Adapt calibration reporting to new calibration implementation

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '1420426'
+ValidationKey: '1447560'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
@@ -7,3 +7,5 @@ AcceptedNotes: Namespaces in Imports field not imported from\:\n *.ggplot2. .kni
   .mip. .piamPlotComparison. .purrr.
 allowLinterWarnings: no
 enforceVersionUpdate: no
+AutocreateCITATION: yes
+skipCoverage: no

.github/workflows/check.yaml

@@ -23,14 +23,14 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            any::lucode2
-            any::covr
-            any::madrat
-            any::magclass
-            any::citation
-            any::gms
-            any::goxygen
-            any::GDPuc
+            lucode2
+            covr
+            madrat
+            magclass
+            citation
+            gms
+            goxygen
+            GDPuc
           # piam packages also available on CRAN (madrat, magclass, citation,
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest version
@@ -44,6 +44,13 @@ jobs:
           [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
           [ -f requirements.txt ] && pip install -r requirements.txt || true
 
+      - name: Run pre-commit checks
+        shell: bash
+        run: |
+          python -m pip install pre-commit
+          python -m pip freeze --local
+          pre-commit run --show-diff-on-failure --color=always --all-files
+
       - name: Verify validation key
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)
@@ -63,6 +70,6 @@ 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"

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
+    rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b  # frozen: v5.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: bae853d82da476eee0e0a57960ee6b741a3b3fb7  # frozen: v0.4.3
+    rev: 3b70240796cdccbe1474b0176560281aaded97e6  # frozen: v0.4.3.9003
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc
@@ -25,4 +25,4 @@ repos:
     -   id: readme-rmd-rendered
     -   id: use-tidy-description
 ci:
-    autoupdate_schedule: quarterly
+    autoupdate_schedule: weekly

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: 'reportbrick: Reporting package for BRICK'
-version: 0.7.1
-date-released: '2024-10-10'
+version: 0.7.2
+date-released: '2025-01-17'
 abstract: This package contains BRICK-specific routines to report model results. The
   main functionality is to generate a mif-file from a given BRICK model run folder.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: reportbrick
 Title: Reporting package for BRICK
-Version: 0.7.1
-Date: 2024-10-10
+Version: 0.7.2
+Date: 2025-01-17
 Authors@R: c(
     person("Robin", "Hasse", , "robin.hasse@pik-potsdam.de",
            role = c("aut", "cre"),

NAMESPACE

@@ -49,6 +49,7 @@ importFrom(tidyr,replace_na)
 importFrom(tidyr,separate)
 importFrom(tidyr,unite)
 importFrom(utils,capture.output)
+importFrom(utils,read.csv)
 importFrom(utils,tail)
 importFrom(utils,write.csv)
 importFrom(yaml,read_yaml)

R/reportCalibration.R

@@ -7,7 +7,8 @@
 #' @author Ricarda Rosemann
 #'
 #' @importFrom tidyr crossing replace_na
-#' @importFrom utils write.csv
+#' @importFrom utils read.csv write.csv
+#' @importFrom yaml read_yaml
 #' @export
 
 reportCalibration <- function(gdx) {
@@ -18,69 +19,87 @@ reportCalibration <- function(gdx) {
   path <- dirname(gdx)
 
   allFiles <- list.files(path = path,
-                         pattern = paste0(sub("\\.gdx$", "", basename(gdx)),
+                         pattern = paste0(sub("_0\\.gdx$", "", basename(gdx)),
                                           "_\\d{1,3}\\.gdx"))
   maxIter <- max(as.numeric(sub(".*_(\\d{1,3})\\.gdx$", "\\1", allFiles)))
 
+  gdxHist <- file.path(path, "historic.gdx")
+
+  # Read config
+  cfg <- read_yaml(file = file.path(path, "config", "config_COMPILED.yaml"))
+
   # Read relevant time periods
-  tCalib <- readGdxSymbol(gdx, "tCalib", asMagpie = FALSE)[["ttot"]]
+  tCalib <- cfg[["calibperiods"]]
 
-  # Read different parameters from gdx files for all iterations
-  # TODO: Could potentially replace this call by mip::getPlotData (but that uses gdxrrw and can only start counting at 1) # nolint
-  targetFunction <- .readGdxIter(gdx, "p_f", maxIter, asMagpie = FALSE)
+  calibOptim <- cfg[["switches"]][["RUNTYPE"]] == "calibrationOptimization"
 
-  stepSize <- .readGdxIter(gdx, "p_alpha", maxIter, asMagpie = FALSE)
+  # Read diagnostic parameters from csv
+  stepSize <- read.csv(file.path(path, "stepSizeParamsIter.csv")) %>%
+    select(-"delta", -"phiDeriv") %>%
+    rename(value = "alpha")
+  descDirCon <- read.csv(file.path(path, "deviationConIter.csv")) %>%
+    rename(value = "d") %>%
+    .replaceVarName()
+  descDirRen <- read.csv(file.path(path, "deviationRenIter.csv")) %>%
+    rename(value = "d")
 
