NEWS.md
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)