A Toolbox for Modelling Species Coexistence in R

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Documentation for package ‘cxr’ version 1.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

abundance	Abundance measurements
abundance_projection	Project abundances from population dynamics models
avg_fitness_diff	Average fitness differences
BH_er_lambdacov_global_effectcov_global_responsecov_global	Effect response Beverton-Holt model with covariate effects on lambda, effect, and response
BH_er_lambdacov_none_effectcov_none_responsecov_none	Effect response model without covariate effects
BH_pm_alpha_global_lambdacov_none_alphacov_none	Beverton-Holt model with a global alpha and no covariate effects
BH_pm_alpha_none_lambdacov_none_alphacov_none	Beverton-Holt model with no alphas and no covariate effects
BH_pm_alpha_pairwise_lambdacov_global_alphacov_global	Beverton-Holt model with pairwise alphas and global covariate effects on lambda and alpha
BH_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise	Beverton-Holt model with pairwise alphas, covariate effects on lambda, and pairwise covariate effects on alpha
BH_pm_alpha_pairwise_lambdacov_none_alphacov_none	Beverton-Holt model with pairwise alphas and no covariate effects
BH_project_alpha_global_lambdacov_none_alphacov_none	Beverton-Holt model for projecting abundances, with a global alpha and no covariate effects
BH_project_alpha_none_lambdacov_none_alphacov_none	Beverton-Holt model for projecting abundances, with no alpha and no covariate effects
BH_project_alpha_pairwise_lambdacov_global_alphacov_global	Beverton-Holt model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
BH_project_alpha_pairwise_lambdacov_global_alphacov_pairwise	Beverton-Holt model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
BH_project_alpha_pairwise_lambdacov_none_alphacov_none	Beverton-Holt model for projecting abundances, with specific alpha values and no covariate effects
build_param	Build param structure
calculate_densities	Obtain species densities from transition matrices
competitive_ability	Competitive ability among pairs of species
cxr_er_bootstrap	standard error estimates for effect and response parameters
cxr_er_fit	General optimization for effect-response models
cxr_generate_test_data	Generate simulated interaction data
cxr_pm_bootstrap	Standard error estimates for model parameters
cxr_pm_fit	General optimization for population models
cxr_pm_multifit	Multi-species parameter optimization
densities_to_df	Converts a densities list to a tidy dataframe
fill_demography_matrix	Fill the vec-permutation demography matrix
fill_dispersal_matrix	Fill the vec-permutation dispersal matrix
fill_transition_matrix	Fill a transition matrix
fitness_ratio	Fitness ratio among two or more species
generate_vital_rate_coefs	Generate coefficients for obtaining vital rates
glm_example_coefs	Generalized linear model coefficients
LV_er_lambdacov_global_effectcov_global_responsecov_global	Effect response Lotka-Volterra model with covariate effects on lambda, effect, and response
LV_er_lambdacov_none_effectcov_none_responsecov_none	Effect response Lotka-Volterra model without covariate effects
LV_pm_alpha_global_lambdacov_none_alphacov_none	Lotka-Volterra model with a global alpha and no covariate effects
LV_pm_alpha_none_lambdacov_none_alphacov_none	Lotka-Volterra model with no alphas and no covariate effects
LV_pm_alpha_pairwise_lambdacov_global_alphacov_global	Lotka-Volterra model with pairwise alphas and global covariate effects on lambda and alpha
LV_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise	Lotka-Volterra model with pairwise alphas, covariate effects on lambda, and pairwise covariate effects on alpha
LV_pm_alpha_pairwise_lambdacov_none_alphacov_none	Lotka-Volterra model with pairwise alphas and no covariate effects
LV_project_alpha_global_lambdacov_none_alphacov_none	Lotka-Volterra model for projecting abundances, with a global alpha and no covariate effects
LV_project_alpha_none_lambdacov_none_alphacov_none	Model for projecting abundances, with no alpha and no covariate effects
LV_project_alpha_pairwise_lambdacov_global_alphacov_global	Lotka-Volterra model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
