## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(EDIutils)
## ----eval=FALSE---------------------------------------------------------------
# # Match all documents with keywords "disturbance" and return only their IDs
# res <- search_data_packages(query = 'q=keyword:disturbance&fl=id')
## ----eval=FALSE---------------------------------------------------------------
# # Match all documents with keywords "disturbance", excluding ecotrends and
# # lter-landsat scopes from the returned results
# query <- 'q=keyword:disturbance&fl=packageid&fq=-scope:(ecotrends+lter-landsat)'
# res <- search_data_packages(query)
## ----eval=FALSE---------------------------------------------------------------
# # Match anything, display all fields, limit to only one document
# res <- search_data_packages(query = 'q=*&fl=*&rows=1')
## ----eval=FALSE---------------------------------------------------------------
# # Find all FCE LTER data packages, displaying the package id, title, and DOI
# query <- 'q=scope:knb-lter-fce&fl=packageid,title,doi&rows=100'
# res <- search_data_packages(query)
#
# # Query on author
# query <- 'q=author:duane+costa&fq=author:costa&fl=id,title,author,score'
# res <- search_data_packages(query)
## ----eval=FALSE---------------------------------------------------------------
# # Query on subject "Primary Production" OR subject "plant". Note that 'subject'
# # is an aggregation of several other fields containing searchable text:
# # 'author', 'organization', 'title', 'keyword', and 'abstract' fields rolled
# # together into a single searchable field.
# query <- paste0('q=subject:("Primary+Production")+OR+subject:plant&fq=',
# '-scope:ecotrends&fq=-scope:lter-landsat*&fl=id,packageid,',
# 'title,author,organization,pubdate,coordinates')
# res <- search_data_packages(query)
## ----eval=FALSE---------------------------------------------------------------
# scope = "edi"
# identifier = "1047"
# revision = list_data_package_revisions(scope, identifier, filter = "newest")
# paste(scope, identifier, revision, sep = ".")
# #> [1] "edi.1047.2"
## ----eval=FALSE---------------------------------------------------------------
# packageId <- "edi.1047.1"
## ----eval=FALSE---------------------------------------------------------------
# # Download data package to path
# read_data_package_archive(packageId, path = tempdir())
# #> |=============================================================| 100%
# dir(tempdir())
# #> [1] ""edi.1047.1.zip"
## ----eval=FALSE---------------------------------------------------------------
# # List data entities of the data package
# res <- read_data_entity_names(packageId)
# res
# #> entityId entityName
# #> 1 3abac5f99ecc1585879178a355176f6d Environmentals.csv
# #> 2 f6bfa89b48ced8292840e53567cbf0c8 ByCatch.csv
# #> 3 c75642ddccb4301327b4b1a86bdee906 Chinook.csv
# #> 4 2c9ee86cc3f3ffc729c5f18bfe0a2a1d Steelhead.csv
# #> 5 785690848dd20f4910637250cdc96819 TrapEfficiencyRelease.csv
# #> 6 58b9000439a5671ea7fe13212e889ba5 TrapEfficiencySummary.csv
# #> 7 86e61c1a501b7dcf0040d10e009bfd87 TrapOperations.csv
#
# # Download Steelhead.csv in raw bytes. Use the entityName and entityID as keys.
# entityName <- "Steelhead.csv"
# entityId <- res$entityId[res$entityName == entityName]
# raw <- read_data_entity(packageId, entityId)
# head(raw)
# #> [1] ef bb bf 44 61 74
## ----eval=FALSE---------------------------------------------------------------
# # These data have a common format are simply parsed
# data <- readr::read_csv(file = raw)
# data
# #> # A tibble: 2,926 x 14
# #> Date trapVisitID subSiteName catchRawID releaseID commonName
# #> <chr> <dbl> <chr> <dbl> <dbl> <chr>
# #> 1 1/12/~ 326 North Chan~ 32123 0 Steelhead ~
# #> 2 1/14/~ 336 North Chan~ 33980 0 Steelhead ~
# #> 3 1/15/~ 337 North Chan~ 32683 0 Steelhead ~
# #> 4 1/16/~ 339 North Chan~ 32971 0 Steelhead ~
# #> 5 1/17/~ 341 North Chan~ 33104 0 Steelhead ~
# #> 6 1/18/~ 342 North Chan~ 33304 0 Steelhead ~
# #> 7 1/19/~ 343 North Chan~ 33432 0 Steelhead ~
# #> 8 1/21/~ 349 North Chan~ 34083 0 Steelhead ~
# #> 9 1/21/~ 349 North Chan~ 34084 0 Steelhead ~
# #> 10 1/23/~ 351 North Chan~ 34384 0 Steelhead ~
# #> # ... with 2,916 more rows, and 8 more variables:
# #> # lifeStage <chr>, forkLength <dbl>, weight <dbl>, n <dbl>,
# #> # mort <chr>, fishOrigin <chr>, markType <chr>,
# #> # CatchRaw.comments <chr>
## ----eval=FALSE---------------------------------------------------------------
# # Read the same data entity but using the physical metadata
# library(xml2)
# eml <- read_metadata(packageId)
# meta <- read_metadata_entity(packageId, entityId)
# fieldDelimiter <- xml_text(xml_find_first(meta, ".//physical//fieldDelimiter"))
# numHeaderLines <- xml_double(xml_find_first(meta, ".//physical//numHeaderLines"))
# data <- readr::read_delim(
# file = raw,
# delim = fieldDelimiter,
# skip = numHeaderLines-1)
# data
# #> # A tibble: 2,926 x 14
# #> Date trapVisitID subSiteName catchRawID releaseID commonName
# #> <chr> <dbl> <chr> <dbl> <dbl> <chr>
# #> 1 1/12/~ 326 North Chan~ 32123 0 Steelhead ~
# #> 2 1/14/~ 336 North Chan~ 33980 0 Steelhead ~
# #> 3 1/15/~ 337 North Chan~ 32683 0 Steelhead ~
# #> 4 1/16/~ 339 North Chan~ 32971 0 Steelhead ~
# #> 5 1/17/~ 341 North Chan~ 33104 0 Steelhead ~
# #> 6 1/18/~ 342 North Chan~ 33304 0 Steelhead ~
# #> 7 1/19/~ 343 North Chan~ 33432 0 Steelhead ~
# #> 8 1/21/~ 349 North Chan~ 34083 0 Steelhead ~
# #> 9 1/21/~ 349 North Chan~ 34084 0 Steelhead ~
# #> 10 1/23/~ 351 North Chan~ 34384 0 Steelhead ~
# #> # ... with 2,916 more rows, and 8 more variables:
# #> # lifeStage <chr>, forkLength <dbl>, weight <dbl>, n <dbl>,
# #> # mort <chr>, fishOrigin <chr>, markType <chr>,
# #> # CatchRaw.comments <chr>