updated readme, and pkg level man file

fix birdlife fxns, and tidy up a bit, fix #100
ropensci · Sep 22, 2017 · df496d9 · df496d9
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diff --git a/R/birdlife.R b/R/birdlife.R
@@ -1,77 +1,61 @@
 #' Get bird habitat information from BirdLife/IUCN
 #'
 #' @export
-#'
 #' @param id A single IUCN species ID
-#'
-#' @return a \code{data.frame} with level 1 and level 2 habitat classes, as well as importance
-#' ratings and occurrence type (e.g. breeding or non-breeding).  The habitat classification
-#' scheme is described at \url{http://bit.ly/1e6gKBr}
+#' @return a \code{data.frame} with level 1 and level 2 habitat classes, as
+#' well as importance ratings and occurrence type (e.g. breeding or
+#' non-breeding). The habitat classification scheme is described
+#' at \url{http://bit.ly/1e6gKBr}
 #' @author David J. Harris \email{harry491@@gmail.com}
+#' @family birdlife
 #' @examples \dontrun{
+#' # Setophaga chrysoparia
 #' birdlife_habitat(22721692)
+#' # Passer domesticus
+#' birdlife_habitat(103818789)
 #' }
-#' @seealso \code{\link{birdlife_threats}}
-
-birdlife_habitat = function(id){
-
+birdlife_habitat <- function(id) {
   stopifnot(length(id) == 1)
-
-  url = paste0(
-    "http://www.birdlife.org/datazone/species/factsheet/",
-    id,
-    "/additional"
-  )
-
+  url <- bl_url(id)
   tables <- make_tables(url)
-
   # Find the table that has "Habitat" as a column name
   habitat_table_number <- which(
-    vapply(tables, function(table) any(grepl("Habitat", colnames(table))), logical(1))
+    vapply(tables, function(table) any(grepl("Habitat", colnames(table))),
+           logical(1))
   )
-
   out <- cbind(id, tables[[habitat_table_number]])
   out[-NROW(out), ] # Drop last row (altitude)
 }
 
 #' Get bird threat information from BirdLife/IUCN
 #'
 #' @export
-#'
-#' @param id A single IUCN species ID
-#'
-#' @return a \code{data.frame} with the species ID and two levels of threat descriptions,
-#' plus stresses, timing, scope, severity, and impact associated with each stressor.
+#' @inheritParams birdlife_habitat
+#' @return a \code{data.frame} with the species ID and two levels of threat
+#' descriptions, plus stresses, timing, scope, severity, and impact associated
+#' with each stressor.
 #' @author David J. Harris \email{harry491@@gmail.com}
+#' @family birdlife
 #' @examples \dontrun{
+#' # Setophaga chrysoparia
 #' birdlife_threats(22721692)
+#' # Aburria aburri
+#' birdlife_threats(22678440)
 #' }
-#' @seealso \code{\link{birdlife_habitat}}
-
-birdlife_threats = function(id){
-
+birdlife_threats <- function(id) {
   stopifnot(length(id) == 1)
-
-  url = paste0(
-    "http://www.birdlife.org/datazone/species/factsheet/",
-    id,
-    "/additional"
-  )
-
+  url <- bl_url(id)
   tables <- make_tables(url)
-
   is_threats <- sapply(
     tables,
     function(x){
       all(c("Scope", "Severity", "Impact", "Timing") %in% unlist(x))
     }
   )
-
-  if(sum(is_threats) > 1){
+  if (sum(is_threats) > 1) {
     stop("Malformed input. Multiple threat tables in ID ", id)
   }
-
-  if(sum(is_threats) == 1){
+  if (sum(is_threats) == 1) {
     threats = tables[is_threats][[1]]
 
     rownums = seq_len(nrow(threats))
@@ -86,10 +70,9 @@ birdlife_threats = function(id){
       severity = threats[rownums %% 5 == 2, 3],
       impact   = threats[rownums %% 5 == 2, 4]
     )
-  }else{
+  } else {
     out = NULL
   }
-
   out
 }
 
