Package: regnans 0.2

Daniel S. Falster

regnans: Package for assembling communities with the plant model

Assembles ecological communities of competing strategies using the plant model, by iterating demography to equilibrium, computing selection gradients and invasion fitness, and solving for evolutionary attractors.

Authors:Daniel S. Falster and Richard G. FitzJohn

regnans_0.2.tar.gz
regnans_0.2.zip(r-4.7-x86_64)regnans_0.2.zip(r-4.7-arm64)regnans_0.2.zip(r-4.6-x86_64)regnans_0.2.zip(r-4.6-arm64)regnans_0.2.zip(r-4.5-x86_64)
regnans_0.2.tgz(r-4.6-x86_64)regnans_0.2.tgz(r-4.6-arm64)regnans_0.2.tgz(r-4.5-x86_64)regnans_0.2.tgz(r-4.5-arm64)
regnans_0.2.tar.gz(r-4.7-arm64)regnans_0.2.tar.gz(r-4.7-x86_64)regnans_0.2.tar.gz(r-4.6-arm64)regnans_0.2.tar.gz(r-4.6-x86_64)
regnans_0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
regnans/json (API)

# Install 'regnans' in R:

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

Bug tracker:https://github.com/traitecoevo/regnans/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.08 score 1 stars 2 scripts 65 exports 74 dependencies

Last updated from:95257c9c05. Checks:13 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	612
linux-devel-x86_64	ERROR	513
source / vignettes	OK	910
linux-release-arm64	ERROR	610
linux-release-x86_64	ERROR	483
macos-release-arm64	ERROR	542
macos-release-x86_64	ERROR	1063
macos-oldrel-arm64	ERROR	662
macos-oldrel-x86_64	ERROR	893
windows-devel-arm64	ERROR	783
windows-devel-x86_64	ERROR	788
windows-release-arm64	ERROR	714
windows-release-x86_64	ERROR	864
windows-oldrel-x86_64	ERROR	766
wasm-release	OK	912

Exports:assembler_control assembler_run assembler_set_traits assembler_start boundary_bisect boundary_control boundary_design boundary_diagram boundary_scout boundary_sweep boundary_switch bounds bounds_infinite canonical_community canonical_control check_bounds check_point community_add community_canonical_equation community_classify_singularity community_continue_boundary community_continue_singularity community_demography community_fitness_gradient community_fitness_hessian community_fitness_landscape community_label community_parameter_map community_parameter_sensitivity community_parameter_values community_pip community_plot_fitness_landscape community_selection_gradient community_selection_gradient_jacobian community_selection_gradient_parameter_jacobian community_solve_boundary community_solve_singularity community_start community_tep community_viable_fitness demographic_step_control derivative_control fitness_landscape_control harness_check_derivatives harness_dd99 harness_dd99_nd harness_explicit harness_fd harness_gk98 harness_gm99 harness_jj12 harness_plant harness_provides max_fitness max_growth_rate mutational_vcv_proportion pip_control pip_mutual plant_community_check_for_inviable_strategies plant_default_assembly_control plant_default_assembly_pars plot_community tidy_assembly trait_matrix util_nlsolve

