Merge pull request #61 from edgararuiz/cran-rel

CRAN release prep
tidymodels · Jun 28, 2018 · eec949f · eec949f
2 parents 318ec18 + 5a92e54
commit eec949f
Show file tree

Hide file tree

Showing 117 changed files with 205 additions and 735 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,3 +9,4 @@
 ^\.Rprofile$
 ^packrat/
 ^to-cor-df\.png$
+revdep
diff --git a/.travis.yml b/.travis.yml
@@ -4,8 +4,7 @@ language: R
 sudo: false
 cache: packages
 
-r_github_packages:
-  - jimhester/covr
-
-after_success:
-  - Rscript -e 'covr::codecov()'
+include:
+  - r: release
+  - r: oldrel
+  - r: devel
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: corrr
 Type: Package
-Version: 0.2.1.9000
+Version: 0.3.0
 Title: Correlations in R
 Description: A tool for exploring correlations.
     It makes it possible to easily perform routine tasks when
@@ -16,8 +16,7 @@ Authors@R: c(
 URL: https://github.com/drsimonj/corrr
 BugReports: https://github.com/drsimonj/corrr/issues
 Depends: 
-    R (>= 3.3.0),
-    dplyr (>= 0.5.0)
+    R (>= 3.3.0)
 LazyData: yes
 License: MIT + file LICENSE
 RoxygenNote: 6.0.1
@@ -29,6 +28,7 @@ Suggests:
     DBI,
     RSQLite
 Imports: 
+    dplyr (>= 0.5.0),
     magrittr (>= 1.5),
     tidyr (>= 0.5.1),
     ggplot2 (>= 2.2.0),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# corrr 0.2.1.9000
+# corrr 0.3.0
 
 ## Small breaking changes
 
@@ -28,6 +28,8 @@ The `diagonal` argument of `as_matrix` and `as_matrix.cor_df` is now an optional
 
 - During the development of this version, ggplot v2.2.0 was released. Many changes in the plotting functions have been made to handle new features in the updated version of ggplot2.
 
+- Improvements to the package folder structure
+
 # corrr 0.2.1
 
 ## New Functionality

diff --git a/R/output.R b/R/output.R
@@ -12,6 +12,7 @@
 #' @export
 #' @examples 
 #' # Examples with correlate()
+#' library(dplyr)
 #' mtcars %>% correlate() %>% fashion()
 #' mtcars %>% correlate() %>% fashion(decimals = 1)
 #' mtcars %>% correlate() %>% fashion(leading_zeros = TRUE)

diff --git a/R/reshape.R b/R/reshape.R
@@ -16,6 +16,7 @@
 #' @return A tbl or, if mirror = TRUE, a cor_df (see \code{\link{correlate}}).
 #' @export
 #' @examples
+#' library(dplyr)
 #' x <- correlate(mtcars)
 #' focus(x, mpg, cyl)  # Focus on correlations of mpg and cyl with all other variables
 #' focus(x, -disp, - mpg, mirror = TRUE)  # Remove disp and mpg from columns and rows
@@ -48,6 +49,7 @@ focus_ <- function(x, ..., .dots, mirror) {
 #' @return A tibble or, if mirror = TRUE, a correlation data frame.
 #' @export
 #' @examples
+#' library(dplyr)
 #' any_greater_than <- function(x, val) {
 #'   mean(abs(x), na.rm = TRUE) > val
 #' }

diff --git a/README-combination-1.png b/README-combination-1.png
diff --git a/README-combination-2.png b/README-combination-2.png
diff --git a/README.Rmd b/README.Rmd
@@ -8,7 +8,7 @@ output: github_document
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
-  fig.path = "README-"
+  fig.path = "tools/readme/"
 )
 ```
 
@@ -24,7 +24,7 @@ knitr::opts_chunk$set(
 
 corrr is a package for exploring **corr**elations in **R**. It focuses on creating and working with **data frames** of correlations (instead of matrices) that can be easily explored via corrr functions or by leveraging tools like those in the [tidyverse](http://tidyverse.org/). This, along with the primary corrr functions, is represented below:
 
-<img src='to-cor-df.png'>
+<img src='tools/readme/to-cor-df.png'>
 
 You can install:
 

diff --git a/README.md b/README.md
@@ -1,59 +1,85 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # corrr <img src="man/figures/logo.png" align="right" />
 
-[![Project Status: Active ? The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![minimal R version](https://img.shields.io/badge/R%3E%3D-3.3.0-6666ff.svg)](https://cran.r-project.org/) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/corrr)](https://cran.r-project.org/package=corrr) [![packageversion](https://img.shields.io/badge/Package%20version-0.2.1.9000-orange.svg?style=flat-square)](commits/master) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--02--03-yellowgreen.svg)](/commits/master) [![Build Status](https://travis-ci.org/drsimonj/corrr.svg?branch=master)](https://travis-ci.org/drsimonj/corrr) [![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/corrr)](http://cran.rstudio.com/web/packages/corrr/index.html)
-
-corrr is a package for exploring **corr**elations in **R**. It focuses on creating and working with **data frames** of correlations (instead of matrices) that can be easily explored via corrr functions or by leveraging tools like those in the [tidyverse](http://tidyverse.org/). This, along with the primary corrr functions, is represented below:
-
-<img src='to-cor-df.png'>
+[![Project Status: Active ? The project has reached a stable, usable
+state and is being actively
+developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![minimal R
+version](https://img.shields.io/badge/R%3E%3D-3.3.0-6666ff.svg)](https://cran.r-project.org/)
+[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/corrr)](https://cran.r-project.org/package=corrr)
+[![packageversion](https://img.shields.io/badge/Package%20version-0.2.1.9000-orange.svg?style=flat-square)](commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2018--05--28-yellowgreen.svg)](/commits/master)
+[![Build
+Status](https://travis-ci.org/drsimonj/corrr.svg?branch=master)](https://travis-ci.org/drsimonj/corrr)
+[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/corrr)](http://cran.rstudio.com/web/packages/corrr/index.html)
+
+corrr is a package for exploring **corr**elations in **R**. It focuses
+on creating and working with **data frames** of correlations (instead of
+matrices) that can be easily explored via corrr functions or by
+leveraging tools like those in the [tidyverse](http://tidyverse.org/).
+This, along with the primary corrr functions, is represented below:
+
+<img src='tools/readme/to-cor-df.png'>
 
 You can install:
 
--   the latest released version from CRAN with
+  - the latest released version from CRAN with
+
+<!-- end list -->
 
