Man pages for cxr
A Toolbox for Modelling Species Coexistence in R

abundanceAbundance measurements
abundance_projectionTitle Project abundances from population dynamics models
avg_fitness_diffAverage fitness differences
BH_er_lambdacov_global_effectcov_global_responsecov_globalEffect response Beverton-Holt model with covariate effects on...
BH_er_lambdacov_none_effectcov_none_responsecov_noneEffect response model without covariate effects
BH_pm_alpha_global_lambdacov_none_alphacov_noneBeverton-Holt model with a global alpha and no covariate...
BH_pm_alpha_none_lambdacov_none_alphacov_noneBeverton-Holt model with no alphas and no covariate effects
BH_pm_alpha_pairwise_lambdacov_global_alphacov_globalBeverton-Holt model with pairwise alphas and global covariate...
BH_pm_alpha_pairwise_lambdacov_global_alphacov_pairwiseBeverton-Holt model with pairwise alphas, covariate effects...
BH_pm_alpha_pairwise_lambdacov_none_alphacov_noneBeverton-Holt model with pairwise alphas and no covariate...
BH_project_alpha_global_lambdacov_none_alphacov_noneBeverton-Holt model for projecting abundances, with a global...
BH_project_alpha_none_lambdacov_none_alphacov_noneBeverton-Holt model for projecting abundances, with no alpha...
BH_project_alpha_pairwise_lambdacov_global_alphacov_globalBeverton-Holt model for projecting abundances, with specific...
BH_project_alpha_pairwise_lambdacov_global_alphacov_pairwiseBeverton-Holt model for projecting abundances, with specific...
BH_project_alpha_pairwise_lambdacov_none_alphacov_noneBeverton-Holt model for projecting abundances, with specific...
competitive_abilityCompetitive ability among pairs of species
cxrcxr
cxr_er_bootstrapstandard error estimates for effect and response parameters
cxr_er_fitGeneral optimization for effect-response models
cxr_generate_test_dataGenerate simulated interaction data
cxr_pm_bootstrapStandard error estimates for model parameters
cxr_pm_fitGeneral optimization for population models
cxr_pm_multifitMulti-species parameter optimization
fitness_ratioFitness ratio among two or more species
LV_er_lambdacov_global_effectcov_global_responsecov_globalEffect response Lotka-Volterra model with covariate effects...
LV_er_lambdacov_none_effectcov_none_responsecov_noneEffect response Lotka-Volterra model without covariate...
LV_pm_alpha_global_lambdacov_none_alphacov_noneLotka-Volterra model with a global alpha and no covariate...
LV_pm_alpha_none_lambdacov_none_alphacov_noneLotka-Volterra model with no alphas and no covariate effects
LV_pm_alpha_pairwise_lambdacov_global_alphacov_globalLotka-Volterra model with pairwise alphas and global...
LV_pm_alpha_pairwise_lambdacov_global_alphacov_pairwiseLotka-Volterra model with pairwise alphas, covariate effects...
LV_pm_alpha_pairwise_lambdacov_none_alphacov_noneLotka-Volterra model with pairwise alphas and no covariate...
LV_project_alpha_global_lambdacov_none_alphacov_noneLotka-Volterra model for projecting abundances, with a global...
LV_project_alpha_none_lambdacov_none_alphacov_noneModel for projecting abundances, with no alpha and no...
LV_project_alpha_pairwise_lambdacov_global_alphacov_globalLotka-Volterra model for projecting abundances, with specific...
LV_project_alpha_pairwise_lambdacov_global_alphacov_pairwiseLotka-Volterra model for projecting abundances, with specific...
LV_project_alpha_pairwise_lambdacov_none_alphacov_noneLotka-Volterra model for projecting abundances, with specific...
LW_er_lambdacov_global_effectcov_global_responsecov_globalEffect response Law-Watkinson model with covariate effects on...
LW_er_lambdacov_none_effectcov_none_responsecov_noneEffect response Law-Watkinson model without covariate effects
LW_pm_alpha_global_lambdacov_none_alphacov_noneLaw-Watkinson model with a global alpha and no covariate...
LW_pm_alpha_none_lambdacov_none_alphacov_noneLaw-Watkinson model with no alphas and no covariate effects
LW_pm_alpha_pairwise_lambdacov_global_alphacov_globalLaw-Watkinson model with pairwise alphas and global covariate...
LW_pm_alpha_pairwise_lambdacov_global_alphacov_pairwiseLaw-Watkinson model with pairwise alphas, covariate effects...
LW_pm_alpha_pairwise_lambdacov_none_alphacov_noneLaw-Watkinson model with pairwise alphas and no covariate...
LW_project_alpha_global_lambdacov_none_alphacov_noneLaw-Watkinson model for projecting abundances, with a global...
LW_project_alpha_none_lambdacov_none_alphacov_noneModel for projecting abundances, with no alpha and no...
LW_project_alpha_pairwise_lambdacov_global_alphacov_globalLaw-Watkinson model for projecting abundances, with specific...
LW_project_alpha_pairwise_lambdacov_global_alphacov_pairwiseLaw-Watkinson model for projecting abundances, with specific...
LW_project_alpha_pairwise_lambdacov_none_alphacov_noneLaw-Watkinson model for projecting abundances, with specific...
neigh_listneighbours and fitness observations
niche_overlapNiche overlap between two species
RK_er_lambdacov_global_effectcov_global_responsecov_globalEffect response Beverton-Holt model with covariate effects on...
RK_er_lambdacov_none_effectcov_none_responsecov_noneEffect response Ricker model without covariate effects
RK_pm_alpha_global_lambdacov_none_alphacov_noneRicker model with a global alpha and no covariate effects
RK_pm_alpha_none_lambdacov_none_alphacov_noneRicker model with no alphas and no covariate effects
RK_pm_alpha_pairwise_lambdacov_global_alphacov_globalRicker model with pairwise alphas and global covariate...
RK_pm_alpha_pairwise_lambdacov_global_alphacov_pairwiseRicker model with pairwise alphas, covariate effects on...
RK_pm_alpha_pairwise_lambdacov_none_alphacov_noneRicker model with pairwise alphas and no covariate effects
RK_project_alpha_global_lambdacov_none_alphacov_noneRicker model for projecting abundances, with a global alpha...
RK_project_alpha_none_lambdacov_none_alphacov_noneModel for projecting abundances, with no alpha and no...
RK_project_alpha_pairwise_lambdacov_global_alphacov_globalRicker model for projecting abundances, with specific alpha...
RK_project_alpha_pairwise_lambdacov_global_alphacov_pairwiseRicker model for projecting abundances, with specific alpha...
RK_project_alpha_pairwise_lambdacov_none_alphacov_noneRicker model for projecting abundances, with specific alpha...
salinity_listSalinity measurements
spatial_samplingspatial arrangement of the observations
species_fitnessFitness of a species
species_ratesSpecies germination and survival rates
summary.cxr_er_fitCXR summary method for effect response model fits
summary.cxr_pm_fitCXR summary method for population model fits
summary.cxr_pm_multifitCXR summary method for multispecies fits
cxr documentation built on April 16, 2021, 5:07 p.m.