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cxr  

A Toolbox for Modelling Species Coexistence in R
View on CRAN: Click here


Download and install cxr package within the R console
Install from CRAN:
install.packages("cxr")

Install from Github:
library("remotes")
install_github("cran/cxr")

Install by package version:
library("remotes")
install_version("cxr", "1.1.1")



Attach the package and use:
library("cxr")
Maintained by
David Garcia-Callejas
[Scholar Profile | Author Map]
First Published: 2021-04-16
Latest Update: 2023-10-26
Description:
Recent developments in modern coexistence theory have advanced our understanding on how species are able to persist and co-occur with other species at varying abundances. However, applying this mathematical framework to empirical data is still challenging, precluding a larger adoption of the theoretical tools developed by empiricists. This package provides a complete toolbox for modelling interaction effects between species, and calculate fitness and niche differences. The functions are flexible, may accept covariates, and different fitting algorithms can be used. A full description of the underlying methods is available in Garc
How to cite:
David Garcia-Callejas (2021). cxr: A Toolbox for Modelling Species Coexistence in R. R package version 1.1.1, https://cran.r-project.org/web/packages/cxr. Accessed 13 Apr. 2025.
Previous versions and publish date:
1.0.0 (2021-04-16 11:20)
Other packages that cited cxr R package
View cxr citation profile
Other R packages that cxr depends, imports, suggests or enhances
Complete documentation for cxr
Functions, R codes and Examples using the cxr R package
Some associated functions: BH_er_lambdacov_global_effectcov_global_responsecov_global . BH_er_lambdacov_none_effectcov_none_responsecov_none . BH_pm_alpha_global_lambdacov_none_alphacov_none . BH_pm_alpha_none_lambdacov_none_alphacov_none . BH_pm_alpha_pairwise_lambdacov_global_alphacov_global . BH_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise . BH_pm_alpha_pairwise_lambdacov_none_alphacov_none . BH_project_alpha_global_lambdacov_none_alphacov_none . BH_project_alpha_none_lambdacov_none_alphacov_none . BH_project_alpha_pairwise_lambdacov_global_alphacov_global . BH_project_alpha_pairwise_lambdacov_global_alphacov_pairwise . BH_project_alpha_pairwise_lambdacov_none_alphacov_none . LV_er_lambdacov_global_effectcov_global_responsecov_global . LV_er_lambdacov_none_effectcov_none_responsecov_none . LV_pm_alpha_global_lambdacov_none_alphacov_none . LV_pm_alpha_none_lambdacov_none_alphacov_none . LV_pm_alpha_pairwise_lambdacov_global_alphacov_global . LV_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise . LV_pm_alpha_pairwise_lambdacov_none_alphacov_none . LV_project_alpha_global_lambdacov_none_alphacov_none . LV_project_alpha_none_lambdacov_none_alphacov_none . LV_project_alpha_pairwise_lambdacov_global_alphacov_global . LV_project_alpha_pairwise_lambdacov_global_alphacov_pairwise . LV_project_alpha_pairwise_lambdacov_none_alphacov_none . LW_er_lambdacov_global_effectcov_global_responsecov_global . LW_er_lambdacov_none_effectcov_none_responsecov_none . LW_pm_alpha_global_lambdacov_none_alphacov_none . LW_pm_alpha_none_lambdacov_none_alphacov_none . LW_pm_alpha_pairwise_lambdacov_global_alphacov_global . LW_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise . LW_pm_alpha_pairwise_lambdacov_none_alphacov_none . LW_project_alpha_global_lambdacov_none_alphacov_none . LW_project_alpha_none_lambdacov_none_alphacov_none . LW_project_alpha_pairwise_lambdacov_global_alphacov_global . LW_project_alpha_pairwise_lambdacov_global_alphacov_pairwise . LW_project_alpha_pairwise_lambdacov_none_alphacov_none . RK_er_lambdacov_global_effectcov_global_responsecov_global . RK_er_lambdacov_none_effectcov_none_responsecov_none . RK_pm_alpha_global_lambdacov_none_alphacov_none . RK_pm_alpha_none_lambdacov_none_alphacov_none . RK_pm_alpha_pairwise_lambdacov_global_alphacov_global . RK_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise . RK_pm_alpha_pairwise_lambdacov_none_alphacov_none . RK_project_alpha_global_lambdacov_none_alphacov_none . RK_project_alpha_none_lambdacov_none_alphacov_none . RK_project_alpha_pairwise_lambdacov_global_alphacov_global . RK_project_alpha_pairwise_lambdacov_global_alphacov_pairwise . RK_project_alpha_pairwise_lambdacov_none_alphacov_none . abundance . abundance_projection . avg_fitness_diff . build_param . calculate_densities . competitive_ability . cxr-package . cxr_er_bootstrap . cxr_er_fit . cxr_generate_test_data . cxr_pm_bootstrap . cxr_pm_fit . cxr_pm_multifit . densities_to_df . fill_demography_matrix . fill_dispersal_matrix . fill_transition_matrix . fitness_ratio . generate_vital_rate_coefs . glm_example_coefs . metapopulation_example_param . neigh_list . niche_overlap . salinity_list . spatial_sampling . species_fitness . species_rates . summary.cxr_er_fit . summary.cxr_pm_fit . summary.cxr_pm_multifit . vec_permutation_matrices . vital_rate . 