 ``` r
 install.packages("corrr")
 ```
 
--   the latest development version from github with
+  - the latest development version from github
+with
+
+<!-- end list -->
 
 ``` r
 install.packages("devtools")  # run this line if devtools is not installed
 devtools::install_github("drsimonj/corrr")
 ```
 
-Using corrr
------------
+## Using corrr
 
-Using `corrr` typically starts with `correlate()`, which acts like the base correlation function `cor()`. It differs by defaulting to pairwise deletion, and returning a correlation data frame (`cor_df`) of the following structure:
+Using `corrr` typically starts with `correlate()`, which acts like the
+base correlation function `cor()`. It differs by defaulting to pairwise
+deletion, and returning a correlation data frame (`cor_df`) of the
+following structure:
 
--   A `tbl` with an additional class, `cor_df`
--   An extra "rowname" column
--   Standardised variances (the matrix diagonal) set to missing values (`NA`) so they can be ignored.
+  - A `tbl` with an additional class, `cor_df`
+  - An extra “rowname” column
+  - Standardised variances (the matrix diagonal) set to missing values
+    (`NA`) so they can be ignored.
 
 ### API
 
-The corrr API is designed with data pipelines in mind (e.g., to use `%>%` from the magrittr package). After `correlate()`, the primary corrr functions take a `cor_df` as their first argument, and return a `cor_df` or `tbl` (or output like a plot). These functions serve one of three purposes:
+The corrr API is designed with data pipelines in mind (e.g., to use
+`%>%` from the magrittr package). After `correlate()`, the primary corrr
+functions take a `cor_df` as their first argument, and return a `cor_df`
+or `tbl` (or output like a plot). These functions serve one of three
+purposes:
 
 Internal changes (`cor_df` out):
 
--   `shave()` the upper or lower triangle (set to NA).
--   `rearrange()` the columns and rows based on correlation strengths.
+  - `shave()` the upper or lower triangle (set to NA).
+  - `rearrange()` the columns and rows based on correlation strengths.
 
 Reshape structure (`tbl` or `cor_df` out):
 
--   `focus()` on select columns and rows.
--   `stretch()` into a long format.
+  - `focus()` on select columns and rows.
+  - `stretch()` into a long format.
 
 Output/visualisations (console/plot out):
 
--   `fashion()` the correlations for pretty printing.
--   `rplot()` the correlations with shapes in place of the values.
--   `network_plot()` the correlations in a network.
+  - `fashion()` the correlations for pretty printing.
+  - `rplot()` the correlations with shapes in place of the values.
+  - `network_plot()` the correlations in a network.
 
-Examples
---------
+## Examples
 
 ``` r
 library(MASS)
@@ -83,31 +109,30 @@ x <- correlate(d)
 class(x)
 #> [1] "cor_df"     "tbl_df"     "tbl"        "data.frame"
 x
-#> # A tibble: 6 × 7
-#>   rowname            v1          v2           v3            v4          v5
-#>     <chr>         <dbl>       <dbl>        <dbl>         <dbl>       <dbl>
-#> 1      v1            NA  0.70986371  0.709330652  0.0001947192 0.021359764
-#> 2      v2  0.7098637068          NA  0.697411266 -0.0132575510 0.009280530
-#> 3      v3  0.7093306516  0.69741127           NA -0.0252752456 0.001088652
-#> 4      v4  0.0001947192 -0.01325755 -0.025275246            NA 0.421380212
-#> 5      v5  0.0213597639  0.00928053  0.001088652  0.4213802123          NA
-#> 6      v6 -0.0435135083 -0.03383145 -0.020057495  0.4424697437 0.425441795
-#> # ... with 1 more variables: v6 <dbl>
+#> # A tibble: 6 x 7
+#>   rowname         v1        v2        v3         v4       v5       v6
+#>   <chr>        <dbl>     <dbl>     <dbl>      <dbl>    <dbl>    <dbl>
+#> 1 v1       NA          0.710     0.709     0.000195  0.0214   -0.0435
+#> 2 v2        0.710     NA         0.697    -0.0133    0.00928  -0.0338
+#> 3 v3        0.709      0.697    NA        -0.0253    0.00109  -0.0201
+#> 4 v4        0.000195  -0.0133   -0.0253   NA         0.421     0.442 
+#> 5 v5        0.0214     0.00928   0.00109   0.421    NA         0.425 
+#> 6 v6       -0.0435    -0.0338   -0.0201    0.442     0.425    NA
 ```
 
-As a `tbl`, we can use functions from data frame packages like `dplyr`, `tidyr`, `ggplot2`:
+As a `tbl`, we can use functions from data frame packages like `dplyr`,
+`tidyr`, `ggplot2`:
 
