VT-Hydroinformatics.github.io/getdata.html at master · VT-Hydroinformatics/VT-Hydroinformatics.github.io · GitHub

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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>

  <meta charset="utf-8" />
  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
  <title>Chapter 7 Joins, Pivots, and USGS dataRetrieval | Hydroinformatics at VT</title>
  <meta name="description" content="This bookdown contains notes and exercises for a course in hydroinformatics at Virginia Tech." />
  <meta name="generator" content="bookdown 0.27 and GitBook 2.6.7" />

  <meta property="og:title" content="Chapter 7 Joins, Pivots, and USGS dataRetrieval | Hydroinformatics at VT" />
  <meta property="og:type" content="book" />

  <meta property="og:description" content="This bookdown contains notes and exercises for a course in hydroinformatics at Virginia Tech." />


  <meta name="twitter:card" content="summary" />
  <meta name="twitter:title" content="Chapter 7 Joins, Pivots, and USGS dataRetrieval | Hydroinformatics at VT" />

  <meta name="twitter:description" content="This bookdown contains notes and exercises for a course in hydroinformatics at Virginia Tech." />


<meta name="author" content="JP Gannon" />


<meta name="date" content="2023-02-09" />

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<li><a href="./">Hydroinformatics</a></li>

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<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Introduction</a>
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<li class="chapter" data-level="1.0.1" data-path="index.html"><a href="index.html#to-help-me-keep-get-an-idea-of-who-is-using-this-resource-so-i-can-improve-it-in-the-future-please-consider-filling-out-any-or-all-of-this-survey-httpsforms.gle6zcntzvr1wzzuh6s7-thanks"><i class="fa fa-check"></i><b>1.0.1</b> To help me keep get an idea of who is using this resource so I can improve it in the future, please consider filling out any or all of this survey: https://forms.gle/6Zcntzvr1wZZUh6S7 Thanks!</a></li>
<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#how-to-use-these-materials"><i class="fa fa-check"></i><b>1.1</b> How to use these materials</a></li>
<li class="chapter" data-level="1.2" data-path="index.html"><a href="index.html#table-of-contents"><i class="fa fa-check"></i><b>1.2</b> Table of contents:</a></li>
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<li class="chapter" data-level="2" data-path="Plotting.html"><a href="Plotting.html"><i class="fa fa-check"></i><b>2</b> Intro to Plotting</a>
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<li class="chapter" data-level="2.1" data-path="Plotting.html"><a href="Plotting.html#download-and-install-tidyverse-library"><i class="fa fa-check"></i><b>2.1</b> Download and install tidyverse library</a></li>
<li class="chapter" data-level="2.2" data-path="Plotting.html"><a href="Plotting.html#reading-data"><i class="fa fa-check"></i><b>2.2</b> Reading data</a></li>
<li class="chapter" data-level="2.3" data-path="Plotting.html"><a href="Plotting.html#our-first-ggplot"><i class="fa fa-check"></i><b>2.3</b> Our first ggplot</a></li>
<li class="chapter" data-level="2.4" data-path="Plotting.html"><a href="Plotting.html#change-point-type"><i class="fa fa-check"></i><b>2.4</b> Change point type</a></li>
<li class="chapter" data-level="2.5" data-path="Plotting.html"><a href="Plotting.html#set-colors"><i class="fa fa-check"></i><b>2.5</b> Set colors</a></li>
<li class="chapter" data-level="2.6" data-path="Plotting.html"><a href="Plotting.html#controlling-color-with-a-third-variable-and-other-functions"><i class="fa fa-check"></i><b>2.6</b> Controlling color with a third variable and other functions</a></li>
<li class="chapter" data-level="2.7" data-path="Plotting.html"><a href="Plotting.html#plotting-multiple-groups"><i class="fa fa-check"></i><b>2.7</b> Plotting multiple groups</a></li>
<li class="chapter" data-level="2.8" data-path="Plotting.html"><a href="Plotting.html#facets"><i class="fa fa-check"></i><b>2.8</b> Facets</a></li>
<li class="chapter" data-level="2.9" data-path="Plotting.html"><a href="Plotting.html#two-variable-faceting"><i class="fa fa-check"></i><b>2.9</b> Two variable faceting</a></li>
<li class="chapter" data-level="2.10" data-path="Plotting.html"><a href="Plotting.html#boxplots"><i class="fa fa-check"></i><b>2.10</b> Boxplots</a></li>
<li class="chapter" data-level="2.11" data-path="Plotting.html"><a href="Plotting.html#more-about-color-size-etc"><i class="fa fa-check"></i><b>2.11</b> More about color, size, etc</a></li>
<li class="chapter" data-level="2.12" data-path="Plotting.html"><a href="Plotting.html#multiple-geoms"><i class="fa fa-check"></i><b>2.12</b> Multiple geoms</a></li>
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<li class="chapter" data-level="3" data-path="Programming.html"><a href="Programming.html"><i class="fa fa-check"></i><b>3</b> R Tidyverse Programming Basics</a>
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<li class="chapter" data-level="3.1" data-path="Programming.html"><a href="Programming.html#introduction-1"><i class="fa fa-check"></i><b>3.1</b> Introduction</a></li>
<li class="chapter" data-level="3.2" data-path="Programming.html"><a href="Programming.html#you-can-use-r-as-a-calculator"><i class="fa fa-check"></i><b>3.2</b> You can use R as a calculator</a></li>
<li class="chapter" data-level="3.3" data-path="Programming.html"><a href="Programming.html#you-can-create-new-objects-using--"><i class="fa fa-check"></i><b>3.3</b> You can create new objects using &lt;-</a></li>
<li class="chapter" data-level="3.4" data-path="Programming.html"><a href="Programming.html#using-functions"><i class="fa fa-check"></i><b>3.4</b> Using functions</a></li>
<li class="chapter" data-level="3.5" data-path="Programming.html"><a href="Programming.html#read-in-some-data."><i class="fa fa-check"></i><b>3.5</b> Read in some data.</a></li>
<li class="chapter" data-level="3.6" data-path="Programming.html"><a href="Programming.html#wait-hold-up.-what-is-a-tibble"><i class="fa fa-check"></i><b>3.6</b> Wait, hold up. What is a tibble?</a></li>
<li class="chapter" data-level="3.7" data-path="Programming.html"><a href="Programming.html#data-wrangling-in-dplyr"><i class="fa fa-check"></i><b>3.7</b> Data wrangling in dplyr</a></li>
<li class="chapter" data-level="3.8" data-path="Programming.html"><a href="Programming.html#filter"><i class="fa fa-check"></i><b>3.8</b> Filter</a>
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<li class="chapter" data-level="3.8.1" data-path="Programming.html"><a href="Programming.html#multiple-conditions"><i class="fa fa-check"></i><b>3.8.1</b> Multiple conditions</a></li>
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<li class="chapter" data-level="3.9" data-path="Programming.html"><a href="Programming.html#arrange"><i class="fa fa-check"></i><b>3.9</b> Arrange</a></li>
<li class="chapter" data-level="3.10" data-path="Programming.html"><a href="Programming.html#select"><i class="fa fa-check"></i><b>3.10</b> Select</a></li>
<li class="chapter" data-level="3.11" data-path="Programming.html"><a href="Programming.html#mutate"><i class="fa fa-check"></i><b>3.11</b> Mutate</a></li>
<li class="chapter" data-level="3.12" data-path="Programming.html"><a href="Programming.html#summarize"><i class="fa fa-check"></i><b>3.12</b> Summarize</a></li>
<li class="chapter" data-level="3.13" data-path="Programming.html"><a href="Programming.html#multiple-operations-with-pipes"><i class="fa fa-check"></i><b>3.13</b> Multiple operations with pipes</a>
<ul>
<li class="chapter" data-level="3.13.1" data-path="Programming.html"><a href="Programming.html#lets-say-we-want-to-tell-r-to-make-a-pbj-sandwich-by-using-the-pbbread-jbread-and-joinslices-functions-and-the-data-ingredients.-if-we-do-this-saving-each-step-if-would-look-like-this"><i class="fa fa-check"></i><b>3.13.1</b> Let’s say we want to tell R to make a PB&amp;J sandwich by using the pbbread(), jbread(), and joinslices() functions and the data “ingredients”. If we do this saving each step if would look like this:</a></li>
