docs + vignettes

cneyens · Jul 18, 2024 · a6d8038 · a6d8038
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: raem
 Title: Analytic Element Modeling of Steady Single-Layer Groundwater Flow
 Version: 0.0.0.9000
 Authors@R: 
-    person("Cas", "Neyens", , "[email protected]", role = c("aut", "cre"))
+    person("Cas", "Neyens", , "[email protected]", role = c("aut", "cre", "cph"))
 Description: Analytic element modeling of steady-state single-layer
     groundwater flow under the Dupuit-Forchheimer assumption. Elements
     such as wells, area-sinks and line-sinks can be placed at arbitrary 

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2024
 COPYRIGHT HOLDER: raem authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2023 raem authors
+Copyright (c) 2024 raem authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.Rmd b/README.Rmd
@@ -4,7 +4,7 @@ output: github_document
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-```{r, include = FALSE}
+```{r knitr-setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
@@ -76,11 +76,10 @@ Find the head and discharge at two locations: `x = -200, y = 200` and `x = 100,
 
 ```{r find-head}
 heads(m, x = c(-200, 100), y = 200)
-
 discharge(m, c(-200, 100), 200, z = top) # m^2/d
 ```
 
-Plot head contours and element locations. First, specify the contouring grid:
+Plot the head contours and element locations. First, specify the contouring grid:
 
 ```{r set-grid}
 xg = seq(-500, 500, length = 100)
@@ -97,7 +96,12 @@ plot(m, add = TRUE)
 Compute particle traces starting along `y = 200` at 20 intervals per year for 5 years and add to the plot:
 
 ```{r plot-traces, dpi = 300}
-paths = tracelines(m, x0 = seq(-450, 450, 50), y0 = 200, z0 = top, times = seq(0, 5 * 365, 365 / 20))
+paths = tracelines(m, 
+                   x0 = seq(-450, 450, 50), 
+                   y0 = 200, 
+                   z0 = top, 
+                   times = seq(0, 5 * 365, 365 / 20))
+
 plot(paths, add = TRUE, col = 'orange')
 ```
 

diff --git a/README.md b/README.md
@@ -73,15 +73,14 @@ heads(m, x = c(-200, 100), y = 200)
 ```
 
 ``` r
-
 discharge(m, c(-200, 100), 200, z = top) # m^2/d
 #>              Qx         Qy Qz
 #> [1,] 0.15028815 -0.2923908  0
 #> [2,] 0.06041242 -0.3347206  0
 ```
 
-Plot head contours and element locations. First, specify the contouring
-grid:
+Plot the head contours and element locations. First, specify the
+contouring grid:
 
 ``` r
 xg = seq(-500, 500, length = 100)
@@ -101,7 +100,12 @@ Compute particle traces starting along `y = 200` at 20 intervals per
 year for 5 years and add to the plot:
 
 ``` r
-paths = tracelines(m, x0 = seq(-450, 450, 50), y0 = 200, z0 = top, times = seq(0, 5 * 365, 365 / 20))
+paths = tracelines(m, 
+                   x0 = seq(-450, 450, 50), 
+                   y0 = 200, 
+                   z0 = top, 
+                   times = seq(0, 5 * 365, 365 / 20))
+
 plot(paths, add = TRUE, col = 'orange')
 ```
 

diff --git a/vignettes/vign-01-overview.Rmd b/vignettes/vign-01-overview.Rmd
diff --git a/vignettes/vign-02-export-spatial.Rmd b/vignettes/vign-02-export-spatial.Rmd
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-`raem` does not contain functions to export output to spatial data formats such as vector data or rasters. This vignette describes a way to create spatial data from `raem` output in R using other packages.
+`raem` does not contain functions to export output to spatial data formats such as vector data or rasters. Other R packages do have this functionality however. This vignette describes a way to create spatial data from `raem` output using other, well-established, packages.
 
 # Create an example AEM model
 
@@ -88,7 +88,7 @@ plot(isolines_sf)
 
 ```
 
-To export the `sf` object to disk, the `sf` package provides the `write_sf()`:
+To export the `sf` object to disk, the `sf` package provides the `write_sf()` function:
 
 ```{r export-shapefile, eval = FALSE}
 # export as shapefile
@@ -97,7 +97,7 @@ write_sf(isolines_sf, 'isolines.shp')
 
 # Exporting as spatial raster
 
-To create and export output as a spatial raster object such as a GeoTIFF, the [terra](https://rspatial.github.io/terra/) can be used. This package is the replacement of the older, widely popular [raster](https://github.com/rspatial/raster) package. Similar to the creation of a spatial vector object, a grid of values for the variable of interest (here hydraulic head) needs to be specified. Optionally, the origin coordinates can be given to georeference the output. The extent of the raster needs to be specified explicitly from the range of the marginal grid vectors.
+To create and export output as a spatial raster object such as a GeoTIFF, the [terra](https://rspatial.github.io/terra/) package can be used. This package is the replacement of the older, widely popular [raster](https://github.com/rspatial/raster) package. Similar to the creation of a spatial vector object, a grid of values for the variable of interest (here hydraulic head) needs to be specified. Optionally, the origin coordinates can be given to georeference the output. The extent of the raster needs to be specified explicitly from the range of the marginal grid vectors.
 
 ```{r terra, message = FALSE}
 library(terra)