Lees docs

.Rprofile

@@ -0,0 +1,2 @@
+install.packages("ALA4R",repos="http://rforge.net/",type="source")
+library(ALA4R)

ALA4R.Rproj

@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source

R/autocomplete.R

@@ -1,27 +1,30 @@
 #' Auto Complete Search
 #' 
-#' This is an autocomplete search for identifying names & identifiers used at
-#' ALA. It is used to provide a dataframe of scientific and common names that
-#' can be used for further analysis that is a match from a supplied partial
-#' name.
+#' An autocomplete search for identifying species names & identifiers used at the ALA based
+#' on matches from a PARTIAL NAME. atocomplete can generate a dataframe of scientific and 
+#' common names that can be used for further analysis in R.
 #' 
+#' If the scientific name, common name or LSID are known, use fulltext_search
 #' 
-#' @param taxon a character string that defines part of the scientific or
-#' common name of the taxa of interest
-#' @param geoOnly logical: if TRUE, only results that have some geospatial occurrence records will be included
-#' @param idxType string: The index type to limit. Values include: TAXON REGION COLLECTION INSTITUTION DATASET
-#' @param limit the maximum number of matches returned (defaults to the server-side value, which is currently 10)
-#' @return A dataframe of taxa given the partial matches where columns are
-#' identified as: \item{guid}{} \item{name}{} \item{occurrenceCount}{}
-#' \item{georeferencedCount}{} \item{scientificNameMatches}{}
-#' \item{commonNameMatches}{} \item{commonName}{} \item{matchedNames}{}
-#' \item{ankId}{} \item{rankString}{} \item{left}{} \item{right}{}
 #' @author Atlas of Living Australia \email{support@@ala.org.au}
 #' @references \url{http://api.ala.org.au/}
+
+#' @param taxon a character string of part of the scientific, common name of the taxa
+#' @param geoOnly logical: if TRUE, only results that have geospatial occurrence records will be included
+#' @param idxType string: The index type to limit. Values include: TAXON REGION COLLECTION INSTITUTION DATASET
+#' @param limit the maximum number of matches returned (defaults to the server-side value - currently 10)
+#' @return A dataframe of taxa given the partial matches where columns are identified as: 
+#' \item{guid}{} \item{name}{} \item{occurrenceCount}{}
+#' \item{georeferencedCount}{} \item{scientificNameMatches}{}
+#' \item{commonNameMatches}{} 
+#' \item{commonName}{} 
+#' \item{matchedNames}{} \item{ankId}{} \item{rankString}{} \item{left}{} \item{right}{}
+#'
 #' @examples
 #' 
-#' 	#find information ALA holds on red kangaroo
+#' 	#find information ALA holds on red kangaroo (Macropus Rufus)
 #' 	autocomplete("red kangaroo")
+#'  autocomplete("Macropus Rufus",geoOnly=TRUE)
 #' 
 #' @export autocomplete
 autocomplete=function(taxon,geoOnly=FALSE,idxType=NULL,limit=NULL) {
@@ -44,7 +47,7 @@ autocomplete=function(taxon,geoOnly=FALSE,idxType=NULL,limit=NULL) {
         this_query$limit=limit
     }
     if (geoOnly) {
-        this_query$geoOnly="true"
+        this_query$geoOnly="true" #Check for taxa that have locations (some have no location)
     }
     if (!is.null(idxType)) {
         this_query$idxType=idxType

R/fulltext_search.R

@@ -1,16 +1,32 @@
 #' Full text search
 #' 
 #' Performs a search across all objects, and selects the closest matches
-#' 
-#' @param taxon a character string for the taxon of interest
-#' @return a dataframe of information with columns being: \item{comp1
-#' }{Description of 'comp1'}
+#'
 #' @author Atlas of Living Australia \email{support@@ala.org.au}
 #' @references \url{http://api.ala.org.au/}
+#'  
+#' @param taxon: a character string for the taxon of interest
+#' @return a dataframe of information with columns being: 
+#' \item{comp1}{Description of 'comp1'} 
+#' $Results
+#' \item{guid}  \item{name}  \item{idxtype}
+#' \item{score} \item{parentGuid}
+#' \item{commonName}  \item{nameComplete}
+#' \item{commonNameSingle}  \item{hasChildren} \item{rank} \item{rankId} \item{rawRank} \item{conservationStatus} \item{conservationStatusAUS}
+#' \item{isAustralian}
+#' \item{highlight}
+#' \item{image} \item{thumbnail} \item{left} \item{right} \item{kingdom}
+#' \item{phylum} \item{class} \item{order} \item{class} \item{order} \item{family} \item{genus} \item{author}
+#' \item{linkIdentifier} \item{occCount} \item{imageSource} \item{imageCount} \item{isEcluded}
+#' \item{imageUrl} \item{largeImageUrl} \item{smallImageUrl} \item{thumbnailUrl} \item{imageMetadataUrl} 
+#' \item{acceptedConceptName} \item{synonomyRelationship} \item{synonomyDescription}
+#' 
 #' @examples
 #' 
 #' 	#find information ALA holds on red kangaroo
 #' 	fulltext_search("red kangaroo")
+#'  fulltext_search("Macropus Rufus")
+#'  fulltext_search("urn:lsid:biodiversity.org.au:afd.taxon:31a9b8b8-4e8f-4343-a15f-2ed24e0bf1ae")
 #' 
 #' @export
 fulltext_search <- function(taxon) {

