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-4.7)ecocomDP_1.3.2.zip(r-4.6)ecocomDP_1.3.2.zip(r-4.5)
ecocomDP_1.3.2.tgz(r-4.6-any)ecocomDP_1.3.2.tgz(r-4.5-any)
ecocomDP_1.3.2.tar.gz(r-4.7-any)ecocomDP_1.3.2.tar.gz(r-4.6-any)
ecocomDP_1.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ecocomDP/json (API)

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

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:

Conda:

7.91 score 37 stars 98 scripts 406 downloads 31 exports 85 dependencies

Last updated from:531bbefc6a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK232
source / vignettesOK244
linux-release-x86_64OK235
macos-release-arm64OK224
macos-oldrel-arm64OK223
windows-develOK201
windows-releaseOK217
windows-oldrelOK199
wasm-releaseOK189

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:arrowaskpassassertthatbase64encbitbit64blobbslibcachemclicpp11curldata.tableDBIdbplyrdigestdownloaderdplyrduckdbduckdbfsEMLemldevaluatefarverfastmapfontawesomefsgenericsgeosphereggplot2gluegtablehighrhtmltoolshttrisobandjosejqrjquerylibjsonldjsonliteknitrlabelinglazyevallifecyclelubridatemagrittrmemoisemimeneonOSneonUtilitiesopensslpbapplypillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttimechangetinytexutf8uuidV8vctrsviridisLitewithrxfunxml2yaml

Shared Practices for Creating ecocomDP Data
Introduction | Getting Started | Identifying a candidate L0 dataset | Understanding the L0 dataset | Resolving issues | Omitting rows | Omitting tables | Creating the Conversion Script | Basics | Do's | Don’ts | Resolving Issues in the L1 Tables | observation | event_id | datetime | taxon_id | variable_name | location | location_id | location_name | latitude and longitude | taxon | dataset_summary | observation_ancillary | location_ancillary | taxon_ancillary | variable_mapping | General Issues | Concepts | Levels of Observation | Determining the Meaningful Level of Observation | Using the Levels of Observation to assign location_id | Determining the Meaningful Level of Observation (Visual Examples) | Frequency of Survey | Determining the Frequency of Survey | Frequency of Survey (Visual Examples) | Value-Added Features | Ontologies and Vocabularies | Natural observation vs. experiment/manipulation | For annotation of metadata and use in the variable_mapping table | Deprecating an L1 Dataset
Rendered fromshared_practices_create.Rmdusingknitr::rmarkdown

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

Convert ecocomDP Data to Another Model Format
DwC-A Event Core
Rendered fromconvert.Rmdusingknitr::rmarkdown

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

Create ecocomDP Data
For archive in a data repository | Example function: | Example function call:
Rendered fromcreate.Rmdusingknitr::rmarkdown

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

ecocomDP Model Overview
Contents | Table descriptions, relationships, and requirements | Overview | Tables | Table: observation | Columns | Table: location | Table: taxon | Table: dataset_summary | Table: observation_ancillary | Table: location_ancillary | Table: taxon_ancillary | Table: variable_mapping | | column name | type | not NULL required? | references | description | example ||---------------|----------|-----------------------|-------------------|--------------|---------|| variable_mapping_id | character |yes| NA | Identifier of the variable mapping information. | 1 || table_name | character |yes| NA | Name of the table containing this variable. | my_observation || variable_name | character |yes| /table/variable_name | Name of the measured variable in another table. | sample_z || mapped_system | character | no| NA | System defining variable_name. | NERC || mapped_id | character | no| NA | Identifier of the definition in mapped_system. | SDN:P07::CFSN0721 || mapped_label | character | no| NA | Label for variable_name in mapped_system. | depth | | Entity Relationship Diagram
Rendered frommodel_overview.Rmdusingknitr::rmarkdown

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

Use ecocomDP Data
Search | Read | Manipulate | Plot | Save
Rendered fromuse.Rmdusingknitr::rmarkdown

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