[custom] fix lesson contents

albhasan · Feb 7, 2023 · af3e28c · af3e28c
1 parent ee731d1
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^\.travis\.yml$
 ^appveyor\.yml$
 ^tic\.R$
diff --git a/episodes/01-raster-structure.Rmd b/episodes/01-raster-structure.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 knitr::opts_chunk$set(fig.height = 6)
 ```
 

diff --git a/episodes/02-raster-plot.Rmd b/episodes/02-raster-plot.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/03-raster-reproject-in-r.Rmd b/episodes/03-raster-reproject-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives
@@ -296,38 +296,42 @@ field site using the `SJER_DSMhill_WGS84.tif` and `SJER_dsmCrop.tif` files.
 
 Reproject the data as necessary to make things line up!
 
-> ## Answers
-> 
-> ```{r challenge-code-reprojection, echo=TRUE}
-> # import DSM
-> DSM_SJER <- raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DSM/SJER_dsmCrop.tif")
-> # import DSM hillshade
-> DSM_hill_SJER_WGS <-
-> raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DSM/SJER_DSMhill_WGS84.tif")
-> 
-> # reproject raster
-> DTM_hill_UTMZ18N_SJER <- projectRaster(DSM_hill_SJER_WGS,
->                                   crs = crs(DSM_SJER),
->                                   res = 1)
-> 
-> # convert to data.frames
-> DSM_SJER_df <- as.data.frame(DSM_SJER, xy = TRUE)
-> 
-> DSM_hill_SJER_df <- as.data.frame(DTM_hill_UTMZ18N_SJER, xy = TRUE)
-> 
-> ggplot() +
->      geom_raster(data = DSM_hill_SJER_df, 
->                  aes(x = x, y = y, 
->                    alpha = SJER_DSMhill_WGS84)
->                  ) +
->      geom_raster(data = DSM_SJER_df, 
->              aes(x = x, y = y, 
->                   fill = SJER_dsmCrop,
->                   alpha=0.8)
->              ) + 
->      scale_fill_gradientn(name = "Elevation", colors = terrain.colors(10)) + 
->      coord_quickmap()
-> ```
+:::::::::::::::  solution
+
+## Answers
+
+```{r challenge-code-reprojection, echo=TRUE}
+# import DSM
+DSM_SJER <- raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DSM/SJER_dsmCrop.tif")
+# import DSM hillshade
+DSM_hill_SJER_WGS <-
+raster("data/NEON-DS-Airborne-Remote-Sensing/SJER/DSM/SJER_DSMhill_WGS84.tif")
+
+# reproject raster
+DTM_hill_UTMZ18N_SJER <- projectRaster(DSM_hill_SJER_WGS,
+                                  crs = crs(DSM_SJER),
+                                  res = 1)
+
+# convert to data.frames
+DSM_SJER_df <- as.data.frame(DSM_SJER, xy = TRUE)
+
+DSM_hill_SJER_df <- as.data.frame(DTM_hill_UTMZ18N_SJER, xy = TRUE)
+
+ggplot() +
+     geom_raster(data = DSM_hill_SJER_df, 
+                 aes(x = x, y = y, 
+                   alpha = SJER_DSMhill_WGS84)
+                 ) +
+     geom_raster(data = DSM_SJER_df, 
+             aes(x = x, y = y, 
+                  fill = SJER_dsmCrop,
+                  alpha=0.8)
+             ) + 
+     scale_fill_gradientn(name = "Elevation", colors = terrain.colors(10)) + 
+     coord_quickmap()
+```
+
+:::::::::::::::::::::::::
 
 If you completed the San Joaquin plotting challenge in the
 [Plot Raster Data in R](02-raster-plot/)

diff --git a/episodes/04-raster-calculations-in-r.Rmd b/episodes/04-raster-calculations-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/05-raster-multi-band-in-r.Rmd b/episodes/05-raster-multi-band-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/06-vector-open-shapefile-in-r.Rmd b/episodes/06-vector-open-shapefile-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/07-vector-shapefile-attributes-in-r.Rmd b/episodes/07-vector-shapefile-attributes-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/08-vector-plot-shapefiles-custom-legend.Rmd b/episodes/08-vector-plot-shapefiles-custom-legend.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/09-vector-when-data-dont-line-up-crs.Rmd b/episodes/09-vector-when-data-dont-line-up-crs.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/10-vector-csv-to-shapefile-in-r.Rmd b/episodes/10-vector-csv-to-shapefile-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/11-vector-raster-integration.Rmd b/episodes/11-vector-raster-integration.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/12-time-series-raster.Rmd b/episodes/12-time-series-raster.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/13-plot-time-series-rasters-in-r.Rmd b/episodes/13-plot-time-series-rasters-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/episodes/14-extract-ndvi-from-rasters-in-r.Rmd b/episodes/14-extract-ndvi-from-rasters-in-r.Rmd
@@ -6,7 +6,7 @@ source: Rmd
 ---
 
 ```{r setup, echo=FALSE}
-source("../setup.R")
+source("setup.R")
 ```
 
 ::::::::::::::::::::::::::::::::::::::: objectives

diff --git a/setup.R → episodes/setup.R b/setup.R → episodes/setup.R
@@ -1,3 +1,4 @@
+options(timeout = max(300, getOption('timeout')))
 ## file structure
 
 if (! file.exists("data/NEON-DS-Site-Layout-Files")) {