Maintenance branch#877

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jbousquin wants to merge 44 commits intodevelopfrom

maintenance-branch

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jbousquin commented Mar 11, 2026

Maintenance & Data Refresh

github-actions bot added 18 commits

March 3, 2026 03:14


          Update reference files

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Collaborator Author

jbousquin commented Mar 11, 2026

Failures seem consistently related to:

::TADA_IDCensoredData(.data)
 13.     └─EPATADA::TADA_FlagMeasureQualifierCode(.data, clean = FALSE)

cristinamullin and others added 3 commits

March 11, 2026 18:07


          Merge branch 'develop' into maintenance-branch

23a6dc1


          Update reference files

dd26533


          Update example data

c43e9c3

Collaborator Author

jbousquin commented Mar 12, 2026

@cristinamullin feel free to take over this branch to resolve maintenance-bug (tests failing) as discussed on today's call


          Address minor bugs

6b6902c

Review and fix TADA_IDCensoredData, TADA_SimpleCensoredMethods and TADA_FlagMeasureQualifierCode

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Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

air

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 289 in 6b6902c

"ResultDetectionConditionText missing"

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 301 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Lines 303 to 304 in 6b6902c

    
           conds <- unique(cens$ResultDetectionConditionText[!is.na(cens$ResultDetectionConditionText)]) 
        
           if (length(conds) > 0 && any(!conds %in% cond.ref$ResultDetectionConditionText)) {

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 313 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 318 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 325 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Lines 327 to 328 in 6b6902c

    
           limits <- unique(cens$DetectionQuantitationLimitTypeName[!is.na(cens$DetectionQuantitationLimitTypeName)]) 
        
           if (length(limits) > 0 && any(!limits %in% limtype.ref$DetectionQuantitationLimitTypeName)) {

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 339 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 347 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 349 in 6b6902c

cens$TADA.Detection_Type %in% c("Non-Detect") &

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 355 in 6b6902c

cens$TADA.Detection_Type %in% c("Over-Detect") &

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 361 in 6b6902c

cens$TADA.Detection_Type %in% c("Other") &

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 368 in 6b6902c

cens$TADA.Detection_Type %in% c("Non-Detect", "Over-Detect", "Other") &

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 374 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 376 in 6b6902c

if ("Conflict between Condition and Limit" %in% cens$TADA.CensoredData.Flag) {

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 385 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 396 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 399 in 6b6902c

cens$TADA.CensoredData.Flag

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 411 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 418 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 426 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Lines 429 to 430 in 6b6902c

    
           idx_conflict <- cens.check$TADA.CensoredData.Flag == "Conflict between Condition and Limit" 
        
           cens.check$TADA.ResultMeasureValueDataTypes.Flag[idx_conflict] <- "Result Value/Unit Cannot Be Estimated From Detection Limit"

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 433 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Lines 565 to 569 in 6b6902c

    
           .data, 
        
           nd_method = "multiplier", 
        
           nd_multiplier = 0.5, 
        
           od_method = "as-is", 
        
           od_multiplier = "null"

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 582 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 588 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 595 in 6b6902c

    
           if (nd_method == "multiplier" & (!is.numeric(nd_multiplier) || length(nd_multiplier) != 1)) {

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 603 in 6b6902c

    
           if (od_method == "multiplier" & (!is.numeric(od_multiplier) || length(od_multiplier) != 1)) {

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 606 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 613 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 634 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 645 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Lines 649 to 650 in 6b6902c

    
           suppressWarnings(nd$TADA.ResultMeasureValue <- as.numeric(nd$TADA.ResultMeasureValue))

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 674 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Lines 678 to 679 in 6b6902c

    
           suppressWarnings(od$TADA.ResultMeasureValue <- as.numeric(od$TADA.ResultMeasureValue))

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 693 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 701 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 709 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/CensoredDataSuite.R

Line 713 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Lines 937 to 940 in 6b6902c

    
           .data, 
        
           clean = FALSE, 
        
           flaggedonly = FALSE, 
        
           define = TRUE

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 949 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Lines 953 to 954 in 6b6902c

	if (isTRUE(define)) TADA_CheckColumns(.data, "ResultIdentifier")

