P-model reference run

This workflow runs the P-model with {rsofun} v4.2 and forcing as used in Stocker et al. (2020). Calibration and evaluation data is also as in Stocker et al. (2020). All data is from files created for Stocker et al. (2020). Results are almost identical as presented in Stocker et al. (2020). Slight deviations are related to the fact that rsofun v4.2 performs time series simulations with continuous acclimation - not for monthly means as done in Stocker et al. (2020). The workflow here provides an exact reproduction of code in sofunBench for v4.2.

Model parameters

Model parameters are determined for this version from calibration. The code for model calibration is not shown. See vignettes/1_p-model_reference_run.Rmd for the code.

params_modl <- list(
    kphio           = 0.09423773,  # pars$par[1],
    soilm_par_a     = 0.33349283,  # pars$par[2],
    soilm_par_b     = 1.45602286,  # pars$par[3],
    tau_acclim_tempstress = 10,   # irrelevant - not calibrated
    par_shape_tempstress  = 0.0   # irrelevant - not calibrated
  )

Model run

output <- rsofun::runread_pmodel_f(
  df_drivers_fluxnet2015 |> 
      dplyr::mutate(forcing = purrr::map(forcing, ~rename(., rain = rainf, snow = snowf))),
  par = params_modl
  )

Run evaluation

This runs the eval_sofun() routine included in the sofunCalVal package, and outputs daily, monthly and annual summary statistics comparing observed with simulated values. We’ll retake this same routine when running on the latest release (i.e. the workflow is equivalent but for the release of the rsofun package)

Results

Level	rsq	rmse	slope	bias	nvals
daily_pooled	0.6822030	2.237670	0.9424125	0.0168156	237777
xdaily_pooled	0.7402749	1.968332	1.0276624	0.0211308	33152
annual_pooled	0.6888402	391.843125	1.0841131	-15.8487457	598
monthly_pooled	0.7655718	1.789852	1.0570757	-0.1032881	7428
spatial	0.7050382	409.730725	1.0358195	-32.6734855	109
anomalies_annual	0.0770564	176.099264	0.4296991	-3.4124489	598
meandoy	0.7358411	1.813804	1.0070837	0.1051432	42844
anomalies_daily	0.2629290	1.569327	0.4433198	-0.0317397	237603
meanxoy	0.7617283	1.696434	1.0315764	0.0872718	5528
anomalies_xdaily	0.1409777	1.214267	0.4071741	-0.0036830	33152

8-daily, spatial and annual

Mean seasonal cycle

Drought response

Consistency with rpmodel

Since rsofun takes time series forcing, overwrite forcing with constant values corresponding to the arguments provided to rpmodel::rpmodel().

Setup ORG

## [1] "Are values equivalent?"

## [1] "- ci:ca: Mean relative difference: 0.00444033"

## [1] "- GPP: Mean relative difference: 0.3456686"

## [1] "- Vcmax: Mean relative difference: 0.3313334"

## [1] "- Vcmax25: Mean relative difference: 0.3313316"

## [1] "- Jmax: Mean relative difference: 0.3450332"

## [1] "- Jmax25: Mean relative difference: 0.3450321"

Setup BRC

## [1] "Are values equivalent for:"

## [1] "- ci:ca: Mean relative difference: 0.00444033"

## [1] "- GPP: Mean relative difference: 0.00254358"

## [1] "- Vcmax: Mean relative difference: 0.01930885"

## [1] "- Vcmax25: Mean relative difference: 0.01931158"

## [1] "- Jmax: Mean relative difference: 0.001575214"

## [1] "- Jmax25: Mean relative difference: 0.001573512"

Appendix

sessionInfo()

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
## 
## time zone: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] RColorBrewer_1.1-3 here_1.0.1         ggthemes_5.1.0     knitr_1.48        
##  [5] lubridate_1.9.3    ggplot2_3.5.1      readr_2.1.5        tidyr_1.3.1       
##  [9] dplyr_1.1.4        rsofun_4.2         rpmodel_1.2.3     
## 
## loaded via a namespace (and not attached):
##  [1] remotes_2.5.0        rlang_1.1.4          magrittr_2.0.3      
##  [4] compiler_4.4.1       mgcv_1.9-1           systemfonts_1.1.0   
##  [7] callr_3.7.6          vctrs_0.6.5          stringr_1.5.1       
## [10] profvis_0.4.0        pkgconfig_2.0.3      crayon_1.5.3        
## [13] fastmap_1.2.0        ellipsis_0.3.2       labeling_0.4.3      
## [16] utf8_1.2.4           promises_1.3.0       rmarkdown_2.28      
## [19] sessioninfo_1.2.2    tzdb_0.4.0           ps_1.8.1            
## [22] nloptr_2.1.1         ragg_1.3.3           purrr_1.0.2         
## [25] bit_4.5.0            xfun_0.48            cachem_1.1.0        
## [28] jsonlite_1.8.9       highr_0.11           later_1.3.2         
## [31] parallel_4.4.1       R6_2.5.1             bslib_0.8.0         
## [34] stringi_1.8.4        boot_1.3-30          pkgload_1.4.0       
## [37] jquerylib_0.1.4      Rcpp_1.0.13          usethis_3.0.0       
## [40] DHARMa_0.4.7         httpuv_1.6.15        Matrix_1.7-0        
## [43] splines_4.4.1        timechange_0.3.0     tidyselect_1.2.1    
## [46] yaml_2.3.10          miniUI_0.1.1.1       curl_5.2.3          
## [49] processx_3.8.4       pkgbuild_1.4.5       plyr_1.8.9          
## [52] lattice_0.22-6       tibble_3.2.1         shiny_1.9.1         
## [55] withr_3.0.2          bridgesampling_1.1-2 coda_0.19-4.1       
## [58] evaluate_1.0.1       desc_1.4.3           urlchecker_1.0.1    
## [61] pillar_1.9.0         generics_0.1.3       vroom_1.6.5         
## [64] rprojroot_2.0.4      hms_1.1.3            BayesianTools_0.1.8 
## [67] munsell_0.5.1        scales_1.3.0         minqa_1.2.8         
## [70] xtable_1.8-4         glue_1.8.0           GenSA_1.1.14.1      
## [73] tools_4.4.1          lme4_1.1-35.5        fs_1.6.4            
## [76] mvtnorm_1.3-1        grid_4.4.1           yardstick_1.3.1     
## [79] devtools_2.4.5       colorspace_2.1-1     nlme_3.1-164        
## [82] cli_3.6.3            textshaping_0.4.0    fansi_1.0.6         
## [85] Brobdingnag_1.2-9    gtable_0.3.6         sass_0.4.9          
## [88] digest_0.6.37        htmlwidgets_1.6.4    farver_2.1.2        
## [91] memoise_2.0.1        htmltools_0.5.8.1    pkgdown_2.1.1       
## [94] lifecycle_1.0.4      mime_0.12            bit64_4.5.2         
## [97] MASS_7.3-60.2

Koen Hufkens and Beni Stocker