FRBCesab · Rekyt · Apr 12, 2024 · Apr 12, 2024 · Apr 15, 2024 · Apr 15, 2024
diff --git a/README.Rmd b/README.Rmd
@@ -26,28 +26,24 @@ pkgload::load_all()
 [![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
 <!-- badges: end -->
 
-
-
-<p align="left">
-  • <a href="#overview">Overview</a><br>
-  • <a href="#features">Features</a><br>
-  • <a href="#installation">Installation</a><br>
-  • <a href="#first-steps">First steps</a><br>
-  • <a href="#long-form-documentations">Long-form documentations</a><br>
-  • <a href="#citation">Citation</a><br>
-  • <a href="#contributing">Contributing</a><br>
-  • <a href="#acknowledgments">Acknowledgments</a><br>
-  • <a href="#references">References</a>
-</p>
-
+- [Overview](#overview)
+- [Features](#features)
+- [Installation](#installation)
+- [First steps](#first-steps)
+- [Long-form documentation (=vignettes)](#long-documentation)
+- [Citation](#citation)
+- [Contributing](#contributing)
+- [Acknowledgments](#acknowledgments)
+- [References](#references)
 
 
 ## Overview
 
-The package `funbiogeo` aims to help users with analyses in functional biogeography (Violle _et al._ 2014) by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.
-
+The package `funbiogeo` aims to help users with analyses in functional biogeography ([Violle _et al._ 2014](#references)), the biogeography of species' traits, by loading and combining data, computing trait coverage, drawing maps, correlating them with the environment, and upscaling assemblages.
 It is aimed at first-timers of functional biogeography as well as more experienced users who want to obtain quick and easy exploratory plots.
 
+Below is a quick introduction to the main features of `funbiogeo`, if you want some more details about them, check [our vignettes](#long-form-documentation).
+
 
 
 ## Features
@@ -59,7 +55,7 @@ It is aimed at first-timers of functional biogeography as well as more experienc
 * Extensive documentation (multiple vignettes, well-documented functions,
   real-life example dataset) to guide you through functional biogeography
   analyses,
-* Nice default plotting functions using outputs from functional diversity
+* Nice default plotting functions fully compatible with the outputs of functional diversity
   packages (`betapart`, `fundiversity`, `hillR`, `mFD`, etc.),
 * Automated standardized report that provide analyses and plots of your data,
 * Functions to easily "upscale" your data to coarser spatial resolutions.
@@ -82,7 +78,7 @@ remotes::install_github("FRBCesab/funbiogeo")
 
 This section will show you some useful functions from `funbiogeo`. For a longer introduction please refer to the ["Get started" vignette](https://frbcesab.github.io/funbiogeo/).
 