<li class="chapter" data-level="3.13.2" data-path="Programming.html"><a href="Programming.html#if-we-nest-the-functions-together-we-get-this"><i class="fa fa-check"></i><b>3.13.2</b> If we nest the functions together we get this</a></li>
<li class="chapter" data-level="3.13.3" data-path="Programming.html"><a href="Programming.html#using-the-pipe-it-would-look-like-this"><i class="fa fa-check"></i><b>3.13.3</b> Using the pipe it would look like this</a></li>
<li class="chapter" data-level="3.13.4" data-path="Programming.html"><a href="Programming.html#when-you-use-the-pipe-it-basically-takes-whatever-came-out-of-the-first-function-and-puts-it-into-the-data-argument-for-the-next-one"><i class="fa fa-check"></i><b>3.13.4</b> When you use the pipe, it basically takes whatever came out of the first function and puts it into the data argument for the next one</a></li>
</ul></li>
<li class="chapter" data-level="3.14" data-path="Programming.html"><a href="Programming.html#save-your-results-to-a-new-tibble"><i class="fa fa-check"></i><b>3.14</b> Save your results to a new tibble</a></li>
<li class="chapter" data-level="3.15" data-path="Programming.html"><a href="Programming.html#what-about-nas"><i class="fa fa-check"></i><b>3.15</b> What about NAs?</a></li>
<li class="chapter" data-level="3.16" data-path="Programming.html"><a href="Programming.html#what-are-some-things-you-think-ill-ask-you-to-do-for-the-activity-next-class"><i class="fa fa-check"></i><b>3.16</b> What are some things you think I’ll ask you to do for the activity next class?</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="introactivity.html"><a href="introactivity.html"><i class="fa fa-check"></i><b>4</b> ACTIVITY Intro Skills</a>
<ul>
<li class="chapter" data-level="4.1" data-path="introactivity.html"><a href="introactivity.html#problem-1"><i class="fa fa-check"></i><b>4.1</b> Problem 1</a></li>
<li class="chapter" data-level="4.2" data-path="introactivity.html"><a href="introactivity.html#problem-2"><i class="fa fa-check"></i><b>4.2</b> Problem 2</a></li>
<li class="chapter" data-level="4.3" data-path="introactivity.html"><a href="introactivity.html#problem-3"><i class="fa fa-check"></i><b>4.3</b> Problem 3</a></li>
<li class="chapter" data-level="4.4" data-path="introactivity.html"><a href="introactivity.html#problem-4"><i class="fa fa-check"></i><b>4.4</b> Problem 4</a></li>
<li class="chapter" data-level="4.5" data-path="introactivity.html"><a href="introactivity.html#problem-5"><i class="fa fa-check"></i><b>4.5</b> Problem 5</a></li>
<li class="chapter" data-level="4.6" data-path="introactivity.html"><a href="introactivity.html#problem-6"><i class="fa fa-check"></i><b>4.6</b> Problem 6</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="stats.html"><a href="stats.html"><i class="fa fa-check"></i><b>5</b> Introduction to Basic Statistics</a>
<ul>
<li class="chapter" data-level="5.1" data-path="stats.html"><a href="stats.html#reading-for-this-section-statistical-methods-in-water-resources-chapter-1"><i class="fa fa-check"></i><b>5.1</b> Reading for this section: Statistical Methods in Water Resources: Chapter 1</a></li>
<li class="chapter" data-level="5.2" data-path="stats.html"><a href="stats.html#questions-for-today"><i class="fa fa-check"></i><b>5.2</b> Questions for today:</a>
<ul>
<li class="chapter" data-level="5.2.1" data-path="stats.html"><a href="stats.html#stack-plots-to-compare-histogram-and-pdf"><i class="fa fa-check"></i><b>5.2.1</b> Stack plots to compare histogram and pdf</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="stats.html"><a href="stats.html#what-is-the-difference-between-a-sample-and-a-population."><i class="fa fa-check"></i><b>5.3</b> What is the difference between a sample and a population.</a></li>
<li class="chapter" data-level="5.4" data-path="stats.html"><a href="stats.html#measuring-our-sample-distribution-central-tendency."><i class="fa fa-check"></i><b>5.4</b> Measuring our sample distribution: central tendency.</a>
<ul>
<li class="chapter" data-level="5.4.1" data-path="stats.html"><a href="stats.html#so-whats-a-weighted-average"><i class="fa fa-check"></i><b>5.4.1</b> So what’s a weighted average?</a></li>
</ul></li>
<li class="chapter" data-level="5.5" data-path="stats.html"><a href="stats.html#measures-of-variability"><i class="fa fa-check"></i><b>5.5</b> Measures of variability</a></li>
<li class="chapter" data-level="5.6" data-path="stats.html"><a href="stats.html#what-is-a-normal-distribution-and-how-can-we-determine-if-we-have-one"><i class="fa fa-check"></i><b>5.6</b> What is a normal distribution and how can we determine if we have one?</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="statsactivity.html"><a href="statsactivity.html"><i class="fa fa-check"></i><b>6</b> ACTIVITY Intro Stats</a>
<ul>
<li class="chapter" data-level="6.1" data-path="statsactivity.html"><a href="statsactivity.html#problem-1-1"><i class="fa fa-check"></i><b>6.1</b> Problem 1</a></li>
<li class="chapter" data-level="6.2" data-path="statsactivity.html"><a href="statsactivity.html#problem-2-1"><i class="fa fa-check"></i><b>6.2</b> Problem 2</a></li>
<li class="chapter" data-level="6.3" data-path="statsactivity.html"><a href="statsactivity.html#problem-3-1"><i class="fa fa-check"></i><b>6.3</b> Problem 3</a></li>
<li class="chapter" data-level="6.4" data-path="statsactivity.html"><a href="statsactivity.html#problem-4-1"><i class="fa fa-check"></i><b>6.4</b> Problem 4</a></li>
<li class="chapter" data-level="6.5" data-path="statsactivity.html"><a href="statsactivity.html#problem-5-1"><i class="fa fa-check"></i><b>6.5</b> Problem 5</a></li>
<li class="chapter" data-level="6.6" data-path="statsactivity.html"><a href="statsactivity.html#problem-6-1"><i class="fa fa-check"></i><b>6.6</b> Problem 6</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="getdata.html"><a href="getdata.html"><i class="fa fa-check"></i><b>7</b> Joins, Pivots, and USGS dataRetrieval</a>
<ul>
<li class="chapter" data-level="7.1" data-path="getdata.html"><a href="getdata.html#goals-for-today"><i class="fa fa-check"></i><b>7.1</b> Goals for today</a></li>
<li class="chapter" data-level="7.2" data-path="getdata.html"><a href="getdata.html#exploring-what-dataretrieval-can-do."><i class="fa fa-check"></i><b>7.2</b> Exploring what dataRetrieval can do.</a></li>
<li class="chapter" data-level="7.3" data-path="getdata.html"><a href="getdata.html#joins"><i class="fa fa-check"></i><b>7.3</b> Joins</a></li>
<li class="chapter" data-level="7.4" data-path="getdata.html"><a href="getdata.html#join-example"><i class="fa fa-check"></i><b>7.4</b> Join example</a></li>
<li class="chapter" data-level="7.5" data-path="getdata.html"><a href="getdata.html#finding-ids-to-download-usgs-data"><i class="fa fa-check"></i><b>7.5</b> Finding IDs to download USGS data</a></li>
<li class="chapter" data-level="7.6" data-path="getdata.html"><a href="getdata.html#ok-lets-download-some-data"><i class="fa fa-check"></i><b>7.6</b> OK let’s download some data!</a></li>
<li class="chapter" data-level="7.7" data-path="getdata.html"><a href="getdata.html#pivoting-wide-and-long-data"><i class="fa fa-check"></i><b>7.7</b> Pivoting: wide and long data</a></li>
<li class="chapter" data-level="7.8" data-path="getdata.html"><a href="getdata.html#pivot-examples"><i class="fa fa-check"></i><b>7.8</b> Pivot Examples</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="joinpivotDR.html"><a href="joinpivotDR.html"><i class="fa fa-check"></i><b>8</b> ACTIVITY: Joins Pivots dataRetrieval</a>
<ul>
<li class="chapter" data-level="8.1" data-path="joinpivotDR.html"><a href="joinpivotDR.html#load-the-tidyverse-dataretrieval-and-patchwork-packages."><i class="fa fa-check"></i><b>8.1</b> Load the tidyverse, dataRetrieval, and patchwork packages.</a></li>
