Man pages for pepfar-datim/datapackr
A Package that Packs and Unpacks all Data Packs and Target Setting Tools
| addcols | Add list of columns as NULL columns to supplied dataframe. |
| add_dp_label | Modify Data Pack Org Unit list to add datapackr IDs. |
| adorn_import_file | Convert a 'PSNU-level' DATIM import file into an... |
| analyze_eid_2mo | Check Data Pack for <90% PMTCT_EID from ≤02 months |
| analyze_indexpos_ratio | Check Data Pack data for low representation of HTS_INDEX_POS |
| analyze_linkage | Check Data Pack data for linkage < 95% or >100% |
| analyze_pmtctknownpos | Check Data Pack data for PMTCT Known Pos Ratio > 75%. |
| analyze_retention | Check Data Pack data for retention < 98% or >100% |
| analyze_tbknownpos | Check Data Pack data for TB Known Pos ratio > 75%. |
| analyze_vmmc_indeterminate | Check Data Pack data for VMMC_CIRC Indeterminate Rate > 5% |
| appendMessage | Title appendMessage |
| appendMessage.MessageQueue | Title appendMessage.MessageQueue |
| appendUnallocatedData | Title appendUnallocatedData |
| cache_is_fresh | Checks whether a cached file is stale |
| calculateFinalDedupeValues | Title calculateFinalDedupeValues |
| canReadFile | Test for file read access |
| can_spawn | Can Spawn |
| checkAnalytics | Check Data Pack data for analytics concerns |
| checkColStructure | checkColStructure(d) |
| checkHasPSNUxIM | Check that a Data Pack tool has a PSNUxIM tab |
| checkInvalidIndicatorCodes | Check for invalid Indicator Codes |
| checkMechanisms | Check Mechanisms |
| checkNonEqualTargets | checkNonEqualTargets extracts all rows from the PSNUxIM tab... |
| checkNonNumericPSNUxIMValues | Title checkNonNumericPSNUxIMValues |
| checkNotPEPFARSupportedPSNUs | Title |
| checkPSNUData | Check PSNUxIM tab Data |
| checkPSNUxIMDisaggs | Title checkPSNUxIMDisaggs |
| compareData_DatapackVsDatim | compareData_DatapackVsDatim |
| compareData_OpuDatapackVsDatim | compareData_OpuDatapackVsDatim |
| cop21_data_pack_schema | Schema describing the correct structure of the COP21 Data... |
| COP21_datapacks_countries | Datapack country groupings |
| cop21_map_DataPack_DATIM_DEs_COCs | Map of COP21 indicators from Data Pack indicator codes to... |
| cop21OPU_data_pack_schema | Schema describing the correct structure of the COP21 OPU Data... |
| cop22_data_pack_schema | Schema describing the correct structure of teh COP22 Data... |
| cop22_map_adorn_import_file | Map from Data Pack to DATIM for the adorning import files |
| cop22_map_DataPack_DATIM_DEs_COCs | Map of COP22 indicators from Data Pack indicator codes to... |
| cop22OPU_data_pack_schema | Schema describing the correct structure of the COP22 OPU Data... |
| cop22_valid_PSNUs | List of valid COP22 PSNUs used for generating Data Packs. |
| cop_validation_rules | COP Validation Rules |
| countryUIDs_homeCell | Location of Country UIDs on Home tab. |
| createAnalytics | createAnalytics(d) |
| createDataPack | Create a new Data Pack |
| createDATIMExport | createDATIMExport |
| createKeychainInfo | Create Keychain Info for use in DataPack object. |
| createPAWExport | createPAWExport |
| create_play_spectrum_output | Create fake Spectrum output for testing |
| createTestDataset | Create a test Targets dataset |
| datapack_cogs | Datapack Category option groups |
| dataPackName_homeCell | Location of Name of the DataPack on the Home tab |
| datapackr | Data Pack on R |
| datapackr_params | Standardized package function parameter definitions |
| datapackrSupports | Supported Tools & COP Years |
| dataset_levels | Structure for DATIM data set levels. |
| default_catOptCombo | Returns 'default' categoryOptionCombo uid. |
| defaultMemoFont | Default Memo Font |
| defaultMemoStyleHeader | Default Memo Header Style |
