Classification: PLS-DA
library(mdatools)
library(kableExtra)
library(tidyverse)The dataset
This dataset is the result of an analysis carried out with an electronic tongue on 72 samples of wine of 6 different types (Pigani et al. 2008)
We have 72 obervations and 1950 variables
df = read.csv('dpv_lingua_vini_bianchi_cleaned.csv', check.names = F)
df = df[-c(1,3,4,5)]
kable(df[, 1:10], row.names = T) %>% kable_styling('striped', fixed_thead = T, full_width = FALSE) %>%
scroll_box( height = "500px")| Type | TR.TS | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Chardonnay Francia | TR | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 |
| 2 | Chardonnay Francia | TR | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 |
| 3 | Chardonnay Francia | TS | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 4 | Chardonnay Francia | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 5 | Chardonnay Francia | TR | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 |
| 6 | Chardonnay Francia | TS | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 7 | Chardonnay Francia | TR | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 |
| 8 | Chardonnay Francia | TR | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 9 | Chardonnay Francia | TS | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 |
| 10 | Chardonnay Francia | TR | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 11 | Chardonnay Francia | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 12 | Chardonnay Francia | TS | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 |
| 13 | Chardonnay Veneto | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 14 | Chardonnay Veneto | TR | 1.3e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 |
| 15 | Chardonnay Veneto | TS | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 16 | Chardonnay Veneto | TR | 8.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 |
| 17 | Chardonnay Veneto | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 18 | Chardonnay Veneto | TS | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 19 | Chardonnay Veneto | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 20 | Chardonnay Veneto | TR | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 21 | Chardonnay Veneto | TS | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 22 | Chardonnay Veneto | TR | 7.0e-07 | 7.0e-07 | 7.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 7.0e-07 |
| 23 | Chardonnay Veneto | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 24 | Chardonnay Veneto | TS | 9.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 25 | Chardonnay Puglia | TR | 9.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 26 | Chardonnay Puglia | TR | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 27 | Chardonnay Puglia | TS | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 28 | Chardonnay Puglia | TR | 1.0e-06 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 29 | Chardonnay Puglia | TR | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 30 | Chardonnay Puglia | TS | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 31 | Chardonnay Puglia | TR | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 8.0e-07 | 9.0e-07 | 8.0e-07 |
| 32 | Chardonnay Puglia | TR | 6.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 | 5.0e-07 |
| 33 | Chardonnay Puglia | TS | 1.0e-06 | 1.0e-06 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 34 | Chardonnay Puglia | TR | 8.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 |
| 35 | Chardonnay Puglia | TR | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 36 | Chardonnay Puglia | TS | 9.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 37 | Trebbiano Emilia | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 38 | Trebbiano Emilia | TR | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 39 | Trebbiano Emilia | TS | 1.3e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 |
| 40 | Trebbiano Emilia | TR | 1.2e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 41 | Trebbiano Emilia | TR | 1.0e-06 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 42 | Trebbiano Emilia | TS | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 43 | Trebbiano Emilia | TR | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 44 | Trebbiano Emilia | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 45 | Trebbiano Emilia | TS | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 |
| 46 | Trebbiano Emilia | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 47 | Trebbiano Emilia | TR | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 9.0e-07 | 9.0e-07 | 1.0e-06 | 9.0e-07 |
| 48 | Trebbiano Emilia | TS | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 49 | Trebbiano Umbria | TR | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 50 | Trebbiano Umbria | TR | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 |
| 51 | Trebbiano Umbria | TS | 1.4e-06 | 1.3e-06 | 1.3e-06 | 1.3e-06 | 1.3e-06 | 1.3e-06 | 1.3e-06 | 1.3e-06 |
