open_sp <- function(spp, shapefile) {
if (shapefile) {
# sort this out later on...
# trycatch()
} else {
ext <- strsplit(spp, "\\.")[[1]]
ext <- ext[length(ext)]
if (ext == "RDS") {
spp <- readRDS(spp)
} else if (ext == "csv") {
spp <- read.csv(spp)
} else if (ext == "txt") {
spp <- read.table(spp)
} else if (ext == "xls" | ext == "xlsx") {
stop(paste("please convert", ext, "file into comma-delimited (.csv)"))
} else {
stop("file format not supported - please use comma-delimited (.csv) or
tab-delimited (with .txt extension) for tables. For R objects please
use the saveRDS function with the .RDS extension to generate the
file.")
}
}
return(spp)
}
check_coord_cols <- function(spp) {
if (all(c("x", "y") %in% colnames(spp))) {
coord_cols <- c("x", "y")
} else if (all(c("lat", "lon") %in% colnames(spp))) {
coord_cols <- c("lat", "lon")
} else if (all(c("lat", "long") %in% colnames(spp))) {
coord_cols <- c("lat", "long")
} else if (all(c("lati", "longi") %in% colnames(spp))) {
coord_cols <- c("lati", "longi")
} else if (all(c("latitude", "longitude") %in% colnames(spp))) {
coord_cols <- c("latitude", "longitude")
} else {
if (ncol(spp) == 2) {
coord_cols <- colnames(spp)
warning("Column names of spp are unexpected - assuming the first column
is latitude and the second is longitude.")
} else {
stop("Cannot find coordinates in spp Columns for coordinates should be
labelled one of:
'x' and 'y',
'lat' and 'lon',
'lat' and 'long',
'lati' and 'longi' or
'latitude' and 'longitude'.")
}
}
return(coord_cols)
}
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