#'@title Useful species
#'
#'@description Get species with a minimum number of occurrences.
#'
#'
#'@param data Vector of characters. Name of the input file.
#'
#'@param rd.frmt Vector of characters. The file format to read.
#'By default it will be read as a R object using the
#' \code{'readRDS'} argument, but it can be read as plain text using the
#' \code{'readTXT'} argument. See details.
#'
#'@param path Vector of characters. Path to the input file.
#'
#'@param cut.off Numeric. Minimal (absolute) number of occurrences for a given
#'species, the default value is 3, as the minimal number of points to draw a polygon.
#'
#'@param wrt.frmt Character. Output file format, by default it uses a \code{'.RDS'}
#'format, although it could save a txt table. See details.
#'
#'@param save.useful.in String. Output file path for useful species (those with
#'occurrences larger than the \code{cut.off} value. See details.
#'
#'@param save.useless.in String. Output file path for useless species (those with
#'occurrences smaller than the \code{cut.off} value. See details.
#'
#'@details
#'To check input/output formats see \code{\link{readAndWrite}}.
#'Column names must follow Darwin Core2[1] standard. See data('ID_DarwinCore).
#'
#'@return A data.frame object and a file for each species.
#'
#'@author R-Alarcon Viviana and Miranda-Esquivel Daniel R.
#'
#'@note See:
#'R-Alarcon V. and Miranda-Esquivel DR.(submitted) geocleaMT: An R package to
#'cleaning geographical data from electronic biodatabases.
#'
#'@seealso \code{\link{readAndWrite}}
#'
#'@references
#'[1] Wieczorek, J. et al. 2012. Darwin core: An evolving community-developed biodiversity data standard.
#' PloS One 7: e29715.
usefulSp <- function(data = NULL,
path = NULL,
cut.off = 3,
rd.frmt = 'readRDS',
wrt.frmt = 'saveRDS',
save.useful.in = NULL,
save.useless.in = NULL){
tab.info <- as.data.frame(matrix(NA, length(data), 3))
colnames(tab.info) <- c('Sp', 'Total.Occ', 'State')
for (i in 1:length(data)){
sp <- readAndWrite(action = 'read',frmt = rd.frmt ,
path = path,name = data[i])
tab.info$Sp[i] <- data[i]
tab.info$Total.Occ[i] <- nrow(sp)
if (nrow(sp) >= cut.off) {
readAndWrite(action = 'write', frmt = wrt.frmt ,
path = save.useful.in, name = data[i], object = sp)
tab.info$State[i] <- 'in'
} else {
readAndWrite(action = 'write', frmt = wrt.frmt ,
path = save.useless.in, name = data[i], object = sp)
tab.info$State[i] <- 'out'
}
print(paste('Species:',data[i]))
}
return(tab.info)
}
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