tweaked metadata in downloadSource

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '34196400'
+ValidationKey: '34569960'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "madrat: May All Data be Reproducible and Transparent (MADRaT) *",
-  "version": "1.85.0",
+  "version": "1.86.0",
   "description": "<p>Provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation.\n    * The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: madrat
 Type: Package
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 1.85.0
+Version: 1.86.0
 Date: 2020-11-20
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "dietrich@pik-potsdam.de", role = c("aut","cre")),
              person("Lavinia", "Baumstark", email = "lavinia@pik-potsdam.de", role = "aut"),
@@ -40,4 +40,3 @@ LazyData: no
 Encoding: UTF-8
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr
-ValidationKey: 34384100

R/calcTauTotal.R

@@ -34,7 +34,7 @@ calcTauTotal <- function(source="paper") {
               note=c('data based on Dietrich J.P., Schmitz C., M\uFCller C., Fader M., Lotze-Campen H., Popp A.,',
                      'Measuring agricultural land-use intensity - A global analysis using a model-assisted approach',
                      'Ecological Modelling, Volume 232, 10 May 2012, Pages 109-118, ISSN 0304-3800, 10.1016/j.ecolmodel.2012.03.002.',
-                     'preprint available \u40 http://edoc.gfz-potsdam.de/pik/display.epl?mode=doc&id=5281'),
+                     'preprint available \u40 https://doi.org/10.1016/j.ecolmodel.2012.03.002'),
               source=bibentry("Article",
                               title="Measuring agricultural land-use intensity - A global analysis using a model-assisted approach",
                               author=c(person("Jan Philipp","Dietrich"),person("Christoph","Schmitz"),person("Christoph","Mueller"),person("Marianela","Fader"),
@@ -43,6 +43,6 @@ calcTauTotal <- function(source="paper") {
                               journal="Ecological Modelling",
                               volume="232",
                               pages="109-118",
-                              url="http://edoc.gfz-potsdam.de/pik/display.epl?mode=doc&id=5281",
+                              url="https://doi.org/10.1016/j.ecolmodel.2012.03.002",
                               doi="10.1016/j.ecolmodel.2012.03.002")))
 }

R/downloadSource.R

@@ -57,15 +57,20 @@ downloadSource <- function(type,subtype=NULL,overwrite=FALSE) {
   if(!all(mandatory %in% names(meta))) {vcat(0, paste0("Missing entries in the meta data of function '",functionname[1],"': ",mandatory[!mandatory %in% names(meta)]))}
 
   # define reserved elements of meta data and check if they already exist
-  reserved <- c("type","subtype","origin","date")
+  reserved <- c("type","subtype","origin","date_downloaded","source_quality")
   if(any(reserved %in% names(meta))) {vcat(0, paste0("The following entries in the meta data of the function '",functionname[1],"' are reserved and will be overwritten: ",reserved[reserved %in% names(meta)]))}
 
   # set reserved meta data elements
   meta$type    <- type
   meta$subtype <- ifelse(is.null(subtype), "none",subtype)
   meta$origin  <- paste0(gsub("\\s{2,}"," ",paste(deparse(match.call()),collapse=""))," -> ",functionname," (madrat ",packageDescription("madrat")$Version," | ",attr(functionname,"pkgcomment"),")")
-  meta$date    <- date()
-  #meta$quality <- quality()
+  meta$date_downloaded <- date()
+  meta$source_quality <- ifelse(!is.null(meta$doi),"gold","silver")
 
-  write_yaml(meta,"DOWNLOAD.yml")
+  # reorder meta entries
+  preferred_order <- c("title","authors","doi","url","license","version","date_released","date_downloaded","origin",
+                       "type","subtype", "source_quality","source")
+  order <- c(intersect(preferred_order,names(meta)),setdiff(names(meta),preferred_order))
+
+  write_yaml(meta[order],"DOWNLOAD.yml")
 }

R/downloadTau.R

@@ -1,19 +1,38 @@
 #' @importFrom utils download.file unzip
 downloadTau <- function(subtype="paper") {
+
+  settings <- list(     paper = list(title = "Cellular (0.5deg), crop-specific land use intensity (tau) for 1995 and 2000",
+                                       url = "https://zenodo.org/record/4282581/files/tau-paper.zip",
+                                       doi = "10.5281/zenodo.4282581"),
+                   historical = list(title = "Historic land use intensity (tau) development",
+                                       url = "https://zenodo.org/record/4282548/files/tau-historical.zip",
+                                       doi = "10.5281/zenodo.4282548"))
+  meta <- toolSubtypeSelect(subtype,settings)
 