| defaultMemoStylePara | Default Memo Paragraph Style |
| dropDuplicatedPSNUxIMColumns | Title dropDuplicatedPSNUxIMColumns |
| dropInvalidMechColumns | Title dropInvalidMechColumns |
| evaluateIndicators | Evaluate Indicators |
| exportDistributedDataToDATIM | exportDistributedDataToDATIM(data) |
| exportPackr | Export output. |
| extractDuplicateRows | Title extractDuplicateRows |
| extractOriginalTargets | Title |
| extractRawColumnData | Title extractRawColumnData |
| extractSNUxIMCombos | Title extractSNUxIMCombos for a given datapack (d) and a... |
| extract_uid | Extract UID. |
| fetchPrioritizationTable | Fetch Prioritization Table |
| formatSetStrings | Title |
| fresh_cache_part | Return the fresh portion of a cache file |
| generateApprovalMemo | Generate COP Approval Memo Target Tables (DOCX Format) |
| generateComparisonTable | Generate Comparison Table |
| generateMemoTemplate | Generate Memo Template File |
| generatePSNUxIMComparison | Title generatePSNUxIMComparison |
| getCodeList | Pull & combine all MER, SUBNAT, IMPATT code lists for... |
| getColumnsToKeep | getColumnsToKeep(d) |
| getCOPDataFromDATIM | Grab all raw data in DATIM for a country for the COP data... |
| getCOPDatasetUids | getCOPDatasetUids |
| getCurrentCOPYear | Returns current COP Year |
| getDataPackOrgUnits | Pull list of Org Units approved for use in Data Packs from... |
| getHeaderColumns | getHeaderColumns returns a vector of header columns provided... |
| getHTSModality | Get HTS Modalities map |
| getMapDataPack_DATIM_DEs_COCs | get_Map_DataPack_DATIM_DEs_COCs |
| getMaxCores | Title |
| getMechanismView | getMechanismView |
| getMemoIndicators | Get COP Memo Indicators |
| getOPUDataFromDATIM | Pull data for packing OPU Data Pack |
| getOUFromCountryUIDs | Get Operating Unit from Country UIDs |
| getPSNUInfo | getPSNUInfo |
| getSaneName | Get Sane Name for Data Pack Tool |
| getValidOrgUnits | Return a data frame of valid organisation units based on the... |
| handshakeFile | Test an input file for read access and type. Prompt if... |
| headerRow | Tool to assist with formatting the header rows |
| interactive_message | Uses r message instead of print if session is interactive. |
| interactive_print | Prints message if session is interactive. |
| interactive_warning | Issue a warning if the session is interactive |
| is_uidish | Is UID-ish |
| listWorkbookContents | listWorkbookContents |
| loadDataPack | Load a DataPack from a supplied filepath. |
| loadSheets | Load a DataPack from a supplied filepath. |
| map_COCs_to_COs | Map categoryoptioncombos to underlying categoryoptions. |
| map_Cs_to_COs | Map categoryoptioncombos to underlying categoryoptions. |
| map_DataPack_DATIM_DEs_COCs | Map of indicators from Data Pack indicator codes to DATIM... |
| memoStructure | COP Memo Target Table Structure |
| mergeDatapack | merge two datapacks into one d object. |
| MessageQueue | Title MessageQueue |
| na-default | Default value for 'NA' |
| null-default | Default value for 'NULL' |
| op-missing-default | Default value for 'missing_arg' |
| packDataPack | Pack a Data Pack |
| packDataPackSheet | Pack data into a Data Pack sheet |
| packDataPackSheets | Loop through and populate normal Data Pack sheets |
| packForDATIM | packForDATIM |
| packOPUDataPack | Pack an OPU Data Pack |
| packPSNUxIM | packPSNUxIM |
| packSNUxIM | packSNUxIM(data) |
| packTool | Pack a requested tool |
| parameter-checks | Standardized Parameter Defaults |
| parse_maybe_number | Parse a value to numeric |
| parsePSNUs | Extract PSNUs from submitted file |
| paste_dataframe | Paste a Dataframe in a string |
| paste_oxford | Compile a list ending with different final collapse |
