readme

README.md

@@ -16,49 +16,53 @@ There are several options available to download data from OBIS, some of which in
 
 - R package [robis](https://github.com/iobis/robis)
 - Python package [pyobis](https://github.com/iobis/pyobis)
-- Full data exports
+- [Full data exports](#full-data-exports)
 - [OBIS homepage search](https://obis.org/) or [advanced dataset search](https://obis.org/datasets)
 - [OBIS Mapper](https://mapper.obis.org/)
 
 
 ### robis
 
 The [robis R package](https://github.com/iobis/robis) connects to the OBIS API from R. The package can be installed from CRAN or from GitHub (latest development version). 
-```
+
+```r
 # install from CRAN
 install.packages("robis")
 
 # latest development version
 remotes::install_github("iobis/robis")
 ```
+
 You can use the package to obtain a list of datasets, a taxon checklist, or raw occurrence data by supplying e.g. a taxon name or [WoRMS AphiaID](https://www.marinespecies.org/about.php). You can also specify whether to include absence records when obtaining occurrence data.
 To download this data, simply export R objects with the write.csv function. If we wanted to obtain Mollusc data from OBIS, some options would be:
 
-```
+```r
 library(robis)
-#obtain occurrence data
-moll<-occurrence("Mollusca")
-moll_abs<-occurrence(“Mollusca”, absence="include") #include absence records
-write.csv(moll, “mollusca-obis.csv”)` #save the data to csv
 
-#obtain a list of datasets for a taxon
-molldata<-dataset(scientificname="Mollusca")
+# obtain occurrence data
+moll <- occurrence("Mollusca")
+moll_abs <- occurrence(“Mollusca”, absence = "include") # include absence records
+write.csv(moll, "mollusca-obis.csv") # save the data to csv
+
+# obtain a list of datasets for a taxon
+molldata <- dataset(scientificname = "Mollusca")
 
 #obtain a checklist of Mollusc species in a certain area
-mollcheck<-checklist(scientificname="Mollusca", geometry = "POLYGON ((2.3 51.8, 2.3 51.6, 2.6 51.6, 2.6 51.8, 2.3 51.8))")
+mollcheck <- checklist(scientificname = "Mollusca", geometry = "POLYGON ((2.3 51.8, 2.3 51.6, 2.6 51.6, 2.6 51.8, 2.3 51.8))")
 ```
 
 #### Filter datasets by keyword
 
 You can use robis to obtain all datasets and then filter based on keywords in the title and/or abstract. See example below where we filter to find datasets related to seamounts. Multiple keywords can be provided by using | to separate each word, e.g. "seamount|deepsea|benthos".
 
-```
-search_terms <- "seamount" #define your search terms
+```r
+search_terms <- "seamount" # define your search terms
 
-datasets <- robis::dataset() #obtain datasets from OBIS
+datasets <- robis::dataset() # obtain datasets from OBIS
 
-seamount_datasets <- datasets[grepl(paste(search_terms, collapse = "|"), datasets$title, ignore.case = TRUE) |
-                                grepl(paste(search_terms, collapse = "|"), datasets$abstract, ignore.case = TRUE),]
+seamount_datasets <- datasets[
+  grepl(paste(search_terms, collapse = "|"), datasets$title, ignore.case = TRUE) |
+  grepl(paste(search_terms, collapse = "|"), datasets$abstract, ignore.case = TRUE),]
 ```
 
 ## Full data exports