NEWS.md

In Rage: Life History Metrics from Matrix Population Models

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.

Rage documentation built on Sept. 30, 2023, 1:06 a.m.