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9b63b774 · Laura A DeCicco · 7af1023f · 9b63b774 · 9b63b774 · 9b63b774
Commit 9b63b774 authored May 19, 2017 by Laura A DeCicco
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,11 +39,11 @@ Imports:
    readr (>= 1.0.0),
    jsonlite
 Suggests:
-    xtable,
+    htmlTable,
    knitr,
    testthat
-VignetteBuilder: knitr
 BuildVignettes: true
+VignetteBuilder: knitr
 BugReports: https://github.com/USGS-R/dataRetrieval/issues
 URL: https://pubs.usgs.gov/tm/04/a10/
 RoxygenNote: 6.0.1
--- a/inst/doc/dataRetrieval.R
+++ b/inst/doc/dataRetrieval.R
-## ----openLibrary, echo=FALSE------------------------------
-library(xtable)
-options(continue=" ")
-options(width=60)
+## ----setup, include=FALSE, message=FALSE------------------
 library(knitr)
+library(dataRetrieval)

-
-## ----include=TRUE ,echo=FALSE,eval=TRUE-------------------
-opts_chunk$set(highlight=TRUE, tidy=TRUE, keep.space=TRUE, keep.blank.space=FALSE, keep.comment=TRUE, tidy=FALSE,comment="")
+options(continue=" ")
+options(width=60)
+knitr::opts_chunk$set(echo = TRUE,
+                      warning = FALSE,
+                      message = FALSE,
+                      fig.height = 7,
+                      fig.width = 7)
+
+opts_chunk$set(highlight=TRUE, 
+               tidy=TRUE, 
+               keep.space=TRUE,
+               keep.blank.space=FALSE,
+               keep.comment=TRUE)
 knit_hooks$set(inline = function(x) {
   if (is.numeric(x)) round(x, 3)})
-knit_hooks$set(crop = hook_pdfcrop)
-
-bold.colHeaders <- function(x) {
-  x <- gsub("\\^(\\d)","$\\^\\1$",x)
-  x <- gsub("\\%","\\\\%",x)
-  x <- gsub("\\_"," ",x)
-  returnX <- paste("\\multicolumn{1}{c}{\\textbf{\\textsf{", x, "}}}", sep = "")
-}
-addSpace <- function(x) ifelse(x != "1", "[5pt]","")
-library(dataRetrieval)

 ## ----workflow, echo=TRUE,eval=FALSE-----------------------
 #  library(dataRetrieval)
@@ -39,38 +37,98 @@ library(dataRetrieval)
 #  pCode <- readNWISpCode(parameterCd)
 #  

-## ----tableParameterCodes, echo=FALSE,results='asis'-------
+## ----echo=FALSE-------------------------------------------
+
+library(htmlTable)
+
+Functions <- c("readNWISdata","",
+               "readNWISdv","","","","",
+               "readNWISqw","","","","",
+               "readNWISuv","","","",
+               "readNWISrating","",
+               "readNWISmeas","","",
+               "readNWISpeak","","",
+               "readNWISgwl","","",
+               "readNWISuse","","","",
+               "readNWISstat","","","","","",
+               "readNWISpCode",
+               "readNWISsite",
+               "whatNWISsites",
+               "whatNWISdata","",
+               "readWQPdata",
+               "readWQPqw","","","",
+               "whatWQPsites")
+Arguments <- c("...","service", #readNWISdata
+               "siteNumber","parameterCd","startDate","endDate","statCd", #readNWISdv
+               "siteNumber","parameterCd","startDate","endDate","expanded", #readNWISqw
+               "siteNumber","parameterCd","startDate","endDate", #readNWISuv
+               "siteNumber","type", #readNWISrating
+               "siteNumber","startDate","endDate", #readNWISmeas
+               "siteNumber","startDate","endDate", #readNWISpeak
+               "siteNumber","startDate","endDate", #readNWISgwl
+               "stateCd","countyCd","years","categories", #readNWISuse
+               "siteNumbers","parameterCd","startDate","endDate","statReportType","statType", #readNWISstat
+               "parameterCd", #readNWISpCode
+               "siteNumber", #readNWISsite
+               "...", #whatNWISsites
+               "siteNumber","service", #whatNWISdata
+               "...", #readWQPdata
+               "siteNumber","parameterCd","startDate","endDate", #readWQPqw
+               "...") #whatWQPsites
+Description <- c("NWIS data using user-specified queries","", #readNWISdata
+                 "NWIS daily data","","","","", #readNWISdv
+                 "NWIS water quality data","","","","", #readNWISqw
+                 "NWIS instantaneous value data","","","", #readNWISuv
+                 "NWIS rating table for active streamgage","", #readNWISrating
+                 "NWIS surface-water measurements","","", #readNWISmeas
+                 "NWIS peak flow data","","", #readNWISpeak
+                 "NWIS groundwater level measurements","","", #readNWISgwl
+                 "NWIS water use","","","", #readNWISuse
+                 "NWIS statistical service","","","","","", #readNWISstat
+                 "NWIS parameter code information", #readNWISpCode
+                 "NWIS site information", #readNWISsite
+                 "NWIS site search using user-specified queries",
+                 "NWIS data availability, including period of record and count","",
+                 "WQP data using user-specified queries",
+                 "WQP data","","","",
+                 "WQP site search using user-specified queries")
+
+data.df <- data.frame(`Function Name` = Functions, Arguments, Description, stringsAsFactors=FALSE)
+
+htmlTable(data.df, 
+          caption="Table 1: dataRetrieval functions",
+          rnames=FALSE, align=c("l","l","l","l"),
+          col.rgroup = c("none", "#F7F7F7"), 
+          css.cell="padding-bottom: 0.0em; padding-right: 0.5em; padding-top: 0.0em;")
+
+
+## ----tableParameterCodes, echo=FALSE----------------------
+
+
 pCode <- c('00060', '00065', '00010','00045','00400')
-shortName <- c("Discharge [ft$^3$/s]","Gage height [ft]","Temperature [C]", "Precipitation [in]", "pH")
+shortName <- c("Discharge [ft<sup>3</sup>/s]","Gage height [ft]","Temperature [C]", "Precipitation [in]", "pH")

