dat > ## Useful Data Frame Functions > -> * `head()` - shown first 6 rows -> * `tail()` - show last 6 rows -> * `dim()` - returns the dimensions +> * `head()` - shows first 6 rows +> * `tail()` - shows last 6 rows +> * `dim()` - returns the dimensions of data frame (i.e. number of rows and number of columns) > * `nrow()` - number of rows > * `ncol()` - number of columns -> * `str()` - structure of each column +> * `str()` - structure of data frame - name, type and preview of data in each column > * `names()` - shows the `names` attribute for a data frame, which gives the column names. {: .callout} See that it is actually a special list: ```{r} -is.list(iris) -class(iris) +is.list(dat) +class(dat) +``` + +Because data frames are rectangular, elements of data frame can be referenced by specifying the row and the column index in single square brackets (similar to matrix). + +```{r} +dat[1,3] ``` +As data frames are also lists, it is possible to refer to columns (which are elements of such list) using the list notation, i.e. either double square brackets or a `$`. + +```{r} +dat[["y"]] +dat$y +``` + +The following table summarizes the one-dimensional and two-dimensional data structures in R in relation to diversity of data types they can contain. + | Dimensions | Homogenous | Heterogeneous | | ------- | ---- | ---- | | 1-D | atomic vector | list | | 2-D | matrix | data frame | +> Lists can contain elements that are themselves muti-dimensional (e.g. a lists can contain data frames or another type of objects). Lists can also contain elements of any length, therefore list do not necessarily have to be "rectangular". However in order for the list to qualify as a data frame, the lenghth of each element has to be the same. +{: .callout} + > ## Column Types in Data Frames > -> Knowing that data frames are lists of lists, can columns be of different type? +> Knowing that data frames are lists, can columns be of different type? > -> What type of structure do you expect on the iris data frame? Hint: Use `str()`. +> What type of structure do you expect to see when you explore the structure of the `iris` data frame? Hint: Use `str()`. > > ~~~ > # The Sepal.Length, Sepal.Width, Petal.Length and Petal.Width columns are all From aca4f12f65bc843b5a1dbfe2dd32c04558724bcf Mon Sep 17 00:00:00 2001 From: Shawn T O'Neil Date: Thu, 1 Dec 2016 13:55:14 -0800 Subject: [PATCH 19/76] Add information about variable naming conventions. Doing this one as part of my Software Carpentry Checkout procedure. Newcomers to R are often confused by the variety of naming conventions they encounter, especially if they come from a language where . is semantically meaningful. A quick digression into best practices for naming can both instill good habits and clear up some of the confusion. --- _episodes_rmd/01-starting-with-data.Rmd | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index 97611564a..d2b0961ca 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -142,6 +142,15 @@ weight_kg <- 57.5 # weight in kilograms is now weight_kg ``` +> ## Variable Naming Conventions +> +> Historically, R programmers have used a variety of conventions for naming variables. The `.` character +> in R can be a valid part of a variable name; thus the above assignment could have easily been `weight.kg <- 57.5`. +> This is often confusing to R newcomers who have programmed in languages where `.` has a more significant meaning. +> Today, most R programmers 1) start variable names with lower case letters, 2) separate words in variable names with +> underscores, and 3) use only lowercase letters, underscores, and numbers in variable names. The book *R Packages* includes +> a [chapter](http://r-pkgs.had.co.nz/style.html) on this and other style considerations. +{: .callout} If we imagine the variable as a sticky note with a name written on it, assignment is like putting the sticky note on a particular value: From 43c4108df3e1c3100ecb6f999699b8da14fc8335 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Wed, 14 Dec 2016 11:08:17 -0600 Subject: [PATCH 20/76] lesson.scss: 2em left padding for lists Example of the problem: see "Ten Things You Need To Know" from http://swcarpentry.github.io/lesson-example/ For numbered lists that have more that 9 elements 1 em padding on the left is not sufficient. The result is that "1" in numbers "10" and above is printed on top of the border of encapsulating HTML block. 2 em padding solves this problem for lists with less that 100 elements. It should be safe to safe to assume that numbered lists in Carpentries' lessons should not have more than 99 items. --- assets/css/lesson.scss | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index 752d7c960..bcc010d0c 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -133,7 +133,7 @@ div.branding { ul, ol { - padding-left: 1em; + padding-left: 2em; } span.fold-unfold { From ad4c372d4f8d763c682b480cacd514d818baf965 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Wed, 14 Dec 2016 11:40:19 -0600 Subject: [PATCH 21/76] Visually separate inline code blocks Change text color, background color and padding around inline code blocks --- assets/css/lesson.scss | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index 752d7c960..e067c8bcb 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -100,9 +100,9 @@ $codeblock-padding: 5px !default; //---------------------------------------- code { - padding: 0 0; - color: inherit; - background-color: inherit; + padding: 2px 5px; + color: #3d90d9; + background-color: #e7e7e7; } img { From 8fb905e07bb97286dd1eaeb72c023268211ab6ed Mon Sep 17 00:00:00 2001 From: Ian Carroll Date: Fri, 30 Dec 2016 20:49:20 -0500 Subject: [PATCH 22/76] changes lesson-rmd target to lesson-md with new recipe --- Makefile | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/Makefile b/Makefile index 0f395a310..457de1ee8 100644 --- a/Makefile +++ b/Makefile @@ -9,6 +9,7 @@ DST=_site # Controls .PHONY : commands clean files +.NOTPARALLEL: all : commands ## commands : show all commands. @@ -16,11 +17,11 @@ commands : @grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g' ## serve : run a local server. -serve : lesson-rmd +serve : lesson-md ${JEKYLL} serve ## site : build files but do not run a server. -site : lesson-rmd +site : lesson-md ${JEKYLL} build # repo-check : check repository settings. @@ -53,7 +54,7 @@ workshop-check : ## ---------------------------------------- ## Commands specific to lesson websites. -.PHONY : lesson-check lesson-rmd lesson-files lesson-fixme +.PHONY : lesson-check lesson-md lesson-files lesson-fixme # RMarkdown files RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd) @@ -79,9 +80,12 @@ HTML_DST = \ $(patsubst _extras/%.md,${DST}/%/index.html,$(wildcard _extras/*.md)) \ ${DST}/license/index.html -## lesson-rmd : convert Rmarkdown files to markdown -lesson-rmd: $(RMD_SRC) - @bin/knit_lessons.sh $(RMD_SRC) +## lesson-md : convert Rmarkdown files to markdown +lesson-md : ${RMD_DST} + +# Use of .NOTPARALLEL makes rule execute only once +${RMD_DST} : ${RMD_SRC} + @bin/knit_lessons.sh ${RMD_SRC} ## lesson-check : validate lesson Markdown. lesson-check : From 61ad44fd0b72accb919ffb5dd8a29d2ed4297cb0 Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Mon, 9 Jan 2017 15:12:30 -0500 Subject: [PATCH 23/76] Using page.previous and page.next for links instead of loop --- _includes/episode_navbar.html | 25 +++++-------------------- 1 file changed, 5 insertions(+), 20 deletions(-) diff --git a/_includes/episode_navbar.html b/_includes/episode_navbar.html index a789d3d99..1f6e033dc 100644 --- a/_includes/episode_navbar.html +++ b/_includes/episode_navbar.html @@ -1,26 +1,11 @@ {% comment %} - Find previous and next episodes (if any). -{% endcomment %} -{% for episode in site.episodes %} - {% if episode.url == page.url %} - {% unless forloop.first %} - {% assign prev_episode = prev %} - {% endunless %} - {% unless forloop.last %} - {% assign next_episode = site.episodes[forloop.index] %} - {% endunless %} - {% endif %} - {% assign prev = episode %} -{% endfor %} - -{% comment %} - Display title and prev/next links. + Navigation bar for an episode. {% endcomment %}

- {% if prev_episode %} - previous episode + {% if page.previous.url %} + previous episode {% else %} lesson home {% endif %} @@ -34,8 +19,8 @@

{{ page.title }}

- {% if next_episode %} - next episode + {% if page.next.url %} + next episode {% else %} lesson home {% endif %} From b357f4e769a06ad73db205b57ebb2780f5ea08fe Mon Sep 17 00:00:00 2001 From: Greg Wilson Date: Mon, 9 Jan 2017 15:14:44 -0500 Subject: [PATCH 24/76] Adding comments on include files purposes --- _includes/carpentries.html | 5 +++-- _includes/episode_keypoints.html | 3 +++ _includes/javascript.html | 3 +++ _includes/lesson_footer.html | 3 +++ _includes/main_title.html | 3 +++ _includes/navbar.html | 3 +++ _includes/workshop_ad.html | 3 +++ _includes/workshop_footer.html | 3 +++ 8 files changed, 24 insertions(+), 2 deletions(-) diff --git a/_includes/carpentries.html b/_includes/carpentries.html index 69e2e1cc5..c42bfcf2f 100644 --- a/_includes/carpentries.html +++ b/_includes/carpentries.html @@ -1,3 +1,6 @@ +{% comment %} + General description of Software and Data Carpentry. +{% endcomment %}
Software Carpentry logo @@ -23,5 +26,3 @@ building on learners' existing knowledge to enable them to quickly apply skills learned to their own research.
- - diff --git a/_includes/episode_keypoints.html b/_includes/episode_keypoints.html index 85378a568..2baa53ef0 100644 --- a/_includes/episode_keypoints.html +++ b/_includes/episode_keypoints.html @@ -1,3 +1,6 @@ +{% comment %} + Display key points for an episode. +{% endcomment %}

Key Points

    diff --git a/_includes/javascript.html b/_includes/javascript.html index 010ae4af1..a2066c202 100644 --- a/_includes/javascript.html +++ b/_includes/javascript.html @@ -1,3 +1,6 @@ +{% comment %} + Javascript used in lesson and workshop pages. +{% endcomment %} diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index a37ba3ece..be46c2d46 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -1,3 +1,6 @@ +{% comment %} + Footer for lesson pages. +{% endcomment %}
    diff --git a/_includes/main_title.html b/_includes/main_title.html index 60b8b0693..8e22ced11 100644 --- a/_includes/main_title.html +++ b/_includes/main_title.html @@ -1 +1,4 @@ +{% comment %} + Main title for lesson pages. +{% endcomment %}

    {{ site.title }}{% if page.title %}: {{ page.title }}{% endif %}

    diff --git a/_includes/navbar.html b/_includes/navbar.html index 6a4df8a7c..effea29db 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -1,3 +1,6 @@ +{% comment %} + Lesson navigation bar. +{% endcomment %}

SetupDowload files used on the lesson.
+ From 4dcf2ed5864ecfccaa5ff14c5439ae196ac63e1c Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Wed, 18 Jan 2017 22:37:17 +0000 Subject: [PATCH 28/76] Add missing class on _includes/syllabus.html --- _includes/syllabus.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_includes/syllabus.html b/_includes/syllabus.html index 0b206cc11..1cee118bb 100644 --- a/_includes/syllabus.html +++ b/_includes/syllabus.html @@ -26,7 +26,7 @@

Schedule

{% assign hours = current | divided_by: 60 %} {% assign minutes = current | modulo: 60 %} - {% if multiday %}{% endif %} + {% if multiday %}{% endif %} @@ -62,7 +62,7 @@

Schedule

{% assign hours = current | divided_by: 60 %} {% assign minutes = current | modulo: 60 %} - {% if multiday %}{% endif %} + {% if multiday %}{% endif %} From 9781de11d1018e400958993bcae8933114ac7629 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Wed, 18 Jan 2017 22:39:47 +0000 Subject: [PATCH 29/76] Add multiday condition on _includes/syllabus.html --- _includes/syllabus.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/syllabus.html b/_includes/syllabus.html index 1cee118bb..3b9a28977 100644 --- a/_includes/syllabus.html +++ b/_includes/syllabus.html @@ -14,7 +14,7 @@

Schedule

Setup Dowload files used on the lesson.
{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} Finish
{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} Finish
- + {% if multiday %}{% endif %} From 3a097992c1ef5e32da87196699d770b02da749c7 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Wed, 18 Jan 2017 22:50:09 +0000 Subject: [PATCH 30/76] Enforce Bootstrap's 12 column layout --- _includes/syllabus.html | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/_includes/syllabus.html b/_includes/syllabus.html index 3b9a28977..118e58489 100644 --- a/_includes/syllabus.html +++ b/_includes/syllabus.html @@ -15,7 +15,7 @@

Schedule

Setup Dowload files used on the lesson.
{% if multiday %}{% endif %} - + @@ -27,7 +27,7 @@

Schedule

{% assign minutes = current | modulo: 60 %} {% if multiday %}{% endif %} - + @@ -38,7 +38,7 @@

Schedule

{% assign minutes = current | modulo: 60 %} {% if multiday %}{% endif %} - + @@ -63,7 +63,7 @@

