lintr formatting

.github/workflows/gotm.yaml

+# SPDX-FileCopyrightText: 2025 Helmholtz-Zentrum hereon GmbH
+# SPDX-License-Identifier: CC0-1.0
+# SPDX-FileContributor Carsten Lemmen <carsten.lemmen@hereon.de>
+
 name: Build and test
 on: push
 jobs:

.gitlab/r.yaml

@@ -10,6 +10,6 @@ lint-r:
   before_script:
     - R -e 'install.packages("lintr", repos="http://cran.rstudio.com")'
   script:
-    - Rscript -e 'lintr::lint("./testcases/light/model_comparison.R")'
-    - Rscript -e 'lintr::lint("./testcases/estuary/plot_output.R")'
-    - Rscript -e 'lintr::lint("./testcases/estuary/setup_data.R")'
+    - Rscript -e 'lintr::lint("./testcases/light/model_comparison.R", linters = with_defaults(object_usage_linter = NULL))'
+    - Rscript -e 'lintr::lint("./testcases/estuary/plot_output.R", linters = with_defaults(object_usage_linter = NULL))'
+    - Rscript -e 'lintr::lint("./testcases/estuary/setup_data.R", linters = with_defaults(object_usage_linter = NULL))'

testcases/estuary/setup_data.R

@@ -14,9 +14,18 @@ as.POSIXct = function(...) base::as.POSIXct(..., format = "%Y-%m-%d %H:%M:%S")
 ## loading observed values for temperature (temp) wind velocity (wind) and wind
 ## direction (dirw) to create forcing file
 
-temp = read.delim("Cuxhaven_DWD!Lufttemperatur.txt", header = FALSE, comment.char = "#")
-wind = read.delim("Cuxhaven_DWD!Windgeschwindigkeit.txt", header = FALSE, comment.char = "#")
-dirw = read.delim("Cuxhaven_DWD!Windrichtung.txt", header = FALSE, comment.char = "#")
+temp = read.delim("Cuxhaven_DWD!Lufttemperatur.txt", 
+                  header = FALSE, 
+                  comment.char = "#"
+)
+wind = read.delim("Cuxhaven_DWD!Windgeschwindigkeit.txt", 
+                  header = FALSE, 
+                  comment.char = "#"
+)
+dirw = read.delim("Cuxhaven_DWD!Windrichtung.txt", 
+                  header = FALSE, 
+                  comment.char = "#"
+)
 
 temp$V1 = as.POSIXct(temp$V1)
 wind$V1 = as.POSIXct(wind$V1)
@@ -34,22 +43,22 @@ temp$temp = temp$V2 + (h_model - h_station) * T_gradient + bias
 ## assuming logarithmic profile
 h_station = 9
 h_model = 10
-w.exponent = 0.14
-wind$V3 = wind$V2 * (h_model / h_station)^w.exponent
+w_exponent = 0.14
+wind$V3 = wind$V2 * (h_model / h_station)^w_exponent
 
 ## merging wind files
 wind = merge(wind, dirw, by = "V1", suffixes = c(".vel", ".dir"))
   
 ## calculating wind components
-wind$u10 = wind$V3 * cos(pi*wind$V2.dir / 180)
-wind$v10 = wind$V3 * sin(pi*wind$V2.dir / 180)
+wind$u10 = wind$V3 * cos(pi * wind$V2.dir / 180)
+wind$v10 = wind$V3 * sin(pi * wind$V2.dir / 180)
 
