R: Principal Components Analysis (PCA) with NA (missing data)

pca {SYNCSA} | R Documentation

## Principal Components Analysis (PCA) with NA (missing data)

### Description

The function use the option "pairwise.complete.obs" (in function `cor`) for calculate the correlation. The correlation between each pair of variables is computed using all complete pairs of observations on those variables.

### Usage

    pca(data)

    ## S3 method for class 'pcasyncsa'
    plot(
      x,
      show = c("variables", "individuals"),
      axis = c(1, 2),
      xlab = axis[1],
      ylab = axis[2],
      arrows = TRUE,
      text = TRUE,
      points = FALSE,
      ...
    )

### Arguments

`data` | A data frame or matrix with individuals in rows and variables in columns.
`x` | A object of class pcasyncsa.
`show` | Draw "variables" or "individuals".
`axis` | Axis for draw, must have length equal to two (Default axis = c(1, 2)).
`xlab` | Text for x label (Default xlab = axis[1]).
`ylab` | Text for y label (Default ylab = axis[2]).
`arrows` | Logical argument (TRUE or FALSE) to specify if arrows are showed for variables (Default arrows = TRUE).
`text` | Logical argument (TRUE or FALSE) to specify if text are showed for individuals (Default text = TRUE).
`points` | Logical argument (TRUE or FALSE) to specify if points are showed for individuals (Default points = FALSE).
`...` | Parameters for `plot` function.

### Value

`decomposition` | list with the results of decomposition of correlation matrix.
`eigenvalues` | Data frame containing all the eigenvalues, the percentage of inertia and the cumulative percentage of inertia.
`individuals` | Coordinates for the individuals.
`variables` | Correlation between original variables and axes.

### Author(s)

Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>

### See Also

`syncsa` `syncsa`

### Examples

    data(ADRS)
    traits<-ADRS$traits
    # Some NA
    traits[c(1,5),1]<-NA
    traits[3,2]<-NA
    traits
    res<-pca(traits)
    res
    plot(res, show = "variables", arrows = TRUE)
    plot(res, show = "individuals", axis = c(1, 2), text = TRUE)
    plot(res, show = "individuals", text = FALSE, points = TRUE)

[Package SYNCSA version 1.3.4 Index]