Schedule

{% assign minutes = current | modulo: 60 %} {% if multiday %}{% endif %} - + From 0958c5fe71b7e68d37018ad0299560040b6d3cdc Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Mon, 23 Jan 2017 14:54:50 -0800 Subject: [PATCH 31/76] bin/lesson_initialize.py: Remove 'example-site' reference The consumer was removed by 079d7d50 (Updating contribution guidelines in boilerplate, 2016-06-26). --- bin/lesson_initialize.py | 1 - 1 file changed, 1 deletion(-) diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index b26bf2877..540bb08c8 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -158,7 +158,6 @@ [dc-lessons]: http://datacarpentry.org/lessons/ [dc-site]: http://datacarpentry.org/ [discuss-list]: http://lists.software-carpentry.org/listinfo/discuss -[example-site]: https://swcarpentry.github.io/lesson-example/ [github]: http://github.com [github-flow]: https://guides.github.com/introduction/flow/ [github-join]: https://github.com/join From 39973eed99fc4b2768bb561b7216b441e76ffcf9 Mon Sep 17 00:00:00 2001 From: Nick Young Date: Tue, 31 Jan 2017 17:10:48 +1300 Subject: [PATCH 32/76] ensure dt elements have an id set --- _includes/javascript.html | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/_includes/javascript.html b/_includes/javascript.html index a2066c202..d0d2249ce 100644 --- a/_includes/javascript.html +++ b/_includes/javascript.html @@ -12,3 +12,16 @@ ga('create', 'UA-37305346-2', 'auto'); ga('send', 'pageview'); + \ No newline at end of file From 0cb3ca5b6814c5ee5dfc4e46d0256a9b2d2e0ada Mon Sep 17 00:00:00 2001 From: Nick Young Date: Wed, 1 Feb 2017 10:19:36 +1300 Subject: [PATCH 33/76] Add javascript comments to the dt-ids snippet --- _includes/javascript.html | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/_includes/javascript.html b/_includes/javascript.html index d0d2249ce..93b515273 100644 --- a/_includes/javascript.html +++ b/_includes/javascript.html @@ -13,15 +13,21 @@ ga('send', 'pageview'); \ No newline at end of file + From ce2ef8d3f1bf31fa836686af17f5a6e694c766fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?R=C3=A9mi=20Emonet?= Date: Sat, 4 Feb 2017 10:34:21 +0100 Subject: [PATCH 34/76] Updating mailmap and AUTHORS before release (Unknown: txemarix007) --- .mailmap | 30 ++++++++++++++++++++++++------ AUTHORS | 8 ++++++++ 2 files changed, 32 insertions(+), 6 deletions(-) diff --git a/.mailmap b/.mailmap index 72cfe3c75..1a854f243 100644 --- a/.mailmap +++ b/.mailmap @@ -12,22 +12,26 @@ Greg Bass Trevor Bekolay Mik Black John Blischak -Andy Boughton +Andy Boughton +Andy Boughton Karl Broman Eric Bruger -Abigail Cabunoc Mayes +Abigail Cabunoc Mayes +Abigail Cabunoc Mayes Scott Chamberlain Daniel Chen Harriet Dashnow Matt Dickenson Alastair Droop Jonah Duckles -Rémi Emonet +Rémi Emonet +Rémi Emonet Marianna Foos Auriel Fournier David Fredman Javier García-Algarra -Noushin Ghaffari +Noushin Ghaffari +Noushin Ghaffari Heather Gibling Jeremy Gray Jessica Guo @@ -65,7 +69,9 @@ Michael Sachs Pat Schloss Peter Schmiedeskamp Beth Signal -Raniere Silva +Raniere Silva +Raniere Silva +Raniere Silva Gavin Simpson Karthik Srinivasan Joseph Stachelek @@ -77,7 +83,19 @@ Andy Teucher Daniel Turek Stephen Turner Lukas Weber -Greg Wilson +Greg Wilson +Greg Wilson Kara Woo Tom Wright Naupaka Zimmerman +Zbigniew Jędrzejewski-Szmek +Evan P. Williamson +Félix-Antoine Fortin +Gabriel A. Devenyi +Greg Bass +Ge Baolai +Jonathan Keane +Kate Hertweck +Zbigniew Jędrzejewski-Szmek +txemarix007 +Zbigniew Jędrzejewski-Szmek diff --git a/AUTHORS b/AUTHORS index 4e9e1a276..b4ec73921 100644 --- a/AUTHORS +++ b/AUTHORS @@ -81,3 +81,11 @@ Greg Wilson Kara Woo Tom Wright Naupaka Zimmerman +Evan P. Williamson +Félix-Antoine Fortin +Gabriel A. Devenyi +Greg Bass +Ge Baolai +Jonathan Keane +Kate Hertweck +Zbigniew Jędrzejewski-Szmek From da5ab8e9f121182c8fc4eec3fd2e4da8aa3b8230 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?R=C3=A9mi=20Emonet?= Date: Sat, 4 Feb 2017 17:40:56 +0100 Subject: [PATCH 35/76] Fixed, more compact, ordered mailmap (+fixes) --- .mailmap | 127 +++++++++++++++---------------------------------------- 1 file changed, 35 insertions(+), 92 deletions(-) diff --git a/.mailmap b/.mailmap index 1a854f243..90d6dd459 100644 --- a/.mailmap +++ b/.mailmap @@ -1,101 +1,44 @@ -Aron Ahmadia -Matthew Aiello-Lammens -Joshua Ainsley -James Allen +Abigail Cabunoc Mayes +Abigail Cabunoc Mayes +Andy Boughton +Andy Teucher Areej Alsheikh-Hussain -Paula Andrea -Jeffrey Arnold -Alex Bajcz -Piotr Banaszkiewicz +Beth Signal +Daniel Chen +Daniel Turek Diego Barneche -Greg Bass -Trevor Bekolay -Mik Black -John Blischak -Andy Boughton -Andy Boughton -Karl Broman +Donna Henderson Eric Bruger -Abigail Cabunoc Mayes -Abigail Cabunoc Mayes -Scott Chamberlain -Daniel Chen -Harriet Dashnow -Matt Dickenson -Alastair Droop -Jonah Duckles -Rémi Emonet -Rémi Emonet -Marianna Foos -Auriel Fournier -David Fredman -Javier García-Algarra -Noushin Ghaffari -Noushin Ghaffari -Heather Gibling -Jeremy Gray -Jessica Guo -Melissa Guzman -Denis Haine -Michael Hansen +Eric Milliman +Evan P. Williamson Fabian Held -Donna Henderson -James Hiebert -Jeff Hollister -Mike Jackson -Elsie Jacobson -W. Trevor King -Michael Levy -Mark Mandel -Carlos Martinez -Ben Marwick +Félix-Antoine Fortin François Michonneau -James Mickley -Eric Milliman -Bill Mills +François Michonneau +Ge Baolai +Greg Bass +Greg Wilson +James Allen +Javier García-Algarra +Jeffrey Arnold Joaquin Moris -Hani Nakhoul -Matthias Nilsson -Aaron O'Leary -Frank Pennekamp -Raissa Philibert -Jon Pipitone -Timothée Poisot -Louis Ranjard -Joey Reid -Scott Ritchie -Natalie Robinson -Michael Sachs -Pat Schloss -Peter Schmiedeskamp -Beth Signal -Raniere Silva -Raniere Silva -Raniere Silva -Gavin Simpson -Karthik Srinivasan Joseph Stachelek -Valentina Staneva -Sarah Stevens -Michael Sumner -Sarah Supp -Andy Teucher -Daniel Turek -Stephen Turner -Lukas Weber -Greg Wilson -Greg Wilson Kara Woo -Tom Wright -Naupaka Zimmerman -Zbigniew Jędrzejewski-Szmek -Evan P. Williamson -Félix-Antoine Fortin -Gabriel A. Devenyi -Greg Bass -Ge Baolai -Jonathan Keane +Karthik Srinivasan Kate Hertweck -Zbigniew Jędrzejewski-Szmek -txemarix007 -Zbigniew Jędrzejewski-Szmek +Louis Ranjard +Melissa Guzman +Michael Sumner +Mik Black +Mike Jackson +Natalie Robinson +Noushin Ghaffari +Noushin Ghaffari +Raniere Silva +Raniere Silva +Rémi Emonet +Rémi Emonet +Sarah Supp +Scott Chamberlain +Timothée Poisot +Valentina Staneva From 0b6467bd8c6d77e0b0d0ccd0face42fe9a144e35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?R=C3=A9mi=20Emonet?= Date: Mon, 6 Feb 2017 22:10:57 +0100 Subject: [PATCH 36/76] Force ordering AUTHORS by lastname --- AUTHORS | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/AUTHORS b/AUTHORS index b4ec73921..1b4a766f9 100644 --- a/AUTHORS +++ b/AUTHORS @@ -7,6 +7,7 @@ Paula Andrea Jeffrey Arnold Alex Bajcz Piotr Banaszkiewicz +Ge Baolai Diego Barneche Greg Bass Trevor Bekolay @@ -19,11 +20,13 @@ Abigail Cabunoc Mayes Scott Chamberlain Daniel Chen Harriet Dashnow +Gabriel A. Devenyi Matt Dickenson Alastair Droop Jonah Duckles Rémi Emonet Marianna Foos +Félix-Antoine Fortin Auriel Fournier David Fredman Javier García-Algarra @@ -36,10 +39,13 @@ Denis Haine Michael Hansen Fabian Held Donna Henderson +Kate Hertweck James Hiebert Jeff Hollister Mike Jackson Elsie Jacobson +Zbigniew Jędrzejewski-Szmek +Jonathan Keane W. Trevor King Michael Levy Mark Mandel @@ -77,15 +83,8 @@ Andy Teucher Daniel Turek Stephen Turner Lukas Weber +Evan P. Williamson Greg Wilson Kara Woo Tom Wright Naupaka Zimmerman -Evan P. Williamson -Félix-Antoine Fortin -Gabriel A. Devenyi -Greg Bass -Ge Baolai -Jonathan Keane -Kate Hertweck -Zbigniew Jędrzejewski-Szmek From c510f14777ca13881b6c9ac02389b085170a1653 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Sat, 18 Feb 2017 17:56:38 +0000 Subject: [PATCH 37/76] Make tables wider Close https://github.com/swcarpentry/styles/issues/101. --- assets/css/bootstrap.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/css/bootstrap.css b/assets/css/bootstrap.css index 46ba03ef1..0fe7cd5b0 100644 --- a/assets/css/bootstrap.css +++ b/assets/css/bootstrap.css @@ -2263,7 +2263,7 @@ th { text-align: left; } .table { - /* width: 100%; -- CHANGE -- */ + width: 100%; max-width: 100%; margin-bottom: 20px; } From 60185ce1c5c73962bd9469f99b479dbd0227a2b8 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Sat, 18 Feb 2017 17:49:06 +0000 Subject: [PATCH 38/76] Improve round corners on block input and output --- assets/css/lesson.scss | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index 0c5f86e1f..fe008e501 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -32,6 +32,7 @@ $color-testimonial: #fc8dc1 !default; color: $color; border-left: solid 5px $color; margin-bottom: 0px; + border-radius: 4px 0 0 4px; } .error { @include cdSetup($color-error); } @@ -45,6 +46,18 @@ $color-testimonial: #fc8dc1 !default; .r { @include cdSetup($color-source); } .sql { @include cdSetup($color-source); } +.error pre, +.output pre, +.source pre, +.bash pre, +.make pre, +.matlab pre, +.python pre, +.r pre, +.sql pre { + border-radius: 0 4px 4px 0; +} + //---------------------------------------- // Specialized blockquote environments for learning objectives, callouts, etc. //---------------------------------------- From 9911100473051835c617b611af486183c691a162 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Thu, 2 Mar 2017 22:01:47 +0000 Subject: [PATCH 39/76] Update copyright year with current year --- _includes/lesson_footer.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index be46c2d46..352dcf06c 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -5,7 +5,7 @@

- Copyright © 2016 + Copyright © 2016–{{ 'now' | date: "%Y" }} {% if site.carpentry == "swc" %} Software Carpentry Foundation {% elsif site.carpentry == "dc" %} From 8dbb992b204150bb1cb7eb7fcf30aed4c29d937a Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Thu, 23 Feb 2017 17:22:53 +0000 Subject: [PATCH 40/76] Add link to Edit on GitHub --- _includes/lesson_footer.html | 4 +++- _includes/navbar.html | 3 ++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 352dcf06c..9d214d54c 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -17,10 +17,12 @@

- Source + Improve this page / Contributing / + Source + / Cite / Contact diff --git a/_includes/navbar.html b/_includes/navbar.html index effea29db..fa8def7bf 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -51,7 +51,6 @@ {% comment %} Show setup instructions, reference guide, and lesson episodes for lessons. {% endcomment %} {% if site.kind == "lesson" %}
  • Setup
    • -
  • Reference
    • @@ -67,6 +66,7 @@
    • From 2093505e4ed2a25389abea2d724399e93b4fb452 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 3 Mar 2017 20:42:00 +0000 Subject: [PATCH 41/76] Change Edit on GitHub link to edit page --- _includes/lesson_footer.html | 2 +- _includes/navbar.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 9d214d54c..afb2be8aa 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -17,7 +17,7 @@

      - Improve this page + Improve this page / Contributing / diff --git a/_includes/navbar.html b/_includes/navbar.html index fa8def7bf..580171a22 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -76,7 +76,7 @@ {% comment %} Always show license. {% endcomment %}
    • License
      • -
    • Edit on GitHub
      • +
    • Edit on GitHub

    From 8874a3fe21d3e4b013c3a9274cde058e386ad8b2 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 3 Mar 2017 20:44:12 +0000 Subject: [PATCH 42/76] Adopt @lexnederbragt suggestion for Edit link https://github.com/swcarpentry/lesson-example/pull/104#issuecomment-283310978 --- _includes/lesson_footer.html | 2 +- _includes/navbar.html | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index afb2be8aa..e9ae2b710 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -17,7 +17,7 @@

    - Improve this page + Edit on GitHub / Contributing / diff --git a/_includes/navbar.html b/_includes/navbar.html index 580171a22..2052ac30a 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -76,7 +76,7 @@ {% comment %} Always show license. {% endcomment %}
  • License
    • -
  • Edit on GitHub
    • +
  • Improve this page
    • From 15da8bb6fa19504624798965a4a221f029688e68 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 3 Mar 2017 20:52:49 +0000 Subject: [PATCH 43/76] Fix issue with link to GitHub from RMarkdown files Jekyll doesn't export the _episodes_rmd so we need to flag the files. Each Rmd file must have in the YAML header source: Rmd --- _includes/lesson_footer.html | 6 ++++++ _includes/navbar.html | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index e9ae2b710..fa5d88870 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -17,7 +17,13 @@

    + {% if page.source %} + {% if page.source == "Rmd" %} + Edit on GitHub + {% endif %} + {% else %} Edit on GitHub + {% endif %} / Contributing / diff --git a/_includes/navbar.html b/_includes/navbar.html index 2052ac30a..6b21afc76 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -76,7 +76,13 @@ {% comment %} Always show license. {% endcomment %}
  • License
    • + {% if page.source %} + {% if page.source == "Rmd" %} +
  • Improve this page
    • + {% endif %} + {% else %}
  • Improve this page
    • + {% endif %}
    From c0eafd4c27f29030ba384e7e6ff0c3bb9fc19da9 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Sat, 18 Feb 2017 17:14:20 +0000 Subject: [PATCH 44/76] Numbering the lessons in the schedule Related with https://github.com/swcarpentry/styles/issues/80. --- _includes/syllabus.html | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/_includes/syllabus.html b/_includes/syllabus.html index 118e58489..86b69c3eb 100644 --- a/_includes/syllabus.html +++ b/_includes/syllabus.html @@ -5,6 +5,7 @@

    Schedule

    + {% assign lesson_number = 0 %} {% assign day = 0 %} {% assign multiday = false %} {% for episode in site.episodes %} @@ -40,7 +41,8 @@