Some associated R codes: BH_competitive_ability.R . BH_demographic_ratio.R . BH_er_lambdacov_global_effectcov_global_responsecov_global.R . BH_er_lambdacov_none_effectcov_none_responsecov_none.R . BH_pm_alpha_global_lambdacov_none_alphacov_none.R . BH_pm_alpha_none_lambdacov_none_alphacov_none.R . BH_pm_alpha_pairwise_lambdacov_global_alphacov_global.R . BH_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . BH_pm_alpha_pairwise_lambdacov_none_alphacov_none.R . BH_project_alpha_global_lambdacov_none_alphacov_none.R . BH_project_alpha_none_lambdacov_none_alphacov_none.R . BH_project_alpha_pairwise_lambdacov_global_alphacov_global.R . BH_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . BH_project_alpha_pairwise_lambdacov_none_alphacov_none.R . BH_species_fitness.R . LV_competitive_ability.R . LV_demographic_ratio.R . LV_er_lambdacov_global_effectcov_global_responsecov_global.R . LV_er_lambdacov_none_effectcov_none_responsecov_none.R . LV_pm_alpha_global_lambdacov_none_alphacov_none.R . LV_pm_alpha_none_lambdacov_none_alphacov_none.R . LV_pm_alpha_pairwise_lambdacov_global_alphacov_global.R . LV_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . LV_pm_alpha_pairwise_lambdacov_none_alphacov_none.R . LV_project_alpha_global_lambdacov_none_alphacov_none.R . LV_project_alpha_none_lambdacov_none_alphacov_none.R . LV_project_alpha_pairwise_lambdacov_global_alphacov_global.R . LV_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . LV_project_alpha_pairwise_lambdacov_none_alphacov_none.R . LV_species_fitness.R . LW_competitive_ability.R . LW_demographic_ratio.R . LW_er_lambdacov_global_effectcov_global_responsecov_global.R . LW_er_lambdacov_none_effectcov_none_responsecov_none.R . LW_pm_alpha_global_lambdacov_none_alphacov_none.R . LW_pm_alpha_none_lambdacov_none_alphacov_none.R . LW_pm_alpha_pairwise_lambdacov_global_alphacov_global.R . LW_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . LW_pm_alpha_pairwise_lambdacov_none_alphacov_none.R . LW_project_alpha_global_lambdacov_none_alphacov_none.R . LW_project_alpha_none_lambdacov_none_alphacov_none.R . LW_project_alpha_pairwise_lambdacov_global_alphacov_global.R . LW_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . LW_project_alpha_pairwise_lambdacov_none_alphacov_none.R . LW_species_fitness.R . RK_competitive_ability.R . RK_demographic_ratio.R . RK_er_lambdacov_global_effectcov_global_responsecov_global.R . RK_er_lambdacov_none_effectcov_none_responsecov_none.R . RK_pm_alpha_global_lambdacov_none_alphacov_none.R . RK_pm_alpha_none_lambdacov_none_alphacov_none.R . RK_pm_alpha_pairwise_lambdacov_global_alphacov_global.R . RK_pm_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . RK_pm_alpha_pairwise_lambdacov_none_alphacov_none.R . RK_project_alpha_global_lambdacov_none_alphacov_none.R . RK_project_alpha_none_lambdacov_none_alphacov_none.R . RK_project_alpha_pairwise_lambdacov_global_alphacov_global.R . RK_project_alpha_pairwise_lambdacov_global_alphacov_pairwise.R . RK_project_alpha_pairwise_lambdacov_none_alphacov_none.R . RK_species_fitness.R . abundance.R . abundance_projection.R . avg_fitness_diff.R . build_param.R . calculate_densities.R . competitive_ability.R . cxr-package.R . cxr_check_initial_values.R . cxr_check_input_data.R . cxr_check_input_er.R . cxr_check_method_boundaries.R . cxr_check_pm_input.R . cxr_competitive_response.R . cxr_demographic_ratio.R . cxr_er_bootstrap.R . cxr_er_fit.R . cxr_er_model_template.R . cxr_generate_test_data.R . cxr_get_init_params.R . cxr_get_model_bounds.R . cxr_init_er_params.R . cxr_model_template.R . cxr_pm_bootstrap.R . cxr_pm_fit.R . cxr_pm_model_template.R . cxr_pm_multifit.R . cxr_retrieve_er_params.R . cxr_retrieve_params.R . cxr_return_init_length.R . cxr_sort_params.R . cxr_structural_fitness_diff.R . densities_to_df.R . fill_demography_matrix.R . fill_dispersal_matrix.R . fill_transition_matrix.R . fitness_ratio.R . generate_vital_rate_coefs.R . get_densities.R . glm_example_coefs.R . metapopulation_example_param.R . neigh_list.R . niche_overlap.R . niche_overlap_MCT.R . niche_overlap_SA.R . salinity_list.R . spatial_sampling.R . species_fitness.R . species_rates.R . summary.R . vec_permutation_matrices.R . vital_rate.R .  Full cxr package functions and examples
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