Updates for v3

DESCRIPTION

@@ -27,7 +27,9 @@ Imports:
     rvest,
     zoo,
     lubridate,
-    recipes
+    recipes,
+    readr,
+    here
 Suggests:
     knitr,
     rmarkdown,

NAMESPACE

@@ -20,4 +20,5 @@ export(fdk_process_lsm)
 export(fdk_release)
 export(fdk_setup_sofun)
 export(fdk_smooth_ts)
+export(fill_netrad)
 export(site_exceptions)

R/data.R

@@ -5,4 +5,18 @@
 #' as their meta-data
 #'
 #' @format DataFrame
+#' \describe{
+#'   \item{sitename}{Site name}
+#'   \item{lon}{Longitude of site}
+#'   \item{lat}{Latitude of site}
+#'   \item{elv}{elevation}
+#'   \item{year_start}{start year of data availability}
+#'   \item{year_end}{end year of data availability}
+#'   \item{koeppen_code}{Koeppen Geiger code}
+#'   \item{igbp_land_use}{IGBP land cover type}
+#'   \item{whc}{Total root zone water holding capacity}
+#'   \item{product}{Data taken from published product}
+#' }
+#'
+
 "fdk_site_info"

R/fdk_convert_lsm.R

@@ -289,14 +289,14 @@ fdk_convert_lsm <- function(
 
     # loop over all rows (variables)
     for (i in seq_len(nrow(replacements))){
-      try(all <-tibble::add_column(all,
+      try(all <- tibble::add_column(all,
             !!(replacements[i, 'variable']) := replacements[i, 'value']
             ),
           silent = TRUE
       )
 
       all <- all |>
-        select(
+        dplyr::select(
           -ends_with(".1")
         )
     }

R/fdk_downsample_fluxnet.R

@@ -158,7 +158,7 @@ fdk_downsample_fluxnet <- function(
       TA_F_MDS = mean(TA_F_MDS, na.rm = FALSE),
       TA_F_QC = mean(TA_F_QC < 1, na.rm = FALSE),
 
-      # temperature is the mean of the HH values
+      # shortwave radiation is the mean of the HH values
       SW_IN_F_MDS = mean(SW_IN_F_MDS, na.rm = FALSE),
       SW_IN_F_MDS_QC = mean(SW_IN_F_MDS_QC < 1, na.rm = FALSE),
 
@@ -174,7 +174,7 @@ fdk_downsample_fluxnet <- function(
       WS_F = mean(WS_F, na.rm = FALSE),
       WS_F_QC = mean(WS_F_QC < 1, na.rm = FALSE),
 
-      # temperature is the mean of the HH values
+      # atmospheric pressure is the mean of the HH values
       PA_F = mean(PA_F, na.rm = FALSE),
       PA_F_QC = mean(PA_F_QC < 1, na.rm = FALSE),
 

R/fdk_process_lsm.R

@@ -128,7 +128,7 @@ fdk_process_lsm <- function(
 
     } else {
 
-      if ( x['product'] == "icos" ){
+      if ( x['product'] == "icos_warmwinter2020" || x['product'] == "icos_drought2018" ){
         infile <- FluxnetLSM::get_fluxnet_files(
           x['data_path'],
           x['sitename'],
@@ -145,7 +145,7 @@ fdk_process_lsm <- function(
         )
       }
 
-      if ( x['product'] == "oneflux" ){
+      if ( x['product'] == "ameriflux" ){
         infile <- FluxnetLSM::get_fluxnet_files(
           x['data_path'],
           x['sitename'],

analysis/00_batch_convert_LSM_data.R

@@ -3,14 +3,14 @@
 options(tidyverse.quiet = TRUE)
 options(dplyr.summarise.inform = FALSE)
 lapply(list.files("R/","*.R", full.names = TRUE), source)
-#library(FluxDataKit)
+library(FluxDataKit)
 library(FluxnetLSM)
 library(dplyr)
 library(ingestr)
 library(rsofun)
 
-input_path <- "/data/scratch/FDK_inputs"
-output_path <- "/data/scratch/beta-v4"
+input_path <- "~/data/FluxDataKit/FDK_inputs"  # "/data/scratch/FDK_inputs"
+output_path <- "~/data/FluxDataKit/v3"  #  "/data/scratch/beta-v4"
 
 # read in all site meta-data, only test on
 # FR-Pue to debug FluxnetLSM for now
@@ -19,16 +19,13 @@ sites <- FluxDataKit::fdk_site_info |>
     data_path = file.path(input_path, "flux_data/")
   )
 
-# CH-Lae
-# CH-Dav
-#
 #---- create a new release ----
 
 fdk_release(
   df = sites,
   input_path = input_path,
   output_path = output_path,
-  overwrite = TRUE
+  overwrite = FALSE
 )
 
 #---- create matching plots ----
@@ -70,3 +67,5 @@ failed_sites <- lapply(sites$sitename, function(site){
 
   return(NULL)
 })
+
+

analysis/01_visualize_fdk_data.R

@@ -26,10 +26,11 @@ failed_sites <- lapply(sites$sitename, function(site){
   df <- suppressWarnings(try(fdk_convert_lsm(
     site = site,
     fluxnet_format = FALSE,
-    path = "/data/scratch/beta-v2/lsm/"
+    path = "~/data/FluxDataKit/v3"
   )
   ))
 
   print(head(df))
 
 })
+

analysis/02_batch_format_rsofun_drivers.R

@@ -9,7 +9,7 @@ library(ingestr)
 library(rsofun)
 lapply(list.files("R/","*.R", full.names = TRUE), source)
 
-input_path <- "/data/scratch/beta-v4/fluxnet/"
+input_path <- "~/data/FluxDataKit/v3"
 
 # read in sites to process
 sites <- FluxDataKit::fdk_site_info

analysis/README.md

@@ -6,7 +6,7 @@ Scripts need to be run in chronological order
 
 ## Scripts
 
-- 00_batch_convert_LSM_data.R - converts FLUXNET data to LSM data
+- 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

data-raw/00_download_plumber_data.R

@@ -6,7 +6,8 @@
 library(rvest)
 
 # set destination path
-dest_path <- "/data/scratch/FDK_inputs/flux_data/plumber/"
+# dest_path <- "/data/scratch/FDK_inputs/flux_data/plumber/"
+dest_path <- "~/data/FluxDataKit/FDK_inputs/plumber/"
 
 # set catalogues
 catalogues <- data.frame(