| pick_schema | Pick correct schema |
| pick_template_path | Pick correct template filepath |
| pickUIDFromType | Title pickUIDFromType is a utility function used to obtain a... |
| prepareExistingDataAnalytics | Prepare Existing Data Analytics |
| prepareMemoData | Prepare Memo Data |
| prepareMemoDataByAgency | Prepare Memo Data By Agency Level |
| prepareMemoDataByPartner | Prepare Memo Data By Partner |
| prepareMemoDataByPrio | Prepare Memo Data By Prioritization Level |
| prepareMemoDataByPSNU | Prepare Memo Data By PSNU |
| prepareMemoMetadata | Populate necessary metadata for the memo |
| prepare_model_data.PSNUxIM | prepare_model_data.PSNUxIM() |
| prepareSheetData | Prepare sheet-specific dataset for writing into a Data Pack... |
| printMessages | Title printMessages |
| printMessages.MessageQueue | Title printMessage.MessageQueue |
| prioritization_dict | Define prioritization values. |
| prioritizations | Mapping of DATIM Prioritization numerals to strings. |
| readSheet | Read data from a DataPack object |
| recalculateDedupeValues | Title recalculateDedupeValues Recalculates dedupe values... |
| reexports | Objects exported from other packages |
| renderAgencyTable | Render Agency-Level Memo Target Table |
| renderPartnerTable | Render Partner-Level Memo Target Tables |
| renderPrioTable | Render Prioritization-Level Memo Target Table |
| round_trunc | Round at 0.5 toward integer with highest absolute value |
| rowMax | Extracts the desired columns for analysis via regular... |
| schema-validations | Standardized Schema Checks |
| separateDataSets | separateDataSets(d) |
| skip_tabs | List of tabs to skip for given tool. |
| strip_wb_NAs | Remove errant NAs in a Data Pack |
| styleGuide | Library of Openxlsx style objects to apply to both Data Pack... |
| supportedCOPYears | Returns COP Years currently supported by the package for a... |
| supportedSeasons | Supported Seasons |
| supportedTools | Supported Tools |
| swapColumns | Swap columns between two dataframes |
| testDropPositiveDedupe | Title testDropPositiveDedupe |
| testImbalancedDistribution | Title testImbalancedDistribution |
| testInvalidDedupeValues | testInvalidDedupeValues |
| testInvalidPSNUs | Title testInvalidPSNUs |
| testMissingDedupeRollupColumns | Title testMissingDedupeRollupColumns |
| testMissingRightSideFormulas | Title testMissingRightSideFormulas |
| testNegativeTargetValues | Title testNegativeTargetValues |
| testRoundDecimalValues | Title testRoundDecimalValues |
| testRoundingDiffs | Title testRoundingDiffs |
| toolName_homeCell | Location of name of the tool on Home tab. |
| uid_pattern | DHIS2 UID pattern |
| unPackCountryUIDs | Extract country uids from submitted file |
| unPackDataChecks | Perform various data quality checks on in-process data from... |
| unPackDataPack | Unpack a submitted Data Pack |
| unPackDataPackName | Extract the name of the datapack |
| unPackDataPackSheet | Unpack a Data Pack sheet. |
| unPackOPUDataPack | Unpack a submitted OPU Data Pack |
| unPackSheets | Unpack data from Data Pack sheets. |
| unPackSNUxIM | unPackSNUxIM(d) |
| unPackTool | Unpack a submitted tool |
| unPackToolSet | unPackToolSet |
| unpackYear2Sheet | Title unpackYear2Sheet |
| update_de_coc_co_map | Generate a map from Data Pack indicators to Data Pack DEs,... |
| updatePSNUxIMTargetValues | Title updatePSNUxIMTargetValues |
| validationSummary | validationSummary(d) |
| valid_OrgUnits | List of valid PSNUs used for generating Data Packs. |
| valid_PSNUs | List of valid PSNUs used for generating Data Packs. |
| writeHomeTab | writeHomeTab(wb, datapack_uid, tool = "Data Pack") |
| writePSNUxIM | Write PSNUxIM Tab |
| writeSpectrumData | writeSpectrumData |
| zerosToDashes | Zeroes to Dashes |
