Package: wddsWizard 0.2.5

Collin Schwantes

wddsWizard: Data Wizard for a Minimal Wildlife Disease Data Standard

Facilitates compliance with and use of the Wildlife Disease Data Standard stored on Zenodo <https://doi.org/10.5281/zenodo.15020049>. It allows users to restructure and validate datasets.

Authors:Collin Schwantes [aut, cre]

wddsWizard_0.2.5.tar.gz
wddsWizard_0.2.5.zip(r-4.7)wddsWizard_0.2.5.zip(r-4.6)wddsWizard_0.2.5.zip(r-4.5)
wddsWizard_0.2.5.tgz(r-4.6-any)wddsWizard_0.2.5.tgz(r-4.5-any)
wddsWizard_0.2.5.tar.gz(r-4.7-any)wddsWizard_0.2.5.tar.gz(r-4.6-any)
wddsWizard_0.2.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
wddsWizard/json (API)

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

Bug tracker:https://github.com/viralemergence/wddswizard/issues

Pkgdown/docs site:https://viralemergence.github.io

Datasets:

On CRAN:

Conda:

software

4.50 score 7 scripts 45 exports 37 dependencies

Last updated from:46e597a2ea. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR221
source / vignettesOK248
linux-release-x86_64ERROR208
macos-release-arm64ERROR216
macos-oldrel-arm64ERROR235
windows-develERROR169
windows-releaseERROR165
windows-oldrelERROR166
wasm-releaseOK192

Exports:batch_download_deposit_versionsclean_field_namescreate_schema_docsdownload_deposit_versionexpand_tidy_dfsextract_metadata_from_doiextract_metadata_oagenerate_metadata_csvgenerate_repeat_dfsget_entityget_required_fieldslist_deposit_versionsmake_simple_dfna_to_blankpaste_reducepaste_reduce_ulprep_affiliationprep_arrayprep_array_objectsprep_atomicprep_creatorsprep_dataprep_descriptionsprep_for_jsonprep_from_metadata_templateprep_fundingReferencesprep_identifierprep_languageprep_methodologyprep_methodsprep_nameIdentifiersprep_objectprep_publicationYearprep_relatedIdentifiersprep_rightsprep_subjectsprep_titlessanitize_versiontranslate_to_dcmiuse_wdds_templatewdds_data_templateswdds_example_datawdds_jsonwdds_to_dcmiwdds_to_pharos

Dependencies:assertthatbitbit64clicliprcpp11crayoncurldplyrfsgenericsglueherehmsjsonlitelifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrrlangrprojrootsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Getting Started
The Whole game | Templates | Disease Data | Project Metadata | Combine disease data and project metadata | Combine components | Make JSON | Validate your json! | Handling Errors | Excuse me? What does this mean? | How do I correct this error? | Best practices for free text fields
Rendered fromwddsWizard.Rmdusingknitr::rmarkdown

Last update: 2025-10-20
Started: 2025-03-12

Schema Overview
Summary | What is a JSON-schema | Wildlife Disease Data Standard (WDDS) Structure | Important vocabulary | Best practices for free text fields | Terms | disease_data | sampleID | animalID | latitude | longitude | spatialUncertainty | collectionDay | collectionMonth | collectionYear | sampleCollectionMethod | sampleMaterial | sampleCollectionBodyPart | hostIdentification | organismSex | liveCapture | hostLifeStage | age | ageUnits | mass | massUnits | length | lengthMeasurement | lengthUnits | organismQuantity | organismQuantityUnits | detectionTarget | detectionMethod | forwardPrimerSequence | reversePrimerSequence | geneTarget | primerCitation | probeTarget | probeType | probeCitation | detectionOutcome | detectionMeasurement | detectionMeasurementUnits | parasiteIdentification | parasiteID | parasiteLifeStage | genbankAccession | project_metadata | methodology | creators | titles | identifier | subjects | publicationYear | rights | descriptions | language | fundingReferences | relatedIdentifiers
Rendered fromschema_overview.Rmdusingknitr::rmarkdown

Last update: 2025-10-20
Started: 2025-03-12

WDDS to Pharos
Read in and Clean up the excel spreadsheet | Differences in required fields | Converting WDDS Data to Pharos Data | Convert the data | Upload data into Pharos | Improve data for upload | Pharos doesn't like NA's
Rendered fromwdds_to_pharos.Rmdusingknitr::rmarkdown

Last update: 2025-10-20
Started: 2025-09-23

Extending the Wildlife Disease Data Standard
Why extend the standard? | Before you extend the standard, review it. | Extending the Disease Data component | Extending the Project Metadata Component | Validate with your extended schema | How to communicate your changes?
Rendered fromextending_wdds.Rmdusingknitr::rmarkdown