| 52 | Trebbiano Umbria | TR | 1.2e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 53 | Trebbiano Umbria | TR | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 54 | Trebbiano Umbria | TS | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 |
| 55 | Trebbiano Umbria | TR | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 56 | Trebbiano Umbria | TR | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 |
| 57 | Trebbiano Umbria | TS | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 58 | Trebbiano Umbria | TR | 1.2e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 59 | Trebbiano Umbria | TR | 1.1e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 |
| 60 | Trebbiano Umbria | TS | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 |
| 61 | Trebbiano Romagna | TR | 3.0e-07 | 3.0e-07 | 3.0e-07 | 3.0e-07 | 3.0e-07 | 3.0e-07 | 3.0e-07 | 3.0e-07 |
| 62 | Trebbiano Romagna | TR | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 | 1.1e-06 |
| 63 | Trebbiano Romagna | TS | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 |
| 64 | Trebbiano Romagna | TR | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 | 1.0e-06 |
| 65 | Trebbiano Romagna | TR | 1.0e-06 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
| 66 | Trebbiano Romagna | TS | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 | 1.2e-06 |
| 67 | Trebbiano Romagna | TR | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 | 8.0e-07 |
| 68 | Trebbiano Romagna | TR | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 69 | Trebbiano Romagna | TS | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 | 6.0e-07 |
| 70 | Trebbiano Romagna | TR | 8.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 | 7.0e-07 |
| 71 | Trebbiano Romagna | TR | 1.0e-06 | 1.0e-06 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 1.0e-06 |
| 72 | Trebbiano Romagna | TS | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 | 9.0e-07 |
We have four different classes corresponding to four types of
wine.
df %>% group_by(Type) %>% summarise(Count = n()) %>% kable() %>% kable_minimal(full_width = F)| Type | Count |
|---|---|
| Chardonnay Francia | 12 |
| Chardonnay Puglia | 12 |
| Chardonnay Veneto | 12 |
| Trebbiano Emilia | 12 |
| Trebbiano Romagna | 12 |
| Trebbiano Umbria | 12 |
Here’s how they look like
dfdata = df[-c(1:2)]
attr(dfdata, "xaxis.name") = "Variables"
attr(dfdata, "xaxis.values") = colnames(dfdata) %>% as.numeric()
mdaplot(dfdata, type = 'l', main = 'Raw data', cgroup = as.factor(df$Type))
Preprocessing
Before performing classification you need to preprocess the data. Start applying only mean-center
\[
x_{ij}\ast = x_{ij} - \overline{x}_j
\]
dfdataMean = scale(dfdata, scale = F) %>% as.data.frame()
mdaplot(dfdataMean, type = 'l', cgroup = factor(df$Type), main = 'Mean-centered data')
Create a new categorical variable by separating the samples in
Chardonnay and Trebbiano
a = rep('Chardonnay', 36)
b = rep('Trebbiano', 36)
CT = c(a, b)
dfclass = cbind('C/T' = CT, 'TR/TS' = df$TR.TS, dfdataMean)
kable(dfclass[, 1:10], row.names = T) %>% kable_styling('striped', fixed_thead = T, full_width = FALSE) %>%
scroll_box( height = "500px")| C/T | TR/TS | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Chardonnay | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 2 | Chardonnay | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 3 | Chardonnay | TS | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 4 | Chardonnay | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 5 | Chardonnay | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 6 | Chardonnay | TS | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 7 | Chardonnay | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 8 | Chardonnay | TR | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 |
| 9 | Chardonnay | TS | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -4e-07 |
| 10 | Chardonnay | TR | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 |
| 11 | Chardonnay | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 12 | Chardonnay | TS | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -4e-07 | -3e-07 |
| 13 | Chardonnay | TR | -1e-07 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 14 | Chardonnay | TR | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 |
| 15 | Chardonnay | TS | 0e+00 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 16 | Chardonnay | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 17 | Chardonnay | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 18 | Chardonnay | TS | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 19 | Chardonnay | TR | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 20 | Chardonnay | TR | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -2e-07 | -3e-07 | -2e-07 |
| 21 | Chardonnay | TS | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -2e-07 | -3e-07 |
| 22 | Chardonnay | TR | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 |
