gen_time,
mature_prob, mature_age,
mpm_to_table, mpm_to_mx. Following this
change, we recommend that users explicitly name their arguments rather
than relying on argument order, since the argument order has changed
with this update. Update your existing code accordingly if you notice
unexpected behaviour.entropy_d to include an option to scale the
entropy calculations to account for population growth/shrinkage. Users
can now choose between the scaled (Caswell, 2001 eqns.
4.94-4.97) or unscaled (from Demetrius 1978) method. The
default is scaled and thus re-running old code will likely
change outputs that relied on entropy_d.plot_life_cycle now includes a logical argument
show_gv which allows users to print the
graphViz code constructed by the function to the screen.
This is useful for use elsewhere, or for debugging plots.entropy_k is being deprecated. We change
the function name to life_elas and recommend use of the new
functions entropy_k_age and entropy_k_stage
for Leslie and Lefkovitch matrices respectively. See the article by de
Vries et al (2023) for the rationale for this change.plot_life_cycle to ensure that nodes are
placed in the correct order. Additional argument node_order
also allows nodes to be placed in any arbitrary order.life_expect_var and
life_expect_mean to ensure that outputs are consistent (as
vectors).is_leslie_matrix function to detect a Leslie
matrix.leslie_collapse function to aggregate a Leslie
matrix to a desired dimension. This function is similar to
mpm_collapse but it will ensure that the returned
aggregated matrix is also in the form of a Leslie matrix. Code
contributed by Richard A. Hinrichsen (@hinrich62).life_expect_var (#193) corrected (contribution
from Chrissy Hernández, @chrissy3815). Note that
life_expect_mean and life_expect_var now
function slightly differently. Be aware!entropy_d entropy_k shape_rep
and shape_surv can now accept matrices directly. In
previous versions, these functions required input of lx
and/or mx trajectories, but now the functions can
optionally use mpm_to_... functions to create these vectors
internally (#174).remove_final argument to
mpm_to_table function. This allows users to optionally
remove the final row of the life table to prevent the artificial
inflation of mortality/hazard caused by the fact that the final
age-class is assumed to be closed (and hence all individuals must
die).Fixed an error in the entropy_d function, which
calculates Demetrius’s entropy.
Added two methods to calculate generation time in
gen_time: average parent-offspring age difference &
expected age at first reproduction (#183).
mpm_to_table and related
functions.lx_crit, conv and
xmax argument values across age-from-stage functions.popbio.ggtern
package. This package was not available for some builds of R and thus
caused problems for CRAN.Released on Github on 25th April 2021
name_stages for (re)naming MPM stages.lifeTimeRepEvents with specific
functions for events (gen_time, life_expect,
longevity).mpm_collapse, mpm_rearrange,
mpm_split, mpm_standardize.vr,
vr_mat, vr_vec.repro_stages and
standard_stages to identify reproductive stages either
logically (TRUE/FALSE) or by the standardised set of reproductive stages
(propagule, pre-reproductive, reproductive and post-reproductive).vitalRates to vital_rates.makeLifeTable to
create new function, mpm_to_table.lifetable_convert function to convert between
types of life table (hazard, survivorship and survival
probability).matrixElementPerturbation and
vitalRatePerturbation functions with enhanced perturbation
functions: perturb_matrix, perturb_stochastic,
perturb_trans, perturb_vr.utils.R) to do various tasks
like check validity of matrices, calculate mean matrices, calculate
matrix inverse.codemeta.json)Released on Github on 14th December 2018
First (pre) release package. Functions include: R0,
dEntropy, kEntropy,
lifeTimeRepEvents, longevity,
makeLifeTable, matrixElementPerturbation,
plotLifeCycle, qsdConverge,
reprodStages, standardizedVitalrates,
vitalRatePerturbation, vitalRates.