    Schedule

    {% if multiday %}

    • {% endif %} {% endif %} - + {% for episode in site.episodes %} {% if episode.start %} {% comment %} Starting a new day? {% endcomment %} From ef92f42fb9a31828c0de3bb118c039e40abf59d1 Mon Sep 17 00:00:00 2001 From: Kristian Tylen Date: Wed, 22 Mar 2017 10:22:10 +0100 Subject: [PATCH 49/76] some-proof-reading Hi there, I made a number of suggestions for edits to make the instructions more clear and the terminology more consistent. best kristian --- _episodes_rmd/01-starting-with-data.Rmd | 38 ++++++++++++------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index 97611564a..784a0624e 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -55,7 +55,7 @@ To do all that, we'll have to learn a little bit about programming. ### Loading Data -To load our inflammation data, first we need to tell our computer where is the file that contains the values. We have been told its name is `inflammation-01.csv`. This is very important in R, if we forget this step we’ll get an error message when trying to read the file. We can change the current working directory using the function `setwd`. For this example, we change the path to the directory we just created: +Let's import the file called `inflammation-01.csv` into our R environment. To import the file, first we need to tell our computer where the file is. We do that by choosing a working directory, that is, a local directory on our computer containing the files we need. This is very important in R. If we forget this step we’ll get an error message saying that the file does not exist. We can set the working directory using the function `setwd`. For this example, we change the path to our new directory at the desktop: ```{r,eval=FALSE} setwd("~/Desktop/r-novice-inflammation/") @@ -64,7 +64,7 @@ setwd("~/Desktop/r-novice-inflammation/") Just like in the Unix Shell, we type the command and then press `Enter` (or `return`). Alternatively you can change the working directory using the RStudio GUI using the menu option `Session` -> `Set Working Directory` -> `Choose Directory...` -The data files are located in the directory `data` inside the working directory. Now we can load the data into R using `read.csv`: +The data file is located in the directory `data` inside the working directory. Now we can load the data into R using `read.csv`: ```{r, results="hide"} read.csv(file = "data/inflammation-01.csv", header = FALSE) @@ -99,16 +99,16 @@ The filename needs to be a character string (or [string]({{ page.root }}/referen > Take a look at `?read.csv` and write the code to load a file called `commadec.txt` that has numeric values with commas as decimal mark, separated by semicolons. {: .challenge} -The utility of a function is that it will perform its given action on whatever value is passed to the named argument(s). -For example, in this case if we provided the name of a different file to the argument `file`, `read.csv` would read it instead. -We'll learn more of the details about functions and their arguments in the next lesson. +A function will perform its given action on whatever value is passed to the argument(s). +For example, in this case if we provided the name of a different file to the argument `file`, `read.csv` would read that instead. +We'll learn more about the details of functions and their arguments in the next lesson. Since we didn't tell it to do anything else with the function's output, the console will display the full contents of the file `inflammation-01.csv`. Try it out. -`read.csv` read the file, but we can't use data unless we assign it to a variable. -A variable is just a name for a value, such as `x`, `current_temperature`, or `subject_id`. -We can create a new variable simply by assigning a value to it using `<-` +`read.csv` reads the file, but we can't use data unless we assign it to a variable. +We can think of a variable as a container with a name, such as `x`, `current_temperature`, or `subject_id` that contains one or more values. +We can create a new variable and assign a value to it using `<-` ```{r} weight_kg <- 55 @@ -121,7 +121,7 @@ In general, R will print to the console any object returned by a function or ope weight_kg ``` -We can do arithmetic with the variable: +We can do arithmetics with the variable: ```{r} # weight in pounds: @@ -135,7 +135,7 @@ We can do arithmetic with the variable: > read it) have an easier time following what the code is doing. {: .callout} -We can also change an object's value by assigning it a new value: +We can also change an variable's value by assigning it a new value: ```{r} weight_kg <- 57.5 @@ -184,15 +184,15 @@ This is different from the way spreadsheets work. > and finally prints the assigned value of the variable `total_weight`. {: .callout} -Now that we know how to assign things to variables, let's re-run `read.csv` and save its result: +Now that we know how to assign things to variables, let's re-run `read.csv` and save its result into a variable called 'dat': ```{r} dat <- read.csv(file = "data/inflammation-01.csv", header = FALSE) ``` -This statement doesn't produce any output because assignment doesn't display anything. -If we want to check that our data has been loaded, we can print the variable's value. -However, for large data sets it is convenient to use the function `head` to display only the first few rows of data. +This statement doesn't produce any output because the assignment doesn't display anything. +If we want to check if our data has been loaded, we can print the variable's value by typing the name of the variable `dat`. However, for large data sets it is convenient to use the function `head` to display only the first few rows of data. + ```{r} head(dat) @@ -213,15 +213,15 @@ head(dat) ### Manipulating Data -Now that our data is loaded in memory, we can start doing things with it. +Now that our data are loaded into R, we can start doing things with them. First, let's ask what type of thing `dat` is: ```{r} class(dat) ``` -The output tells us that is a data frame. Think of this structure as a spreadsheet in MS Excel that many of us are familiar with. -Data frames are very useful for storing data and you will find them elsewhere when programming in R. A typical data frame of experimental data contains individual observations in rows and variables in columns. +The output tells us that it is a data frame. We can think of this as a spreadsheet in MS Excel, which many of us are familiar with. +Data frames are very useful for organizing data and you will find them elsewhere when programming in R. A typical data frame of experimental data contains individual observations in rows and variables in columns. We can see the shape, or [dimensions]({{ page.root }}/reference/#dimensions), of the data frame with the function `dim`: @@ -231,7 +231,7 @@ dim(dat) This tells us that our data frame, `dat`, has `r nrow(dat)` rows and `r ncol(dat)` columns. -If we want to get a single value from the data frame, we can provide an [index]({{ page.root }}/reference/#index) in square brackets, just as we do in math: +If we want to get a single value from the data frame, we can provide an [index]({{ page.root }}/reference/#index) in square brackets. The first number specifies the row and the second the column: ```{r} # first value in dat @@ -277,7 +277,7 @@ dat[, 16] > You can learn more about subsetting by column name in this supplementary [lesson]({{ page.root }}/10-supp-addressing-data/). {: .callout} -Now let's perform some common mathematical operations to learn about our inflammation data. +Now let's perform some common mathematical operations to learn more about our inflammation data. When analyzing data we often want to look at partial statistics, such as the maximum value per patient or the average value per day. One way to do this is to select the data we want to create a new temporary data frame, and then perform the calculation on this subset: From 3c0d46925ea59a62b8595be613234cf2d8e932ab Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Mon, 27 Mar 2017 14:44:53 -0400 Subject: [PATCH 50/76] remove .swp bin file from #244 --- .swp | Bin 12288 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 .swp diff --git a/.swp b/.swp deleted file mode 100644 index 1d20d4a5c74af9b9fd2d8ce044eb917560f3ea7d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12288 zcmeI&y>8S%5C`xL6=?t^FEF_@L?l+eB;XzZiGl`{G$_)I?Y-P8yX#{=P82NoQL!tyD)Pl0H{%inAaG9t>nBHt2m9?}+oLVo+&H69gat0SG_<0uX=z1Rwwb2tWV= zk5GW+J%95|slO8K`~Ttj|K_<;*AiC}e##5SUsyQ)D13SIj9Z$2bl4(4RVs`Qk`*K7T+bUc6 zBt4G16lc6~+0%k;9_}(BCi;>&BxCz?PS=M0s;bk&zce$UzRe`|^{OU+9qOH%h4wVl zc0SFPYMt2FNL)5Kb*Yiv+)CpnreMn4Hd`n)nM_pQ@k`m$=iP(x@!5{rrcd2A%r{NL q*4o_f;fGQmiEV6X#!~+Fs;t3@R;7%N6k9d6!seW?3>dQNSp5UK+n0I( From 3ee403989124343ffa8d47a08d54efb0ff8b38d5 Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Mon, 27 Mar 2017 17:22:55 -0400 Subject: [PATCH 51/76] fix typo from #262 and #253 --- _episodes_rmd/04-cond.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_episodes_rmd/04-cond.Rmd b/_episodes_rmd/04-cond.Rmd index 9d596ef4e..0000f2e0c 100644 --- a/_episodes_rmd/04-cond.Rmd +++ b/_episodes_rmd/04-cond.Rmd @@ -411,7 +411,7 @@ analyze_all <- function(pattern) { Now we can save all of the results with just one line of code: ```{r} -analyze_all("inflammation*.csv") +analyze_all("inflammation.*csv") ``` Now if we need to make any changes to our analysis, we can edit the `analyze` function and quickly regenerate all the figures with `analyze_all`. From c5ae83f37056e55c12ccffdd314df8f3c92c9a47 Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Mon, 27 Mar 2017 18:57:43 -0400 Subject: [PATCH 52/76] formatting from PR #263 --- _episodes_rmd/01-starting-with-data.Rmd | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index effa5362c..5288e6bad 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -146,10 +146,10 @@ weight_kg > > Historically, R programmers have used a variety of conventions for naming variables. The `.` character > in R can be a valid part of a variable name; thus the above assignment could have easily been `weight.kg <- 57.5`. -> This is often confusing to R newcomers who have programmed in languages where `.` has a more significant meaning. -> Today, most R programmers 1) start variable names with lower case letters, 2) separate words in variable names with +> This is often confusing to R newcomers who have programmed in languages where `.` has a more significant meaning. +> Today, most R programmers 1) start variable names with lower case letters, 2) separate words in variable names with > underscores, and 3) use only lowercase letters, underscores, and numbers in variable names. The book *R Packages* includes -> a [chapter](http://r-pkgs.had.co.nz/style.html) on this and other style considerations. +> a [chapter](http://r-pkgs.had.co.nz/style.html) on this and other style considerations. {: .callout} If we imagine the variable as a sticky note with a name written on it, @@ -432,7 +432,7 @@ We'll learn why this is so in the next lesson. > > whichPatients <- seq(2,40,2) > > whichDays <- c(1:5) > > dat2 <- dat -> > dat2[whichDays,whichPatients] <- dat2[whichDays,whichPatients]/2 +> > dat2[whichDays, whichPatients] <- dat2[whichDays, whichPatients]/2 > > (dat2) > > ~~~ > > {: .r} From 64502b2ca4015499174751eaa5bd8aa3eba350fc Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Mon, 27 Mar 2017 19:07:40 -0400 Subject: [PATCH 53/76] update md files from source rmd files Updates from the following PRs: #244 #243 #246 #248 #252 #268 more: #253 #262 #254 #263 #269 #264 #267 #266 --- _episodes/01-starting-with-data.md | 78 ++++++++++----- _episodes/02-func-R.md | 2 +- _episodes/04-cond.md | 2 +- _episodes/05-cmdline.md | 22 +++-- _episodes/08-making-packages-R.md | 5 +- _episodes/11-supp-read-write-csv.md | 2 +- _episodes/13-supp-data-structures.md | 142 +++++++++++++++++++++------ _episodes/15-supp-loops-in-depth.md | 4 +- 8 files changed, 191 insertions(+), 66 deletions(-) diff --git a/_episodes/01-starting-with-data.md b/_episodes/01-starting-with-data.md index 3e9f6f79b..dee4800aa 100644 --- a/_episodes/01-starting-with-data.md +++ b/_episodes/01-starting-with-data.md @@ -33,7 +33,7 @@ keypoints: We are studying inflammation in patients who have been given a new treatment for arthritis, and need to analyze the first dozen data sets. -The data sets are stored in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-(csv)) (CSV) format. Each row holds the observations for just one patient. Each column holds the inflammation measured in a day, so we have a set of values in successive days. +The data sets are stored in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-csv) (CSV) format. Each row holds the observations for just one patient. Each column holds the inflammation measured in a day, so we have a set of values in successive days. The first few rows of our first file look like this: @@ -56,7 +56,7 @@ To do all that, we'll have to learn a little bit about programming. ### Loading Data -To load our inflammation data, first we need to tell our computer where is the file that contains the values. We have been told its name is `inflammation-01.csv`. This is very important in R, if we forget this step we’ll get an error message when trying to read the file. We can change the current working directory using the function `setwd`. For this example, we change the path to the directory we just created: +Let's import the file called `inflammation-01.csv` into our R environment. To import the file, first we need to tell our computer where the file is. We do that by choosing a working directory, that is, a local directory on our computer containing the files we need. This is very important in R. If we forget this step we’ll get an error message saying that the file does not exist. We can set the working directory using the function `setwd`. For this example, we change the path to our new directory at the desktop: ~~~ @@ -67,7 +67,7 @@ setwd("~/Desktop/r-novice-inflammation/") Just like in the Unix Shell, we type the command and then press `Enter` (or `return`). Alternatively you can change the working directory using the RStudio GUI using the menu option `Session` -> `Set Working Directory` -> `Choose Directory...` -The data files are located in the directory `data` inside the working directory. Now we can load the data into R using `read.csv`: +The data file is located in the directory `data` inside the working directory. Now we can load the data into R using `read.csv`: ~~~ @@ -104,16 +104,16 @@ The filename needs to be a character string (or [string]({{ page.root }}/referen > Take a look at `?read.csv` and write the code to load a file called `commadec.txt` that has numeric values with commas as decimal mark, separated by semicolons. {: .challenge} -The utility of a function is that it will perform its given action on whatever value is passed to the named argument(s). -For example, in this case if we provided the name of a different file to the argument `file`, `read.csv` would read it instead. -We'll learn more of the details about functions and their arguments in the next lesson. +A function will perform its given action on whatever value is passed to the argument(s). +For example, in this case if we provided the name of a different file to the argument `file`, `read.csv` would read that instead. +We'll learn more about the details of functions and their arguments in the next lesson. Since we didn't tell it to do anything else with the function's output, the console will display the full contents of the file `inflammation-01.csv`. Try it out. -`read.csv` read the file, but we can't use data unless we assign it to a variable. -A variable is just a name for a value, such as `x`, `current_temperature`, or `subject_id`. -We can create a new variable simply by assigning a value to it using `<-` +`read.csv` reads the file, but we can't use data unless we assign it to a variable. +We can think of a variable as a container with a name, such as `x`, `current_temperature`, or `subject_id` that contains one or more values. +We can create a new variable and assign a value to it using `<-` ~~~ @@ -137,7 +137,7 @@ weight_kg ~~~ {: .output} -We can do arithmetic with the variable: +We can do arithmetics with the variable: ~~~ @@ -160,7 +160,7 @@ We can do arithmetic with the variable: > read it) have an easier time following what the code is doing. {: .callout} -We can also change an object's value by assigning it a new value: +We can also change an variable's value by assigning it a new value: ~~~ @@ -176,6 +176,15 @@ weight_kg [1] 57.5 ~~~ {: .output} +> ## Variable Naming Conventions +> +> Historically, R programmers have used a variety of conventions for naming variables. The `.` character +> in R can be a valid part of a variable name; thus the above assignment could have easily been `weight.kg <- 57.5`. +> This is often confusing to R newcomers who have programmed in languages where `.` has a more significant meaning. +> Today, most R programmers 1) start variable names with lower case letters, 2) separate words in variable names with +> underscores, and 3) use only lowercase letters, underscores, and numbers in variable names. The book *R Packages* includes +> a [chapter](http://r-pkgs.had.co.nz/style.html) on this and other style considerations. +{: .callout} If we imagine the variable as a sticky note with a name written on it, assignment is like putting the sticky note on a particular value: @@ -262,7 +271,7 @@ This is different from the way spreadsheets work. > and finally prints the assigned value of the variable `total_weight`. {: .callout} -Now that we know how to assign things to variables, let's re-run `read.csv` and save its result: +Now that we know how to assign things to variables, let's re-run `read.csv` and save its result into a variable called 'dat': ~~~ @@ -270,9 +279,9 @@ dat <- read.csv(file = "data/inflammation-01.csv", header = FALSE) ~~~ {: .r} -This statement doesn't produce any output because assignment doesn't display anything. -If we want to check that our data has been loaded, we can print the variable's value. -However, for large data sets it is convenient to use the function `head` to display only the first few rows of data. +This statement doesn't produce any output because the assignment doesn't display anything. +If we want to check if our data has been loaded, we can print the variable's value by typing the name of the variable `dat`. However, for large data sets it is convenient to use the function `head` to display only the first few rows of data. + ~~~ @@ -322,7 +331,7 @@ head(dat) ### Manipulating Data -Now that our data is loaded in memory, we can start doing things with it. +Now that our data are loaded into R, we can start doing things with them. First, let's ask what type of thing `dat` is: @@ -338,10 +347,10 @@ class(dat) ~~~ {: .output} -The output tells us that is a data frame. Think of this structure as a spreadsheet in MS Excel that many of us are familiar with. -Data frames are very useful for storing data and you will find them elsewhere when programming in R. A typical data frame of experimental data contains individual observations in rows and variables in columns. +The output tells us that it is a data frame. We can think of this as a spreadsheet in MS Excel, which many of us are familiar with. +Data frames are very useful for organizing data and you will find them elsewhere when programming in R. A typical data frame of experimental data contains individual observations in rows and variables in columns. -We can see the shape, or [dimensions]({{ page.root }}/reference/#dimensions), of the data frame with the function `dim`: +We can see the shape, or [dimensions]({{ page.root }}/reference/#dimensions-of-an-array), of the data frame with the function `dim`: ~~~ @@ -358,7 +367,7 @@ dim(dat) This tells us that our data frame, `dat`, has 60 rows and 40 columns. -If we want to get a single value from the data frame, we can provide an [index]({{ page.root }}/reference/#index) in square brackets, just as we do in math: +If we want to get a single value from the data frame, we can provide an [index]({{ page.root }}/reference/#index) in square brackets. The first number specifies the row and the second the column: ~~~ @@ -496,7 +505,7 @@ dat[, 16] > You can learn more about subsetting by column name in this supplementary [lesson]({{ page.root }}/10-supp-addressing-data/). {: .callout} -Now let's perform some common mathematical operations to learn about our inflammation data. +Now let's perform some common mathematical operations to learn more about our inflammation data. When analyzing data we often want to look at partial statistics, such as the maximum value per patient or the average value per day. One way to do this is to select the data we want to create a new temporary data frame, and then perform the calculation on this subset: @@ -612,6 +621,31 @@ sd(dat[, 7]) ~~~ {: .output} +R also has a function that summaries the previous common calculations: + + +~~~ +# Summarize function +summary(dat[,1:4]) +~~~ +{: .r} + + + +~~~ + V1 V2 V3 V4 + Min. :0 Min. :0.00 Min. :0.000 Min. :0.00 + 1st Qu.:0 1st Qu.:0.00 1st Qu.:1.000 1st Qu.:1.00 + Median :0 Median :0.00 Median :1.000 Median :2.00 + Mean :0 Mean :0.45 Mean :1.117 Mean :1.75 + 3rd Qu.:0 3rd Qu.:1.00 3rd Qu.:2.000 3rd Qu.:3.00 + Max. :0 Max. :1.00 Max. :2.000 Max. :3.00 +~~~ +{: .output} + +For every column in the data frame, the function "summary" calculates: the minimun value, the first quartile, the median, the mean, the third quartile and the max value, given helpful details about the sample distribution. + + What if we need the maximum inflammation for all patients, or the average for each day? As the diagram below shows, we want to perform the operation across a margin of the data frame: @@ -724,7 +758,7 @@ We'll learn why this is so in the next lesson. > > whichPatients <- seq(2,40,2) > > whichDays <- c(1:5) > > dat2 <- dat -> > dat2[whichDays,whichPatients] <- dat2[whichDays,whichPatients]/2 +> > dat2[whichDays, whichPatients] <- dat2[whichDays, whichPatients]/2 > > (dat2) > > ~~~ > > {: .r} diff --git a/_episodes/02-func-R.md b/_episodes/02-func-R.md index b36fb75a8..24847f8e9 100644 --- a/_episodes/02-func-R.md +++ b/_episodes/02-func-R.md @@ -248,7 +248,7 @@ Real-life functions will usually be larger than the ones shown here--typically h > 2. 