I would like to extract casts ("ctd_files") from unique ctd file in order to applied formulas from the package oce in all the casts with lapply function. Nevertheless, I obtain this error:
Error in files[ifile] : object of type 'S4' is not subsettable
For that I use this dataframe (sample):
df <-
structure(list(ctd_file = c("2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-02T162038 SBE0251090", "2018-08-02T162038 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T090018 SBE0251090", "2018-08-03T090018 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-03T183128 SBE0251090", "2018-08-03T183128 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T092503 SBE0251090", "2018-08-05T092503 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090",
"2018-08-05T190218 SBE0251090", "2018-08-05T190218 SBE0251090"
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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), row.names = c(NA, -100L
), class = c("tbl_df", "tbl", "data.frame"))
That I transform in ctd file
library(oce)
library(tidyverse)
ctd.df <- df %>% as.ctd(.,salinity, temperature, pressure)
And after I apply the following code given by this website:
## preallocate the container to store the individual
casts <- list()
### Loop the CNV file and create a list of casted CTD
for (ctd_files in 1:length(ctd.df)) {
casts[[ctd_files]] <- read.oce(ctd.df[ctd_files])
}
This is were the error come...
The original code is below (I do an extra step to transform the dataframe in ctd file), if that can help
files <- dir(pattern='*.cnv')
casts <- list()
for (ifile in 1:length(files)) {
casts[[ifile]] <- read.oce(files[ifile])
}
I have found a way to reach the wanted result with the function mapply.
By first, spliting the dataset df in a list and after transform the dataframe within the list in a ctd files.
#Transform the dataframe in list
spl_1 <- split(df,
f = list(PdataLaKo$ctd_file),
sep = '-', drop = TRUE)
#Transform the list in ctd files
spl_1 <- mapply(function(dat, nm) {
as.ctd(dat, salinity, temperature, pressure)
},
dat = spl_1, nm = names(spl_1))
It is also possible to split the list in different ctd files within the Global Environment
list2env(spl_2, envir = .GlobalEnv)