5 Packages & data downloads

5.1 Install & import DWQ’s R packages

devtools::install_github('utah-dwq/wqTools')
devtools::install_github('utah-dwq/irTools')

library(wqTools)
library(irTools)

5.2 Download and import data

5.2.1 Data download

downloadWQP(outfile_path='01-raw-data',start_date='10/01/2008', end_date='09/30/2014', zip=TRUE, unzip=TRUE, retrieve=c("narrowresult", "activity", "detquantlim"))
downloadWQP(outfile_path='01-raw-data', zip=FALSE, retrieve="sites")

Note– Downloading all sites separately (query w/o date range), then subsetting to just those included in narrowresult.

sites=read.csv(file='01-raw-data/sites-2019-04-04.csv')
nr=read.csv(file='01-raw-data/narrowresult-2019-04-04.csv')
sites=sites[sites$MonitoringLocationIdentifier %in% nr$MonitoringLocationIdentifier,]
write.csv(file='01-raw-data/sites-2019-04-04.csv', sites, row.names=F)
rm(sites)

5.2.2 Data imports

Read raw data into R, remove duplicates and check for orphans

irdata <- readWQPFiles(file_select=FALSE,
            narrowresult_file = "01-raw-data\\narrowresult-2019-04-04.csv",
            sites_file = "01-raw-data\\sites-2019-04-04.csv",
            activity_file = "01-raw-data\\activity-2019-04-04.csv",
            detquantlim_file = "01-raw-data\\detquantlim-2019-04-04.csv",
            orph_check = TRUE)

## [1] "------------READING IN FILES--------------"
## [1] "----REMOVING EXACT DUPLICATES-----"
## [1] "-----PERFORMING ORPHAN RECORD CHECKS------"
## [1] "3 orphan records detected in sites file with no match to narrowresult."
## [1] "narrowresult_sites_orphans object created containing orphan records."
## [1] "Date forms between narrowresult and activity often cause erroneous orphans. Check date forms below. If date forms do not match, prior conversion using as.Date() is needed."
## [1] "narrowresult file:"
## [1] 2010-07-13 2010-07-13 2010-07-13 2010-07-13 2010-07-13 2010-07-13
## 1775 Levels: 2008-10-01 2008-10-02 2008-10-03 2008-10-04 ... 2014-09-30
## [1] "activity file:"
## [1] 2010-07-13 2010-07-13 2010-07-13 2010-07-13 2010-07-13 2010-07-13
## 1777 Levels: 2008-10-01 2008-10-02 2008-10-03 2008-10-04 ... 2014-09-30
## [1] "98 orphan records detected in activity file with no match to narrowresult."
## [1] "narrowresult_activity_orphans object created containing orphan records."
## [1] "NOTE: narrowresult will likely have many orphan records not represented in detquantlim. This occurs for a few reasons: (1) labs sometimes do not report detection quantitation limits, and (2) field measurements often do not report detection quantitation limits."
## [1] "684950 orphan records detected in narrowresult file with no match to detquantlim."
## [1] "narrowresult_detquantlim_orphans object created containing orphan records."
## [1] "Need to figure out non-numeric data in numeric columns conundrum."

## Warning in wqTools::facToNum(wqpdat$merged_results$ResultMeasureValue): NAs
## introduced by coercion

## [1] "----FILES SUCCESSFULLY ADDED TO R OBJECT LIST----"

objects(irdata)

## [1] "detquantlim"                      "merged_results"                  
## [3] "narrowresult_activity_orphans"    "narrowresult_detquantlim_orphans"
## [5] "narrowresult_site_orphans"        "sites"