Problem with for loop when downloading species occurrence data - r

Question

I want to download the occurrence data from gbif website and I use the following R script. When I run the script, I got an error with the following message "Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : arguments imply differing number of rows: 1, 0)". It would be highly appreciated if anyone could help me with this.
My data: data
My R script:
flist<-read_excel("Mekong fish.xlsx",sheet="Sheet1")
##Loop
fname<-list()
Occ<-list()
datfish<-list()
name_list<-unique(flist$Updated_name)
# create for loop to produce ggplot2 graphs
for (i in seq_along(name_list)) {
# create plot for each Occurrence in df
Occ[[i]] <-occ_search(scientificName = name_list[i], limit=2)
fname[[i]]<-occ_search(scientificName = name_list[i],
fields = c("species", "country","decimalLatitude", "decimalLongitude"),
hasCoordinate=T, limit= Occ[[i]]$meta[4],return ="data")
datfish[[i]]<-as.data.frame(fname[[i]]$data)
}

Answer 1

I got a different error:
Expecting logical in D1424 / R1424C4: got 'in Lao'Expecting logical in D1426 / R1426C4: got 'in China'Expecting logical in D1467 / R1467C4: got 'only Cambodia'Expecting logical in D1469 / R1469C4: got 'only in VN'Expecting logical in D1473 / R1473C4: got 'only in China'Expecting logical in D1486 / R1486C4: got 'only in Malaysia'Expecting logical in D1488 / R1488C4: got 'only 1 point in VN'
I think the problem is caused in some fields in the 4th column. I don't have the right packages installed to run your code. But I got a different error (package missing) once i dropped the fourth column.
flist<-read_excel("~/Downloads/Mekong fish.xlsx",sheet="Sheet1")
flist <=subset(flist, select = -4)
...
EDIT:
This worked for me. read_excel assigned column 4 the type boolean. When I explicitly set it to text it worked.
library(readxl)
library(rgbif)
library(raster)
flist<-read_excel("~/Downloads/Mekong fish.xlsx",
sheet="Sheet1",
col_types = c("numeric", "text", "numeric", "text"))
flist
##Loop
fname<-list()
Occ<-list()
datfish<-list()
name_list<-unique(flist$Updated_name)
# create for loop to produce ggplot2 graphs
for (i in seq_along(name_list[1:2])) {
message(i)
# # create plot for each Occurrence in df
Occ[[i]] <-occ_search(scientificName = name_list[i], limit=2)
message(Occ[[i]])
fname[[i]]<-occ_search(scientificName = name_list[i],
fields = c("species", "country","decimalLatitude", "decimalLongitude"),
hasCoordinate=T, limit= Occ[[i]]$meta[4],return ="data")
message(fname[[i]])
datfish[[i]]<-as.data.frame(fname[[i]]$data)
message(datfish[[i]])
}
> 1
> list(offset = 0, limit = 2, endOfRecords = FALSE, count = >15)list(list(name = c("Animalia", "Chordata", "Actinopterygii",
> "Cypriniformes", "Cyprinidae", "Aaptosyax", "Aaptosyax grypus"), key = > > c("1", "44", "204", "1153", "7336", "2363805", "2363806"),
> etc...