diff --git a/README.md b/README.md
index 89adf09432d775d48c617b033426524e6a7f1370..8350e906846466bb942436953debd161fe44b764 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-dataRetrieval
+`dataRetrieval`
=============
[](https://ci.appveyor.com/project/USGS-R/dataretrieval)
@@ -9,23 +9,20 @@ R package source for data retrieval specifically for the EGRET R package:
Please visit the EGRET wiki for more information:
[EGRET Wiki](https://github.com/USGS-R/EGRET/wiki)
-Disclaimer
-----------
-This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at [http://www.usgs.gov/visual-id/credit_usgs.html#copyright](http://www.usgs.gov/visual-id/credit_usgs.html#copyright)
+##Disclaimer
+This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey, an agency of the United States Department of Interior. For more information, see the [official USGS copyright policy](http://www.usgs.gov/visual-id/credit_usgs.html#copyright/ "official USGS copyright policy")
-Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.
+Although this software program has been used by the U.S. Geological Survey (USGS), no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.
This software is provided "AS IS."
-Subscribe
----------
+##Subscribe
Please email questions, comments, and feedback to:
egret_comments@usgs.gov
Additionally, to subscribe to an email list concerning updates to these R packages, please send a request to egret_comments@usgs.gov.
-Package Installation
----------------------------------
+##Package Installation
While the dataRetreival package is in development (and not on CRAN), the zoo package must first be manually installed. To install the dataRetrieval package, you must be using R 3.0 or greater and run the following commands:
install.packages("dataRetrieval",
@@ -34,27 +31,31 @@ While the dataRetreival package is in development (and not on CRAN), the zoo pac
type="both")
-Version updates
+##Version updates
---------------
-dataRetrieval 1.4.0-in developement
-===========
-* Changed naming convention:
-getDVData -> getNWISDaily
-getSampleData -> getNWISSample
-getSTORETData* -> getWQPSample
-getSampleDataFromFile -> getUserSample
-getDailyDataFromFile -> getUserDaily
-getMetaData -> splits into getNWISInfo and getUserInfo
-getSiteFileData <- getNWISSiteInfo
-getParameterInfo <- getNWISPcodeInfo
-getDataAvailability <- getNWISDataAvailability
-'retrieve' functions changed to 'get'
-* Changed WaterML2 rbind fill from plyr function to dplyr. Removed plyr import, added dplyr.
-*
-
-
-dataRetrieval 1.3.3
-===========
+###dataRetrieval 1.4.0-in developement
+Changed naming convention:
+
+
+
+|Original Name | New Name |
+| ------------- |:-------------|
+|getDVData | getNWISDaily |
+|getSampleData | getNWISSample |
+|getSTORETData* | getWQPSample |
+|getSampleDataFromFile | getUserSample |
+|getDailyDataFromFile | getUserDaily |
+|getMetaData | splits into getNWISInfo and getUserInfo |
+|getSiteFileData | getNWISSiteInfo |
+|getParameterInfo | getNWISPcodeInfo |
+|getDataAvailability | getNWISDataAvailability |
+|'retrieve' functions | 'get' |
+
+Changed WaterML2 rbind fill from plyr function to dplyr. Removed plyr import, added dplyr.
+
+
+
+###dataRetrieval 1.3.3
* Updated getNWISSiteInfo to retrieve multiple site file datasets at once using a vector of siteNumbers as input argument.
* Updated error-handling for Web service calls. More information is returned when errors happen
@@ -62,8 +63,7 @@ dataRetrieval 1.3.3
* Added very generalized NWIS and WQP retrieval functions (getNWISData, getNWISSites, getGeneralWQPData, and getWQPSites) which allow the user to use any argument available on the Web service platform.
-dataRetrieval 1.3.2
-===========
+###dataRetrieval 1.3.2
* Deprecated getQWData, updated getWQPData to take either parameter code or characteristic name.
* Changed the name of raw data retrievals to: getNWISqwData, getNWISunitData, getNWISdvData, and getWQPqwData (from: getNWISqwData, retrieveUnitNWISData, retrieveNWISData, getRawQWData)
@@ -71,8 +71,7 @@ dataRetrieval 1.3.2
* Updated mergeReport to allow for Sample data with different measurements taken on the same day
-Sample Workflow
----------------
+##Sample Workflow
Load data from web services:
diff --git a/inst/doc/dataRetrieval.Rnw b/inst/doc/dataRetrieval.Rnw
index 72dab59a7f668c87068799d663b8f00538743104..0e5c361355590dd43d6b4c3a08d251f7acea0b23 100644
--- a/inst/doc/dataRetrieval.Rnw
+++ b/inst/doc/dataRetrieval.Rnw
@@ -545,7 +545,7 @@ url_uv <- constructNWISURL(siteNumber,"00060",startDate,endDate,'uv')
\section{Water Quality Portal Web Retrievals}
\label{sec:usgsSTORET}
%------------------------------------------------------------
-There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}). These data sets can be housed in either the STORET (data from EPA), NWIS database (data from USGS), STEWARDS database (USDA), and additional databases are slated to be included. Because only USGS uses parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied. The \texttt{getWQPqwData} function can take either a USGS parameter code, or a more general cahracteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin.
