differences for PR #444

01-raster-structure.md

@@ -6,6 +6,17 @@ source: Rmd
 ---
 
 
+``` warning
+Warning in
+download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip",
+: cannot open URL
+'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip':
+HTTP status was '500 Internal Server Error'
+```
+
+``` error
+Error in download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip", : cannot open URL 'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip'
+```
 
 ::::::::::::::::::::::::::::::::::::::: objectives
 
@@ -463,7 +474,7 @@ raster: surface elevation in meters for one time period.
 
 A raster dataset can contain one or more bands. We can use the `rast()`
 function to import one single band from a single or multi-band raster. We can
-view the number of bands in a raster using the `nlyr()` function.
+view the number of bands in a raster using the `nly()` function.
 
 
 ``` r
@@ -474,8 +485,11 @@ nlyr(DSM_HARV)
 [1] 1
 ```
 
-However, raster data can also be multi-band, meaning that one raster file contains data for more than one variable or time period for each cell.
-Jump to a later episode in this series for information on working with multi-band rasters:
+However, raster data can also be multi-band, meaning that one raster file
+contains data for more than one variable or time period for each cell. By
+default the `raster()` function only imports the first band in a raster
+regardless of whether it has one or more bands. Jump to a later episode in
+this series for information on working with multi-band rasters:
 [Work with Multi-band Rasters in R](05-raster-multi-band-in-r/).
 
 ## Dealing with Missing Data

02-raster-plot.md

@@ -6,6 +6,17 @@ source: Rmd
 ---
 
 
+``` warning
+Warning in
+download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip",
+: cannot open URL
+'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip':
+HTTP status was '500 Internal Server Error'
+```
+
+``` error
+Error in download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip", : cannot open URL 'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip'
+```
 
 ::::::::::::::::::::::::::::::::::::::: objectives
 
@@ -79,19 +90,24 @@ unique(DSM_HARV_df$fct_elevation)
 Levels: (305,342] (342,379] (379,416]
 ```
 
-And we can get the count of values in each group using `dplyr`'s `count()` function:
+And we can get the count of values in each group using `dplyr`'s `group_by()` 
+and `count()` functions:
 
 
 ``` r
 DSM_HARV_df %>%
-        count(fct_elevation)
+        group_by(fct_elevation) %>%
+        count()
 ```
 
 ``` output
+# A tibble: 3 × 2
+# Groups:   fct_elevation [3]
   fct_elevation       n
-1     (305,342]  418891
-2     (342,379] 1530073
-3     (379,416]  370835
+  <fct>           <int>
+1 (305,342]      418891
+2 (342,379]     1530073
+3 (379,416]      370835
 ```
 
 We might prefer to customize the cutoff values for these groups.
@@ -143,14 +159,18 @@ And we can get the count of values in each group in the same way we did before:
 
 ``` r
 DSM_HARV_df %>%
-  count(fct_elevation_2)
+  group_by(fct_elevation_2) %>%
+  count()
 ```
 