11 > 3. 23 > 4. 30 -> 2. If mySum(3) == 13, why does mySum(b=3) return an error? +> 2. If `mySum(3)` returns 13, why does `mySum(input_2 = 3)` return an error? {: .challenge} ### Testing and Documenting diff --git a/_episodes/04-cond.md b/_episodes/04-cond.md index 4a9daca18..bb9ff1f4a 100644 --- a/_episodes/04-cond.md +++ b/_episodes/04-cond.md @@ -564,7 +564,7 @@ Now we can save all of the results with just one line of code: ~~~ -analyze_all("inflammation*.csv") +analyze_all("inflammation.*csv") ~~~ {: .r} diff --git a/_episodes/05-cmdline.md b/_episodes/05-cmdline.md index 57d4d9ec9..7913c0ec2 100644 --- a/_episodes/05-cmdline.md +++ b/_episodes/05-cmdline.md @@ -50,7 +50,7 @@ $ Rscript readings.R --max data/inflammation-*.csv Our overall requirements are: -1. If no filename is given on the command line, read data from [standard input]({{ page.root }}/reference/#standard-input). +1. If no filename is given on the command line, read data from [standard input]({{ page.root }}/reference/#standard-input-stdin). 2. If one or more filenames are given, read data from them and report statistics for each file separately. 3. Use the `--min`, `--mean`, or `--max` flag to determine what statistic to print. @@ -82,11 +82,17 @@ Rscript session-info.R ~~~ -R version 3.1.2 (2014-10-31) -Platform: x86_64-apple-darwin13.4.0 (64-bit) +R version 3.3.3 (2017-03-06) +Platform: x86_64-pc-linux-gnu (64-bit) +Running under: Antergos Linux locale: -[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 + [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C + [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 + [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 + [7] LC_PAPER=en_US.UTF-8 LC_NAME=C + [9] LC_ADDRESS=C LC_TELEPHONE=C +[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets base @@ -112,7 +118,7 @@ cat(args, sep = "\n") The function `commandArgs` extracts all the command line arguments and returns them as a vector. The function `cat`, similar to the `cat` of the Unix Shell, outputs the contents of the variable. -Since we did not specify a filename for writing, `cat` sends the output to [standard output]({{ page.root }}/reference/#standard-output-(stdout)), +Since we did not specify a filename for writing, `cat` sends the output to [standard output]({{ page.root }}/reference/#standard-output-stdout), which we can then pipe to other Unix functions. Because we set the argument `sep` to `"\n"`, which is the symbol to start a new line, each element of the vector is printed on its own line. Let's see what happens when we run this program in the Unix Shell: @@ -127,7 +133,7 @@ Rscript print-args.R ~~~ -/Library/Frameworks/R.framework/Resources/bin/exec/R +/usr/lib64/R/bin/exec/R --slave --no-restore --file=print-args.R @@ -156,7 +162,7 @@ R --slave --no-restore --file=print-args.R --args ~~~ -/Library/Frameworks/R.framework/Resources/bin/exec/R +/usr/lib64/R/bin/exec/R --slave --no-restore --file=print-args.R @@ -176,7 +182,7 @@ Rscript print-args.R first second third ~~~ -/Library/Frameworks/R.framework/Resources/bin/exec/R +/usr/lib64/R/bin/exec/R --slave --no-restore --file=print-args.R diff --git a/_episodes/08-making-packages-R.md b/_episodes/08-making-packages-R.md index 4ecdbfb0d..0d95b97ea 100644 --- a/_episodes/08-making-packages-R.md +++ b/_episodes/08-making-packages-R.md @@ -6,7 +6,10 @@ questions: - "How do I collect my code together so I can reuse it and share it?" - "How do I make my own packages?" objectives: -- "Quick summary on how (and why) making R packages." +- "Describe the required structure of R packages." +- "Create the required structure of a simple R package." +- "Write documentation comments that can be automatically compiled to R's native help and documentation format." + keypoints: - "A package is the basic unit of reusability in R." - "Every package must have a DESCRIPTION file and an R directory containing code." diff --git a/_episodes/11-supp-read-write-csv.md b/_episodes/11-supp-read-write-csv.md index 3f94d90fa..66685fbad 100644 --- a/_episodes/11-supp-read-write-csv.md +++ b/_episodes/11-supp-read-write-csv.md @@ -19,7 +19,7 @@ keypoints: The most common way that scientists store data is in Excel spreadsheets. While there are R packages designed to access data from Excel spreadsheets (e.g., gdata, RODBC, XLConnect, xlsx, RExcel), -users often find it easier to save their spreadsheets in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-(csv)) files (CSV) +users often find it easier to save their spreadsheets in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-csv) files (CSV) and then use R's built in functionality to read and manipulate the data. In this short lesson, we'll learn how to read data from a .csv and write to a new .csv, and explore the [arguments]({{ page.root }}/reference/#argument) that allow you read and write the data correctly for your needs. diff --git a/_episodes/13-supp-data-structures.md b/_episodes/13-supp-data-structures.md index 2fd97960f..10f32560d 100644 --- a/_episodes/13-supp-data-structures.md +++ b/_episodes/13-supp-data-structures.md @@ -1,21 +1,21 @@ --- title: "Data Types and Structures" +keypoints: +- R's basic data types are character, numeric, integer, complex, and logical. +- R's basic data structures include the vector, list, matrix, data frame, and factors. +- Objects may have attributes, such as name, dimension, and class. +objectives: +- Expose learners to the different data types in R. +- Learn how to create vectors of different types. +- Be able to check the type of vector. +- Learn about missing data and other special values. +- Getting familiar with the different data structures (lists, matrices, data frames). +questions: +- What are the different data types in R? +- What are the different data structures in R? +- How do I access data within the various data structures? teaching: 45 exercises: 0 -questions: -- "What are the different data types in R?" -- "What are the different data structures in R?" -- "How do I access data within the various data structures?" -objectives: -- "Expose learners to the different data types in R." -- "Learn how to create vectors of different types." -- "Be able to check the type of vector." -- "Learn about missing data and other special values." -- "Getting familiar with the different data structures (lists, matrices, data frames)." -keypoints: -- "R's basic data types are character, numeric, integer, complex, and logical." -- "R's basic data structures include the vector, list, matrix, data frame, and factors." -- "Objects may have attributes, such as name, dimension, and class." --- @@ -727,6 +727,21 @@ mdat ~~~ {: .output} +Elements of a matrix can be referenced by specifying the index along each dimension (e.g. "row" and "column") in single square brackets. + + +~~~ +mdat[2,3] +~~~ +{: .r} + + + +~~~ +[1] 13 +~~~ +{: .output} + ### List In R lists act as containers. Unlike atomic vectors, the contents of a list are @@ -779,6 +794,7 @@ length(x) ~~~ {: .output} +The content of elements of a list can be retrieved by using double square brackets. ~~~ @@ -793,6 +809,7 @@ NULL ~~~ {: .output} +Vectors can be coerced to lists as follows: ~~~ @@ -813,6 +830,9 @@ length(x) 2. What about `x[[1]]`? +Elements of a list can be named (i.e. lists can have the `names` atttibute) + + ~~~ xlist <- list(a = "Karthik Ram", b = 1:10, data = head(iris)) xlist @@ -839,16 +859,30 @@ $data ~~~ {: .output} + + +~~~ +names(xlist) +~~~ +{: .r} + + + +~~~ +[1] "a" "b" "data" +~~~ +{: .output} + 1. What is the length of this object? What about its structure? -Lists can be extremely useful inside functions. You can “staple” together lots +Lists can be extremely useful inside functions. Because the functions in R are able to return only a single object, you can "staple" together lots of different kinds of results into a single object that a function can return. A list does not print to the console like a vector. Instead, each element of the list starts on a new line. Elements are indexed by double brackets. Single brackets will still return -a(nother) list. +a(nother) list. If the elements of a list are named, they can be referenced by the `$` notation (i.e. `xlist$data`). ### Data Frame @@ -856,7 +890,7 @@ a(nother) list. A data frame is a very important data type in R. It's pretty much the *de facto* data structure for most tabular data and what we use for statistics. -A data frame is a special type of list where every element of the list has same length. +A data frame is a *special type of list* where every element of the list has same length (i.e. data frame is a "rectangular" list). Data frames can have additional attributes such as `rownames()`, which can be useful for annotating data, like `subject_id` or `sample_id`. But most of the @@ -864,12 +898,11 @@ time they are not used. Some additional information on data frames: -* Usually created by `read.csv()` and `read.table()`. -* Can convert to matrix with `data.matrix()` (preferred) or `as.matrix()` -* Coercion will be forced and not always what you expect. -* Can also create with `data.frame()` function. +* Usually created by `read.csv()` and `read.table()`, i.e. when importing the data into R. +* Assuming all columns in a data frame are of same type, data frame can be converted to a matrix with data.matrix() (preferred) or as.matrix(). Otherwise type coercion will be enforced and the results may not always be what you expect. +* Can also create a new data frame with `data.frame()` function. * Find the number of rows and columns with `nrow(dat)` and `ncol(dat)`, respectively. -* Rownames are usually 1, 2, ..., n. +* Rownames are often automatically generated and look like 1, 2, ..., n. Consistency in numbering of rownames may not be honored when rows are reshuffled or subset. ### Creating Data Frames by Hand @@ -901,12 +934,12 @@ dat > ## Useful Data Frame Functions > -> * `head()` - shown first 6 rows -> * `tail()` - show last 6 rows -> * `dim()` - returns the dimensions +> * `head()` - shows first 6 rows +> * `tail()` - shows last 6 rows +> * `dim()` - returns the dimensions of data frame (i.e. number of rows and number of columns) > * `nrow()` - number of rows > * `ncol()` - number of columns -> * `str()` - structure of each column +> * `str()` - structure of data frame - name, type and preview of data in each column > * `names()` - shows the `names` attribute for a data frame, which gives the column names. {: .callout} @@ -914,7 +947,7 @@ See that it is actually a special list: ~~~ -is.list(iris) +is.list(dat) ~~~ {: .r} @@ -928,7 +961,7 @@ is.list(iris) ~~~ -class(iris) +class(dat) ~~~ {: .r} @@ -939,17 +972,66 @@ class(iris) ~~~ {: .output} +Because data frames are rectangular, elements of data frame can be referenced by specifying the row and the column index in single square brackets (similar to matrix). + + +~~~ +dat[1,3] +~~~ +{: .r} + + + +~~~ +[1] 11 +~~~ +{: .output} + +As data frames are also lists, it is possible to refer to columns (which are elements of such list) using the list notation, i.e. either double square brackets or a `$`. + + +~~~ +dat[["y"]] +~~~ +{: .r} + + + +~~~ + [1] 11 12 13 14 15 16 17 18 19 20 +~~~ +{: .output} + + + +~~~ +dat$y +~~~ +{: .r} + + + +~~~ + [1] 11 12 13 14 15 16 17 18 19 20 +~~~ +{: .output} + +The following table summarizes the one-dimensional and two-dimensional data structures in R in relation to diversity of data types they can contain. + | Dimensions | Homogenous | Heterogeneous | | ------- | ---- | ---- | | 1-D | atomic vector | list | | 2-D | matrix | data frame | +> Lists can contain elements that are themselves muti-dimensional (e.g. a lists can contain data frames or another type of objects). Lists can also contain elements of any length, therefore list do not necessarily have to be "rectangular". However in order for the list to qualify as a data frame, the lenghth of each element has to be the same. +{: .callout} + > ## Column Types in Data Frames > -> Knowing that data frames are lists of lists, can columns be of different type? +> Knowing that data frames are lists, can columns be of different type? > -> What type of structure do you expect on the iris data frame? Hint: Use `str()`. +> What type of structure do you expect to see when you explore the structure of the `iris` data frame? Hint: Use `str()`. > > ~~~ > # The Sepal.Length, Sepal.Width, Petal.Length and Petal.Width columns are all diff --git a/_episodes/15-supp-loops-in-depth.md b/_episodes/15-supp-loops-in-depth.md index 74f501e98..74da96c4a 100644 --- a/_episodes/15-supp-loops-in-depth.md +++ b/_episodes/15-supp-loops-in-depth.md @@ -219,7 +219,7 @@ system.time(avg2 <- analyze2(filenames)) ~~~ user system elapsed - 0.076 0.004 0.149 + 0.057 0.004 0.060 ~~~ {: .output} @@ -249,7 +249,7 @@ system.time(avg3 <- analyze3(filenames)) ~~~ user system elapsed - 0.050 0.002 0.054 + 0.047 0.003 0.047 ~~~ {: .output} From 11e00b91b91c9a8997628b696db0bba77f6c3acc Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Fri, 31 Mar 2017 13:42:15 -0400 Subject: [PATCH 54/76] update md files from #271 #251 8c8c28cab7c640986fc3e5483ddc4c6228f7b329 --- _episodes/06-best-practices-R.md | 32 +++++++++++++++------------- _episodes/13-supp-data-structures.md | 1 + _episodes/15-supp-loops-in-depth.md | 4 ++-- 3 files changed, 20 insertions(+), 17 deletions(-) diff --git a/_episodes/06-best-practices-R.md b/_episodes/06-best-practices-R.md index 96c2f36e3..e51b68c4f 100644 --- a/_episodes/06-best-practices-R.md +++ b/_episodes/06-best-practices-R.md @@ -7,7 +7,7 @@ questions: objectives: - "Define best formatting practices when writing code in R scripts." - "Synthesize a consistent personal coding style to increase code readability, consistency, and repeatability." -- "Apply this style to one's own code." +- "Apply this style to your own code." keypoints: - "Start each program with a description of what it does." - "Then load all required packages." @@ -27,16 +27,16 @@ keypoints: -1. Start your code with an annotated description of what the code does when it is run: +1. Start your code with an annotated description of what the code does: ~~~ -# This is code to replicate the analyses and figures from my 2014 Science paper. -# Code developed by Sarah Supp, Tracy Teal, and Jon Borelli +#This is code to replicate the analyses and figures from my 2014 Science paper. +#Code developed by Sarah Supp, Tracy Teal, and Jon Borelli ~~~ {: .r} -2. Next, load all of the packages that will be necessary to run your code (using `library`): +2. Next, load all of the packages needed to run your code (using `library()`): ~~~ @@ -46,14 +46,16 @@ library(vegan) ~~~ {: .r} +If you use only one or two functions from a package, it is sometimes useful to note that fact in a comment, e.g. `library(reshape2) ## for melt()` + 3. Set your working directory before `source()`ing a script, or start `R` inside your project folder: -One should exercise caution when using `setwd()`. Changing directories in a script file can limit reproducibility: +Exercise caution when using `setwd()`. Changing directories in a script file can limit reproducibility: -* `setwd()` will return an error if the directory to which you're trying to change doesn't exit or if the user doesn't have the correct permissions to access that directory. This becomes a problem when sharing scripts between users who have organized their directories differently. -* If/when your script terminates with an error, you might leave the user in a different directory than the one they started in, and if they then call the script again, this will cause further problems. If you must use `setwd()`, it is best to put it at the top of the script to avoid these problems. +* `setwd()` will return an error if the directory you're trying to change to doesn't exist or if the user doesn't have the correct permissions to access that directory. This becomes a problem when sharing scripts between users who have organized their directories differently. +* If/when your script terminates with an error, you might leave the user in a different directory than the one they started in, which will cause further problems if they then call the script again. If you must use `setwd()`, it is best to put it at the top of the script to avoid these problems. Putting a commented-out `setwd()` call at the top of your code can be a reasonable compromise: it reminds you where on your machine your material is living, is easy to copy-and-paste if necessary, but doesn't commit other users. -The following error message indicates that R has failed to set the working directory you specified: +This error message indicates that R has failed to set the working directory you specified: ``` Error in setwd("~/path/to/working/directory") : cannot change working directory @@ -63,7 +65,7 @@ It is best practice to have the user running the script begin in a consistent di 4. Annotate and mark your code using `#` or `#-` to set off sections of your code and to make finding specific parts of your code easier. -5. If you create only one or a few custom functions in your script, put them toward the top of your code so they are among the first objects created. If you have written many functions, put them all in their own .R file and then `source` those files. `source` will define all of these functions so that your code can make use of them as needed. For the reasons listed above, try to avoid using `setwd()` (or other functions that have side-effects in the user's workspace) in scripts you `source`. +5. If you create only a few custom functions in your script, put them toward the top of your code so they are among the first objects created. If you have written many functions, put them all in their own .R file and then `source()` those files. `source()` will define all of these functions so that your code can use them as needed. For the reasons listed