Merge pull request #607 from ldecicco-USGS/main

dataProfile examples

.Rbuildignore

@@ -50,3 +50,5 @@ vignettes/tutorial.Rmd
 vignettes/phosData.rds
 vignettes/waterservices.png
 .gitlab-ci.yml
+sample_large_pull.R
+

.github/workflows/R-CMD-check.yaml

+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
+    branches: main
   pull_request:
-    branches:
-      - main
+    branches: main
 
 name: R-CMD-check
 
@@ -20,68 +20,30 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
-        run: |
-          install.packages(c('remotes', 'zoo', 'sf'))
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
-      - name: mac dependencies
-        if: runner.os == 'macOS'
-        run: brew install pkg-config gdal proj geos udunits
-        
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages(c('remotes', 'zoo', 'sf'))
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
+          extra-packages: rcmdcheck
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v1
 
       - name: Show testthat output
         if: always()
@@ -90,7 +52,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          path: check
\ No newline at end of file

DESCRIPTION

 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
-Version: 2.7.10.1
+Version: 2.7.11
 Authors@R: c(
     person("Laura", "DeCicco", role = c("aut","cre"),
             email = "ldecicco@usgs.gov",

NEWS

@@ -2,6 +2,8 @@ dataRetrieval 2.7.11
 ==================
 * Updated some documentation to improve examples.
 * Changed the check for internet to better account for proxies.
+* Fixed bug due to new behavior in NWIS parameter code service.
+* Updated documentation for readWQPdata and readWQPsummary
 
 dataRetrieval 2.7.10
 ==================

R/importWQP.R

@@ -157,43 +157,11 @@ importWQP <- function(obs_url, zip=TRUE, tz="UTC",
     }
   }
 
-  retval <- suppressWarnings(readr::read_delim(doc, 
-                       col_types = readr::cols(`ActivityStartTime/Time` = readr::col_character(),
-                                        `ActivityEndTime/Time` = readr::col_character(),
-                                        USGSPCode = readr::col_character(),
-                                        ResultCommentText = readr::col_character(),
-                                        ResultSampleFractionText = readr::col_character(),
-                                        ActivityDepthAltitudeReferencePointText = readr::col_character(),
-                                        ActivityConductingOrganizationText = readr::col_character(),
-                                        ActivityCommentText = readr::col_character(),
-                                        ResultWeightBasisText = readr::col_character(),
-                                        ResultTimeBasisText = readr::col_character(),
-                                        ResultParticleSizeBasis  = readr::col_character(),
-                                        ResultDepthAltitudeReferencePointText = readr::col_character(),
-                                        ResultLaboratoryCommentText = readr::col_character(),
-                                        ResultTemperatureBasisText = readr::col_character(),
-                                        ResultDetectionConditionText = readr::col_character(),
-                                        ResultParticleSizeBasisText = readr::col_character(),
-                                        `ActivityDepthHeightMeasure/MeasureValue` = readr::col_number(),
-                                        `DetectionQuantitationLimitMeasure/MeasureValue` = readr::col_number(),
-                                        ResultMeasureValue = readr::col_character(),
-                                        `WellDepthMeasure/MeasureValue` = readr::col_number(),
-                                        `WellHoleDepthMeasure/MeasureValue` = readr::col_number(),
-                                        DetectionQuantitationLimitTypeName = readr::col_character(),
-                                        LaboratoryName = readr::col_character(),
-                                        MethodDescriptionText = readr::col_character(),
-                                        `ResultAnalyticalMethod/MethodName` = readr::col_character(),
-                                        `ResultAnalyticalMethod/MethodIdentifier` = readr::col_character(),
-                                        `ResultAnalyticalMethod/MethodIdentifierContext` = readr::col_character(),
-                                        SampleTissueAnatomyName = readr::col_character(),
-                                        SubjectTaxonomicName = readr::col_character(),
-                                        ResultDepthAltitudeReferencePointText = readr::col_character(),
-                                        `ResultDepthHeightMeasure/MeasureUnitCode` = readr::col_character(),
-                                        `DetectionQuantitationLimitMeasure/MeasureUnitCode` = readr::col_character(),
-                                        `HUCEightDigitCode` = readr::col_character(), 
-                                        `ActivityEndTime/TimeZoneCode` = readr::col_character()),
+  retval <- suppressWarnings(readr::read_delim(doc,
+                       col_types = readr::cols(.default = "c"),
                        quote = ifelse(csv,'\"',""),
-                       delim = ifelse(csv,",","\t")))
+                       delim = ifelse(csv,",","\t"), 
+                       guess_max = totalPossible))
     
