updated to roxygen new ver, and added error handling to parsms that c…

…hanged names
ropensci · Apr 16, 2014 · ed949cb · ed949cb
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diff --git a/NAMESPACE b/NAMESPACE
@@ -1,3 +1,5 @@
+# Generated by roxygen2 (4.0.0): do not edit by hand
+
 S3method(gbifdata,gbifdens)
 S3method(gbifdata,gbiflist)
 S3method(gbifdata,gbiflist_na)

diff --git a/NEWS b/NEWS
@@ -4,12 +4,14 @@ rgbif 0.6.0
 BUG FIXES
 
 * A number of variables changed names to better follow the Darwin Core standard. `latitude` is now `decimalLatitude`. `longitude` is now `decimalLongitude`. `clazz` is now `class`. Code in this package changed to accomodate these changes. `date` is now `eventDate`. `georeferenced` is now `hasCoordinate`. Beware of these changes in your own code using `rgbif` - find and replace for these should be easy.
+* Changed `altitude` parameter in `occ_search()` to `elevation` - should have been `elevation` the whole time. 
 
 IMPROVEMENTS
 
 * Better checking and parsing of response data from GBIF: Across all functions, we now check that the response content type is `application/json`, then parse JSON ourselves using `RJSONIO::fromJSON` (instead of httr doing it).
 * Across all functions, we now return all potenital character class columns as character class (instead of factor), by passing `stringsAsFactors = FALSE` to all `data.frame()` calls.
 * Now using assertthat package in various places to give better error messages when the wrong input is passed to a function.
+* Four parameters have name changes. These parameters are still in the function definition, but if called they throw a useful warning telling you the correct parameter names. (#75)
 
 NEW FEATURES
 

diff --git a/R/occ_search.r b/R/occ_search.r
@@ -161,14 +161,19 @@
 #' nrow(out)
 #' }
 
-occ_search <- function(taxonKey=NULL, scientificName=NULL, country=NULL, publishingCountry=NULL, 
+occ_search <- function(taxonKey=NULL, scientificName=NULL, country=NULL, publishingCountry=NULL,
   hasCoordinate=NULL, typeStatus=NULL, recordNumber=NULL, lastInterpreted=NULL, continent=NULL,
   geometry=NULL, collectorName=NULL, basisOfRecord=NULL, datasetKey=NULL, eventDate=NULL, 
   catalogNumber=NULL, year=NULL, month=NULL, decimalLatitude=NULL, decimalLongitude=NULL, 
   elevation=NULL, depth=NULL, institutionCode=NULL, collectionCode=NULL, 
   spatialIssues=NULL, search=NULL, callopts=list(), limit=20, start=NULL, 
   fields = 'minimal', return='all')
 {
+  calls <- names(sapply(match.call(), deparse))[-1]
+  calls_vec <- c("georeferenced","altitude","latitude","longitude") %in% calls
+  if(any(calls_vec))
+    stop("Parameter name changes: \n georeferenced -> hasCoordinate\n altitude -> elevation\n latitude -> decimalLatitude\n longitude - > decimalLongitude")
+
   url = 'http://api.gbif.org/v0.9/occurrence/search'
   getdata <- function(x=NULL, itervar=NULL)
   {

diff --git a/man/blanktheme.Rd b/man/blanktheme.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{blanktheme}
 \alias{blanktheme}
 \title{Custom ggplot2 theme}

diff --git a/man/check_wkt.Rd b/man/check_wkt.Rd
@@ -1,11 +1,12 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{check_wkt}
 \alias{check_wkt}
 \title{Check input WKT}
 \usage{
 check_wkt(wkt = NULL)
 }
 \arguments{
-  \item{wkt}{A Well Known Text object}
+\item{wkt}{A Well Known Text object}
 }
 \description{
 Check input WKT

diff --git a/man/commas_to_periods.Rd b/man/commas_to_periods.Rd
@@ -1,11 +1,12 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{commas_to_periods}
 \alias{commas_to_periods}
 \title{Convert commas to periods in lat/long data}
 \usage{
 commas_to_periods(dataframe)
 }
 \arguments{
-  \item{dataframe}{A data.frame}
+\item{dataframe}{A data.frame}
 }
 \description{
 Convert commas to periods in lat/long data

diff --git a/man/count_facet.Rd b/man/count_facet.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{count_facet}
 \alias{count_facet}
 \title{Facetted count occurrence search.}
@@ -6,16 +7,14 @@ count_facet(keys = NULL, by = "country", countries = 10,
   removezeros = FALSE)
 }
 \arguments{
-  \item{keys}{(numeric) GBIF keys, a vector.}
+\item{keys}{(numeric) GBIF keys, a vector.}
 
