Files in EDIorg/ecocomDP
Tools to Create, Use, and Convert ecocomDP Data

.Rbuildignore
.gitignore
.travis.yml
CODE_OF_CONDUCT.md CONTRIBUTING.md
DESCRIPTION
GBIF/pasta2gbif.py
LICENSE
LICENSE.md
NAMESPACE
NEON_dev_script/TESTING_NEON_mappings.r NEON_dev_script/TESTING_plotting_fxns.r NEON_dev_script/draft tutorials/ecocomDP_plots_doc.Rmd NEON_dev_script/draft tutorials/ecocomDP_plots_doc.pdf NEON_dev_script/draft tutorials/ecocomDP_plots_doc_v20210921.Rmd
NEON_dev_script/draft tutorials/images/tables_image.png
NEON_dev_script/old dev files/EcocomDP_MAM_SP.R NEON_dev_script/old dev files/aggregateDivPresenceData.R NEON_dev_script/old dev files/map_neon.ecocomdp.10003.001.001_20220717.R NEON_dev_script/old dev files/map_neon.ecocomdp.10022.001.001_20220717.R NEON_dev_script/old dev files/map_neon.ecocomdp.10043.001.001_20220324.R NEON_dev_script/old dev files/map_neon.ecocomdp.10072.001.001_20220712.R NEON_dev_script/old dev files/map_neon.ecocomdp.20107.001.001_20220713.R NEON_dev_script/old dev files/plot_taxa_20230718.R NEON_dev_script/old dev files/working_mos_mapping_20230719.R NEON_dev_script/old testing files/TESTING_20210510.r NEON_dev_script/old testing files/TESTING_ecocomDP_calls_with_NEON_updates_20201215.R NEON_dev_script/old testing files/TESTING_edi_193.r NEON_dev_script/old testing files/TESTING_for_CRAN.r NEON_dev_script/old testing files/TESTING_local_neon_save_20210320.R NEON_dev_script/old testing files/TESTING_mos_mapping_fix_20220323-2.R NEON_dev_script/old testing files/TESTING_mos_mapping_fix_20220323.R NEON_dev_script/old testing files/TESTING_plotting.r NEON_dev_script/working.R NEWS.md R/EAL_make_eml.R R/EAL_template_arguments.R R/EAL_validate.R R/annotation_dictionary.R R/convert_to_dwca.R R/create_dataset_summary.R R/create_eml.R R/create_location.R R/create_location_ancillary.R R/create_observation.R R/create_observation_ancillary.R R/create_taxon.R R/create_taxon_ancillary.R R/create_variable_mapping.R R/data.R R/flatten_data.R R/map_neon.ecocomdp.10003.001.001.R R/map_neon.ecocomdp.10022.001.001.R R/map_neon.ecocomdp.10022.001.002.R R/map_neon.ecocomdp.10043.001.001.R R/map_neon.ecocomdp.10058.001.001.R R/map_neon.ecocomdp.10072.001.001.R R/map_neon.ecocomdp.10092.001.001.R R/map_neon.ecocomdp.10093.001.001.R R/map_neon.ecocomdp.20107.001.001.R R/map_neon.ecocomdp.20120.001.001.R R/map_neon.ecocomdp.20166.001.001.R R/map_neon.ecocomdp.20219.001.001.R R/map_neon_data_to_ecocomDP.r R/neon_helper_functions.r R/plot_taxa.R R/read_data.R R/save_data.R R/search_data.R R/taxonomyCleanr.R R/utilities.R R/validate_arguments.R R/validate_data.R R/zzz.R README.Rmd README.md
_pkgdown.yml
codemeta.json
cran-comments.md data-raw/create_ants_L0_flat.R data-raw/create_ants_L1.R
data/ants_L0_flat.rda
data/ants_L1.rda
docs/404.html
docs/CODE_OF_CONDUCT.html
docs/CONTRIBUTING.html
docs/LICENSE-text.html
docs/LICENSE.html
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docs/articles/convert.html
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docs/reference/create_taxon.html
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docs/reference/make_eml_dwca.html
docs/reference/make_taxonomicCoverage.html
docs/reference/map_neon_data_to_ecocomDP.html
docs/reference/not_all_NAs.html
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docs/reference/read_dir.html
docs/reference/read_eml.html
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docs/reference/resolve_sci_taxa.html
docs/reference/save_data.html
