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TADA_CreateParamRef() and TADA_CreateParamUseRef() #555

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33429a3
TADA_CreateParamRef() and TADA_CreateParamUseRef()
wokenny13 Dec 13, 2024
7e5c6dd
pushed devtool document()
wokenny13 Dec 13, 2024
785e4c7
Merge branch 'develop' into Create-Module-3-Reference-Tables
wokenny13 Dec 13, 2024
359d20e
Update WORDLIST
hillarymarler Dec 16, 2024
df513ad
Update R documentation for errors
wokenny13 Dec 16, 2024
2816e3e
updates
wokenny13 Dec 16, 2024
c9d4ad2
arg input name misspell fix and removal of intermediate objects
wokenny13 Dec 16, 2024
67da081
Update CriteriaInputs.R
wokenny13 Dec 16, 2024
fb47bfd
Update CriteriaInputs.R
wokenny13 Dec 16, 2024
c513fb7
Changed order of creating ATTAINS_param_all variable
wokenny13 Dec 16, 2024
75be2ec
Update test-URLChecker.R
hillarymarler Dec 16, 2024
8514702
Update CriteriaInputs.R
hillarymarler Dec 16, 2024
797230f
Update CriteriaInputs.R
hillarymarler Dec 17, 2024
b328058
Updated ATTAINS.FlagParameterName
wokenny13 Dec 17, 2024
14a7f8c
Mod 3 vignette testing and updates
wokenny13 Dec 18, 2024
5359692
Update documentation and excel formula logic
wokenny13 Dec 20, 2024
ab32395
Speed up loops within both functions and additional edits
wokenny13 Dec 20, 2024
4461bfa
Additional comments and further updates
wokenny13 Dec 23, 2024
44f9246
Addressed some ref documentation
wokenny13 Dec 23, 2024
38912fd
Merge branch 'develop' into Create-Module-3-Reference-Tables
cristinamullin Dec 23, 2024
45df19d
run spelling check and update wordlist
cristinamullin Dec 23, 2024
22c0f68
Merge branch 'Create-Module-3-Reference-Tables' of https://github.com…
wokenny13 Dec 24, 2024
7b69b29
Update CST EPA 304a Ref table
wokenny13 Dec 24, 2024
e6b7357
CreateParamUseRef() and CST ref
wokenny13 Dec 24, 2024
661a63e
further updates to reflect dependencies on CST ref file changes
wokenny13 Dec 24, 2024
6cc04b1
Format updates, text updates, mod 3 vignette updates
wokenny13 Dec 27, 2024
b4c3a71
Merge branch 'develop' into Create-Module-3-Reference-Tables
wokenny13 Dec 27, 2024
98c22b9
Update CriteriaInputs.R
wokenny13 Dec 27, 2024
17f59e7
update mod 3 vignette
wokenny13 Dec 27, 2024
20e0ddc
mod 3 vignette update
wokenny13 Dec 30, 2024
bb694df
global variables message fix
wokenny13 Dec 31, 2024
42c06f3
Updates, global variable message handling, and text fixes
wokenny13 Dec 31, 2024
8970ec5
Notes and minor fixes
wokenny13 Jan 2, 2025
7396485
Removed function CreateAUIDRef()
wokenny13 Jan 3, 2025
6947abc
mods 1 and 3 review
cristinamullin Jan 3, 2025
b0bd5b4
Merge branch 'Create-Module-3-Reference-Tables' of https://github.com…
cristinamullin Jan 3, 2025
bd3a842
update example data
cristinamullin Jan 7, 2025
7db1fb1
update docs
cristinamullin Jan 7, 2025
7988b1b
update WQX ref and add test
cristinamullin Jan 8, 2025
2d0908a
AURef update, and CST.csv update
wokenny13 Jan 8, 2025
c2f5236
fix pH unit harmonization