Last update: 2025-09-29
Started: 2025-09-29

Project Metadata
Required fields | Load in the CSV and clean it up | Restructure data | Make the json! | Validate Project metadata | What if we just use the project metadata template?
Rendered fromproject_metadata.Rmdusingknitr::rmarkdown

Last update: 2025-09-23
Started: 2025-02-06

WDDS to Zenodo
What is Zenodo? | Whats the difference between WDDS project metadata and Zenodo deposit metadata? | Read in project metadata | Map fields to DCMI | Getting started with deposits | Create deposit
Rendered fromwdds_to_zenodo.Rmdusingknitr::rmarkdown

Last update: 2025-09-23
Started: 2025-09-23

Wildlife Disease Data
Required fields | Read in and Clean up the excel spreadsheet | Check for required Fields | Rename Fields to match standard | Prep for JSON | Validate disease data
Rendered fromdisease_data.Rmdusingknitr::rmarkdown

Last update: 2025-07-17
Started: 2025-02-06

Readme and manuals

Help Manual

Help pageTopics
Batch download deposit versionsbatch_download_deposit_versions
Becker et al. datasetbecker_disease_data
Becker et al. project metadatabecker_project_metadata
Clean Field Namesclean_field_names
Create Docs Section for a schema objectcreate_object_docs
Create Documentation for a schemacreate_schema_docs
Datacite Data Stadnarddatacite_schema
Required fields in the disease data objectdisease_data_required_fields
Wildlife Disease Data Standard - datadisease_data_schema
Download deposit versiondownload_deposit_version
Rate limited download of OA itemsdownload_oa_item
Expand tidy dataframes to project metadata template formatexpand_tidy_dfs
Extract Project Metadata from DOIextract_metadata_from_doi
Extract Metadata from Open Alex recordextract_metadata_oa
Generate minimal project metadata templategenerate_metadata_csv
generate_repeat_dfsgenerate_repeat_dfs
Get entityget_entity
Get schema referencesget_ref
Get the required fieldsget_required_fields
Increase documentation depthincrease_docs_depth
List Versions of a deposit on Zenodolist_deposit_versions
File paths for wdds templateslist_wdds_templates
A convenience function for making non-repeating itemsmake_simple_df
An example of minimal disease dataminimal_disease_data
An example of minimal project metadataminimal_project_metadata
Convert NA's to blanksna_to_blank
Paste Reducepaste_reduce
Paste Reduce unordered list itempaste_reduce_ul
prep affiliationprep_affiliation
Prep arrayprep_array
Prepare an array of objectsprep_array_objects
Prepare atomicprep_atomic
Prepare creatorsprep_creators
Prepare Dataprep_data
Prepare descriptionsprep_descriptions
Prepare data for jsonprep_for_json
Prepare metadata created from the metadata template for conversion to JSONprep_from_metadata_template
Prepare funding referencesprep_fundingReferences
Prep identifierprep_identifier
Prep languageprep_language
Prep methodology for conversion to jsonprep_methodology
Prepare methodsprep_methods
Prepare Name identifiersprep_nameIdentifiers
Prepare an objectprep_object
Prepare publication year itemsprep_publicationYear
Prepare related identifiersprep_relatedIdentifiers
Prepare rightsprep_rights
Prepare subjectsprep_subjects
Prepare Titlesprep_titles
Required fields in the project metadata objectproject_metadata_required_fields
Wildlife Disease Data Standard - project_metadataproject_metadata_schema
Sanitize version idssanitize_version
Schema Objectschema_obj
Wildlife Disease Data Standard - schema propertiesschema_properties
Wildlife Disease Data Standard required fieldsschema_required_fields
Wildlife Disease Data Standard - schema termsschema_terms
Set the wdds version for the packageset_wdds_version
Data frame of SPDX licensesspdx_licenses
translate to dcmitranslate_to_dcmi
Use a wildlife disease data standard templateuse_wdds_template
Provides Access to Versioned Data Template Fileswdds_data_templates
Provides Access to Versioned Example Data Fileswdds_example_data
Provides Access to Versioned Schema Fileswdds_json
Wildlife Disease Data Standardwdds_schema
WDDS to the Dublin Core Metadata Initiativewdds_to_dcmi
WDDS to DCMI metadata mappingwdds_to_dcmi_map
Convert WDDS disease data to PHAROS datawdds_to_pharos
WDDS to PHAROS metadata mappingwdds_to_pharos_map