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_pkgdown.yml
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_pkgdown.yml
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url: https://evolecolgroup.github.io/tidysdm/
template:
bootstrap: 5
development:
mode: auto
reference:
- title: "Data preparation"
desc: "Functions for sampling background/pseudo-absences points and thinning the data."
contents:
- sample_background
- sample_background_time
- sample_pseudoabs
- sample_pseudoabs_time
- thin_by_cell
- thin_by_cell_time
- thin_by_dist
- thin_by_dist_time
- title: "Choice of predictor variables"
desc: "Functions for removing collinearity and visualising the distribution of predictors."
contents:
- filter_collinear
- plot_pres_vs_bg
- geom_split_violin
- dist_pres_vs_bg
- title: "Recipes"
desc: "Functions for recipes with spatial SDM data (additional steps can be added with standard `recipes` functions)."
contents:
- recipe.sf
- spatial_recipe
- check_sdm_presence
- title: "Models specification"
desc: "Predefined model specifications (custom models can be added with standard `parsnip` model specifications)."
contents:
- sdm_spec_glm
- sdm_spec_gam
- gam_formula
- sdm_spec_rand_forest
- sdm_spec_boost_tree
- sdm_spec_maxent
- maxent
- regularization_multiplier
- feature_classes
- title: "Data splitting"
desc: "Functions for splitting the data into folds (in additiona to standard `spatialsample` functions."
contents:
- spatial_initial_split
- blockcv2rsample
- check_splits_balance
- autoplot.spatial_initial_split
- grid_offset
- grid_cellsize
- title: "Metrics"
desc: "Specialised metrics for SDM, and methods of metrics from `yardstick` adapted to work on `sf` objects"
contents:
- sdm_metric_set
- optim_thresh
- boyce_cont
- kap_max
- tss_max
- tss
- prob_metrics_sf
- title: "Ensemble"
desc: "Functions for creating an ensemble selecting the best set of
parameters for each model."
contents:
- simple_ensemble
- autoplot.simple_ensemble
- repeat_ensemble
- add_member
- add_repeat
- collect_metrics.simple_ensemble
- collect_metrics.repeat_ensemble
- control_ensemble_grid
- control_ensemble_resamples
- control_ensemble_bayes
- explain_tidysdm
- title: "Project SDM to present, past and future"
desc: "Functions for making predictions."
contents:
- has_keyword("predict")
- title: "Managing extrapolation"
desc: "Functions for managing extrapolation."
contents:
- has_keyword("extrapolation")
- title: "Other"
desc: "Additional helpful functions."
contents:
- niche_overlap
- km2m
- y2d
- filter_high_cor
- title: "Example data"
desc: "Example datasets and simple models used in the documentation"
contents:
- horses
- lacerta
- lacertidae_background
- lacerta_ensemble
- lacerta_rep_ens