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minor tweaks #89

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Merged
jakegreif merged 1 commit into from
May 13, 2022
Merged

minor tweaks #89

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12 changes: 6 additions & 6 deletions vignettes/WQPDataHarmonization.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@ Load TADA library and update internal TADA package validation and reference tabl
library(TADA)
UpdateWQXCharValRef()
UpdateMeasureUnitRef()
HarmonizationRefTable()
```

Read in WQP data using WQP web services directly
Expand Down Expand Up @@ -59,18 +58,18 @@ TADAProfileRaw=TADAdataRetrieval()

#Run all dependencies
TADAProfileClean=MeasureValueSpecialCharacters(TADAProfileRaw)
TADAProfileClean1=autoclean(TADAProfileClean)
#runs as part of retrieval: TADAProfileClean1=autoclean(TADAProfileClean)
TADAProfileClean2=DepthProfileData(TADAProfileClean)
TADAProfileClean3=AggregatedContinuousData(TADAProfileClean2, clean=TRUE)
TADAProfileClean4=WQXTargetUnits(TADAProfileClean3, convert=TRUE)
TADAProfileClean4=WQXTargetUnits(TADAProfileClean3, transform=TRUE)
```

Run result flag functions and address flagged data
```{r}
TADAProfileClean5=UncommonAnalyticalMethodID(TADAProfileClean4)
TADAProfileClean6=PotentialDuplicateRowID(TADAProfileClean5, clean=TRUE)
TADAProfileClean7=AboveNationalWQXUpperThreshold(TADAProfileClean6, clean=TRUE)
TADAProfileClean8=BelowNationalWQXUpperThreshold(TADAProfileClean6, clean=TRUE)
TADAProfileClean7=AboveNationalWQXUpperThreshold(TADAProfileClean6, transform=TRUE)
TADAProfileClean8=BelowNationalWQXUpperThreshold(TADAProfileClean6, transform=TRUE)
TADAProfileClean9=QAPPapproved(TADAProfileClean6)
TADAProfileClean10=QAPPDocAvailable(TADAProfileClean6)
TADAProfileClean11=InvalidCoordinates(TADAProfileClean6)
Expand All @@ -81,5 +80,6 @@ TADAProfileClean14=InvalidResultUnit(TADAProfileClean13, clean=TRUE)

Transform Characteristic, Speciation, and Unit values to TADA Standards
```{r}
TADAProfileClean15=HarmonizeData(TADAProfileClean14, transform=TRUE)
TADAProfileClean15=HarmonizationRefTable(TADAProfileClean14)
TADAProfileClean16=HarmonizeData(TADAProfileClean15, transform=TRUE)
```
2 changes: 1 addition & 1 deletion vignettes/testing.Rmd
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Expand Up @@ -48,7 +48,7 @@ WQP query URL: https://www.waterqualitydata.us/#statecode=US%3A42&characteristic

```{r}
#get PA nutrient data
TADAProfileRaw=readWQPwebservice("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A09&countycode=US%3A09%3A003&characteristicType=Nutrient&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
TADAProfileRaw=readWQPwebservice("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A42&siteType=Lake%2C%20Reservoir%2C%20Impoundment&sampleMedia=water&sampleMedia=Water&characteristicType=Nutrient&startDateLo=01-01-2019&startDateHi=01-01-2022&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
```


Expand Down