Package index

1 Data variability and exploration

  Diagnostics and filtering

diagnose_cube()

Diagnose data quality of a processed data cube

filter_cube()

Filter a processed data cube using diagnostic rules

  Sensitivity analysis

cross_validate_cube()

Leave-one-out cross-validation for data cubes

2 Indicator uncertainty and interpretation

  Bootstrapping and confidence interval calculation

bootstrap_cube()

Perform bootstrapping over a data cube for a calculated statistic

calculate_bootstrap_ci()

Calculate confidence intervals from bootstrap results

  Effect classification

add_effect_classification()

Add effect classifications to a dataframe by comparing the confidence intervals with a reference and thresholds

3 Diagnostic utilities

  Diagnostic rule groups

basic_cube_rules()

Basic diagnostic rules for data cubes

  Diagnostic rules

rule_obs_min_records()

Minimum number of records diagnostic rule

rule_obs_min_total()

Minimum total number of observations diagnostic rule

rule_spatial_max_uncertainty()

Maximal coordinate uncertainty diagnostic rule

rule_spatial_min_cells()

Spatial minimum grid cells diagnostic rule

rule_spatial_miss_uncertainty()

Missing coordinate uncertainty diagnostic rule

rule_taxon_min_taxa()

Taxonomic minimum taxa diagnostic rule

rule_temporal_min_years()

Temporal minimum years diagnostic rule

rule_temporal_missing_years()

Temporal gaps diagnostic rule

  Diagnostic methods

plot(<cube_diagnostics>)

Plot cube diagnostics

print(<cube_diagnostics>)

Print cube diagnostics

summary(<cube_diagnostics>)

Summarise cube diagnostics

4 Bootstrap utilities

  Bootstrap helpers

boot_list_to_dataframe()

Convert a list of 'boot' objects to a tidy dataframe

bootstrap_cube_raw()

Perform bootstrapping over a dataframe for a calculated statistic

calculate_acceleration()

Calculate acceleration for a statistic in a dataframe

calculate_boot_ci_from_boot()

Calculate confidence intervals from a 'boot' object

resolve_bootstrap_method()

Resolve bootstrap method including use of the boot package

  Bootstrap interval types

basic_ci()

Calculate basic bootstrap confidence interval

bca_ci()

Calculate Bias-Corrected and Accelerated (BCa) bootstrap confidence interval

norm_ci()

Calculate normal bootstrap confidence interval

perc_ci()

Calculate percentile bootstrap confidence interval