Rage 1.9.0

• is_leslie_matrix now explicitly documents and supports plus-group Leslie matrices where A[n,n] > 0, representing an open-ended oldest age class. Fixed a bug in the internal leslie_expand function where the plus-group survival term A[n,n] was silently dropped during matrix expansion, causing leslie_collapse to produce incorrect results for such matrices.

• Added function stage_at_death_dist which calculates the distribution of stages at death for a synthetic population. The initial starting vector must be specified.

• Added function evenness_shannon to calculate the evenness of the stages at death.

• Added function scale_mpm_to_lambda1 to rescale an MPM so that the dominant eigenvalue of the projection matrix is 1.

• Improved consistency in the handling of total reproduction matrices (matR) in mpm_to_mx, mpm_to_table, gen_time, and net_repro_rate.

• plot_life_cycle now handles NA transitions explicitly, labels them as NA, and produces a tighter plot with less surrounding whitespace.

• Fixed an edge case in mpm_collapse that could produce NaN values when collapsing groups of stages with zero stable-stage weight.

• Added short notes to fecundity- and reproduction-related documentation clarifying interpretation under pre- versus post-breeding census designs.

• Improved documentation for entropy_k_stage.

• Fixed error in gen_time which caused an over estimate of generation time under method = "cohort" of 1 year.

Rage 1.8.0

• Improved consistency in the handling of reproductive matrices (F (sexual reproduction), C (clonal reproduction), R (clonal and sexual reproduction combined)) across multiple functions. These are: 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.
• Modified 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.

Rage 1.7.0

• 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.
• The function 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.

Rage 1.6.0

• Bug fix in 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.
• Changes to life_expect_var and life_expect_mean to ensure that outputs are consistent (as vectors).
• Improved test coverage (still >95%)

Rage 1.5.1

• Patch to fix test errors on older systems (r-oldrel-macos-arm64). No changes to main package code.

Rage 1.5.0

• added is_leslie_matrix function to detect a Leslie matrix.
• added 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).
• Error in 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!
• performance enhancements to speed up code and make it more robust.
• increased unit test coverage to >95%

Rage 1.4.0

• 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).
• added 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).

Rage 1.3.0

• 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).

Rage 1.2.0

• Improved documentation of mpm_to_table and related functions.
• Standardised the lx_crit, conv and xmax argument values across age-from-stage functions.
• Minor edits to documentation for stylistic consistency.
• Removed dependency on the package popbio.
• Added vignette with suggested quality control.

Rage 1.1.0

• Removed the vignette that made heavy use of ggtern package. This package was not available for some builds of R and thus caused problems for CRAN.

Rage 1.0.0

• Released on CRAN

Rage 0.2.0

Released on Github on 25th April 2021

• Name changes of functions to consistent snake_case.
• Improved documentation with fuller descriptions and executable examples.
• Grouped functions by type in the documentation.
• Improved vignettes by greatly expanding them.
• Added support using stage names in addition to stage number, plus helper function name_stages for (re)naming MPM stages.
• Replaced old function lifeTimeRepEvents with specific functions for events (gen_time, life_expect, longevity).
• Added functions for manipulating matrices: mpm_collapse, mpm_rearrange, mpm_split, mpm_standardize.
• Added functions to calculate various vital rates vr, vr_mat, vr_vec.
• Added utility functions 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).
• Renamed vitalRates to vital_rates.
• Renamed (and modified) old function makeLifeTable to create new function, mpm_to_table.
• Added lifetable_convert function to convert between types of life table (hazard, survivorship and survival probability).
• Replaced matrixElementPerturbation and vitalRatePerturbation functions with enhanced perturbation functions: perturb_matrix, perturb_stochastic, perturb_trans, perturb_vr.
• Added utility functions (utils.R) to do various tasks like check validity of matrices, calculate mean matrices, calculate matrix inverse.
• Expanded use of unit tests for all functions.
• Updated DESCRIPTION with contributors
• Added build checks via continuous integration on Travis, Appveyor and Github actions (including weekly checks).
• Added machine-readable codemeta-data information (codemeta.json)

Rage 0.1.0

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.