-The package contains default example data named `species_traits`, `site_species`, and `site_locations`. You can for example visualize to completeness of your trait dataset using the `fb_plot_species_traits_completeness()` function:
+The package contains default example data named `species_traits`, `site_species`, and `site_locations`. You can for example visualize to completeness of your trait dataset (which traits are known for which proportion of species) using the `fb_plot_species_traits_completeness()` function:
 
 ```{r plot-sp-tr-complete}
 fb_plot_species_traits_completeness(species_traits)
@@ -98,26 +94,27 @@ See more features of `funbiogeo` in the [vignettes of the package](https://frbce
 
 
 
-## Long-form documentations
+## Long-form documentation
 
 `funbiogeo` provides four vignettes to explain its functioning:
 
 * A ["Get started" vignette](https://frbcesab.github.io/funbiogeo/articles/funbiogeo.html)
   that describes its core features and guide you through a typical analysis.
-* A [vignette on all diagnostic plots](https://frbcesab.github.io/funbiogeo/articles/diagnostic-plots.html)
+* A vignette on [all diagnostic plots](https://frbcesab.github.io/funbiogeo/articles/diagnostic-plots.html)
   provided in the package, which details how to use each plotting function and
   how to interpret their output.
-* A [vignette on formatting your data](https://frbcesab.github.io/funbiogeo/articles/long-format.html)
-  to the needs of `funbiogeo`, which shows you the use of specific functions.
-* And a [specific vignette on upscaling](https://frbcesab.github.io/funbiogeo/articles/upscaling.html)
-  which explains how to aggregate automatically your data to coarser grain and
-  use it in further analyses.
+* A vignette on [the data format](https://frbcesab.github.io/funbiogeo/articles/long-format.html)
+  that `funbiogeo` needs, which shows you the use of specific functions to format your data to work well within `funbiogeo`.
+* A vignette on [data upscaling](https://frbcesab.github.io/funbiogeo/articles/upscaling.html)
+  which explains how to leverage `funbiogeo` to aggregate automatically your data to coarser grain and
+  use them in further analyses.
 
 
 
 ## Citation
 
-For the moment `funbiogeo` doesn't offer a companion paper. But if you happen to use it in your paper you can cite the package through:
+For the moment `funbiogeo` doesn't offer a companion paper nor is it on CRAN.
+But if you happen to use it in your paper you can cite the package through:
 
 > Casajus N & Grenié M (2024). _funbiogeo: Functional Biogeography Analyses_. R package version 0.0.0.9000, <https://github.com/frbcesab/funbiogeo>.
 
@@ -131,7 +128,8 @@ citation("funbiogeo")
 
 ## Contributing
 
-All types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/FRBCesab/funbiogeo/blob/main/CONTRIBUTING.md).
+All types of contributions are encouraged and valued.
+For more information, check out our [Contributor Guidelines](https://github.com/FRBCesab/funbiogeo/blob/main/CONTRIBUTING.md).
 
 Please note that the `funbiogeo` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
 

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# funbiogeo <img src="man/figures/logo.png" align="right" style="float:right; height:120px;"/>
+# funbiogeo - Streamlining functional biogeography analyses <img src="man/figures/logo.png" align="right" style="float:right; height:120px;"/>
 
 <!-- badges: start -->
 
@@ -13,28 +13,29 @@ status](https://www.r-pkg.org/badges/version/funbiogeo)](https://CRAN.R-project.
 v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
 <!-- badges: end -->
 
-<p align="left">
-• <a href="#overview">Overview</a><br> •
-<a href="#features">Features</a><br> •
-<a href="#installation">Installation</a><br> •
-<a href="#first-steps">First steps</a><br> •
-<a href="#long-form-documentations">Long-form documentations</a><br> •
-<a href="#citation">Citation</a><br> •
-<a href="#contributing">Contributing</a><br> •
-<a href="#acknowledgments">Acknowledgments</a><br> •
-<a href="#references">References</a>
-</p>
+- [Overview](#overview)
+- [Features](#features)
+- [Installation](#installation)
+- [First steps](#first-steps)
+- [Long-form documentation (=vignettes)](#long-documentation)
+- [Citation](#citation)
+- [Contributing](#contributing)
+- [Acknowledgments](#acknowledgments)
+- [References](#references)
 
 ## Overview
 
 The package `funbiogeo` aims to help users with analyses in functional
-biogeography (Violle *et al.* 2014) by loading and combining data,
-computing trait coverage, as well as computing functional diversity
-indices, drawing maps, correlating them with the environment, and
-upscaling assemblages.
+biogeography ([Violle *et al.* 2014](#references)), the biogeography of
+species’ traits, by loading and combining data, computing trait
+coverage, drawing maps, correlating them with the environment, and
+upscaling assemblages. It is aimed at first-timers of functional
+biogeography as well as more experienced users who want to obtain quick
+and easy exploratory plots.
 
-It is aimed at first-timers of functional biogeography as well as more
-experienced users who want to obtain quick and easy exploratory plots.
+Below is a quick introduction to the main features of `funbiogeo`, if
+you want some more details about them, check [our
+vignettes](#long-form-documentation).
 
 ## Features
 
@@ -47,8 +48,9 @@ experienced users who want to obtain quick and easy exploratory plots.
 - Extensive documentation (multiple vignettes, well-documented
   functions, real-life example dataset) to guide you through functional
   biogeography analyses,
-- Nice default plotting functions using outputs from functional
-  diversity packages (`betapart`, `fundiversity`, `hillR`, `mFD`, etc.),
+- Nice default plotting functions fully compatible with the outputs of
+  functional diversity packages (`betapart`, `fundiversity`, `hillR`,
+  `mFD`, etc.),
 - Automated standardized report that provide analyses and plots of your
   data,
 - Functions to easily “upscale” your data to coarser spatial
@@ -72,8 +74,9 @@ vignette](https://frbcesab.github.io/funbiogeo/).
 
 The package contains default example data named `species_traits`,
 `site_species`, and `site_locations`. You can for example visualize to
-completeness of your trait dataset using the
-`fb_plot_species_traits_completeness()` function:
+completeness of your trait dataset (which traits are known for which
+proportion of species) using the `fb_plot_species_traits_completeness()`
+function:
 