LV_project_alpha_pairwise_lambdacov_global_alphacov_pairwise	Lotka-Volterra model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
LV_project_alpha_pairwise_lambdacov_none_alphacov_none	Lotka-Volterra model for projecting abundances, with specific alpha values and no covariate effects
LW_er_lambdacov_global_effectcov_global_responsecov_global	Effect response Law-Watkinson model with covariate effects on lambda, effect, and response
LW_er_lambdacov_none_effectcov_none_responsecov_none	Effect response Law-Watkinson model without covariate effects
LW_pm_alpha_global_lambdacov_none_alphacov_none	Law-Watkinson model with a global alpha and no covariate effects
LW_pm_alpha_none_lambdacov_none_alphacov_none	Law-Watkinson model with no alphas and no covariate effects
LW_pm_alpha_pairwise_lambdacov_global_alphacov_global	Law-Watkinson model with pairwise alphas and global covariate effects on lambda and alpha
LW_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise	Law-Watkinson model with pairwise alphas, covariate effects on lambda, and pairwise covariate effects on alpha
LW_pm_alpha_pairwise_lambdacov_none_alphacov_none	Law-Watkinson model with pairwise alphas and no covariate effects
LW_project_alpha_global_lambdacov_none_alphacov_none	Law-Watkinson model for projecting abundances, with a global alpha and no covariate effects
LW_project_alpha_none_lambdacov_none_alphacov_none	Model for projecting abundances, with no alpha and no covariate effects
LW_project_alpha_pairwise_lambdacov_global_alphacov_global	Law-Watkinson model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
LW_project_alpha_pairwise_lambdacov_global_alphacov_pairwise	Law-Watkinson model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
LW_project_alpha_pairwise_lambdacov_none_alphacov_none	Law-Watkinson model for projecting abundances, with specific alpha values and no covariate effects
metapopulation_example_param	Metapopulation dynamics coefficients
neigh_list	neighbours and fitness observations
niche_overlap	Niche overlap between two species
RK_er_lambdacov_global_effectcov_global_responsecov_global	Effect response Beverton-Holt model with covariate effects on lambda, effect, and response
RK_er_lambdacov_none_effectcov_none_responsecov_none	Effect response Ricker model without covariate effects
RK_pm_alpha_global_lambdacov_none_alphacov_none	Ricker model with a global alpha and no covariate effects
RK_pm_alpha_none_lambdacov_none_alphacov_none	Ricker model with no alphas and no covariate effects
RK_pm_alpha_pairwise_lambdacov_global_alphacov_global	Ricker model with pairwise alphas and global covariate effects on lambda and alpha
RK_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise	Ricker model with pairwise alphas, covariate effects on lambda, and pairwise covariate effects on alpha
RK_pm_alpha_pairwise_lambdacov_none_alphacov_none	Ricker model with pairwise alphas and no covariate effects
RK_project_alpha_global_lambdacov_none_alphacov_none	Ricker model for projecting abundances, with a global alpha and no covariate effects
RK_project_alpha_none_lambdacov_none_alphacov_none	Model for projecting abundances, with no alpha and no covariate effects
RK_project_alpha_pairwise_lambdacov_global_alphacov_global	Ricker model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
RK_project_alpha_pairwise_lambdacov_global_alphacov_pairwise	Ricker model for projecting abundances, with specific alpha values and global covariate effects on alpha and lambda
RK_project_alpha_pairwise_lambdacov_none_alphacov_none	Ricker model for projecting abundances, with specific alpha values and no covariate effects
salinity_list	Salinity measurements
spatial_sampling	spatial arrangement of the observations
species_fitness	Fitness of a species
species_rates	Species germination and survival rates
summary.cxr_er_fit	CXR summary method for effect response model fits
summary.cxr_pm_fit	CXR summary method for population model fits
summary.cxr_pm_multifit	CXR summary method for multispecies fits
vec_permutation_matrices	Generate templates for dispersal, demography, and permutation matrices
vital_rate	Vital rate calculation