@@ -98,3 +81,6 @@ make_tables <- function(x) {
   tables <- xml2::xml_find_all(html, "//table")
   rvest::html_table(tables, fill = TRUE)
 }
+
+bl_base <- "http://datazone.birdlife.org/species/factsheet"
+bl_url <- function(x) sprintf("%s/%s/details", bl_base, x)
diff --git a/R/traits-package.r b/R/traits-package.r
@@ -1,6 +1,7 @@
 #' traits - Species trait data from around the web
 #'
-#' Currently included in \code{traits} with the associated function prefix:
+#' Currently included in \code{traits} with the associated function name or
+#' function prefix:
 #' \itemize{
 #'  \item BETYdb \url{http://www.betydb.org} - \code{betydb_}
 #'  \item National Center for Biotechnology Information - NCBI
@@ -11,6 +12,9 @@
 #'  \code{birdlife_}
 #'  \item LEDA Traitbase http://www.leda-traitbase.org/LEDAportal/index.jsp -
 #'  \code{leda_}
+#'  \item USDA Plants Database - \code{\link{tr_usda}}
+#'  \item Zanne et al. plant dataset - \code{\link{tr_zanne}}
+#'  \item Amniote life history dataset - \code{\link{tr_ernest}}
 #'  \item More to come ...
 #' }
 #'

diff --git a/README.Rmd b/README.Rmd
@@ -6,8 +6,7 @@ knitr::opts_chunk$set(
   comment = "#>",
   collapse = TRUE,
   warning = FALSE,
-  message = FALSE,
-  cache.path = "inst/readmecache/"
+  message = FALSE
 )
 ```
 
@@ -18,17 +17,17 @@ knitr::opts_chunk$set(
 
 R client for various sources of species trait data.
 
-Included in `traits` with the associated function prefix:
+Included in `traits` with the associated function prefix or function name:
 
 * [BETYdb](http://www.betydb.org) - `betydb_`
 * [National Center for Biotechnology Information - NCBI](http://www.ncbi.nlm.nih.gov/) - `ncbi_`
-* [Global Invasive Species Database - GISD](http://www.issg.org/database/welcome/) - `g_`
-* [Encyclopedia of Life Invasive Species](http://eol.org/collections/38204) - `eol_`
 * [Encyclopedia of Life Traitbank](http://eol.org/info/516) - `traitbank_`
 * [Coral Traits Database](http://coraltraits.org/) - `coral_`
-* [Flora Europaea](http://rbg-web2.rbge.org.uk/FE/fe.html) - `fe_`
 * [Birdlife International](http://rbg-web2.rbge.org.uk/FE/fe.html) - `birdlife_`
 * LEDA Traitbase - `leda_`
+* USDA Plants Database - `tr_usda`
+* Zanne et al. plant dataset - `tr_zanne`
+* Amniote life history dataset - `tr_ernest`
 * More to come ...
 
 Talk to us on the [issues page](https://github.com/ropensci/traits/issues) if you know of a source of traits data with an API, and we'll see about including it.
@@ -78,54 +77,28 @@ salix %>%
 
 ```
 
-## GISD invasive species data
-
-```{r}
-sp <- c("Carpobrotus edulis", "Rosmarinus officinalis")
-g_invasive(sp)
-```
-
-Or as simplified output
-
-```{r}
-g_invasive(sp, simplify = TRUE)
-```
-
-## EOL invasive species data
-
-```{r}
-eol_invasive_('Brassica oleracea', dataset = 'gisd')
-```
-
-Another example, with more species, and from
-
-```{r}
-eol_invasive_(c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
-              dataset = 'i3n')
-```
-
 ## EOL's traitbank trait data
 
-Searching for _Mesoplodon bidens_, page id `328566`
+Searching for _Balaenoptera musculus_ (blue whale), page id `328574`
 
-```{r cache=TRUE}
-res <- traitbank(846827)
+```{r cache=FALSE}
+res <- traitbank(328574)
 res$graph %>%
-  select(`dwc:measurementtype.@id`, `dwc:measurementtype.rdfs:label.en`) %>%
-  filter(!is.na(`dwc:measurementtype.rdfs:label.en`))
+  select(`dwc:measurementtype`) %>%
+  filter(!is.na(`dwc:measurementtype`))
 ```
 
 ## Coral
 
 Get the species list and their ids
 
-```{r cache=TRUE}
+```{r cache=FALSE}
 coral_species()
 ```
 
 Get data by taxon
 
-```{r cache=TRUE}
+```{r cache=FALSE}
 coral_taxa(80)
 ```
 
@@ -142,5 +115,7 @@ birdlife_habitat(22721692)
 * Please [report any issues or bugs](https://github.com/ropensci/traits/issues).
 * License: MIT
 * Get citation information for `traits` in R doing `citation(package = 'traits')`
+* Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). 
+By participating in this project you agree to abide by its terms.
 
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