 ``` r
 fb_plot_species_traits_completeness(species_traits)
@@ -94,31 +97,32 @@ fb_map_site_traits_completeness(site_locations, site_species, species_traits)
 See more features of `funbiogeo` in the [vignettes of the
 package](https://frbcesab.github.io/funbiogeo/articles/)
 
-## Long-form documentations
+## Long-form documentation
 
 `funbiogeo` provides four vignettes to explain its functioning:
 
 - A [“Get started”
   vignette](https://frbcesab.github.io/funbiogeo/articles/funbiogeo.html)
   that describes its core features and guide you through a typical
   analysis.
-- A [vignette on all diagnostic
+- A vignette on [all diagnostic
   plots](https://frbcesab.github.io/funbiogeo/articles/diagnostic-plots.html)
   provided in the package, which details how to use each plotting
   function and how to interpret their output.
-- A [vignette on formatting your
-  data](https://frbcesab.github.io/funbiogeo/articles/long-format.html)
-  to the needs of `funbiogeo`, which shows you the use of specific
-  functions.
-- And a [specific vignette on
+- A vignette on [the data
+  format](https://frbcesab.github.io/funbiogeo/articles/long-format.html)
+  that `funbiogeo` needs, which shows you the use of specific functions
+  to format your data to work well within `funbiogeo`.
+- A vignette on [data
   upscaling](https://frbcesab.github.io/funbiogeo/articles/upscaling.html)
-  which explains how to aggregate automatically your data to coarser
-  grain and use it in further analyses.
+  which explains how to leverage `funbiogeo` to aggregate automatically
+  your data to coarser grain and use them in further analyses.
 
 ## Citation
 
-For the moment `funbiogeo` doesn’t offer a companion paper. But if you
-happen to use it in your paper you can cite the package through:
+For the moment `funbiogeo` doesn’t offer a companion paper nor is it on
+CRAN. But if you happen to use it in your paper you can cite the package
+through:
 
 > Casajus N & Grenié M (2024). *funbiogeo: Functional Biogeography
 > Analyses*. R package version 0.0.0.9000,