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docs/reference/set_taxonomic_coverage.html
docs/reference/to_docbook.html
docs/reference/update_neon_summary_info.html
docs/reference/url_env.html
docs/reference/validate_arguments.html
docs/reference/validate_column_classes.html
docs/reference/validate_column_names.html
docs/reference/validate_column_presence.html
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docs/reference/validate_elevation.html
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docs/reference/validate_taxonomic_coverage_authority_system.html
docs/reference/validate_taxonomic_coverage_column_names.html
docs/reference/validate_taxonomic_coverage_completeness.html
docs/reference/validate_templates.html
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docs/reference/view_descriptions.html
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docs/reference/write_tables.html
docs/reference/xml_val.html
docs/sitemap.xml
documentation/model/ecocomDP.png
documentation/model/table_description.md documentation/model/table_visualization.md
inst/extdata/L1_versions.txt
inst/extdata/create_ecocomDP.R
inst/extdata/dwca_event_core/annotations.txt
inst/extdata/dwca_event_core/attributes_event.txt
inst/extdata/dwca_event_core/attributes_extendedmeasurementorfact.txt
inst/extdata/dwca_event_core/attributes_occurrence.txt
inst/extdata/dwca_event_core/keywords.txt
inst/extdata/dwca_event_core/meta.xml
inst/extdata/eal_templates/abstract.docx
inst/extdata/eal_templates/abstract.md
inst/extdata/eal_templates/abstract.txt
inst/extdata/eal_templates/additional_info.docx
inst/extdata/eal_templates/additional_info.md
inst/extdata/eal_templates/additional_info.txt
inst/extdata/eal_templates/annotation_defaults.txt
inst/extdata/eal_templates/annotations.txt
inst/extdata/eal_templates/arguments.txt
inst/extdata/eal_templates/bounding_boxes.txt
inst/extdata/eal_templates/categorical_variables.txt
inst/extdata/eal_templates/custom_units.txt
inst/extdata/eal_templates/geographic_coverage.txt
inst/extdata/eal_templates/intellectual_rights.txt
inst/extdata/eal_templates/intellectual_rights_cc0.txt
inst/extdata/eal_templates/intellectual_rights_ccby4.0.txt
inst/extdata/eal_templates/keywords.txt
inst/extdata/eal_templates/methods.docx
inst/extdata/eal_templates/methods.md
inst/extdata/eal_templates/methods.txt
inst/extdata/eal_templates/personnel.txt
inst/extdata/eal_templates/provenance.txt
inst/extdata/eal_templates/table_attributes.txt
inst/extdata/eal_templates/taxonomic_coverage.txt
inst/extdata/eal_templates/template_characteristics.txt
inst/extdata/ecocomDP/abstract.txt
inst/extdata/ecocomDP/annotations.txt
inst/extdata/ecocomDP/attributes_dataset_summary.txt
inst/extdata/ecocomDP/attributes_location.txt
inst/extdata/ecocomDP/attributes_location_ancillary.txt
inst/extdata/ecocomDP/attributes_observation.txt
inst/extdata/ecocomDP/attributes_observation_ancillary.txt
inst/extdata/ecocomDP/attributes_taxon.txt
inst/extdata/ecocomDP/attributes_taxon_ancillary.txt
inst/extdata/ecocomDP/attributes_variable_mapping.txt
inst/extdata/ecocomDP/intellectual_rights.txt
inst/extdata/ecocomDP/keywords.txt
inst/extdata/ecocomDP/methods.txt
inst/extdata/neon-field-sites.csv
inst/extdata/neon_data_products_for_ecocomDP.txt
inst/extdata/table_descriptions.txt
inst/extdata/template_characteristics.txt
inst/extdata/validation_criteria.txt
