| 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... |
| 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... |
| 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... |
| BH_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise | Beverton-Holt model with pairwise alphas, covariate effects... |
| BH_pm_alpha_pairwise_lambdacov_none_alphacov_none | Beverton-Holt model with pairwise alphas and no covariate... |
| BH_project_alpha_global_lambdacov_none_alphacov_none | Beverton-Holt model for projecting abundances, with a global... |
| BH_project_alpha_none_lambdacov_none_alphacov_none | Beverton-Holt model for projecting abundances, with no alpha... |
| BH_project_alpha_pairwise_lambdacov_global_alphacov_global | Beverton-Holt model for projecting abundances, with specific... |
| BH_project_alpha_pairwise_lambdacov_global_alphacov_pairwise | Beverton-Holt model for projecting abundances, with specific... |
| BH_project_alpha_pairwise_lambdacov_none_alphacov_none | Beverton-Holt model for projecting abundances, with specific... |
| 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-package | cxr: A Toolbox for Modelling Species Coexistence in R |
| 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... |
| LV_er_lambdacov_none_effectcov_none_responsecov_none | Effect response Lotka-Volterra model without covariate... |
| LV_pm_alpha_global_lambdacov_none_alphacov_none | Lotka-Volterra model with a global alpha and no covariate... |
| 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... |
| LV_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise | Lotka-Volterra model with pairwise alphas, covariate effects... |
| LV_pm_alpha_pairwise_lambdacov_none_alphacov_none | Lotka-Volterra model with pairwise alphas and no covariate... |
| LV_project_alpha_global_lambdacov_none_alphacov_none | Lotka-Volterra model for projecting abundances, with a global... |
| LV_project_alpha_none_lambdacov_none_alphacov_none | Model for projecting abundances, with no alpha and no... |
| LV_project_alpha_pairwise_lambdacov_global_alphacov_global | Lotka-Volterra model for projecting abundances, with specific... |
| LV_project_alpha_pairwise_lambdacov_global_alphacov_pairwise | Lotka-Volterra model for projecting abundances, with specific... |
| LV_project_alpha_pairwise_lambdacov_none_alphacov_none | Lotka-Volterra model for projecting abundances, with specific... |
| LW_er_lambdacov_global_effectcov_global_responsecov_global | Effect response Law-Watkinson model with covariate effects on... |
| 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... |
| 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... |
| LW_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise | Law-Watkinson model with pairwise alphas, covariate effects... |
| LW_pm_alpha_pairwise_lambdacov_none_alphacov_none | Law-Watkinson model with pairwise alphas and no covariate... |
| LW_project_alpha_global_lambdacov_none_alphacov_none | Law-Watkinson model for projecting abundances, with a global... |
| LW_project_alpha_none_lambdacov_none_alphacov_none | Model for projecting abundances, with no alpha and no... |
| LW_project_alpha_pairwise_lambdacov_global_alphacov_global | Law-Watkinson model for projecting abundances, with specific... |
| LW_project_alpha_pairwise_lambdacov_global_alphacov_pairwise | Law-Watkinson model for projecting abundances, with specific... |
| LW_project_alpha_pairwise_lambdacov_none_alphacov_none | Law-Watkinson model for projecting abundances, with specific... |
| 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... |
| 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... |
| RK_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise | Ricker model with pairwise alphas, covariate effects on... |
| 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... |
| RK_project_alpha_none_lambdacov_none_alphacov_none | Model for projecting abundances, with no alpha and no... |
| RK_project_alpha_pairwise_lambdacov_global_alphacov_global | Ricker model for projecting abundances, with specific alpha... |
| RK_project_alpha_pairwise_lambdacov_global_alphacov_pairwise | Ricker model for projecting abundances, with specific alpha... |
| RK_project_alpha_pairwise_lambdacov_none_alphacov_none | Ricker model for projecting abundances, with specific alpha... |
| 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... |
| vital_rate | Vital rate calculation |