<li class="chapter" data-level="8.2" data-path="joinpivotDR.html"><a href="joinpivotDR.html#problem-1-2"><i class="fa fa-check"></i><b>8.2</b> Problem 1</a></li>
<li class="chapter" data-level="8.3" data-path="joinpivotDR.html"><a href="joinpivotDR.html#problem-2-2"><i class="fa fa-check"></i><b>8.3</b> Problem 2</a></li>
<li class="chapter" data-level="8.4" data-path="joinpivotDR.html"><a href="joinpivotDR.html#problem-3-2"><i class="fa fa-check"></i><b>8.4</b> Problem 3</a></li>
<li class="chapter" data-level="8.5" data-path="joinpivotDR.html"><a href="joinpivotDR.html#problem-4-2"><i class="fa fa-check"></i><b>8.5</b> Problem 4</a></li>
<li class="chapter" data-level="8.6" data-path="joinpivotDR.html"><a href="joinpivotDR.html#problem-5-2"><i class="fa fa-check"></i><b>8.6</b> Problem 5</a></li>
<li class="chapter" data-level="8.7" data-path="joinpivotDR.html"><a href="joinpivotDR.html#problem-6-2"><i class="fa fa-check"></i><b>8.7</b> Problem 6</a></li>
<li class="chapter" data-level="8.8" data-path="joinpivotDR.html"><a href="joinpivotDR.html#problem-7"><i class="fa fa-check"></i><b>8.8</b> Problem 7</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="Summative1.html"><a href="Summative1.html"><i class="fa fa-check"></i><b>9</b> ACTIVITY Summative 1</a>
<ul>
<li class="chapter" data-level="9.0.1" data-path="Summative1.html"><a href="Summative1.html#instructions"><i class="fa fa-check"></i><b>9.0.1</b> Instructions</a></li>
<li class="chapter" data-level="9.1" data-path="Summative1.html"><a href="Summative1.html#problem-1-3"><i class="fa fa-check"></i><b>9.1</b> Problem 1</a></li>
<li class="chapter" data-level="9.2" data-path="Summative1.html"><a href="Summative1.html#problem-2-3"><i class="fa fa-check"></i><b>9.2</b> Problem 2</a></li>
<li class="chapter" data-level="9.3" data-path="Summative1.html"><a href="Summative1.html#problem-3-3"><i class="fa fa-check"></i><b>9.3</b> Problem 3</a></li>
<li class="chapter" data-level="9.4" data-path="Summative1.html"><a href="Summative1.html#problem-4-3"><i class="fa fa-check"></i><b>9.4</b> Problem 4</a></li>
<li class="chapter" data-level="9.5" data-path="Summative1.html"><a href="Summative1.html#problem-5-3"><i class="fa fa-check"></i><b>9.5</b> Problem 5</a></li>
<li class="chapter" data-level="9.6" data-path="Summative1.html"><a href="Summative1.html#problem-6-3"><i class="fa fa-check"></i><b>9.6</b> Problem 6</a></li>
<li class="chapter" data-level="9.7" data-path="Summative1.html"><a href="Summative1.html#problem-7-1"><i class="fa fa-check"></i><b>9.7</b> Problem 7</a></li>
<li class="chapter" data-level="9.8" data-path="Summative1.html"><a href="Summative1.html#problem-8"><i class="fa fa-check"></i><b>9.8</b> Problem 8</a></li>
<li class="chapter" data-level="9.9" data-path="Summative1.html"><a href="Summative1.html#problem-9"><i class="fa fa-check"></i><b>9.9</b> Problem 9</a></li>
<li class="chapter" data-level="9.10" data-path="Summative1.html"><a href="Summative1.html#problem-10"><i class="fa fa-check"></i><b>9.10</b> Problem 10</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="fdcs.html"><a href="fdcs.html"><i class="fa fa-check"></i><b>10</b> Flow Duration Curves</a>
<ul>
<li class="chapter" data-level="10.1" data-path="fdcs.html"><a href="fdcs.html#get-data"><i class="fa fa-check"></i><b>10.1</b> Get data</a></li>
<li class="chapter" data-level="10.2" data-path="fdcs.html"><a href="fdcs.html#review-describe-the-distribution"><i class="fa fa-check"></i><b>10.2</b> Review: describe the distribution</a></li>
<li class="chapter" data-level="10.3" data-path="fdcs.html"><a href="fdcs.html#ecdfs"><i class="fa fa-check"></i><b>10.3</b> ECDFs</a></li>
<li class="chapter" data-level="10.4" data-path="fdcs.html"><a href="fdcs.html#calculate-flow-exceedence-probabilities"><i class="fa fa-check"></i><b>10.4</b> Calculate flow exceedence probabilities</a></li>
<li class="chapter" data-level="10.5" data-path="fdcs.html"><a href="fdcs.html#plot-a-flow-duration-curve-using-the-probabilities"><i class="fa fa-check"></i><b>10.5</b> Plot a Flow Duration Curve using the probabilities</a></li>
<li class="chapter" data-level="10.6" data-path="fdcs.html"><a href="fdcs.html#make-an-almost-fdc-with-stat_ecdf"><i class="fa fa-check"></i><b>10.6</b> Make an almost FDC with stat_ecdf</a></li>
<li class="chapter" data-level="10.7" data-path="fdcs.html"><a href="fdcs.html#example-use-of-an-fdc"><i class="fa fa-check"></i><b>10.7</b> Example use of an FDC</a></li>
<li class="chapter" data-level="10.8" data-path="fdcs.html"><a href="fdcs.html#compare-to-a-boxplot-of-the-same-data"><i class="fa fa-check"></i><b>10.8</b> Compare to a boxplot of the same data</a></li>
<li class="chapter" data-level="10.9" data-path="fdcs.html"><a href="fdcs.html#challenge-examining-flow-regime-change-at-the-grand-canyon"><i class="fa fa-check"></i><b>10.9</b> Challenge: Examining flow regime change at the Grand Canyon</a></li>
</ul></li>
<li class="chapter" data-level="11" data-path="lfas.html"><a href="lfas.html"><i class="fa fa-check"></i><b>11</b> Low Flow Analysis</a>
<ul>
<li class="chapter" data-level="11.1" data-path="lfas.html"><a href="lfas.html#what-are-low-flow-statistics"><i class="fa fa-check"></i><b>11.1</b> What are low flow statistics?</a></li>
<li class="chapter" data-level="11.2" data-path="lfas.html"><a href="lfas.html#get-data-1"><i class="fa fa-check"></i><b>11.2</b> Get data</a></li>
<li class="chapter" data-level="11.3" data-path="lfas.html"><a href="lfas.html#create-the-x-days-average-flow-record"><i class="fa fa-check"></i><b>11.3</b> Create the X days average flow record</a></li>
<li class="chapter" data-level="11.4" data-path="lfas.html"><a href="lfas.html#look-at-what-a-rolling-mean-does."><i class="fa fa-check"></i><b>11.4</b> Look at what a rolling mean does.</a></li>
<li class="chapter" data-level="11.5" data-path="lfas.html"><a href="lfas.html#calculate-yearly-minimums"><i class="fa fa-check"></i><b>11.5</b> Calculate yearly minimums</a></li>
<li class="chapter" data-level="11.6" data-path="lfas.html"><a href="lfas.html#calculate-return-interval"><i class="fa fa-check"></i><b>11.6</b> Calculate return interval</a></li>
<li class="chapter" data-level="11.7" data-path="lfas.html"><a href="lfas.html#fit-to-pearson-type-iii-distribution"><i class="fa fa-check"></i><b>11.7</b> Fit to Pearson Type III distribution</a></li>
<li class="chapter" data-level="11.8" data-path="lfas.html"><a href="lfas.html#distribution-free-method"><i class="fa fa-check"></i><b>11.8</b> Distribution-free method</a></li>
</ul></li>
<li class="chapter" data-level="12" data-path="floods.html"><a href="floods.html"><i class="fa fa-check"></i><b>12</b> Flood Frequency Analysis and Creating Functions</a>
<ul>
<li class="chapter" data-level="12.1" data-path="floods.html"><a href="floods.html#template-repository"><i class="fa fa-check"></i><b>12.1</b> Template Repository</a></li>
<li class="chapter" data-level="12.2" data-path="floods.html"><a href="floods.html#intro"><i class="fa fa-check"></i><b>12.2</b> Intro</a></li>
<li class="chapter" data-level="12.3" data-path="floods.html"><a href="floods.html#challenge-create-a-function"><i class="fa fa-check"></i><b>12.3</b> Challenge: Create a function</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="rgeospatial.html"><a href="rgeospatial.html"><i class="fa fa-check"></i><b>13</b> Geospatial data in R - Vector</a>
<ul>
<li class="chapter" data-level="13.1" data-path="rgeospatial.html"><a href="rgeospatial.html#goals"><i class="fa fa-check"></i><b>13.1</b> Goals</a></li>
<li class="chapter" data-level="13.2" data-path="rgeospatial.html"><a href="rgeospatial.html#intro-to-tmap"><i class="fa fa-check"></i><b>13.2</b> Intro to tmap</a></li>
<li class="chapter" data-level="13.3" data-path="rgeospatial.html"><a href="rgeospatial.html#data-wrangling-with-tidyverse-principles"><i class="fa fa-check"></i><b>13.3</b> Data wrangling with tidyverse principles</a></li>
