Merge branch 'main' into patch-2

Author: dafnidrake

.gitignore

@@ -58,4 +58,4 @@ __pycache__
 vendor/
 .docker-vendor/
 Gemfile.lock
-.*history
+.*history

episodes/01-raster-structure.Rmd

@@ -318,16 +318,14 @@ 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 `nly()` function.
+view the number of bands in a raster using the `nlyr()` function.
 
 ```{r view-raster-bands}
 nlyr(DSM_HARV)
 ```
 
-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.
+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

episodes/02-raster-plot.Rmd

@@ -85,13 +85,11 @@ values of `fct_elevation`:
 unique(DSM_HARV_df$fct_elevation)
 ```
 
-And we can get the count of values in each group using `dplyr`'s `group_by()` 
-and `count()` functions:
+And we can get the count of values in each group using `dplyr`'s `count()` function:
 
 ```{r breaks-count}
 DSM_HARV_df %>%
-        group_by(fct_elevation) %>%
-        count()
+        count(fct_elevation)
 ```
 
 We might prefer to customize the cutoff values for these groups.
@@ -133,8 +131,7 @@ And we can get the count of values in each group in the same way we did before:
 
 ```{r break-count-custom}
 DSM_HARV_df %>%
-  group_by(fct_elevation_2) %>%
-  count()
+  count(fct_elevation_2)
 ```
 
 We can use those groups to plot our raster data, with each group being a 

episodes/05-raster-multi-band-in-r.Rmd

@@ -55,7 +55,7 @@ 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 parater would read 
+specific raster bands (i.e. the first one); omitting this parameter would read 
 instead all bands.
 
 ```{r read-single-band}

episodes/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://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")
+  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")
 }
 
 if (! file.exists("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")
+  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")
 }

renv/activate.R

@@ -2,11 +2,13 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.5"
+  version <- "1.0.7"
   attr(version, "sha") <- NULL
 
   # the project directory
-  project <- getwd()
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
 
   # use start-up diagnostics if enabled
   diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
@@ -129,6 +131,21 @@ local({
 
   }
 
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    paste(substring(lines, common), collapse = "\n")
+  
+  }
+  
   startswith <- function(string, prefix) {
     substring(string, 1, nchar(prefix)) == prefix
   }
@@ -631,6 +648,9 @@ local({
 
     # if the user has requested an automatic prefix, generate it
     auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
     if (auto %in% c("TRUE", "True", "true", "1"))
       return(renv_bootstrap_platform_prefix_auto())
 
@@ -822,24 +842,23 @@ local({
 
     # the loaded version of renv doesn't match the requested version;
     # give the user instructions on how to proceed
-    remote <- if (!is.null(description[["RemoteSha"]])) {
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
       paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
-    } else {
+    else
       paste("renv", description[["Version"]], sep = "@")
-    }
 
     # display both loaded version + sha if available
     friendly <- renv_bootstrap_version_friendly(
       version = description[["Version"]],
-      sha     = description[["RemoteSha"]]
+      sha     = if (dev) description[["RemoteSha"]]
     )
 
-    fmt <- paste(
-      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
-      "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
-      "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
-      sep = "\n"
-    )
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
     catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
 
     FALSE