Package: mpmsim 3.0.0

Owen Jones

mpmsim:Simulation of Matrix Population Models with Defined Life History Characteristics

Allows users to simulate matrix population models with particular characteristics based on aspects of life history such as mortality trajectories and fertility trajectories. Also allows the exploration of sampling error due to small sample size.

Authors:Owen Jones [aut, cre]

mpmsim_3.0.0.tar.gz
mpmsim_3.0.0.tar.gz(r-4.5-noble)mpmsim_3.0.0.tar.gz(r-4.4-noble)
mpmsim_3.0.0.tgz(r-4.4-emscripten)mpmsim_3.0.0.tgz(r-4.3-emscripten)
mpmsim.pdf |mpmsim.html✨
mpmsim/json (API)
NEWS

# Installmpmsim in R:

install.packages('mpmsim',repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jonesor/mpmsim/issues

17 exports 0.36 score 87 dependencies 140 downloads

Last updated 4 days agofrom:a4c2a98c9b

Exports:add_mpm_error calculate_errors compute_ci compute_ci_U driven_vital_rate generate_mpm_set make_leslie_mpm model_fertility model_mortality model_survival plot_matrix rand_lefko_mpm rand_lefko_set rand_leslie_set random_mpm reorganise_matrices summarise_mpms

Dependencies:base64enc bit bit64 bslib cachem cli clipr coda colorspace cpp11 crayon DiagrammeR digest dplyr evaluate expm fansi farver fastmap fontawesome fs generics ggplot2 glue gtable highr hms htmltools htmlwidgets igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix MatrixModels mcmc MCMCpack memoise mgcv mime munsell nlme pillar pkgconfig plyr popbio popdemo prettyunits progress purrr quantreg R6 Rage rappdirs RColorBrewer Rcompadre Rcpp readr reshape rlang rmarkdown rstudioapi sass scales SparseM stringi stringr survival tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite visNetwork vroom withr xfun yaml

Generate Lefkovitch matrices

Owen Jones

Rendered fromgenerate_lefkovitch_models.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2024-07-02
Started: 2024-07-02

Generate Leslie matrices

Owen Jones

Rendered fromgenerate_leslie_models.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2024-07-02
Started: 2024-07-02

Sampling error and its propagation

Rendered fromerror_propagation.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2023-09-29
Started: 2023-04-18

Citation

Readme and manuals

Help Manual

Help page	Topics
Add sampling error to matrix population models (MPMs) based on expected values of transition rates and sample sizes	add_mpm_error
Calculate error (standard error or 95%CI) in elements of a matrix population model.	calculate_errors
Compute 95% confidence intervals for derived estimates from a matrix population model	compute_ci
Compute 95% confidence intervals for derived estimates from the U submatrix of a matrix population model	compute_ci_U
Calculate driven vital rates	driven_vital_rate
Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes	generate_mpm_set
Create a Leslie matrix population model	make_leslie_mpm
Model fertility with age using set functional forms	model_fertility
Model mortality hazard, survivorship and age-specific survival probability using a mortality model	model_mortality model_survival
Plot a matrix as a heatmap	plot_matrix
Generate random Lefkovitch matrix population models (MPMs) based on life history archetypes	rand_lefko_mpm
Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes	rand_lefko_set
Generate a set of random Leslie Matrix Population Models	rand_leslie_set
Generate random Lefkovitch matrix population models (MPMs) based on life history archetypes	random_mpm
Reorganise Matrix Population Models	reorganise_matrices
Summarise Matrix Population Models	summarise_mpms

Package: mpmsim 3.0.0

mpmsim:Simulation of Matrix Population Models with Defined Life History Characteristics

Generate Lefkovitch matrices

Generate Leslie matrices

Sampling error and its propagation

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)