   if(!file.exists(obs_url)){
     actualNumReturned <- nrow(retval)
@@ -202,18 +170,24 @@ importWQP <- function(obs_url, zip=TRUE, tz="UTC",
       warning("Number of rows returned not matched in header")
     } 
   }
-  suppressWarnings({
-    val <- tryCatch(as.numeric(retval$ResultMeasureValue),
-                    warning = function(w) w)
+  
+  valueCols <- names(retval)[grep("MeasureValue", names(retval))]
+  countCols <- names(retval)[grep("Count", names(retval))]
+  yearCols <- names(retval)[grep("Year", names(retval))]
+  
+  for(numberCol in unique(c(valueCols, countCols, yearCols))){
+    suppressWarnings({
+      val <- tryCatch(as.numeric(retval[[numberCol]]),
+                      warning = function(w) w)
+      # we don't want to convert it to numeric if there are non-numeric chars
+      # If we leave it to the user, it will probably break a lot of code
+      if(!"warning" %in% class(val)){
+        retval[[numberCol]] <- val
+      }
+    })
+  }
+  
 
-    # we don't want to convert it to numeric if there are non-numeric chars
-    # they often happen after readr has decided the column type if we left it to readr
-    # If we leave it to the user, it will probably break a lot of code
-    # If we bump up readr's guess_max...the computational time becomes really really long
-    if(!"warning" %in% class(val)){
-      retval$ResultMeasureValue <- val
-    }
-  })
 
   if(length(grep("ActivityStartTime",names(retval))) > 0){
     

R/readNWISdata.r

@@ -146,8 +146,10 @@ readNWISdata <- function(..., asDateTime=TRUE,convertType=TRUE,tz="UTC"){
   if(any(service %in% c("qw", "qwdata"))){
     .Deprecated(old = "readNWISdata", package = "dataRetrieval",
                 new = "readWQPdata",
-                msg = "NWIS qw web services are being retired. Please see the vignette 
-'Changes to NWIS QW services' for more information.")
+                msg = "NWIS qw web services are being retired. 
+Please see vignette('qwdata_changes', package = 'dataRetrieval') 
+for more information.
+https://cran.r-project.org/web/packages/dataRetrieval/vignettes/qwdata_changes.html")
   }
   
   values <- sapply(valuesList$values, function(x) URLencode(x))
@@ -276,21 +278,22 @@ countyCdLookup <- function(state, county, outputType = "id"){
     stop("No county code provided")
   }
   
+  if(length(state) > 1){
+    stop("Only one state allowed in countyCdLookup.")
+  }
+  
   #first turn state into stateCd postal name
   stateCd <- stateCdLookup(state,outputType = "postal")
+  state_counties <- countyCd[countyCd$STUSAB == stateCd,]
   
   if(is.numeric(county) | !is.na(suppressWarnings(as.numeric(county)))){
     county_i <- which(as.numeric(county) == as.numeric(countyCd$COUNTY) & stateCd == countyCd$STUSAB)
   } else {
-    # if no suffix was added, this will figure out what it should be (or throw a helpful error)
-    allSuffixes <- unique(tolower(unlist(lapply(strsplit(countyCd$COUNTY_NAME,split=" "), tail, 1))))
+
+    county_in_state <- grep(tolower(county), tolower(state_counties$COUNTY_NAME))
     
-    county_i <- unlist(lapply(allSuffixes, function(suffix, stateCd, county){
-      currentSuffixExistsInString <- grepl(paste0('(?i)\\', suffix, '$'), tolower(county))
-      retCounty <- ifelse(currentSuffixExistsInString, county, paste(county, suffix))
-      retCounty_i <- which(tolower(retCounty) == tolower(countyCd$COUNTY_NAME) & stateCd == countyCd$STUSAB)
-      return(retCounty_i)
-    }, stateCd, county))
+    county_i <- which(countyCd$STUSAB == stateCd &
+                        countyCd$COUNTY_NAME == state_counties$COUNTY_NAME[county_in_state] )
     
     if(length(county_i) == 0){
       stop(paste("Could not find", county, "(county),", stateCd, 

