---
title: "How to Use writeResults"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{writeResults}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

## Overview

This vignette outlines the use of the `writeResults()` function. 

`writeResults()` is a function to calculate coordinates and clustering results and write them to a CSV file outside the GUI.


## Input

There are 5 main types of inputs to the function. Of these the first 3 are necessary inputs: Data frames, settings and file name. There are also optional inputs that can be described by two types: space properties and coordinate functions.

#### Data frames

`cluster` is the clustering space and `linked` is the linked space. These should be two data frames with the same number of rows in each.

#### Settings

Settings are options from the GUI. Settings are passed as a named list in the form: `settings=list(k= , linkage= , metric= )`

| Settings | Description |
|:-----------|:---------------------------------------------|
| `k=`       | Numeric, number of clusters                  |
| `linkage=` | Linkage used by `stats::hclust`              |
| `metric=`  | Metric used by `getDists`                    |

#### File name

`filename` specifies the file name or connection to write to.

#### Coordinate functions

`getCoords.space1` and `getCoords.space2` specify the coordinate functions for the clustering and linked space respectively. By default, `getCoords.space1` will be `normCoords()` and `getCoords.space2` will be `rawCoords()`. These can be specified to be other coordinate functions; see `vignette("get-coords")` for more information on coordinate functions.

#### Space properties

Each space can have a covariance matrix, inverse covariance matrix or reference point defined. These are used by some coordinate functions and will need to be provided if used.

## Output

`writeResults()` will write a CSV file to the provided file name.
The first columns of the CSV will be linked space coordinates, then the clustering space coordinates. 
**clstr** will be an integer giving the clustering assignment of each point.
**BM** identifies the benchmarks of each cluster, where 0 means the point is not a benchmark and 1 means the point is a benchmark.

The typical output of is as follows for the bikes data:

```
A1,A2,A3,A4,A5,A6,A7,A8,yr,temp,weathersit,atemp,hum,windspeed,clstr,BM
0.953,1.200,1.649,0.473,-0.593,-0.891,-0.910,1.887,0,0.344,2,0.363,0.805,0.160,1,0
0.700,-0.606,0.800,0.619,-0.593,-0.891,-0.910,1.080,0,0.363,2,0.353,0.696,0.248,3,0
-0.621,-0.771,-0.696,2.530,-0.593,-0.891,-0.910,-0.605,0,0.196,1,0.189,0.437,0.248,3,0
-0.621,-0.189,-0.696,2.18,-0.593,-0.891,-0.910,-0.3606,0,0.2,1,0.212,0.590,0.160,3,0

```