 ``` r
 library(dplyr)
 
 # Filter rows by correlation size
 x %>% filter(v1 > .6)
-#> # A tibble: 2 × 7
-#>   rowname        v1        v2        v3          v4          v5
-#>     <chr>     <dbl>     <dbl>     <dbl>       <dbl>       <dbl>
-#> 1      v2 0.7098637        NA 0.6974113 -0.01325755 0.009280530
-#> 2      v3 0.7093307 0.6974113        NA -0.02527525 0.001088652
-#> # ... with 1 more variables: v6 <dbl>
+#> # A tibble: 2 x 7
+#>   rowname    v1     v2     v3      v4      v5      v6
+#>   <chr>   <dbl>  <dbl>  <dbl>   <dbl>   <dbl>   <dbl>
+#> 1 v2      0.710 NA      0.697 -0.0133 0.00928 -0.0338
+#> 2 v3      0.709  0.697 NA     -0.0253 0.00109 -0.0201
 ```
 
 corrr functions work in pipelines (`cor_df` in; `cor_df` or `tbl` out):
@@ -136,7 +161,7 @@ fashion(x)
 rplot(x)
 ```
 
-![](README-combination-1.png)
+![](tools/readme/combination-1.png)<!-- -->
 
 ``` r
 
@@ -148,4 +173,4 @@ datasets::airquality %>%
 #> Missing treated using: 'pairwise.complete.obs'
 ```
 
-![](README-combination-2.png)
+![](tools/readme/combination-2.png)<!-- -->
diff --git a/README_files/figure-markdown_github/combination-1.png b/README_files/figure-markdown_github/combination-1.png
diff --git a/README_files/figure-markdown_github/rplot-1.png b/README_files/figure-markdown_github/rplot-1.png
diff --git a/README_files/figure-markdown_github/rplot_arranged-1.png b/README_files/figure-markdown_github/rplot_arranged-1.png
diff --git a/README_files/figure-markdown_github/rplot_arranged-2.png b/README_files/figure-markdown_github/rplot_arranged-2.png
diff --git a/README_files/figure-markdown_github/rplot_arranged-3.png b/README_files/figure-markdown_github/rplot_arranged-3.png
diff --git a/README_files/figure-markdown_github/unnamed-chunk-3-1.png b/README_files/figure-markdown_github/unnamed-chunk-3-1.png
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,23 +1,26 @@
-## Test environments
-* local Windows 10 install, R 3.3.1
-* ubuntu 12.04.5 LTS (on travis-ci), R 3.3.1
-* win-builder (devel and release)
+## Release summary
 
-## R CMD check results
+- `as_cordf` will coerce lists or matrices into correlation data frames if possible
+
+- `focus_if` enables conditional variable selection
+
+- Can use arithmetic operators (e.g., `+` or `-`) with correlation data frames
+
+- `correlate()` now supports data frame with a SQL back-end (`tbl_sql`)
 
-Except for win-builder, there were no ERRORs, WARNINGs or NOTEs.
+- Small breaking change: The `diagonal` argument of `as_matrix` and `as_matrix.cor_df` is now an optional argument rather than set to `1` by default 
 
-Via win-builder, there was 1 NOTE:
+- Other improvements and fixes
+
+## Test environments
+* local Windows 10 install, R 3.5.0
+* ubuntu 14.04 (on travis-ci)
+* Ubuntu 14.04.5 LTS with RStudio Server, R 3.4.3 
+
+## R CMD check results
 
-  * checking CRAN incoming feasibility ... NOTE
-  Maintainer: 'Simon Jackson <[email protected]>'
-
-  License components with restrictions and base license permitting such:
-    MIT + file LICENSE
-  File 'LICENSE':
-    YEAR: 2016
-    COPYRIGHT HOLDER: Simon Jackson
+- 0 errors | 0 warnings | 0 notes
 
-## Downstream dependencies
+## revdep check results
 
-There are currently no downstream dependencies for this package.
+- 0 packages
diff --git a/man/fashion.Rd b/man/fashion.Rd
diff --git a/man/focus.Rd b/man/focus.Rd
diff --git a/man/focus_if.Rd b/man/focus_if.Rd