General Biodiversity Indicators for Biodiversity Data Cubes

Documentation for package ‘b3gbi’ version 1.1.3

Help Pages

-- A --

ab_rarity_map	Calculate Rarity Over Time or Space
ab_rarity_ts	Calculate Rarity Over Time or Space
add_ci	Add Confidence Intervals to an Indicator Object
area_rarity_map	Calculate Rarity Over Time or Space
area_rarity_ts	Calculate Rarity Over Time or Space
available_indicators	Indicators Available for Use in the Package

-- C --

calc_ci	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.ab_rarity	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.area_rarity	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.default	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.hill0	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.hill1	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.hill2	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.newness	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.occ_density	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.pielou_evenness	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.spec_occ	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.spec_range	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.spec_richness_density	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.total_occ	Calculate Confidence Intervals for a Biodiversity Indicator
calc_ci.williams_evenness	Calculate Confidence Intervals for a Biodiversity Indicator
calc_map	Calculate Biodiversity Indicators Over Space
calc_map.ab_rarity	Calculate Biodiversity Indicators Over Space
calc_map.area_rarity	Calculate Biodiversity Indicators Over Space
calc_map.completeness	Calculate Biodiversity Indicators Over Space
calc_map.hill0	Calculate Biodiversity Indicators Over Space
calc_map.hill1	Calculate Biodiversity Indicators Over Space
calc_map.hill2	Calculate Biodiversity Indicators Over Space
calc_map.newness	Calculate Biodiversity Indicators Over Space
calc_map.obs_richness	Calculate Biodiversity Indicators Over Space
calc_map.occ_density	Calculate Biodiversity Indicators Over Space
calc_map.pielou_evenness	Calculate Biodiversity Indicators Over Space
calc_map.relative_occupancy	Calculate Biodiversity Indicators Over Space
calc_map.spec_occ	Calculate Biodiversity Indicators Over Space
calc_map.spec_range	Calculate Biodiversity Indicators Over Space
calc_map.spec_richness_density	Calculate Biodiversity Indicators Over Space
calc_map.tax_distinct	Calculate Biodiversity Indicators Over Space
calc_map.total_occ	Calculate Biodiversity Indicators Over Space
calc_map.williams_evenness	Calculate Biodiversity Indicators Over Space
calc_ts	Calculate Biodiversity Indicators Over Time
calc_ts.ab_rarity	Calculate Biodiversity Indicators Over Time
calc_ts.area_rarity	Calculate Biodiversity Indicators Over Time
calc_ts.completeness	Calculate Biodiversity Indicators Over Time
calc_ts.cum_richness	Calculate Biodiversity Indicators Over Time
calc_ts.default	Calculate Biodiversity Indicators Over Time
calc_ts.hill0	Calculate Biodiversity Indicators Over Time
calc_ts.hill1	Calculate Biodiversity Indicators Over Time
calc_ts.hill2	Calculate Biodiversity Indicators Over Time
calc_ts.newness	Calculate Biodiversity Indicators Over Time
calc_ts.obs_richness	Calculate Biodiversity Indicators Over Time
calc_ts.occ_density	Calculate Biodiversity Indicators Over Time
calc_ts.occ_turnover	Calculate Biodiversity Indicators Over Time
calc_ts.pielou_evenness	Calculate Biodiversity Indicators Over Time
calc_ts.relative_occupancy	Calculate Biodiversity Indicators Over Time
calc_ts.spec_occ	Calculate Biodiversity Indicators Over Time
calc_ts.spec_range	Calculate Biodiversity Indicators Over Time
calc_ts.spec_richness_density	Calculate Biodiversity Indicators Over Time
calc_ts.tax_distinct	Calculate Biodiversity Indicators Over Time
calc_ts.total_occ	Calculate Biodiversity Indicators Over Time
calc_ts.williams_evenness	Calculate Biodiversity Indicators Over Time
completeness_map	Calculate Completeness (Sample Coverage) Over Space or Time
completeness_ts	Calculate Completeness (Sample Coverage) Over Space or Time
compute_indicator_workflow	Calculate Biodiversity Indicators Over Space or Time
convert_eqdgc_latlong	Convert extended quarter-degree grid cell codes to latitude and longitude
create_sf_from_utm	Create an sf object from UTM coordinates, handling multiple zones correctly.
cum_richness_ts	Calculate Cumulative Species Richness

