Catching all columns as character

R/importWQP.R

@@ -158,48 +158,7 @@ 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(),
-                                        `ResultAnalyticalMethod/MethodIdentifier` = readr::col_character(), 
-                                        `ResultAnalyticalMethod/MethodIdentifierContext` = readr::col_character(),
-                                        ResultStatusIdentifier = readr::col_character(),
-                                        `SampleCollectionMethod/MethodIdentifier` = readr::col_character(),
-                                        `SampleCollectionMethod/MethodIdentifierContext` = readr::col_character(),
-                                        MonitoringLocationIdentifier = readr::col_character(),
-                                        ProjectIdentifier = readr::col_character(),
-                                        ActivityIdentifier = readr::col_character()),
+                       col_types = readr::cols(.default = "c"),
                        quote = ifelse(csv,'\"',""),
                        delim = ifelse(csv,",","\t"), 
                        guess_max = totalPossible))
@@ -211,18 +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))

R/readNWISqw.r

@@ -83,7 +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 vignette('qwdata_changes', package = 'dataRetrieval') 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

@@ -223,31 +223,19 @@ readWQPdata <- function(..., querySummary=FALSE, tz="UTC",
       
       attr(retval, "siteInfo") <- siteInfo
       
-      if(all(c("CharacteristicName","USGSPCode",
-               "ResultMeasure.MeasureUnitCode","ResultSampleFractionText") %in% names(retval))){
-        retvalVariableInfo <- retval[,c("CharacteristicName","USGSPCode",
-                                        "ResultMeasure.MeasureUnitCode","ResultSampleFractionText")]
+      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$CharacteristicName,
-                                   parameterCd=retval$USGSPCode,
                                    param_units=retval$ResultMeasure.MeasureUnitCode,
                                    valueType=retval$ResultSampleFractionText,
                                    stringsAsFactors=FALSE)
         
-        if(!anyNA(variableInfo$parameterCd)){
-          pcodes <- unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)])
-          pcodes <- pcodes["" != pcodes]
-          paramINFO <- readNWISpCode(pcodes)
-          names(paramINFO)["parameter_cd" == names(paramINFO)] <- "parameterCd"
-          
-          pCodeToName <- pCodeToName
-          varExtras <- pCodeToName[pCodeToName$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
       }
 

R/readWQPdots.R

@@ -60,6 +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=":")