Merge branch 'treecover' into 'main'

adding TimeAvgMapTreeCover metric also as a default

See merge request lpjml/lpjmlstats!21

.buildlibrary

@@ -1,8 +1,9 @@
-ValidationKey: '1000700'
+ValidationKey: '1202100'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes: checking installed package size
 allowLinterWarnings: no
 enforceVersionUpdate: no
+skipCoverage: no

.github/workflows/check.yaml

@@ -63,6 +63,6 @@ jobs:
         shell: Rscript {0}
         run: |
           nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
-          if(length(nonDummyTests) > 0) covr::codecov(quiet = FALSE)
+          if(length(nonDummyTests) > 0 && !lucode2:::loadBuildLibraryConfig()[["skipCoverage"]]) covr::codecov(quiet = FALSE)
         env:
           NOT_CRAN: "true"

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'lpjmlstats: Statistical tools for LPJmL data analysis'
-version: 0.5.0
-date-released: '2024-10-18'
+version: 0.6.0
+date-released: '2024-11-08'
 abstract: This package provides statistical tools for LPJmL data analysis to be used
   for benchmarking LPJmL outputs.
 authors:
@@ -14,6 +14,10 @@ authors:
   given-names: Jannes
   email: [email protected]
   orcid: https://orcid.org/0000-0002-9055-6904
+- family-names: Müller
+  given-names: Christoph
+  email: [email protected]
+  orcid: https://orcid.org/0000-0002-9491-3550
 license: AGPL-3.0
 repository-code: https://github.com/PIK-LPJmL/lpjmlstats
 

DESCRIPTION

@@ -1,9 +1,10 @@
 Package: lpjmlstats
 Title: Statistical tools for LPJmL data analysis
-Version: 0.5.0
+Version: 0.6.0
 Authors@R: c(
     person("David","Hötten", , "[email protected]", role = c("aut", "cre")),
-    person("Jannes","Breier", , "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-9055-6904"))
+    person("Jannes","Breier", , "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-9055-6904")),
+    person("Christoph","Müller", , "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-9491-3550"))
   )
 Description: This package provides statistical tools for LPJmL data analysis
     to be used for benchmarking LPJmL outputs.
@@ -44,4 +45,4 @@ Config/testthat/edition: 3
 VignetteBuilder: knitr
 Depends:
     R (>= 3.5.0)
-Date: 2024-10-18
+Date: 2024-11-08

NAMESPACE

@@ -21,6 +21,7 @@ export(GlobSumTimeseries)
 export(LPJmLDataCalc)
 export(Metric)
 export(TimeAvgMap)
+export(TimeAvgMapTreeCover)
 export(TimeAvgMapWithAbs)
 export(aggregate)
 export(benchmark)

R/Metric_subclasses.R

@@ -691,3 +691,50 @@ GlobSumAnnTimeseriesFPC <- R6::R6Class( # nolint: object_name_linter.
     }
   )
 )
+
+#' @title TimeAvgMapTreeCover
+#' @description
+#' TimeAvgMapTreeCover metric
+#' @export
+TimeAvgMapTreeCover <- # nolint: object_name_linter.
+  R6::R6Class(
+    "TimeAvgMapTreeCover",
+    inherit = TimeAvgMapWithAbs,
+    public = list(
+      #' @description
+      #' add up bands for tree fpcs
+      #' @param data LPJmLDataCalc object to be summarized
+      summarize = function(data) {
+        bands <- data$meta$band_names
+        data <- subset(data, band = bands[grep("tree", bands)])
+        data$add_band("treecover_band", function(x) sum(x))
+        data <- subset(data, band = "treecover_band")
+        data <- aggregate(data, time = list(to = "sim_period", stat = "mean"))
+      },
+
+      #' @field m_options
+      #' See \link{TimeAvgMapWithAbs} for the documentation of the options of this metric.
+      m_options = list(
+        font_size = 4,
+        highlight = NULL,
+        quantiles = c(0.05, 0.95),
+        sep_cmp_lims = TRUE,
+        year_subset = as.character(1991:2000),
+        cell_subset = NULL,
+        n_breaks = 8,
+        num_cols = 3,
+        var_subheading = FALSE,
+        band_subheading = FALSE
+      ),
+
+      #' @field title
+      #' Section header used in the report
+      title = "Time Average Maps With Absolute Values of total Tree Cover",
+
+      #' @field description
+      #' Description used in the report
+      description = "The cell-time values of each variable are averaged over time.
+        Bands that contain the string `tree` are added up.
+        The resulting sum is then plotted on a map. \n"
+    )
+  )

R/default_settings.R

@@ -20,7 +20,7 @@ default_settings <- list(
   mbnf  = c(GlobSumTimeAvgTable, GlobSumAnnAvgTimeseries, TimeAvgMap),
   firec = c(GlobSumTimeAvgTable, GlobSumAnnAvgTimeseries, TimeAvgMap),
   flux_estab = c(GlobSumTimeAvgTable, GlobSumAnnAvgTimeseries, TimeAvgMap),
-  fpc = c(GlobSumTimeAvgTableFPC, GlobSumAnnTimeseriesFPC, TimeAvgMap),
+  fpc = c(GlobSumTimeAvgTableFPC, GlobSumAnnTimeseriesFPC, TimeAvgMap, TimeAvgMapTreeCover),
   mgpp = c(GlobSumTimeAvgTable, GlobSumAnnAvgTimeseries, TimeAvgMap),
   mnpp = c(GlobSumTimeAvgTable, GlobSumAnnAvgTimeseries, TimeAvgMap),
   anbp = c(GlobSumTimeAvgTable, GlobSumAnnAvgTimeseries, TimeAvgMap),

README.md

@@ -1,6 +1,6 @@
 # Statistical tools for LPJmL data analysis
 
-R package **lpjmlstats**, version **0.5.0**
+R package **lpjmlstats**, version **0.6.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lpjmlstats)](https://cran.r-project.org/package=lpjmlstats)  [![R build status](https://github.com/PIK-LPJmL/lpjmlstats/workflows/check/badge.svg)](https://github.com/PIK-LPJmL/lpjmlstats/actions) [![codecov](https://codecov.io/gh/PIK-LPJmL/lpjmlstats/branch/master/graph/badge.svg)](https://app.codecov.io/gh/PIK-LPJmL/lpjmlstats) [![r-universe](https://pik-piam.r-universe.dev/badges/lpjmlstats)](https://pik-piam.r-universe.dev/builds)
 
@@ -48,16 +48,16 @@ In case of questions / problems please contact David Hötten <davidho@pik-potsda
 
 To cite package **lpjmlstats** in publications use:
 
-Hötten D, Breier J (2024). _lpjmlstats: Statistical tools for LPJmL data analysis_. R package version 0.5.0, <https://github.com/PIK-LPJmL/lpjmlstats>.
+Hötten D, Breier J, Müller C (2024). _lpjmlstats: Statistical tools for LPJmL data analysis_. R package version 0.6.0, <https://github.com/PIK-LPJmL/lpjmlstats>.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
 @Manual{,
   title = {lpjmlstats: Statistical tools for LPJmL data analysis},
-  author = {David Hötten and Jannes Breier},
+  author = {David Hötten and Jannes Breier and Christoph Müller},
   year = {2024},
-  note = {R package version 0.5.0},
+  note = {R package version 0.6.0},
   url = {https://github.com/PIK-LPJmL/lpjmlstats},
 }
 ```