Package: ecocomDP 1.3.2

Colin Smith

ecocomDP: Tools to Create, Use, and Convert ecocomDP Data

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>.

Authors:Colin Smith [aut, cre, cph], Eric Sokol [aut], Margaret O'Brien [aut], Matt Bitters [ctb], Melissa Chen [ctb], Savannah Gonzales [ctb], Matt Helmus [ctb], Brendan Hobart [ctb], Ruvi Jaimes [ctb], Lara Janson [ctb], Marta Jarzyna [ctb], Michael Just [ctb], Daijiang Li [ctb], Wynne Moss [ctb], Kari Norman [ctb], Stephanie Parker [ctb], Rafael Rangel [ctb], Natalie Robinson [ctb], Thilina Surasinghe [ctb], Kyle Zollo-Venecek [ctb]

ecocomDP_1.3.2.tar.gz
ecocomDP_1.3.2.zip(r-4.5)ecocomDP_1.3.2.zip(r-4.4)ecocomDP_1.3.2.zip(r-4.3)
ecocomDP_1.3.2.tgz(r-4.4-any)ecocomDP_1.3.2.tgz(r-4.3-any)
ecocomDP_1.3.2.tar.gz(r-4.5-noble)ecocomDP_1.3.2.tar.gz(r-4.4-noble)
ecocomDP_1.3.2.tgz(r-4.4-emscripten)ecocomDP_1.3.2.tgz(r-4.3-emscripten)
ecocomDP.pdf |ecocomDP.html✨
ecocomDP/json (API)
NEWS

# Install 'ecocomDP' in R:
install.packages('ecocomDP', repos = c('https://ediorg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ediorg/ecocomdp/issues

Datasets:
  • ants_L0_flat - Joined and flat version of EDI data package knb-lter-hfr.118.33
  • ants_L1 - The ecocomDP (L1) version of EDI data package knb-lter-hfr.118.33

On CRAN:

31 exports 32 stars 2.93 score 83 dependencies 73 scripts 401 downloads

Last updated 1 months agofrom:7cd8ff51ee. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 19 2024
R-4.5-winNOTEAug 19 2024
R-4.5-linuxNOTEAug 19 2024
R-4.4-winNOTEAug 19 2024
R-4.4-macNOTEAug 19 2024
R-4.3-winNOTEAug 19 2024
R-4.3-macNOTEAug 19 2024

Exports:annotation_dictionarycalc_geo_extent_bounding_box_m2calc_length_of_survey_yearscalc_number_of_years_sampledcalc_std_dev_interval_betw_yearsconvert_to_dwcacreate_dataset_summarycreate_emlcreate_locationcreate_location_ancillarycreate_observationcreate_observation_ancillarycreate_taxoncreate_taxon_ancillarycreate_variable_mappingflatten_dataplot_sample_space_timeplot_sitesplot_taxa_abundplot_taxa_accum_sitesplot_taxa_accum_timeplot_taxa_diversityplot_taxa_occur_freqplot_taxa_rankplot_taxa_sample_timeplot_taxa_shared_sitesread_datasave_datasearch_datavalidate_datawrite_tables

Dependencies:askpassbase64encbslibcachemclicolorspacecpp11curldata.tabledigestdownloaderdplyrEMLemldevaluatefansifarverfastmapfontawesomefsgenericsgeosphereggplot2gluegtablehighrhtmltoolshttrisobandjqrjquerylibjsonldjsonliteknitrlabelinglatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellneonOSneonUtilitiesnlmeopensslpbapplypillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesspstringistringrsystibbletidyrtidyselecttimechangetinytexutf8uuidV8vctrsviridisLitewithrxfunxml2yaml

Convert ecocomDP Data to Another Model Format

Rendered fromconvert.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2023-06-12
Started: 2021-05-25

Create ecocomDP Data

Rendered fromcreate.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2023-06-12
Started: 2021-04-12

ecocomDP Model Overview

Rendered frommodel_overview.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2023-06-12
Started: 2021-10-16

Shared Practices for Creating ecocomDP Data

Rendered fromshared_practices_create.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2023-06-19
Started: 2021-10-16

Use ecocomDP Data

Rendered fromuse.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2023-06-12
Started: 2021-04-12

Readme and manuals

Help Manual

Help pageTopics
Annotations of published dataannotation_dictionary
Joined and flat version of EDI data package knb-lter-hfr.118.33ants_L0_flat
The ecocomDP (L1) version of EDI data package knb-lter-hfr.118.33ants_L1
Calculate geo_extent_bounding_box_m2 for the dataset_summary tablecalc_geo_extent_bounding_box_m2
Calculate length_of_survey_years for the dataset_summary tablecalc_length_of_survey_years
Calculate number_of_years_sampled for the dataset_summary tablecalc_number_of_years_sampled
Calculate std_dev_interval_betw_years for the dataset_summary tablecalc_std_dev_interval_betw_years
Convert a dataset to the Darwin Core Archive formatconvert_to_dwca
Create the dataset_summary tablecreate_dataset_summary
Create EML metadatacreate_eml
Create the location tablecreate_location
Create the location_ancillary tablecreate_location_ancillary
Create the observation tablecreate_observation
Create the observation_ancillary tablecreate_observation_ancillary
Create the taxon tablecreate_taxon
Create the taxon_ancillary tablecreate_taxon_ancillary
Create the variable_mapping tablecreate_variable_mapping
Flatten a datasetflatten_data
Plot dates and times samples were collected or observations were madeplot_sample_space_time
Plot sites on US mapplot_sites
Plot mean taxa abundances per 'observation_id'plot_taxa_abund
Plot taxa accumulation by site accumulationplot_taxa_accum_sites
Plot taxa accumulation through timeplot_taxa_accum_time
Plot diversity (taxa richness) through timeplot_taxa_diversity
Plot taxon occurrence frequenciesplot_taxa_occur_freq
Plot taxa ranksplot_taxa_rank
Plot number of unique taxa shared across sitesplot_taxa_shared_sites
Read published dataread_data
Save a datasetsave_data
Search published datasearch_data
Validate tables against the modelvalidate_data
Write tables to filewrite_tables