update schedule and raster 2

05_Raster.Rmd

@@ -106,7 +106,7 @@ getData("ISO3")%>%
   as.data.frame%>%
   filter(NAME=="Tunisia")
 
-country=getData('GADM', country='TUN', level=1)
+country=getData('GADM', country='TUN', level=2)
 
 country%>% 
   gSimplify(0.01)%>%
@@ -266,7 +266,7 @@ Use `projectRaster()` to _warp_ to a different projection.
 `method=` `ngb` (for categorical) or `bilinear` (continuous)
 
 ```{r}
-r2=projectRaster(r,crs="+proj=sinu +lon_0=0",method = )
+r2=projectRaster(r,crs="+proj=sinu +lon_0=0",method = "ngb")
 
 par(mfrow=c(1,2));plot(r);plot(r2)
 
@@ -434,8 +434,14 @@ rf_min <- focal(r1, w=matrix(1,11,11), fun=min)
 rf_max <- focal(r1, w=matrix(1,11,11), fun=max)
 rf_range=rf_max-rf_min
 
-## or just use the range function
-rf_range2 <- focal(r1, w=matrix(1,11,11), fun=range)
+## or do it all at once
+range2=function(x,na.rm=F) {
+  max(x,na.rm)-min(x,na.rm)
+}
+
+rf_range2 <- focal(r1, w=matrix(1,11,11), fun=range2)
+
+plot(rf_range)
 plot(rf_range2)
 ```
 

Schedule.Rmd

@@ -11,13 +11,13 @@ Course content is designed to be flexible to accommodate student interest and ab
 | 9/14 | **Data Wrangling 2** | Filtering, selecting, joining data sets. Data gymnastics with dplyr. |  Homework #1 due before class  | 1 |
 | 9/21 | **Graphics** | More base graphics (scatterplots, histograms).  The _grammar of graphics_: ggplot2 and extensions (ggmap, rasterVis, etc.). |  | 2 |
 | 9/28 | **Spatial Data** | Spatial Libraries: raster, sp, rgeos, rgdal. Integrating ‘traditional GIS’ analyses with statistical modelling.  Data intersection (e.g. connecting points with polygons and rasters), overlays, zonal statistics | Homework # 2 | 3 |
-| 10/5 | **Spatial Raster I** | Working with gridded spatial data | Project Proposal Due | 4| 
-| 10/12 | **Spatial Raster II** | Raster calculations, working with climate datasets.  |     | 5| 
-| 10/19 | **Spatial Raster III** | A 'mini' project - looking at sea level rise in Bangladesh | | 6 | 
-| 10/26 | **Reproducible Research & Literate Programming** | RMarkdown to create dynamic research outputs.  Publishing to github/word/html/etc.| Homework # 3  | 7| 
-| 11/2 | **Weather/Climate Data Processing ** | Processing daily weather data from NOAA  |  First draft of project for peer assessment   | 8 |
-| 11/9 | **Satellite Data Processing** | Working with MODIS Satellite data | Peer Evaluation Due | 9 |
-| 11/16 | **High Performance Computing & Software Integration** | Parallel processing and high performance computing in R, Calling other programs from within R. | Homework # 4 | 10 |
+| 10/5 | **Spatial Raster I** | Working with gridded spatial data | Project Proposal Due 10/10 | 4| 
+| 10/12 | **Spatial Raster II** | A 'mini' project - looking at sea level rise in Bangladesh |     | 5| 
+| 10/19 | **Reproducible Research & Literate Programming** | RMarkdown to create dynamic research outputs.  Publishing to github/word/html/etc. | | 6 | 
+| 10/26 | **Weather/Climate Data Processing ** | Processing daily weather data from NOAA  | Homework # 3  | 7| 
+| 11/2 | **Satellite Data Processing** | Working with MODIS Satellite data |  First draft of project for peer assessment   | 8 |
+| 11/9 | **High Performance Computing & Software Integration** | Parallel processing and high performance computing in R, Calling other programs from within R. | Peer Evaluation Due | 9 |
+| 11/16 |  | | Homework # 4 | 10 |
 | 11/23 | **Thanksgiving** | (no class)   |  | |
 | 11/30 |  **Version Control** |  Managing code with "version control"" using Github. | Second draft of project Due 12/1 at midnight | |
 | 12/7 | **Final Project Presentations** | | 5 minute presentation of your final project | |