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 959 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 965 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 969 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 973 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 979 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 988 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 998 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1010 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1016 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1022 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1028 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Lines 1035 to 1038 in 6b6902c

    
           any(.x %in% flag.lists$suspect,     na.rm = TRUE) ~ "Suspect", 
        
           any(.x %in% flag.lists$nondetect,   na.rm = TRUE) ~ "Non-Detect", 
        
           any(.x %in% flag.lists$overdetect,  na.rm = TRUE) ~ "Over-Detect", 
        
           any(.x %in% flag.lists$pass,        na.rm = TRUE) ~ "Pass",

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1046 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Lines 1051 to 1052 in 6b6902c

	codes <- codes[!is.na(codes)] # drop NA to avoid if(NA) error

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1068 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1078 in 6b6902c

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1087 in 6b6902c

    
           if (sum(final.data$TADA.MeasureQualifierCode.Flag != "Suspect", na.rm = TRUE) == 0) {

[air] _{reported by reviewdog 🐶}

EPATADA/R/ResultFlagsDependent.R

Line 1103 in 6b6902c

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cristinamullin and others added 3 commits

March 12, 2026 13:39


          Merge branch 'develop' into maintenance-branch

d538c21


          [pre-commit.ci] auto fixes from pre-commit.com hooks

943afcd

for more information, see https://pre-commit.ci


          Update WORDLIST

c949617

Contributor

github-actions bot commented Mar 12, 2026 •

edited

Loading

coverage-report

File	Coverage		Missing
All files	`38%`	✅
R/ATTAINSCrosswalks.R	`24%`	✅	`72-884` `1094-1109` `1113-1117` `1122-1127` `1132` `1138-1158` `1164-1167` `1172-1193` `1204-1219` `1272-1275` `1448-1504` `1511-1774` `1959-1971` `1975-1978` `1983` `2011-2014` `2026-2029` `2037-2041` `2057-2061` `2077-2083` `2091-2106` `2111` `2117-2130` `2150-2153` `2306-2315` `2320-2330` `2490-2763` `2960-3491` `3646-3665` `3669-3672` `3681-3694` `3701-3721` `3729-3733` `3746-3750` `3781-3891` `3943-4100` `4105-4108` `4115-4258`
R/ATTAINSRefTables.R	`0%`	❌	`17-150`
R/autoClean.R	`89%`	✅	`152-153` `248-254` `413-414` `424-428`
R/autoFilter.R	`45%`	✅	`31-228` `346-348` `354` `384` `416-428`
R/CensoredDataSuite.R	`88%`	✅	`126-127` `245-246` `605-606` `611-613` `619` `622-624` `630` `637` `688-695` `698-699` `706-720` `726-729`
R/CriteriaComparison.R	`87%`	✅	`173-177` `182` `191-193` `240-265`
R/CriteriaMethods.R	`15%`	✅	`227-238` `242-244` `261-263` `268-270` `275-277` `287-300` `308-335` `505-509` `525-529` `635-961` `979-1158` `1186-1235` `1269-1829` `1847-2162`
R/CriteriaRefTables.R	`35%`	✅	`65-292` `308` `344` `348` `352` `358-368` `373-378` `405-470` `509` `519-521` `527` `570-572` `578` `611` `621-623` `629`
R/DataDiscoveryRetrieval.R	`31%`	✅	`199` `210-213` `230-233` `246-249` `255` `259` `276-751` `765-767` `775` `777` `782-789` `797` `803` `805` `809` `811` `817` `821` `823` `833` `835` `839` `845` `847` `851` `853` `858` `860` `864` `871-878` `886` `898-916` `927-933` `962-980` `994-1012` `1031` `1128-1159` `1264-1271` `1369-1405` `1498-1501` `1570-1748`
R/DepthProfile.R	`0%`	❌	`102-2020`
R/Figures.R	`0%`	❌	`64-1521`
R/GeospatialFunctions.R	`55%`	✅	`115-119` `194-196` `224-226` `310` `372-373` `376-378` `444-446` `501-503` `517` `583-585` `725` `804-809` `813` `871-873` `879-882` `949-953` `964-969` `975-980` `986-991` `998-1002` `1049-1050` `1057-1062` `1066` `1074-1244` `1386-1392` `1399-1681` `1785-1788` `1793-1816` `1861-1864` `1933` `1990-1998` `2103-2106` `2151-2155` `2207-2238` `2453-2463` `2510-2520` `2555-2557` `2623` `2627` `2656-2658` `2662` `2666-2691` `2783-2871` `3019-3048` `3175` `3196-3780`
