Class 21 slides

agroimpacts · Apr 3, 2024 · 597848b · 597848b
1 parent e056aca
commit 597848b
Show file tree

Hide file tree

Showing 5 changed files with 346 additions and 2 deletions.
diff --git a/docs/class21.Rmd b/docs/class21.Rmd
@@ -0,0 +1,89 @@
+---
+title: "Geospatial Analysis with R"
+subtitle: Class 20
+output:
+  xaringan::moon_reader:
+    lib_dir: libs
+    css: ["default", "lucy", "middlebury-fonts", "themes/class18.css"]
+    nature:
+      highlightStyle: github
+      highlightLines: true
+      countIncrementalSlides: false
+---
+
+---
+
+## Today
+
+- `terra` (raster) intro
+  - agg/disagg, masking
+  - assigning values
+  - zonal
+  - focal
+  - global
+  - terrain
+
+---
+- Load data
+```{r, eval=FALSE}
+library(geospaar)
+farmers <- system.file("extdata/farmer_spatial.csv", package = "geospaar") %>% 
+  read_csv() %>% 
+  st_as_sf(coords = c("x", "y"))
+districts <- st_read(
+  system.file("extdata/districts.geojson", package = "geospaar")
+)
+roads <- read_sf(system.file("extdata/roads.geojson", package = "geospaar"))
+
+chirps <- terra::rast(system.file("extdata/chirps.tif", package = "geospaar"))
+```
+
+---
+```{r, eval=FALSE}
+districts <- districts %>% mutate(ID = 1:nrow(.))
+distsr <- districts %>% 
+  rasterize(x = ., y = raintot, field = "ID") %>% 
+  print()
+
+chirpsz <- mask(chirps, districts) 
+raintot <- app(chirpsz, sum)
+```
+
+
+---
+## Climate data summaries and zonal stats
+
+```{r, eval=FALSE}
+tmax <- geodata::worldclim_country("Zambia", var = "tmax", path = tempdir())
+dt <- as.Date(gsub("Y", "", names(chirpsz)), format = "%y%j")
+dt <- lubridate::parse_date_time(gsub("Y", "", names(chirpsz)), orders = "yj")
+wk <- lubridate::week(dt)
+weekly_rainfall <- lapply(unique(wk), function(x) {
+  which(wk == x)
+  app(chirpsz[[which(wk == x)]], sum)
+}) %>% do.call(c, .)
+names(weekly_rainfall) <- paste0("wk", unique(wk))
+
+rflim <- range(global(weekly_rainfall, range, na.rm = TRUE))
+plot(weekly_rainfall, zlim = rflim)
+```
+
+---
+## Distance
+- plot distance from points
+- points must be in same projection as model raster
+```{r, message = F}
+set.seed(1)
+randsamp <- spatSample(raintot, size = 10, xy = TRUE, na.rm = TRUE) %>%
+  st_as_sf(coords = c("x", "y"), crs = 4326)
+
+ptdistr <- distance(raintot, vect(randsamp))
+ptdistrmsk <- mask(ptdistr, raintot)
+plot(ptdistrmsk)
+
+```
+
+
+
+
+
diff --git a/docs/class21.html b/docs/class21.html
@@ -0,0 +1,252 @@
+<!DOCTYPE html>
+<html lang="" xml:lang="">
+  <head>
+    <title>Geospatial Analysis with R</title>
+    <meta charset="utf-8" />
+    <script src="libs/header-attrs-2.25/header-attrs.js"></script>
+    <link href="libs/remark-css-0.0.1/default.css" rel="stylesheet" />
+    <link href="libs/remark-css-0.0.1/lucy.css" rel="stylesheet" />
+    <link href="libs/remark-css-0.0.1/middlebury-fonts.css" rel="stylesheet" />
+    <link rel="stylesheet" href="themes/class18.css" type="text/css" />
+  </head>
+  <body>
+    <textarea id="source">
+class: center, middle, inverse, title-slide
+
+.title[
+# Geospatial Analysis with R
+]
+.subtitle[
+## Class 20
+]
+
+---
+
+
+---
+
+## Today
+
+- `terra` (raster) intro
+  - agg/disagg, masking
+  - assigning values
+  - zonal
+  - focal
+  - global
+  - terrain
+
+---
+- Load data
+
+```r
+library(geospaar)
+farmers &lt;- system.file("extdata/farmer_spatial.csv", package = "geospaar") %&gt;% 
+  read_csv() %&gt;% 
+  st_as_sf(coords = c("x", "y"))
+districts &lt;- st_read(
+  system.file("extdata/districts.geojson", package = "geospaar")
+)
+roads &lt;- read_sf(system.file("extdata/roads.geojson", package = "geospaar"))
