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Merged
cristinamullin merged 12 commits into from
Nov 25, 2025
Merged

Updates to mod3 functions and vignettes #713

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9ffdda5
code cleanup and minor bug fixes
wokenny13 Nov 22, 2025
00bf089
handle of invalid arg inputs in TADA_DefineCriteriaMethods
wokenny13 Nov 24, 2025
ae68b0f
bug fixes
wokenny13 Nov 24, 2025
71c0cec
Update R/ATTAINSCrosswalks.R
wokenny13 Nov 24, 2025
60c0884
handle test failure and run styler
wokenny13 Nov 24, 2025
78a0164
mod 3 vignette knit eval = T
wokenny13 Nov 24, 2025
6934580
Merge branch 'develop' into Updates-to-Mod3-Functions-and-Vignettes
cristinamullin Nov 24, 2025
6ac76da
Merge branch 'Updates-to-Mod3-Functions-and-Vignettes' of https://git…
wokenny13 Nov 24, 2025
cc4b695
Updates to Mod3Vignette
wokenny13 Nov 24, 2025
84eefe0
Update ExampleMod3Workflow.Rmd
wokenny13 Nov 24, 2025
ed80109
Update ExampleMod3Workflow.Rmd
wokenny13 Nov 25, 2025
e14140c
Update ExampleMod3Workflow.Rmd
wokenny13 Nov 25, 2025
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133 changes: 61 additions & 72 deletions R/ATTAINSCrosswalks.R
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Original file line number Diff line number Diff line change
Expand Up @@ -923,6 +923,7 @@ TADA_UpdateATTAINSAUMLCrosswalk <- function(org_id = NULL,
#'
TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assign = c("None", "All", "Org"),
excel = FALSE, overwrite = FALSE) {
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[air] reported by reviewdog 🐶

Suggested change
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
) {

# argument input selection for auto_assign
auto_assign <- match.arg(auto_assign)

# Return an empty dataframe with column names only if a user does not define any arg inputs.
Expand Down Expand Up @@ -961,10 +962,7 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi
stop("TADA.CreateParamRef: org_id must be a character vector")
}

# Allows for users to crosswalk parameters by multiple orgs.
org_id <- as.list(org_id)

# If more than 1 org, it will create n duplicate rows for each TADA.ComparableDataIdentifier.
# If more than 1 org, it will create n duplicate rows for each TADA.ComparableDataIdentifier.
if (length(org_id) > 1) {
print(paste0(
"TADA.CreateParamRef: More than one org_name was defined in your dataframe. ",
Expand Down Expand Up @@ -1028,10 +1026,20 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi

# Pulls in all unique combinations of TADA.ComparableDataIdentifier in user's dataframe.
TADA_param <- dplyr::distinct(
.data[, c("TADA.CharacteristicName", "TADA.ComparableDataIdentifier")]
.data[, c("TADA.ComparableDataIdentifier"), drop = FALSE]
) %>%
tidyr::uncount(weights = length(org_id)) %>%
dplyr::mutate(ATTAINS.OrganizationIdentifier = as.character(rep(org_id, nrow(.) / length(org_id))))
dplyr::distinct() %>%
dplyr::mutate(ATTAINS.OrganizationIdentifier = NA_character_) %>%
tidyr::complete(
TADA.ComparableDataIdentifier,
ATTAINS.OrganizationIdentifier = org_id
) %>%
dplyr::filter(!is.na(ATTAINS.OrganizationIdentifier)) %>%
dplyr::left_join(
.data[, c("TADA.ComparableDataIdentifier", "TADA.CharacteristicName")],
relationship = "many-to-many"
) %>%
dplyr::distinct()

# Pulls in all domain values of parameter and use names in ATTAINS.
ATTAINS_param_all <- utils::read.csv(
Expand Down Expand Up @@ -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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[air] reported by reviewdog 🐶

Suggested change
TADA.CharacteristicName, TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier,
TADA.CharacteristicName,
TADA.ComparableDataIdentifier,
ATTAINS.OrganizationIdentifier,

ATTAINS.ParameterName # , EPA304A.PollutantName
) %>%
dplyr::left_join(ATTAINSParameterWQPCharRef, by = c("TADA.CharacteristicName" = "CharacteristicName"), relationship = "many-to-many") %>%
dplyr::left_join(
ATTAINSParameterWQPCharRef,
by = c("TADA.CharacteristicName" = "CharacteristicName"),
relationship = "many-to-many"
) %>%
dplyr::mutate(ATTAINS.ParameterName = ATTAINS.ParameterName.y) %>%
dplyr::select(
TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier,
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[air] reported by reviewdog 🐶

