ecocomDP1.3.2 package

Tools to Create, Use, and Convert ecocomDP Data

create_eml

Create EML metadata

annotation_dictionary

Annotations of published data

calc_geo_extent_bounding_box_m2

Calculate geo_extent_bounding_box_m2 for the dataset_summary table

calc_length_of_survey_years

Calculate length_of_survey_years for the dataset_summary table

calc_number_of_years_sampled

Calculate number_of_years_sampled for the dataset_summary table

calc_std_dev_interval_betw_years

Calculate std_dev_interval_betw_years for the dataset_summary table

convert_to_dwca

Convert a dataset to the Darwin Core Archive format

create_dataset_summary

Create the dataset_summary table

create_location_ancillary

Create the location_ancillary table

create_location

Create the location table

create_observation_ancillary

Create the observation_ancillary table

create_observation

Create the observation table

create_taxon_ancillary

Create the taxon_ancillary table

create_taxon

Create the taxon table

create_variable_mapping

Create the variable_mapping table

flatten_data

Flatten a dataset

plot_sample_space_time

Plot dates and times samples were collected or observations were made

plot_sites

Plot sites on US map

plot_taxa_abund

Plot mean taxa abundances per 'observation_id'

plot_taxa_accum_sites

Plot taxa accumulation by site accumulation

plot_taxa_accum_time

Plot taxa accumulation through time

plot_taxa_diversity

Plot diversity (taxa richness) through time

plot_taxa_occur_freq

Plot taxon occurrence frequencies

plot_taxa_rank

Plot taxa ranks

plot_taxa_sample_time

Plot dates and times samples were taken (DEPRECATED)

plot_taxa_shared_sites

Plot number of unique taxa shared across sites

read_data

Read published data

save_data

Save a dataset

search_data

Search published data

validate_data

Validate tables against the model

write_tables

Write tables to file

Work with the Ecological Community Data Design Pattern. 'ecocomDP' is a flexible data model for harmonizing ecological community surveys, in a research question agnostic format, from source data published across repositories, and with methods that keep the derived data up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.

  • Maintainer: Colin Smith
  • License: MIT + file LICENSE
  • Last published: 2024-08-16