Merge branch 'feat/fix-issue-#33' into dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: duflor
 Title: Plant Image Analysis For Determination of Leaf- and Root-Area 
-Version: 0.0.1.9026
+Version: 0.0.1.9027
 Author: Claudius Appel
 Authors@R: c(
     person("Claudius", "Appel", email =   "claudius.appel@freenet.de" , role = c("aut", "cre"))

README.Rmd

@@ -13,18 +13,18 @@ knitr::opts_chunk$set(
 )
 ```
 
-# duflor <a href="https://github.com/Claudius-Appel/duflor/"><img src="man/figures/logo.png" align="right" height="139" alt="duflor website" /></a>
+# duflor <a href="https://github.com/Claudius-Appel/duflor/"><img src="man/figures/logo.png" alt="duflor website" align="right" height="139"/></a>
 
 <!-- badges: start -->
-[![R-CMD-check: Dev](https://github.com/Claudius-Appel/duflor/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/Claudius-Appel/duflor/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/Claudius-Appel/duflor/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Claudius-Appel/duflor?branch=master)
+
+[![R-CMD-check: Dev](https://github.com/Claudius-Appel/duflor/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/Claudius-Appel/duflor/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/Claudius-Appel/duflor/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Claudius-Appel/duflor?branch=master)
+
 <!-- badges: end -->
 
 ## Overview
 
 Duflor is a package to detect and quantify number of pixels in any subrange(s) of HSV-color space declared by an upper and lower bound. While the package is principally task-agnostic and could work on any sort of HSV-range(s), it is developed for the detection and quantification of plant area.
 
-
 ## Installation
 
 You can install the development and release versions of `duflor` like so:
@@ -47,41 +47,52 @@ devtools::install_github("https://github.com/Claudius-Appel/duflor@dev"
 
 Vignettes are rendered documents discussing specific topics within a package. Installing them is recommended, but not required for utilising the package itself.
 
+**If the front-end shiny-application within the `duflor_gui`-package is to be used, it is strongly recommended to follow the installation-guide for that package instead.**
+
 ### Prerequisites
 
 Installing this package from GitHub requires the installation of the R-package `devtools`:
 
-``` r 
+``` r
 install.packages("devtools")
 ```
 
+#### Install Rtools (windows-only) {#install-rtools-windows-only}
+
+On windows, Rtools must be installed for your respective R-Version in order to compile this package from source (as it contains `cpp`-code). For more information, refer to "<https://r-pkgs.org/setup.html#setup-tools>".
+
+If you are not on windows, you can skip this step. There are certain scenarios in which you will be unable to build packages from source on MacOS and linux machines as well. In these cases, refer to the documentation provided for the respective platform in the link above.
+
+For windows, the R-package `installr` may be used to check if Rtools is already installed, and whether or not it has been found by R. Additionally, it will notify the user if a new R-update is available (major and minor versions only, ignores patch versions):
+
+``` r
+install.packages("installr") # once pkgbuild is installed, run: installr::install.Rtools(check = T,check_r_update = T,GUI = T)
+```
+
 ## Usage
 
-For detailed documentation, refer to https://claudius-appel.github.io/duflor/
+For detailed documentation, refer to <https://claudius-appel.github.io/duflor/>
 
 Additionally, various topics have more detailed articles, accessible on the aforementioned website, as well as within R via `browseVignettes()`. While access from within R is possible, it is generally recommended to view the articles via the website.
 
 ### A small sidenote on options set by duflor:
 
+Upon loading, duflor will set the following options via `options(XX)`:
 
-Upon loading, duflor will set the following options via `options(XX)`: 
+-   `duflor.default_hsv_spectrums`: default HSV-ranges for
+    -   drought leaf-area
+    -   green leaf-area
+    -   complete leaf-area
+    -   identifier area
+-   `duflor.default_identifier_area`: the size of the `identifier_dot` in [cm\^2].
 
-- duflor.default_hsv_spectrums: default HSV-ranges for
-    - drought leaf-area
-    - green leaf-area
-    - complete leaf-area
-    - identifier area
-- duflor.default_identifier_area: the size of the `identifier_dot` in [cm^2].
+Their values can be retrieved via `getOption(option)`:
 
-Their values can be retrieved via `getOption(option)`.
 ``` r
 getOption("duflor.default_hsv_spectrums")
 getOption("duflor.default_identifier_area")
 ```
 
-`duflor.default_hsv_spectrums` is merely used as a shortcut to load the currently-set default hsv ranges. It is not intended to be modified; as it serves no internal use.
-`duflor.default_identifier_area` is more likely to require modification. Before calculating the area for each spectrum via  `duflor::pixels_to_area(pixel.counts)`, the true area of the identifier-dot must be set via this option. The default is set to `r 0.503`. All areas are assumed to be in [cm^2].
-
+-   `duflor.default_hsv_spectrums` is merely used as a shortcut to load the currently-set default hsv ranges. It is not intended to be modified; as it serves no internal use.
 
