Renata Diaz 2020-12-19
Download from Zenodo (https://zenodo.org/record/166725)
zip_download_dest <- "~/Documents/sad-comparison.zip"
download.file("https://zenodo.org/record/166725/files/weecology/sad-comparison-peerj.2.zip?download=1",zip_download_dest , quiet = TRUE, mode = "wb")
unzip("~/Documents/sad-comparison.zip", exdir = "~/Documents/sad-comparison")
file.remove(zip_download_dest)
## [1] TRUE
Load data files from Zenodo downloads
zenodo_dir <- list.dirs("~/Documents/sad-comparison/", full.names = T)
zenodo_dir <- zenodo_dir[ which(grepl("sad-data", zenodo_dir))]
BBS:
bbs_zenodo <- read.csv(file.path(zenodo_dir, "bbs_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
bbs_github <- read.csv(here::here("working-data", "abund_data", "bbs_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
any(!(bbs_github == bbs_zenodo))
## [1] FALSE
FIA:
fia_zenodo <- read.csv(file.path(zenodo_dir, "fia_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
fia_github <- read.csv(here::here("working-data", "abund_data", "fia_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
any(!(fia_github == fia_zenodo))
## [1] FALSE
Gentry:
gentry_zenodo <- read.csv(file.path(zenodo_dir, "gentry_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
gentry_github <- read.csv(here::here("working-data", "abund_data", "gentry_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
any(!(gentry_github == gentry_zenodo), na.rm = T)
## [1] FALSE
any(!(which(is.na(gentry_github)) == which(is.na(gentry_zenodo))))
## [1] FALSE
MCDB:
mcdb_zenodo <- read.csv(file.path(zenodo_dir, "mcdb_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
mcdb_github <- read.csv(here::here("working-data", "abund_data", "mcdb_spab.csv"), stringsAsFactors = F, header = F, skip = 2)
any(!(mcdb_github == mcdb_zenodo))
## [1] FALSE
All the data files downloaded from GitHub exactly match their counterparts on Zenodo. (This is not surprising but good to check).
The analyses for this manuscript were done using the files downloaded
from GitHub. RMD doesn’t think it’s necessary (or really appropriate) to
re-write download_data
to download from Zenodo instead. This report
demonstrates that the analyses should be replicable using the data files
from Zenodo, should that be the only/the preferred option in the future.
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