 data.df <- data.frame(pCode, shortName, stringsAsFactors=FALSE)

-print(xtable(data.df,
-       label="tab:params",
-       caption="Common USGS Parameter Codes"),
-       caption.placement="top",
-       size = "\\footnotesize",
-       latex.environment=NULL,
-       sanitize.text.function = function(x) {x},
-       sanitize.colnames.function =  bold.colHeaders,
-       sanitize.rownames.function = addSpace
-      )
+htmlTable(data.df, 
+          caption="Table 2: Common USGS Parameter Codes",
+          rnames=FALSE, align=c("c","c"), col.rgroup = c("none", "#F7F7F7"), 
+          css.cell="padding-bottom: 0.0em; padding-right: 0.5em; padding-top: 0.0em;")


-## ----tableStatCodes, echo=FALSE,results='asis'------------
+
+## ----tableStatCodes, echo=FALSE---------------------------
 StatCode <- c('00001', '00002', '00003','00008')
 shortName <- c("Maximum","Minimum","Mean", "Median")

 data.df <- data.frame(StatCode, shortName, stringsAsFactors=FALSE)

-print(xtable(data.df,label="tab:stat",
-           caption="Commonly used USGS Stat Codes"),
-       caption.placement="top",
-       size = "\\footnotesize",
-       latex.environment=NULL,
-       sanitize.colnames.function = bold.colHeaders,
-       sanitize.rownames.function = addSpace
-      )
+htmlTable(data.df, 
+          caption="Table 3: Commonly used USGS Stat Codes",
+          rnames=FALSE, align=c("c","c"), col.rgroup = c("none", "#F7F7F7"), 
+          css.cell="padding-bottom: 0.0em; padding-right: 0.5em; padding-top: 0.0em;")
+
+


 ## ----getSite, echo=TRUE, eval=FALSE-----------------------
@@ -89,33 +147,28 @@ print(xtable(data.df,label="tab:stat",
 #  
 #  

