---
title: "Example : Minimal"
output:
   rmarkdown::html_vignette:
     tabset: true
bibliography: references.bib
vignette: >
  %\VignetteIndexEntry{The phytoclass package}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

This vignette outlines the simplest possible usage of phytoclass's simulated annealing.

# Preparing the S Matrix
To run phytoclass you must prepare a sample matrix (aka the `S matrix`).
For this we recommend creating a comma-separated-value (`.csv`) file.
Several example files are included in the [`./vignettes/` directory of the phytoclass source code](https://github.com/phytoclass/phytoclass/tree/main/vignettes). 
`.csv` files can be created in any plain text editor.
Below is an example S-matrix `.csv` file content:

```
"","Per","X19but","Fuco","Neox","Pra","Viol","X19hex","Allo","Zea","Lut","ChlcMGDG18","ChlcMGDG14","Chl_b","Tchla"
"1",0,0.03024,0.06225,0.00557,0.01407,0.00759,0.08224,0.00188,0.00201,0,0,0,0.08661,0.45851
"2",0,0.01084,0.02864,0.00111,0.00351,0.00144,0.01497,0.00144,0.00191,0,0,0,0.01473,0.14571
"3",0,0.0156,0.2172,0.0064,0.0092,0,0.0174,0.0058,0.0036,0,0,0,0.057,0.6127
"4",0,0.0177,0.2347,0.007,0.0115,0,0.0189,0.0054,0.0038,0,0,0,0.0619,0.6207
"5",0,0.0252,0.2952,0.0099,0.013,0,0.0211,0.0014,0.0076,0,0,0,0.0578,0.5302
"6",0.0102,0.0222,0.2275,0.0076,0.0107,0,0.019,0,0.003,0,0,0,0.0453,0.4057
"7",0,0.0151,0.1417,0.004,0.008,0.0026,0.0255,8e-04,0.001,0,0,0,0.0312,0.2117
"8",0,0.0452,0.4484,0.0037,0.0065,0,0.1317,0.0044,0.0023,0,0,0,0.0093,0.6885
"9",0,0.0518,0.6228,0.0049,0.0075,0.004,0.1321,0.0597,0.0035,0,0,0,0.0121,1.0849
"10",0,0.022,0.109,0.004,0.008,0.003,0.042,0.003,0.003,0,0,0,0.032,0.206
"11",0,0.049062693,0.526641835,0.017334346,0.034463572,0,0.120442872,0.029990012,0.039966194,0,0,0,0.153250497,1.039660729
"12",0,0.020526621,0.271493439,0.017692288,0.019947584,0,0.030115477,0,0.030828916,0,0,0,0.09243326,0.481204323
"13",0,0.022161768,0.165425707,0.012242414,0.019562855,0,0.027210489,0,0.017661542,0,0,0,0.087205952,0.340907892
"14",0,0.014385454,0.255559406,0.020671983,0.047363662,0.011507712,0.021676506,0.009032764,0.018938989,0,0,0,0.142134419,0.489290176
```

This example includes only 14 samples (rows), with the pigment concentration of each sample included on each row.
14 is the minumum number of rows required to apply simulated annealing.
The first row includes the names for each pigment.
These **pigment abbreviations must match exactly** to the pigments in the F-matrix. For this example we are using the default `phytoclass:Fm` F matrix, and the column names in the example above should be used.

> NOTE: Instead of using a plain text editor, `.csv` files can also be created using a spreadsheet editor (MS Excel, Google Docs, LibreOffice Calc, etc.) by using "save as" or "export" to `.csv`.

# Simulated Annealing
To run the simulated annealing call the function with your S matrix passed as the only argument.
```{R}
#| eval: false
# load the sample matrix from a file
S_matrix <- read.csv("vignettes/custom-example-S.csv")

# run simulated annealing 
results <- phytoclass::simulated_annealing(S_matrix)
```

# Viewing Results
Results of the simulated annealing run are in the `results` object returned by the function.

```{R}
#| eval: false
results$`condition number`
results$RMSE
results$MAE
results$Error
results$`Class abundances`
results$Figure
```