<li class="chapter" data-level="13.4" data-path="rgeospatial.html"><a href="rgeospatial.html#plot-maps-side-by-side"><i class="fa fa-check"></i><b>13.4</b> Plot maps side by side</a></li>
<li class="chapter" data-level="13.5" data-path="rgeospatial.html"><a href="rgeospatial.html#built-in-styles-like-themes-in-ggplot"><i class="fa fa-check"></i><b>13.5</b> Built in styles, like themes in ggplot</a></li>
<li class="chapter" data-level="13.6" data-path="rgeospatial.html"><a href="rgeospatial.html#interactive-maps"><i class="fa fa-check"></i><b>13.6</b> Interactive Maps</a>
<ul>
<li class="chapter" data-level="13.6.1" data-path="rgeospatial.html"><a href="rgeospatial.html#tmap"><i class="fa fa-check"></i><b>13.6.1</b> tmap</a></li>
<li class="chapter" data-level="13.6.2" data-path="rgeospatial.html"><a href="rgeospatial.html#leaflet"><i class="fa fa-check"></i><b>13.6.2</b> Leaflet</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="14" data-path="summative2.html"><a href="summative2.html"><i class="fa fa-check"></i><b>14</b> Summative Assessment 2</a>
<ul>
<li class="chapter" data-level="14.1" data-path="summative2.html"><a href="summative2.html#info-for-assessment"><i class="fa fa-check"></i><b>14.1</b> Info for assessment</a></li>
</ul></li>
<li class="chapter" data-level="15" data-path="rgeoraster.html"><a href="rgeoraster.html"><i class="fa fa-check"></i><b>15</b> Geospatial R Raster - Hydro Analyses</a>
<ul>
<li class="chapter" data-level="15.1" data-path="rgeoraster.html"><a href="rgeoraster.html#introduction-2"><i class="fa fa-check"></i><b>15.1</b> Introduction</a></li>
<li class="chapter" data-level="15.2" data-path="rgeoraster.html"><a href="rgeoraster.html#read-in-dem"><i class="fa fa-check"></i><b>15.2</b> Read in DEM</a></li>
<li class="chapter" data-level="15.3" data-path="rgeoraster.html"><a href="rgeoraster.html#plot-dem"><i class="fa fa-check"></i><b>15.3</b> Plot DEM</a></li>
<li class="chapter" data-level="15.4" data-path="rgeoraster.html"><a href="rgeoraster.html#generate-a-hillshade"><i class="fa fa-check"></i><b>15.4</b> Generate a hillshade</a>
<ul>
<li class="chapter" data-level="15.4.1" data-path="rgeoraster.html"><a href="rgeoraster.html#how-whitebox-tools-functions-work"><i class="fa fa-check"></i><b>15.4.1</b> How whitebox tools functions work</a></li>
</ul></li>
<li class="chapter" data-level="15.5" data-path="rgeoraster.html"><a href="rgeoraster.html#prepare-dem-for-hydrology-analyses"><i class="fa fa-check"></i><b>15.5</b> Prepare DEM for Hydrology Analyses</a></li>
<li class="chapter" data-level="15.6" data-path="rgeoraster.html"><a href="rgeoraster.html#visualize-filled-sinks-and-breached-depressions"><i class="fa fa-check"></i><b>15.6</b> Visualize filled sinks and breached depressions</a></li>
<li class="chapter" data-level="15.7" data-path="rgeoraster.html"><a href="rgeoraster.html#d8-flow-accumulation"><i class="fa fa-check"></i><b>15.7</b> D8 Flow Accumulation</a></li>
<li class="chapter" data-level="15.8" data-path="rgeoraster.html"><a href="rgeoraster.html#d-infinity-flow-accumulation"><i class="fa fa-check"></i><b>15.8</b> D infinity flow accumulation</a></li>
<li class="chapter" data-level="15.9" data-path="rgeoraster.html"><a href="rgeoraster.html#topographic-wetness-index"><i class="fa fa-check"></i><b>15.9</b> Topographic Wetness Index</a></li>
<li class="chapter" data-level="15.10" data-path="rgeoraster.html"><a href="rgeoraster.html#downslope-twi"><i class="fa fa-check"></i><b>15.10</b> Downslope TWI</a></li>
<li class="chapter" data-level="15.11" data-path="rgeoraster.html"><a href="rgeoraster.html#map-stream-network"><i class="fa fa-check"></i><b>15.11</b> Map Stream Network</a></li>
<li class="chapter" data-level="15.12" data-path="rgeoraster.html"><a href="rgeoraster.html#extract-raster-values-to-point-locations"><i class="fa fa-check"></i><b>15.12</b> Extract raster values to point locations</a>
<ul>
<li class="chapter" data-level="15.12.1" data-path="rgeoraster.html"><a href="rgeoraster.html#import-and-plot-points"><i class="fa fa-check"></i><b>15.12.1</b> Import and plot points</a></li>
<li class="chapter" data-level="15.12.2" data-path="rgeoraster.html"><a href="rgeoraster.html#extract-values-from-multiple-rasters-at-once"><i class="fa fa-check"></i><b>15.12.2</b> Extract values from multiple rasters at once</a></li>
</ul></li>
<li class="chapter" data-level="15.13" data-path="rgeoraster.html"><a href="rgeoraster.html#view-raster-data-as-a-pdf-or-histogram"><i class="fa fa-check"></i><b>15.13</b> View raster data as a PDF or histogram</a></li>
<li class="chapter" data-level="15.14" data-path="rgeoraster.html"><a href="rgeoraster.html#subsetting-a-raster-for-visualization"><i class="fa fa-check"></i><b>15.14</b> Subsetting a raster for visualization</a></li>
<li class="chapter" data-level="15.15" data-path="rgeoraster.html"><a href="rgeoraster.html#raster-math"><i class="fa fa-check"></i><b>15.15</b> Raster Math</a></li>
<li class="chapter" data-level="15.16" data-path="rgeoraster.html"><a href="rgeoraster.html#extra-plot-topo-characteristics-against-one-another"><i class="fa fa-check"></i><b>15.16</b> Extra: plot topo characteristics against one another</a></li>
</ul></li>
<li class="chapter" data-level="16" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html"><i class="fa fa-check"></i><b>16</b> Geospatial R Raster - Watershed Delineation</a>
<ul>
<li class="chapter" data-level="16.1" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#introduction-3"><i class="fa fa-check"></i><b>16.1</b> Introduction</a></li>
<li class="chapter" data-level="16.2" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#the-watershed-delineation-toolprocess"><i class="fa fa-check"></i><b>16.2</b> The watershed delineation tool/process</a></li>
<li class="chapter" data-level="16.3" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#read-in-dem-1"><i class="fa fa-check"></i><b>16.3</b> Read in DEM</a></li>
<li class="chapter" data-level="16.4" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#generate-a-hillshade-1"><i class="fa fa-check"></i><b>16.4</b> Generate a hillshade</a></li>
<li class="chapter" data-level="16.5" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#prepare-dem-for-hydrology-analyses-1"><i class="fa fa-check"></i><b>16.5</b> Prepare DEM for Hydrology Analyses</a></li>
<li class="chapter" data-level="16.6" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#create-flow-accumulation-and-pointer-grids"><i class="fa fa-check"></i><b>16.6</b> Create flow accumulation and pointer grids</a></li>
<li class="chapter" data-level="16.7" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#setting-pour-points"><i class="fa fa-check"></i><b>16.7</b> Setting pour points</a></li>
<li class="chapter" data-level="16.8" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#delineate-watersheds"><i class="fa fa-check"></i><b>16.8</b> Delineate watersheds</a></li>
<li class="chapter" data-level="16.9" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#convert-watersheds-to-shapefiles"><i class="fa fa-check"></i><b>16.9</b> Convert watersheds to shapefiles</a></li>
<li class="chapter" data-level="16.10" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#extract-data-based-on-watershed-outline"><i class="fa fa-check"></i><b>16.10</b> Extract data based on watershed outline</a></li>
<li class="chapter" data-level="16.11" data-path="rgeowatersheds.html"><a href="rgeowatersheds.html#bonus-make-a-3d-map-of-your-watershed-with-rayshader"><i class="fa fa-check"></i><b>16.11</b> BONUS: Make a 3d map of your watershed with rayshader</a></li>
</ul></li>
<li class="chapter" data-level="17" data-path="modelingintro.html"><a href="modelingintro.html"><i class="fa fa-check"></i><b>17</b> Intro to Modeling - Getting Started with HBV</a>
<ul>
<li class="chapter" data-level="17.1" data-path="modelingintro.html"><a href="modelingintro.html#introduction-4"><i class="fa fa-check"></i><b>17.1</b> Introduction</a></li>