above, avoid using `setwd()` (or other functions that have side-effects in the user's workspace) in scripts you `source()`. ~~~ @@ -71,7 +73,7 @@ source("my_genius_fxns.R") ~~~ {: .r} -6. Use a consistent style within your code. For example, name all matrices something ending in `.mat`. Consistency makes code easier to read and problems easier to spot. +6. Use a consistent style within your code. For example, name all matrices something ending in `.mat`. Indent consistently and decide on a scheme for multi-word variable names (e.g. `resource.use`, `resource_use`, or `resourceUse`). Consistency makes code easier to read and problems easier to spot. 7. Keep your code in bite-sized chunks. If a single function or loop gets too long, consider looking for ways to break it into smaller pieces. @@ -93,22 +95,22 @@ dat <- read.csv(file = "/Users/Karthik/Documents/sannic-project/files/dataset-20 ~~~ {: .r} -10. R can run into memory issues. It is a common problem to run out of memory after running R scripts for a long time. To inspect the objects in your current R environment, you can list the objects, search current packages, and remove objects that are currently not in use. A good practice when running long lines of computationally intensive code is to remove temporary objects after they have served their purpose. However, sometimes, R will not clean up unused memory for a while after you delete objects. You can force R to tidy up its memory by using `gc()`. +10. R can run into memory issues. R scripts that run for a long time often run out of memory. To inspect the objects in your current R environment, you can list the objects, search current packages, and remove objects that are currently not in use. A good practice when running long chunks of computationally intensive code is to remove temporary objects after they have served their purpose. However, R will not always clean up unused memory immediately after you delete objects. You can force R to tidy up its memory by using `gc()`. ~~~ interim_object <- data.frame(rep(1:100,10),rep(101:200,10),rep(201:300,10)) # Sample dataset of 1000 rows object.size(interim_object) # Reports the memory size allocated to the object -rm(interim_object) # Removes only the object itself and not necessarily the memory allotted to it +rm("interim_object") # Removes only the object itself and not necessarily the memory allotted to it gc() # Force R to release memory it is no longer using ls() # Lists all the objects in your current workspace rm(list = ls()) # If you want to delete all the objects in the workspace and start with a clean slate ~~~ {: .r} -11. Don't save a session history (the default option in R, when it asks if you want an `RData` file). Instead, start in a clean environment so that older objects don't remain in your environment any longer than they need to. If that happens, it can lead to unexpected results. +11. Don't save your workspace (the default option in R, when it asks if you want to "Save workspace image [y/n/c]?"). Instead, start in a clean workspace without old objects cluttering it. Leftover objects from previous sessions can lead to unexpected, hard-to-debug results. Do *not* put `rm(list=ls())` (which removes all objects in your current workspace, as shown in the previous code example) at the top of your code, as this is a trap for other users who might `source()` or copy-and-paste your code in the course of their R session. Instead, restart R when you want to start fresh. -12. Wherever possible, keep track of `sessionInfo()` somewhere in your project folder. Session information is invaluable because it captures all of the packages used in the current project. If a newer version of a package changes the way a function behaves, you can always go back and reinstall the version that worked (Note: At least on CRAN, all older versions of packages are permanently archived). +12. Wherever possible, keep track of `sessionInfo()` somewhere in your project folder. Session information is invaluable because it captures all of the packages used in the current project. If a newer version of a package changes the way a function behaves, you can always go back and reinstall the version that worked (Note: At least on CRAN, all older versions of packages are permanently archived). For more complex projects, you may want to use the [packrat](https://CRAN.R-project.org/package=packrat) package. 13. Collaborate. Grab a buddy and practice "code review". Review is used for preparing experiments and manuscripts; why not use it for code as well? Our code is also a major scientific achievement and the product of lots of hard work! diff --git a/_episodes/13-supp-data-structures.md b/_episodes/13-supp-data-structures.md index 10f32560d..15e0978fa 100644 --- a/_episodes/13-supp-data-structures.md +++ b/_episodes/13-supp-data-structures.md @@ -941,6 +941,7 @@ dat > * `ncol()` - number of columns > * `str()` - structure of data frame - name, type and preview of data in each column > * `names()` - shows the `names` attribute for a data frame, which gives the column names. +> * `sapply(dataframe, class)` - shows the class of each column in the data frame {: .callout} See that it is actually a special list: diff --git a/_episodes/15-supp-loops-in-depth.md b/_episodes/15-supp-loops-in-depth.md index 74da96c4a..564b0dd82 100644 --- a/_episodes/15-supp-loops-in-depth.md +++ b/_episodes/15-supp-loops-in-depth.md @@ -219,7 +219,7 @@ system.time(avg2 <- analyze2(filenames)) ~~~ user system elapsed - 0.057 0.004 0.060 + 0.080 0.003 0.084 ~~~ {: .output} @@ -249,7 +249,7 @@ system.time(avg3 <- analyze3(filenames)) ~~~ user system elapsed - 0.047 0.003 0.047 + 0.064 0.004 0.068 ~~~ {: .output} From 7f64b0abdd63d57a8fe155613bbaaf774dfce0d0 Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Thu, 6 Apr 2017 15:26:54 -0400 Subject: [PATCH 55/76] fix merge conflicts and incorporate changes from #270 --- README.md | 10 +++++----- _episodes_rmd/01-starting-with-data.Rmd | 2 +- _episodes_rmd/03-loops-R.Rmd | 5 +++-- _episodes_rmd/04-cond.Rmd | 2 +- _episodes_rmd/06-best-practices-R.Rmd | 3 ++- _extras/guide.md | 10 ++++------ 6 files changed, 16 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index baa72e61d..54b32ba9c 100644 --- a/README.md +++ b/README.md @@ -11,13 +11,13 @@ Maintainers: The goal of this lesson is to teach novice programmers to write modular code to perform a data analysis. R is used to teach these skills because it is a commonly used programming language in many scientific disciplines. However, the -emphasis is not on teaching every aspect of R, but instead the focus is on +emphasis is not on teaching every aspect of R, but instead on language agnostic principles like automation with loops and encapsulation with functions (see [Best Practices for Scientific Computing][best-practices] to -learn more). In fact, this lesson is a translation of the [Python version][py], -and the lesson is also available in [MATLAB][]. +learn more). This lesson is a translation of the [Python version][py], +and is also available in [MATLAB][MATLAB]. -The example used in this lesson is analyzing a set of 12 data files with +The example used in this lesson analyzes a set of 12 data files with inflammation data collected from a trial for a new treatment for arthritis (the data was simulated). Learners are shown how it is better to create a function and apply it to each of the 12 files using a loop instead of using copy-paste @@ -42,7 +42,7 @@ To view how the changes will look, when viewed in a web browser, you can render Once you've made your edits and rendered the corresponding html files, you need to add, commit, and push just the source R Markdown file(s) -and any supporting files (e.g. data files). Changes generated by the `make preview` command should not be committed or included in a pull request. These changes will be taken care off by the lesson maintainer when the PR is merged. +and any supporting files (e.g. data files). Changes generated by the `make preview` command should not be committed or included in a pull request. These changes will be taken care of by the lesson maintainer when the PR is merged. ## Getting Help diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index fde84d6f6..ea919ea93 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -430,7 +430,7 @@ We'll learn why this is so in the next lesson. > > ## Solution > > ~~~ > > whichPatients <- seq(2,40,2) -> > whichDays <- c(1:5) +> > whichDays <- 1:5 > > dat2 <- dat > > dat2[whichDays, whichPatients] <- dat2[whichDays, whichPatients]/2 > > (dat2) diff --git a/_episodes_rmd/03-loops-R.Rmd b/_episodes_rmd/03-loops-R.Rmd index 08c8a7d39..320f1693f 100644 --- a/_episodes_rmd/03-loops-R.Rmd +++ b/_episodes_rmd/03-loops-R.Rmd @@ -103,7 +103,7 @@ print_words <- function(sentence) { print_words(best_practice) ``` -This is shorter---certainly shorter than something that prints every character in a hundred-letter string---and more robust as well: +This is shorter - certainly shorter than something that prints every character in a hundred-letter string - and more robust as well: ```{r} print_words(best_practice[-6]) @@ -120,7 +120,8 @@ for (variable in collection) { We can name the [loop variable]({{ page.root }}/reference/#loop-variable) anything we like (with a few [restrictions][], e.g. the name of the variable cannot start with a digit). `in` is part of the `for` syntax. -Note that the body of the loop is enclosed in curly braces `{ }`. +Note that the condition (`variable in collection`) is enclosed in parentheses, +and the body of the loop is enclosed in curly braces `{ }`. For a single-line loop body, as here, the braces aren't needed, but it is good practice to include them as we did. [restrictions]: http://cran.r-project.org/doc/manuals/R-intro.html#R-commands_003b-case-sensitivity-etc diff --git a/_episodes_rmd/04-cond.Rmd b/_episodes_rmd/04-cond.Rmd index 0000f2e0c..30d90e594 100644 --- a/_episodes_rmd/04-cond.Rmd +++ b/_episodes_rmd/04-cond.Rmd @@ -152,7 +152,7 @@ sign(0) sign(2/3) ``` -Note that when combining `else` and `if` in an `else if` statement (similar to `elif` in Python), the `if` portion still requires a direct input condition. This is never the case for the `else` statement alone, which is only executed if all other conditions go unsatisfied. +Note that when combining `else` and `if` in an `else if` statement, the `if` portion still requires a direct input condition. This is never the case for the `else` statement alone, which is only executed if all other conditions go unsatisfied. Note that the test for equality uses two equal signs, `==`. > ## Other Comparisons diff --git a/_episodes_rmd/06-best-practices-R.Rmd b/_episodes_rmd/06-best-practices-R.Rmd index 807c5e44a..5808443ee 100644 --- a/_episodes_rmd/06-best-practices-R.Rmd +++ b/_episodes_rmd/06-best-practices-R.Rmd @@ -19,7 +19,7 @@ keypoints: - "Factor out common operations rather than repeating them." - "Keep all of the source files for a project in one directory and use relative paths to access them." - "Keep track of the memory used by your program." -- "Always start with a clean environment instead of saving session history." +- "Always start with a clean environment instead of saving the workspace." - "Keep track of session information in your project folder." - "Have someone else review your code." - "Use version control." @@ -50,6 +50,7 @@ If you use only one or two functions from a package, it is sometimes useful to n Exercise caution when using `setwd()`. Changing directories in a script file can limit reproducibility: + * `setwd()` will return an error if the directory you're trying to change to doesn't exist or if the user doesn't have the correct permissions to access that directory. This becomes a problem when sharing scripts between users who have organized their directories differently. * If/when your script terminates with an error, you might leave the user in a different directory than the one they started in, which will cause further problems if they then call the script again. If you must use `setwd()`, it is best to put it at the top of the script to avoid these problems. Putting a commented-out `setwd()` call at the top of your code can be a reasonable compromise: it reminds you where on your machine your material is living, is easy to copy-and-paste if necessary, but doesn't commit other users. diff --git a/_extras/guide.md b/_extras/guide.md index 8e08ec5f8..590284185 100644 --- a/_extras/guide.md +++ b/_extras/guide.md @@ -79,13 +79,11 @@ line and this should resolve the issue. ## Teaching Notes * Watching the instructor grow programs step by step - is as helpful to learners as anything to do with Python. - Resist the urge to update a single cell repeatedly + is as helpful to learners as anything to do with R. + Resist the urge to clean up your R script as you go (which is what you'd probably do in real life). - Instead, - clone the previous cell and write the update in the new copy - so that learners have a complete record of how the program grew. - Once you've done this, + Instead, keep intermediate steps in your script. + Once you've reached the final version you can say, "Now why don't we just breaks things into small functions right from the start?" From af17754a008697e373fc6c32f996013e4bc1537c Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Thu, 6 Apr 2017 15:45:58 -0400 Subject: [PATCH 56/76] undo c() for further discussion --- _episodes_rmd/01-starting-with-data.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index ea919ea93..fde84d6f6 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -430,7 +430,7 @@ We'll learn why this is so in the next lesson. > > ## Solution > > ~~~ > > whichPatients <- seq(2,40,2) -> > whichDays <- 1:5 +> > whichDays <- c(1:5) > > dat2 <- dat > > dat2[whichDays, whichPatients] <- dat2[whichDays, whichPatients]/2 > > (dat2) From 2c2b2df9c1751df4c0b110502a4dbdc1857871c1 Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Thu, 6 Apr 2017 15:47:07 -0400 Subject: [PATCH 57/76] updates from #270 --- _episodes/03-loops-R.md | 5 +++-- _episodes/04-cond.md | 2 +- _episodes/06-best-practices-R.md | 3 ++- _episodes/15-supp-loops-in-depth.md | 4 ++-- 4 files changed, 8 insertions(+), 6 deletions(-) diff --git a/_episodes/03-loops-R.md b/_episodes/03-loops-R.md index ff82f3dc2..bbd821d73 100644 --- a/_episodes/03-loops-R.md +++ b/_episodes/03-loops-R.md @@ -163,7 +163,7 @@ print_words(best_practice) ~~~ {: .output} -This is shorter---certainly shorter than something that prints every character in a hundred-letter string---and more robust as well: +This is shorter - certainly shorter than something that prints every character in a hundred-letter string - and more robust as well: ~~~ @@ -195,7 +195,8 @@ for (variable in collection) { We can name the [loop variable]({{ page.root }}/reference/#loop-variable) anything we like (with a few [restrictions][], e.g. the name of the variable cannot start with a digit). `in` is part of the `for` syntax. -Note that the body of the loop is enclosed in curly braces `{ }`. +Note that the condition (`variable in collection`) is enclosed in parentheses, +and the body of the loop is enclosed in curly braces `{ }`. For a single-line loop body, as here, the braces aren't needed, but it is good practice to include them as we did. [restrictions]: http://cran.r-project.org/doc/manuals/R-intro.html#R-commands_003b-case-sensitivity-etc diff --git a/_episodes/04-cond.md b/_episodes/04-cond.md index bb9ff1f4a..a026faaac 100644 --- a/_episodes/04-cond.md +++ b/_episodes/04-cond.md @@ -220,7 +220,7 @@ sign(2/3) ~~~ {: .output} -Note that when combining `else` and `if` in an `else if` statement (similar to `elif` in Python), the `if` portion still requires a direct input condition. This is never the case for the `else` statement alone, which is only executed if all other conditions go unsatisfied. +Note that when combining `else` and `if` in an `else if` statement, the `if` portion still requires a direct input condition. This is never the case for the `else` statement alone, which is only executed if all other conditions go unsatisfied. Note that the test for equality uses two equal signs, `==`. > ## Other Comparisons diff --git a/_episodes/06-best-practices-R.md b/_episodes/06-best-practices-R.md index e51b68c4f..1cdd17c80 100644 --- a/_episodes/06-best-practices-R.md +++ b/_episodes/06-best-practices-R.md @@ -19,7 +19,7 @@ keypoints: - "Factor out common operations rather than repeating them." - "Keep all of the source files for a project in one directory and use relative paths to access them." - "Keep track of the memory used by your program." -- "Always start with a clean environment instead of saving session history." +- "Always start with a clean environment instead of saving the workspace." - "Keep track of session information in your project folder." - "Have someone else review your code." - "Use version control." @@ -52,6 +52,7 @@ If you use only one or two functions from a package, it is sometimes useful to n Exercise caution when using `setwd()`. Changing directories in a script file can limit reproducibility: + * `setwd()` will return an error if the directory you're trying to change to doesn't exist or if the user doesn't have the correct permissions to access that directory. This becomes a problem when sharing scripts between users who have organized their directories differently. * If/when your script terminates with an error, you might leave the user in a different directory than the one they started in, which will cause further problems if they then call the script again. If you must use `setwd()`, it is best to put it at the top of the script to avoid these problems. Putting a commented-out `setwd()` call at the top of your code can be a reasonable compromise: it reminds you where on your machine your material is living, is easy to copy-and-paste if necessary, but doesn't commit other users. diff --git a/_episodes/15-supp-loops-in-depth.md b/_episodes/15-supp-loops-in-depth.md index 564b0dd82..618327b25 100644 --- a/_episodes/15-supp-loops-in-depth.md +++ b/_episodes/15-supp-loops-in-depth.md @@ -219,7 +219,7 @@ system.time(avg2 <- analyze2(filenames)) ~~~ user system elapsed - 0.080 0.003 0.084 + 0.023 0.000 0.023 ~~~ {: .output} @@ -249,7 +249,7 @@ system.time(avg3 <- analyze3(filenames)) ~~~ user system elapsed - 0.064 0.004 0.068 + 0.020 0.000 0.022 ~~~ {: .output} From 38307ff35b01ef8c1521473676a43742b5f9601a Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Tue, 4 Apr 2017 08:02:53 +0100 Subject: [PATCH 58/76] Add Library Carpentry to the workshop template Includes @drjwbaker's description of Library Carpentry. --- _includes/dc/intro.html | 18 +++++++ _includes/dc/schedule.html | 24 +++++++++ _includes/dc/syllabus.html | 96 +++++++++++++++++++++++++++++++++ _includes/dc/who.html | 8 +++ _includes/lc/intro.html | 19 +++++++ _includes/lc/schedule.html | 24 +++++++++ _includes/lc/syllabys.html | 69 ++++++++++++++++++++++++ _includes/lc/who.html | 8 +++ _includes/navbar.html | 14 +---- _includes/sc/intro.html | 18 +++++++ _includes/sc/schedule.html | 24 +++++++++ _includes/sc/syllabus.html | 96 +++++++++++++++++++++++++++++++++ _includes/sc/who.html | 8 +++ _includes/workshop_footer.html | 19 +++++-- assets/img/lc-icon-black.png | Bin 0 -> 18753 bytes 15 files changed, 428 insertions(+), 17 deletions(-) create mode 100644 _includes/dc/intro.html create mode 100644 _includes/dc/schedule.html create mode 100644 _includes/dc/syllabus.html create mode 100644 _includes/dc/who.html create mode 100644 _includes/lc/intro.html create mode 100644 _includes/lc/schedule.html create mode 100644 _includes/lc/syllabys.html create mode 100644 _includes/lc/who.html create mode 100644 _includes/sc/intro.html create mode 100644 _includes/sc/schedule.html create mode 100644 _includes/sc/syllabus.html create mode 100644 _includes/sc/who.html create mode 100644 assets/img/lc-icon-black.png diff --git a/_includes/dc/intro.html b/_includes/dc/intro.html new file mode 100644 index 000000000..741aeebb5 --- /dev/null +++ b/_includes/dc/intro.html @@ -0,0 +1,18 @@ +

