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Check water quality exchange (wqx) metadata input

Source: R/checkMWRwqx.R
checkMWRwqx.Rd

Check water quality exchange (wqx) metadata input

Usage

checkMWRwqx(wqxdat, warn = TRUE)

Arguments

wqxdat

input data frame

warn

logical to return warnings to the console (default)

Value

wqxdat is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding. Checks with warnings can be fixed at the discretion of the user before proceeding.

Details

This function is used internally within readMWRwqx to run several checks on the input data for conformance with downstream functions

The following checks are made:

  • Column name spelling: Should be the following: Parameter, Sampling Method Context, Method Speciation, Result Sample Fraction, Analytical Method, Analytical Method Context

  • Columns present: All columns from the previous check should be present

  • Unique parameters: Values in Parameter should be unique (no duplicates)

  • Parameter: Should match parameter names in the Simple Parameter or WQX Parameter columns of the paramsMWR data (warning only)

Examples

library(dplyr)

wqxpth <- system.file('extdata/ExampleWQX.xlsx', package = 'MassWateR')

wqxdat <- readxl::read_excel(wqxpth, na = c('NA', 'na', ''), col_types = 'text')
    
checkMWRwqx(wqxdat)
#> Running checks on WQX metadata...
#> 	Checking column names... OK
#> 	Checking all required columns are present... OK
#> 	Checking unique parameters... OK
#> 	Checking Parameter formats... OK
#> 
#> All checks passed!
#> # A tibble: 8 × 6
#>   Parameter    Sampling Method Cont…¹ `Method Speciation` Result Sample Fracti…²
#>   <chr>        <chr>                  <chr>               <chr>                 
#> 1 Water Temp   NA                     NA                  NA                    
#> 2 pH           NA                     NA                  NA                    
#> 3 DO           NA                     NA                  NA                    
#> 4 Sp Conducta… NA                     NA                  NA                    
#> 5 TP           MassWateR              as P                Unfiltered            
#> 6 Nitrate      MassWateR              as N                Unfiltered            
#> 7 Ammonia      MassWateR              as N                Unfiltered            
#> 8 E.coli       MassWateR              NA                  NA                    
#> # ℹ abbreviated names: ¹​`Sampling Method Context`, ²​`Result Sample Fraction`
#> # ℹ 2 more variables: `Analytical Method` <chr>,
#> #   `Analytical Method Context` <chr>