   # Potentially shift the time filter to a later stage if I want to save and plot pure stock/flow data
-  p_stock <- .readGdxIter(gdx, "p_stock", maxIter, asMagpie = FALSE, ttotFilter = tCalib, replaceVar = TRUE)
+  v_stock <- .readGdxIter(gdx,
+                          if (calibOptim) "p_stock" else "v_stock",
+                          maxIter, asMagpie = FALSE, ttotFilter = tCalib, replaceVar = TRUE)
 
-  p_construction <- .readGdxIter(gdx, "p_construction", maxIter,
+  v_construction <- .readGdxIter(gdx,
+                                 if (calibOptim) "p_construction" else "v_construction",
+                                 maxIter,
                                  asMagpie = FALSE, ttotFilter = tCalib, replaceVar = TRUE)
 
-  p_renovation <- .readGdxIter(gdx, "p_renovation", maxIter,
+  v_renovation <- .readGdxIter(gdx,
+                               if (calibOptim) "p_renovation" else "v_renovation", maxIter,
                                asMagpie = FALSE, ttotFilter = tCalib)
 
   # Read historical gdx files
-  p_stockHist <- .replaceVarName(readGdxSymbol(gdx, "p_stockHist", asMagpie = FALSE))
+  p_stockHist <- .replaceVarName(readGdxSymbol(gdxHist, "p_stockHist", asMagpie = FALSE))
 
-  p_constructionHist <- .replaceVarName(readGdxSymbol(gdx, "p_constructionHist", asMagpie = FALSE))
+  p_constructionHist <- .replaceVarName(readGdxSymbol(gdxHist, "p_constructionHist", asMagpie = FALSE))
 
-  p_renovationHist <- readGdxSymbol(gdx, "p_renovationHist", asMagpie = FALSE)
+  p_renovationHist <- readGdxSymbol(gdxHist, "p_renovationHist", asMagpie = FALSE)
 
 
   # COMPUTE DEVIATIONS ---------------------------------------------------------
 
-  p_stockDev <- .computeDeviation(p_stock, p_stockHist)
+  v_stockDev <- .computeDeviation(v_stock, p_stockHist)
 
-  p_constructionDev <- .computeDeviation(p_construction, p_constructionHist)
+  v_constructionDev <- .computeDeviation(v_construction, p_constructionHist)
 
-  p_renovationDev <- .computeDeviation(p_renovation, p_renovationHist)
+  v_renovationDev <- .computeDeviation(v_renovation, p_renovationHist)
 
-  # Start writing output quantities --------------------------------------------
+  # WRITE DIAGNOSTIC OUTPUT ----------------------------------------------------
 
   out <- list()
 
-  out[["targetFunction"]] <- targetFunction
-
   out[["stepSize"]] <- stepSize
 
+  out[["descDirCon"]] <- .computeAvg(descDirCon, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr", "ttot"))
+
+  out[["descDirRen"]] <- .computeAvg(descDirRen, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr", "ttot"))
+
   # AGGREGATE QUANTITIES -------------------------------------------------------
 
   # Aggregate across all dimensions
-  out[["stockDevAgg"]] <- .computeSumSq(p_stockDev, rprt = c("iteration", "reg", "typ", "loc", "inc"))
+  out[["stockDevAgg"]] <- .computeSumSq(v_stockDev, rprt = c("iteration", "reg", "typ", "loc", "inc"))
 
-  out[["conDevAgg"]] <- .computeSumSq(p_constructionDev, rprt = c("iteration", "reg", "typ", "loc", "inc"))
+  out[["conDevAgg"]] <- .computeSumSq(v_constructionDev, rprt = c("iteration", "reg", "typ", "loc", "inc"))
 
-  out[["renDevAgg"]] <- .computeSumSq(p_renovationDev, rprt = c("iteration", "reg", "typ", "loc", "inc"))
+  out[["renDevAgg"]] <- .computeSumSq(v_renovationDev, rprt = c("iteration", "reg", "typ", "loc", "inc"))
 
   out[["flowDevAgg"]] <- .computeFlowSum(out[["conDevAgg"]], out[["renDevAgg"]])
 
   # Aggregate by heating system (hs)
-  out[["stockDevHs"]] <- .computeSumSq(p_stockDev, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr"))
+  out[["stockDevHs"]] <- .computeSumSq(v_stockDev, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr"))
 
-  out[["conDevHs"]] <- .computeSumSq(p_constructionDev, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr"))
+  out[["conDevHs"]] <- .computeSumSq(v_constructionDev, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr"))
 