diff --git a/man/figures/README-plot-sp-tr-complete-1.png b/man/figures/README-plot-sp-tr-complete-1.png
diff --git a/man/rmdchunks/_table-plot-functions.Rmd b/man/rmdchunks/_table-plot-functions.Rmd
@@ -1,15 +1,15 @@
-| Function name                                | Site x species | Species x traits | Site x locations | Species category | Additional input |
-| :------------------------------------------- |:-------------: | :--------------: | :--------------: | :--------------: | :--------------: |
-| `fb_plot_distribution_site_trait_coverage()` |        ✅       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_plot_number_sites_by_species()`          |        ✅       |        ❌         |        ❌         |         ❌        |         ❌        |
-| `fb_plot_number_species_by_trait()`          |        ❌       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_plot_number_traits_by_species()`         |        ❌       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_plot_site_environment()`                 |        ❌       |        ❌         |        ✅         |         ❌        |         ✅        |
-| `fb_plot_site_traits_completeness()`         |        ✅       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_plot_species_traits_completeness()`      |        ❌       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_plot_species_traits_missingness()`       |        ❌       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_plot_trait_combination_frequencies()`    |        ❌       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_plot_trait_correlation()`                |        ❌       |        ✅         |        ❌         |         ✅        |         ❌        |
-| `fb_map_raster()`                            |        ❌       |        ❌         |        ❌         |         ❌        |         ✅        |
-| `fb_map_site_data()`                         |        ❌       |        ❌         |        ✅         |         ❌        |         ✅        |
-| `fb_map_site_traits_completeness()`          |        ✅       |        ✅         |        ✅         |         ❌        |         ❌        |
+| Function name                                | Site<br>x<br>species | Species<br>x<br>traits | Site<br>x<br>locations | Species category | Additional input |
+| :------------------------------------------- | :--------------: | :----------------: | :----------------: | :--------------: | :--------------: |
+| `fb_plot_distribution_site_trait_coverage()` |         ✳️       |         ✳️         |         ➖         |          🟠       |         ➖        |
+| `fb_plot_number_sites_by_species()`          |         ✳️       |         ➖         |         ➖         |         ➖        |         ➖        |
+| `fb_plot_number_species_by_trait()`          |         ➖       |         ✳️         |         ➖         |         🟠        |         ➖        |
+| `fb_plot_number_traits_by_species()`         |         ➖       |         ✳️         |         ➖         |         🟠        |         ➖        |
+| `fb_plot_site_environment()`                 |         ➖       |         ➖         |         ✳️         |         ➖        |         ✳️        |
+| `fb_plot_site_traits_completeness()`         |         ✳️       |         ✳️         |         ➖         |         🟠️        |         ➖        |
+| `fb_plot_species_traits_completeness()`      |         ➖       |         ✳️         |         ➖         |         🟠        |         ➖        |
+| `fb_plot_species_traits_missingness()`       |         ➖       |         ✳️         |         ➖         |         🟠        |         ➖        |
+| `fb_plot_trait_combination_frequencies()`    |         ➖       |         ✳️         |         ➖         |         🟠        |         ➖        |
+| `fb_plot_trait_correlation()`                |         ➖       |         ✳️         |         ➖         |         🟠        |         ➖        |
+| `fb_map_raster()`                            |         ➖       |         ➖         |         ➖         |         ➖        |         ✳️        |
+| `fb_map_site_data()`                         |         ➖       |         ➖         |         ✳️         |         ➖        |         ✳️        |
+| `fb_map_site_traits_completeness()`          |         ✳️       |         ✳️         |         ✳️         |         ➖        |         ➖        |
diff --git a/vignettes/diagnostic-plots.Rmd b/vignettes/diagnostic-plots.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "Diagnostic Plots in funbiogeo"
+title: "Diagnostic plots in funbiogeo"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Diagnostic Plots in funbiogeo}
+  %\VignetteIndexEntry{Diagnostic plots in funbiogeo}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -28,9 +28,8 @@ displaying information by each category of species (family, order, endemism stat
 ```{r child="../man/rmdchunks/_table-plot-functions.Rmd"}
 ```
 
-Table: A table of available plotting functions in `funbiogeo` ordered
-alphabetically with their required arguments. The "Additional input" column
-reflects the need for other argument that are not of the standard object type.
+Table: required ✳️; optional 🟠; absent ➖<br>
+"Additional input" means other types of arguments
 
 Let's first load the package and example datasets included in the `funbiogeo`.
 
@@ -314,9 +313,6 @@ The plot displays the number of species with known and missing traits. It shows
 each trait in separate line as a proportional bar chart with the total numbers
 included within each bar.
 
-~~Here we see that 53 species have all of their traits known while 96 don't.
-Adult body mass is known for 123 species and missing for 26.~~
-
 
 ### Displaying traits combinations