---
title: "Plotting nomenclatural changes"
output: rmarkdown::html_vignette
resource_files:
    - cumulative_discovery_Luetzelburgia.png
vignette: >
  %\VignetteIndexEntry{Plotting nomenclatural changes}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{css, echo=FALSE}
p.caption {
  font-size: 0.8em;
}
.table{
  width: auto;
  font-size: 14px;
}
.table caption {
  font-size: 1em;
}
```

Information concerning the year of publication of a species and its current status, obtained from the taxonomically validated [Plants of the World Online (POWO)](https://powo.science.kew.org/) database, can offer valuable insights into temporal trends related to changes in species nomenclature.\

Employing the World Checklist of Vascular Plants (WCVP) accessible via RBG Kew’s 
Plants of the World Online (POWO) database entails a thorough examination of type specimens, representative herbarium material, protologues, and other pertinent literature housed in the herbariums, some of which required detailed systematic study.\

In the pursuit of advancing this knowledge, our objective was to automatically generate graphics that delineate the resolution of nomenclatural issues, the creation of new combinations and new
names proposed over time. Additionally, the graphics also should depict validated names of taxa.\

In this article, we illustrate the utilization of the package's `accGraph` function for automatically generate graphics that showcase the nomenclatural changes over time. This versatile function is capable of producing two distinct types of graphics: one depicting the accumulation of formally described species within each genus or family, and the other illustrating changes in species nomenclature over time. The second type of graphic (focus of this article) allows for the comparison of variations in the data, accommodating multimodal distributions, such as those with multiple peaks representing years characterized by numerous changes in nomenclature.\

To employ this function effectively, it is necessary to have data stored in a spreadsheet or dataset generated using the `powoSpecies` function with the `synonyms` argument set to TRUE.
\

## Setup

Install the latest developmental version of __expowo__ from 
[GitHub](https://github.com/):

``` r
#install.packages("devtools")
devtools::install_github("DBOSlab/expowo")
```
```{r package load, message=FALSE, warning=FALSE}
library(expowo)
```

\

## 1. Plotting nomenclatural changes for the entire dataset

If your dataset comprises species from multiple genera, the `accGraph` function has the capability to automatically generate a graphical representation illustrating historical changes in species nomenclature using the data from those genera.

In this example, it is noteworthy that the parameter `spp_acc` is set as TRUE. It is because the argument `spp_acc` will define the creation of the second type of graphic that depicts nomenclatural changes over time. The dynamics of nomenclatural changes are visually represented through the varying densities of curves and circles between the publication years. Currently accepted names are depicted in gray, and their size is proportionally scaled to the associated homotypic or heterotypic synonyms (in yellow) that were published. 

First, to get the graphic, we extracted all data of the genera _Achillea_, _Matricaria_ and _Launaea_ from Plants of the World Online using `powoSpecies` as follows:

```{r, eval = FALSE}
newdata <- powoSpecies(family = "Asteraceae",
                       genus = c("Achillea", "Matricaria", "Launaea"),
                       synonyms = TRUE,
                       save = FALSE,
                       dir = "Asteraceae_results",
                       filename = "Asteraceae_spp")
```

Then, we used the newly developed function `accGraph` to plot a violin graph for 
the three genera within Asteraceae.


```{r, eval = FALSE}
accGraph(inputdf = newdata,
         verbose = TRUE,
         spp_acc = FALSE,
         spp_changes = TRUE,
         spp_changes_col = "genus",
         genus_plots = TRUE,
         save = TRUE,
         dir = "results_accGraph",
         filename = "cumulative_discovery_Asteraceae_",
         format = "jpg")
```
\

```{r, echo = FALSE, out.width = "600px", fig.cap = "FIGURE 1. The temporal dynamics of nomenclatural changes in three genera."}
knitr::include_graphics("figures/cumulative_discovery_Asteraceae_all_data.png", 
                        dpi = 300)
```

\