+There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}). These data sets can be housed in either the STORET database (data from EPA), NWIS database (data from USGS), STEWARDS database (data from USDA), and additional databases are slated to be included. Because only USGS uses parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied. The \texttt{getWQPqwData} function can take either a USGS parameter code, or a more general characteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin.
<<label=getQWData, echo=TRUE, eval=FALSE>>=
@@ -553,6 +553,7 @@ specificCond <- getWQPqwData('WIDNR_WQX-10032762',
'Specific conductance','2011-05-01','2011-09-30')
@
+Guidance for finding characteristic names can be found at: \url{http://www.waterqualitydata.us/webservices_documentation.jsp}.
\FloatBarrier
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index 86ec1ffbcb43e4db99cd84b9363a0b606e6dc2c2..79241a6cf35a9767c84309da885f9ac66a573649 100644
Binary files a/inst/doc/dataRetrieval.pdf and b/inst/doc/dataRetrieval.pdf differ
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 3c7c784432853188f0761b6c12eee44226db94c9..7fa17698e20d5c90bf79dfa462958e1408da497d 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -2,7 +2,7 @@
1 127 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 8 1 9 0 %
24 1 3 0 21 1 4 0 6 1 8 0 18 1 3 0 25 1 1 4 19 1 9 0 %
6 1 7 0 22 1 8 0 16 1 2 0 11 1 23 0 22 1 9 0 20 1 3 0 %
-6 1 17 0 28 1 12 0 10 1 9 0 20 1 4 0 14 1 4 0 32 1 17 %
+6 1 17 0 28 1 12 0 10 1 9 0 20 1 4 0 14 1 4 0 33 1 17 %
0 39 1 14 0 18 1 2 0 14 1 2 0 49 1 4 0 7 1 4 0 11 1 2 %
0 17 1 7 0 22 1 8 0 21 1 4 0 9 1 4 0 79 1 1 2 9 1 1 4 %
4 1 20 0 44 1 4 0 30 1 4 0 22 1 4 0 21 1 26 0 13 1 9 %
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index 72dab59a7f668c87068799d663b8f00538743104..0e5c361355590dd43d6b4c3a08d251f7acea0b23 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -545,7 +545,7 @@ url_uv <- constructNWISURL(siteNumber,"00060",startDate,endDate,'uv')
\section{Water Quality Portal Web Retrievals}
\label{sec:usgsSTORET}
%------------------------------------------------------------
-There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}). These data sets can be housed in either the STORET (data from EPA), NWIS database (data from USGS), STEWARDS database (USDA), and additional databases are slated to be included. Because only USGS uses parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied. The \texttt{getWQPqwData} function can take either a USGS parameter code, or a more general cahracteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin.
+There are additional water quality data sets available from the Water Quality Data Portal (\url{http://www.waterqualitydata.us/}). These data sets can be housed in either the STORET database (data from EPA), NWIS database (data from USGS), STEWARDS database (data from USDA), and additional databases are slated to be included. Because only USGS uses parameter codes, a \texttt{"}characteristic name\texttt{"} must be supplied. The \texttt{getWQPqwData} function can take either a USGS parameter code, or a more general characteristic name in the parameterCd input argument. The Water Quality Data Portal includes data discovery tools and information on characteristic names. The following example retrieves specific conductance from a DNR site in Wisconsin.
<<label=getQWData, echo=TRUE, eval=FALSE>>=
@@ -553,6 +553,7 @@ specificCond <- getWQPqwData('WIDNR_WQX-10032762',
'Specific conductance','2011-05-01','2011-09-30')
@
+Guidance for finding characteristic names can be found at: \url{http://www.waterqualitydata.us/webservices_documentation.jsp}.
\FloatBarrier
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
index 34e15212d0f5fcdb8088cbe5d584476e4e21f9a8..f42cd96770911ed2ecb7777508ad00d71e1afc8c 100644
Binary files a/vignettes/figure/egretEx.pdf and b/vignettes/figure/egretEx.pdf differ
diff --git a/vignettes/figure/getNWIStemperaturePlot.pdf b/vignettes/figure/getNWIStemperaturePlot.pdf
index a870020ddb117d1148e8cfbdedd8a5b2efae8384..0928119a77a42de2606498470844f7bc9bea2db4 100644
Binary files a/vignettes/figure/getNWIStemperaturePlot.pdf and b/vignettes/figure/getNWIStemperaturePlot.pdf differ
diff --git a/vignettes/figure/getQWtemperaturePlot.pdf b/vignettes/figure/getQWtemperaturePlot.pdf
index 6fded0320e03ac082ba87d1c08c8bd616801e941..b72d9d183ad5dbdff0a9695cfde7b0bfbd9a4b52 100644
Binary files a/vignettes/figure/getQWtemperaturePlot.pdf and b/vignettes/figure/getQWtemperaturePlot.pdf differ