Suggested change
TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier,
TADA.ComparableDataIdentifier,
ATTAINS.OrganizationIdentifier,

Expand Down Expand Up @@ -1165,69 +1177,21 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi
"No Crosswalk was provided and no exact matches were found for this organization."
)
) %>%
dplyr::filter(!is.na(ATTAINS.ParameterName)) %>%
dplyr::distinct()
}

# User provides their own user supplied parameter crosswalk
if (!is.null(paramRef)) {
# Identifies NEW rows in your current CreateParamRef data frame that are missing from your paramRef input -
# i.e. current WQP Characteristics that you have not defined a crosswalk for
Flag1 <- CreateParamRef %>%
# anti_join will identify observations that exist in your 1st data frame, but not in the 2nd data frame.
dplyr::anti_join(
paramRef,
by =
c(
"TADA.ComparableDataIdentifier", "ATTAINS.OrganizationIdentifier"
# "ATTAINS.ParameterName", ATTAINS.FlagParameterName) # Exclude any dynamic values or possible NAs
)
) %>%
dplyr::mutate(
Flag.ParameterInput =
"Suspect: Your paramRef argument did not include this TADA.ComparableDataIdentifier. Please ensure this is not a new WQP Characteristic Name entry that needs to be crosswalked."
)

# identifies if a user has MODIFIED any ATTAINS.ParameterName values by TADA.ComparableDataIdentifier and ATTAINS.OrganizationIdentifier
Flag2 <- paramRef %>%
dplyr::anti_join(
CreateParamRef,
by = c(
"TADA.ComparableDataIdentifier", "ATTAINS.ParameterName", "ATTAINS.OrganizationIdentifier"
)
) %>%
dplyr::mutate(
Flag.ParameterInput =
"This ATTAINS.ParameterName crosswalk was MODIFIED by your input(s) for this TADA.ComparableDataIdentifier."
) %>%
dplyr::mutate(
ATTAINS.FlagParameterName = dplyr::case_when(
ATTAINS.ParameterName == "No parameter match for TADA.ComparableDataIdentifier" | is.na(ATTAINS.ParameterName) ~
"No parameter crosswalk provided for TADA.ComparableDataIdentifier. Parameter will not be used for assessment.",
!ATTAINS.ParameterName %in% ATTAINS_param_all$ATTAINS.ParameterName ~
"Parameter name is not included in ATTAINS, contact ATTAINS to add parameter name to Domain List.",
ATTAINS.ParameterName %in% ATTAINS_param_all$ATTAINS.ParameterName & !paste(ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName) %in% paste(ATTAINS_param_all$ATTAINS.OrganizationIdentifier, ATTAINS_param_all$ATTAINS.ParameterName) ~
"Parameter name is listed as a prior cause in ATTAINS, but not for this organization.",
paste(ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName) %in% paste(ATTAINS_param_all$ATTAINS.OrganizationIdentifier, ATTAINS_param_all$ATTAINS.ParameterName) ~
"Parameter name is listed as a prior cause in ATTAINS for this organization."
)
)

CreateParamRef <- paramRef %>%
dplyr::select("TADA.ComparableDataIdentifier", "ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName") %>%
dplyr::full_join(
Flag1 %>%
dplyr::full_join(
Flag2,
by =
c(
"TADA.ComparableDataIdentifier", "ATTAINS.OrganizationIdentifier",
"ATTAINS.ParameterName", "ATTAINS.FlagParameterName", "Flag.ParameterInput"
)
),
by = c("TADA.ComparableDataIdentifier", "ATTAINS.OrganizationIdentifier", "ATTAINS.ParameterName")
) %>%
dplyr::mutate(Flag.ParameterInput = dplyr::if_else(is.na(ATTAINS.ParameterName), NA, Flag.ParameterInput)) %>%
dplyr::rows_patch(CreateParamRef, by = "TADA.ComparableDataIdentifier") %>%
paramRef <- paramRef %>%
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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[air] reported by reviewdog 🐶

Suggested change
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"
) %>%

dplyr::filter(!is.na(ATTAINS.ParameterName))

CreateParamRef <- CreateParamRef %>%
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")]) %>%
Comment on lines +1192 to +1194
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[air] reported by reviewdog 🐶

