fixed problems

pik-piam · Apr 24, 2024 · db0aa18 · db0aa18
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commit db0aa18
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Showing 12 changed files with 67 additions and 11 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@
 ^\.Rproj\.user$
 ^.lintr$
 ^tests/.lintr$
+^codecov\.yml$
diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '376922837'
+ValidationKey: '198370'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

diff --git a/CITATION.cff b/CITATION.cff
@@ -2,13 +2,39 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'mrlandcore: One-line description of this awesome package'
-version: 0.0.1.9001
+version: 0.1.0
 date-released: '2024-04-24'
 abstract: One-paragraph description of this awesome package.
 authors:
+- family-names: Beier
+  given-names: Felicitas
+  email: beier@pik-potsdam.de
 - family-names: Karstens
   given-names: Kristine
-  email: karstens@pik-potsdam.de
+- family-names: Alves
+  given-names: Marcos
+- family-names: Philipp Dietrich
+  given-names: Jan
+- family-names: Leon Bodirsky
+  given-names: Benjamin
+- family-names: Hoetten
+  given-names: David
+- family-names: Humpenoeder
+  given-names: Florian
+- family-names: Heinke
+  given-names: Jens
+- family-names: v. Jeetze
+  given-names: Patrick
+- family-names: Mishra
+  given-names: Abhijeet
+- family-names: Beier
+  given-names: Felcitas
+- family-names: Wirth
+  given-names: Stephen
+- family-names: Chen
+  given-names: David
+- family-names: Kreidenweis
+  given-names: Ulrich
 license: LGPL-3.0
 repository-code: https://github.com/pik-piam/mrlandcore
 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: mrlandcore
 Title: One-line description of this awesome package
-Version: 0.0.1.9001
+Version: 0.1.0
 Date: 2024-04-24
 Authors@R:
     c(person("Felicitas", "Beier", email = "beier@pik-potsdam.de", role = c("aut","cre")),
@@ -26,8 +26,10 @@ Depends:
     magclass (>= 3.17),
     madrat (>= 2.20.9),
     mrdrivers (>= 1.0.0),
+    mrfaocore,
     mstools
 Imports:
+    dplyr,
     lpjclass,
     lpjmlkit,
     luscale,

diff --git a/NAMESPACE b/NAMESPACE
@@ -8,8 +8,10 @@ export(toolLPJmLVersion)
 import(madrat)
 import(magclass)
 import(mrdrivers)
+import(mrfaocore)
 import(mstools)
 importFrom(SPEI,thornthwaite)
+importFrom(dplyr,"%>%")
 importFrom(lpjclass,read.LPJ_input)
 importFrom(lpjclass,readLPJ)
 importFrom(lpjmlkit,read_io)
@@ -44,6 +46,9 @@ importFrom(magclass,setYears)
 importFrom(magclass,where)
 importFrom(magpiesets,addLocation)
 importFrom(magpiesets,findset)
+importFrom(mrfaocore,toolExtrapolateFodder)
+importFrom(mrfaocore,toolFAOcombine)
+importFrom(mstools,toolConv2CountryByCelltype)
 importFrom(mstools,toolHoldConstant)
 importFrom(ncdf4,nc_open)
 importFrom(nleqslv,nleqslv)
@@ -62,8 +67,10 @@ importFrom(terra,ext)
 importFrom(terra,project)
 importFrom(terra,rast)
 importFrom(terra,subset)
+importFrom(terra,terraOptions)
 importFrom(utils,download.file)
 importFrom(utils,head)
+importFrom(utils,person)
 importFrom(utils,read.csv)
 importFrom(utils,read.delim)
 importFrom(utils,tail)

diff --git a/R/calcLUH2v2.R b/R/calcLUH2v2.R
@@ -22,6 +22,7 @@
 #' calcOutput("LUH2v2")
 #' }
 #' @importFrom magclass getNames
+#' @importFrom mstools toolConv2CountryByCelltype
 #' @importFrom magpiesets findset
 
 calcLUH2v2 <- function(landuse_types = "magpie", irrigation = FALSE, # nolint

diff --git a/R/imports.R b/R/imports.R
@@ -1,4 +1,4 @@
 # Generated by lucode2: do not edit by hand
 
-#' @import magclass madrat mrdrivers mstools
+#' @import magclass madrat mrdrivers mrfaocore mstools
 NULL
diff --git a/R/readLPJmL_new.R b/R/readLPJmL_new.R
@@ -20,6 +20,7 @@
 #' @importFrom magpiesets addLocation
 #' @importFrom lpjclass readLPJ
 #' @importFrom stringr str_subset str_trim str_split
+#' @importFrom dplyr %>%
 
 readLPJmL_new <- function(subtype = "LPJmL4_for_MAgPIE_44ac93de:GSWP3-W5E5:historical:soilc") { # nolint
 

diff --git a/R/readLUH2v2.R b/R/readLUH2v2.R
@@ -8,7 +8,7 @@
 #' Jan Philipp Dietrich, Patrick v. Jeetze
 #'
 #' @importFrom ncdf4 nc_open
-#' @importFrom terra rast ext subset aggregate project ext<-
+#' @importFrom terra rast ext subset aggregate project ext<- terraOptions
 #' @importFrom magclass as.magpie mbind
 #' @importFrom withr local_tempdir defer
 #' @importFrom stringr str_match str_count str_subset

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # One-line description of this awesome package
 
-R package **mrlandcore**, version **0.0.1.9001**
+R package **mrlandcore**, version **0.1.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrlandcore)](https://cran.r-project.org/package=mrlandcore)  [![R build status](https://github.com/pik-piam/mrlandcore/workflows/check/badge.svg)](https://github.com/pik-piam/mrlandcore/actions) [![codecov](https://codecov.io/gh/pik-piam/mrlandcore/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrlandcore) 
 
@@ -32,22 +32,22 @@ update.packages()
 
 ## Questions / Problems
 
-In case of questions / problems please contact Kristine Karstens <karstens@pik-potsdam.de>.
+In case of questions / problems please contact Felicitas Beier <beier@pik-potsdam.de>.
 
 ## Citation
 
 To cite package **mrlandcore** in publications use:
 
-Karstens K (2024). _mrlandcore: One-line description of this awesome package_. R package version 0.0.1.9001, <https://github.com/pik-piam/mrlandcore>.
+Beier F, Karstens K, Alves M, Philipp Dietrich J, Leon Bodirsky B, Hoetten D, Humpenoeder F, Heinke J, v. Jeetze P, Mishra A, Beier F, Wirth S, Chen D, Kreidenweis U (2024). _mrlandcore: One-line description of this awesome package_. R package version 0.1.0, <URL: https://github.com/pik-piam/mrlandcore>.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Manual{,
   title = {mrlandcore: One-line description of this awesome package},
-  author = {Kristine Karstens},
+  author = {Felicitas Beier and Kristine Karstens and Marcos Alves and Jan {Philipp Dietrich} and Benjamin {Leon Bodirsky} and David Hoetten and Florian Humpenoeder and Jens Heinke and Patrick {v. Jeetze} and Abhijeet Mishra and Felcitas Beier and Stephen Wirth and David Chen and Ulrich Kreidenweis},
   year = {2024},
-  note = {R package version 0.0.1.9001},
+  note = {R package version 0.1.0},
   url = {https://github.com/pik-piam/mrlandcore},
 }
 ```
diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,18 @@
+comment: true
+github_checks:
+  annotations: false
+coverage:
+  precision: 2
+  round: down
+  range: "0...95"
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true