I'm opening ebird data with auk, having trouble creating a path for the file. I set the path to a folder. When I try to change it to a file it says the path is not true.
with the Sys.getenv()
I can see the path is set to a folder. with the auk_get_ebd_path()
command I see the same thing. When I try to change the path to a file inside that folder with the auk_set_ebd_path()
command I receive an error message.
library(auk)
auk_get_ebd_path()
[1] "/Users/lucypullen/Documents/bird/data"
auk_set_ebd_path("/Users/lucypullen/Documents/bird/data/ebd_CA_relApr-2019.txt", overwrite = TRUE)
[1] Error: dir.exists(paths = path) is not TRUE
other attempts yeilded an Error in file(con, "r") : cannot open the connection
message
Warning messages: 1: In file(con, "r") :
'raw = FALSE' but '/Users.....data/CA' is not a regular file
2: In file(con, "r") :
cannot open file '/Users/lucypullen/Documents/bird/data/CA': it is a directory
seems like they want the path to go to a file. I thought the path would be complete with the system.file()
command. I've tried a bunch of variations:
input_file <- system.file("/Users/lucypullen/Documents/bird/data/CA/ebd_CA_relApr-2019.txt", package = "auk")
or
input_file <- system.file("ebd_CA_relApr-2019.txt", package = "auk")
or
input_file <- system.file("~/ebd_CA_relApr-2019.txt", package = "auk")
I suspect you should be doing this, since there appears to have been some sort of setup operation that preceded this question:
my_ebd_path = auk_get_ebd_path() # since you appear to already set it.
my_full_file_loc <- paste0(my_ebd_path, ”/“, "ebd_CA_relApr-2019.txt")
my_ebd_data <- read_ebd(my_full_file_loc)
str(my_ebd_data)
# ------what I get with the sample file in the package--------------
Classes ‘tbl_df’, ‘tbl’ and 'data.frame': 494 obs. of 45 variables:
$ checklist_id : chr "S6852862" "S14432467" "S39033556" "S38303088" ...
$ global_unique_identifier : chr "URN:CornellLabOfOrnithology:EBIRD:OBS97935965" "URN:CornellLabOfOrnithology:EBIRD:OBS201605886" "URN:CornellLabOfOrnithology:EBIRD:OBS530638734" "URN:CornellLabOfOrnithology:EBIRD:OBS520887169" ...
$ last_edited_date : chr "2016-02-22 14:59:49" "2013-06-16 17:34:19" "2017-09-06 13:13:34" "2017-07-24 15:17:16" ...
$ taxonomic_order : num 20145 20145 20145 20145 20145 ...
$ category : chr "species" "species" "species" "species" ...
$ common_name : chr "Green Jay" "Green Jay" "Green Jay" "Green Jay" ...
$ scientific_name : chr "Cyanocorax yncas" "Cyanocorax yncas" "Cyanocorax yncas" "Cyanocorax yncas" ...
$ observation_count : chr "4" "2" "1" "1" ...
$ breeding_bird_atlas_code : chr NA NA NA NA ...
#----snipped a bunch of output---------
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