Blog Entry Number One

animals <- read.csv2("tbk_animals.csv") #note that it is the "continental" csv version!

library(knitr)
kable(animals)

cornet <- function(x, y = NULL, use = "pairwise", method = "pearson", round = 3, row.labels, col.labels, ...) {
  
  require(psych)
  
  ct <- corr.test(x, y, use, method,adjust="bonferroni")    # calculate correlation
  r <- ct$r                             # get correlation coefs
  p <- ct$p                             # get p-values
  
  sig <- ifelse(p < .05, 1,0) # generate significance stars
  poscorr<-ifelse(r > 0, 1,0)
  
  m <- matrix(NA, nrow = nrow(r) , ncol = ncol(r)) # create empty matrix
  
  rlab <- if(missing(row.labels)) rownames(r) else row.labels # add row labels
  clab <- if(missing(col.labels)) {
    if(is.null(colnames(r)))
      deparse(substitute(y))
    else
      colnames(r)
  } else {
    col.labels # add column labels
  }
  
  rows <- 1:nrow(m)                     # row indices
  cols <- 1:ncol(m)                     # column indices
  
  m[rows, cols] <- sig*poscorr
  
  colnames(m) <- c( clab)           # add colnames
  rownames(m) <- c( rlab)           # add colnames
  m                                     # return matrix
}

adj <- cornet(na.omit(animals[,3:25]))

## Lade nötiges Paket: psych

## Warning in abbreviate(colnames(r), minlength = 5): abbreviate mit
## nicht-ASCII Zeichen genutzt

library(GGally)

ggnet2(adj, mode = "fruchtermanreingold", size = 24, label = rownames(adj), label.size = 3, alpha=0.8)

## Lade nötiges Paket: network

## network: Classes for Relational Data
## Version 1.13.0 created on 2015-08-31.
## copyright (c) 2005, Carter T. Butts, University of California-Irvine
##                     Mark S. Handcock, University of California -- Los Angeles
##                     David R. Hunter, Penn State University
##                     Martina Morris, University of Washington
##                     Skye Bender-deMoll, University of Washington
##  For citation information, type citation("network").
##  Type help("network-package") to get started.

## Lade nötiges Paket: sna

## sna: Tools for Social Network Analysis
## Version 2.3-2 created on 2014-01-13.
## copyright (c) 2005, Carter T. Butts, University of California-Irvine
##  For citation information, type citation("sna").
##  Type help(package="sna") to get started.

## 
## Attache Paket: 'sna'

## Das folgende Objekt ist maskiert 'package:network':
## 
##     %c%

## Lade nötiges Paket: scales

## 
## Attache Paket: 'scales'

## Die folgenden Objekte sind maskiert von 'package:psych':
## 
##     alpha, rescale