-  # Meta data to be provided by the user
-  meta <- list(url      = "http://www.pik-potsdam.de/members/dietrich/",
-               title    = "Agricultural Land Use Intensity Tau",
-               authors  = "Jan Philipp Dietrich",
-               license  = "Creative Commons Attribution-ShareAlike 4.0 International License"
-               #version <- 
-               #date_released <- 
-               #doi <- 
-  )
-
-  file <- toolSubtypeSelect(subtype,c(paper="tau-paper.zip",historical="tau-historical.zip"))
-  download.file(paste0(meta$url,file), destfile = "tau.zip")
+  download.file(meta$url, destfile = "tau.zip")
   unzip("tau.zip")
   unlink("tau.zip")
-  return(meta)
+
+  return(list(url           = meta$url,
+              doi           = meta$doi,
+              title         = meta$title,
+              authors       = person("Jan Philipp","Dietrich", email="dietrich@pik-potsdam.de", comment=c(ORCID="0000-0002-4309-6431")),
+              version       = "1.0",
+              date_released = "2012-05-10",
+              license  = "Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0)",
+              source   = bibentry("Article",
+                                  title="Measuring agricultural land-use intensity - A global analysis using a model-assisted approach",
+                                  author=c(person("Jan Philipp","Dietrich", email="dietrich@pik-potsdam.de", comment=c(ORCID="0000-0002-4309-6431")),
+                                           person("Christoph","Schmitz"),
+                                           person("Christoph","Mueller"),
+                                           person("Marianela","Fader"),
+                                           person("Hermann","Lotze-Campen"),
+                                           person("Alexander","Popp")),
+                                  year="2012",
+                                  journal="Ecological Modelling",
+                                  volume="232",
+                                  pages="109-118",
+                                  url="https://doi.org/10.1016/j.ecolmodel.2012.03.002",
+                                  doi="10.1016/j.ecolmodel.2012.03.002"))
+  )
 }

R/toolSubtypeSelect.R

@@ -6,7 +6,7 @@
 #' 
 #' 
 #' @param subtype A chosen subtype (character)
-#' @param files A named vector. The names of the vector correspond to the
+#' @param files A named vector or list. The names of the vector correspond to the
 #' allowed subtypes and the content of the vector are the corresponding file
 #' names.
 #' @return The file name corresponding to the given subtype
@@ -23,5 +23,5 @@
 toolSubtypeSelect <- function(subtype, files) {
     if(is.null(subtype)) stop('Subtype has to be set! Available subtypes are: ',paste(names(files),collapse=", "))
     if(!(subtype %in% names(files))) stop('Unknown subtype "',subtype,'"! Available subtypes are: ',paste(names(files),collapse=", "))
-    return(files[subtype])
+    return(files[[subtype]])
 } 

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **1.85.0**
+R package **madrat**, version **1.86.0**
 
 [![Travis build status](https://travis-ci.com/pik-piam/madrat.svg?branch=master)](https://travis-ci.com/pik-piam/madrat) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1115490.svg)](https://doi.org/10.5281/zenodo.1115490) [![codecov](https://codecov.io/gh/pik-piam/madrat/branch/master/graph/badge.svg)](https://codecov.io/gh/pik-piam/madrat)
 
@@ -36,7 +36,7 @@ update.packages()
 The package comes with a vignette describing the basic functionality of the package and how to use it. You can load it with the following command (the package needs to be installed):
 
 ```r
-vignette(madrat) # Data preparation with MADRaT
+vignette("madrat") # Data preparation with MADRaT
 ```
 
 ## Questions / Problems
@@ -47,9 +47,9 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **madrat** in publications use:
 
-Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Kreidenweis U, Klein D (2020). _madrat: May All Data be Reproducible
-and Transparent (MADRaT)_. doi: 10.5281/zenodo.1115490 (URL: https://doi.org/10.5281/zenodo.1115490), R package version 1.85.0, <URL:
-https://github.com/pik-piam/madrat>.
+Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Kreidenweis U, Klein D (2020). _madrat:
+May All Data be Reproducible and Transparent (MADRaT)_. doi: 10.5281/zenodo.1115490 (URL:
+https://doi.org/10.5281/zenodo.1115490), R package version 1.86.0, <URL: https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -58,7 +58,7 @@ A BibTeX entry for LaTeX users is
   title = {madrat: May All Data be Reproducible and Transparent (MADRaT)},
   author = {Jan Philipp Dietrich and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Ulrich Kreidenweis and David Klein},
   year = {2020},
-  note = {R package version 1.85.0},
+  note = {R package version 1.86.0},
   doi = {10.5281/zenodo.1115490},
   url = {https://github.com/pik-piam/madrat},
 }