R/readNWISqw.r

@@ -83,8 +83,10 @@ readNWISqw <- function (siteNumbers,parameterCd,startDate="",endDate="",
                         expanded=TRUE,reshape=FALSE,tz="UTC"){  
   
   .Deprecated(new = "readWQPqw", package = "dataRetrieval", 
-              msg = "NWIS qw web services are being retired. Please see the vignette 
-'Changes to NWIS QW services' for more information.")
+              msg = "NWIS qw web services are being retired. 
+Please see vignette('qwdata_changes', package = 'dataRetrieval') 
+for more information.
+https://cran.r-project.org/web/packages/dataRetrieval/vignettes/qwdata_changes.html")
   
   pgrp <- c("INF", "PHY", "INM", "INN", "NUT", "MBI", "BIO", "IMM", "IMN", "TOX",
             "OPE", "OPC", "OOT", "RAD", "XXX", "SED", "POP",

R/readWQPdata.R

@@ -129,10 +129,54 @@
 #'                               querySummary=TRUE)
 #'                               
 #' # querying by county
-#' dailyLexingtonVA <- readWQPdata(statecode = "Virginia", 
-#'                                 countycode="Lexington", 
-#'                                 parameterCd = "00010") 
+#' DeWitt <- readWQPdata(statecode = "Illinois", 
+#'                       countycode= "DeWitt", 
+#'                       characteristicName = "Nitrogen") 
 #'                                 
+#' # Data profiles: "Organization Data"
+#' org_data <- readWQPdata(statecode = "WI",
+#'                         countycode = "Dane",
+#'                         service = "Organization")
+#' 
+#' # Data profiles: "Site Data Only" 
+#' site_data <- readWQPdata(statecode = "WI",
+#'                          countycode = "Dane",
+#'                          service = "Station")
+#'                          
+#' # Data profiles: "Project Data"
+#' project_data <- readWQPdata(statecode = "WI",
+#'                          countycode = "Dane",
+#'                          service = "Project")
+#'                          
+#' # Data profiles: "Project Monitoring Location Weighting Data"
+#' proj_mlwd <- readWQPdata(statecode = "WI",
+#'                          countycode = "Dane",
+#'                          service = "ProjectMonitoringLocationWeighting")
+#'                          
+#' # Data profiles: "Sample Results (physical/chemical metadata)":
+#' samp_data <- readWQPdata(siteid = "USGS-04024315",
+#'                          dataProfile = "resultPhysChem")
+#'                          
+#' # Data profiles: "Sample Results (biological metadata)"
+#' samp_bio <- readWQPdata(siteid="USGS-04024315",
+#'                         dataProfile = "biological")
+#'                          
+#' # Data profiles: "Sample Results (narrow)"
+#' samp_narrow <- readWQPdata(siteid="USGS-04024315",
+#'                            dataProfile = "narrowResult")
+#'                            
+#' # Data profiles: "Sampling Activity"
+#' samp_activity <- readWQPdata(siteid="USGS-04024315",
+#'                              dataProfile = "activityAll")
+#'                              
+#' # Data profile: "Sampling Activity Metrics"
+#' act_metrics <- readWQPdata(statecode = "WI",
+#'                            countycode = "Dane",
+#'                            service = "ActivityMetric")
+#'                            
+#' # Data profile: "Result Detection Quantitation Limit Data"
+#' dl_data <- readWQPdata(siteid="USGS-04024315",
+#'                        service = "ResultDetectionQuantitationLimit")
 #' }
 readWQPdata <- function(..., querySummary=FALSE, tz="UTC", 
                         ignore_attributes = FALSE){
@@ -177,33 +221,24 @@ readWQPdata <- function(..., querySummary=FALSE, tz="UTC",
         siteInfo <- cbind(siteInfoCommon, siteInfo)        
       }
       
-      retvalVariableInfo <- retval[,c("CharacteristicName","USGSPCode",
-                                      "ResultMeasure.MeasureUnitCode","ResultSampleFractionText")]
-      retvalVariableInfo <- unique(retvalVariableInfo)
-      
-      variableInfo <- data.frame(characteristicName=retval$CharacteristicName,
-                                 parameterCd=retval$USGSPCode,
-                                 param_units=retval$ResultMeasure.MeasureUnitCode,
-                                 valueType=retval$ResultSampleFractionText,
-                                 stringsAsFactors=FALSE)
+      attr(retval, "siteInfo") <- siteInfo
       