 ``` output
+# A tibble: 3 × 2
+# Groups:   fct_elevation_2 [3]
   fct_elevation_2       n
-1       (300,350]  741815
-2       (350,400] 1567316
-3       (400,450]   10668
+  <fct>             <int>
+1 (300,350]        741815
+2 (350,400]       1567316
+3 (400,450]         10668
 ```
 
 We can use those groups to plot our raster data, with each group being a 

05-raster-multi-band-in-r.md

@@ -6,6 +6,17 @@ source: Rmd
 ---
 
 
+``` warning
+Warning in
+download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip",
+: cannot open URL
+'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip':
+HTTP status was '500 Internal Server Error'
+```
+
+``` error
+Error in download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip", : cannot open URL 'https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip'
+```
 
 ::::::::::::::::::::::::::::::::::::::: objectives
 
@@ -49,7 +60,7 @@ Each RGB image is a 3-band raster. The same steps would apply to working with a
 multi-spectral image with 4 or more bands - like Landsat imagery.
 
 By using the `rast()` function along with the `lyrs` parameter, we can read 
-specific raster bands (i.e. the first one); omitting this parameter would read 
+specific raster bands (i.e. the first one); omitting this parater would read 
 instead all bands.
 
 
@@ -364,7 +375,7 @@ well between 0 and 255.
 Let's explore what happens with NoData values when working with RasterStack 
 objects and using the `plotRGB()` function. We will use the 
 `HARV_Ortho_wNA.tif` GeoTIFF file in the 
-`NEON-DS-Airborne-Remote-Sensing/HARVRGB_Imagery/` directory.
+`NEON-DS-Airborne-Remote-Sensing/HARV/RGB_Imagery/` directory.
 
 1. View the files attributes. Are there `NoData` values assigned for this file?
 2. If so, what is the `NoData` Value?

md5sum.txt

@@ -4,11 +4,11 @@
 "about.md" "2ae9402fd9f37560bd85430a98bf4847" "site/built/about.md" "2024-06-04"
 "config.yaml" "8f4c7a49b9d32beef686bcd8ae3e4c5f" "site/built/config.yaml" "2024-06-04"
 "index.md" "8704017272467874007912c316744a00" "site/built/index.md" "2024-06-04"
-"episodes/01-raster-structure.Rmd" "fd0024d668eb41109e4761a558c3d855" "site/built/01-raster-structure.md" "2024-06-15"
-"episodes/02-raster-plot.Rmd" "5de487340aa50257089b12295059018b" "site/built/02-raster-plot.md" "2024-06-15"
+"episodes/01-raster-structure.Rmd" "c819b6903d870befad6add128c4f9274" "site/built/01-raster-structure.md" "2024-06-15"
+"episodes/02-raster-plot.Rmd" "3bc30659ae4d91c31a1175ff7127531a" "site/built/02-raster-plot.md" "2024-06-15"
 "episodes/03-raster-reproject-in-r.Rmd" "d11ff839db427f11b0f0d5e8f7825c80" "site/built/03-raster-reproject-in-r.md" "2024-06-04"
 "episodes/04-raster-calculations-in-r.Rmd" "a100233c7c80bcae34c0112d10980d0d" "site/built/04-raster-calculations-in-r.md" "2024-06-04"
-"episodes/05-raster-multi-band-in-r.Rmd" "ed98c238c11fbe7706bf924813f17d20" "site/built/05-raster-multi-band-in-r.md" "2024-06-15"
+"episodes/05-raster-multi-band-in-r.Rmd" "575875af5ca9a106473a84c1fc41804d" "site/built/05-raster-multi-band-in-r.md" "2024-06-15"
 "episodes/06-vector-open-shapefile-in-r.Rmd" "9966d5678aea06e445f5b660a079482e" "site/built/06-vector-open-shapefile-in-r.md" "2024-06-04"
 "episodes/07-vector-shapefile-attributes-in-r.Rmd" "726f78cdabe6ebe90a609b31127674ca" "site/built/07-vector-shapefile-attributes-in-r.md" "2024-06-04"
 "episodes/08-vector-plot-shapefiles-custom-legend.Rmd" "733bf768d8f27d9c7e548e7f835fda67" "site/built/08-vector-plot-shapefiles-custom-legend.md" "2024-06-04"

setup.R

@@ -2,43 +2,43 @@ options(timeout = max(300, getOption('timeout')))
 ## file structure
 
 if (! file.exists("data/NEON-DS-Site-Layout-Files")) {
-  dest <- tempfile()
-  download.file("https://ndownloader.figshare.com/files/3708751", dest,
-                mode = "wb")
-  unzip(dest, exdir = "data")
+    dest <- tempfile()
+    download.file("https://ndownloader.figshare.com/files/3708751", dest,
+                  mode = "wb")
+    unzip(dest, exdir = "data")
 }
 
 if (! file.exists("data/NEON-DS-Airborne-Remote-Sensing")) {
-  dest <- tempfile()
-  download.file("https://ndownloader.figshare.com/files/3701578", dest,
-                mode = "wb")
-  unzip(dest, exdir = "data")
+    dest <- tempfile()
+    download.file("https://ndownloader.figshare.com/files/3701578", dest,
+                  mode = "wb")
+    unzip(dest, exdir = "data")
 }
 
 if (! file.exists("data/NEON-DS-Met-Time-Series")) {
-  dest <- tempfile()
-  download.file("https://ndownloader.figshare.com/files/3701572", dest,
-                mode = "wb")
-  unzip(dest, exdir = "data")
+    dest <- tempfile()
+    download.file("https://ndownloader.figshare.com/files/3701572", dest,
+                  mode = "wb")
+    unzip(dest, exdir = "data")
 }
 
 if (! file.exists("data/NEON-DS-Landsat-NDVI")) {
-  dest <- tempfile()
-  download.file("https://ndownloader.figshare.com/files/4933582", dest,
-                mode = "wb")
-  unzip(dest, exdir = "data")
+    dest <- tempfile()
+    download.file("https://ndownloader.figshare.com/files/4933582", dest,
+                  mode = "wb")
+    unzip(dest, exdir = "data")
 }
 
 if (! file.exists("data/Global/Boundaries/ne_110m_graticules_all")) {
-  dest <- tempfile()
-  download.file("https://naciscdn.org/naturalearth/110m/physical/ne_110m_graticules_all.zip",
-                dest, mode = "wb")
-  unzip(dest, exdir = "data/Global/Boundaries/ne_110m_graticules_all")
+    dest <- tempfile()
+    download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_graticules_all.zip",
+                  dest, mode = "wb")
+    unzip(dest, exdir = "data/Global/Boundaries/ne_110m_graticules_all")
 }
 
 if (! file.exists("data/Global/Boundaries/ne_110m_land")) {
-  dest <- tempfile()
-  download.file("https://naciscdn.org/naturalearth/110m/physical/ne_110m_land.zip",
-                dest, mode = "wb")
-  unzip(dest, exdir = "data/Global/Boundaries/ne_110m_land")
+    dest <- tempfile()
+    download.file("https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/110m/physical/ne_110m_land.zip",
+                  dest, mode = "wb")
+    unzip(dest, exdir = "data/Global/Boundaries/ne_110m_land")
 }