docs/05_Raster.html

@@ -501,7 +501,7 @@ <h2 id="your-turn">Your turn</h2>
   filter(NAME==&quot;Tunisia&quot;)</code></pre>
 <pre><code>##   ISO3    NAME
 ## 1  TUN Tunisia</code></pre>
-<pre class="r"><code>country=getData(&#39;GADM&#39;, country=&#39;TUN&#39;, level=1)
+<pre class="r"><code>country=getData(&#39;GADM&#39;, country=&#39;TUN&#39;, level=2)
 
 country%&gt;% 
   gSimplify(0.01)%&gt;%
@@ -671,7 +671,7 @@ <h2>Spatial Projections</h2>
 <h2>Warping rasters</h2>
 <p>Use <code>projectRaster()</code> to <em>warp</em> to a different projection.</p>
 <p><code>method=</code> <code>ngb</code> (for categorical) or <code>bilinear</code> (continuous)</p>
-<pre class="r"><code>r2=projectRaster(r,crs=&quot;+proj=sinu +lon_0=0&quot;,method = )</code></pre>
+<pre class="r"><code>r2=projectRaster(r,crs=&quot;+proj=sinu +lon_0=0&quot;,method = &quot;ngb&quot;)</code></pre>
 <pre><code>## Warning in rgdal::rawTransform(projto_int, projfrom, nrow(xy), xy[, 1], :
 ## 48 projected point(s) not finite</code></pre>
 <pre class="r"><code>par(mfrow=c(1,2));plot(r);plot(r2)</code></pre>
@@ -874,10 +874,17 @@ <h2>Focal (“moving window”)</h2>
 rf_max &lt;- focal(r1, w=matrix(1,11,11), fun=max)
 rf_range=rf_max-rf_min
 
-## or just use the range function
-rf_range2 &lt;- focal(r1, w=matrix(1,11,11), fun=range)
-plot(rf_range2)</code></pre>
+## or do it all at once
+range2=function(x,na.rm=F) {
+  max(x,na.rm)-min(x,na.rm)
+}
+
+rf_range2 &lt;- focal(r1, w=matrix(1,11,11), fun=range2)
+
+plot(rf_range)</code></pre>
 <p><img src="05_Raster_files/figure-html/unnamed-chunk-38-1.png" width="2100" /></p>
+<pre class="r"><code>plot(rf_range2)</code></pre>
+<p><img src="05_Raster_files/figure-html/unnamed-chunk-38-2.png" width="2100" /></p>
 <div class="well">
 <h2 id="your-turn-3">Your turn</h2>
 <p>Plot the focal standard deviation of <code>r1</code> over a 3x3 window.</p>

docs/07_Reproducibile.html

@@ -553,9 +553,11 @@ <h2>Literate statistical programming</h2>
 </blockquote>
 <p>For example… Let’s calculate the current time in R.</p>
 <pre class="r"><code>time &lt;- format(Sys.time(), &quot;%a %d %b %X %Y&quot;)</code></pre>
+<pre><code>## Warning in as.POSIXlt.POSIXct(x, tz): unknown timezone &#39;default/America/
+## New_York&#39;</code></pre>
 <p>The text and R code are interwoven in the output:</p>
 <p>The time is <code>`r time`</code></p>
-<p>The time is Thu 28 Sep 09:21:22 2017</p>
+<p>The time is Thu 12 Oct 13:25:37 2017</p>
 </div>
 <div id="literate-programming-for-and-against" class="section level2 columns-2">
 <h2>Literate programming: for and against</h2>
@@ -729,8 +731,9 @@ <h2>Step 1: Load packages</h2>
 CODE HERE
 #```</code></pre>
 <p>Load these packages in a code chunk (you may need to install some packages):</p>
-<pre class="r"><code>library(dplyr)
-library(ggplot2)
+<pre class="r"><code>library(dplyr)</code></pre>
+<pre><code>## Warning: package &#39;dplyr&#39; was built under R version 3.4.2</code></pre>
+<pre class="r"><code>library(ggplot2)
 library(maps)
 library(spocc)</code></pre>
 <blockquote>

