Package: iidda 1.0.0

Steve Walker

iidda: Processing Infectious Disease Datasets in IIDDA.

Part of an open toolchain for processing infectious disease datasets available through the IIDDA data repository.

Authors:Steve Walker [aut, cre], Samara Manzin [aut], Michael Roswell [aut], Gabrielle MacKinnon [aut], Ronald Jin [aut]

iidda_1.0.0.tar.gz
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iidda.pdf |iidda.html✨
iidda/json (API)

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

Peer review:

Bug tracker:https://github.com/canmod/iidda-tools/issues

Datasets:

On CRAN:

5.05 score 3 packages 6 scripts 160 exports 55 dependencies

Last updated 17 hours agofrom:a34ec14fa0. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winNOTENov 20 2024
R-4.5-linuxNOTENov 20 2024
R-4.4-winNOTENov 20 2024
R-4.4-macNOTENov 20 2024
R-4.3-winNOTENov 20 2024
R-4.3-macNOTENov 20 2024

Exports:%_%%-%%.%%+%add_basal_diseaseadd_column_summariesadd_filter_group_valuesadd_metadataadd_provenanceall_prep_script_outcomesbasal_diseaseblob_to_rawcell_blockcheck_metadata_colscheck_tidy_data_colscollapse_xlsx_value_columnscombine_weeksconvert_harmonized_metadataconvert_metadata_pathcp_git_versioncsv_to_json_filesdata_to_json_filesdisease_coverage_heatmapdo_time_scale_cross_checkdrop_empty_rowsempty_column_reportempty_is_blankempty_to_naepiweek_end_dateerror_tarextract_all_between_parenextract_between_parenextract_char_or_blankextract_or_blankfailed_prep_script_outcomesfill_and_wrapfill_re_templatefix_csvfreq_to_byfreq_to_daysget_all_dependenciesget_canmod_digitization_metadataget_dataset_metadataget_dataset_pathget_elementsget_firstsget_itemsget_lookup_tableget_main_scriptget_source_pathget_tracking_metadataget_unique_col_valuesget_with_keygroup_with_dashicd_finderidentify_scalesiidda_data_dictionaryiidda_from_single_filein_git_repoin_projis_emptyiso_3166_codesiso_8601_daterangesiso_8601_datesiso_codesjson_files_to_csvjson_files_to_datakey_vallist_dataset_idslist_dataset_ids_by_sourcelist_dependency_idslist_dependency_ids_for_sourcelist_dependency_pathslist_extractlist_file_idlist_prep_script_idslist_resource_idslist_source_idslist_xpathlookupmake_age_hash_tablemake_compilation_dependenciesmake_configmake_data_cite_tidy_datamake_dataset_dependenciesmake_dataset_metadatamake_resource_metadatamake_source_directorymake_source_metadatamelt_tracking_table_keysmemoise_remove_ageMissingHandlersmock_api_hooknlistnon_numeric_reportnormalize_diseasesopen_all_resources_locallyopen_digitizations_locallyopen_locallyopen_resources_locallyopen_scans_locallyor_patternpad_weekspagerparse_columnspipeline_exploration_starterproj_pathproj_rootraw_githubread_column_metadataread_data_columnsread_data_frameread_digitized_dataread_global_metadataread_lookupread_prerequisite_dataread_prerequisite_metadataread_prerequisite_pathsread_resource_metadataread_tidy_dataread_tracking_tablesreadme_classic_iiddaregister_prep_scriptrelative_pathsremote_iidda_gitremove_ageremove_between_parenreturn_matched_age_boundrm_leading_slashrm_trailing_slashsave_resultset_extset_iidda_col_typesset_typessource_from_digitization_idsprintf_namedstatcan_mort_prepstrip_blob_githubsuccessful_prep_script_outcomessum_timescalessummarise_datessummarise_diseasessummarise_integerssummarise_locationssummarise_periodssummarise_periods_vecsummarise_stringstest_resulttime_series_islandstracking_table_keystracking_tables_with_columntwo_field_formatunlist_char_listvsubwrap_age_patternswrite_data_framewrite_local_data_dictionarieswrite_tidy_dataxlsx_diffxlsx_to_csv

Dependencies:bitbit64cachemclicliprcolorspacecpp11crayondplyrfansifarverfastmapgenericsggplot2gluegtablehmsisobandjsonlitelabelinglatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpitonpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangscalesstringistringrtibbletidyrtidyselecttidyxltimechangetzdbutf8vctrsviridisLitevroomwithr

