RinAction - Basic Statistics - Association & Correlations

gistfile1.r

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# -------- Test of independence & Association -------- #
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##########################
# Evidence of Independence
##########################

# X-square
library(vcd)
mytable <- xtabs(~Treatment+Improved, data=Arthritis)
chisq.test(mytable)
mytable <- xtabs(~Improved+Sex, data=Arthritis)
chisq.test(mytable)
           
# Fisher's exact test
mytable <- xtabs(~Treatment+Improved, data=Arthritis)
fisher.test(mytable)
           
# Chochran-Mantel-Haenszel test
           
mytable <- xtabs(~Treatment+Improved+Sex, data=Arthritis)
mantelhaen.test(mytable)
           
##########################
# Strength of Association
##########################
           
library(vcd)
mytable <- xtabs(~Treatment+Improved, data=Arthritis)
assocstats(mytable)
       

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# --------          Correlations              -------- #
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# Covariances and correlations
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# 1. Square matrix
states <- state.x77[, 1:6]
cov(states)
cor(states)
cor(states, method="spearman")
cor(states, use="all.obs", method='pearson') # assumes no missing data, missing will produce an error
cor(states, use="everything", method='pearson') # any correlation involving a case with missing is set to missing
cor(states, use="complete.obs", method='pearson') # listwise deletion
cor(states, use="pairwise.complete.obs", method='pearson') # pairwise deletion
  
# 2. Nonsquare matrix
x <- states[, c("Population", "Income", "Illiteracy", "HS Grad")]
y <- states[, c("Life Exp", "Murder")]
cor(x, y)
           
######################
# Partial Correlations
######################

#partial correlation of population and murder rate, controlling
# for income, illiteracy rate, and HS graduation rate
  
install.packages("ggm")
library(ggm)
pcor(c(1, 5, 2, 3, 6), cov(states))


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# Testing correlations for significance
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# 1. Testing one correlation at a time
cor.test(states[, 3], states[, 5])

# 2. Correlation matrix and tests of significance via corr.test
           
library(psych)
corr.test(states, use = "complete")
corr.test(states, use = "pairwise")