Simplify cohorts
simplifyCohorts.RdReduce the number of cohorts / pixel groups for LANDIS-II, which only supports (integer) initial community map codes between 0 and 65535.
Details
Biomass is CONSERVED across the merge. Each merged community takes, per species,
the mean of the stand totals of the pixel groups it pools, and that total is then
divided among the retained age classes in proportion to age, so the oldest class
still carries the most. Before 0.0.128 each age class instead received its own
scaled copy of the mean COHORT biomass, so a community's biomass grew with the
number of age classes pooled into it rather than being conserved: measured on one
landscape, initial communities carried a median 440 t/ha against 116 t/ha observed,
and exceeded the succession extension's own maxB by four to thirteen times.
The shares are computed over the DISTINCT retained age classes, because
prepInitialCommunities() deduplicates its rows: partitioning across duplicate
rows would lose whatever those duplicates carried. Integer rounding leaves the
per-species total within a few g/m2 of the target.
Conservation is per merged community, and the mean it takes over the pooled pixel groups is UNWEIGHTED: a pixel group covering one cell counts the same as one covering a thousand. Landscape biomass is therefore conserved only up to that weighting, and on a landscape where 1.6 million pixel groups collapse to 4,153 communities the unweighted community mean sat about 1.2 times the pixel-group mean (151 against 126 t/ha), because small communities count equally with large ones. Weighting by pixel count would remove that; it is deliberately left alone here because it changes which stands the communities represent, not just their arithmetic.