R/load_safe.R
insert_dataset.RdIf files are embargoed or restricted, then users may request the datafiles from the authors. This function allows provided files to be incorporated into a SAFE data directory, so that they will then work seamlessly alongside openly available data.
insert_dataset(record_id, files)A SAFE dataset record id
A vector of files to insert into the data directory
set_example_safe_dir()
#> Loading and caching index
#> Validating directory
files <- system.file("safedata_example_dir",
"template_ClareWfunctiondata.xlsx",
package = "safedata")
insert_dataset(1237719, files)
#> Inserting files: template_ClareWfunctiondata.xlsx
#> Warning: '/tmp/RtmpTl0AoJ/safedata_example_dir/1198840/1237719' already exists
dat <- load_safe_data(1237719, "Data")
str(dat)
#> SAFE dataset
#> Concept: 1198840; Record 1237719; Worksheet: Data
#> 'data.frame': 34 obs. of 11 variables:
#> $ taxon_name : chr "Anguilla.borneensis" "Anguilla.marmorata" "Barbodes.sealei" "Barbonymus.balleroides" ...
#> $ Body_size : num 24.14 30.56 8.51 11.36 7.59 ...
#> $ body_shape : Factor w/ 3 levels "Compressed","Cylindrical",..: 2 2 1 1 1 2 1 2 1 2 ...
#> $ trophic_position : Factor w/ 4 levels "Herbivore","Higher carnivore",..: 2 2 4 3 3 2 2 1 3 1 ...
#> $ mouth_position : Factor w/ 3 levels "Inferior","Superior",..: 3 3 3 3 3 3 3 1 3 1 ...
#> $ presence_teeth : Factor w/ 2 levels "no","yes": 2 2 1 1 2 2 1 1 1 1 ...
#> $ gregariousness : Factor w/ 2 levels "no","yes": 1 1 2 2 1 1 1 2 2 2 ...
#> $ presence_barbels : Factor w/ 2 levels "no","yes": 2 2 2 2 1 2 2 2 1 2 ...
#> $ vertical_position_water : Factor w/ 4 levels "Benthic","Benthopelagic",..: 2 2 3 3 2 2 2 2 3 1 ...
#> $ air.breathing_capability: chr "yes" "yes" "no" "no" ...
#> $ air-breathing_capability: Factor w/ 0 levels: NA NA NA NA NA NA NA NA NA NA ...
unset_example_safe_dir()
#> Loading and caching index
#> Validating directory