A Toolbox for Modelling Species Coexistence in R
Ricker model with a global alpha and no covariate effects
Ricker model with no alphas and no covariate effects
Ricker model with pairwise alphas and global covariate effects on lamb...
Ricker model with pairwise alphas, covariate effects on lambda, and pa...
Ricker model with pairwise alphas and no covariate effects
Ricker model for projecting abundances, with a global alpha and no cov...
Model for projecting abundances, with no alpha and no covariate effect...
Ricker model for projecting abundances, with specific alpha values and...
Ricker model for projecting abundances, with specific alpha values and...
Ricker model for projecting abundances, with specific alpha values and...
Law-Watkinson model for projecting abundances, with specific alpha val...
Law-Watkinson model for projecting abundances, with specific alpha val...
Law-Watkinson model for projecting abundances, with specific alpha val...
Niche overlap between two species
Effect response Beverton-Holt model with covariate effects on lambda, ...
Effect response Ricker model without covariate effects
Average fitness differences
Project abundances from population dynamics models
Beverton-Holt model for projecting abundances, with specific alpha val...
Beverton-Holt model for projecting abundances, with specific alpha val...
Build param structure
Obtain species densities from transition matrices
Effect response Lotka-Volterra model without covariate effects
Lotka-Volterra model with a global alpha and no covariate effects
Lotka-Volterra model with no alphas and no covariate effects
Lotka-Volterra model with pairwise alphas and global covariate effects...
Lotka-Volterra model with pairwise alphas, covariate effects on lambda...
Lotka-Volterra model with pairwise alphas and no covariate effects
Lotka-Volterra model for projecting abundances, with a global alpha an...
Model for projecting abundances, with no alpha and no covariate effect...
Lotka-Volterra model for projecting abundances, with specific alpha va...
Lotka-Volterra model for projecting abundances, with specific alpha va...
Lotka-Volterra model for projecting abundances, with specific alpha va...
Effect response Law-Watkinson model with covariate effects on lambda, ...
Effect response Law-Watkinson model without covariate effects
Law-Watkinson model with a global alpha and no covariate effects
Law-Watkinson model with no alphas and no covariate effects
Law-Watkinson model with pairwise alphas and global covariate effects ...
Law-Watkinson model with pairwise alphas, covariate effects on lambda,...
Law-Watkinson model with pairwise alphas and no covariate effects
Law-Watkinson model for projecting abundances, with a global alpha and...
Model for projecting abundances, with no alpha and no covariate effect...
Beverton-Holt model with pairwise alphas and no covariate effects
Beverton-Holt model for projecting abundances, with a global alpha and...
Beverton-Holt model for projecting abundances, with no alpha and no co...
Beverton-Holt model for projecting abundances, with specific alpha val...
Effect response Beverton-Holt model with covariate effects on lambda, ...
Effect response model without covariate effects
Beverton-Holt model with a global alpha and no covariate effects
Beverton-Holt model with no alphas and no covariate effects
Beverton-Holt model with pairwise alphas and global covariate effects ...
Beverton-Holt model with pairwise alphas, covariate effects on lambda,...
Competitive ability among pairs of species
cxr: A Toolbox for Modelling Species Coexistence in R
standard error estimates for effect and response parameters
General optimization for effect-response models
Generate simulated interaction data
Effect response Lotka-Volterra model with covariate effects on lambda,...
Standard error estimates for model parameters
General optimization for population models
Multi-species parameter optimization
Converts a densities list to a tidy dataframe
Fill the vec-permutation demography matrix
Fill the vec-permutation dispersal matrix
Fill a transition matrix
Fitness ratio among two or more species
Generate coefficients for obtaining vital rates
Fitness of a species
CXR summary method for effect response model fits
CXR summary method for population model fits
CXR summary method for multispecies fits
Generate templates for dispersal, demography, and permutation matrices
Vital rate calculation
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 García-Callejas, D., Godoy, O., and Bartomeus, I. (2020) <doi:10.1111/2041-210X.13443>. Furthermore, the package provides a series of functions to calculate dynamics for stage-structured populations across sites.