Unverified Commit d875e0ac authored by Laura A DeCicco's avatar Laura A DeCicco Committed by GitHub
Browse files

Merge pull request #420 from ldecicco-USGS/gh-pages

https
parents 521650fe 1aa00a59
#bigTable td{
font-size: 0.8em;
width: 1500px;
}
.title-slide hgroup h1 {
color: #515151;
font-size: 40px;
letter-spacing: -3px;
line-height: 1.4;
}
h2 {
color: #515151;
font-size: 35px;
letter-spacing: -2px;
line-height: 1.2em;
}
slides > slide > hgroup + article{
margin-top:10px;
}
#study-sites-tributaries {
margin-top: 10px;
}
#testingStuff{
width:100%
}
#leftSideDiv{
width:75%;
float:left;
}
#leftSideThird{
width:33%;
float:left;
}
#rightSideThird{
width:33%;
float:right;
}
#middleThird{
width:33%;
float:left;
}
.diffH2 h2{
line-height:0px;
}
#rightSideDiv{
width:33%;
float:right;
}
table.rmdtable td, table th {
font-size: 18px;
padding: 0.5em 0.5em;
}
table.rmdtable tr > td:first-child, table th {
font-weight: normal;
color: #515151;
}
article.smaller table td {
font-size: 14px;
font-weight: normal;
color: #515151;
}
article.rmdtable table th {
font-size: 16px;
font-weight: normal;
color: #FFF;
}
.testingStuff b, strong {
font-weight: bold;
color: #FF0000;
}
slides > slide {
background-image: url(../img/usgs.png), url(../img/simple-shadow.png);
background-size: 150px, 35px;
background-repeat: no-repeat;
background-position: 3% 98%, 98% 98%;
}
...@@ -8,11 +8,11 @@ knit: (function(inputFile, encoding) { ...@@ -8,11 +8,11 @@ knit: (function(inputFile, encoding) {
out_dir <- 'test'; out_dir <- 'test';
rmarkdown::render(inputFile, rmarkdown::render(inputFile,
encoding=encoding, encoding=encoding,
output_file='../dataRetrieval.html') }) output_file='dataRetrieval.html') })
output: output:
ioslides_presentation: ioslides_presentation:
css: ../styles.css css: css/stylesSlides.css
logo: ../images/simple-shadow.png logo: img/simple-shadow.png
smaller: yes smaller: yes
widescreen: yes widescreen: yes
--- ---
...@@ -48,7 +48,7 @@ How to discover data? ...@@ -48,7 +48,7 @@ How to discover data?
## Overview ## Overview
<img src="../images/2015-12-15_13-52-29.png" alt="Overview" style="width: 800px;"/> <img src="img/2015-12-15_13-52-29.png" alt="Overview" style="width: 800px;"/>
## Installation ## Installation
...@@ -62,11 +62,11 @@ Bug fixes and feature upgrades are vetted through a version of `dataRetrieval` t ...@@ -62,11 +62,11 @@ Bug fixes and feature upgrades are vetted through a version of `dataRetrieval` t
```{r echo=TRUE, eval=FALSE} ```{r echo=TRUE, eval=FALSE}
install.packages("dataRetrieval", install.packages("dataRetrieval",
repos=c("http://owi.usgs.gov/R", repos=c("https://owi.usgs.gov/R",
getOption("repos"))) getOption("repos")))
``` ```
More information can be found at [http://owi.usgs.gov/R/gran.html](http://owi.usgs.gov/R/gran.html). More information can be found at [https://owi.usgs.gov/R/gran.html](https://owi.usgs.gov/R/gran.html).