-  \item{by}{(character) One of georeferenced,
-  basisOfRecord, country, hostCountry, or
-  publishingCountry.}
+\item{by}{(character) One of georeferenced, basisOfRecord, country, hostCountry, or
+publishingCountry.}
 
-  \item{countries}{(numeric) Number of countries to facet
-  on, or a vector of country names}
+\item{countries}{(numeric) Number of countries to facet on, or a vector of country names}
 
-  \item{removezeros}{(logical) Default is FALSE}
+\item{removezeros}{(logical) Default is FALSE}
 }
 \description{
 Facetted count occurrence search.

diff --git a/man/create_gist.Rd b/man/create_gist.Rd
@@ -1,19 +1,19 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{create_gist}
 \alias{create_gist}
 \title{Function that takes a list of files and creates payload for API}
 \usage{
 create_gist(filenames, description = "", public = TRUE)
 }
 \arguments{
-  \item{filenames}{names of files to post}
+\item{filenames}{names of files to post}
 
-  \item{description}{brief description of gist (optional)}
+\item{description}{brief description of gist (optional)}
 
-  \item{public}{whether gist is public (defaults to TRUE)}
+\item{public}{whether gist is public (defaults to TRUE)}
 }
 \description{
-Function that takes a list of files and creates payload for
-API
+Function that takes a list of files and creates payload for API
 }
 \keyword{internal}
 
diff --git a/man/dataset_metrics.Rd b/man/dataset_metrics.Rd
@@ -1,18 +1,19 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{dataset_metrics}
 \alias{dataset_metrics}
 \title{Geta details on a dataset.}
 \usage{
 dataset_metrics(uuid, callopts = list())
 }
 \arguments{
-  \item{uuid}{A dataset UUID.}
+\item{uuid}{A dataset UUID.}
 
-  \item{callopts}{Pass on options to GET.}
+\item{callopts}{Pass on options to GET.}
 }
 \description{
-You should be able to pass in more than one uuid to this
-function, but I have not yet found more than the one uuid
-below in the example that actually has data available.
+You should be able to pass in more than one uuid to this function, but I have
+not yet found more than the one uuid below in the example that actually has
+data available.
 }
 \examples{
 \dontrun{