man/annotation_dictionary.Rd man/ants_L0_flat.Rd man/ants_L1.Rd man/calc_geo_extent_bounding_box_m2.Rd man/calc_length_of_survey_years.Rd man/calc_number_of_years_sampled.Rd man/calc_std_dev_interval_betw_years.Rd man/convert_to_dwca.Rd man/create_dataset_summary.Rd man/create_eml.Rd man/create_location.Rd man/create_location_ancillary.Rd man/create_observation.Rd man/create_observation_ancillary.Rd man/create_taxon.Rd man/create_taxon_ancillary.Rd man/create_variable_mapping.Rd
man/figures/logo.png
man/flatten_data.Rd man/plot_sample_space_time.Rd man/plot_sites.Rd man/plot_taxa_abund.Rd man/plot_taxa_accum_sites.Rd man/plot_taxa_accum_time.Rd man/plot_taxa_diversity.Rd man/plot_taxa_occur_freq.Rd man/plot_taxa_rank.Rd man/plot_taxa_sample_time.Rd man/plot_taxa_shared_sites.Rd man/read_data.Rd man/save_data.Rd man/search_data.Rd man/validate_data.Rd man/write_tables.Rd model/README.md
model/ecocomDP.png
model/ecocomDP.svg
model/table_description.md model/table_visualization.md
pkgdown/favicon/apple-touch-icon-120x120.png
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postgreSQL/README.md
postgreSQL/create_1_optional_tables_ecocomDP.sql
postgreSQL/create_7tables_ecocomDP_postgres.sql
postgreSQL/drop_7tables_ecocomDP_postgres.sql
postgreSQL/html/anomalies.html
postgreSQL/html/columns.byAuto.html
postgreSQL/html/columns.byColumn.html
postgreSQL/html/columns.byDefault.html
postgreSQL/html/columns.byNulls.html
postgreSQL/html/columns.bySize.html
postgreSQL/html/columns.byTable.html
postgreSQL/html/columns.byType.html
postgreSQL/html/constraints.html
postgreSQL/html/deletionOrder.txt
postgreSQL/html/diagrams/.DS_Store
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postgreSQL/html/edi_sandbox.ecocom_dp.xml
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postgreSQL/html/index.html
postgreSQL/html/insertionOrder.txt
postgreSQL/html/jquery.js
postgreSQL/html/relationships.html
postgreSQL/html/schemaSpy.css
postgreSQL/html/schemaSpy.js
postgreSQL/html/tables/dataset_summary.html
postgreSQL/html/tables/event.html
postgreSQL/html/tables/event_ancillary.html
postgreSQL/html/tables/location.html
postgreSQL/html/tables/location_ancillary.html
postgreSQL/html/tables/observation.html
postgreSQL/html/tables/observation_ancillary.html
postgreSQL/html/tables/sampling_location.html
postgreSQL/html/tables/sampling_location_ancillary.html
postgreSQL/html/tables/taxon.html
postgreSQL/html/tables/taxon_ancillary.html
postgreSQL/html/tables/variable_mapping.html
postgreSQL/html/utilities.html
tests/testthat.R tests/testthat/test_convert_to_dwca.R tests/testthat/test_create_dataset_summary.R tests/testthat/test_create_eml.R tests/testthat/test_create_location.R tests/testthat/test_create_location_ancillary.R tests/testthat/test_create_observation.R tests/testthat/test_create_observation_ancillary.R tests/testthat/test_create_taxon.R tests/testthat/test_create_taxon_ancillary.R tests/testthat/test_create_variable_mapping.R tests/testthat/test_flatten_data.R tests/testthat/test_plot_taxa.R tests/testthat/test_read_data.R tests/testthat/test_save_data.R tests/testthat/test_search_data.R tests/testthat/test_utilities.R tests/testthat/test_validate_arguments.R tests/testthat/test_validate_data.R
vignettes/.gitignore
vignettes/LevelOfSurvey_final_long2.png
vignettes/MLO_final_long2.png
vignettes/convert.Rmd
vignettes/coords_final_wide2.png
vignettes/create.Rmd
vignettes/deprecated.jpg
vignettes/model.png
vignettes/model_overview.Rmd vignettes/shared_practices_create.Rmd vignettes/use.Rmd
vignettes/workflow.png
EDIorg/ecocomDP documentation built on Aug. 22, 2024, 9:34 a.m.