    + Data Carpentry + aims to help researchers get their work done + in less time and with less pain + by teaching them basic research computing skills. + This hands-on workshop will cover basic concepts and tools, + including program design, version control, data management, + and task automation. + Participants will be encouraged to help one another + and to apply what they have learned to their own research problems. +

    +

    + + For more information on what we teach and why, + please see our paper + "Best Practices for Scientific Computing". + +

    diff --git a/_includes/dc/schedule.html b/_includes/dc/schedule.html new file mode 100644 index 000000000..6894a19e3 --- /dev/null +++ b/_includes/dc/schedule.html @@ -0,0 +1,24 @@ +
    +
    +

    Day 1

    +
    Setup Dowload files used on the lesson.
    {% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} Finish
    {% if episode.start %}Day {{ day }}{% endif %}{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} {{ episode.title }}
    {% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} Finish
    {% if episode.start %}Day {{ day }}{% endif %}{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }} - {{ episode.title }} + {% assign lesson_number = lesson_number | plus: 1 %} + {{ lesson_number }}. {{ episode.title }} {% if episode.break %} From f994dfbedc0b992a73ae966a21d2c82aaf9c7c25 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 3 Mar 2017 21:37:22 +0000 Subject: [PATCH 45/76] Revert "ensure dt elements have an id set" --- _includes/javascript.html | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/_includes/javascript.html b/_includes/javascript.html index 93b515273..a2066c202 100644 --- a/_includes/javascript.html +++ b/_includes/javascript.html @@ -12,22 +12,3 @@ ga('create', 'UA-37305346-2', 'auto'); ga('send', 'pageview'); - From 6739c209db200c12b94f8d9a0c36f1f789378194 Mon Sep 17 00:00:00 2001 From: Stefan Topfstedt Date: Sat, 4 Mar 2017 18:21:04 -0800 Subject: [PATCH 46/76] fixed variable positioning switcheroo. --- _episodes/01-starting-with-data.md | 2 +- _episodes_rmd/01-starting-with-data.Rmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_episodes/01-starting-with-data.md b/_episodes/01-starting-with-data.md index fc9cfd005..3e9f6f79b 100644 --- a/_episodes/01-starting-with-data.md +++ b/_episodes/01-starting-with-data.md @@ -724,7 +724,7 @@ We'll learn why this is so in the next lesson. > > whichPatients <- seq(2,40,2) > > whichDays <- c(1:5) > > dat2 <- dat -> > dat2[whichPatients,whichDays] <- dat2[whichPatients,whichDays]/2 +> > dat2[whichDays,whichPatients] <- dat2[whichDays,whichPatients]/2 > > (dat2) > > ~~~ > > {: .r} diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index 97611564a..1ffff1d8e 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -413,7 +413,7 @@ We'll learn why this is so in the next lesson. > > whichPatients <- seq(2,40,2) > > whichDays <- c(1:5) > > dat2 <- dat -> > dat2[whichPatients,whichDays] <- dat2[whichPatients,whichDays]/2 +> > dat2[whichDays,whichPatients] <- dat2[whichDays,whichPatients]/2 > > (dat2) > > ~~~ > > {: .r} From b452d7c2581d8c9f08a301e6a697c3e672803ac4 Mon Sep 17 00:00:00 2001 From: Nick Young Date: Wed, 8 Mar 2017 12:59:21 +1300 Subject: [PATCH 47/76] fix anchor links --- _episodes_rmd/01-starting-with-data.Rmd | 4 ++-- _episodes_rmd/05-cmdline.Rmd | 4 ++-- _episodes_rmd/11-supp-read-write-csv.Rmd | 2 +- index.md | 2 +- reference.md | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index 97611564a..628ad7eee 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -36,7 +36,7 @@ knitr_fig_path("01-starting-with-data-") We are studying inflammation in patients who have been given a new treatment for arthritis, and need to analyze the first dozen data sets. -The data sets are stored in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-(csv)) (CSV) format. Each row holds the observations for just one patient. Each column holds the inflammation measured in a day, so we have a set of values in successive days. +The data sets are stored in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-csv) (CSV) format. Each row holds the observations for just one patient. Each column holds the inflammation measured in a day, so we have a set of values in successive days. The first few rows of our first file look like this: ```{r echo = FALSE} @@ -223,7 +223,7 @@ class(dat) The output tells us that is a data frame. Think of this structure as a spreadsheet in MS Excel that many of us are familiar with. Data frames are very useful for storing data and you will find them elsewhere when programming in R. A typical data frame of experimental data contains individual observations in rows and variables in columns. -We can see the shape, or [dimensions]({{ page.root }}/reference/#dimensions), of the data frame with the function `dim`: +We can see the shape, or [dimensions]({{ page.root }}/reference/#dimensions-of-an-array), of the data frame with the function `dim`: ```{r} dim(dat) diff --git a/_episodes_rmd/05-cmdline.Rmd b/_episodes_rmd/05-cmdline.Rmd index 02ea5c0c4..c24974bd0 100644 --- a/_episodes_rmd/05-cmdline.Rmd +++ b/_episodes_rmd/05-cmdline.Rmd @@ -52,7 +52,7 @@ $ Rscript readings.R --max data/inflammation-*.csv Our overall requirements are: -1. If no filename is given on the command line, read data from [standard input]({{ page.root }}/reference/#standard-input). +1. If no filename is given on the command line, read data from [standard input]({{ page.root }}/reference/#standard-input-stdin). 2. If one or more filenames are given, read data from them and report statistics for each file separately. 3. Use the `--min`, `--mean`, or `--max` flag to determine what statistic to print. @@ -92,7 +92,7 @@ cat print-args.R The function `commandArgs` extracts all the command line arguments and returns them as a vector. The function `cat`, similar to the `cat` of the Unix Shell, outputs the contents of the variable. -Since we did not specify a filename for writing, `cat` sends the output to [standard output]({{ page.root }}/reference/#standard-output-(stdout)), +Since we did not specify a filename for writing, `cat` sends the output to [standard output]({{ page.root }}/reference/#standard-output-stdout), which we can then pipe to other Unix functions. Because we set the argument `sep` to `"\n"`, which is the symbol to start a new line, each element of the vector is printed on its own line. Let's see what happens when we run this program in the Unix Shell: diff --git a/_episodes_rmd/11-supp-read-write-csv.Rmd b/_episodes_rmd/11-supp-read-write-csv.Rmd index 4c06e1f2c..94e1c9ee7 100644 --- a/_episodes_rmd/11-supp-read-write-csv.Rmd +++ b/_episodes_rmd/11-supp-read-write-csv.Rmd @@ -21,7 +21,7 @@ source('../bin/chunk-options.R') The most common way that scientists store data is in Excel spreadsheets. While there are R packages designed to access data from Excel spreadsheets (e.g., gdata, RODBC, XLConnect, xlsx, RExcel), -users often find it easier to save their spreadsheets in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-(csv)) files (CSV) +users often find it easier to save their spreadsheets in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-csv) files (CSV) and then use R's built in functionality to read and manipulate the data. In this short lesson, we'll learn how to read data from a .csv and write to a new .csv, and explore the [arguments]({{ page.root }}/reference/#argument) that allow you read and write the data correctly for your needs. diff --git a/index.md b/index.md index 88659e661..2305bada6 100644 --- a/index.md +++ b/index.md @@ -23,7 +23,7 @@ and to use that language *well*. We are studying inflammation in patients who have been given a new treatment for arthritis, and need to analyze the first dozen data sets of their daily inflammation. -The data sets are stored in [comma-separated values]({{ page.root }}/reference/#comma-separated-values) (CSV) format: +The data sets are stored in [comma-separated values]({{ page.root }}/reference/#comma-separated-values-csv) (CSV) format: each row holds information for a single patient, and the columns represent successive days. The first few rows of our first file look like this: diff --git a/reference.md b/reference.md index ae2a25c53..2e6099065 100644 --- a/reference.md +++ b/reference.md @@ -174,10 +174,10 @@ stack frame : A data structure that provides storage for a function's local variables. Each time a function is called, a new stack frame is created and put on the top of the [call stack](#call-stack). When the function returns, the stack frame is discarded. standard input (stdin) -: A process's default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a [pipe](#pipe), it receives data from the [standard output](#standard-output) of the preceding process. +: A process's default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a [pipe](#pipe), it receives data from the [standard output](#standard-output-stdout) of the preceding process. standard output (stdout) -: A process's default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a [pipe](#pipe), it is passed to the [standard input](#standard-input) of the next process. +: A process's default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a [pipe](#pipe), it is passed to the [standard input](#standard-input-stdin) of the next process. string : Short for "character string", a sequence of zero or more characters. From 12506a4b66016088a5c8582ac6e34ccb2cdb13f3 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Tue, 14 Mar 2017 14:22:16 +0000 Subject: [PATCH 48/76] Improve wording on syllabus.html As suggested by @gcapes. --- _includes/syllabus.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/syllabus.html b/_includes/syllabus.html index 118e58489..1adfac44a 100644 --- a/_includes/syllabus.html +++ b/_includes/syllabus.html @@ -17,7 +17,7 @@

