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testing vignette #81

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Merged
jakegreif merged 1 commit into from
May 10, 2022
Merged

testing vignette #81

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42 changes: 0 additions & 42 deletions R/Utilities.R
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Original file line number Diff line number Diff line change
@@ -1,26 +1,3 @@
#' Apply Conversions
#'
#' **placeholder text for function description
#'
#' @param .data TADA dataset
#' @param Include Conversions to execute (should input be a column name? Or
#' groups of columns, which have their own group ID? Where would we put this
#' group ID info, another reference table? within the function?)
#' @param Exclude ibid, but conversions to not execute
#'
#' @return Full TADA dataset with data conversions executed. Function defaults
#' to convert the following: (**note all columns/type of data included in
#' conversions).
#' Users can specify which conversions to exclude.
#' @export
#'


ApplyConversions <- function(.data, Include, Exclude){

}


#' AutoFilter
#'
#' This function can be used to autofilter and simplify a WQP dataset.
Expand All @@ -39,7 +16,6 @@ ApplyConversions <- function(.data, Include, Exclude){
#' @export



AutoFilter <- function(.data, clean = TRUE){

field.names <- colnames(.data)
Expand Down Expand Up @@ -71,24 +47,6 @@ AutoFilter <- function(.data, clean = TRUE){
}


#' Filter
#'
#' @param .data TADA dataset
#'
#' @return Full TADA dataset with data removed
#'
#' @export


Filter <- function(.data){

# Remove all data where media name does NOT equal WATER (ignore punctuation)
dplyr::filter(.data, ActivityMediaName == "Water")

return(.data)
}


#' RemoveEmptyColumns
#'
#' @param .data TADA dataset
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36 changes: 36 additions & 0 deletions vignettes/testing.Rmd
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Expand Up @@ -16,8 +16,12 @@ knitr::opts_chunk$set(
)
```

Load TADA library and update internal TADA package validation and reference tables
```{r setup}
library(TADA)
UpdateWQXCharValRef()
#UpdateMeasureUnitRef()
#HarmonizationRefTable()
```

Read in WQP data using WQP web services directly
Expand All @@ -43,12 +47,44 @@ original data filters, but it cannot be used to download the data.
WQP query URL: https://www.waterqualitydata.us/#statecode=US%3A42&characteristicType=Nutrient&mimeType=csv&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET

```{r}
#get PA nutrient data
TADAProfileRaw=readWQPwebservice("https://www.waterqualitydata.us/data/Result/search?statecode=US%3A42&characteristicType=Nutrient&mimeType=csv&zip=yes&dataProfile=resultPhysChem&providers=NWIS&providers=STEWARDS&providers=STORET")
```


Clean raw data for TADA use case
```{r}
#autoclean
TADAProfileClean=AggregatedContinuousData(TADAProfileClean)
```

Run result flag functions and address flagged data
```{r}
#TADAProfileClean=UncommonAnalyticalMethodID(TADAProfileClean)
TADAProfileClean=PotentialDuplicateRowID(TADAProfileClean)
TADAProfileClean=AboveNationalWQXUpperThreshold(TADAProfileClean)
TADAProfileClean=BelowNationalWQXUpperThreshold(TADAProfileClean)
TADAProfileClean=QAPPapproved(TADAProfileClean)
TADAProfileClean=QAPPDocAvailable(TADAProfileClean)
TADAProfileClean=InvalidCoordinates(TADAProfileClean)
TADAProfileClean=InvalidFraction(TADAProfileClean)
TADAProfileClean=InvalidSpeciation(TADAProfileClean)
TADAProfileClean=InvalidResultUnit(TADAProfileClean)
```

Address result values with special characters
```{r}
MeasureValueSpecialCharacters
```

Apply unit conversions
```{r}
DepthProfileData
WQXTargetUnits
```

Transform Characteristic, Speciation, and Unit values to TADA Standards
```{r}
HarmonizeData
```