Finally, the absolute cutting-edge version of `dataRetrieval` can be installed using the `devtools` package which pulls from GitHub: Finally, the absolute cutting-edge version of `dataRetrieval` can be installed using the `devtools` package which pulls from GitHub:
...@@ -106,11 +106,9 @@ Finally, if there are still questions that the vignette and help files don't ans ...@@ -106,11 +106,9 @@ Finally, if there are still questions that the vignette and help files don't ans
|Unit Data| |Unit Data|
|---------| |---------|
|Data reported at the frequency it is collected – e.g. 15 minute| |Data reported at the frequency it is collected – e.g. 15 minute|
|Generally available back to 2007 (big improvement from 120 days!)|
|Includes current real-time data| |Includes current real-time data|
|Daily Data| |Daily Data|
|----------| |----------|
|Data aggregated to a daily statistic such as mean, min, or max| |Data aggregated to a daily statistic such as mean, min, or max|
...@@ -270,7 +268,7 @@ siteInfo <- attr(yahara, "siteInfo") ...@@ -270,7 +268,7 @@ siteInfo <- attr(yahara, "siteInfo")
ts <- ts + ts <- ts +
xlab("") + xlab("") +
ylab(parameterInfo$parameter_desc) + ylab(parameterInfo$variableDescription) +
ggtitle(siteInfo$station_nm) ggtitle(siteInfo$station_nm)
ts ts
``` ```
...@@ -334,7 +332,7 @@ Environmental Data Discovery and Transformation tool: [http://cida.usgs.gov/endd ...@@ -334,7 +332,7 @@ Environmental Data Discovery and Transformation tool: [http://cida.usgs.gov/endd
For dataRetrieval: For dataRetrieval:
Become familiar with the possibilities of the web services [http://waterservices.usgs.gov/](http://waterservices.usgs.gov/) Become familiar with the possibilities of the web services [http://waterservices.usgs.gov/](http://waterservices.usgs.gov/)
<img src="../images/waterservices.png" alt="Overview" style="width: 450px;"/> <img src="img/waterservices.png" alt="Overview" title="dataRetrieval Overview" style="width: 450px;"/>
## USGS Advanced Retrievals: readNWISdata ## USGS Advanced Retrievals: readNWISdata
...@@ -418,8 +416,6 @@ meas <- readNWISdata(state_cd="WI",service="measurements",format="rdb_expanded") ...@@ -418,8 +416,6 @@ meas <- readNWISdata(state_cd="WI",service="measurements",format="rdb_expanded")
[Water Quality Portal](http://www.waterqualitydata.us/) [Water Quality Portal](http://www.waterqualitydata.us/)
<div class="columns-2">
* Multiple agencies * Multiple agencies
+ USGS data comes from the NWIS database + USGS data comes from the NWIS database
+ EPA data comes from the STORET database (this includes many state, tribal, NGO, and academic groups) + EPA data comes from the STORET database (this includes many state, tribal, NGO, and academic groups)
...@@ -430,9 +426,6 @@ meas <- readNWISdata(state_cd="WI",service="measurements",format="rdb_expanded") ...@@ -430,9 +426,6 @@ meas <- readNWISdata(state_cd="WI",service="measurements",format="rdb_expanded")
* To get non-NWIS data, need to use CharacteristicName instead of parameter code. * To get non-NWIS data, need to use CharacteristicName instead of parameter code.
<img src="../images/WQP.png" alt="Overview" style="width: 300px;"/>
</div>
## Water Quality Portal Basic Retrieval: readWQPqw ## Water Quality Portal Basic Retrieval: readWQPqw
...@@ -510,7 +503,7 @@ unique(phosData$ResultMeasure.MeasureUnitCode) ...@@ -510,7 +503,7 @@ unique(phosData$ResultMeasure.MeasureUnitCode)
``` ```
```{r echo=FALSE, eval=TRUE} ```{r echo=FALSE, eval=TRUE}
phosData <- readRDS("phosData.rds") phosData <- readRDS("img/phosData.rds")
unique(phosData$ResultMeasure.MeasureUnitCode) unique(phosData$ResultMeasure.MeasureUnitCode)
``` ```
...@@ -699,7 +692,8 @@ pander(sitesVA.1[,c("site_no","station_nm","begin_date","end_date")]) ...@@ -699,7 +692,8 @@ pander(sitesVA.1[,c("site_no","station_nm","begin_date","end_date")])
Get samples that have both parameters: Get samples that have both parameters:
```{r echo=TRUE, eval = FALSE} ```{r echo=TRUE, eval = FALSE}
comboData <- readNWISqw(sitesVA.1$site_no[1], pCode, reshape = TRUE) %>% comboData <- readNWISqw(sitesVA.1$site_no[1],
pCode, reshape = TRUE) %>%
filter(!is.na(result_va_00665) & !is.na(result_va_80154)) filter(!is.na(result_va_00665) & !is.na(result_va_80154))
variableInfo <- attr(comboData, "variableInfo") variableInfo <- attr(comboData, "variableInfo")
...@@ -781,9 +775,6 @@ plotResid ...@@ -781,9 +775,6 @@ plotResid
## Supplemental Slides: USGS Basic Web Retrievals: readNWISdv ## Supplemental Slides: USGS Basic Web Retrievals: readNWISdv
Unit value discharge data is 15 minute data availabe back to 2007.
Daily mean data is available for far longer.
```{r echo=TRUE, eval=FALSE} ```{r echo=TRUE, eval=FALSE}
siteNo <- "05427718" siteNo <- "05427718"
...@@ -793,26 +784,27 @@ daily <- readNWISdv(siteNo, pCode, "1990-01-01","2014-12-31") ...@@ -793,26 +784,27 @@ daily <- readNWISdv(siteNo, pCode, "1990-01-01","2014-12-31")
daily <- renameNWISColumns(daily) daily <- renameNWISColumns(daily)
dd <- ggplot(daily, aes(Date,Flow)) + dd <- ggplot(daily, aes(Date,Flow)) +
xlab("") + xlab("") +
ylab(attr(daily,"variableInfo")$parameter_nm) + ylab(attr(daily,"variableInfo")$variableName) +
geom_line() geom_line()
dd dd
``` ```
## Supplemental Slides: USGS Basic Web Retrievals: readNWISdv ## Supplemental Slides: USGS Basic Web Retrievals: readNWISdv
Unit value discharge data is 15 minute data availabe back to 2007.