-## ----tablegda, echo=FALSE,eval=FALSE----------------------
-#  tableData <- with(dailyDataAvailable,
-#        data.frame(
-#        siteNumber= site_no,
-#        srsname=srsname,
-#        startDate=as.character(begin_date),
-#        endDate=as.character(end_date),
-#        count=as.character(count_nu),
-#        units=parameter_units,
-#  #       statCd = stat_cd,
-#        stringsAsFactors=FALSE)
-#        )
-#  
-#  tableData$units[which(tableData$units == "ft3/s")] <- "ft$^3$/s"
-#  tableData$units[which(tableData$units == "uS/cm @25C")] <- "$\\mu$S/cm @25C"
-#  
-#  
-#  print(xtable(tableData,label="tab:gda",
-#      caption="Reformatted version of output from \\texttt{whatNWISdata} function for the Choptank River near Greensboro, MD, and from Seneca Creek at Dawsonville, MD from the daily values service [Some columns deleted for space considerations]"),
-#         caption.placement="top",
-#         size = "\\footnotesize",
-#         latex.environment=NULL,
-#         sanitize.text.function = function(x) {x},
-#         sanitize.colnames.function =  bold.colHeaders,
-#         sanitize.rownames.function = addSpace
-#        )
-#  
+## ----echo=FALSE-------------------------------------------
+
+tableData <- data.frame(
+  siteNumber = c("01491000","01491000","01645000","01491000","01491000","01491000"),
+  srsname = c("Temperature, water","Stream flow, mean daily",
+              "Stream flow, mean daily",
+              "Specific conductance",
+              "Suspended sediment concentration (SSC)",
+              "Suspended sediment discharge" ),
+  startDate = c("2010-10-01","1948-01-01","1930-09-26","2010-10-01","1980-10-01","1980-10-01"),
+  endDate = c("2012-05-09","2017-05-17","2017-05-17","2012-05-09","1991-09-30","1991-09-30"),
+  count = c("529","25340","31646","527","4017","4017"),
+  units = c("deg C","ft<sup>3</sup>/s","ft<sup>3</sup>/s","uS/cm @25C","mg/l","tons/day"),
+  stringsAsFactors = FALSE)
+
+
+htmlTable(tableData, 
+          caption="Table 4: Reformatted version of output from the whatNWISdata function for the Choptank River near Greensboro, MD, and from Seneca Creek at Dawsonville, MD from the daily values service [Some columns deleted for space considerations]",
+          rnames=FALSE, 
+          col.rgroup = c("none", "#F7F7F7"), 
+          css.cell="padding-bottom: 0.0em; padding-right: 0.5em; padding-top: 0.0em;")
+

 ## ----label=getPCodeInfo, echo=TRUE, eval=FALSE------------
 #  # Using defaults:
@@ -167,7 +220,7 @@ variableInfo <- attr(temperatureAndFlow, "variableInfo")
 siteInfo <- attr(temperatureAndFlow, "siteInfo")


-## ----getNWIStemperaturePlot, echo=TRUE, fig.cap="Temperature and discharge plot of Choptank River in 2012.",out.width='1\\linewidth',out.height='1\\linewidth',fig.show='hold'----
+## ---------------------------------------------------------
 variableInfo <- attr(temperatureAndFlow, "variableInfo")
 siteInfo <- attr(temperatureAndFlow, "siteInfo")

@@ -205,8 +258,8 @@ legend("topleft", variableInfo$param_units,
 #        startDate, endDate)
 #  
 #  # Or the wide return:
-#  # dfWide <- readNWISqw(siteNumber, parameterCd,
-#  #       startDate, endDate, reshape=TRUE)
+#  dfWide <- readNWISqw(siteNumber, parameterCd,
+#        startDate, endDate, reshape=TRUE)
 #  

 ## ----qwmeta, echo=TRUE, eval=FALSE------------------------
@@ -232,15 +285,57 @@ legend("topleft", variableInfo$param_units,
 #  surfaceData <- readNWISmeas(siteNumber)
 #  

+## ----eval=FALSE-------------------------------------------
+#  allegheny <- readNWISuse(stateCd = "Pennsylvania",
+#                           countyCd = "Allegheny")
+#  
+#  
+#  national <- readNWISuse(stateCd = NULL,
+#                          countyCd = NULL,
+#                          transform = TRUE)
+#  
+
+## ----eval=FALSE-------------------------------------------
+#  discharge_stats <- readNWISstat(siteNumbers=c("02319394"),
+#                     parameterCd=c("00060"),
+#                     statReportType="annual")
+#  
+
 ## ----label=getQWData, echo=TRUE, eval=FALSE---------------
 #  specificCond <- readWQPqw('WIDNR_WQX-10032762',
-#                  'Specific conductance','2011-05-01','2011-09-30')
+#                            'Specific conductance',
+#                            '2011-05-01','2011-09-30')

 ## ----siteSearch, eval=FALSE-------------------------------
 #  sites <- whatNWISsites(bBox=c(-83.0,36.5,-81.0,38.5),
 #                        parameterCd=c("00010","00060"),
 #                        hasDataTypeCd="dv")

