update documentation

ropensci · Feb 19, 2015 · 63ca1e3 · 63ca1e3
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commit 63ca1e3
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Showing 7 changed files with 18 additions and 11 deletions.
diff --git a/R/locations.R b/R/locations.R
@@ -1,3 +1,5 @@
+## Consider information from: Countries | FAO areas | Ecosystems | Occurrences | Point map | Introductions | Faunaf
+
 #' locations
 #' 
 #' return a table of species locations as reported in FishBASE.org FAO location data
@@ -7,6 +9,8 @@
 #' @export
 #' @examples
 #' locations(species_list(Genus='Labroides'))
+#' @details currently this is ~ FAO areas table (minus "note" field)
+#' e.g. http://www.fishbase.us/Country/FaoAreaList.php?ID=5537
 locations <- function(species_list, server = SERVER, limit = 100){
   codes <- speccodes(species_list)
   bind_rows(lapply(codes, faoareas))
@@ -36,3 +40,8 @@ faoarrefs <- function(area_code, server = SERVER, limit = 100){
   data <- check_and_parse(resp)
 }
 
+
+
+## FIXME: Reproduce the ECOSYSTEMS table: 
+# see `ecosystems` sql-table
+# http://www.fishbase.us/trophiceco/EcosysList.php?ID=5537
diff --git a/R/species_info.R b/R/species_info.R
@@ -2,7 +2,6 @@
 #' 
 #' Provide wrapper to work with species lists. 
 #' @param species_list A vector of scientific names (each element as "genus species"). 
-#'   (FishBase SpecCodes can be given as numeric values in place of a scientific name.)
 #' @param limit The maximum number of matches from a single API call (e.g. per species). Function
 #'   will warn if this needs to be increased, otherwise can be left as is. 
 #' @param server base URL to the FishBase API, should leave as default.

diff --git a/man/commonnames.Rd b/man/commonnames.Rd
@@ -8,8 +8,7 @@ commonnames(species_list, limit = 100, server = SERVER,
   fields = c("ComName", "Language", "C_Code", "SpecCode"))
 }
 \arguments{
-\item{species_list}{A vector of scientific names (each element as "genus species").
-(FishBase SpecCodes can be given as numeric values in place of a scientific name.)}
+\item{species_list}{A vector of scientific names (each element as "genus species").}
 
 \item{limit}{The maximum number of matches from a single API call (e.g. per species). Function
 will warn if this needs to be increased, otherwise can be left as is.}

diff --git a/man/ecology.Rd b/man/ecology.Rd
@@ -7,8 +7,7 @@
 ecology(species_list, server = SERVER, limit = 100, fields = NULL)
 }
 \arguments{
-\item{species_list}{A vector of scientific names (each element as "genus species").
-(FishBase SpecCodes can be given as numeric values in place of a scientific name.)}
+\item{species_list}{A vector of scientific names (each element as "genus species").}
 
 \item{server}{base URL to the FishBase API, should leave as default.}
 

diff --git a/man/locations.Rd b/man/locations.Rd
@@ -7,8 +7,7 @@
 locations(species_list, server = SERVER, limit = 100)
 }
 \arguments{
-\item{species_list}{A vector of scientific names (each element as "genus species").
-(FishBase SpecCodes can be given as numeric values in place of a scientific name.)}
+\item{species_list}{A vector of scientific names (each element as "genus species").}
 
 \item{server}{base URL to the FishBase API, should leave as default.}
 
@@ -18,6 +17,10 @@ will warn if this needs to be increased, otherwise can be left as is.}
 \description{
 return a table of species locations as reported in FishBASE.org FAO location data
 }
+\details{
+currently this is ~ FAO areas table (minus "note" field)
+e.g. http://www.fishbase.us/Country/FaoAreaList.php?ID=5537
+}
 \examples{
 locations(species_list(Genus='Labroides'))
 }

diff --git a/man/species_info.Rd b/man/species_info.Rd
@@ -7,8 +7,7 @@
 species_info(species_list, server = SERVER, limit = 100, fields = NULL)
 }
 \arguments{
-\item{species_list}{A vector of scientific names (each element as "genus species").
-(FishBase SpecCodes can be given as numeric values in place of a scientific name.)}
+\item{species_list}{A vector of scientific names (each element as "genus species").}
 
 \item{server}{base URL to the FishBase API, should leave as default.}
 

diff --git a/man/synonyms.Rd b/man/synonyms.Rd
@@ -9,8 +9,7 @@ synonyms(species_list, limit = 50, server = SERVER, fields = c("SynGenus",
   "SpecCode", "SynCode", "CoL_ID", "TSN", "WoRMS_ID"))
 }
 \arguments{
-\item{species_list}{A vector of scientific names (each element as "genus species").
-(FishBase SpecCodes can be given as numeric values in place of a scientific name.)}
+\item{species_list}{A vector of scientific names (each element as "genus species").}
 
 \item{limit}{The maximum number of matches from a single API call (e.g. per species). Function
 will warn if this needs to be increased, otherwise can be left as is.}