CRS error in extract() with readchl functions

[KimBaldry]

Error when using

read_oc_sochla
readchla
readcha_mean

Error in spTransform(y1, projection(dummy)) :
second argument needs to be of class CRS

error origin is .big.extract

Will try to find a fix today.

[KimBaldry]

Have written the below function to work with extract - only pulls MODISA daily files. This will do for now. @mdsumner would be good for you to check the function. Based off readCHL_month but had to add a couple of lines to make it work with extract().

---

readCHL_daily <- function(date,time.resolution = "daily", xylim = NULL, ..., inputfiles = NULL, latest = TRUE,lon180 = FALSE,
nobsonly = FALSE,
returnfiles = FALSE) {
if (is.null(inputfiles)) {
## memoize this call
files <- ocfiles("daily", product = "MODISA", varnam = "CHL", type = "L3m")
} else {
files <- inputfiles
}
if (returnfiles)
return(files)
if (missing(date)) {
if (latest) date <- max(files$date) else date <- min(files$date)
}
date <- raadtools:::timedateFrom(date)
files <- .processFiles(date, files, "daily")
rl <- lapply(files$fullname, raster::raster, varname = "chlor_a")
if (!is.null(xylim)) rl <- lapply(rl, raster::crop, raster::extent(xylim))
raster::setZ(raster::brick(rl), date)
}