+
+chirps &lt;- terra::rast(system.file("extdata/chirps.tif", package = "geospaar"))
+```
+
+---
+
+```r
+districts &lt;- districts %&gt;% mutate(ID = 1:nrow(.))
+distsr &lt;- districts %&gt;% 
+  rasterize(x = ., y = raintot, field = "ID") %&gt;% 
+  print()
+
+chirpsz &lt;- mask(chirps, districts) 
+raintot &lt;- app(chirpsz, sum)
+```
+
+
+---
+## Climate data summaries and zonal stats
+
+
+```r
+tmax &lt;- geodata::worldclim_country("Zambia", var = "tmax", path = tempdir())
+dt &lt;- as.Date(gsub("Y", "", names(chirpsz)), format = "%y%j")
+dt &lt;- lubridate::parse_date_time(gsub("Y", "", names(chirpsz)), orders = "yj")
+wk &lt;- lubridate::week(dt)
+weekly_rainfall &lt;- lapply(unique(wk), function(x) {
+  which(wk == x)
+  app(chirpsz[[which(wk == x)]], sum)
+}) %&gt;% do.call(c, .)
+names(weekly_rainfall) &lt;- paste0("wk", unique(wk))
+
+rflim &lt;- range(global(weekly_rainfall, range, na.rm = TRUE))
+plot(weekly_rainfall, zlim = rflim)
+```
+
+---
+## Distance
+- plot distance from points
+- points must be in same projection as model raster
+
+```r
+set.seed(1)
+randsamp &lt;- spatSample(raintot, size = 10, xy = TRUE, na.rm = TRUE) %&gt;%
+  st_as_sf(coords = c("x", "y"), crs = 4326)
+
+ptdistr &lt;- distance(raintot, vect(randsamp))
+```
+
+```
+## 
+|---------|---------|---------|---------|
+=========================================
+
+```
+
+```r
+ptdistrmsk &lt;- mask(ptdistr, raintot)
+plot(ptdistrmsk)
+```
+
+![](/home/rstudio/geospaar/docs/class21_files/figure-html/unnamed-chunk-4-1.png)&lt;!-- --&gt;
+
+
+
+
+
+    </textarea>
+<style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
+<script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
+<script>var slideshow = remark.create({
+"highlightStyle": "github",
+"highlightLines": true,
+"countIncrementalSlides": false
+});
+if (window.HTMLWidgets) slideshow.on('afterShowSlide', function (slide) {
+  window.dispatchEvent(new Event('resize'));
+});
+(function(d) {
+  var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
+  if (!r) return;
+  s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
+  d.head.appendChild(s);
+})(document);
+
+(function(d) {
+  var el = d.getElementsByClassName("remark-slides-area");
+  if (!el) return;
+  var slide, slides = slideshow.getSlides(), els = el[0].children;
+  for (var i = 1; i < slides.length; i++) {
+    slide = slides[i];
+    if (slide.properties.continued === "true" || slide.properties.count === "false") {
+      els[i - 1].className += ' has-continuation';
+    }
+  }
+  var s = d.createElement("style");
+  s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
+  d.head.appendChild(s);
+})(document);
+// delete the temporary CSS (for displaying all slides initially) when the user
+// starts to view slides
+(function() {
+  var deleted = false;
+  slideshow.on('beforeShowSlide', function(slide) {
+    if (deleted) return;
+    var sheets = document.styleSheets, node;
+    for (var i = 0; i < sheets.length; i++) {
+      node = sheets[i].ownerNode;
+      if (node.dataset["target"] !== "print-only") continue;
+      node.parentNode.removeChild(node);
+    }
+    deleted = true;
+  });
+})();
+// add `data-at-shortcutkeys` attribute to <body> to resolve conflicts with JAWS
+// screen reader (see PR #262)
+(function(d) {
+  let res = {};
+  d.querySelectorAll('.remark-help-content table tr').forEach(tr => {
+    const t = tr.querySelector('td:nth-child(2)').innerText;
+    tr.querySelectorAll('td:first-child .key').forEach(key => {
+      const k = key.innerText;
+      if (/^[a-z]$/.test(k)) res[k] = t;  // must be a single letter (key)
