make-data.Rmd
# REQUIRED ARGUMENTS
dir.orig.data = "C:/Users/jburnett/OneDrive - DOI/research/cormorants/dubcorm-data-backup/"
dir.proj = "C:/users/jburnett/OneDrive - DOI/research/cormorants/do-not-edit/"
species = c("wood thrush")
species.abbr = c("woothr") # see ebird filenames for abbreviation
usgs.layer = "US_BBS_Route-Paths-Snapshot_Taken-Feb-2020" # name of the USGS BBS route shapefile
cws.layer = "ALL_ROUTES" # name of the Canadian (CWS) BBS route shapefile.
mmyyyy = "dec-2021" # the month and year of the eBird data downloads on file
states = c("us-ia", "us-il", "us-mo")
countries = c("US") ## string of countries Call /code{bbsebird::iso.codes} to find relevant
year.range = 2008:2019
base.julian.date = lubridate::ymd(paste0(min(year.range), c("-01-01")))
crs.target = 4326 #target CRS for all created spatial layers
grid.size = 0.75 # size in decimal degrees (for US/CAN a good est is 1.00dec deg == 111.11km)
min.yday = 91
max.yday = 245
## Munge the states and countries indexes for use in dir/proj dir reation
if(!exists("states")) states <- NULL
if(!is.null(states)){regions <- states}else{regions <- countries}
stopifnot(all(tolower(states) %in% tolower(bbsAssistant::region_codes$iso_3166_2)))Specify and create directories
subdir.proj <- set_proj_shorthand(species.abbr, regions, grid.size, year.range)
dirs <- dir_spec(dir.orig.data = dir.orig.data,
dir.proj = dir.proj,
subdir.proj = subdir.proj) # create and/or specify The following chunk creates a spatial sampling grid of size grid.size with units defaulting to the units of crs.target.
study_area <- make_spatial_grid(
dir.out = dirs[['dir.spatial.out']],
states = states,
countries = countries,
crs.target = crs.target,
grid.size = grid.size,
hexagonal = FALSE,
adjacency.mat = "euclid",
overwrite = FALSE
)
if(is.list(study_area)){
neighborhood <- study_area$neighborhood
study_area <- study_area$grid
overlay <- study_area$overlay
}
# plot(study_area)Create the BBS data. This chunk relieson R package /code{bbsAssistant}. The resulting data is aligned with the spatial grid (see above).
## if the files already exist, don't overwrite unless you've made changes to data specs
if("bbs_obs.rds" %in% list.files(dirs$dir.bbs.out)){bbs_obs <- readRDS(list.files(dirs$dir.bbs.out, "bbs_obs.rds", full.names=TRUE))}else{
bbs_orig <- bbsAssistant::grab_bbs_data(bbs_dir = dirs$dir.bbs.out)
bbs_obs <- bbsAssistant::munge_bbs_data(
bbs_list = bbs_orig,
states = states,
species = species,
year.range = year.range)
bbs_obs <- bbsebird:::match_col_names(bbs_obs) # munge column names to mesh with eBird
saveRDS(bbs_obs, paste0(dirs$dir.bbs.out, "/bbs_obs.rds")) # suggest saving data to file for easy access
}
# Overlay BBS and study area / sampling grid
### note, sometimes when running this in a notebook/rmd a random .rdf" path error occurs.
#### I have no clue what this bug is. Just try running it again. See also https://github.com/rstudio/rstudio/issues/6260
if("bbs_spatial.rds" %in% list.files(dirs$dir.bbs.out)){bbs_spatial <- readRDS(list.files(dirs$dir.bbs.out, "bbs_spatial.rds", full.names=TRUE))}else{
bbs_spatial <- make_bbs_spatial(
df = bbs_obs,
cws.routes.dir = dirs$cws.routes.dir,
usgs.routes.dir = dirs$usgs.routes.dir,
# plot.dir = dirs$dir.plots,
crs.target = crs.target,
print.plots = FALSE,
grid = study_area,
dir.out = dirs$dir.spatial.out,
overwrite = FALSE
)
saveRDS(bbs_spatial, paste0(dirs$dir.bbs.out, "/bbs_spatial.rds"))
}
## check out the bbs spatial data to ensure things look ok
# plot(bbs_spatial['area']) # cell area
## check the specified ebird original data directory for files.
(fns.ebird <- id_ebird_files(
dir.ebird.in = dirs$dir.ebird.in,
dir.ebird.out = dirs$dir.ebird.out,
mmyyyy = mmyyyy,
species = species.abbr,
states.ind = states
))
stopifnot(length(fns.ebird) > 1)
# Import and munge the desired files
ebird <- munge_ebird_data(
fns.ebird = fns.ebird,
species = c(species, species.abbr),
dir.ebird.out = dirs$dir.ebird.out,
countries = countries,
states = states,
overwrite = FALSE, ## this function checks for existing, munged files iin dir.ebird.out..
years = year.range
)
# Create spatial ebird
ebird_spatial <- make_ebird_spatial(
df = ebird,
crs.target = crs.target,
grid = study_area,
overwrite = TRUE, # this fun checks for existing spatial ebird file in dir.spatial.out
dir.out = dirs$dir.spatial.out
)
## visualizing the ebird_spatial data takes a while, do not recommend.Create a list of lists and indexes for use in JAGS or elsewhere. We suggest creating a list using make_bundle and subsequently grabbing useful data from there.
make_bundle creates site-level covariates in both long (vector) and wide (matrix) form. Matrix form are housed inside Xsite matrix, whereas long-form are within list elements ‘bbs.df’ and ‘ebird.df’. Note, however, that the Xsite matrices include missing covariate data.
message("[note] sometimes when running this chunk in notebook/rmarkdown it crashes. try restarting session or running interactively/n")
### make a teeny little bundle for model dev/debugging
bundle.dev <- make_bundle(
bbs = bbs_spatial,
ebird = ebird_spatial,
grid = study_area,
dev.mode = TRUE
)
## recommend saving to file in case you have crashes due to memory or modeling
saveRDS(bundle.dev, paste0(dirs$dir.proj,"/dev-bundle.rds"))
### make full sized bundle
bundle <- make_bundle(
# data
bbs = bbs_spatial,
ebird = ebird_spatial,
grid = study_area,
# optional args
dev.mode = FALSE
)
saveRDS(bundle, paste0(dirs$dir.proj,"/bundle.rds"))
# dir.copy <- "C:/Users/jburnett/DOI/Royle, Andy - aaaaa/"
# saveRDS(overlay, paste0(dirs$dir.proj,"/overlay.rds"))
# saveRDS(neighborhood, paste0(dirs$dir.proj,"/neighborhood.rds"))
# file.copy(paste0(dirs$dir.proj,"/bundle.rds"), dir.copy)
# file.copy(paste0(dirs$dir.proj,"/overlay.rds"), dir.copy)
# file.copy(paste0(dirs$dir.proj,"/dev-bundle.rds"), dir.copy)
# file.copy(paste0(dirs$dir.proj,"/overlay.rds"), dir.copy)
# file.copy(paste0(dirs$dir.proj,"/neighborhood.rds"), dir.copy)