-      if(!anyNA(variableInfo$parameterCd)){
-        pcodes <- unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)])
-        pcodes <- pcodes["" != pcodes]
-        paramINFO <- readNWISpCode(pcodes)
-        names(paramINFO)["parameter_cd" == names(paramINFO)] <- "parameterCd"
+      if(all(c("CharacteristicName",
+               "ResultMeasure.MeasureUnitCode",
+               "ResultSampleFractionText") %in% names(retval))){
+        retvalVariableInfo <- retval[,c("CharacteristicName",
+                                        "ResultMeasure.MeasureUnitCode",
+                                        "ResultSampleFractionText")]
+        retvalVariableInfo <- unique(retvalVariableInfo)
+        
+        variableInfo <- data.frame(characteristicName=retval$CharacteristicName,
+                                   param_units=retval$ResultMeasure.MeasureUnitCode,
+                                   valueType=retval$ResultSampleFractionText,
+                                   stringsAsFactors=FALSE)
         
-        pCodeToName <- pCodeToName
-        varExtras <- pCodeToName[pCodeToName$parm_cd %in% unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)]),]
-        names(varExtras)[names(varExtras) == "parm_cd"] <- "parameterCd"
-        variableInfo <- merge(variableInfo, varExtras, by="parameterCd", all = TRUE)
-        variableInfo <- merge(variableInfo, paramINFO, by="parameterCd", all = TRUE)
-        variableInfo <- unique(variableInfo)
+        attr(retval, "variableInfo") <- variableInfo
       }
-      
-      attr(retval, "siteInfo") <- siteInfo
-      attr(retval, "variableInfo") <- variableInfo
-      
+
     } else {
       if(!ignore_attributes){
         message("The following url returned no data:\n")

R/readWQPdots.R

@@ -23,7 +23,20 @@ readWQPdots <- function(...){
     service <- "Result"
   }
   
-  match.arg(service, c("Result", "Station", "Activity",
+  if("dataProfile" %in% names(matchReturn)){
+    profile <- matchReturn$dataProfile
+    if(profile == "activityAll"){
+      service <- "Activity"
+      matchReturn$service <- NULL
+    } else if(profile %in% c("resultPhysChem",
+                             "biological",
+                             "narrowResult")){
+      service <- "Result"
+      matchReturn$service <- NULL
+    }
+  }
+  
+  match.arg(service, c("Result", "Station", "Activity", "Organization",
                        "ActivityMetric", "SiteSummary",
                        "Project", "ProjectMonitoringLocationWeighting",
                        "ResultDetectionQuantitationLimit", "BiologicalMetric"))
@@ -47,6 +60,10 @@ readWQPdots <- function(...){
   names(values)[names(values) == "countyCd"] <- "countycode"
   if(all(c("countycode","statecode") %in% names(values))){
     stCd <- gsub("US:", "", values["statecode"])
+    # This will error if more than 1 state is requested
+    # It's possible that someone could requst more than one state
+    # in WQP, but if they also then request county codes,
+    # it gets really confusing, and the WQP developers don't recommend.
     values["countycode"] <- paste(values["statecode"], 
                                   countyCdLookup(stCd, values["countycode"], "id"),
                                   sep=":")

R/setAccess.R

@@ -65,7 +65,8 @@ setAccess = function(access="public"){
   pkg.env$ProjectMonitoringLocationWeighting = "https://www.waterqualitydata.us/data/ProjectMonitoringLocationWeighting/search"
   pkg.env$ResultDetectionQuantitationLimit = "https://www.waterqualitydata.us/data/ResultDetectionQuantitationLimit/search"
   pkg.env$BiologicalMetric = "https://www.waterqualitydata.us/data/BiologicalMetric/search"
-  
+  pkg.env$Organization = "https://www.waterqualitydata.us/data/Organization/search"
+
   pkg.env$NGWMN = "https://cida.usgs.gov/ngwmn_cache/sos"
 
 }

R/tabbedDataRetrievals.R

@@ -86,8 +86,9 @@ NULL
 
 #' US State Code Lookup Table
 #'
-#' Data pulled from \url{https://www2.census.gov/geo/docs/reference/state.txt}
-#' on April 1, 2015. 
+#' Data originally pulled from \url{https://www2.census.gov/geo/docs/reference/state.txt}
+#' on April 1, 2015. On Feb. 11, 2022, the fields were updated with the
+#' file found in inst/extdata, which is used internally with NWIS retrievals. 
 #'
 #' @name stateCd
 #' @return stateCd data frame.
@@ -108,8 +109,9 @@ NULL
 