+## ----echo=FALSE-------------------------------------------
+
+Service <- c("dv","iv","gwlevels","qwdata","measurements","peak","stat")
+Description <- c("Daily","Instantaneous","Groundwater Levels","Water Quality","Surface Water Measurements","Peak Flow","Statistics Service")
+URL <- c("<a href='https://waterservices.usgs.gov/rest/DV-Test-Tool.html' target='_blank'>https://waterservices.usgs.gov/rest/DV-Test-Tool.html<a>",
+         "<a href='https://waterservices.usgs.gov/rest/IV-Test-Tool.html' target='_blank'>https://waterservices.usgs.gov/rest/IV-Test-Tool.html<a>",
+         "<a href='https://waterservices.usgs.gov/rest/GW-Levels-Test-Tool.html' target='_blank'>https://waterservices.usgs.gov/rest/GW-Levels-Test-Tool.html<a>",
+         "<a href='https://nwis.waterdata.usgs.gov/nwis/qwdata' target='_blank'>https://nwis.waterdata.usgs.gov/nwis/qwdata<a>",
+         "<a href='https://waterdata.usgs.gov/nwis/measurements/' target='_blank'>https://waterdata.usgs.gov/nwis/measurements/<a>",
+         "<a href='https://nwis.waterdata.usgs.gov/usa/nwis/peak/' target='_blank'>https://nwis.waterdata.usgs.gov/usa/nwis/peak/<a>",
+         "<a href='https://waterservices.usgs.gov/rest/Statistics-Service-Test-Tool.html' target='_blank'>https://waterservices.usgs.gov/rest/Statistics-Service-Test-Tool.html<a>")
+
+tableData <- data.frame(Service,
+                        Description,
+                        URL,
+  stringsAsFactors = FALSE)
+
+
+htmlTable(tableData, 
+          caption="Table 5: NWIS general data calls",
+          rnames=FALSE, align=c("l","l","l"),
+          col.rgroup = c("none", "#F7F7F7"), 
+          css.cell="padding-bottom: 0.0em; padding-right: 0.5em; padding-top: 0.0em;")
+
+
 ## ----dataExample, eval=FALSE------------------------------
 #  dischargeWI <- readNWISdata(service="dv",
 #                             stateCd="WI",
@@ -258,10 +353,19 @@ legend("topleft", variableInfo$param_units,
 #  

 ## ----phData, eval=FALSE-----------------------------------
-#  
 #  dataPH <- readWQPdata(statecode="US:55",
 #                   characteristicName="pH")
-#  
+
+## ----eval=FALSE-------------------------------------------
+#  type <- "Stream"
+#  sites <- whatWQPdata(countycode="US:55:025",siteType=type)
+
+## ----eval=FALSE-------------------------------------------
+#  site <- whatWQPsamples(siteid="USGS-01594440")
+
+## ----eval=FALSE-------------------------------------------
+#  type <- "Stream"
+#  sites <- whatWQPmetrics(countycode="US:55:025",siteType=type)

 ## ----meta1, eval=FALSE------------------------------------
 #  
@@ -289,10 +393,7 @@ legend("topleft", variableInfo$param_units,
 #  comment(peakData)
 #  
 #  #Which is equivalent to:
-#  # attr(peakData, "comment")
-
-## ----helpFunc,eval = FALSE--------------------------------
-#  ?readNWISpCode
+#  attr(peakData, "comment")

 ## ----seeVignette,eval = FALSE-----------------------------
 #  vignette(dataRetrieval)

--- a/inst/doc/dataRetrieval.Rmd
+++ b/inst/doc/dataRetrieval.Rmd
--- a/inst/doc/dataRetrieval.Rnw
+++ b/inst/doc/dataRetrieval.Rnw
--- a/inst/doc/dataRetrieval.html
+++ b/inst/doc/dataRetrieval.html
--- a/inst/doc/dataRetrieval.pdf
+++ b/inst/doc/dataRetrieval.pdf
--- a/vignettes/dataRetrieval.Rmd
+++ b/vignettes/dataRetrieval.Rmd
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
--- a/vignettes/figure/egretEx.pdf
+++ b/vignettes/figure/egretEx.pdf
--- a/vignettes/figure/getNWISUnitPlot.pdf
+++ b/vignettes/figure/getNWISUnitPlot.pdf
--- a/vignettes/figure/getNWIStemperaturePlot-1.pdf
+++ b/vignettes/figure/getNWIStemperaturePlot-1.pdf
--- a/vignettes/figure/getQWtemperaturePlot-1.pdf
+++ b/vignettes/figure/getQWtemperaturePlot-1.pdf
--- a/vignettes/figure/getQWtemperaturePlot.pdf
+++ b/vignettes/figure/getQWtemperaturePlot.pdf