Updates to mod3 functions and vignettes#713
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cristinamullin merged 12 commits intodevelopfrom Nov 25, 2025
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Handle errors in TADA_ExampleMod3Workflow vignette
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| TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assign = c("None", "All", "Org"), | ||
| excel = FALSE, overwrite = FALSE) { |
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| TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assign = c("None", "All", "Org"), | |
| excel = FALSE, overwrite = FALSE) { | |
| TADA_CreateParamRef <- function( | |
| .data, | |
| org_id = NULL, | |
| paramRef = NULL, | |
| auto_assign = c("None", "All", "Org"), | |
| excel = FALSE, | |
| overwrite = FALSE | |
| ) { |
| @@ -1087,7 +1095,11 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi | |||
| TADA.CharacteristicName, TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, | |||
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| TADA.CharacteristicName, TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, | |
| TADA.CharacteristicName, | |
| TADA.ComparableDataIdentifier, | |
| ATTAINS.OrganizationIdentifier, |
| ) %>% | ||
| dplyr::mutate(ATTAINS.ParameterName = ATTAINS.ParameterName.y) %>% | ||
| dplyr::select( | ||
| TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, |
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| TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, | |
| TADA.ComparableDataIdentifier, | |
| ATTAINS.OrganizationIdentifier, |
| dplyr::bind_rows(paramRef[,c("ATTAINS.OrganizationIdentifier", "TADA.ComparableDataIdentifier", "ATTAINS.ParameterName", "Flag.ParameterInput")]) %>% | ||
| dplyr::mutate( | ||
| ATTAINS.FlagParameterName = dplyr::case_when( | ||
| ATTAINS.ParameterName == "Not Applicable for Analysis." | is.na(ATTAINS.ParameterName) ~ |
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| ATTAINS.ParameterName == "Not Applicable for Analysis." | is.na(ATTAINS.ParameterName) ~ | |
| ATTAINS.ParameterName == "Not Applicable for Analysis." | | |
| is.na(ATTAINS.ParameterName) ~ |
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| dplyr::select(ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName, ATTAINS.UseName, IncludeOrExclude) %>% | ||
| dplyr::left_join(paramRef, by = c("ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName", "IncludeOrExclude")) | ||
| dplyr::left_join(paramRef, by = c("ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName")) |
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| dplyr::select(ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName, ATTAINS.UseName, IncludeOrExclude) %>% | |
| dplyr::left_join(paramRef, by = c("ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName", "IncludeOrExclude")) | |
| dplyr::left_join(paramRef, by = c("ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName")) | |
| dplyr::select( | |
| ATTAINS.OrganizationIdentifier, | |
| ATTAINS.ParameterName, | |
| ATTAINS.UseName, | |
| IncludeOrExclude | |
| ) %>% | |
| dplyr::left_join( | |
| paramRef, | |
| by = c("ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName") | |
| ) |
| dplyr::left_join(paramRef, by = c("ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName", "IncludeOrExclude")) | ||
| dplyr::left_join(paramRef, by = c("ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName")) | ||
| } else { | ||
| print("IncludeOrExclude was not found as a column name in your user supplied, assuming all parameter and uses are applicable for your analysis.") |
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| print("IncludeOrExclude was not found as a column name in your user supplied, assuming all parameter and uses are applicable for your analysis.") | |
| print( | |
| "IncludeOrExclude was not found as a column name in your user supplied, assuming all parameter and uses are applicable for your analysis." | |
| ) |
|
|
||
| # If user supplies criteria methods table, then auto_assign = T for any non-matched values | ||
| if (!is.null(criteriaMethods)) { | ||
| print("A criteriaMethods table was provided. auto_assign will be set to 'TRUE' to determine any missing or non-matching inputs.") |
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| print("A criteriaMethods table was provided. auto_assign will be set to 'TRUE' to determine any missing or non-matching inputs.") | |
| print( | |
| "A criteriaMethods table was provided. auto_assign will be set to 'TRUE' to determine any missing or non-matching inputs." | |
| ) |
| # Invalid function input combos - MLSummaryRef and auto_assign = TRUE cannot be used together | ||
| if (!is.null(MLSummaryRef) && auto_assign == TRUE) { | ||
| stop("TADA_DefineCriteriaMethodology: MLSummaryRef is provided and autofill = TRUE are not valid function argument input combinations.") | ||
| stop("TADA_DefineCriteriaMethodology: MLSummaryRef is provided and auto_assign = TRUE are not valid function argument input combinations.") |
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| stop("TADA_DefineCriteriaMethodology: MLSummaryRef is provided and auto_assign = TRUE are not valid function argument input combinations.") | |
| stop( | |
| "TADA_DefineCriteriaMethodology: MLSummaryRef is provided and auto_assign = TRUE are not valid function argument input combinations." | |
| ) |
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
run styler, keep dataframe type, and explicit dplyr package call fix.
