Merge pull request #297 from fabern/revise-for-manuscript

Revise for manuscript

Author: stineb

.gitignore

@@ -6,13 +6,6 @@
 .DS_Store
 .idea
 
-# VS Code local settings
-.vscode/
-
-# act local config & secrets
-.actrc
-.secrets
-
 # source files
 src/*.o
 src/*.so
@@ -25,5 +18,4 @@ vignettes/*.html
 # documentation dir
 docs/
 
-# CRAN submission archives
 CRAN-SUBMISSION

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rsofun
 Title: The P-Model and BiomeE Modelling Framework
-Version: 5.0.0.9000
+Version: 5.0.1
 Authors@R: c(
             person(
               family = "Stocker",
@@ -75,15 +75,12 @@ ByteCompile: true
 NeedsCompilation: yes
 RoxygenNote: 7.3.2
 Suggests:
-    constructive,
     covr,
     rcmdcheck,
     testthat,
     rmarkdown,
     ggplot2,
     knitr,
-    lubridate,
-    rlang,
     sensitivity
 VignetteBuilder: knitr
 Encoding: UTF-8

NEWS.md

@@ -5,6 +5,12 @@ available forcing data
 * Breaking change: biomee drivers' `init_cohort$init_n_cohorts` column has been phased out and must not be present in  
 drivers to protect against data corruption.
 
+# rsofun v5.0.1
+
+* This model version behaves exactly as the version before.
+* Update was necessary to include description of scripts and data used for the model documentation paper into archive on Zenodo
+
+
 # rsofun v5.0.0
 
 * new BiomeE forcing data matching that of P-model

R/run_pmodel_f_bysite.R

@@ -156,35 +156,6 @@ run_pmodel_f_bysite <- function(
     as.integer() %>%
     abs()
 
-  # Default value for tc_home
-  if ('tc_home' %in% names(site_info)) {stop("Unexpectedly received site_info$tc_home for p-model.")}
-  # Calculate tc_home (mean maximum temperature of the warmest month)
-  site_info$tc_home <- forcing %>%
-    dplyr::mutate(
-      year = format(.data$date, "%Y"), month = format(.data$date, "%m")
-    ) %>%
-    dplyr::group_by(.data$year, .data$month) %>%
-    dplyr::summarise(
-      mean_tmax_month = mean(.data$tmax, na.rm = TRUE), .groups = "drop"
-    ) %>%
-    dplyr::group_by(.data$year) %>%
-    dplyr::summarise(
-      warmest_month_tmax = max(.data$mean_tmax_month, na.rm = TRUE),
-      .groups = "drop"
-    ) %>%
-    dplyr::summarise(tc_home = mean(.data$warmest_month_tmax, na.rm = TRUE)) %>%
-    dplyr::pull(.data$tc_home)
-
-  # Validation
-  if (is.na(site_info$tc_home) || length(site_info$tc_home) == 0) {
-    if (verbose) {
-      warning(
-        "Calculated tc_home is NA or missing; setting default to 25C."
-      )
-    }
-    site_info$tc_home <- 25
-  }
-
   # re-define units and naming of forcing dataframe
   # keep the order of columns - it's critical for Fortran (reading by column number)
   forcing_features <- c(
@@ -337,7 +308,6 @@ run_pmodel_f_bysite <- function(
       latitude                  = as.numeric(site_info$lat),
       altitude                  = as.numeric(site_info$elv),
       whc                       = as.numeric(site_info$whc),
-      tc_home                   = as.numeric(site_info$tc_home),
       n                         = as.integer(nrow(forcing)), # number of rows in matrix (pre-allocation of memory)
       par                       = c(as.numeric(params_modl$kphio), # model parameters as vector in order
                                     as.numeric(params_modl$kphio_par_a),

README.md

@@ -118,6 +118,22 @@ pars <- calib_sofun(
   )
 ```
 
+## Data and code for model documentation paper
+
+Scripts to reproduce the plots in the model documentation paper are located in the `analysis` subfolder (`01-sensitivity-analysis.R`, `02-bayesian-calibration.R`, and `03-uncertainty-estimation.R`) and the outputs
+are archived in the `analysis/paper_results_files` subfolder.
+
+Data used in the model documentation paper is located in the `data` subfolder (`p_model_drivers.rda` and `p_model_validation.rda`).
+
+The data is based on the publicly available FLUXNET2015 data for the site FR-Pue containing years 2007 to 2012 (available as FluxDataKit v3.4.2 under DOI 10.5281/zenodo.14808331).
+It is generated with the script `data-raw/generate_pmodel_drivers.R`.
+
+Versions of {rsofun} (including the exact version used in the model documentation paper) are publicly archived on Zenodo (https://doi.org/10.5281/zenodo.3712928).
+
+The model documentation paper is currently under review.
+A preprint is available at: https://www.biorxiv.org/content/10.1101/2023.11.24.568574v3
+
+
 ## References
 
 Stocker, B. D., Wang, H., Smith, N. G., Harrison, S. P., Keenan, T. F., Sandoval, D., Davis, T., and Prentice, I. C.: P-model v1.0: an optimality-based light use efficiency model for simulating ecosystem gross primary production, Geosci. Model Dev., 13, 1545–1581, https://doi.org/10.5194/gmd-13-1545-2020, 2020.

analysis/paper_inputs_csvs/p_model_drivers_forcing.csv

@@ -0,0 +1,2 @@
+spinup,spinupyears,recycle,outdt,ltre,ltne,ltrd,ltnd,lgr3,lgn3,lgr4
+TRUE,10,1,1,FALSE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE

analysis/paper_inputs_csvs/p_model_drivers_params_siml.csv

@@ -0,0 +1,2 @@
+lon,lat,elv,whc
+3.5957,43.7413,270,432.375