<li class="chapter" data-level="17.2" data-path="modelingintro.html"><a href="modelingintro.html#creating-the-hbv-model-function"><i class="fa fa-check"></i><b>17.2</b> Creating the HBV model function</a></li>
<li class="chapter" data-level="17.3" data-path="modelingintro.html"><a href="modelingintro.html#read-in-precip-and-temp"><i class="fa fa-check"></i><b>17.3</b> Read in Precip and Temp</a></li>
<li class="chapter" data-level="17.4" data-path="modelingintro.html"><a href="modelingintro.html#calculate-pet"><i class="fa fa-check"></i><b>17.4</b> Calculate PET</a></li>
<li class="chapter" data-level="17.5" data-path="modelingintro.html"><a href="modelingintro.html#hbv-parameters"><i class="fa fa-check"></i><b>17.5</b> HBV Parameters</a></li>
<li class="chapter" data-level="17.6" data-path="modelingintro.html"><a href="modelingintro.html#first-model-run"><i class="fa fa-check"></i><b>17.6</b> First model run</a></li>
<li class="chapter" data-level="17.7" data-path="modelingintro.html"><a href="modelingintro.html#import-observed-streamflow-data"><i class="fa fa-check"></i><b>17.7</b> Import observed streamflow data</a></li>
<li class="chapter" data-level="17.8" data-path="modelingintro.html"><a href="modelingintro.html#compare-observed-and-modeled-discharge-graphically"><i class="fa fa-check"></i><b>17.8</b> Compare observed and modeled discharge graphically</a></li>
<li class="chapter" data-level="17.9" data-path="modelingintro.html"><a href="modelingintro.html#compare-observed-and-modelled-discharge-with-interactive-graph"><i class="fa fa-check"></i><b>17.9</b> Compare observed and modelled discharge with interactive graph</a></li>
<li class="chapter" data-level="17.10" data-path="modelingintro.html"><a href="modelingintro.html#measure-how-well-the-model-fits-with-nse"><i class="fa fa-check"></i><b>17.10</b> Measure how well the model fits with NSE</a></li>
<li class="chapter" data-level="17.11" data-path="modelingintro.html"><a href="modelingintro.html#assess-model-fit-with-a-different-measure-snow"><i class="fa fa-check"></i><b>17.11</b> Assess model fit with a different measure: Snow</a></li>
<li class="chapter" data-level="17.12" data-path="modelingintro.html"><a href="modelingintro.html#calibrate-hbv-manually"><i class="fa fa-check"></i><b>17.12</b> Calibrate HBV manually</a></li>
</ul></li>
<li class="chapter" data-level="18" data-path="modelingcalibration.html"><a href="modelingcalibration.html"><i class="fa fa-check"></i><b>18</b> Intro to Modeling - Calibrate HBV</a>
<ul>
<li class="chapter" data-level="18.1" data-path="modelingcalibration.html"><a href="modelingcalibration.html#introduction-5"><i class="fa fa-check"></i><b>18.1</b> Introduction</a></li>
<li class="chapter" data-level="18.2" data-path="modelingcalibration.html"><a href="modelingcalibration.html#challenge-write-a-for-loop"><i class="fa fa-check"></i><b>18.2</b> Challenge: Write a for loop</a></li>
<li class="chapter" data-level="18.3" data-path="modelingcalibration.html"><a href="modelingcalibration.html#prep-data-for-hbv"><i class="fa fa-check"></i><b>18.3</b> Prep data for HBV</a></li>
<li class="chapter" data-level="18.4" data-path="modelingcalibration.html"><a href="modelingcalibration.html#calculate-pet-1"><i class="fa fa-check"></i><b>18.4</b> Calculate PET</a></li>
<li class="chapter" data-level="18.5" data-path="modelingcalibration.html"><a href="modelingcalibration.html#monte-carlo-step-1-generate-random-parameter-sets"><i class="fa fa-check"></i><b>18.5</b> Monte Carlo step 1: generate random parameter sets</a></li>
<li class="chapter" data-level="18.6" data-path="modelingcalibration.html"><a href="modelingcalibration.html#run-the-model-for-each-parameter-set"><i class="fa fa-check"></i><b>18.6</b> Run the model for each parameter set</a></li>
<li class="chapter" data-level="18.7" data-path="modelingcalibration.html"><a href="modelingcalibration.html#find-the-best-parameter-set"><i class="fa fa-check"></i><b>18.7</b> Find the best parameter set</a></li>
<li class="chapter" data-level="18.8" data-path="modelingcalibration.html"><a href="modelingcalibration.html#investigating-a-much-bigger-monte-carlo"><i class="fa fa-check"></i><b>18.8</b> Investigating a much bigger Monte Carlo</a></li>
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<div id="getdata" class="section level1 hasAnchor" number="7">
<h1><span class="header-section-number">Chapter 7</span> Joins, Pivots, and USGS dataRetrieval<a href="getdata.html#getdata" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Use Template Repository from github:</p>
<p>Readings: Introduction to the dataRetrieval package <a href="https://cran.r-project.org/web/packages/dataRetrieval/vignettes/dataRetrieval.html" class="uri">https://cran.r-project.org/web/packages/dataRetrieval/vignettes/dataRetrieval.html</a></p>
<p>Chapter 12 &amp; 13 of R for Data Science <a href="https://r4ds.had.co.nz/tidy-data.html" class="uri">https://r4ds.had.co.nz/tidy-data.html</a></p>
<div id="goals-for-today" class="section level2 hasAnchor" number="7.1">
<h2><span class="header-section-number">7.1</span> Goals for today<a href="getdata.html#goals-for-today" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<ul>
<li>Get familiar with the dataRetrieval package</li>
<li>Intro to joins</li>
<li>Learn about long vs. wide data and how to change between them</li>
</ul>
<p>Prep question: How would you get data from the USGS NWIS (non-R)?</p>
<p>Install the dataRetrieval package. Load it and the tidyverse.</p>
<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb111-1"><a href="getdata.html#cb111-1" aria-hidden="true" tabindex="-1"></a><span class="co">#install.packages(&quot;dataRetrieval&quot;)</span></span>
<span id="cb111-2"><a href="getdata.html#cb111-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dataRetrieval)</span></code></pre></div>
<pre><code>## Warning: package &#39;dataRetrieval&#39; was built under R version 4.1.2</code></pre>
<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb113-1"><a href="getdata.html#cb113-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span>
<span id="cb113-2"><a href="getdata.html#cb113-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(lubridate)</span></code></pre></div>
</div>
<div id="exploring-what-dataretrieval-can-do." class="section level2 hasAnchor" number="7.2">
<h2><span class="header-section-number">7.2</span> Exploring what dataRetrieval can do.<a href="getdata.html#exploring-what-dataretrieval-can-do." class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Think about the dataRetrieval as a way to interact with same public data you can access through waterdata.usgs.gov but without having to click on buttons and search around. It makes getting data or doing analyses with USGS data much more reproducible and fast!</p>
<p>To explore a few of the capabilities (NOT ALL!!) we will start with the USGS gage on the New River at Radford. The gage number is 03171000.</p>
<p>The documentation for the package is extremely helpful: <a href="https://cran.r-project.org/web/packages/dataRetrieval/vignettes/dataRetrieval.html" class="uri">https://cran.r-project.org/web/packages/dataRetrieval/vignettes/dataRetrieval.html</a></p>
<p>I always have to look up how to do things because the package is very specialized! This is the case with most website APIs, in my experience. It’s a good argument for getting good at navigating package documentation! Basically you just look through and try to piece together the recipe for what you want to do using the examples they give in the document.</p>
<p>First, let’s get information about the site using the readNWISsite() and whatNWISdata() functions. Try each out and see what they tell you.</p>
<p>Remember, all the parameter codes and site names get passed to dataRetrieval functions as characters, so they must be in quotes.</p>
<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb114-1"><a href="getdata.html#cb114-1" aria-hidden="true" tabindex="-1"></a><span class="co">#important: note the site number gets input as a character</span></span>
