Merge pull request #16 from luisDVA/lvchanges

Fix some spelling, added an error for lets.presab., document datasets, add test

R/Data_helps.R

@@ -1,64 +1,73 @@
-#'@name IUCN
-#'@aliases IUCN
-#'@docType data
-#'@title IUCN avaliation for frogs of Phyllomedusa genus 
-#'@usage data(IUCN)
-#'@description Result of the function \code{\link{lets.iucn}} 
-#'applied to Southern American frog genera Phyllomedusa in 2014. 
+#' IUCN evaluation for frogs of the genus Phyllomedusa
+#' 
+#' Result of the (deprecated) function \code{\link{lets.iucn}} 
+#' applied to South American frog genus Phyllomedusa in 2014.
+#'
+#'@format A data frame with 32 rows and 7 columns:
+#'\describe{
+#'  \item{Species}{Scientific name}
+#'  \item{Family}{Family}
+#'  \item{Status}{Red List Status}
+#'  \item{Criteria}{Criteria for listing as threatened}
+#'  \item{Population}{Population trend per IUCN}
+#'  \item{Description_Year}{Year described}
+#'  \item{Country}{Presence in country}
+#'}
+#'
+#'@source IUCN - \url{https://www.iucnredlist.org/}. 2014.  
+"IUCN" 
 
-NULL
 
-#'@name PAM
-#'@aliases PAM
-#'@docType data
-#'@title PresenceAbsence object for frogs of Phyllomedusa genus
-#'@usage data(PAM)
-#'@description PresenceAbsence object obtained using the function \code{\link{lets.presab}} 
-#'in the Geographic distribution of the Southern American frog genus \link{Phyllomedusa}.
-#'@source IUCN - \url{https://www.iucnredlist.org/}. 2014.
+#' PresenceAbsence object for frogs of the genus Phyllomedusa
+#' 
+#' PresenceAbsence object obtained using the function \code{\link{lets.presab}} 
+#' for the Geographic distribution of the South American frog genus \link{Phyllomedusa}.
+#' @format A PresenceAbsence object
+#' @source Generated from IUCN Spatial Data - \url{https://www.iucnredlist.org/}. 2014.
+"PAM"
 
-NULL
+#' Phyllomedusa
+#' 
+#' Geographic distribution of the South American frog genus Phyllomedusa. 
+# 'Data modified from the IUCN Red List spatial dataset, downloaded 05/2014).
+#'
+#' See the IUCN Red List Attribute Information for Species Ranges. 
+#'
+#' @format A simple feature collection for 32 species with 46 features and 4 fields.
+#' 
+#' \describe{
+#'  \item{binomial}{Scientific name}
+#'  \item{presence}{IUCN Red List distributional code}
+#'  \item{origin}{IUCN Red List distributional code}
+#'  \item{seasonal}{IUCN Red List distributional code}
+#' }
+#' @source IUCN - \url{https://www.iucnredlist.org/}. 2014.
+"Phyllomedusa"
 
-#'@name Phyllomedusa
-#'@aliases Phyllomedusa
-#'@docType data
-#'@title Geographic distribution of Phyllomedusa genus
-#'@usage data(Phyllomedusa)
-#'@description Geographic distribution of the Southern American frog genera Phyllomedusa. 
-#'Data was modfied from IUCN (\url{https://www.iucnredlist.org/}, downloaded in 05/2014). 
-#'There are 32 species and 46 polygons.
-#'@source IUCN - \url{https://www.iucnredlist.org/}. 2014.
 
-NULL
+#' Mean temperature raster for the world.
+#'
+#' Mean temperature raster in degrees Celsius (multiplied by 100) 
+#' for the world in 10 arc min of resolution. 
+#' @format A PackedStatRaster object.
+#' @source Data was modified from WorldClim (\url{https://worldclim.com/}, downloaded 05/2014).
+#' 
+#' Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis, 2005. 
+#' Very high resolution interpolated climate surfaces for global land areas. 
+#' International Journal of Climatology 25: 1965-1978.
+"temp"
 
-#'@name temp
-#'@aliases temp
-#'@docType data
-#'@title Avarege temperature raster for the world.
-#'@usage data(temp)
-#'@description Average temperature raster in Celsius degrees(multiplied by 100) 
-#'for the world in 10 arc min of resolution. Data was modfied from 
-#'WorldClim (\url{https://worldclim.com/}, downloaded in 05/2014).
-#'@source Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis, 2005. 
-#'Very high resolution interpolated climate surfaces for global land areas. 
-#'International Journal of Climatology 25: 1965-1978.
 