diff --git a/man/dataset_search.Rd b/man/dataset_search.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{dataset_search}
 \alias{dataset_search}
 \title{Search datasets in GBIF.}
@@ -10,82 +11,68 @@ dataset_search(query = NULL, country = NULL, type = NULL,
   return = "all")
 }
 \arguments{
-  \item{callopts}{Pass on options to httr::GET for more
-  refined control of http calls, and error handling}
-
-  \item{limit}{Number of records to return}
-
-  \item{start}{Record number to start at}
-
-  \item{query}{Query term(s) for full text search.  The
-  value for this parameter can be a simple word or a
-  phrase. Wildcards can be added to the simple word
-  parameters only, e.g. q=*puma*}
-
-  \item{country}{NOT YET IMPLEMENTED. Filters by country as
-  given in isocodes$gbif_name, e.g. country=CANADA.}
-
-  \item{type}{Type of dataset, options include OCCURRENCE,
-  etc.}
-
-  \item{keyword}{Keyword to search by. Datasets can be
-  tagged by keywords, which you can search on. The search
-  is done on the merged collection of tags, the dataset
-  keywordCollections and temporalCoverages.}
-
-  \item{owning_org}{Owning organization. A uuid string. See
-  \code{\link{organizations}}}
-
-  \item{hosting_org}{Hosting organization. A uuid string.
-  See \code{\link{organizations}}}
-
-  \item{publishing_country}{Publishing country. See options
-  at isocodes$gbif_name}
-
-  \item{decade}{Decade, e.g., 1980. Filters datasets by
-  their temporal coverage broken down to decades. Decades
-  are given as a full year, e.g. 1880, 1960, 2000, etc, and
-  will return datasets wholly contained in the decade as
-  well as those that cover the entire decade or more. Facet
-  by decade to get the break down, e.g.
-  /search?facet=DECADE&facet_only=true (see example below)}
-
-  \item{pretty}{Print informative metadata using
-  \code{\link{cat}}. Not easy to manipulate output though.}
-
-  \item{facet}{A list of facet names used to retrieve the
-  100 most frequent values for a field. Allowed facets are:
-  dataset_key, highertaxon_key, rank, status, extinct,
-  habitat, and name_type. Additionally threat and
-  nomenclatural_status are legal values but not yet
-  implemented, so data will not yet be returned for them.}
-
-  \item{facet_only}{Used in combination with the facet
-  parameter. Set facet_only=true to exclude search
-  results.}
-
-  \item{facet_mincount}{Used in combination with the facet
-  parameter. Set facet_mincount={#} to exclude facets with
-  a count less than {#}, e.g.  http://bit.ly/1bMdByP only
-  shows the type value 'ACCEPTED' because the other
-  statuses have counts less than 7,000,000}
-
-  \item{facet_multiselect}{Used in combination with the
-  facet parameter. Set facet_multiselect=true to still
-  return counts for values that are not currently filtered,
-  e.g. http://bit.ly/19YLXPO still shows all status values
-  even though status is being filtered by status=ACCEPTED}
-
-  \item{return}{What to return. One of meta, descriptions,
-  data, facets, or all (Default).}
+\item{callopts}{Pass on options to httr::GET for more refined control of
+http calls, and error handling}
+
+\item{limit}{Number of records to return}
+
+\item{start}{Record number to start at}
+
+\item{query}{Query term(s) for full text search.  The value for this parameter
+can be a simple word or a phrase. Wildcards can be added to the simple word
+parameters only, e.g. q=*puma*}
+
+\item{country}{NOT YET IMPLEMENTED. Filters by country as given in isocodes$gbif_name,
+e.g. country=CANADA.}
+
+\item{type}{Type of dataset, options include OCCURRENCE, etc.}
+
+\item{keyword}{Keyword to search by. Datasets can be tagged by keywords, which
+you can search on. The search is done on the merged collection of tags, the
+dataset keywordCollections and temporalCoverages.}
+
+\item{owning_org}{Owning organization. A uuid string. See \code{\link{organizations}}}
+
+\item{hosting_org}{Hosting organization. A uuid string. See \code{\link{organizations}}}
+
+\item{publishing_country}{Publishing country. See options at isocodes$gbif_name}
+
+\item{decade}{Decade, e.g., 1980. Filters datasets by their temporal coverage
+broken down to decades. Decades are given as a full year, e.g. 1880, 1960, 2000,
+etc, and will return datasets wholly contained in the decade as well as those
+that cover the entire decade or more. Facet by decade to get the break down,
+e.g. /search?facet=DECADE&facet_only=true (see example below)}
+
+\item{pretty}{Print informative metadata using \code{\link{cat}}. Not easy to
+manipulate output though.}
+
+\item{facet}{A list of facet names used to retrieve the 100 most frequent values
+for a field. Allowed facets are: dataset_key, highertaxon_key, rank, status,
+extinct, habitat, and name_type. Additionally threat and nomenclatural_status
+are legal values but not yet implemented, so data will not yet be returned for them.}
+
+\item{facet_only}{Used in combination with the facet parameter. Set facet_only=true
+to exclude search results.}
+
+\item{facet_mincount}{Used in combination with the facet parameter. Set
+facet_mincount={#} to exclude facets with a count less than {#}, e.g.
+http://bit.ly/1bMdByP only shows the type value 'ACCEPTED' because the other
+statuses have counts less than 7,000,000}
+
+\item{facet_multiselect}{Used in combination with the facet parameter. Set
+facet_multiselect=true to still return counts for values that are not currently
+filtered, e.g. http://bit.ly/19YLXPO still shows all status values even though
+status is being filtered by status=ACCEPTED}
+
+\item{return}{What to return. One of meta, descriptions, data, facets,
+or all (Default).}
 }
 \value{
-A data.frame, list, or message printed to console (using
-pretty=TRUE).
+A data.frame, list, or message printed to console (using pretty=TRUE).
 }
 \description{
-This function does not search occurrence data, only
-metadata on the datasets that contain occurrence data.
+This function does not search occurrence data, only metadata on the datasets
+that contain occurrence data.
 }
 \examples{
 \dontrun{

diff --git a/man/dataset_suggest.Rd b/man/dataset_suggest.Rd
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
 \name{dataset_suggest}
 \alias{dataset_suggest}
 \title{Suggest datasets in GBIF.}
@@ -9,66 +10,54 @@ dataset_suggest(query = NULL, country = NULL, type = NULL,
   description = FALSE)
 }
 \arguments{
-  \item{callopts}{Pass on options to httr::GET for more
-  refined control of http calls, and error handling}
+\item{callopts}{Pass on options to httr::GET for more refined control of
+http calls, and error handling}
 