<span id="cb114-2"><a href="getdata.html#cb114-2" aria-hidden="true" tabindex="-1"></a>site <span class="ot">&lt;-</span> <span class="st">&quot;03171000&quot;</span></span>
<span id="cb114-3"><a href="getdata.html#cb114-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb114-4"><a href="getdata.html#cb114-4" aria-hidden="true" tabindex="-1"></a><span class="co">#Information about the site</span></span>
<span id="cb114-5"><a href="getdata.html#cb114-5" aria-hidden="true" tabindex="-1"></a>siteinfo <span class="ot">&lt;-</span> <span class="fu">readNWISsite</span>(site)</span>
<span id="cb114-6"><a href="getdata.html#cb114-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb114-7"><a href="getdata.html#cb114-7" aria-hidden="true" tabindex="-1"></a><span class="co">#What data is available for the site?</span></span>
<span id="cb114-8"><a href="getdata.html#cb114-8" aria-hidden="true" tabindex="-1"></a><span class="co">#Daily values, mean values</span></span>
<span id="cb114-9"><a href="getdata.html#cb114-9" aria-hidden="true" tabindex="-1"></a>dataAvailable <span class="ot">&lt;-</span> <span class="fu">whatNWISdata</span>(<span class="at">siteNumber =</span> site, <span class="at">service =</span> <span class="st">&quot;dv&quot;</span>, <span class="at">statCd =</span> <span class="st">&quot;00003&quot;</span>)</span>
<span id="cb114-10"><a href="getdata.html#cb114-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb114-11"><a href="getdata.html#cb114-11" aria-hidden="true" tabindex="-1"></a>dataAvailable</span></code></pre></div>
<pre><code>##   agency_cd  site_no               station_nm site_tp_cd dec_lat_va dec_long_va
## 2      USGS 03171000 NEW RIVER AT RADFORD, VA         ST   37.14179   -80.56922
## 3      USGS 03171000 NEW RIVER AT RADFORD, VA         ST   37.14179   -80.56922
## 4      USGS 03171000 NEW RIVER AT RADFORD, VA         ST   37.14179   -80.56922
##   coord_acy_cd dec_coord_datum_cd  alt_va alt_acy_va alt_datum_cd   huc_cd
## 2            U              NAD83 1711.99       0.13       NAVD88 05050001
## 3            U              NAD83 1711.99       0.13       NAVD88 05050001
## 4            U              NAD83 1711.99       0.13       NAVD88 05050001
##   data_type_cd parm_cd stat_cd  ts_id loc_web_ds medium_grp_cd parm_grp_cd
## 2           dv   00010   00003 241564         NA           wat        &lt;NA&gt;
## 3           dv   00060   00003 145684         NA           wat        &lt;NA&gt;
## 4           dv   00095   00003 145685         NA           wat        &lt;NA&gt;
##    srs_id access_cd begin_date   end_date count_nu
## 2 1645597         0 2006-12-20 2009-03-18      704
## 3 1645423         0 1907-10-01 2023-02-08    33368
## 4 1646694         0 2006-12-20 2008-09-29      534</code></pre>
</div>
<div id="joins" class="section level2 hasAnchor" number="7.3">
<h2><span class="header-section-number">7.3</span> Joins<a href="getdata.html#joins" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>When we look at what whatNWISdata returns, we see it gives us parameter codes, but doesn’t tell us what they mean. This is a common attribute of databases: you use a common identifier but then have the full information in a lookup file. In this case, the look-up information telling us what the parameter codes mean is in “parameterCdFile” which loads with the dataRetrieval package.</p>
<p>So, you could look at that and see what the parameters mean.</p>
<p>OR We could have R do it and add a column that tells us what the parameters mean. Enter JOINS!</p>
<p>Joins allow us to combine the data from two different data sets that have a column in common. At its most basic, a join looks for a matching row with the same key in both datasets (for example, a USGS gage number) and then combines the rows. So now you have all the data from both sets, matched on the key.</p>
<p>But you have to make some decisions: what if a key value exists in one set but not the other? Do you just drop that observation? Do you add an NA? Let’s look at the different options.</p>
<p>Take for example the two data sets, FlowTable and SizeTable. The SiteName values are the key values and the MeanFlow and WSsize values are the data.</p>
<div class="figure">
<img src="images/joinsetup.png" title="Join setup" width="400" alt="" />
<p class="caption">Join Setup</p>
</div>
<p>Note River1 and River2 match up, but River3 and River5 only exist in one data set or the other.</p>
<p>The first way to deal with this is an <strong>INNER JOIN: inner_join()</strong> In an inner join, you only keep records that match. So the rows for River3 and River5 will be dropped because there is no corresponding data in the other set. See below:</p>
<div class="figure">
<img src="images/innerjoin.png" title="Inner Join" alt="" />
<p class="caption">Inner Join</p>
</div>
<p>But what if you don’t want to lose the values in one or the other or both?!</p>
<p>For instance, let’s say you have a bunch of discharge data for a stream, and then chemistry grab samples. You want to join the chemistry to the discharge based on the dates and times they were taken. But when you do this, you don’t want to delete all the discharge data where there is no chemistry! We need another option. Enter OUTER JOINS</p>
<p><strong>LEFT JOIN, left_join():</strong> Preserves all values from the LEFT data set, and pastes on the matching ones from the right. This creates NAs where there is a value on the left but not the right. (this is what you’d want to do in the discharge - chemistry example above)</p>
<div class="figure">
<img src="images/leftjoin1.png" title="Left Join" alt="" />
<p class="caption">Left Join</p>
</div>
<p><strong>RIGHT JOIN, right_join():</strong> Preserves all values from the RIGHT data set, and pastes on the matching ones from the left. This creates NAs where there is a value on the right but not the left.</p>
<div class="figure">
<img src="images/rightjoin.png" title="Right Join" alt="" />
<p class="caption">Right Join</p>
</div>
<p><strong>FULL JOIN, full_join():</strong> KEEP EVERYTHING! The hoarder of the joins. No matching record on the left? create an NA on the right! No matching value on the right? Create an NA on the left! NAs for everyone!</p>
<div class="figure">
<img src="images/fulljoin.png" title="Full Join" alt="" />
<p class="caption">Full Join</p>
</div>
<p>When you do this in R, you use the functions identified in the descriptions with the following syntax (see example below):</p>
<p><strong>if the column is named the same in both data sets</strong>
&gt; xxx_join(left_tibble, right_tibble, by = “key_column”)**</p>
<p><strong>if the column is named differently in both data sets</strong>
&gt; xxx_join(left_tibble, right_tibble, by = c(“left_key” = “right_key”)</p>
<div class="figure">
<img src="images/leftjoin2.png" title="Left Join with differing column names" alt="" />
<p class="caption">Left Join Differing Col Names</p>
</div>
<p>Note in both of the above, when you specify which column to use as “by” you have to put it in quotes.</p>
</div>
<div id="join-example" class="section level2 hasAnchor" number="7.4">
<h2><span class="header-section-number">7.4</span> Join example<a href="getdata.html#join-example" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>So in the chunk below let’s get add information about the parameters in dataAvailable by joining it with the key file: parameterCdFile. The column with the parameter codes is called parm_cd in dataAvailable and parameter_cd in parameterCdFile</p>
<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb116-1"><a href="getdata.html#cb116-1" aria-hidden="true" tabindex="-1"></a>dataAvailable <span class="ot">&lt;-</span> <span class="fu">left_join</span>(dataAvailable, parameterCdFile, </span>
<span id="cb116-2"><a href="getdata.html#cb116-2" aria-hidden="true" tabindex="-1"></a>                           <span class="at">by =</span> <span class="fu">c</span>(<span class="st">&quot;parm_cd&quot;</span> <span class="ot">=</span> <span class="st">&quot;parameter_cd&quot;</span>))</span>
