A Toolbox for Modelling Species Coexistence in R

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Documentation for package ‘cxr’ version 1.0.0

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abundance Abundance measurements
abundance_projection Title 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
competitive_ability Competitive ability among pairs of species
cxr cxr
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
fitness_ratio Fitness ratio among two or more species
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
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