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 +47,53 @@ 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 R-build-toolchain {#install-rbuild-chain}
+
+This package contains C++ code. As it is distributed as source-code, users will require the appropriate R-build-toolchain for their respective operating system. For further information and setup-instructions, refer to "<https://r-pkgs.org/setup.html#setup-tools>".
+
+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)
+```
+
+###  {data-link="Installation-steps"}
+
 ## 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 +57,26 @@ R-package `devtools`:
 install.packages("devtools")
 ```
 
+#### Install R-build-toolchain
+
+This package contains C++ code. As it is distributed as source-code,
+users will require the appropriate R-build-toolchain for their
+respective operating system. For further information and
+setup-instructions, refer to
+“<https://r-pkgs.org/setup.html#setup-tools>”.
+
+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 +91,27 @@ 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 \[cm^2\].