    Schedule

    {% if multiday %}    		 SetupDowload files used on the lesson.Download files required for the lesson
    + + + + + + +
    09:00 Automating tasks with the Unix shell
    10:30 Coffee
    12:00 Lunch break
    13:00 Building programs with Python
    14:30 Coffee
    16:00 Wrap-up
    + +
    +

    Day 2

    + + + + + + + +
    09:00 Version control with Git
    10:30 Coffee
    12:00 Lunch break
    13:00 Managing data with SQL
    14:30 Coffee
    16:00 Wrap-up
    +
    + diff --git a/_includes/dc/syllabus.html b/_includes/dc/syllabus.html new file mode 100644 index 000000000..a325ceec2 --- /dev/null +++ b/_includes/dc/syllabus.html @@ -0,0 +1,96 @@ +
    +
    +

    The Unix Shell

    +
      +
    • Files and directories
      • +
    • History and tab completion
      • +
    • Pipes and redirection
      • +
    • Looping over files
      • +
    • Creating and running shell scripts
      • +
    • Finding things
      • +
    • Reference...
      • +
    +
    +
    +

    Programming in Python

    +
      +
    • Using libraries
      • +
    • Working with arrays
      • +
    • Reading and plotting data
      • +
    • Creating and using functions
      • +
    • Loops and conditionals
      • +
    • Defensive programming
      • +
    • Using Python from the command line
      • +
    • Reference...
      • +
    +
    + + +
    + +
    +
    +

    Version Control with Git

    +
      +
    • Creating a repository
      • +
    • Recording changes to files: add, commit, ...
      • +
    • Viewing changes: status, diff, ...
      • +
    • Ignoring files
      • +
    • Working on the web: clone, pull, push, ...
      • +
    • Resolving conflicts
      • +
    • Open licenses
      • +
    • Where to host work, and why
      • +
    • Reference...
      • +
    +
    + +
    +

    Open Refine

    +
      +
    • Introduction to OpenRefine
      • +
    • Importing data
      • +
    • Basic functions
      • +
    • Advanced Functions
      • +
    • Reference...
      • +
    +
    +
    diff --git a/_includes/dc/who.html b/_includes/dc/who.html new file mode 100644 index 000000000..2d8e94ae3 --- /dev/null +++ b/_includes/dc/who.html @@ -0,0 +1,8 @@ +

    + Who: + The course is aimed at graduate students and other researchers. + + You don't need to have any previous knowledge of the tools + that will be presented at the workshop. + +

    diff --git a/_includes/lc/intro.html b/_includes/lc/intro.html new file mode 100644 index 000000000..6794b542c --- /dev/null +++ b/_includes/lc/intro.html @@ -0,0 +1,19 @@ +

    + Library Carpentry + is made by librarians, for librarians to help you: +

    +
      +
    • automate repetitive, boring, error-prone tasks
      • +
    • create, maintain and analyse sustainable and reusable data
      • +
    • work effectively with IT and systems colleagues
      • +
    • better understand the use of software in research
      • +
    • and much more...
      • +
    +

    + + Library Carpentry introduces you to the fundamentals of computing + and provides you with a platform for further self-directed learning. + For more information on what we teach and why, please see our paper + "Library Carpentry: software skills training for library professionals". + +

    diff --git a/_includes/lc/schedule.html b/_includes/lc/schedule.html new file mode 100644 index 000000000..cc2b59202 --- /dev/null +++ b/_includes/lc/schedule.html @@ -0,0 +1,24 @@ +
    +
    +

    Day 1

    + + + + + + + +
    09:00 Data Intro for Librarians
    10:30 Coffee
    12:00 Lunch break
    13:00 Shell Lessons for Libraries
    14:30 Coffee
    16:00 Wrap-up
    +
    +
    +

    Day 2

    + + + + + + + +
    09:00 Git Intro for Librarians
    10:30 Coffee
    12:00 Lunch break
    13:00 OpenRefine for Librarians
    14:30 Coffee
    16:00 Wrap-up
    +
    +
    diff --git a/_includes/lc/syllabys.html b/_includes/lc/syllabys.html new file mode 100644 index 000000000..4dc20776d --- /dev/null +++ b/_includes/lc/syllabys.html @@ -0,0 +1,69 @@ +
    +
    +

    Data Intro

    +
      +
    • Intro to data
      • +
    • Jargon busting
      • +
    • Keyboard shortcuts
      • +
    • Plain text formats
      • +
    • Naming files
      • +
    • Regular expressions
      • +
    • Reference...
      • +
    +
    +
    +

    The Unix Shell

    +
      +
    • Files and directories
      • +
    • History and tab completion
      • +
    • Counting and sorting contents in files
      • +
    • Pipes and redirection
      • +
    • Mining or searching in files
      • +
    • Reference...
      • +
    +
    + +
    + +
    +
    +

    Version Control with Git

    +
      +
    • Creating a repository
      • +
    • Configuring git
      • +
    • Recording changes to files: add, commit, ...
      • +
    • Viewing state changes with status
      • +
    • Working on the web: clone, pull, push, ...
      • +
    • Where to host work, and why
      • +
    • Reference...
      • +
    +
    +
    +
    +

    Open Refine

    +
      +
    • Introduction to OpenRefine
      • +
    • Importing data
      • +
    • Basic functions
      • +
    • Advanced Functions
      • +
    • Reference...
      • +
    +
    +
    +
    + diff --git a/_includes/lc/who.html b/_includes/lc/who.html new file mode 100644 index 000000000..fd9b38c47 --- /dev/null +++ b/_includes/lc/who.html @@ -0,0 +1,8 @@ +

    + Who: + The course is for librarians, archivists, and other information workers. + + You don't need to have any previous knowledge of the tools that + will be presented at the workshop. + +

    diff --git a/_includes/navbar.html b/_includes/navbar.html index 6b21afc76..00fd328ba 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -22,19 +22,7 @@ {% elsif page.carpentry == "lc" %} - - - {% elsif site.carpentry == "swc" %} - - - - {% elsif site.carpentry == "dc" %} - - - - {% elsif site.carpentry == "lc" %} - - + {% endif %} diff --git a/_includes/sc/intro.html b/_includes/sc/intro.html new file mode 100644 index 000000000..7b9fbf57b --- /dev/null +++ b/_includes/sc/intro.html @@ -0,0 +1,18 @@ +

    + Software Carpentry + aims to help researchers get their work done + in less time and with less pain + by teaching them basic research computing skills. + This hands-on workshop will cover basic concepts and tools, + including program design, version control, data management, + and task automation. + Participants will be encouraged to help one another + and to apply what they have learned to their own research problems. +

    +

    + + For more information on what we teach and why, + please see our paper + "Best Practices for Scientific Computing". + +

    diff --git a/_includes/sc/schedule.html b/_includes/sc/schedule.html new file mode 100644 index 000000000..6894a19e3 --- /dev/null +++ b/_includes/sc/schedule.html @@ -0,0 +1,24 @@ +
    +
    +

    Day 1

    + + + + + + + +
    09:00 Automating tasks with the Unix shell
    10:30 Coffee
    12:00 Lunch break
    13:00 Building programs with Python
    14:30 Coffee
    16:00 Wrap-up
    +
    +
    +

    Day 2

    + + + + + + + +
    09:00 Version control with Git
    10:30 Coffee
    12:00 Lunch break
    13:00 Managing data with SQL
    14:30 Coffee
    16:00 Wrap-up
    +
    +
    diff --git a/_includes/sc/syllabus.html b/_includes/sc/syllabus.html new file mode 100644 index 000000000..a325ceec2 --- /dev/null +++ b/_includes/sc/syllabus.html @@ -0,0 +1,96 @@ +
    +
    +

    The Unix Shell

    +
      +
    • Files and directories
      • +
    • History and tab completion
      • +
    • Pipes and redirection
      • +
    • Looping over files
      • +
    • Creating and running shell scripts
      • +
    • Finding things
      • +
    • Reference...
      • +
    +
    +
    +

    Programming in Python

    +
      +
    • Using libraries
      • +
    • Working with arrays
      • +
    • Reading and plotting data
      • +
    • Creating and using functions
      • +
    • Loops and conditionals
      • +
    • Defensive programming
      • +
    • Using Python from the command line
      • +
    • Reference...
      • +
    +
    + + +
    + +
    +
    +

    Version Control with Git

    +
      +
    • Creating a repository
      • +
    • Recording changes to files: add, commit, ...
      • +
    • Viewing changes: status, diff, ...
      • +
    • Ignoring files
      • +
    • Working on the web: clone, pull, push, ...
      • +
    • Resolving conflicts
      • +
    • Open licenses
      • +
    • Where to host work, and why
      • +
    • Reference...
      • +
    +
    + +
    +

    Open Refine

    +
      +
    • Introduction to OpenRefine
      • +
    • Importing data
      • +
    • Basic functions
      • +
    • Advanced Functions
      • +
    • Reference...
      • +
    +
    +
    diff --git a/_includes/sc/who.html b/_includes/sc/who.html new file mode 100644 index 000000000..2d8e94ae3 --- /dev/null +++ b/_includes/sc/who.html @@ -0,0 +1,8 @@ +

    + Who: + The course is aimed at graduate students and other researchers. + + You don't need to have any previous knowledge of the tools + that will be presented at the workshop. + +

