Removed rsofun mentions

.gitignore

@@ -9,3 +9,4 @@ data-raw/cloud_cover/
 data-raw/modis/
 data/tmp/
 docs/
+.idea/

analysis/00_batch_convert_LSM_data.R

@@ -8,7 +8,6 @@ library(FluxDataKit)
 library(FluxnetLSM)
 library(dplyr)
 library(ingestr)
-library(rsofun)
 
 input_path <- "/data_2/FluxDataKit/FDK_inputs/"
 output_path <- "/data_2/FluxDataKit/v3.4/"

analysis/03_screen_data.R

@@ -0,0 +1,77 @@
+# Determine longest good-quality sequence by site
+library(tidyverse)
+library(FluxDataKit)
+
+path <- "/data_2/FluxDataKit/v3.4"
+
+sites <- FluxDataKit::fdk_site_info |>
+  filter(!(sitename %in% c("MX-Tes", "US-KS3")))
+
+# # site subset------------------
+# # xxx debug
+# # chose representative sites for LES book
+# use_sites <- c(
+#   # "FI-Hyy", # Boreal Forests/Taiga
+#   # "US-SRM", # Deserts & Xeric Shrublands
+#   # "FR-Pue", # Mediterranean Forests, Woodlands & Scrub
+#   # "DE-Hai", # Temperate Broadleaf & Mixed Forests
+#   "IT-Ro1"
+#   # "US-Tw1", # Temperate Grasslands, Savannas & Shrublands
+#   # "AU-How", # Tropical & Subtropical Grasslands, Savannas & Shrubland
+#   # "BR-Sa3", # Tropical
+#   # "ZM-Mon", # Tropical deciduous forest (xeric woodland)
+#   # "US-ICh"  # Tundra
+# )
+# sites <- sites |>
+#   filter(sitename %in% use_sites)
+# #----------------------------
+
+# determine longest sequence of good-quality data for each site
+list_seq <- lapply(sites$sitename, function(site){
+  message(sprintf("Analysing %s ----", site))
+
+  # get file name path
+  filn <- list.files(
+    file.path(path, "fluxnet"),
+    pattern = paste0("FLX_", site, ".*_FULLSET_DD.*.csv"),
+    recursive = TRUE
+  )
+
+  df <- read.csv(file.path(file.path(path, "fluxnet"), filn))
+
+  df_seq <- suppressMessages(
+    suppressWarnings(
+      try(fdk_get_sequence(
+        df,
+        site = site,
+        qc_threshold = 0.25,
+        leng_threshold = 90,
+        do_plot = TRUE,
+        out_path = file.path(path, "plots")
+      )
+      )
+    )
+  )
+
+  if(inherits(df_seq, "try-error")){
+    message("!!! plotting failed !!!")
+    return(NULL)
+  }
+
+  return(df_seq)
+})
+
+
+fdk_site_fullyearsequence <- bind_rows(list_seq)
+
+# write CSV file
+save(fdk_site_fullyearsequence,
+     file = here::here("data/fdk_site_fullyearsequence.rda"),
+     compress = "xz"
+     )
+
+# write CSV file for upload to Zenodo
+readr::write_csv(
+  fdk_site_fullyearsequence,
+  file = "/data_2/FluxDataKit/v3.4/fdk_site_fullyearsequence.csv"
+)

analysis/README.md

@@ -9,8 +9,11 @@ Scripts need to be run in chronological order
 - 00_batch_convert_LSM_data.R - converts FLUXNET data (standard CSV files) to LSM data (NetCDF)
  - the output is land surface model (LSM) compatible data in a netcdf format 
 - 01_visualize_fdk_data.R - Plots all converted data for visual checks (not mandatory)
-- 03_batch_convert_to_CSV_data.R - converts LSM data to FLUXNET compatible CSVs
+- 03_screen_data.R - converts LSM data to FLUXNET compatible CSVs
  - this data is downsampled to a daily time step
  - the data sticks to FLUXNET formatting
-- 04_batch_format_rsofun_drivers.R - converts data to `rsofun` model inputs
- - conversion to ensure compatibility with the `rsofun` package for modelling
+- 04_create_zenodo_upload.R
+
+Optional scripts:
+- b_02_batch_format_rsofun_drivers.R
+- b_06_p-model_run.R

vignettes/03_data_generation.Rmd

@@ -163,13 +163,16 @@ library(rsofun)
 
 # processing of the half hourly data to
 # p-model input drivers for rsofun
-rsofun_data <- fdk_format_drivers(
+rsofun_driver <- rsofun::fdk_format_drivers(
   site_info = FluxDataKit::fdk_site_info |>
     filter(sitename == "FR-Fon"),
   path = paste0(tempdir(),"/"),
   verbose = TRUE
 )
 
+# Please make sure the parameter names correspond to your version of rsofun.
+# See rsofun documentation
+
 # optimized parameters from previous work
 params_modl <- list(
   kphio           = 0.09423773,
@@ -181,7 +184,7 @@ params_modl <- list(
 
 # run the model for these parameters
 output <- rsofun::runread_pmodel_f(
-  rsofun_data,
+  rsofun_driver,
   par = params_modl
 )
 
@@ -194,7 +197,7 @@ print(head(model_data))
 
 ```{r eval = evaluate}
 
-validation_data <- rsofun_data |>
+validation_data <- rsofun_driver |>
   filter(sitename == "FR-Fon") |>
   tidyr::unnest(forcing)