adjusted the p3k14c parser to use a .csv input file

ropensci · Feb 1, 2022 · c995165 · c995165
1 parent 1a334b7
commit c995165
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 12 deletions.
diff --git a/R/get_p3k14c.R b/R/get_p3k14c.R
@@ -5,14 +5,16 @@ get_p3k14c <- function(db_url = get_db_url("p3k14c")) {
   check_connection_to_url(db_url)
 
   # download and unzip data
-  temp <- tempfile()
-  utils::download.file(db_url, temp, quiet = TRUE)
-  load(temp)
-
-  p3k14c_data$d13C[p3k14c_data$d13C == 0.0] <- NA
-  suppressWarnings(p3k14c_data$d13C <- as.numeric(p3k14c_data$d13C))
-
-  p3k14c <- p3k14c_data %>%
+  p3k14c <- db_url %>%
+    data.table::fread(
+      colClasses = "character",
+      showProgress = FALSE,
+      na.strings = ""
+    ) %>%
+    dplyr::mutate(
+      d13C = suppressWarnings(as.numeric(.data[["d13C"]])),
+      d13C = ifelse(.data[["d13C"]] == 0, NA, .data[["d13C"]])
+    ) %>%
     dplyr::transmute(
       labnr = .data[["LabID"]],
       c14age = .data[["Age"]],
@@ -27,7 +29,7 @@ get_p3k14c <- function(db_url = get_db_url("p3k14c")) {
       country = .data[["Country"]],
       lat = .data[["Lat"]],
       lon = .data[["Long"]],
-      shortref = .data[["Reference"]]
+      shortref = ifelse(is.na(.data[["Reference"]]), .data[["Source"]], .data[["Reference"]])
     ) %>%
     dplyr::mutate(
       sourcedb = "p3k14c",

diff --git a/data-raw/db_info_table.csv b/data-raw/db_info_table.csv
@@ -27,4 +27,4 @@ agrichange,2021-05-21,1,https://zenodo.org/record/4541470/files/AgriChange_14Cda
 caribbean,2021-05-21,1,https://raw.githubusercontent.com/philriris/caribbean-14C/main/data/caribbean_14C.csv
 aida,today,1,https://raw.githubusercontent.com/apalmisano82/AIDA/main/dates.csv
 sard,2021-03-01,1,https://raw.githubusercontent.com/emmaloftus/Southern-African-Radiocarbon-Database/main/SARD_Mar2021_14C.csv
-p3k14c,2021-08-03,1,https://github.com/people3k/p3k14c/raw/1.0.0/data/p3k14c_data.rda
+p3k14c,2021-08-03,1,https://raw.githubusercontent.com/people3k/p3k14c/1.0.0/inst/p3k14c_scrubbed_fuzzed.csv
diff --git a/data-raw/variable_reference.csv b/data-raw/variable_reference.csv
@@ -610,5 +610,4 @@ site,p3k14c,SiteName
 country,p3k14c,Country
 ,p3k14c,Province
 region,p3k14c,Continent
-,p3k14c,Source
-shortref,p3k14c,Reference
+shortref,p3k14c,Reference;Source
diff --git a/data/db_info_table.rda b/data/db_info_table.rda