NEWS.md
stage_at_death_dist which calculates the distribution of stages at death for a synthetic population. The initial starting vector must be specified.evenness_shannon to calculate the evenness of the stages at death.entropy_k_stage.gen_time which caused an over estimate of generation time under method = "cohort" of 1 year.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)