test: Fix testing path for R CMD CHECK

analysis/pmodel_use_newdata.R

@@ -6,8 +6,8 @@ library(tidyr)
 library(khroma)
 
 ## ----------------------------------------------------------------------------------------------------------------------
-p_model_drivers = readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
-p_model_validation = readRDS(file = here::here("data/p_model_validation_newformat.rds"))
+p_model_drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
+# p_model_validation <- rsofun::p_model_validation_format2024_08
 
 ## ----------------------------------------------------------------------------------------------------------------------
 # define model parameter values from previous work

tests/testthat/test-calibration-pmodel.R

@@ -3,8 +3,7 @@ set.seed(10)
 
 test_that("test GPP calibration routine p-model (BT, likelihood maximization)", {
   skip_on_cran()
-  #drivers <- rsofun::p_model_drivers # TODO: NOT YET UPDATED FOR PHYDRO
-  drivers <- readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
+  drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
   drivers$params_siml[[1]]$use_gs     <- TRUE
 
 
@@ -60,8 +59,7 @@ test_that("test GPP calibration routine p-model (BT, likelihood maximization)",
 
 test_that("test GPP calibration routine p-model (GenSA, rmse, all params)", {
   skip_on_cran()
-  #drivers <- rsofun::p_model_drivers # TODO: NOT YET UPDATED FOR PHYDRO
-  drivers <- readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
+  drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
   drivers$params_siml[[1]]$use_gs     <- TRUE
   obs <- rsofun::p_model_validation
 
@@ -218,8 +216,7 @@ test_that("test Vcmax25 calibration routine p-model (GenSA, rmse)", {
 test_that("test joint calibration routine p-model (BT, likelihood maximization)", {
   skip_on_cran()
   drivers <- rbind(
-    gpp     = # TODO: rsofun::p_model_drivers is NOT YET UPDATED FOR PHYDRO 
-      readRDS(file = here::here("data/p_model_drivers_newformat.rds")), 
+    gpp     =   rsofun::p_model_drivers_format2024_08, # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
     vcmax25 = rsofun::p_model_drivers_vcmax25  |>
       # TODO: NOT YET UPDATED FOR PHYDRO
       # # specify additionally needed params_siml flags:
@@ -270,7 +267,6 @@ test_that("test joint calibration routine p-model (BT, likelihood maximization)"
       err_vcmax25 = list(lower = 0.0001, upper = 0.1, init = 0.005)
     )
   )
-  # debug(rsofun::runread_pmodel_f)
   pars <- rsofun::calib_sofun(
     drivers = drivers,
     obs = obs,
@@ -284,4 +280,4 @@ test_that("test joint calibration routine p-model (BT, likelihood maximization)"
 
   # test for correctly returned values
   expect_type(pars, "list")
-})
+})

tests/testthat/test-model-runs.R

@@ -1,6 +1,5 @@
 context("test models and their parameters")
 set.seed(10)
-
 test_that("run_pmodel_f_bysite()", {
   skip_on_cran()
 
@@ -18,8 +17,7 @@ test_that("run_pmodel_f_bysite()", {
   )
 
   # read in demo data
-  #df_drivers <- p_model_drivers # TODO: NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
-  df_drivers <- readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
+  df_drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
 
   # check run_pmodel_f_bysite() ##########################
   # run the SOFUN Fortran P-model using the internal function `run_pmodel_f_bysite`
@@ -154,9 +152,9 @@ test_that("run_pmodel_f_bysite()", {
     dpsi      = c(0, 0, 0, 0, 0, 0), 
     psi_leaf  = c(0, 0, 0, 0, 0, 0)
   )
-  expect_equal(slice(tibble(mod1), c(1, 70, 1200, 1400, 2000, 2180)), ref1, tolerance = 1e-7)
-  expect_equal(slice(tibble(mod2), c(1, 70, 1200, 1400, 2000, 2180)), ref2, tolerance = 1e-7)
-  expect_equal(slice(tibble(mod3), c(1, 70, 1200, 1400, 2000, 2180)), ref3, tolerance = 1e-7)
+  expect_equal(slice(tibble(mod1), c(1, 70, 1200, 1400, 2000, 2180)), ref1, tolerance = 1e-6)
+  expect_equal(slice(tibble(mod2), c(1, 70, 1200, 1400, 2000, 2180)), ref2, tolerance = 1e-6)
+  expect_equal(slice(tibble(mod3), c(1, 70, 1200, 1400, 2000, 2180)), ref3, tolerance = 1e-6)
 
 })
 test_that("runread_pmodel_f()", {
@@ -176,8 +174,7 @@ test_that("runread_pmodel_f()", {
   )
 
   # read in demo data
-  #df_drivers <- p_model_drivers # TODO: NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
-  df_drivers <- readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
+  df_drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
 
   df_output_singlecore <- rsofun::runread_pmodel_f(
     df_drivers,
@@ -290,8 +287,7 @@ test_that("phydro-model run check LE and AET", {
   )
 
   # read in demo data
-  #df_drivers <- p_model_drivers # TODO: NOT YET UPDATED FOR PHYDRO
-  df_drivers <- readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
+  df_drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
   df_drivers$params_siml[[1]]$use_gs     <- TRUE
 