-- E --

example_cube_1	Cube of GBIF Mammal Occurrences in Denmark
example_indicator_map1	Map of Observed Species Richness for Mammals in Denmark
example_indicator_ts1	Time Series of Observed Species Richness for Mammals in Denmark
example_indicator_ts2	Time Series of Cumulative Species Richness for Bryophytes in South Africa

-- G --

get_observed_years

Extract Years With Observations

-- H --

hill0_map	Calculate Estimated Hill Diversity Over Space or Time
hill0_ts	Calculate Estimated Hill Diversity Over Space or Time
hill1_map	Calculate Estimated Hill Diversity Over Space or Time
hill1_ts	Calculate Estimated Hill Diversity Over Space or Time
hill2_map	Calculate Estimated Hill Diversity Over Space or Time
hill2_ts	Calculate Estimated Hill Diversity Over Space or Time

-- L --

list_species

Extract Species Names.

-- M --

mgrs_to_latlong_bbox

Create a Longitude/Latitude Bounding Box from MGRS Data

-- N --

newness_map	Calculate Mean Year of Occurrence Over Time or Space
newness_ts	Calculate Mean Year of Occurrence Over Time or Space

-- O --

obs_richness_map	Calculate Observed Species Richness Over Space or Time
obs_richness_ts	Calculate Observed Species Richness Over Space or Time
occ_density_map	Calculate Occurrence Density Over Space or Time
occ_density_ts	Calculate Occurrence Density Over Space or Time
occ_turnover_ts	Calculate Occupancy Turnover

-- P --

pielou_evenness_map	Calculate Evenness Over Time or Space
pielou_evenness_ts	Calculate Evenness Over Time or Space
plot_map	Plot Biodiversity Indicator Map
plot_mv	Plot Interactive Biodiversity Indicator Map
plot_species_map	Plot Occurrence Map or Range Map of Individual Species
plot_species_ts	Plot Occurrence Trends or Range Size Trends for Individual Species
plot_ts	Plot Biodiversity Indicator Trend
prepare_indicator_bootstrap	Prepare bootstrap and confidence interval parameters for an indicator
print.available_indicators	Print Available Indicators
print.indicator_map	Print an Indicator Map Object
print.indicator_ts	Print an Indicator Time Series Object
print.processed_cube	Print a Processed Data Cube Object
print.processed_cube_dsinfo	Print a Processed Data Cube Object with Dataset Information
print.sim_cube	Print a Simulated Data Cube Object
process_cube	Process GBIF Data Cubes

-- R --

relative_occupancy_map	Calculate Species Relative Occupancy Over Space or Time
relative_occupancy_ts	Calculate Species Relative Occupancy Over Space or Time
replace_na	Replace NA Values in Indicator Objects

-- S --

spec_occ_map	Calculate Species Occurrences Over Space or Time
spec_occ_ts	Calculate Species Occurrences Over Space or Time
spec_range_map	Calculate Species Ranges Over Space or Time
spec_range_ts	Calculate Species Ranges Over Space or Time
spec_richness_density_map	Calculate Species Richness Density Over Space or Time
spec_richness_density_ts	Calculate Species Richness Density Over Space or Time
sum_by_taxon	Sum Observations by Taxonomic Rank

-- T --

tax_distinct_map	Calculate Taxonomic Distinctness Over Space or Time
tax_distinct_ts	Calculate Taxonomic Distinctness Over Space or Time
total_occ_map	Calculate Total Occurrences Over Space or Time
total_occ_ts	Calculate Total Occurrences Over Space or Time

-- W --

williams_evenness_map	Calculate Evenness Over Time or Space
williams_evenness_ts	Calculate Evenness Over Time or Space