 ## creating the meteofile
 meteofile = merge(temp, wind)
 meteofile = subset(meteofile, 
                    get.year(V1) >= 2004 & !is.na(temp) & !is.na(v10) & !is.na(u10),
                    select=c(V1, temp, u10, v10)
-                   )
+)
 
 meteofile$V1 = meteofile$V1 + 1 # adding 1 sec to avoid a bug with gotm config
 colnames(meteofile) = paste0("#", colnames(meteofile))

testcases/light/model_comparison.R

@@ -30,9 +30,16 @@ col_ref = "black"
 N = length(rpar[1,])
 
 png(filename = "./light_validation.png",
-    width = 600, height = 600)
+    width = 600, 
+    height = 600
+)
+
+par(mfrow = c(3, 2), 
+    mai = 2 * c(0.42, 0.42, 0.21, 0.21), 
+    oma = 2 * c(1, 1, 0.5, 0.5), 
+    las = 1
+)
 
-par(mfrow = c(3, 2), mai = 2 * c(0.42, 0.42, 0.21, 0.21), oma = 2 * c(1, 1, 0.5, 0.5), las = 1)
 hist(100 * (bpar - rpar) / (rpar + bpar),
      main = "difference in par relatiave to reference (%)",
      xlim = c(-100, 100),
@@ -40,52 +47,50 @@ hist(100 * (bpar - rpar) / (rpar + bpar),
      freq = FALSE,
      border = NA,
      n = 50
-     )
-
-  hist(100 * (bphy - rphy) / (rphy + bphy),
-       xlim = c(-100, 100),
-       xlab = "",
-       main = "difference in ALG1 relatiave to reference (%)",
-       freq = FALSE,
-       border = NA,
-       n = 50
-       )
-
-  plot(rpar, bpar,
-       col = "lightgray",
-       pch = 20,
-       xlab = "reference ALG1",
-       ylab = "dobgc_light ALG1"
-       )
-  abline(a = 0, b = 1)
-  
-  
-  plot(rphy, bphy,
-       col = "lightgray",
-       pch = 20,
-       xlab = "reference ALG1",
-       ylab = "dobgc_light ALG1"
-       )
-  abline(a = 0, b = 1)
-
-  plot(rowMeans(rpar[,1:(N / 2 + 1)]), 
-       type = "l",
-       col = col_ref,
-       main = "par in the surface",
-       xlab = "",
-       ylab = "W m-2"
-       )
-  lines(rowMeans(bpar[,1:(N / 2 + 1)]), type = "l", col = col_sim)
-  
-
-  plot(rowMeans(rphy[,1:(N / 2 + 1)]),
-       type = "l",
-       col = col_ref,
-       main = "ALG1 in the surface",
-       xlab = "",
-       ylab = "mmol-C m-3"
-       )
-  lines(rowMeans(bphy[,1:(N / 2 + 1)]),type = "l",col = col_sim)
+)
+
+hist(100 * (bphy - rphy) / (rphy + bphy),
+     xlim = c(-100, 100),
+     xlab = "",
+     main = "difference in ALG1 relatiave to reference (%)",
+     freq = FALSE,
+     border = NA,
+     n = 50
+)
+
+plot(rpar, bpar,
+     col = "lightgray",
+     pch = 20,
+     xlab = "reference ALG1",
+     ylab = "dobgc_light ALG1"
+)
+abline(a = 0, b = 1)
+
+plot(rphy, bphy,
+     col = "lightgray",
+     pch = 20,
+     xlab = "reference ALG1",
+     ylab = "dobgc_light ALG1"
+)
+abline(a = 0, b = 1)
+
+plot(rowMeans(rpar[, 1:(N / 2 + 1)]), 
+     type = "l",
+     col = col_ref,
+     main = "par in the surface",
+     xlab = "",
+     ylab = "W m-2"
+)
+lines(rowMeans(bpar[, 1:(N / 2 + 1)]), type = "l", col = col_sim)
+
+plot(rowMeans(rphy[, 1:(N / 2 + 1)]),
+     type = "l",
+     col = col_ref,
+     main = "ALG1 in the surface",
+     xlab = "",
+     ylab = "mmol-C m-3"
+)
+lines(rowMeans(bphy[, 1:(N / 2 + 1)]),type = "l",col = col_sim)
 dev.off()