fix #62 (see also #61) put dwc terms inside of pkg to avoid breaking pkg when file moves on the web

Author: sckott

DESCRIPTION

@@ -4,7 +4,7 @@ Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
     Functions allow searching by many parameters, including 'taxonomic' names,
     places, and dates. In addition, there is an interface for conducting spatially
     delimited searches, and another for requesting large 'datasets' via email.
-Version: 0.6.0.9100
+Version: 0.6.2
 Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
 Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
 License: MIT + file LICENSE

NEWS.md

@@ -1,3 +1,13 @@
+rvertnet 0.6.2
+===============
+
+### BUG FIXES 
+
+* A small data source used in one function was on the web, and
+was moved - that data source now within the pkg as quite small, and 
+now pkg won't break when the file is moved again (#61) (#62)
+
+
 rvertnet 0.6.0
 ===============
 
@@ -24,7 +34,7 @@ allows to optionally only return Darwin Core fields
 
 ### BUG FIXES 
 
-* Small fix to `vertsummary()` (59)
+* Small fix to `vertsummary()` (#59)
 
 
 rvertnet 0.5.0

R/vert_id.R

@@ -11,7 +11,15 @@
 #' @return A list, with data frame of search results, and list of metadata
 #' @references \url{http://bit.ly/vertnet-wiki}
 #' @details VertNet IDs can be a variety of things, some URIs 
-#' (i.e., with http://...), while others start with \code{urn}. 
+#' (i.e., with http://...), while others start with \code{urn}.
+#' 
+#' Internally in this function we filter data to darwin core terms only. To 
+#' see what terms we use, do 
+#' \code{readLines(
+#' system.file("extdata", "simple_dwc_terms.txt", package = "rvertnet"))}. 
+#' Get in touch with us if these terms need correcting/are out of date. The
+#' terms are from 
+#' https://github.com/tdwg/dwc/blob/master/dist/simple_dwc_horizontal.csv
 #'
 #' @examples \dontrun{
 #' vert_id(ids = "urn:catalog:CM:Herps:116520")
@@ -21,8 +29,7 @@
 #' res <- vert_id(ids)
 #' res$data$occurrenceid
 #' 
-#' # Lots
-#' out <- vertsearch(taxon = "aves", state = "california", limit = 20)
+#' out <- vertsearch(taxon = "aves", state = "california", limit = 5)
 #' (ids <- out$data$occurrenceid)
 #' res <- vert_id(ids)
 #' identical(sort(res$data$occurrenceid), sort(ids))

R/zzz.R

@@ -34,10 +34,10 @@ vertwrapper <- function(fxn = "", args = NULL, lim = NULL, rfile = NULL,
 
 mssg <- function(v, ...) if (v) message(...)
 
-get_terms <- function(){
-  url <- "https://raw.githubusercontent.com/tdwg/dwc/master/dist/simple_dwc_horizontal.csv"
-  res <- crul::HttpClient$new(url)$get()$parse("UTF-8")
-  tolower(strsplit(res, split = ",")[[1]])
+get_terms <- function() {
+  readLines(
+    system.file("extdata", "simple_dwc_terms.txt", package = "rvertnet")
+  )
 }
 
 vert_GET <- function(fxn="searchbyterm", args, limit = 1000, messages = TRUE, 

cran-comments.md

@@ -1,7 +1,7 @@
 ## Test environments
 
-* local OS X install, R 3.4.1 patched
-* ubuntu 12.04 (on travis-ci), R 3.4.1
+* local OS X install, R 3.4.2 patched
+* ubuntu 12.04 (on travis-ci), R 3.4.2
 * win-builder (devel and release)
 
 ## R CMD check results
@@ -22,8 +22,7 @@
 
 --------
 
-This release includes a new function, swaps a dependency, and some minor
-changes and bug fixes.
+This release includes a bug fix for a data source that moved on the web.
 
 Sincerely,
 Scott Chamberlain

inst/extdata/simple_dwc_terms.txt

@@ -0,0 +1,169 @@
+type
+modified
+language
+license
+rightsholder
+accessrights
+bibliographiccitation
+references
+institutionid
+collectionid
+datasetid
+institutioncode
+collectioncode
+datasetname
+ownerinstitutioncode
+basisofrecord
+informationwithheld
+datageneralizations
+dynamicproperties
+occurrenceid
+catalognumber
+recordnumber
+recordedby
+individualcount
+organismquantity
+organismquantitytype
+sex
+lifestage
+reproductivecondition
+behavior
+establishmentmeans
+occurrencestatus
+preparations
+disposition
+associatedmedia
+associatedreferences
+associatedsequences
+associatedtaxa
+othercatalognumbers
+occurrenceremarks
+organismid
+organismname
+organismscope
+associatedoccurrences
+associatedorganisms
+previousidentifications
+organismremarks
+materialsampleid
+eventid
+parenteventid
+fieldnumber
+eventdate
+eventtime
+startdayofyear
+enddayofyear
+year
+month
+day
+verbatimeventdate
+habitat
+samplingprotocol
+samplesizevalue
+samplesizeunit
+samplingeffort
+fieldnotes
+eventremarks
+locationid
+highergeographyid
+highergeography
+continent
+waterbody
+islandgroup
+island
+country
+countrycode
+stateprovince
+county
+municipality
+locality
+verbatimlocality
+minimumelevationinmeters
+maximumelevationinmeters
+verbatimelevation
+minimumdepthinmeters
+maximumdepthinmeters
+verbatimdepth
+minimumdistanceabovesurfaceinmeters
+maximumdistanceabovesurfaceinmeters
+locationaccordingto
+locationremarks
+decimallatitude
+decimallongitude
+geodeticdatum
+coordinateuncertaintyinmeters
+coordinateprecision
+pointradiusspatialfit
+verbatimcoordinates
+verbatimlatitude
+verbatimlongitude
+verbatimcoordinatesystem
+verbatimsrs
+footprintwkt
+footprintsrs
+footprintspatialfit
+georeferencedby
+georeferenceddate
+georeferenceprotocol
+georeferencesources
+georeferenceverificationstatus
+georeferenceremarks
+geologicalcontextid
+earliesteonorlowesteonothem
+latesteonorhighesteonothem
+earliesteraorlowesterathem
+latesteraorhighesterathem
+earliestperiodorlowestsystem
+latestperiodorhighestsystem
+earliestepochorlowestseries
+latestepochorhighestseries
+earliestageorloweststage
+latestageorhigheststage
+lowestbiostratigraphiczone
+highestbiostratigraphiczone
+lithostratigraphicterms
+group
+formation
+member
+bed
+identificationid
+identificationqualifier
+typestatus
+identifiedby
+dateidentified
+identificationreferences
+identificationverificationstatus
+identificationremarks
+taxonid
+scientificnameid
+acceptednameusageid
+parentnameusageid
+originalnameusageid
+nameaccordingtoid
+namepublishedinid
+taxonconceptid
+scientificname
+acceptednameusage
+parentnameusage
+originalnameusage
+nameaccordingto
+namepublishedin
+namepublishedinyear
+higherclassification
+kingdom
+phylum
+class
+order
+family
+genus
+subgenus
+specificepithet
+infraspecificepithet
+taxonrank
+verbatimtaxonrank
+scientificnameauthorship
+vernacularname
+nomenclaturalcode
+taxonomicstatus
+nomenclaturalstatus
+taxonremarks