Struggling with data loss when using read.table in R
I downloaded the entire World Checklist of Vascular Plant Database version 9:
http://sftp.kew.org/pub/data-repositories/WCVP/
unzip the file and to get wcvp_v9_jun_2022.txt and use control + F to search "Corymbia", and you will find many rows of data where genus=="Corymbia", the same is also true for genus=="Eucalyptus" and genus=="Angophora"
imported it into R studio with the following line
WCVP <- read.table("wcvp_v9_jun_2022.txt",sep = "|", fill = T, header = T)
and check for the data
WCVP[WCVP$genus=="Corymbia",]
WCVP[WCVP$genus=="Eucalyptus",]
WCVP[WCVP$genus=="Angophora",]
I got the response
WCVP[WCVP$genus=="Corymbia",]
[1] kew_id family genus species
[5] infraspecies taxon_name authors rank
[9] taxonomic_status accepted_kew_id accepted_name accepted_authors
[13] parent_kew_id parent_name parent_authors reviewed
[17] publication original_name_id
<0 rows> (or 0-length row.names)
While data for the other 2 genera are intact and R spits out rows of data?
Why is the data for Genus Corymbia missing after the .txt is imported into R studio? is there a bug or how do I troubleshoot?
Many thanks
There are embedded single-quotes (singles, not always paired) in the data that are throwing off reading it in. Set quote="" and you should see all the data.
WCVP <- read.table("wcvp_v9_jun_2022.txt",
sep = "|", fill = TRUE, header = TRUE)
nrow(WCVP)
# [1] 605649
WCVP[WCVP$genus=="Corymbia",]
# [1] kew_id family genus species infraspecies taxon_name authors rank taxonomic_status accepted_kew_id accepted_name accepted_authors parent_kew_id
# [14] parent_name parent_authors reviewed publication original_name_id
# <0 rows> (or 0-length row.names)
WCVP <- read.table("wcvp_v9_jun_2022.txt",
sep = "|", fill = TRUE, header = TRUE, quote = "")
nrow(WCVP)
# [1] 1232931 ## DIFFERENT!
head(WCVP[WCVP$genus=="Corymbia",], 3)
# kew_id family genus species infraspecies taxon_name authors rank taxonomic_status accepted_kew_id accepted_name accepted_authors parent_kew_id parent_name
# 758307 986238-1 Myrtaceae Corymbia Corymbia K.D.Hill & L.A.S.Johnson GENUS Accepted
# 758308 986307-1 Myrtaceae Corymbia abbreviata Corymbia abbreviata (Blakely & Jacobs) K.D.Hill & L.A.S.Johnson SPECIES Accepted 986238-1 Corymbia
# 758309 986248-1 Myrtaceae Corymbia abergiana Corymbia abergiana (F.Muell.) K.D.Hill & L.A.S.Johnson SPECIES Accepted 986238-1 Corymbia
# parent_authors reviewed publication original_name_id
# 758307 Reviewed Telopea 6: 214 (1995)
# 758308 K.D.Hill & L.A.S.Johnson Reviewed Telopea 6: 344 (1995) 592646-1
# 758309 K.D.Hill & L.A.S.Johnson Reviewed Telopea 6: 244 (1995) 592647-1