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don't renumber years in speciesEcoregion #80

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don't renumber years in speciesEcoregion #80

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31 changes: 24 additions & 7 deletions Biomass_core.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1001,14 +1001,31 @@ Init <- function(sim, verbose = getOption("LandR.verbose", TRUE)) {
doAssertion = getOption("LandR.assertions", TRUE))

sim$lastReg <- 0
speciesEcoregion[, identifier := year > P(sim)$successionTimestep]
speciesEcoregion_True <- speciesEcoregion[identifier == TRUE, ]
speciesEcoregion_False <- speciesEcoregion[identifier == FALSE, ]
if (NROW(speciesEcoregion_False)) {
speciesEcoregion_True_addon <- speciesEcoregion_False[year == max(year), ]
speciesEcoregion_True <- rbindlist(list(speciesEcoregion_True_addon, speciesEcoregion_True))

## the code below makes sure the first year of traits is used even if it's < successionTimestep
## if all(year == start(sim)), all become 0, which is ok because only the most recent
## year of trait data up time(sim) is used (so if all year == 0, year 0's traits
## are used during the first growth event). HOWEVER, this will be problematic if
## speciesEcoregion contains projected values for the entire simulation as only the last
## year of values would be used since all become lower than time(sim)

# speciesEcoregion[, identifier := year > P(sim)$successionTimestep]
# speciesEcoregion_True <- speciesEcoregion[identifier == TRUE, ]
# speciesEcoregion_False <- speciesEcoregion[identifier == FALSE, ]
# if (NROW(speciesEcoregion_False)) {
# speciesEcoregion_True_addon <- speciesEcoregion_False[year == max(year), ]
# speciesEcoregion_True <- rbindlist(list(speciesEcoregion_True_addon, speciesEcoregion_True))
# }
# sim$speciesEcoregion <- speciesEcoregion_True[, ':='(year = year - min(year), identifier = NULL)]

## proposed fix: check that year 0 exists and if not, add it -- LANDIS-II doc requires a year 0 to be present
if (!any(speciesEcoregion$year == 0)) {
message("Could not find 'year == 0' in 'speciesEcoregion' table.")
message("Using the first year of trait values as 'year 0'")
firstYrSppEcoregion <- sim$speciesEcoregion[year == min(year)]
firstYrSppEcoregion$year <- 0L
sim$speciesEcoregion <- rbind(firstYrSppEcoregion, sim$speciesEcoregion)
}
sim$speciesEcoregion <- speciesEcoregion_True[, ':='(year = year - min(year), identifier = NULL)]

sim$lastFireYear <- "noFire"

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