<span id="cb116-3"><a href="getdata.html#cb116-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb116-4"><a href="getdata.html#cb116-4" aria-hidden="true" tabindex="-1"></a>dataAvailable</span></code></pre></div>
<pre><code>##   agency_cd  site_no               station_nm site_tp_cd dec_lat_va dec_long_va
## 1      USGS 03171000 NEW RIVER AT RADFORD, VA         ST   37.14179   -80.56922
## 2      USGS 03171000 NEW RIVER AT RADFORD, VA         ST   37.14179   -80.56922
## 3      USGS 03171000 NEW RIVER AT RADFORD, VA         ST   37.14179   -80.56922
##   coord_acy_cd dec_coord_datum_cd  alt_va alt_acy_va alt_datum_cd   huc_cd
## 1            U              NAD83 1711.99       0.13       NAVD88 05050001
## 2            U              NAD83 1711.99       0.13       NAVD88 05050001
## 3            U              NAD83 1711.99       0.13       NAVD88 05050001
##   data_type_cd parm_cd stat_cd  ts_id loc_web_ds medium_grp_cd parm_grp_cd
## 1           dv   00010   00003 241564         NA           wat        &lt;NA&gt;
## 2           dv   00060   00003 145684         NA           wat        &lt;NA&gt;
## 3           dv   00095   00003 145685         NA           wat        &lt;NA&gt;
##    srs_id access_cd begin_date   end_date count_nu parameter_group_nm
## 1 1645597         0 2006-12-20 2009-03-18      704           Physical
## 2 1645423         0 1907-10-01 2023-02-08    33368           Physical
## 3 1646694         0 2006-12-20 2008-09-29      534           Physical
##                                                                                 parameter_nm
## 1                                                        Temperature, water, degrees Celsius
## 2                                                           Discharge, cubic feet per second
## 3 Specific conductance, water, unfiltered, microsiemens per centimeter at 25 degrees Celsius
##   casrn                  srsname parameter_units
## 1             Temperature, water           deg C
## 2       Stream flow, mean. daily           ft3/s
## 3           Specific conductance      uS/cm @25C</code></pre>
<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb118-1"><a href="getdata.html#cb118-1" aria-hidden="true" tabindex="-1"></a><span class="co">#that made a lot of columns, let&#39;s clean it up</span></span>
<span id="cb118-2"><a href="getdata.html#cb118-2" aria-hidden="true" tabindex="-1"></a>dataAvailClean <span class="ot">&lt;-</span> dataAvailable <span class="sc">%&gt;%</span> <span class="fu">select</span>(site_no, </span>
<span id="cb118-3"><a href="getdata.html#cb118-3" aria-hidden="true" tabindex="-1"></a>                                           station_nm,</span>
<span id="cb118-4"><a href="getdata.html#cb118-4" aria-hidden="true" tabindex="-1"></a>                                           parm_cd, </span>
<span id="cb118-5"><a href="getdata.html#cb118-5" aria-hidden="true" tabindex="-1"></a>                                           srsname, </span>
<span id="cb118-6"><a href="getdata.html#cb118-6" aria-hidden="true" tabindex="-1"></a>                                           parameter_units,</span>
<span id="cb118-7"><a href="getdata.html#cb118-7" aria-hidden="true" tabindex="-1"></a>                                           begin_date, </span>
<span id="cb118-8"><a href="getdata.html#cb118-8" aria-hidden="true" tabindex="-1"></a>                                           end_date)</span>
<span id="cb118-9"><a href="getdata.html#cb118-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb118-10"><a href="getdata.html#cb118-10" aria-hidden="true" tabindex="-1"></a>dataAvailClean</span></code></pre></div>
<pre><code>##    site_no               station_nm parm_cd                  srsname
## 1 03171000 NEW RIVER AT RADFORD, VA   00010       Temperature, water
## 2 03171000 NEW RIVER AT RADFORD, VA   00060 Stream flow, mean. daily
## 3 03171000 NEW RIVER AT RADFORD, VA   00095     Specific conductance
##   parameter_units begin_date   end_date
## 1           deg C 2006-12-20 2009-03-18
## 2           ft3/s 1907-10-01 2023-02-08
## 3      uS/cm @25C 2006-12-20 2008-09-29</code></pre>
</div>
<div id="finding-ids-to-download-usgs-data" class="section level2 hasAnchor" number="7.5">
<h2><span class="header-section-number">7.5</span> Finding IDs to download USGS data<a href="getdata.html#finding-ids-to-download-usgs-data" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>You can find sites via map and just enter the id like we did in the chunks above: <a href="https://maps.waterdata.usgs.gov/mapper/index.html" class="uri">https://maps.waterdata.usgs.gov/mapper/index.html</a></p>
<p>Below we will look at two other ways to get sites: using a bounding box of a geographic region, or search terms like State and drainage area</p>
<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb120-1"><a href="getdata.html#cb120-1" aria-hidden="true" tabindex="-1"></a><span class="co">#find sites in a bounding box</span></span>
<span id="cb120-2"><a href="getdata.html#cb120-2" aria-hidden="true" tabindex="-1"></a><span class="co">#coords of bottom left, top right</span></span>
<span id="cb120-3"><a href="getdata.html#cb120-3" aria-hidden="true" tabindex="-1"></a>swva <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="sc">-</span><span class="fl">81.36</span>, <span class="fl">36.72</span>, <span class="sc">-</span><span class="fl">80.27</span>, <span class="fl">37.32</span>)</span>
<span id="cb120-4"><a href="getdata.html#cb120-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb120-5"><a href="getdata.html#cb120-5" aria-hidden="true" tabindex="-1"></a><span class="co">#get sites in this bounding box that have daily water temperature and discharge</span></span>
<span id="cb120-6"><a href="getdata.html#cb120-6" aria-hidden="true" tabindex="-1"></a>swva_sites <span class="ot">&lt;-</span> <span class="fu">whatNWISsites</span>(<span class="at">bBox =</span> swva, </span>
<span id="cb120-7"><a href="getdata.html#cb120-7" aria-hidden="true" tabindex="-1"></a>                            <span class="at">parameterCd =</span> <span class="fu">c</span>(<span class="st">&quot;00060&quot;</span>, <span class="st">&quot;00010&quot;</span>), </span>
<span id="cb120-8"><a href="getdata.html#cb120-8" aria-hidden="true" tabindex="-1"></a>                            <span class="at">hasDataTypeCd =</span> <span class="st">&quot;dv&quot;</span>)</span>
<span id="cb120-9"><a href="getdata.html#cb120-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb120-10"><a href="getdata.html#cb120-10" aria-hidden="true" tabindex="-1"></a>swva_sites</span></code></pre></div>
<pre><code>##    agency_cd  site_no                                      station_nm
## 1       USGS 03473500             M F HOLSTON RIVER AT GROSECLOSE, VA
## 2       USGS 03175140         WEST FORK COVE CREEK NEAR BLUEFIELD, VA
## 3       USGS 03177710              BLUESTONE RIVER AT FALLS MILLS, VA
## 4       USGS 03177700                BLUESTONE RIVER AT BLUEFIELD, VA
## 5       USGS 03166000                  CRIPPLE CREEK NEAR IVANHOE, VA
## 6       USGS 03164500                      NEW RIVER NEAR GRAYSON, VA
## 7       USGS 03165500                        NEW RIVER AT IVANHOE, VA
## 8       USGS 03166880  WEST SP AT NAT FISH HAT NEAR GRAHAMS FORGE, VA
## 9       USGS 03166800                GLADE CREEK AT GRAHAMS FORGE, VA
## 10      USGS 03166900 BOILING SP AT NAT FISH HAT NR GRAHAMS FORGE, VA
## 11      USGS 03167000                 REED CREEK AT GRAHAMS FORGE, VA
## 12      USGS 03175500                     WOLF CREEK NEAR NARROWS, VA
## 13      USGS 03168500                       PEAK CREEK AT PULASKI, VA
## 14      USGS 03168000                      NEW RIVER AT ALLISONIA, VA
## 15      USGS 03167500        BIG REED ISLAND CREEK NEAR ALLISONIA, VA
## 16      USGS 03172500              WALKER CREEK AT STAFFORDSVILLE, VA
## 17      USGS 03173000                        WALKER CREEK AT BANE, VA
## 18      USGS 03171500                      NEW