Readme and manuals

Help Manual

Help pageTopics
Add Basal Diseaseadd_basal_disease
Add Column Summariesadd_column_summaries
Add Filter Group Valuesadd_filter_group_values
Add Metadataadd_metadata
Add Provenanceadd_provenance
Prep Script Outcomesall_prep_script_outcomes error_tar failed_prep_script_outcomes successful_prep_script_outcomes
Basal Diseasebasal_disease
Blob to Rawblob_to_raw
Cell Blockcell_block
Error if columns in the tidy data are not in metadata Schema and if all values in a column are NAcheck_metadata_cols
Error if columns in the metadata Schema are not in tidy datacheck_tidy_data_cols
Collapse xlsx Value Columnscollapse_xlsx_value_columns
Combine Weekscombine_weeks
Convert Harmonized Metadataconvert_harmonized_metadata
Convert Metadata Pathconvert_metadata_path
Copy old git File Versioncp_git_version
CSV to JSON Filescsv_to_json_files
Data to JSON Filesdata_to_json_files
Creates a heatmap that shows disease coverage over the yearsdisease_coverage_heatmap
Time Scale Cross Checkdo_time_scale_cross_check
Drop Empty Rowsdrop_empty_rows
Empty Column Reportempty_column_report
Empty is Blankempty_is_blank
Convert all missing values to NAempty_to_na
End-Dates of Epiweeksepiweek_end_date
Extract Substring Between Parenthesesextract_all_between_paren extract_between_paren
Extract Character or Blankextract_char_or_blank
Extract or Blankextract_or_blank
Fill Template and Wrap the Resultsfill_and_wrap
Fill Regex Templatefill_re_template
Fix CSVfix_csv
Frequency to Byfreq_to_by
Frequency to Daysfreq_to_days
Get all Dependenciesget_all_dependencies
Get CANMOD Digitization Metadataget_canmod_digitization_metadata
Get Dataset Metadataget_dataset_metadata
Get Dataset pathget_dataset_path
Get Elementsget_elements
Get Firstsget_firsts
Get Itemsget_items
Get Lookup Tableget_lookup_table
Get Main Scriptget_main_script
Get Source Pathget_source_path
Read Tracking Metadataget_tracking_metadata
Unique Column Valuesget_unique_col_values
Get with Key by Regexget_with_key
Convert GitHub URLs into Raw Format (not working)git_path_to_raw_github
Simplify String with List of Numbers Grouped by Dashesgroup_with_dash
Harmonization Lookup Tablesharmonization_lookup_tables
ICD Findericd_finder
Identify Scalesidentify_scales
IIDDA Data Dictionaryiidda_data_dictionary
Create New IIDDA Dataset from Single Fileiidda_from_single_file
In Git Repoin_git_repo
Is Emptyis_empty
ISO-3166 and ISO-3166-2 Codesiso_3166_codes
ISO-8601 Date Rangesiso_8601_dateranges
ISO-8601 Datesiso_8601_dates
Iso Codesiso_codes
JSON Files to CSVjson_files_to_csv
JSON Files to Datajson_files_to_data
Key-Valuekey_val
List Dataset IDslist_dataset_ids
List Dataset IDs by Sourcelist_dataset_ids_by_source
List Dependency IDslist_dependency_ids
List Dependency IDs for Sourcelist_dependency_ids_for_source
List Dependency Pathslist_dependency_paths
List Extractlist_extract
List File IDlist_file_id
List Prep Script IDslist_prep_script_ids
List Resources IDslist_resource_ids
List Source IDslist_source_ids
List XPathlist_xpath
Lookup Valuelookup
Make Age Hash Tablemake_age_hash_table
Make Compilation Dependenciesmake_compilation_dependencies
Create IIDDA Config Filemake_config
Make DataCite JSON Metadatamake_data_cite_tidy_data
Make Dataset Dependenciesmake_dataset_dependencies
Make Dataset Metadatamake_dataset_metadata
Make Resource Metadatamake_resource_metadata
Make Source Directorymake_source_directory
Make Source Metadatamake_source_metadata
Melt Tracking Table Keys (Deprecated)melt_tracking_table_keys
Missing HandlersMissingHandlers
Mock API Hookmock_api_hook
Self-Naming Listnlist
Non-Numeric Reportnon_numeric_report
Normalize Diseasesnormalize_diseases
Open a Path on Mac OS or Windowsopen_all_resources_locally open_digitizations_locally open_locally open_resources_locally open_scans_locally
Or Patternor_pattern
Pad Weekspad_weeks
Pagerpager
Parse Columnsparse_columns
Paste Operators%+% %-% %.% %_% paste_operators
Pipeline Exploration Quick-Startpipeline_exploration_starter
Project Pathproj_path
Project Rootin_proj proj_root
Construct an URL to Download Single Files from GitHubraw_github
Read Column Metadataread_column_metadata
Read Data Columnsread_data_columns
Read Data Frameread_data_frame
Read Digitized Dataread_digitized_data
Read Global Metadataread_global_metadata
Read Lookupread_lookup
Read Prerequisite Dataread_prerequisite_data
Read Prerequisite Metadataread_prerequisite_metadata
Read Prerequisite Pathsread_prerequisite_paths
Read Resource Metadataread_resource_metadata
Read Tidy Data and Metadata filesread_tidy_data
Read Tracking Tablesread_tracking_tables
README File Templatereadme_classic_iidda
Register Prep Scriptregister_prep_script
Relative Pathsrelative_paths
Remote IIDDA Gitremote_iidda_git
Remove Agememoise_remove_age remove_age
Remove Parenthesized Substringremove_between_paren
Matched Age Boundreturn_matched_age_bound
Remove Trailing / Leading Slashrm_leading_slash rm_trailing_slash
Save Results of a Data Prep Scriptsave_result
Set Extensionset_ext
Set IIDDA Column Typesset_iidda_col_types
Set Data Frame Column Typesset_types
Source from Digitization IDsource_from_digitization_id
Lightweight Templatingsprintf_named
Standardsstandards
Prepare Mortality Data from Statistics Canadastatcan_mort_prep
Strip Blobstrip_blob_github
Sum Timescalessum_timescales
Summarise Datessummarise_dates
Summarise Diseasessummarise_diseases
Summarise Integerssummarise_integers
Summarise Locationssummarise_locations
Summarise Periodssummarise_periods summarise_periods_vec
Summarise Stringssummarise_strings
Test Resultstest_result
Time Series Islandstime_series_islands
Tracking Table Keystracking_table_keys
Which Tracking Tables have a Particular Columntracking_tables_with_column
Two Field Formattwo_field_format
Unlist a List of Character Vectorsunlist_char_list
Vectorized String Substitutionvsub
Wrap Age Patternswrap_age_patterns
Write Data Framewrite_data_frame
Write Local Data Dictionarieswrite_local_data_dictionaries
Write Tidy Digitized Data and Metadatawrite_tidy_data
Compare Two Excel Filesxlsx_diff
Excel to CSVxlsx_to_csv