cristinamullin Jan 8, 2025
3863ef5
style, update example data
cristinamullin Jan 8, 2025
dad6805
Mod 3 update and TADA_CreateAURef() function included
wokenny13 Jan 8, 2025
cf8c378
Merge branch 'Create-Module-3-Reference-Tables' of https://github.com…
wokenny13 Jan 8, 2025
d221275
Removed AU_ML crosswalk draft from this branch
wokenny13 Jan 8, 2025
cb3606a
remove export of in development functions in namespace
wokenny13 Jan 10, 2025
5bdc2a7
update TADAModule1_AdvancedTraining.Rmd
cristinamullin Jan 10, 2025
8a68960
use PH_NA_NA_STD UNITS
cristinamullin Jan 10, 2025
4c9702f
Update TADAModule3.Rmd
wokenny13 Jan 10, 2025
c9e85a0
Merge branch 'Create-Module-3-Reference-Tables' of https://github.com…
wokenny13 Jan 10, 2025
9acdd69
flag suspect pH units
cristinamullin Jan 10, 2025
8df3e2b
Merge branch 'Create-Module-3-Reference-Tables' of https://github.com…
wokenny13 Jan 10, 2025
80a4c70
update TADA_GetATTAINS docs
cristinamullin Jan 10, 2025
fc8dd69
Merge branch 'Create-Module-3-Reference-Tables' of https://github.com…
wokenny13 Jan 10, 2025
660a6dd
update refs, mod 3 updates
cristinamullin Jan 10, 2025
1a3ac3b
Mod 3 vignette updates
wokenny13 Jan 10, 2025
56542f9
Merge branch 'Create-Module-3-Reference-Tables' of https://github.com…
wokenny13 Jan 10, 2025
99831f7
Created a Dataframe with button function
wokenny13 Jan 10, 2025
b0820fd
Added missing @param
wokenny13 Jan 10, 2025
8414798
Update TADA_CreateParamUseRef.Rd
wokenny13 Jan 10, 2025
9a5d59a
Update TADAModule3.Rmd
wokenny13 Jan 14, 2025
3fa96ca
Update TADAModule3.Rmd
wokenny13 Jan 15, 2025
2339205
Update test-Utilities.R
wokenny13 Jan 21, 2025
38aabd8
Update CriteriaInputs.R
wokenny13 Jan 21, 2025
73b030c
Update TADAModule3.Rmd
hillarymarler Jan 21, 2025
d4b81e7
Update TADAModule3.Rmd
hillarymarler Jan 21, 2025
91363a1
Changed Organization_name to Organization_identifier
wokenny13 Jan 24, 2025
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3 changes: 2 additions & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,8 @@ Imports:
nhdplusTools,
arcgislayers,
httr,
jsonlite
jsonlite,
openxlsx
Depends:
R (>= 3.5.0)
Suggests:
Expand Down
4 changes: 4 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ export(TADA_ConvertResultUnits)
export(TADA_ConvertSpecialChars)
export(TADA_CreateComparableID)
export(TADA_CreatePairRef)
export(TADA_CreateParamRef)
export(TADA_CreateParamUseRef)
export(TADA_CreateUnitRef)
export(TADA_DataRetrieval)
export(TADA_DepthProfilePlot)
Expand All @@ -41,10 +43,12 @@ export(TADA_FlagSpeciation)
export(TADA_FlaggedSitesMap)
export(TADA_FormatDelimitedString)
export(TADA_GetATTAINS)
export(TADA_GetATTAINSParamUseOrgRef)
export(TADA_GetActivityTypeRef)
export(TADA_GetCharacteristicRef)
export(TADA_GetDetCondRef)
export(TADA_GetDetLimitRef)
export(TADA_GetEPA304aRef)
export(TADA_GetMeasureQualifierCodeRef)
export(TADA_GetMeasureUnitRef)
export(TADA_GetMonLocTypeRef)
Expand Down
699 changes: 699 additions & 0 deletions R/CriteriaInputs.R

