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Fixed bug in get_ereefs_ts() in mmp check. #35

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Fixed bug in get_ereefs_ts() in mmp check. #35

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747371b
Fixed bug in get_ereefs_ts() in mmp check.
BarbaraRobson May 22, 2023
72ffc12
Fixed warn() error (changed to warning())
BarbaraRobson May 23, 2023
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: ereefs
Title: Useful Functions to Handle eReefs and EMS model Output
Version: 3.2.4
Version: 3.2.5
Encoding: UTF-8
Authors@R: c(person("Barbara", "Robson", email="[email protected]",
role = c("aut", "cre")),
Expand Down Expand Up @@ -43,7 +43,7 @@ URL: https://ereefs.info
Date: 2021-08-18
License: MIT + file LICENSE
LazyData: true
Imports: ncdf4 (>= 1.16),
Imports: ncdf4 (== 1.19),
plyr (>= 1.8.4),
dplyr (>= 0.7.6),
magrittr,
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15 changes: 13 additions & 2 deletions R/data_extraction_functions.R
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Expand Up @@ -526,7 +526,7 @@ get_ereefs_ts <- function(var_names=c('Chl_a_sum', 'TN'),
if (layer=='integrated') return(get_ereefs_depth_integrated_ts(var_names, location_latlon, start_date, end_date, input_file, input_grid, eta_stem, override_positive))
if ((layer=='bottom')&&(length(location_latlon[,1])>1)) stop('Only one location can be given if layer==bottom')
# if (layer=='bottom') return(get_ereefs_bottom_ts(var_names, location_latlon, start_date, end_date, input_file, input_grid, eta_stem, override_positive))
if (location_latlon[[1]]=="mmp") {
if (location_latlon[[1]][1]=="mmp") {
location_latlon <- data.frame(latitude=mmp_sites$latitude, longitude=mmp_sites$longitude)
mmp <- TRUE
} else {
Expand Down Expand Up @@ -554,7 +554,7 @@ get_ereefs_ts <- function(var_names=c('Chl_a_sum', 'TN'),
if (length(ilat)) {
location_latlon <- data.frame(latitude = location_latlon[, ilat], longitude = location_latlon[, ilon])
} else {
warn("Assuming that the first column of location_latlon is latitude and the second column is longitude")
warning("Assuming that the first column of location_latlon is latitude and the second column is longitude")
}
names(location_latlon)[1:2] <- c("latitude", "longitude")
grid_index <- apply(location_latlon,1, function(ll) which.min((latitude - ll[1])^2 + (longitude - ll[2])^2))
Expand Down Expand Up @@ -651,6 +651,9 @@ get_ereefs_ts <- function(var_names=c('Chl_a_sum', 'TN'),
}
#input_file <- paste0(input_file, '?', var_list, ',time')
nc <- safe_nc_open(input_file)
## tindyc:
## nc <- tindync::tidync(input_file)

# if ((ereefs_case[2] == "1km")||(ereefs_case[2] == "4km")) {
# if (!is.null(nc$var[['t']])) {
# d <- as.Date(safe_ncvar_get(nc, "t"), origin = as.Date("1990-01-01"))[from_day:(from_day+day_count-1)]
Expand All @@ -670,14 +673,22 @@ get_ereefs_ts <- function(var_names=c('Chl_a_sum', 'TN'),
dims <- nc$var[[var_names[j]]][['size']]
if (is.null(dims)) stop(paste(var_names[j], ' not found in netcdf file.'))
ndims[j] <- length(dims)
## tidync:
## ndims[j] <- dim(nc %>% tidync::activate(var_names[j]) %>% hyper_dims())[1]
}
if (layer == 'surface') {
dims <- nc$var[[var_names[j]]][['size']]
layer_actual <- dims[3]
## tidync:
## layer_actual <- nc %>% tidync::hyper_dims() %>% dplyr::filter(name=="k") %>% dplyr::select("length")
} else if (layer == 'bottom') {
# find the bottom layer -- assume it is the first layer that is not NA
if (ndims[j] == 4) {
dum1 <- safe_ncvar_get(nc, var_names[j], start=c(startv,1,from_day), count=c(countv,-1,1))
## tidync: [need to check whether dims of startv and countv are the right way around
## dum1 <- nc %>% tidync::activate(var_names[j]) %>%
## tidync::hyper_filter(i = dplyr::between(i, startv[1], startv[1]+countv[1]), j = dply::between(j, startv[2], startv[2]+countv[2]), time = time == from_day) %>%
## tidync::hyper_array()
if (length(which(!is.na(dum1)))==0) stop('Location given is a dry cell at start time. It is probably on land.')
layer <- min(which(!is.na(dum1)))
layer_actual <- layer
Expand Down