Dependencies:backports BB bbotk BH checkmate cli codetools cpp11 crayon data.table dfoptim digest dplyr evaluate farver future future.apply generics ggplot2 globals glue gtable isoband labeling lgr lhs lifecycle listenv logger magrittr matrixStats mirai mlbench mlr3 mlr3learners mlr3mbo mlr3measures mlr3misc mlr3tuning moocore mvtnorm nanonext nleqslv odelia palmerpenguins paradox parallelly phylloptim pillar pkgconfig plant PRROC purrr quadprog R6 rbibutils RColorBrewer Rcpp Rdpack rlang S7 scales spacefillr stringi stringr tibble tidyr tidyselect utf8 uuid vctrs viridisLite withr yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Options controllings community assembly process.	assembler_control
Take specified number of steps with assembler.	assembler_run
Set traits on an assembler	assembler_set_traits
start community assembly process.	assembler_start
Bisect coexistence boundaries along rays	boundary_bisect print.boundary_points
Coexistence boundary settings	boundary_control
Scouting design in a parameter box	boundary_design
A diagram of coexistence boundaries	as.data.frame.boundary_diagram boundary_diagram plot.boundary_diagram
Scout a parameter design for coexistence	boundary_scout print.boundary_labels
Sweep a path for hysteresis	boundary_sweep print.boundary_sweep
Start the branch an event seeds	boundary_switch
Trait bounds	bounds bounds_infinite check_bounds check_point
Community along a canonical-equation trajectory	canonical_community
Canonical-equation settings	canonical_control
Add strategies to a community	community_add
Canonical equation with branching	community_canonical_equation
Classify a singular strategy or coalition (1-D and N-D)	community_classify_singularity print.singularity_classification
Continue a coexistence boundary in two parameters	as.data.frame.regnans_branch community_continue_boundary plot.regnans_branch print.regnans_branch
Continuation of a singular strategy or coalition along a parameter	community_continue_singularity print.singularity_path
Update demography of community	community_demography
Fitness gradient in the mutant direction	community_fitness_gradient
Fitness Hessian in the mutant direction	community_fitness_hessian
Fitness Landscape	community_fitness_landscape
Label a community by the species its parameters support	community_label
Parameter map for an explicit harness	community_parameter_map
Parameter sensitivity of a singular strategy or coalition	community_parameter_sensitivity
Parameter values of a community	community_parameter_values
Pairwise invasibility plot	community_pip
Plot an invasion-fitness landscape	community_plot_fitness_landscape
Selection gradient of the residents	community_selection_gradient
Resident Jacobian of the selection gradient	community_selection_gradient_jacobian
Parameter Jacobian of the selection gradient	community_selection_gradient_parameter_jacobian
Solve for a coexistence boundary point	community_solve_boundary
Solve for a singular strategy or coalition (N-dimensional)	community_solve_singularity
Initialise a community object	community_start
Trait-evolution plot	community_tep
Compute region of positive fitness for a community	community_viable_fitness
Options controllings community assembly process.	demographic_step_control
Derivative settings	derivative_control
Options controlling fitness-landscape construction	fitness_landscape_control
Verify model-supplied derivatives	harness_check_derivatives
DD99 (Dieckmann & Doebeli 1999) harness	harness_dd99
DD99 multi-trait harness	harness_dd99_nd
Explicit (toy-model) harness	harness_explicit
Finite-difference derivatives for a harness	harness_fd
GK98 (Geritz et al. 1998 soft-selection) harness	harness_gk98
GM99 (Geritz et al. 1999 seed-size) harness	harness_gm99
JJ12 (Johansson & Jonzen 2012 bird arrival) harness	harness_jj12
plant model harness	harness_plant
Query a harness's derivatives	harness_provides
Returns number taken by an 'assembler' object	length.assembler
Returns number of types in 'community'	length.community
Find point of maximum fitness within some range	max_fitness
Fitness of trait values against a community	max_growth_rate
Generate mutational covariance matrices	mutational_vcv_proportion
Pairwise-invasibility settings	pip_control
Mutual invasibility	pip_mutual
Check low-abundance strategies for viability	plant_community_check_for_inviable_strategies
Default plant control for community assembly	plant_default_assembly_control
Default plant parameters for assembly	plant_default_assembly_pars
Plot the residents of an assembled community	plot_community
Plot a canonical-equation run	autoplot.canonical_equation plot.canonical_equation
Plot a pairwise or mutual invasibility surface	autoplot.pip plot.pip
Plot a trait-evolution plot	autoplot.tep plot.tep
Tidies output from assembler_run into tidy dataframe.	tidy_assembly
Create trait matrix	trait_matrix
Solve a nonlinear system	util_nlsolve