A benchmark option has been added to functions project3(), invade3(), and batch_project3().
Unit tests added.
Processing of age-related parameters in batch projection of Leslie MPMs fixed.
Processing of supplements in batch_project3() no longer leads to an occasional memory leak.
Trait axes now include individual covariate values that can be used to create variants.
Density dependence through the additive limit and absolute limit functions has been added to projection and invasion functions.
Equivalence frames and density frames can now be added per annual matrix.
Community projections with projection3() can now handle post-processing of
pre-existing MPMs with argument supplemental.
Function batch_project3() now runs batches of community projections using
vectors of alterations input as matrix element offsets, given rate changes,
and multipliers.
Function summary.adaptProjBatch() now summarizes batch community
projections.
Function project3() now includes aggregate density in the output.
Function summary.adaptProj() now also outputs mean final population sizes
for each MPM across replicates.
Function plot.adaptInv() now processes the first variable trait in the trait
axis as the source of axis labels by default to PIPs, and to the x axis in
elasticity plots.
comm_out renamed to structure, and with its own structure changing such
that the top-level list refers to replicates, and the lower-level list refers
to input MPMs.Projection via vrm_input with deviance terms now no longer crashes.
Function project3() no longer always incorporates the current MPMs start vector as the vector at time 0, but instead incorporates it only as the correct start time.
Corrected issue resulting in Leslie-format function-based MPMs yielding matrices full of NAs if the format vector is missing.
Fixed fatal error in project3() occurring when the number of MPMs entered is smaller than the times projected using unequal stage weights across MPMs.
Fixed bug that led function summary.adaptProj() to acknowledge only a single
replicate.
ESS trait value optimization now handled via Golden section Nelder-Mead search algorithm.
Standard error bootstrapping example added to invasibility analysis vignette.
Corrections to documentation.
Corrected default axis labels in function plot.adaptInv().
Corrected optimization trait axis calculations in cases where traits span both positive and negative values.
Corrected ESS trait value calculations in cases where traits span both positive and negative values.
Function plot.adaptInv() now correctly labels axes with user-supplied values.
Function summary.adaptInv() now gives the correct number of variants tested.
Functions plot.adaptProj() and summary.adaptProj() created to plot and summarize community projections, respectively.
ESS optimization routine enabled for function invade3().
New invasibility analysis vignette added.
Threshold values for 0s created for function invade3().
Function invade3() added to run invasibility analyses.
Function plot.adaptInv() created to plot the results of pairwise invasibility analyses.
Functions ta_skeletion() and trait_axis() created to develop quick trait axis data frames.