# How to Use writeResults

## 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