RIVER AT EGGLESTON, VA
## 19      USGS 03171000                        NEW RIVER AT RADFORD, VA
## 20      USGS 03170000                 LITTLE RIVER AT GRAYSONTOWN, VA
## 21      USGS 03169500             LITTLE RIVER NEAR COPPER VALLEY, VA
##    site_tp_cd dec_lat_va dec_long_va colocated           queryTime
## 1          ST   36.88873   -81.34733     FALSE 2023-02-09 11:20:29
## 2          ST   37.18428   -81.32982     FALSE 2023-02-09 11:20:29
## 3          ST   37.27151   -81.30482     FALSE 2023-02-09 11:20:29
## 4          ST   37.25595   -81.28177     FALSE 2023-02-09 11:20:29
## 5          ST   36.85984   -80.98036     FALSE 2023-02-09 11:20:29
## 6          ST   36.75985   -80.95619     FALSE 2023-02-09 11:20:29
## 7          ST   36.83485   -80.95258     FALSE 2023-02-09 11:20:29
## 8          SP   36.93429   -80.90313     FALSE 2023-02-09 11:20:29
## 9          ST   36.93095   -80.90036     FALSE 2023-02-09 11:20:29
## 10         SP   36.93068   -80.89619     FALSE 2023-02-09 11:20:29
## 11         ST   36.93901   -80.88730     FALSE 2023-02-09 11:20:29
## 12         ST   37.30568   -80.84980     FALSE 2023-02-09 11:20:29
## 13         ST   37.04721   -80.78472     FALSE 2023-02-09 11:20:29
## 14         ST   36.93762   -80.74563     FALSE 2023-02-09 11:20:29
## 15         ST   36.88901   -80.72757     FALSE 2023-02-09 11:20:29
## 16         ST   37.24179   -80.71090     FALSE 2023-02-09 11:20:29
## 17         ST   37.26818   -80.70951     FALSE 2023-02-09 11:20:29
## 18         ST   37.28957   -80.61673     FALSE 2023-02-09 11:20:29
## 19         ST   37.14179   -80.56922     FALSE 2023-02-09 11:20:29
## 20         ST   37.03763   -80.55672     FALSE 2023-02-09 11:20:29
## 21         ST   36.99652   -80.52144     FALSE 2023-02-09 11:20:29</code></pre>
<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb122-1"><a href="getdata.html#cb122-1" aria-hidden="true" tabindex="-1"></a><span class="co">#find sites with other criteria, VA, less than 20 sqmi, other criteria can be used..</span></span>
<span id="cb122-2"><a href="getdata.html#cb122-2" aria-hidden="true" tabindex="-1"></a><span class="co">#check out the CRAN documentation</span></span>
<span id="cb122-3"><a href="getdata.html#cb122-3" aria-hidden="true" tabindex="-1"></a>smallVA <span class="ot">&lt;-</span> <span class="fu">readNWISdata</span>(<span class="at">service =</span> <span class="st">&quot;dv&quot;</span>,</span>
<span id="cb122-4"><a href="getdata.html#cb122-4" aria-hidden="true" tabindex="-1"></a>                           <span class="at">stateCd =</span> <span class="st">&quot;VA&quot;</span>,</span>
<span id="cb122-5"><a href="getdata.html#cb122-5" aria-hidden="true" tabindex="-1"></a>                           <span class="at">parameterCd =</span> <span class="st">&quot;00060&quot;</span>,</span>
<span id="cb122-6"><a href="getdata.html#cb122-6" aria-hidden="true" tabindex="-1"></a>                           <span class="at">drainAreaMax =</span> <span class="st">&quot;20&quot;</span>,</span>
<span id="cb122-7"><a href="getdata.html#cb122-7" aria-hidden="true" tabindex="-1"></a>                           <span class="at">statCd =</span> <span class="st">&quot;00003&quot;</span>)</span></code></pre></div>
</div>
<div id="ok-lets-download-some-data" class="section level2 hasAnchor" number="7.6">
<h2><span class="header-section-number">7.6</span> OK let’s download some data!<a href="getdata.html#ok-lets-download-some-data" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>We are going to use readNWISdv(), which downloads daily values.</p>
<p>We will tell it which sites to download, which parameters to download, and then what time period to download.</p>
<p>siteNumber gets the sites we want to download, USGS site numbers, as a character. We will use the swva_sites data we generated (yep, you can download multiple sites at once!)</p>
<p>startDate and endDate get the…. start and end dates. IMPORTANT: These must be in YYY-MM-DD format, but you don’t have to tell R they are dates before you give them to the function, it’ll do that for you.</p>
<p>parameterCd is the parameters you want to download. We want water temperature and discharge, which are “00060” and “00010”, respectively.</p>
<p>Once we have the data, the column names correspond to the keys that identify them, for example, discharge will be 00060 something something. Fortunately the dataRetrieval package also provides “renameNWISColumns()” which translates these into words, making them more easily understood by humans. We can pipe the results of our download to that function after we get the data to make the column names easier to understand.</p>
<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb123-1"><a href="getdata.html#cb123-1" aria-hidden="true" tabindex="-1"></a>start <span class="ot">&lt;-</span> <span class="st">&quot;2006-10-01&quot;</span></span>
<span id="cb123-2"><a href="getdata.html#cb123-2" aria-hidden="true" tabindex="-1"></a>end <span class="ot">&lt;-</span> <span class="st">&quot;2008-09-30&quot;</span></span>
<span id="cb123-3"><a href="getdata.html#cb123-3" aria-hidden="true" tabindex="-1"></a>params <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">&quot;00010&quot;</span>, <span class="st">&quot;00060&quot;</span>)</span>
<span id="cb123-4"><a href="getdata.html#cb123-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb123-5"><a href="getdata.html#cb123-5" aria-hidden="true" tabindex="-1"></a>swva_dat <span class="ot">&lt;-</span> <span class="fu">readNWISdv</span>(<span class="at">siteNumber =</span> swva_sites<span class="sc">$</span>site_no, </span>
<span id="cb123-6"><a href="getdata.html#cb123-6" aria-hidden="true" tabindex="-1"></a>                       <span class="at">parameterCd =</span> params, </span>
<span id="cb123-7"><a href="getdata.html#cb123-7" aria-hidden="true" tabindex="-1"></a>                       <span class="at">startDate =</span> start, </span>
<span id="cb123-8"><a href="getdata.html#cb123-8" aria-hidden="true" tabindex="-1"></a>                       <span class="at">endDate =</span> end) <span class="sc">%&gt;%</span> </span>
<span id="cb123-9"><a href="getdata.html#cb123-9" aria-hidden="true" tabindex="-1"></a>            <span class="fu">renameNWISColumns</span>()</span></code></pre></div>
<p>Let’s plot the water temperature data as a line and control the color of the lines with the different sites.</p>
<p>What could be better about this plot?</p>
<div class="sourceCode" id="cb124"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb124-1"><a href="getdata.html#cb124-1" aria-hidden="true" tabindex="-1"></a>swva_dat <span class="sc">%&gt;%</span> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> Date, <span class="at">y =</span> Wtemp, <span class="at">color =</span> site_no)) <span class="sc">+</span></span>
<span id="cb124-2"><a href="getdata.html#cb124-2" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_line</span>()</span></code></pre></div>
<pre><code>## Warning: Removed 2218 row(s) containing missing values (geom_path).</code></pre>
<p><img src="Hydroinformatics_Bookdown_files/figure-html/unnamed-chunk-62-1.png" width="672" /></p>
<p>We can add site names with….More joins! Our swva_sites data has the names of the sites in human-friendly language. The column in the downloaded data and in the swva_sites data is called “site_no” so we just give that to the “by” argument. Perform a left join to add the names of the sites to the data.</p>
<p>Then use select to remove some of the unnecessary columns.</p>
<p>Then make the plot and then snazz it up with labels and a non-junky theme.</p>
<div class="sourceCode" id="cb126"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb126-1"><a href="getdata.html#cb126-1" aria-hidden="true" tabindex="-1"></a>swva_dat_clean <span class="ot">&lt;-</span> <span class="fu">left_join</span>(swva_dat, swva_sites, <span class="at">by =</span> <span class="st">&quot;site_no&quot;</span>) <span class="sc">%&gt;%</span></span>