R/GeospatialUtilities.R	`9%`	❌	`108` `132` `188-1748` `1808-1810` `1846`
R/MaintenanceScheduled.R	`0%`	❌	`42-433`
R/Maps.R	`5%`	❌	`26-640` `752` `761-905`
R/RequiredCols.R	`30%`	✅	`405-648`
R/ResultFlagsDependent.R	`59%`	✅	`60-62` `67` `110-119` `144-151` `254` `291-295` `317-320` `327-330` `346-362` `423` `446-448` `454-455` `461` `509-520` `526-533` `596-599` `611` `623-634` `656-658` `671-677` `748-875` `944-947` `1085-1087` `1101-1108`
R/ResultFlagsIndependent.R	`69%`	✅	`70-72` `78` `123-157` `265-267` `272` `276` `280` `290` `388-391` `403-435` `525-527` `532-534` `543` `663-681` `696-721` `810-812` `817-819` `828` `948-966` `981-1168` `1213` `1235-1254` `1267-1272` `1412` `1416` `1474-1489` `1494` `1498-1505` `1569-1570` `1665-1681` `1753-1758` `1879-1893`
R/Tables.R	`93%`	✅	`19-30`
R/TADAGeospatialRefLayers.R	`0%`	❌	`8-13`
R/TADARefTables.R	`10%`	✅	`86-88` `105-111` `234` `268-772` `837` `846-1210`
R/Transformations.R	`86%`	✅	`76-77` `82-84` `221-232` `394-395` `444-447` `515` `792` `822-837` `924-925` `942` `973-984` `987-1004` `1008-1016`
R/UnitConversions.R	`81%`	✅	`147` `307-315` `421` `428` `435` `442-444` `451` `458-460` `469-472` `482-484` `634-716` `738-784` `807` `855` `868-882` `1115-1119` `1199` `1276-1279` `1321`
R/Utilities.R	`58%`	✅	`12-16` `504` `622-623` `627` `632-634` `729` `858-869` `1013-1015` `1049-1050` `1080-1084` `1194-1195` `1199-1200` `1210-1214` `1219-1224` `1266-1625` `1651-1652` `1665-1668` `1739-2109` `2136-2140` `2149-2153` `2370` `2423` `2429-2432` `2436` `2447` `2466-2467` `2469-2484` `2486` `2488` `2490-2491` `2493-2494` `2496-2499` `2501` `2503` `2506` `2521` `2527` `2535` `2540` `2548-2553` `2558-2563` `2582` `2592-2593`
R/WQPWQXRefTables.R	`70%`	✅	`92-141` `164-200` `241-330` `340` `363-383` `747-749` `1033-1042` `1052-1061` `1064-1074` `1088-1154` `1176-1178` `1199-1208` `1235` `1256-1265` `1292` `1313-1322` `1346` `1367-1376` `1398-1403` `1424-1502` `1532-1534` `1555-1564` `1584` `1613` `1617` `1626` `1637` `1648` `1664` `1667` `1680` `1686-1700` `1714-1723`

Minimum allowed coverage is 10%

Generated by 🐒 cobertura-action against ac115b6


          address check notes

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pre-commit-ci bot and others added 2 commits

March 12, 2026 19:07


          [pre-commit.ci] auto fixes from pre-commit.com hooks

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          Update TADA_SimpleCensoredMethods.Rd

dbe3838

Collaborator

cristinamullin commented Mar 12, 2026

It's Thursday so the WQX/WQP data retrieval is failing. Will try the tests again tomorrow.

github-actions bot and others added 3 commits

March 13, 2026 03:11


          Update reference files

7d4a184


          Update example data

395de32


          update refs and example data

ac115b6

cristinamullin mentioned this pull request

Refactor ref file code and add tests #878

Open

20 tasks

Collaborator

cristinamullin commented Mar 13, 2026

No longer working on this branch, continuing the work here: #878

github-actions bot added 13 commits

March 14, 2026 03:08


          Update reference files

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          Update example data

3d9f4d0


          Update reference files

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          Update reference files

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          Update example data

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          Update reference files

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          Update example data

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          Update reference files

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          Update reference files


          Update example data

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