docs/Schedule.html

@@ -454,48 +454,48 @@ <h1 class="title toc-ignore">Course Schedule</h1>
 <td align="left">10/5</td>
 <td align="left"><strong>Spatial Raster I</strong></td>
 <td align="left">Working with gridded spatial data</td>
-<td align="left">Project Proposal Due</td>
+<td align="left">Project Proposal Due 10/10</td>
 <td align="right">4</td>
 </tr>
 <tr class="odd">
 <td align="left">10/12</td>
 <td align="left"><strong>Spatial Raster II</strong></td>
-<td align="left">Raster calculations, working with climate datasets.</td>
+<td align="left">A ‘mini’ project - looking at sea level rise in Bangladesh</td>
 <td align="left"></td>
 <td align="right">5</td>
 </tr>
 <tr class="even">
 <td align="left">10/19</td>
-<td align="left"><strong>Spatial Raster III</strong></td>
-<td align="left">A ‘mini’ project - looking at sea level rise in Bangladesh</td>
+<td align="left"><strong>Reproducible Research &amp; Literate Programming</strong></td>
+<td align="left">RMarkdown to create dynamic research outputs. Publishing to github/word/html/etc.</td>
 <td align="left"></td>
 <td align="right">6</td>
 </tr>
 <tr class="odd">
 <td align="left">10/26</td>
-<td align="left"><strong>Reproducible Research &amp; Literate Programming</strong></td>
-<td align="left">RMarkdown to create dynamic research outputs. Publishing to github/word/html/etc.</td>
+<td align="left"><strong>Weather/Climate Data Processing </strong></td>
+<td align="left">Processing daily weather data from NOAA</td>
 <td align="left">Homework # 3</td>
 <td align="right">7</td>
 </tr>
 <tr class="even">
 <td align="left">11/2</td>
-<td align="left"><strong>Weather/Climate Data Processing </strong></td>
-<td align="left">Processing daily weather data from NOAA</td>
+<td align="left"><strong>Satellite Data Processing</strong></td>
+<td align="left">Working with MODIS Satellite data</td>
 <td align="left">First draft of project for peer assessment</td>
 <td align="right">8</td>
 </tr>
 <tr class="odd">
 <td align="left">11/9</td>
-<td align="left"><strong>Satellite Data Processing</strong></td>
-<td align="left">Working with MODIS Satellite data</td>
+<td align="left"><strong>High Performance Computing &amp; Software Integration</strong></td>
+<td align="left">Parallel processing and high performance computing in R, Calling other programs from within R.</td>
 <td align="left">Peer Evaluation Due</td>
 <td align="right">9</td>
 </tr>
 <tr class="even">
 <td align="left">11/16</td>
-<td align="left"><strong>High Performance Computing &amp; Software Integration</strong></td>
-<td align="left">Parallel processing and high performance computing in R, Calling other programs from within R.</td>
+<td align="left"></td>
+<td align="left"></td>
 <td align="left">Homework # 4</td>
 <td align="right">10</td>
 </tr>

docs/scripts/05_Raster.R

@@ -244,7 +244,7 @@ projection(r)
 #' `method=` `ngb` (for categorical) or `bilinear` (continuous)
 #' 
 ## ------------------------------------------------------------------------
-r2=projectRaster(r,crs="+proj=sinu +lon_0=0",method = )
+r2=projectRaster(r,crs="+proj=sinu +lon_0=0",method = "ngb")
 
 par(mfrow=c(1,2));plot(r);plot(r2)
 
@@ -408,8 +408,14 @@ rf_min <- focal(r1, w=matrix(1,11,11), fun=min)
 rf_max <- focal(r1, w=matrix(1,11,11), fun=max)
 rf_range=rf_max-rf_min
 
-## or just use the range function
-rf_range2 <- focal(r1, w=matrix(1,11,11), fun=range)
+## or do it all at once
+range2=function(x,na.rm=F) {
+  max(x,na.rm)-min(x,na.rm)
+}
+
+rf_range2 <- focal(r1, w=matrix(1,11,11), fun=range2)
+
+plot(rf_range)
 plot(rf_range2)
 
 #' 

scripts/05_Raster.R

@@ -244,7 +244,7 @@ projection(r)
 #' `method=` `ngb` (for categorical) or `bilinear` (continuous)
 #' 
 ## ------------------------------------------------------------------------
-r2=projectRaster(r,crs="+proj=sinu +lon_0=0",method = )
+r2=projectRaster(r,crs="+proj=sinu +lon_0=0",method = "ngb")
 
 par(mfrow=c(1,2));plot(r);plot(r2)
 
@@ -408,8 +408,14 @@ rf_min <- focal(r1, w=matrix(1,11,11), fun=min)
 rf_max <- focal(r1, w=matrix(1,11,11), fun=max)
 rf_range=rf_max-rf_min
 
-## or just use the range function
-rf_range2 <- focal(r1, w=matrix(1,11,11), fun=range)
+## or do it all at once
+range2=function(x,na.rm=F) {
+  max(x,na.rm)-min(x,na.rm)
+}
+
+rf_range2 <- focal(r1, w=matrix(1,11,11), fun=range2)
+
+plot(rf_range)
 plot(rf_range2)
 
 #'