-## Further Documentation
-TODO
+-   `duflor.default_identifier_area` is more likely to require modification. Before calculating the area for each spectrum via `duflor::pixels_to_area(pixel.counts)`, the true area of the identifier-dot must be set via this option. The default is set to `r 0.503`. All areas are assumed to be in [cm\^2].

README.md

@@ -1,13 +1,14 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# duflor <a href="https://github.com/Claudius-Appel/duflor/"><img src="man/figures/logo.png" align="right" height="139" alt="duflor website" /></a>
+# duflor <a href="https://github.com/Claudius-Appel/duflor/"><img src="man/figures/logo.png" alt="duflor website" align="right" height="139"/></a>
 
 <!-- badges: start -->
 
 [![R-CMD-check:
 Dev](https://github.com/Claudius-Appel/duflor/actions/workflows/R-CMD-check.yaml/badge.svg?branch=dev)](https://github.com/Claudius-Appel/duflor/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/Claudius-Appel/duflor/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Claudius-Appel/duflor?branch=master)
+
 <!-- badges: end -->
 
 ## Overview
@@ -43,6 +44,10 @@ Vignettes are rendered documents discussing specific topics within a
 package. Installing them is recommended, but not required for utilising
 the package itself.
 
+**If the front-end shiny-application within the `duflor_gui`-package is
+to be used, it is strongly recommended to follow the installation-guide
+for that package instead.**
+
 ### Prerequisites
 
 Installing this package from GitHub requires the installation of the
@@ -52,6 +57,27 @@ R-package `devtools`:
 install.packages("devtools")
 ```
 
+#### Install Rtools (windows-only)
+
+On windows, Rtools must be installed for your respective R-Version in
+order to compile this package from source (as it contains `cpp`-code).
+For more information, refer to
+“<https://r-pkgs.org/setup.html#setup-tools>”.
+
+If you are not on windows, you can skip this step. There are certain
+scenarios in which you will be unable to build packages from source on
+MacOS and linux machines as well. In these cases, refer to the
+documentation provided for the respective platform in the link above.
+
+For windows, the R-package `installr` may be used to check if Rtools is
+already installed, and whether or not it has been found by R.
+Additionally, it will notify the user if a new R-update is available
+(major and minor versions only, ignores patch versions):
+
+``` r
+install.packages("installr") # once pkgbuild is installed, run: installr::install.Rtools(check = T,check_r_update = T,GUI = T)
+```
+
 ## Usage
 
 For detailed documentation, refer to
@@ -66,29 +92,27 @@ view the articles via the website.
 
 Upon loading, duflor will set the following options via `options(XX)`:
 
-- duflor.default_hsv_spectrums: default HSV-ranges for
+- `duflor.default_hsv_spectrums`: default HSV-ranges for
   - drought leaf-area
   - green leaf-area
   - complete leaf-area
   - identifier area
-- duflor.default_identifier_area: the size of the `identifier_dot` in
+- `duflor.default_identifier_area`: the size of the `identifier_dot` in
   \[cm^2\].
 
-Their values can be retrieved via `getOption(option)`.
+Their values can be retrieved via `getOption(option)`:
 
 ``` r
 getOption("duflor.default_hsv_spectrums")
 getOption("duflor.default_identifier_area")
 ```
 
-`duflor.default_hsv_spectrums` is merely used as a shortcut to load the
-currently-set default hsv ranges. It is not intended to be modified; as
-it serves no internal use. `duflor.default_identifier_area` is more
-likely to require modification. Before calculating the area for each
-spectrum via `duflor::pixels_to_area(pixel.counts)`, the true area of
-the identifier-dot must be set via this option. The default is set to
-0.503. All areas are assumed to be in \[cm^2\].
-
-## Further Documentation
+- `duflor.default_hsv_spectrums` is merely used as a shortcut to load
+  the currently-set default hsv ranges. It is not intended to be
+  modified; as it serves no internal use.
 
-TODO
+- `duflor.default_identifier_area` is more likely to require
+  modification. Before calculating the area for each spectrum via
+  `duflor::pixels_to_area(pixel.counts)`, the true area of the
+  identifier-dot must be set via this option. The default is set to
+  0.503. All areas are assumed to be in \[cm^2\].