# pca: Principal Components Analysis (PCA) with NA (missing data) In SYNCSA: Analysis of Functional and Phylogenetic Patterns in Metacommunities

## 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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14``` ```pca(data) ## S3 method for class 'pcasyncsa' plot( x, show = c("variables", "individuals"), axis = c(1, 2), xlab = axis, ylab = axis, 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). `ylab` Text for y label (Default ylab = axis). `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>

`syncsa` `syncsa`
 ``` 1 2 3 4 5 6 7 8 9 10 11``` ```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) ```