 #' US County Code Lookup Table
 #'
-#' Data pulled from \url{https://www2.census.gov/geo/docs/reference/codes/files/national_county.txt}
-#' on April 1, 2015. 
+#' Data originally pulled from \url{https://www2.census.gov/geo/docs/reference/codes/files/national_county.txt}
+#' on April 1, 2015. On Feb. 11, 2022, the fields were updated with the
+#' file found in inst/extdata, which is used internally with NWIS retrievals.
 #'
 #' @name countyCd
 #' @return countyCd data frame.
@@ -127,4 +129,48 @@ NULL
 #' @keywords USGS countyCd
 #' @examples
 #' head(countyCd)
-NULL
\ No newline at end of file
+NULL
+
+# Here's how to incorporate the state_county.json into the historic
+# sysdata.rda. The original data included some IDs that aren't in the json
+# We're leaving those in for now because maybe it's helpful,
+# even though to my knowledge it's not used in any dataRetrieval query.
+
+# #Step 1: open the json file, parse out what's needed:
+# x <- jsonlite::read_json("inst/extdata/state_county.json")
+# states <- x[["US"]]
+# state_df <- data.frame("STATE" = names(sapply(states$state_cd, function(x) x[[1]])),
+#                        "STATE_NAME" = as.character(sapply(states$state_cd, function(x) x[[1]])))
+# #Step 2: join it into the original stateCd data frame:
+# # This preserves STATE_NAME, which is nice
+#
+# library(dplyr)
+# state_df <- state_df %>%
+#   left_join(stateCd, by = c("STATE", "STATE_NAME"))
+#
+# state_df$STUSAB[state_df$STATE_NAME == "Virgin Islands"] <- "VI"
+# 
+# #Step 3: now get the county names/ids:
+# y <- sapply(states$state_cd, function(x) x[["county_cd"]])
+# 
+# county_df <- data.frame()
+# 
+# for(st in state_df$STATE){
+#   county_nums <- names(y[[st]])
+#   county_names <- as.character(unlist(y[[st]]))
+#   county_df_st <- data.frame(STATE = st,
+#                              COUNTY = county_nums,
+#                              COUNTY_NAME = county_names)
+#   county_df <- dplyr::bind_rows(county_df, county_df_st)
+# }
+# 
+# county_df_full <- county_df %>%
+#   left_join(select(state_df, STUSAB, STATE), by = "STATE") %>%
+#   left_join(select(countyCd, STATE, STUSAB, COUNTY, COUNTY_ID),
+#             by = c("STATE", "STUSAB", "COUNTY"))
+# 
+# countyCd <- county_df_full
+# stateCd <- state_df
+# save(countyCd, stateCd, parameterCdFile, pCodeToName,
+#      file = "R/sysdata.rda", compress = "xz")
+

R/whatWQPsites.R

@@ -143,22 +143,27 @@ whatWQPsites <- function(...){
 #' @export
 #' @examplesIf is_dataRetrieval_user()
 #' \donttest{
+#' # Summary of a single site for the last 5 years:
 #' site_5 <- readWQPsummary(siteid="USGS-07144100",
 #'                         summaryYears=5)
 #'                         
+#' # Summary of a single site for the full period of record:
 #' site_all <- readWQPsummary(siteid="USGS-07144100",
 #'                            summaryYears="all")
-#'                            
+#' 
+#' # Summary of the data available from streams in a single county:       
 #' dane_county_data <- readWQPsummary(countycode = "US:55:025",
 #'                         summaryYears = 5,
 #'                         siteType = "Stream")
 #' 
-#' 
+#' # Summary of the data all available from lakes in a single county:
 #' lake_sites <- readWQPsummary(siteType = "Lake, Reservoir, Impoundment",
 #'                          countycode = "US:55:025")
-#'                            
-#' # Very slow:
-#' #state1 <- readWQPsummary(statecode="NJ")
+#' 
+#' # Summary of the data available for the last 5 years in New Jersey:
+#' state1 <- readWQPsummary(statecode="NJ",
+#'                          summaryYears = 5,
+#'                          siteType = "Stream")
 #' }
 readWQPsummary <- function(...){
   