   # run the SOFUN Fortran PHYDRO-model

tests/testthat/test-quantitative-validation.R

@@ -21,9 +21,8 @@ test_that("p-model quantitative check versus observations (FR-Pue)", {
     whc                = 2000 # site info, water holding capacity in mm: TODO: does this make sense with soilm_thetastar in mm units?
   )
 
-  #df_drivers <- p_model_drivers # TODO: NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
-  df_drivers <- readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
-
+  df_drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
+
   # run the model for these parameters
   res <- rsofun::runread_pmodel_f(
     drivers = df_drivers,

vignettes/pmodel_use_newdata.Rmd

@@ -201,18 +201,20 @@ The package includes two demo datasets to run and validate pmodel output using G
 #                   lubridate::year(date) <= 2012) |>
 #          list()
 #     ))
-# 
-# saveRDS(p_model_drivers, file = here::here("data/p_model_drivers_newformat.rds"))
-# 
-# saveRDS(p_model_validation, file = here::here("data/p_model_validation_newformat.rds"))
+#
+# Save to subfolder data/ and export it to make it available for package users:
+# p_model_drivers_format2024_08 <- p_model_drivers
+# usethis::use_data(p_model_drivers_format2024_08)  # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
+# p_model_validation_format2024_08 <- p_model_validation
+# usethis::use_data(p_model_validation_format2024_08) 
 ```
 
 ### Read drivers
 
 ```{r}
-p_model_drivers = readRDS(file = here::here("data/p_model_drivers_newformat.rds"))
+p_model_drivers <- rsofun::p_model_drivers_format2024_08 # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
 
-p_model_validation = readRDS(file = here::here("data/p_model_validation_newformat.rds"))
+p_model_validation <- rsofun::p_model_validation_format2024_08
 ```
 
 ### Visualize drivers
@@ -243,9 +245,9 @@ These are real data from the French FR-Pue fluxnet site. Information about data
 Another two datasets are provided as an example to validate the model against leaf traits data, rather than fluxes. Measurements of Vcmax25 (aggregated over species) for a subset of 4 sites from the GlobResp database (Atkin et al., 2015) are given in `p_model_validation_vcmax25` and the corresponding forcing for the P-model is given in `p_model_drivers_vcmax25`. Since leaf traits are only measured once per site, the forcing used is a single year of average climate (the average measurements between 2001 and 2015 on each day of the year).
 
 ```{r}
-p_model_drivers_vcmax25
+rsofun::p_model_drivers_vcmax25
 
-p_model_validation_vcmax25
+rsofun::p_model_validation_vcmax25
 ```
 
 For the remainder of this vignette, we will use the GPP flux datasets. The workflow is exactly the same for leaf traits data.

vignettes/sensitivity_analysis.Rmd

@@ -61,11 +61,12 @@ ll_pmodel <- function(
   rsofun::cost_likelihood_pmodel(        # reuse likelihood cost function
     as.list(par_v), # must be a named list
     obs = rsofun::p_model_validation,
-    drivers = readRDS(file = here::here("data/p_model_drivers_newformat.rds")), #TODO rsofun::p_model_drivers is NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
+    drivers = rsofun::p_model_drivers_format2024_08, #TODO rsofun::p_model_drivers is NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
     targets = "gpp"
   )
 }
 
+
 # Compute log-likelihood for a given set of parameters
 ll_pmodel( 
   par_v = c(
@@ -269,7 +270,7 @@ settings_calib <- list(
 
 # Calibrate kphio-related parameters and err_gpp 
 par_calib <- calib_sofun(
-  drivers = readRDS(file = here::here("data/p_model_drivers_newformat.rds")), #TODO rsofun::p_model_drivers is NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
+  drivers = rsofun::p_model_drivers_format2024_08, # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
   obs = p_model_validation,
   settings = settings_calib,
   par_fixed = list(
@@ -309,7 +310,7 @@ settings_calib <- list(
 )
 
 par_calib <- calib_sofun(
-  drivers = readRDS(file = here::here("data/p_model_drivers_newformat.rds")), #TODO rsofun::p_model_drivers is NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
+  drivers = rsofun::p_model_drivers_format2024_08, # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
   obs = p_model_validation,
   settings = settings_calib,
   par_fixed = list(
@@ -405,7 +406,7 @@ run_pmodel <- function(sample_par){
   # and also adds the new observation error
   
   out <- runread_pmodel_f(
-    drivers = readRDS(file = here::here("data/p_model_drivers_newformat.rds")), #TODO rsofun::p_model_drivers is NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
+    drivers = rsofun::p_model_drivers_format2024_08, # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
     par =  list(                      # copied from par_fixed above
       kphio = sample_par$kphio,
       kphio_par_a = sample_par$kphio_par_a,
@@ -514,7 +515,7 @@ plot_gpp_error +
 # 
 # Plot observed and predicted GPP, with a 95% confidence interval using err_gpp
 plot_gpp_error <- ggplot(data = runread_pmodel_f(
-    drivers = readRDS(file = here::here("data/p_model_drivers_newformat.rds")), #TODO rsofun::p_model_drivers is NOT YET UPDATED FOR PHYDRO (a newformat, b add phydro_ parameters)
+    drivers = rsofun::p_model_drivers_format2024_08, # TODO: NOT YET UPDATED FOR PHYDRO (still add default phydro_* parameters)
     par =  list(                       
       kphio = par_calib$par[1],        # values from posterior
       kphio_par_a = par_calib$par[2],