-NULL
-
-
-
-#'@name wrld_simpl
-#'@aliases wrld_simpl
-#'@docType data
-#'@title Simplified world country polygons
-#'@usage data(temp)
-#'@description Shapefile in sf format. The object was obtained from maptools
-#'  package and converted to sf.
-#'@source Originally
-#'  “https://mappinghacks.com/data/TM_WORLD_BORDERS_SIMPL-0.2.zip”, 
+#' Simplified world country polygons
+#' 
+#' World map in sf format. Obtained from maptools 
+#' and converted to sf.
+#'  
+#' @format A simple feature collection with 246 features and 11 fields.
+#' @source Originally
+#'  \url{https://mappinghacks.com/data/TM_WORLD_BORDERS_SIMPL-0.2.zip}, 
 #'  now available from
-#'  https://github.com/nasa/World-Wind-Java/tree/master/WorldWind/testData/shapefiles
-
+#'  \url{https://github.com/nasa/World-Wind-Java/tree/master/WorldWind/testData/shapefiles}.
+"wrld_simpl"
 
 
-NULL

R/lets_presab.R

@@ -8,17 +8,17 @@
 #'@param shapes Object of class \code{SpatVect} or \code{Spatial} (see packages
 #'  \code{\link{terra}} and  \code{\link{sf}} to read these files) containing
 #'  the distribution of one or more species. Species names should be stored in
-#'  the object as BINOMIAL/binomial or SCINAME/sciname.
-#'@param xmx Maximun longitude used to construct the grid in which the matrix
+#'  the object as BINOMIAL/binomial or SCINAME/sciname. 
+#'@param xmx Maximum longitude used to construct the grid in which the matrix
 #'  will be based (i.e. the [gridded] geographic domain of interest). 
 #'  If NULL, limits will be calculated based on the limits of the shapes object.
-#'@param xmn Minimun longitude used to construct the grid in which the matrix
+#'@param xmn Minimum longitude used to construct the grid in which the matrix
 #'  will be based (i.e. the [gridded] geographic domain of interest).
 #'  If NULL, limits will be calculated based on the limits of the shapes object.
-#'@param ymx Maximun latitude used to construct the grid in which the matrix
+#'@param ymx Maximum latitude used to construct the grid in which the matrix
 #'  will be based (i.e. the [gridded] geographic domain of interest).
 #'  If NULL, limits will be calculated based on the limits of the shapes object.
-#'@param ymn Minimun latitude used to construct the grid in which the matrix
+#'@param ymn Minimum latitude used to construct the grid in which the matrix
 #'  will be based (i.e. the [gridded] geographic domain of interest).
 #'  If NULL, limits will be calculated based on the limits of the shapes object.
 #'@param resol Numeric vector of length 1 or 2 to set the grid resolution. 
@@ -59,29 +59,29 @@
 #' *But see the optional argument \code{show.matrix}.
 #'
 #'
-#'@details The function creates the presence-absence matrix based on a raster
+#'@details This function creates the presence-absence matrix based on a raster
 #'  object. Depending on the cell size, extension used and number of species it
 #'  may require a lot of memory, and may take some time to process it. Thus,
 #'  during the process, if \code{count} argument is set \code{TRUE}, a counting
-#'  window will open so you can see the progress (i.e. in what polygon/shapefile
-#'  the function is working). Note that the number of polygons is not the same
-#'  as the number of species that you have (i.e. a species may have more than
+#'  window will open to display the progress (i.e. the polygon/shapefile
+#'  that the function is working on). Note that the number of polygons is not the same
+#'  as the number of species (i.e. a species may have more than
 #'  one polygon/shapefiles).
 #'
 #'@seealso \code{\link{plot.PresenceAbsence}}
 #'@seealso \code{\link{lets.presab.birds}}
 #'@seealso \code{\link{lets.shFilter}}
 #'
 #' @examples \dontrun{
-#' # Spatial distribution polygons of south american frogs
+#' # Spatial distribution polygons of South American frogs
 #' # of genus Phyllomedusa.
 #' data(Phyllomedusa)
 #' PAM <- lets.presab(Phyllomedusa)
 #' summary(PAM)
 #' # Species richness map
 #' plot(PAM, xlab = "Longitude", ylab = "Latitude",
 #'      main = "Phyllomedusa species richness")
-#' # Map of the specific species
+#' # Map of individual species
 #' plot(PAM, name = "Phyllomedusa nordestina")
 #'}
 #'
@@ -108,7 +108,14 @@ lets.presab <- function(shapes,
                         seasonal = NULL,
                         count = FALSE) {
 
-
+  # look for species names
+  if(!any(c("binomial","BINOMIAL","SCINAME","sciname") %in% names(shapes)))
+  {
+    stop(paste0("species names missing from shapes ",
+                "or column name in data does not match required names"))
+  }
+
+
   shapes <- .check_shape(shapes)
 
   # Projection set for spatial polygons
@@ -234,7 +241,7 @@ lets.presab <- function(shapes,
 
 
 
-# Axuliar function to avoid code repetition inside the loop <<<<<<<<<
+# Helper function to avoid code repetition inside the loop <<<<<<<<<
 
 # Function to extract cell positions in the raster
 .extractpos <- function(ras,