README.Rmd

@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 ```
 
 
-# dataRetrieval <img src="man/figures/logo.png" alt="dataRetrieval" height="150px" align="right" />
+# dataRetrieval <img src="man/figures/logo.png" alt="dataRetrieval" style="width:150px;height:auto;" align="right" />
 
 [![R build status](https://github.com/USGS-R/dataRetrieval/workflows/R-CMD-check/badge.svg)](https://github.com/USGS-R/dataRetrieval/actions)[![Coverage Status](https://coveralls.io/repos/github/USGS-R/dataRetrieval/badge.svg?branch=main)](https://coveralls.io/github/USGS-R/dataRetrieval?branch=main) [![status](https://img.shields.io/badge/USGS-Core-green.svg)](https://owi.usgs.gov/R/packages.html#core) [![CRAN version](http://www.r-pkg.org/badges/version/dataRetrieval)](https://cran.r-project.org/package=dataRetrieval) [![](http://cranlogs.r-pkg.org/badges/dataRetrieval)](https://cran.r-project.org/package=dataRetrieval) [![](http://cranlogs.r-pkg.org/badges/grand-total/dataRetrieval)](https://cran.r-project.org/package=dataRetrieval)
 

README.md

-# dataRetrieval <img src="man/figures/logo.png" alt="dataRetrieval" height="150px" align="right" />
+# dataRetrieval <img src="man/figures/logo.png" alt="dataRetrieval" style="width:150px;height:auto;" align="right" />
  
 Retrieval functions for USGS and EPA hydrologic and water quality data.
 

code.json

@@ -3,7 +3,7 @@
     "name": "dataRetrieval",
     "organization": "U.S. Geological Survey",
     "description": "This R package is designed to obtain USGS or EPA water quality sample data, streamflow data, and metadata directly from web services",
-    "version": "2.7.9",
+    "version": "2.7.11",
     "status": "Production",
 
     "permissions": {
@@ -11,13 +11,13 @@
       "licenses": [
         {
           "name": "Public Domain, CC0-1.0",
-          "URL": "https://code.usgs.gov/WMA-Data-Science/dataRetrieval/blob/master/LICENSE.note"
+          "URL": "https://code.usgs.gov/water/dataRetrieval/blob/master/LICENSE.note"
         }
       ]
     },
 
     "homepageURL": "https://code.usgs.gov/water/dataRetrieval",
-    "downloadURL": "https://code.usgs.gov/water/dataRetrieval/-/archive/v2.7.9/dataRetrieval-v2.7.9.zip",
+    "downloadURL": "https://code.usgs.gov/water/dataRetrieval/-/archive/v2.7.11/dataRetrieval-v2.7.11.zip",
     "disclaimerURL": "https://code.usgs.gov/water/dataRetrieval/blob/master/DISCLAIMER.md",
     "repositoryURL": "https://code.usgs.gov/water/dataRetrieval.git",
     "vcs": "git",
@@ -41,7 +41,7 @@
     },
 
     "date": {
-      "metadataLastUpdated": "2021-07-29"
+      "metadataLastUpdated": "2022-02-11"
     }
   }
 ]

man/countyCd.Rd

@@ -17,8 +17,9 @@ COUNTY_ID \tab character \tab County id \cr
 }
 }
 \description{
-Data pulled from \url{https://www2.census.gov/geo/docs/reference/codes/files/national_county.txt}
-on April 1, 2015.
+Data originally pulled from \url{https://www2.census.gov/geo/docs/reference/codes/files/national_county.txt}
+on April 1, 2015. On Feb. 11, 2022, the fields were updated with the
+file found in inst/extdata, which is used internally with NWIS retrievals.
 }
 \examples{
 head(countyCd)

man/readWQPdata.Rd

@@ -142,10 +142,54 @@ wqp.summary_WI <- readWQPdata(arg_3, statecode="WI",
                               querySummary=TRUE)
                               
 # querying by county
-dailyLexingtonVA <- readWQPdata(statecode = "Virginia", 
-                                countycode="Lexington", 
-                                parameterCd = "00010") 
+DeWitt <- readWQPdata(statecode = "Illinois", 
+                      countycode= "DeWitt", 
+                      characteristicName = "Nitrogen")