Generate watercourse_100mseg & watercourse_100msegpoints: initial code

.gitignore

@@ -19,3 +19,5 @@ src/private_code.R
 *.qgs
 *.bak
 *.qgz
+grass_*/
+watercourse_segments/

src/generate_watercourse_100mseg/10_generate_watercourse_100mseg.Rmd

@@ -0,0 +1,93 @@
+# Making the data source
+
+We will create a master dataset of watercourse segments (`watercourse_100mseg`), in order to derive sampling frames of lotic types (3260 in particular).
+
+It is a processed data source, derived from the raw data source `watercourse_segments`.
+The segments have a 100 m length, except at the end of the linestrings in `watercourse_segments`.
+
+Further we derive a second data source `watercourse_100msegpoints` which represent the endpoints of the segments.
+
+```{r}
+local_root <- find_root(has_file("generate_watercourse_100mseg.Rproj"))
+datapath <- file.path(local_root, "data")
+if (!dir.exists(datapath)) dir.create(datapath)
+finalpath_segments <- find_root_file("n2khab_data/20_processed/watercourse_100mseg", 
+                                     criterion = has_dir("n2khab_data"))
+if (!dir.exists(finalpath_segments)) dir.create(finalpath_segments)
+finalpath_segmentpoints <- find_root_file("n2khab_data/20_processed/watercourse_100msegpoints", 
+                                          criterion = has_dir("n2khab_data"))
+if (!dir.exists(finalpath_segmentpoints)) dir.create(finalpath_segmentpoints)
+```
+
+```{r}
+grass_location <- file.path(datapath, "grass_watercourse_segments")
+if (!dir.exists(grass_location)) dir.create(file.path(grass_location, "PERMANENT"),
+                                            recursive = TRUE)
+grass_exists <- file.exists(file.path(grass_location, "PERMANENT/PROJ_INFO"))
+if (.Platform$OS.type == "unix") {
+  Sys.setenv(GRASS_PYTHON = system("which python3", intern = TRUE))
+}
+```
+
+
+## Geoprocessing steps in GRASS
+
+<!-- Read the `watercourse_segments` data source (this needs improvement). -->
+
+<!-- ```{r paged.print=FALSE} -->
+<!-- watercourse_segments <- read_sf("data/watercourse_segments") -->
+<!-- ``` -->
+
+Initialize GRASS project if non-existant:
+
+```{r eval=!grass_exists}
+initGRASS(gisBase = link2GI::findGRASS()[1, 1],
+          home = tempdir(),
+          gisDbase = datapath, location = grass_location, 
+          mapset = "PERMANENT", override = TRUE)
+execGRASS("g.proj", flags = c("c", "quiet"), 
+          georef = file.path(datapath, "watercourse_segments"))
+b_box <- st_bbox(watercourse_segments)
+execGRASS("g.region", flags = c("quiet"), 
+          n = as.character(b_box["ymax"]), s = as.character(b_box["ymin"]), 
+          e = as.character(b_box["xmax"]), w = as.character(b_box["xmin"]), 
+          res = "1")
+use_sf()
+```
+
+Add `watercourse_segments` data source to GRASS:
+
+```{r eval=!grass_exists}
+execGRASS("v.in.ogr",
+          input = file.path(datapath, "watercourse_segments"),
+          output = "watercourse_segments")
+```
+
+### Generate `watercourse_100mseg` in GRASS
+
+```{r eval=!grass_exists}
+execGRASS("v.split",
+          flags = c("f", "overwrite"),
+          input = "watercourse_segments",
+          output = "watercourse_100mseg",
+          length = 100)
+```
+
+```{r eval=!grass_exists}
+system("v.category input=watercourse_100mseg option=report")
+```
+
+
+
+### Generate `watercourse_100msegpoints` in GRASS
+
+```{r eval=!grass_exists}
+execGRASS("v.to.points",
+          flags = c("overwrite"),
+          input = "watercourse_100mseg",
+          output = "watercourse_100msegpoints",
+          use = "end")
+```
+
+# Checks on the data source
+

src/generate_watercourse_100mseg/99_sessioninfo.Rmd

@@ -0,0 +1,22 @@
+# Used environment
+
+```{r session-info, results = "asis", echo=FALSE}
+si <- devtools::session_info()
+p <- si$platform %>%
+  do.call(what = "c")
+if ("sf" %in% si$packages$package) p <- c(p, sf_extSoftVersion())
+if ("rgrass7" %in% si$packages$package) {
+  p <- c(p, GRASS = link2GI::findGRASS()[1, "version"])
+}
+sprintf("- **%s**:\n %s\n", names(p), p) %>%
+  cat()
+```
+
+```{r results = "asis", echo=FALSE}
+si$packages %>%
+    as_tibble %>%
+    select(package, loadedversion, date, source) %>%
+pander::pandoc.table(caption = "(\\#tab:sessioninfo)Loaded R packages",
+                     split.table = Inf)
+```
+

src/generate_watercourse_100mseg/_bookdown.yml

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+book_filename: "generating_watercourse_segments.Rmd"
+new_session: FALSE
+rmd_files: # specifies the order of Rmd files; NOT needed when you use index.Rmd and an alphabetical order for other Rmd files
+    # - index.Rmd

src/generate_watercourse_100mseg/generate_watercourse_100mseg.Rproj

@@ -0,0 +1,18 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: XeLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Website

src/generate_watercourse_100mseg/index.Rmd

@@ -0,0 +1,51 @@
+---
+title: "Generate watercourse segments"
+# subtitle: "x"
+date: "`r lubridate::now()`"
+link-citations: true
+linkcolor: link.colour
+citecolor: link.colour
+urlcolor: link.colour
+geometry: margin=1in
+mainfont: "Calibri"
+fontsize: 11pt
+documentclass: "article"
+# csl: ../inbo.csl
+# bibliography: ../references.bib
+site: bookdown::bookdown_site
+output:
+  bookdown::html_document2:
+    code_folding: show
+    keep_md: TRUE
+    number_sections: yes
+    fig_caption: yes
+    df_print: paged
+    toc: TRUE
+    toc_float:
+      collapsed: FALSE
+      smooth_scroll: FALSE
+    includes:
+        in_header: ../header.html
+---
+
+```{r setup, include=FALSE}
+library(sf)
+library(dplyr)
+library(knitr)
+library(rprojroot)
+library(ggplot2)
+library(rgrass7)
+opts_chunk$set(
+  echo = TRUE,
+  dpi = 300
+)
+library(mapview)
+mapviewOptions(fgb = FALSE)
+```
+
+**Note: this is a bookdown project, supposed to be run from within the `src/generate_watercourse_100mseg` subfolder. You can use the `generate_watercourse_100mseg.Rproj` RStudio project file in this subfolder to run it.**
+
+
+
+
+