# A Toolbox for Modelling Species Coexistence in R

## Documentation for package ‘cxr’ version 1.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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