removing one of the cohort

[trotsiuk]

This issue appears if one of the cohort is thinned to 0. Unfortunately, the last thinning for Picea able_1 provide NA, and cause all the simulation to be NA afterwards.

f_loc <- ""
 out_3PG <- run_3PG(site        = read_xlsx(f_loc, 'site'),
                    species     = read_xlsx(f_loc, 'species'),
                    climate     = prepare_climate(climate = read_xlsx(f_loc, 'climate'), from = read_xlsx(f_loc, sheet = 'site')$from, to = read_xlsx(f_loc, sheet = 'site')$to),
                    thinning    = read_xlsx(f_loc, 'thinning'),
                    parameters  = read_xlsx(f_loc, 'parameters'),
                    size_dist   = read_xlsx(f_loc, 'sizeDist'),
                    settings    = list(light_model = 2, transp_model = 2, phys_model = 2, height_model = 2, correct_bias = 1, calculate_d13c = 0),
                    check_input = TRUE, df_out = TRUE)

This issue is not occurring if I test with the internal data.

library(r3PG)
library(dplyr)
library(ggplot2)

d_thinning$stems_n <- c(500.1, 600.8, 0)

out_3PG <- run_3PG(
  site        = d_site, 
  species     = d_species, 
  climate     = d_climate, 
  thinning    = d_thinning,
  parameters  = d_parameters, 
  size_dist   = d_sizeDist,
  settings    = list(light_model = 2, transp_model = 2, phys_model = 2, 
    height_model = 1, correct_bias = 0, calculate_d13c = 0),
  check_input = TRUE, df_out = TRUE)

sel_var <- c('biom_stem', 'biom_foliage', 'biom_root', 'stems_n')

out_3PG %>%
  filter( variable %in% sel_var ) %>%
  ggplot( aes(date, value, color = species) ) +
  geom_line() +
  facet_wrap(~variable, scales = 'free') +
  theme_classic()

1019000_input.xlsx

[trotsiuk]

from @DavidForrester

if a cohort is removed from a simulation (by thinning or dying)
before the simulation is supposed to end, the simulation ends prematurely.
I have also added an example of this "1015002_input.xlsx".

1015003_input.xlsx

[trotsiuk]

DONE

@DavidForrester