-  \item{limit}{Number of records to return}
+\item{limit}{Number of records to return}
 
-  \item{start}{Record number to start at}
+\item{start}{Record number to start at}
 
-  \item{query}{Query term(s) for full text search.  The
-  value for this parameter can be a simple word or a
-  phrase. Wildcards can be added to the simple word
-  parameters only, e.g. q=*puma*}
+\item{query}{Query term(s) for full text search.  The value for this parameter
+can be a simple word or a phrase. Wildcards can be added to the simple word
+parameters only, e.g. q=*puma*}
 
-  \item{country}{NOT YET IMPLEMENTED. Filters by country as
-  given in isocodes$gbif_name, e.g. country=CANADA.}
+\item{country}{NOT YET IMPLEMENTED. Filters by country as given in isocodes$gbif_name,
+e.g. country=CANADA.}
 
-  \item{type}{Type of dataset, options include OCCURRENCE,
-  etc.}
+\item{type}{Type of dataset, options include OCCURRENCE, etc.}
 
-  \item{keyword}{Keyword to search by. Datasets can be
-  tagged by keywords, which you can search on. The search
-  is done on the merged collection of tags, the dataset
-  keywordCollections and temporalCoverages.}
+\item{keyword}{Keyword to search by. Datasets can be tagged by keywords, which
+you can search on. The search is done on the merged collection of tags, the
+dataset keywordCollections and temporalCoverages.}
 
-  \item{owning_org}{Owning organization. A uuid string. See
-  \code{\link{organizations}}}
+\item{owning_org}{Owning organization. A uuid string. See \code{\link{organizations}}}
 
-  \item{hosting_org}{Hosting organization. A uuid string.
-  See \code{\link{organizations}}}
+\item{hosting_org}{Hosting organization. A uuid string. See \code{\link{organizations}}}
 
-  \item{publishing_country}{Publishing country. See options
-  at isocodes$gbif_name}
+\item{publishing_country}{Publishing country. See options at isocodes$gbif_name}
 
-  \item{decade}{Decade, e.g., 1980. Filters datasets by
-  their temporal coverage broken down to decades. Decades
-  are given as a full year, e.g. 1880, 1960, 2000, etc, and
-  will return datasets wholly contained in the decade as
-  well as those that cover the entire decade or more. Facet
-  by decade to get the break down, e.g.
-  /search?facet=DECADE&facet_only=true (see example below)}
+\item{decade}{Decade, e.g., 1980. Filters datasets by their temporal coverage
+broken down to decades. Decades are given as a full year, e.g. 1880, 1960, 2000,
+etc, and will return datasets wholly contained in the decade as well as those
+that cover the entire decade or more. Facet by decade to get the break down,
+e.g. /search?facet=DECADE&facet_only=true (see example below)}
 
-  \item{pretty}{Print informative metadata using
-  \code{\link{cat}}. Not easy to manipulate output though.}
+\item{pretty}{Print informative metadata using \code{\link{cat}}. Not easy to
+manipulate output though.}
 
-  \item{subtype}{NOT YET IMPLEMENTED. Will allow filtering
-  of datasets by their dataset subtypes, DC or EML.}
+\item{subtype}{NOT YET IMPLEMENTED. Will allow filtering of datasets by their
+dataset subtypes, DC or EML.}
 
-  \item{continent}{Not yet implemented, but will eventually
-  allow filtering datasets by their continent(s) as given
-  in our Continent enum.}
+\item{continent}{Not yet implemented, but will eventually allow filtering datasets
+by their continent(s) as given in our Continent enum.}
 
-  \item{description}{Return descriptions only (TRUE) or all
-  data (FALSE, default)}
+\item{description}{Return descriptions only (TRUE) or all data (FALSE, default)}
 }
 \value{
-A data.frame, list, or message printed to console (using
-pretty=TRUE).
+A data.frame, list, or message printed to console (using pretty=TRUE).
 }
 \description{
-Search that returns up to 20 matching datasets. Results are
-ordered by relevance.
+Search that returns up to 20 matching datasets. Results are ordered by relevance.
 }
 \examples{
 \dontrun{