| 23 | Chardonnay | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 24 | Chardonnay | TS | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 25 | Chardonnay | TR | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 26 | Chardonnay | TR | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 27 | Chardonnay | TS | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 1e-07 | 1e-07 | 0e+00 | 0e+00 |
| 28 | Chardonnay | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 29 | Chardonnay | TR | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 30 | Chardonnay | TS | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 31 | Chardonnay | TR | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 32 | Chardonnay | TR | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 |
| 33 | Chardonnay | TS | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 34 | Chardonnay | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 35 | Chardonnay | TR | 1e-07 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 1e-07 | 0e+00 |
| 36 | Chardonnay | TS | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 37 | Trebbiano | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 38 | Trebbiano | TR | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 39 | Trebbiano | TS | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 | 4e-07 |
| 40 | Trebbiano | TR | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 |
| 41 | Trebbiano | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 42 | Trebbiano | TS | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 43 | Trebbiano | TR | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 | 0e+00 |
| 44 | Trebbiano | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 45 | Trebbiano | TS | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 |
| 46 | Trebbiano | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 47 | Trebbiano | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 48 | Trebbiano | TS | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 | -3e-07 |
| 49 | Trebbiano | TR | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 |
| 50 | Trebbiano | TR | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 |
| 51 | Trebbiano | TS | 5e-07 | 5e-07 | 5e-07 | 5e-07 | 5e-07 | 5e-07 | 5e-07 | 5e-07 |
| 52 | Trebbiano | TR | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 |
| 53 | Trebbiano | TR | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 54 | Trebbiano | TS | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 55 | Trebbiano | TR | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 56 | Trebbiano | TR | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 |
| 57 | Trebbiano | TS | -1e-07 | 0e+00 | 0e+00 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 58 | Trebbiano | TR | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 2e-07 | 2e-07 | 2e-07 |
| 59 | Trebbiano | TR | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 60 | Trebbiano | TS | -1e-07 | -1e-07 | -1e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 |
| 61 | Trebbiano | TR | -6e-07 | -6e-07 | -5e-07 | -5e-07 | -5e-07 | -6e-07 | -6e-07 | -6e-07 |
| 62 | Trebbiano | TR | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 | 2e-07 |
| 63 | Trebbiano | TS | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 64 | Trebbiano | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 65 | Trebbiano | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 66 | Trebbiano | TS | 4e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 | 3e-07 |
| 67 | Trebbiano | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 68 | Trebbiano | TR | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 |
| 69 | Trebbiano | TS | -3e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 | -2e-07 |
| 70 | Trebbiano | TR | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 | -1e-07 |
| 71 | Trebbiano | TR | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
| 72 | Trebbiano | TS | 0e+00 | 0e+00 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 | 1e-07 |
dfclassTR = dfclass[dfclass$`TR/TS` == 'TR',]
dfclassTS = dfclass[dfclass$`TR/TS` == 'TS',]
model = plsda(dfclassTR[-c(1,2)], dfclassTR$`C/T`, cv = list('ven', 5), center = F, lim.type = 'jm')par(mfrow = c(1,1))
plotRMSE(model)
plotSensitivity(model)
model = selectCompNum(model , 4)
plot(model)
Classification’s \(R^2\) for 4 latent variables is 0.8137212
Now validate the model using the test set
modelp = predict(model, dfclassTS[-c(1,2)], c.ref = dfclassTS$`C/T`)
plotPredictions(modelp)
Classification’s \(R^2\) for 4 latent
variables is 0.8559592
References
Pigani, L., G. Foca, K. Ionescu, V. Martina, A. Ulrici, F. Terzi, M.
Vignali, C. Zanardi, and R. Seeber. 2008. “Amperometric Sensors
Based on Poly(3,4-Ethylenedioxythiophene)-Modified Electrodes:
Discrimination of White Wines.” Analytica Chimica Acta
614 (2): 213–22. https://doi.org/10.1016/j.aca.2008.03.029.
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