R/species_info.R

@@ -1,22 +1,21 @@
-#' Fetch species profile
+#' Fetch a taxon profile given a scientific name or LSID
 #' 
-#' Retrieve species profile given either the scientific name or GUID
-#' 
-#' 
-#' @param scientificname string: scientific name of the species of interest
-#' @param guid string: GUID of species of interest
-#' @param verbose boolean value defining how much progress information to display; default is set by ala_config().
-#' @return species profile in the form of a named list
 #' @author Atlas of Living Australia \email{support@@ala.org.au}
 #' @references \url{http://api.ala.org.au/}
+#' 
+#' @param scientificname string: scientific name of the taxon of interest (species, genus, family etc) 
+#' @param LSID string: The Life Science Identifier of the taxon of interest
+#' @param verbose boolean value: How much progress information to display; default is set by ala_config().
+#' @return species profile in the form of a named list
+
 #' @examples
 #' 
 #' species_info("Grevillea humilis subsp. maritima")
 #' species_info(guid="urn:lsid:biodiversity.org.au:apni.taxon:248651")
 #' 
 #' @export species_info
 
-# TODO: support multiple names or guids passed as a vector?
+# TODO: support multiple names or guids passed as a vector? (LB:low priority)
 
 species_info=function(scientificname=NULL,guid=NULL,verbose=ala_config()$verbose) {
     if (is.null(scientificname) && is.null(guid)) {

R/specieslist.R

@@ -1,23 +1,23 @@
-#' Get list of taxa and occurrence counts
-#' 
-#' Get list of taxa and their occurrence counts, matching a taxonomic query
-#' and/or within a specified spatial area
+#' Get list of taxa and their occurrence counts, with/without a matching
+#' taxonomic query within an optionally-defined WKT-defined polygon
 #' 
+#' @author Atlas of Living Australia \email{support@@ala.org.au}
+#' @references \url{http://api.ala.org.au/} 
+#' \url{http://www.geoapi.org/3.0/javadoc/org/opengis/referencing/doc-files/WKT.html}
 #' 
-#' @param taxon Taxonomic query, e.g. "macropus" or "macropodidae"
-#' @param wkt A WKT (well-known text) string providing a spatial polygon within
-#' which to search, e.g. "POLYGON((140 -37,151 -37,151 -26,140.1310 -26,140
-#' -37))"
+#' @param taxon: Text of taxon, e.g. "Macropus rufus" or "macropodidae"
+#' @param wkt: Numeric vector string of WKT (well-known text) defining a polygon within
+#' which to limit taxon search, e.g. "POLYGON((140 -37,151 -37,151 -26,140 -26,140 -37))"
 #' @param page_size Maximum number of records to return (may not be honoured by
-#' the ALA server). Default=NA, meaning that the server default value
-#' (currently 10) will be used.
+#' the ALA server). Default=NA, meaning that the server default value (currently 10) will be used.
 #' @return Data frame with (at least) the columns
-#' "Scientific.name","Common.name","Taxon.rank","LSID","N.occurrences"
-#' @author Atlas of Living Australia \email{support@@ala.org.au}
-#' @references \url{http://api.ala.org.au/}
+#' \item {family} \item{Scientific.name} \item{Common.name} \item{Taxon.rank}
+#' \item{GUID} \item{N.occurrences}
 #' @examples
 #' 
-#' x=specieslist(taxon="macropus",wkt="POLYGON((140 -37,151 -37,151 -26,140.1310 -26,140 -37))")
+#' x=specieslist(taxon="macropus",wkt="POLYGON((140 -37,151 -37,151 -26,140 -26,140 -37))")
+#' x=specieslist(wkt="POLYGON((140 -37,151 -37,151 -26,140 -26,140 -37))")
+#' x=specieslist(wkt="POLYGON((147.62 -42.83,147.60 -42.86,147.65 -42.87,147.70 -42.86,147.62 -42.83))",page_size=30)
 #' 
 #' @export specieslist
 specieslist=function(taxon="",wkt="",page_size=NA) {