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| dplyr::select(ATTAINS.OrganizationIdentifier, TADA.ComparableDataIdentifier, ATTAINS.ParameterName) %>% | ||
| dplyr::mutate(Flag.ParameterInput = "This crosswalk was provided through a user supplied table") %>% |
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| dplyr::select(ATTAINS.OrganizationIdentifier, TADA.ComparableDataIdentifier, ATTAINS.ParameterName) %>% | |
| dplyr::mutate(Flag.ParameterInput = "This crosswalk was provided through a user supplied table") %>% | |
| dplyr::select( | |
| ATTAINS.OrganizationIdentifier, | |
| TADA.ComparableDataIdentifier, | |
| ATTAINS.ParameterName | |
| ) %>% | |
| dplyr::mutate( | |
| Flag.ParameterInput = "This crosswalk was provided through a user supplied table" | |
| ) %>% |
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| dplyr::select(ATTAINS.OrganizationIdentifier, TADA.ComparableDataIdentifier, ATTAINS.ParameterName, Flag.ParameterInput) %>% | ||
| dplyr::filter(!TADA.ComparableDataIdentifier %in% paramRef$TADA.ComparableDataIdentifier) %>% | ||
| dplyr::bind_rows(paramRef[, c("ATTAINS.OrganizationIdentifier", "TADA.ComparableDataIdentifier", "ATTAINS.ParameterName", "Flag.ParameterInput")]) %>% |
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| dplyr::select(ATTAINS.OrganizationIdentifier, TADA.ComparableDataIdentifier, ATTAINS.ParameterName, Flag.ParameterInput) %>% | |
| dplyr::filter(!TADA.ComparableDataIdentifier %in% paramRef$TADA.ComparableDataIdentifier) %>% | |
| dplyr::bind_rows(paramRef[, c("ATTAINS.OrganizationIdentifier", "TADA.ComparableDataIdentifier", "ATTAINS.ParameterName", "Flag.ParameterInput")]) %>% | |
| dplyr::select( | |
| ATTAINS.OrganizationIdentifier, | |
| TADA.ComparableDataIdentifier, | |
| ATTAINS.ParameterName, | |
| Flag.ParameterInput | |
| ) %>% | |
| dplyr::filter( | |
| !TADA.ComparableDataIdentifier %in% | |
| paramRef$TADA.ComparableDataIdentifier | |
| ) %>% | |
| dplyr::bind_rows(paramRef[, c( | |
| "ATTAINS.OrganizationIdentifier", | |
| "TADA.ComparableDataIdentifier", | |
| "ATTAINS.ParameterName", | |
| "Flag.ParameterInput" | |
| )]) %>% |
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| TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName, | ||
| ATTAINS.FlagParameterName, Flag.ParameterInput |
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| TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName, | |
| ATTAINS.FlagParameterName, Flag.ParameterInput | |
| TADA.ComparableDataIdentifier, | |
| ATTAINS.OrganizationIdentifier, | |
| ATTAINS.ParameterName, | |
| ATTAINS.FlagParameterName, | |
| Flag.ParameterInput |
|
|
||
| # remove intermediate object Flag1 | ||
| rm(Flag1, Flag2) | ||
|
|
| @@ -19,7 +19,6 @@ ATTAINSParamToWQPCharRef_Cached <- NULL | |||
| #' | |||
| #' @export | |||
| TADA_GetATTAINSParamToWQPCharRef <- function(charAliasType = c("All", "ATTAINS")) { | |||
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| TADA_GetATTAINSParamToWQPCharRef <- function(charAliasType = c("All", "ATTAINS")) { | |
| TADA_GetATTAINSParamToWQPCharRef <- function( | |
| charAliasType = c("All", "ATTAINS") | |
| ) { |
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| AssessPeriod = as.character(NA), AssessPeriodStartDate = as.Date(NA), AssessPeriodEndDate = as.Date(NA), | ||
| Season = as.character(NA), SeasonStartDate = as.Date(NA), SeasonEndDate = as.Date(NA), | ||
| DistrCount = as.numeric(NA), DistrPeriod = as.character(NA), DistrMinSample = as.numeric(NA), Notes = as.character(NA) |
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| AssessPeriod = as.character(NA), AssessPeriodStartDate = as.Date(NA), AssessPeriodEndDate = as.Date(NA), | |