+    });
+  });
+  d.body.setAttribute('data-at-shortcutkeys', JSON.stringify(res));
+})(document);
+(function() {
+  "use strict"
+  // Replace <script> tags in slides area to make them executable
+  var scripts = document.querySelectorAll(
+    '.remark-slides-area .remark-slide-container script'
+  );
+  if (!scripts.length) return;
+  for (var i = 0; i < scripts.length; i++) {
+    var s = document.createElement('script');
+    var code = document.createTextNode(scripts[i].textContent);
+    s.appendChild(code);
+    var scriptAttrs = scripts[i].attributes;
+    for (var j = 0; j < scriptAttrs.length; j++) {
+      s.setAttribute(scriptAttrs[j].name, scriptAttrs[j].value);
+    }
+    scripts[i].parentElement.replaceChild(s, scripts[i]);
+  }
+})();
+(function() {
+  var links = document.getElementsByTagName('a');
+  for (var i = 0; i < links.length; i++) {
+    if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
+      links[i].target = '_blank';
+    }
+  }
+})();
+// adds .remark-code-has-line-highlighted class to <pre> parent elements
+// of code chunks containing highlighted lines with class .remark-code-line-highlighted
+(function(d) {
+  const hlines = d.querySelectorAll('.remark-code-line-highlighted');
+  const preParents = [];
+  const findPreParent = function(line, p = 0) {
+    if (p > 1) return null; // traverse up no further than grandparent
+    const el = line.parentElement;
+    return el.tagName === "PRE" ? el : findPreParent(el, ++p);
+  };
+
+  for (let line of hlines) {
+    let pre = findPreParent(line);
+    if (pre && !preParents.includes(pre)) preParents.push(pre);
+  }
+  preParents.forEach(p => p.classList.add("remark-code-has-line-highlighted"));
+})(document);</script>
+
+<script>
+slideshow._releaseMath = function(el) {
+  var i, text, code, codes = el.getElementsByTagName('code');
+  for (i = 0; i < codes.length;) {
+    code = codes[i];
+    if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
+      text = code.textContent;
+      if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
+          /^\$\$(.|\s)+\$\$$/.test(text) ||
+          /^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
+        code.outerHTML = code.innerHTML;  // remove <code></code>
+        continue;
+      }
+    }
+    i++;
+  }
+};
+slideshow._releaseMath(document);
+</script>
+<!-- dynamically load mathjax for compatibility with self-contained -->
+<script>
+(function () {
+  var script = document.createElement('script');
+  script.type = 'text/javascript';
+  script.src  = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
+  if (location.protocol !== 'file:' && /^https?:/.test(script.src))
+    script.src  = script.src.replace(/^https?:/, '');
+  document.getElementsByTagName('head')[0].appendChild(script);
+})();
+</script>
+  </body>
+</html>
diff --git a/docs/index.Rmd b/docs/index.Rmd
@@ -103,6 +103,7 @@ The class materials were designed by Lyndon Estes and Lei Song.
 
 ### Week 12 (April 1, 3)
   - [Class 20 slides](class20.html)
+  - [Class 21 slides](class21.html)
   - Assignment 5 (Unit 2 Module 2) 
 
 ### Week 13-15 (April 8, 11, 15, 17, 22, 24, 29)

diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/index.md b/docs/index.md
@@ -3,7 +3,7 @@
 
 ## Spring 2024
 
-Updated on: 2024-04-01
+Updated on: 2024-04-03
 
 <center>
 
@@ -112,6 +112,7 @@ The class materials were designed by Lyndon Estes and Lei Song.
 ### Week 12 (April 1, 3)
 
 - [Class 20 slides](class20.html)
+- [Class 21 slides](class21.html)
 - Assignment 5 (Unit 2 Module 2)
 
 ### Week 13-15 (April 8, 11, 15, 17, 22, 24, 29)