renaming files + processing

analysis/04_batch_format_rsofun_drivers.R → analysis/02_batch_format_rsofun_drivers.R

@@ -5,14 +5,16 @@ options(dplyr.summarise.inform = FALSE)
 library(dplyr)
 library(tidyr)
 library(ggplot2)
+library(ingestr)
 library(rsofun)
 lapply(list.files("R/","*.R", full.names = TRUE), source)
 
 input_path <- "/data/scratch/beta-v4/fluxnet/"
 
 # read in sites to process
 sites <- FluxDataKit::fdk_site_info
-#site <- c("FR-Pue", "CH-Lae", "CH-Dav")
+
+#site <- c("FR-Pue", "CH-Lae")
 
 # subset sites
 # sites <- sites |>

analysis/05_screen_rsofun_data.R → analysis/03_screen_rsofun_data.R

@@ -60,7 +60,8 @@ data_fix_years <- df |>
   nest() |>
   rename(
     forcing = data
-  )
+  ) |>
+  ungroup()
 
 df1 <- df |>
   filter(tolower(sitename) %in% tolower(screen$sitename)) |>
@@ -76,3 +77,47 @@ data <- bind_rows(df1, df2)
 
 # save data
 saveRDS(data, "data/rsofun_driver_data_clean.rds", compress = "xz")
+
+data |>
+  group_by(sitename) |>
+  do({
+
+    tmp <- .$forcing[[1]] |>
+      tidyr::pivot_longer(
+        col = !contains("date"),
+        names_to = "measurement",
+        values_to = "value"
+      )
+
+    sitename <- .$sitename[1]
+
+    l <- seq(as.Date("1990/1/1"), as.Date("2023/1/1"), "years")
+
+    p <- ggplot(data = tmp) +
+      geom_line(
+        aes(
+          date,
+          value
+        ),
+        colour = "red"
+      ) +
+      geom_vline(xintercept = l) +
+      labs(
+        title = sitename
+      ) +
+      theme_bw() +
+      theme(panel.grid.minor = element_line()
+      ) +
+      facet_grid(
+        measurement ~ .,
+        scales = "free"
+        )
+
+    ggsave(
+      paste0("manuscript/rsofun_input/",sitename,".png"),
+      width = 12,
+      height = 14,
+      dpi = 175
+    )
+
+  })

analysis/04_create_zenodo_upload.R

@@ -0,0 +1,100 @@
+# This script does the final renaming of all the files
+# to a consistent format, as well as zipping them up
+# for uploading to Zenodo
+#
+# This script uses bash system calls
+# as well as the "rename" function which
+# is not installed by default. Run on linux
+# or a bash compatible system.
+#
+# Compressed data should be uploaded to
+# the Zenodo repository:
+# https://zenodo.org/record/7258291
+
+input_path <- "/data/scratch/beta-v4/"
+tmp_path <- "/data/scratch/upload"z
+
+#---- purge old data -----
+
+# remove temporary path
+system(sprintf("rm -rf %s", tmp_path))
+
+# recreate temporary path
+dir.create(tmp_path)
+
+#---- copy new data over ----
+system(
+  sprintf(
+    "cp -R %s/lsm %s/lsm",
+  input_path,
+  tmp_path
+  )
+)
+
+system(
+  sprintf(
+    "cp -R %s/fluxnet %s/fluxnet",
+    input_path,
+    tmp_path
+  )
+)
+
+#---- rename all files in place ----
+
+# rename LSM data
+
+system(
+  sprintf(
+    "rename 's/FLUXNET2015/FLUXDATAKIT/g' %s/lsm/*.nc",
+    tmp_path
+  )
+)
+
+system(
+  sprintf(
+    "rename 's/OxFlux/FLUXDATAKIT/g' %s/lsm/*.nc",
+    tmp_path
+  )
+)
+
+system(
+  sprintf(
+    "rename 's/LaThuile/FLUXDATAKIT/g' %s/lsm/*.nc",
+    tmp_path
+  )
+)
+
+# rename FLUXNET data
+
+system(
+  sprintf(
+    "rename 's/PLUMBER/FLUXDATAKIT/g' %s/fluxnet/*.csv",
+    tmp_path
+  )
+)
+
+#---- zip up all data -----
+
+# compress LSM data
+system(
+  sprintf(
+  "
+  cd %s/lsm;
+  tar -czvf %s/FLUXDATAKIT_LSM.tar.gz *.nc
+  ",
+  tmp_path,
+  tmp_path
+  )
+)
+
+# compress FLUXNET data
+system(
+  sprintf(
+    "
+  cd %s/fluxnet;
+  tar -czvf %s/FLUXDATAKIT_FLUXNET.tar.gz *.csv
+  ",
+    tmp_path,
+    tmp_path
+  )
+)

analysis/06_p-model_run.R

@@ -28,7 +28,7 @@ for(i in driver_data$sitename){
       output <- try(rsofun::runread_pmodel_f(
         df,
         par = params_modl,
-        makecheck = TRUE
+        makecheck = FALSE
       ))
 
       print(output)
@@ -68,7 +68,7 @@ for(i in driver_data$sitename){
 
       ggsave(
         file.path(
-          "./manuscript/figures/",
+          "./manuscript/rsofun_output/",
           paste0(df$sitename,".png")
         ),
         width = 12,