Suggested change
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"
)]) %>%

dplyr::mutate(
ATTAINS.FlagParameterName = dplyr::case_when(
ATTAINS.ParameterName == "Not Applicable for Analysis." | is.na(ATTAINS.ParameterName) ~
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[air] reported by reviewdog 🐶

Suggested change
ATTAINS.ParameterName == "Not Applicable for Analysis." | is.na(ATTAINS.ParameterName) ~
ATTAINS.ParameterName == "Not Applicable for Analysis." |
is.na(ATTAINS.ParameterName) ~

Expand All @@ -1243,11 +1207,37 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi
dplyr::select(
TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName,
ATTAINS.FlagParameterName, Flag.ParameterInput
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[air] reported by reviewdog 🐶

Suggested change
TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName,
ATTAINS.FlagParameterName, Flag.ParameterInput
TADA.ComparableDataIdentifier,
ATTAINS.OrganizationIdentifier,
ATTAINS.ParameterName,
ATTAINS.FlagParameterName,
Flag.ParameterInput

) %>%
dplyr::distinct()
)

# remove intermediate object Flag1
rm(Flag1, Flag2)

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[air] reported by reviewdog 🐶

Suggested change

# paramRef %>%
# dplyr::select(ATTAINS.OrganizationIdentifier, TADA.ComparableDataIdentifier, ATTAINS.ParameterName) %>%
# dplyr::full_join(
# CreateParamRef,
# by = dplyr::join_by(ATTAINS.OrganizationIdentifier, TADA.ComparableDataIdentifier)) %>%
# dplyr::mutate(
# Flag.ParameterInput = dplyr::if_else(
# paste(TADA.ComparableDataIdentifier, ATTAINS.ParameterName) %in% paste(paramRef$TADA.ComparableDataIdentifier, paramRef$ATTAINS.ParameterName),
# "This crosswalk was provided through a user supplied table",
# Flag.ParameterInput
# )
# ) %>%
# dplyr::mutate(
# ATTAINS.FlagParameterName = dplyr::case_when(
# ATTAINS.ParameterName == "Not Applicable for Analysis." | is.na(ATTAINS.ParameterName) ~
# "No ATTAINS.ParameterName crosswalk provided for TADA.ComparableDataIdentifier. Parameter will not be used for assessment.",
# !ATTAINS.ParameterName %in% ATTAINS_param_all$ATTAINS.ParameterName ~
# "Parameter name is not included in ATTAINS, contact ATTAINS to add ATTAINS.ParameterName name to Domain List.",
# ATTAINS.ParameterName %in% ATTAINS_param_all$ATTAINS.ParameterName & !paste(ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName) %in% paste(ATTAINS_param_all$ATTAINS.OrganizationIdentifier, ATTAINS_param_all$ATTAINS.ParameterName) ~
# "Parameter name is listed as a prior cause in ATTAINS, but not for this organization.",
# paste(ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName) %in% paste(ATTAINS_param_all$ATTAINS.OrganizationIdentifier, ATTAINS_param_all$ATTAINS.ParameterName) ~
# "Parameter name is listed as a prior cause in ATTAINS for this organization"
# )
# ) %>%
# dplyr::select(
# TADA.ComparableDataIdentifier, ATTAINS.OrganizationIdentifier, ATTAINS.ParameterName,
# ATTAINS.FlagParameterName, Flag.ParameterInput
# )
}

# Excel ref files to be stored in the Downloads folder location.
Expand Down Expand Up @@ -1491,7 +1481,6 @@ TADA_CreateParamRef <- function(.data, org_id = NULL, paramRef = NULL, auto_assi
#' argument input, by joining the ATTAINS.WaterType of the AUs defined in
#' your useAURef to the ATTAINS.WaterType found from ATTAINS Expert Query.
#'
#'
#' Otherwise, users can still
#' proceed by overriding the data validation by value pasting in Excel.
#' Users will be warned in the ATTAINS.FlagUseName column if they choose to
Expand Down Expand Up @@ -1866,7 +1855,7 @@ TADA_CreateUseParamRef <- function(.data, org_id = NULL, paramRef = NULL, usePar
if ("IncludeOrExclude" %in% names(useParamRef)) {
useParamRef <- useParamRef %>%
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"))
Comment on lines 1857 to +1858
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[air] reported by reviewdog 🐶

Suggested change
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")
)

} 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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[air] reported by reviewdog 🐶

Suggested change
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."
)

useParamRef <- useParamRef %>%
Expand Down
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