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37 changes: 37 additions & 0 deletions R/TADARefTables.R
Original file line number Diff line number Diff line change
@@ -1,3 +1,40 @@
#' ATTAINS Parameter and Use Name by Organization Reference Key
#'
#' Function downloads and returns the newest available ATTAINS domain values
#' reference dataframe summarized by parameter, use and organization.
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Add clarifying language about parameters (listed as cause by org in previous assessments)

#' This dataframe is used in TADA_CreateParamRef() and
#' TADA_CreateParamUseRef() as the basis for the pulling in prior ATTAINS
#' parameter names and use name by organization name. This helps to filter
#' selections of drop down values and creating parameter and use combination
#' summaries that will need to be defined.
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I think you could remove "that will need to be defined"

#'
#' @return Dataframe of ATTAINS parameter and use name by organization
#'
#' @export

TADA_GetATTAINSParamUseOrgRef <- function() {
ref <- utils::read.csv(system.file("extdata", "ATTAINSParamUseEntityRef.csv", package = "EPATADA"))
return(ref)
}

#' EPA304a Criteria Search Tool Reference Key
#'
#' Function downloads and returns the newest available EPA 304a Criteria Search Tool
#' reference dataframe. This dataframe is used in TADA_CreateParamRef() and
#' TADA_CreateParamUseRef() as the basis for the pulling in EPA304a recommended
#' pollutant name and use_name for assessment under the CWA.
#'
#' (Currently only numeric priority characteristic in TADA are the focus.)
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Add info on where to find list of TADA priority chars?

#'
#' @return Dataframe of EPA304a recommended standards for a pollutant and use name.
#'
#' @export

TADA_GetEPA304aRef <- function() {
ref <- utils::read.csv(system.file("extdata", "CST.csv", package = "EPATADA"))
return(ref)
}

#' Nutrient Summation Reference Key
#'
#' Function downloads and returns the newest available nutrient summation
Expand Down
21 changes: 21 additions & 0 deletions inst/WORDLIST
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ BiologicalIntentName
CCO
CNENVSER
CRS
CWA
CalculateTotalNP
CalculateTotalNitrogen
CensoredData
Expand All @@ -43,6 +44,7 @@ CharacteristicsForDepthProfile
Chilton
ComparableDataIdentifier
ComparableDataIdentifiers
ComparableDataIentifier
ConsolidatedDepth
ConstructionDateText
ContinuousData
Expand All @@ -54,7 +56,10 @@ ConvertSpecialChars
CountyCode
CreateComparableID
CreatePairRef
CreateParamRef
CreateParamUseRef
CreateUnitRef
CriteriaSearchTool
DataQuality
DataRetreival
DataRetrieval
Expand Down Expand Up @@ -88,8 +93,10 @@ FlagDepthCategory
FlagFraction
FlagMeasureQualifierCode
FlagMethod
FlagParameterName
FlagResultUnit
FlagSpeciation
FlagUseName
FractionAssumptions
FullPhysChem
Geospatial
Expand Down Expand Up @@ -151,6 +158,7 @@ Msr
MultipleOrgDupGroupID
MultipleOrgDuplicate
NA's
NCTC
NCTCShepherdstown
ND's
NHD
Expand All @@ -166,6 +174,7 @@ NutrientSummationGroup
OA
ORs
Okabe
OrgName
OrganizationFormalName
OrganizationIdentifier
OutsideUSA
Expand All @@ -175,7 +184,10 @@ PUEBLOOFTESUQUE
PairReplicates
PairingGroup
PairingGroupRank
ParameterName
ParameterNames
Pojoaque
PollutantName
ProjectFileUrl
ProjectName
QAPP
Expand Down Expand Up @@ -228,6 +240,7 @@ ResultWeightBasisText
RetainRequired
Rmd
Rtools
RunKeyFlagFunctions
SFNOES
STORET
SampleCollectionEquipmentName
Expand All @@ -247,6 +260,7 @@ StringB
SubstituteDeprecatedChars
SummarizeColumn
SuspectCoordinates
Sys
TADA
TADADataRetrieval
TADAGeospatialRefLayers
Expand All @@ -259,6 +273,7 @@ TargetUnit
Tesuque
UG
USEPA
USERPROFILE
USGS
USGS's
Uncomment
Expand Down Expand Up @@ -317,6 +332,7 @@ countycode
cristinamullin
crs
csv
cwa
dailyagg
dataProfile
dataRetrieval
Expand Down Expand Up @@ -346,6 +362,7 @@ geospatially
getFeatureLayer
getLayer
getPopup
getenv
ggplot
github
gitignore
Expand All @@ -362,6 +379,7 @@ magrittr
manys
mimeType
mlt
myfileRef
nd
nondetections
nonstandardized
Expand All @@ -372,6 +390,7 @@ orgs
ousideUSA
outsideUSA
param
paramRef
params
pch
pchIcons
Expand Down Expand Up @@ -414,7 +433,9 @@ waterdata
waterqualitydata
webserviceurl
wikipedia
wqs
wqx
writeLayer
www
xlsx
σ
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