    diff --git a/_includes/workshop_footer.html b/_includes/workshop_footer.html index 3ae63e6dc..7b2f22ce7 100644 --- a/_includes/workshop_footer.html +++ b/_includes/workshop_footer.html @@ -3,11 +3,22 @@ {% endcomment %} From 1e56203d492a1a13d86756fb5e9d754ed2cae0f8 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Sat, 6 May 2017 10:07:40 +0100 Subject: [PATCH 68/76] Remove CONDUCT.md since it should be generate by bin/lesson_initialize.py --- CONDUCT.md | 45 --------------------------------------------- 1 file changed, 45 deletions(-) delete mode 100644 CONDUCT.md diff --git a/CONDUCT.md b/CONDUCT.md deleted file mode 100644 index 5e4943b4c..000000000 --- a/CONDUCT.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -layout: page -title: "Contributor Code of Conduct" -permalink: /conduct/ ---- -As contributors and maintainers of this project, -we pledge to respect all people who contribute through reporting issues, -posting feature requests, -updating documentation, -submitting pull requests or patches, -and other activities. - -We are committed to making participation in this project a harassment-free experience for everyone, -regardless of level of experience, -gender, -gender identity and expression, -sexual orientation, -disability, -personal appearance, -body size, -race, -ethnicity, -age, -or religion. - -Examples of unacceptable behavior by participants include the use of sexual language or imagery, -derogatory comments or personal attacks, -trolling, -public or private harassment, -insults, -or other unprofessional conduct. - -Project maintainers have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions -that are not aligned to our [Code of Conduct][coc]. -Project maintainers who do not follow the Code of Conduct may be removed from the project team. - -Instances of abusive, harassing, or otherwise unacceptable behavior -may be reported by following our [reporting guidelines][coc-reporting]. - - -- [Software and Data Carpentry Code of Conduct][coc] -- [Code of Conduct Reporting Guide][coc-reporting] - -{% include links.md %} From 98e4bc69b4b03055125a6f888e08b7d08e5cba67 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Sat, 6 May 2017 10:19:56 +0100 Subject: [PATCH 69/76] Fix bug with Python script --- bin/lesson_initialize.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index 513597a40..fc7baf7d8 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -278,7 +278,7 @@ FIXME ''' -ROOT_SETUP_MD = '''\ +ROOT_AIO_MD = '''\ --- layout: page permalink: /aio/ From 9f34e6e952d0d3ab25df0eef4e65a521d2ba4c88 Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Wed, 10 May 2017 11:05:10 +0100 Subject: [PATCH 70/76] Revert "Remove CONDUCT.md since it should be generate by bin/lesson_initialize.py" This reverts commit 1e56203d492a1a13d86756fb5e9d754ed2cae0f8. --- CONDUCT.md | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 CONDUCT.md diff --git a/CONDUCT.md b/CONDUCT.md new file mode 100644 index 000000000..5e4943b4c --- /dev/null +++ b/CONDUCT.md @@ -0,0 +1,45 @@ +--- +layout: page +title: "Contributor Code of Conduct" +permalink: /conduct/ +--- +As contributors and maintainers of this project, +we pledge to respect all people who contribute through reporting issues, +posting feature requests, +updating documentation, +submitting pull requests or patches, +and other activities. + +We are committed to making participation in this project a harassment-free experience for everyone, +regardless of level of experience, +gender, +gender identity and expression, +sexual orientation, +disability, +personal appearance, +body size, +race, +ethnicity, +age, +or religion. + +Examples of unacceptable behavior by participants include the use of sexual language or imagery, +derogatory comments or personal attacks, +trolling, +public or private harassment, +insults, +or other unprofessional conduct. + +Project maintainers have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to our [Code of Conduct][coc]. +Project maintainers who do not follow the Code of Conduct may be removed from the project team. + +Instances of abusive, harassing, or otherwise unacceptable behavior +may be reported by following our [reporting guidelines][coc-reporting]. + + +- [Software and Data Carpentry Code of Conduct][coc] +- [Code of Conduct Reporting Guide][coc-reporting] + +{% include links.md %} From c13550da0628bb6638633dc366b48dd8fcdbdf3c Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Wed, 10 May 2017 11:18:25 +0100 Subject: [PATCH 71/76] Add files from bin/lesson_initialize.py --- CONTRIBUTING.md | 9 ++++----- aio.md | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+), 5 deletions(-) create mode 100644 aio.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4ec80f76c..9de5a12a3 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -46,8 +46,8 @@ and to meet some of our community members. ## Where to Contribute 1. If you wish to change this lesson, - please work in , - which can be viewed at . + please work in , + which can be viewed at . 2. If you wish to change the example lesson, please work in , @@ -140,13 +140,12 @@ You can also [reach us by email][contact]. [dc-lessons]: http://datacarpentry.org/lessons/ [dc-site]: http://datacarpentry.org/ [discuss-list]: http://lists.software-carpentry.org/listinfo/discuss -[example-site]: https://swcarpentry.github.io/lesson-example/ [github]: http://github.com [github-flow]: https://guides.github.com/introduction/flow/ [github-join]: https://github.com/join [how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github -[issues]: https://github.com/swcarpentry/r-novice-inflammation/issues/ -[repo]: https://github.com/swcarpentry/r-novice-inflammation/ +[issues]: https://github.com/swcarpentry/FIXME/issues/ +[repo]: https://github.com/swcarpentry/FIXME/ [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry [swc-lessons]: http://software-carpentry.org/lessons/ [swc-site]: http://software-carpentry.org/ diff --git a/aio.md b/aio.md new file mode 100644 index 000000000..6d9385238 --- /dev/null +++ b/aio.md @@ -0,0 +1,36 @@ +--- +layout: page +permalink: /aio/ +--- + +{% comment %} +Create anchor for each one of the episodes. +{% endcomment %} +{% for episode in site.episodes %} +
    +{% endfor %} From d35955a0a1be55c62f3fb3aa44b592caa8e2a318 Mon Sep 17 00:00:00 2001 From: Ben Bolker Date: Mon, 22 May 2017 11:11:08 -0400 Subject: [PATCH 72/76] add missing backtick --- _episodes_rmd/02-func-R.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_episodes_rmd/02-func-R.Rmd b/_episodes_rmd/02-func-R.Rmd index 495796ad3..cd54443a0 100644 --- a/_episodes_rmd/02-func-R.Rmd +++ b/_episodes_rmd/02-func-R.Rmd @@ -123,7 +123,7 @@ Real-life functions will usually be larger than the ones shown here--typically h > e.g. `x <- c("A", "B", "C")` creates a vector `x` with three elements. > Furthermore, we can extend that vector again using `c`, e.g. `y <- c(x, "D")` creates a vector `y` with four elements. > Write a function called `fence` that takes two vectors as arguments, called -> original` and `wrapper`, and returns a new vector that has the wrapper vector +> `original` and `wrapper`, and returns a new vector that has the wrapper vector > at the beginning and end of the original: > > ```{r, echo=-1} From 199a1af047f882d1037cd41545f59b000cde15c7 Mon Sep 17 00:00:00 2001 From: Ben Bolker Date: Mon, 22 May 2017 11:11:08 -0400 Subject: [PATCH 73/76] add missing backtick --- _episodes_rmd/02-func-R.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_episodes_rmd/02-func-R.Rmd b/_episodes_rmd/02-func-R.Rmd index 495796ad3..cd54443a0 100644 --- a/_episodes_rmd/02-func-R.Rmd +++ b/_episodes_rmd/02-func-R.Rmd @@ -123,7 +123,7 @@ Real-life functions will usually be larger than the ones shown here--typically h > e.g. `x <- c("A", "B", "C")` creates a vector `x` with three elements. > Furthermore, we can extend that vector again using `c`, e.g. `y <- c(x, "D")` creates a vector `y` with four elements. > Write a function called `fence` that takes two vectors as arguments, called -> original` and `wrapper`, and returns a new vector that has the wrapper vector +> `original` and `wrapper`, and returns a new vector that has the wrapper vector > at the beginning and end of the original: > > ```{r, echo=-1} From b0a8f8d90f285e2bbf891b3cf296b8cd809a9a31 Mon Sep 17 00:00:00 2001 From: Alisa Postma Date: Fri, 23 Jun 2017 08:58:47 +0200 Subject: [PATCH 74/76] Added APS to title --- _episodes_rmd/01-starting-with-data.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index fde84d6f6..7cbb7cf3f 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -1,5 +1,5 @@ --- -title: "Analyzing Patient Data" +title: "Analyzing Patient Data - APS" teaching: 45 exercises: 0 questions: From 9320d92b7d972924560afe6b897b1cc715da3b6b Mon Sep 17 00:00:00 2001 From: Alisa Postma Date: Fri, 23 Jun 2017 11:36:47 +0200 Subject: [PATCH 75/76] Provided solution for 'Subsetting more data' --- _episodes_rmd/01-starting-with-data.Rmd | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/_episodes_rmd/01-starting-with-data.Rmd b/_episodes_rmd/01-starting-with-data.Rmd index 7cbb7cf3f..2cb2e4600 100644 --- a/_episodes_rmd/01-starting-with-data.Rmd +++ b/_episodes_rmd/01-starting-with-data.Rmd @@ -1,5 +1,5 @@ --- -title: "Analyzing Patient Data - APS" +title: "Analyzing Patient Data" teaching: 45 exercises: 0 questions: @@ -55,7 +55,7 @@ To do all that, we'll have to learn a little bit about programming. ### Loading Data -Let's import the file called `inflammation-01.csv` into our R environment. To import the file, first we need to tell our computer where the file is. We do that by choosing a working directory, that is, a local directory on our computer containing the files we need. This is very important in R. If we forget this step we’ll get an error message saying that the file does not exist. We can set the working directory using the function `setwd`. For this example, we change the path to our new directory at the desktop: +Let's import the file called `inflammation-01.csv` into our R environment. To import the file, first we need to tell our computer where the file is. We do that by choosing a working directory, that is, a local directory on our computer containing the files we need. This is very important in R. If we forget this step we???ll get an error message saying that the file does not exist. We can set the working directory using the function `setwd`. For this example, we change the path to our new directory at the desktop: ```{r,eval=FALSE} setwd("~/Desktop/r-novice-inflammation/") @@ -416,6 +416,14 @@ We'll learn why this is so in the next lesson. > 2. `max(dat[3:7, 5])` > 3. `max(dat[5, 3:7])` > 4. `max(dat[5, 3, 7])` +> +> > ## Solution +> > +> > Answer: 3 +> > +> > Explanation: You want to extract the part of the dataframe representing data for patient 5 from days three to seven. In this dataframe, patient data is organised in columns and the days are represented by the rows. Subscripting in R follows the `[i,j]` principle, where `i=columns` and `j=rows`. Thus, answer 3 is correct since the patient is represented by the value for i (5) and the days are represented by the values in j, which is a slice spanning day 3 to 7. +> > +> {: .solution} {: .challenge} > ## Slicing and Re-Assignment From d6ed0b26f813ae30c22cb0335d6d010c6fce7257 Mon Sep 17 00:00:00 2001 From: Daniel Chen Date: Sun, 16 Jul 2017 11:27:05 -0500 Subject: [PATCH 76/76] md updates from PRs --- _episodes/01-starting-with-data.md | 44 +++++++++++++++++------------ _episodes/02-func-R.md | 2 +- _episodes/08-making-packages-R.md | 6 ++-- _episodes/15-supp-loops-in-depth.md | 4 +-- 4 files changed, 32 insertions(+), 24 deletions(-) diff --git a/_episodes/01-starting-with-data.md b/_episodes/01-starting-with-data.md index dee4800aa..bfb20f7a4 100644 --- a/_episodes/01-starting-with-data.md +++ b/_episodes/01-starting-with-data.md @@ -56,7 +56,7 @@ To do all that, we'll have to learn a little bit about programming. ### Loading Data -Let's import the file called `inflammation-01.csv` into our R environment. To import the file, first we need to tell our computer where the file is. We do that by choosing a working directory, that is, a local directory on our computer containing the files we need. This is very important in R. If we forget this step we’ll get an error message saying that the file does not exist. We can set the working directory using the function `setwd`. For this example, we change the path to our new directory at the desktop: +Let's import the file called `inflammation-01.csv` into our R environment. To import the file, first we need to tell our computer where the file is. We do that by choosing a working directory, that is, a local directory on our computer containing the files we need. This is very important in R. If we forget this step we???ll get an error message saying that the file does not exist. We can set the working directory using the function `setwd`. For this example, we change the path to our new directory at the desktop: ~~~ @@ -633,13 +633,13 @@ summary(dat[,1:4]) ~~~ - V1 V2 V3 V4 - Min. :0 Min. :0.00 Min. :0.000 Min. :0.00 - 1st Qu.:0 1st Qu.:0.00 1st Qu.:1.000 1st Qu.:1.00 - Median :0 Median :0.00 Median :1.000 Median :2.00 - Mean :0 Mean :0.45 Mean :1.117 Mean :1.75 - 3rd Qu.:0 3rd Qu.:1.00 3rd Qu.:2.000 3rd Qu.:3.00 - Max. :0 Max. :1.00 Max. :2.000 Max. :3.00 + V1 V2 V3 V4 + Min. :0 Min. :0.00 Min. :0.000 Min. :0.00 + 1st Qu.:0 1st Qu.:0.00 1st Qu.:1.000 1st Qu.:1.00 + Median :0 Median :0.00 Median :1.000 Median :2.00 + Mean :0 Mean :0.45 Mean :1.117 Mean :1.75 + 3rd Qu.:0 3rd Qu.:1.00 3rd Qu.:2.000 3rd Qu.:3.00 + Max. :0 Max. :1.00 Max. :2.000 Max. :3.00 ~~~ {: .output} @@ -692,31 +692,31 @@ We'll learn why this is so in the next lesson. > A subsection of a data frame is called a [slice]({{ page.root }}/reference/#slice). > We can take slices of character vectors as well: > -> +> > ~~~ > animal <- c("m", "o", "n", "k", "e", "y") > # first three characters > animal[1:3] > ~~~ > {: .r} -> -> -> +> +> +> > ~~~ > [1] "m" "o" "n" > ~~~ > {: .output} -> -> -> +> +> +> > ~~~ > # last three characters > animal[4:6] > ~~~ > {: .r} -> -> -> +> +> +> > ~~~ > [1] "k" "e" "y" > ~~~ @@ -742,6 +742,14 @@ We'll learn why this is so in the next lesson. > 2. `max(dat[3:7, 5])` > 3. `max(dat[5, 3:7])` > 4. `max(dat[5, 3, 7])` +> +> > ## Solution +> > +> > Answer: 3 +> > +> > Explanation: You want to extract the part of the dataframe representing data for patient 5 from days three to seven. In this dataframe, patient data is organised in columns and the days are represented by the rows. Subscripting in R follows the `[i,j]` principle, where `i=columns` and `j=rows`. Thus, answer 3 is correct since the patient is represented by the value for i (5) and the days are represented by the values in j, which is a slice spanning day 3 to 7. +> > +> {: .solution} {: .challenge} > ## Slicing and Re-Assignment diff --git a/_episodes/02-func-R.md b/_episodes/02-func-R.md index 24847f8e9..5e8d8f29e 100644 --- a/_episodes/02-func-R.md +++ b/_episodes/02-func-R.md @@ -171,7 +171,7 @@ Real-life functions will usually be larger than the ones shown here--typically h > e.g. `x <- c("A", "B", "C")` creates a vector `x` with three elements. > Furthermore, we can extend that vector again using `c`, e.g. `y <- c(x, "D")` creates a vector `y` with four elements. > Write a function called `fence` that takes two vectors as arguments, called -> original` and `wrapper`, and returns a new vector that has the wrapper vector +> `original` and `wrapper`, and returns a new vector that has the wrapper vector > at the beginning and end of the original: > > diff --git a/_episodes/08-making-packages-R.md b/_episodes/08-making-packages-R.md index 0d95b97ea..3f399c273 100644 --- a/_episodes/08-making-packages-R.md +++ b/_episodes/08-making-packages-R.md @@ -120,16 +120,16 @@ Place each function into a separate R script and add documentation like this: ~~~ -#' Convert Fahrenheit to Kelvin +#' Converts Fahrenheit to Kelvin #' #' This function converts input temperatures in Fahrenheit to Kelvin. -#' @param temp The input temperature. +#' @param temp The temperature in Fahrenheit. +#' @return The temperature in Kelvin. #' @export #' @examples #' fahr_to_kelvin(32) fahr_to_kelvin <- function(temp) { - #Converts Fahrenheit to Kelvin kelvin <- ((temp - 32) * (5/9)) + 273.15 kelvin } diff --git a/_episodes/15-supp-loops-in-depth.md b/_episodes/15-supp-loops-in-depth.md index 618327b25..51a3a2985 100644 --- a/_episodes/15-supp-loops-in-depth.md +++ b/_episodes/15-supp-loops-in-depth.md @@ -219,7 +219,7 @@ system.time(avg2 <- analyze2(filenames)) ~~~ user system elapsed - 0.023 0.000 0.023 + 0.038 0.000 0.039 ~~~ {: .output} @@ -249,7 +249,7 @@ system.time(avg3 <- analyze3(filenames)) ~~~ user system elapsed - 0.020 0.000 0.022 + 0.039 0.000 0.039 ~~~ {: .output}