| Season = as.character(NA), SeasonStartDate = as.Date(NA), SeasonEndDate = as.Date(NA), | |
| DistrCount = as.numeric(NA), DistrPeriod = as.character(NA), DistrMinSample = as.numeric(NA), Notes = as.character(NA) | |
| AssessPeriod = as.character(NA), | |
| AssessPeriodStartDate = as.Date(NA), | |
| AssessPeriodEndDate = as.Date(NA), | |
| Season = as.character(NA), | |
| SeasonStartDate = as.Date(NA), | |
| SeasonEndDate = as.Date(NA), | |
| DistrCount = as.numeric(NA), | |
| DistrPeriod = as.character(NA), | |
| DistrMinSample = as.numeric(NA), | |
| Notes = as.character(NA) |
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| use_name = USE_CLASS_NAME_LOCATION_ETC, CRITERION_VALUE, | ||
| CRITERIATYPEAQUAHUMHLTH, CRITERIATYPEFRESHSALTWATER, | ||
| CRITERIATYPE_ACUTECHRONIC, CRITERIATYPE_WATERORG, UNIT_NAME |
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| use_name = USE_CLASS_NAME_LOCATION_ETC, CRITERION_VALUE, | |
| CRITERIATYPEAQUAHUMHLTH, CRITERIATYPEFRESHSALTWATER, | |
| CRITERIATYPE_ACUTECHRONIC, CRITERIATYPE_WATERORG, UNIT_NAME | |
| use_name = USE_CLASS_NAME_LOCATION_ETC, | |
| CRITERION_VALUE, | |
| CRITERIATYPEAQUAHUMHLTH, | |
| CRITERIATYPEFRESHSALTWATER, | |
| CRITERIATYPE_ACUTECHRONIC, | |
| CRITERIATYPE_WATERORG, | |
| UNIT_NAME |
| #' @export | ||
| TADA_GetCriteriaSearchToolRef <- function(){ | ||
| TADA_GetCriteriaSearchToolRef <- function() { | ||
| CST.raw <- openxlsx::read.xlsx("https://cfpub.epa.gov/wqsits/wqcsearch/criteria-search-tool-data.xlsx") |
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| CST.raw <- openxlsx::read.xlsx("https://cfpub.epa.gov/wqsits/wqcsearch/criteria-search-tool-data.xlsx") | |
| CST.raw <- openxlsx::read.xlsx( | |
| "https://cfpub.epa.gov/wqsits/wqcsearch/criteria-search-tool-data.xlsx" | |
| ) |
| # extract unique ATTAINS parameter names | ||
| ref <- ATTAINS.raw[, "name"] | ||
| old <- utils::read.csv(system.file("extdata", "ATTAINSParamToWQPCharRef.csv", package = "EPATADA"))[,"ATTAINS.ParameterName"] | ||
| old <- utils::read.csv(system.file("extdata", "ATTAINSParamToWQPCharRef.csv", package = "EPATADA"))[, "ATTAINS.ParameterName"] |
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| old <- utils::read.csv(system.file("extdata", "ATTAINSParamToWQPCharRef.csv", package = "EPATADA"))[, "ATTAINS.ParameterName"] | |
| old <- utils::read.csv(system.file( | |
| "extdata", | |
| "ATTAINSParamToWQPCharRef.csv", | |
| package = "EPATADA" | |
| ))[, "ATTAINS.ParameterName"] |
| dplyr::distinct() | ||
| ref <- CST$POLLUTANT_NAME | ||
| old <- utils::read.csv(system.file("extdata", "CriteriaSearchToolRef.csv", package = "EPATADA"))[,"POLLUTANT_NAME"] | ||
| old <- utils::read.csv(system.file("extdata", "CriteriaSearchToolRef.csv", package = "EPATADA"))[, "POLLUTANT_NAME"] |
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| old <- utils::read.csv(system.file("extdata", "CriteriaSearchToolRef.csv", package = "EPATADA"))[, "POLLUTANT_NAME"] | |
| old <- utils::read.csv(system.file( | |
| "extdata", | |
| "CriteriaSearchToolRef.csv", | |
| package = "EPATADA" | |
| ))[, "POLLUTANT_NAME"] |
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system.file to read in example criteria table
updated criteria_table.rda read in
display data table for each chunk
cristinamullin
approved these changes
Nov 25, 2025
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some minor updates to handle errors in the mod 3 vignette.
MT.ParamRef.All <- TADA_CreateParamRef( tada.MT.clean, org_id = c("MTDEQ", "MDE_EASP", "21ARIZ"), auto_assign = "Org", excel = FALSE )MT.Criteria.auto3 <- TADA_DefineCriteriaMethodology( tada.MT.clean, org_id = c("MTDEQ","MDE_EASP", "21ARIZ"), # add other org_id to see output auto_assign = TRUE, epa304a = TRUE, displayUniqueId = TRUE, excel = FALSE )