-  out[["renDevHs"]] <- .computeSumSq(p_renovationDev, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr"))
+  out[["renDevHs"]] <- .computeSumSq(v_renovationDev, rprt = c("iteration", "reg", "typ", "loc", "inc", "hsr"))
 
   out[["flowDevHs"]] <- .computeFlowSum(out[["conDevHs"]], out[["renDevHs"]])
 
@@ -141,7 +160,7 @@ reportCalibration <- function(gdx) {
   # Loop over all iterations and read in gdx files
   res <- data.frame()
   for (i in seq(0, maxIter)) {
-    fileName <- file.path(dirname(gdx), paste0(gsub("\\.gdx$", "", basename(gdx)), "_", i, ".gdx"))
+    fileName <- file.path(dirname(gdx), paste0(gsub("_0\\.gdx$", "", basename(gdx)), "_", i, ".gdx"))
     if (file.exists(fileName)) {
       res <- rbind(res, readGdxSymbol(fileName, symbol, asMagpie = asMagpie) %>%
                      mutate(iteration = i))
@@ -209,6 +228,22 @@ reportCalibration <- function(gdx) {
 
 }
 
+#' Compute the sum of the squares in a data frame
+#'
+#' @param df data frame, containing the data to be evaluated
+#' @param rprt character, column names for which the sum of the squares should be reported separately
+#' @returns data frame averages as value column
+#'
+#' @importFrom dplyr %>% across any_of .data group_by summarise
+#'
+.computeAvg <- function(df, rprt = "") {
+
+  df %>%
+    group_by(across(any_of(rprt))) %>%
+    summarise(value = mean(.data[["value"]], na.rm = TRUE), .groups = "drop")
+
+}
+
 #' Compute the sum of the squares in a data frame
 #'
 #' @param df data frame, containing the data to be evaluated

README.md

@@ -1,8 +1,8 @@
 # Reporting package for BRICK
 
-R package **reportbrick**, version **0.7.1**
+R package **reportbrick**, version **0.7.2**
 
-[![CRAN status](https://www.r-pkg.org/badges/version/reportbrick)](https://cran.r-project.org/package=reportbrick)  [![R build status](https://github.com/pik-piam/reportbrick/workflows/check/badge.svg)](https://github.com/pik-piam/reportbrick/actions) [![codecov](https://codecov.io/gh/pik-piam/reportbrick/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/reportbrick) [![r-universe](https://pik-piam.r-universe.dev/badges/reportbrick)](https://pik-piam.r-universe.dev/builds)
+[![CRAN status](https://www.r-pkg.org/badges/version/reportbrick)](https://cran.r-project.org/package=reportbrick) [![R build status](https://github.com/pik-piam/reportbrick/workflows/check/badge.svg)](https://github.com/pik-piam/reportbrick/actions) [![codecov](https://codecov.io/gh/pik-piam/reportbrick/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/reportbrick) [![r-universe](https://pik-piam.r-universe.dev/badges/reportbrick)](https://pik-piam.r-universe.dev/builds)
 
 ## Purpose and Functionality
 
@@ -38,16 +38,15 @@ In case of questions / problems please contact Robin Hasse <robin.hasse@pik-pots
 
 To cite package **reportbrick** in publications use:
 
-Hasse R, Rosemann R (2024). _reportbrick: Reporting package for BRICK_. R package version 0.7.1, <https://github.com/pik-piam/reportbrick>.
+Hasse R, Rosemann R (2025). "reportbrick: Reporting package for BRICK - Version 0.7.2."
 
 A BibTeX entry for LaTeX users is
 
  ```latex
-@Manual{,
-  title = {reportbrick: Reporting package for BRICK},
+@Misc{,
+  title = {reportbrick: Reporting package for BRICK - Version 0.7.2},
   author = {Robin Hasse and Ricarda Rosemann},
-  year = {2024},
-  note = {R package version 0.7.1},
-  url = {https://github.com/pik-piam/reportbrick},
+  date = {2025-01-17},
+  year = {2025},
 }
 ```

inst/plotsCalibrationReporting/plotsCalibration.Rmd

@@ -107,14 +107,6 @@ if (length(filePath) == 1) {
 
 ```
 
-## Target function
-
-```{r target function}
-
-.createCalibrationPlot(data, "targetFunction", outPath, outName = outName,
-                       color = color, savePlots = savePlots)
-
-```
 
 ## Absolute stock and flow deviations
 
@@ -189,6 +181,7 @@ if (length(filePath) == 1) {
 
 ```
 
+
 ## Step size
 
 ```{r step size}
@@ -197,3 +190,14 @@ if (length(filePath) == 1) {
                        color = color, savePlots = savePlots)
 ```
 
+
+## Descent direction by heating system
+
+```{r descent direction}
+
+.createCalibrationPlot(data, "descDirCon", outPath, outName = outName,
+                       color = "hsr", savePlots = savePlots)
+
+.createCalibrationPlot(data, "descDirRen", outPath, outName = outName,
+                       color = "hsr", savePlots = savePlots)
+```