Daily mean data is available for far longer.
```{r echo=FALSE, eval=TRUE} ```{r echo=FALSE, eval=TRUE}
siteNo <- "05427718" siteNo <- "05427718"
pCode <- "00060" pCode <- "00060"
daily <- readNWISdv(siteNo, pCode, "1990-01-01","2014-12-31") daily <- readNWISdv(siteNo, pCode, "1990-01-01","2014-12-31")
daily <- renameNWISColumns(daily) daily <- renameNWISColumns(daily)
dd <- ggplot(daily, aes(Date,Flow)) + dd <- ggplot(daily, aes(Date,Flow)) +
xlab("") + xlab("") +
ylab(attr(daily,"variableInfo")$parameter_nm) + ylab(attr(daily,"variableInfo")$variableName) +
geom_line() geom_line()
dd dd
``` ```
...@@ -828,7 +820,10 @@ The NWIS functions can be used to get multiple sites and multiple parameters in ...@@ -828,7 +820,10 @@ The NWIS functions can be used to get multiple sites and multiple parameters in
sites <- c("05427850","05427718") # 2 stations on Yahara sites <- c("05427850","05427718") # 2 stations on Yahara
pCodes <- c("00060","00010") #Temperature and discharge pCodes <- c("00060","00010") #Temperature and discharge
multi <- readNWISuv(sites,pCodes, "2016-03-01","2016-03-08") today <- Sys.Date()
last.week <- Sys.Date()-7
multi <- readNWISuv(sites,pCodes, last.week, today)
multi <- renameNWISColumns(multi) multi <- renameNWISColumns(multi)
names(multi) names(multi)
...@@ -966,8 +961,9 @@ longMulti <- gather(wideMulti, variable, value, -site_no, -dateTime) %>% ...@@ -966,8 +961,9 @@ longMulti <- gather(wideMulti, variable, value, -site_no, -dateTime) %>%
mutate(variable = as.factor(variable)) %>% mutate(variable = as.factor(variable)) %>%
mutate(site_no = as.factor(site_no)) mutate(site_no = as.factor(site_no))
levels(longMulti$variable) <- paramInfo$param_units levels(longMulti$variable) <- paramInfo$unit[which(paste0("X_",paramInfo$variableCode,"_00000") %in% levels(longMulti$variable))]
levels(longMulti$site_no) <- siteInfo$station_nm
levels(longMulti$site_no) <- siteInfo$station_nm[which(siteInfo$site_no %in% levels(longMulti$site_no))]
gp <- ggplot(longMulti, gp <- ggplot(longMulti,
aes(dateTime, value, color=site_no)) + aes(dateTime, value, color=site_no)) +
......
#bigTable td{
font-size: 0.8em;
width: 1500px;
}
.title-slide hgroup h1 {
color: #515151;
font-size: 40px;
letter-spacing: -3px;
line-height: 1.4;
}
h2 {
color: #515151;
font-size: 35px;
letter-spacing: -2px;
line-height: 1.2em;
}
slides > slide > hgroup + article{
margin-top:10px;
}
#study-sites-tributaries {
margin-top: 10px;
}
#testingStuff{
width:100%
}
#leftSideDiv{
width:75%;
float:left;
}
#leftSideThird{
width:33%;
float:left;
}
#rightSideThird{
width:33%;
float:right;
}
#middleThird{
width:33%;
float:left;
}
.diffH2 h2{
line-height:0px;
}
#rightSideDiv{
width:33%;
float:right;
}
table.rmdtable td, table th {
font-size: 18px;
padding: 0.5em 0.5em;
}
table.rmdtable tr > td:first-child, table th {
font-weight: normal;
color: #515151;
}
article.smaller table td {
font-size: 14px;
font-weight: normal;
color: #515151;
}
article.rmdtable table th {
font-size: 16px;
font-weight: normal;
color: #FFF;
}
.testingStuff b, strong {
font-weight: bold;
color: #FF0000;
}
slides > slide {
background-image: url(images/usgs.png), url(images/simple-shadow.png);
background-size: 150px, 35px;
background-repeat: no-repeat;
background-position: 3% 98%, 98% 98%;
}
This diff is collapsed.
...@@ -90,8 +90,8 @@ article.rmdtable table th { ...@@ -90,8 +90,8 @@ article.rmdtable table th {
} }
slides > slide { slides > slide {
background-image: url(images/usgs.png), url(images/simple-shadow.png), url(images/paper_fibers.png); background-image: url(images/usgs.png), url(images/simple-shadow.png);
background-size: 150px, 35px, cover; background-size: 150px, 35px;
background-repeat: no-repeat; background-repeat: no-repeat;
background-position: 3% 98%, 98% 98%; background-position: 3% 98%, 98% 98%;
} }
......
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