library(readr)
## Warning: package 'readr' was built under R version 3.6.1
mice <- read_csv("~/RPy Analytics/Dr Manatsa/mice.csv")
## Parsed with column specification:
## cols(
## `Lab Number` = col_character(),
## drug = col_character(),
## status = col_character(),
## tem_gene = col_character()
## )
#View(mice)
attach(mice)
library(gmodels)
## Warning: package 'gmodels' was built under R version 3.6.1
library(Rmisc)
## Warning: package 'Rmisc' was built under R version 3.6.1
## Loading required package: lattice
## Loading required package: plyr
## Warning: package 'plyr' was built under R version 3.6.1
drug=as.factor(drug)
status=as.factor(status)
tem_gene=as.factor(tem_gene)
mytable <- table(drug,tem_gene) # A will be rows, B will be columns
mytable # print table
## tem_gene
## drug gene absent gene present
## Amoxycillin/Clavulinic acid 30 10
## Ampicillin 30 10
## Cefotaxime 30 10
## Ceftazidime. 30 10
## Imipenem 30 10
margin.table(mytable, 1) # A frequencies (summed over B)
## drug
## Amoxycillin/Clavulinic acid Ampicillin
## 40 40
## Cefotaxime Ceftazidime.
## 40 40
## Imipenem
## 40
margin.table(mytable, 2) # B frequencies (summed over A)
## tem_gene
## gene absent gene present
## 150 50
prop.table(mytable) # cell percentages
## tem_gene
## drug gene absent gene present
## Amoxycillin/Clavulinic acid 0.15 0.05
## Ampicillin 0.15 0.05
## Cefotaxime 0.15 0.05
## Ceftazidime. 0.15 0.05
## Imipenem 0.15 0.05
prop.table(mytable, 1) # row percentages
## tem_gene
## drug gene absent gene present
## Amoxycillin/Clavulinic acid 0.75 0.25
## Ampicillin 0.75 0.25
## Cefotaxime 0.75 0.25
## Ceftazidime. 0.75 0.25
## Imipenem 0.75 0.25
prop.table(mytable, 2) # column percentages
## tem_gene
## drug gene absent gene present
## Amoxycillin/Clavulinic acid 0.2 0.2
## Ampicillin 0.2 0.2
## Cefotaxime 0.2 0.2
## Ceftazidime. 0.2 0.2
## Imipenem 0.2 0.2
# 2-Way Frequency Table
mytable <- table(status,tem_gene) # A will be rows, B will be columns
mytable # print table
## tem_gene
## status gene absent gene present
## resistance 20 14
## susceptibility 130 36
margin.table(mytable, 1) # A frequencies (summed over B)
## status
## resistance susceptibility
## 34 166
margin.table(mytable, 2) # B frequencies (summed over A)
## tem_gene
## gene absent gene present
## 150 50
prop.table(mytable) # cell percentages
## tem_gene
## status gene absent gene present
## resistance 0.10 0.07
## susceptibility 0.65 0.18
prop.table(mytable, 1) # row percentages
## tem_gene
## status gene absent gene present
## resistance 0.5882353 0.4117647
## susceptibility 0.7831325 0.2168675
prop.table(mytable, 2) # column percentages
## tem_gene
## status gene absent gene present
## resistance 0.1333333 0.2800000
## susceptibility 0.8666667 0.7200000
#Mantel-Haenszel chi-squared test with continuity correction
mantelhaen.test(drug,status,tem_gene)
##
## Cochran-Mantel-Haenszel test
##
## data: drug and status and tem_gene
## Cochran-Mantel-Haenszel M^2 = 48.458, df = 4, p-value = 7.575e-10
# 3-Way Frequency Table
mytable <- xtabs(~drug+status+tem_gene, data=mice)
ftable(mytable) # print table
## tem_gene gene absent gene present
## drug status
## Amoxycillin/Clavulinic acid resistance 4 2
## susceptibility 26 8
## Ampicillin resistance 10 10
## susceptibility 20 0
## Cefotaxime resistance 6 2
## susceptibility 24 8
## Ceftazidime. resistance 0 0
## susceptibility 30 10
## Imipenem resistance 0 0
## susceptibility 30 10
summary(mytable) # chi-square test of indepedence
## Call: xtabs(formula = ~drug + status + tem_gene, data = mice)
## Number of cases in table: 200
## Number of factors: 3
## Test for independence of all factors:
## Chisq = 71.49, df = 13, p-value = 4.271e-10
## Chi-squared approximation may be incorrect
## cross tabultaions using gmodel package
## cardiovascular deseases
CrossTable(status,tem_gene)
##
##
## Cell Contents
## |-------------------------|
## | N |
## | Chi-square contribution |
## | N / Row Total |
## | N / Col Total |
## | N / Table Total |
## |-------------------------|
##
##
## Total Observations in Table: 200
##
##
## | tem_gene
## status | gene absent | gene present | Row Total |
## ---------------|--------------|--------------|--------------|
## resistance | 20 | 14 | 34 |
## | 1.186 | 3.559 | |
## | 0.588 | 0.412 | 0.170 |
## | 0.133 | 0.280 | |
## | 0.100 | 0.070 | |
## ---------------|--------------|--------------|--------------|
## susceptibility | 130 | 36 | 166 |
## | 0.243 | 0.729 | |
## | 0.783 | 0.217 | 0.830 |
## | 0.867 | 0.720 | |
## | 0.650 | 0.180 | |
## ---------------|--------------|--------------|--------------|
## Column Total | 150 | 50 | 200 |
## | 0.750 | 0.250 | |
## ---------------|--------------|--------------|--------------|
##
##
CrossTable(drug,tem_gene)
##
##
## Cell Contents
## |-------------------------|
## | N |
## | Chi-square contribution |
## | N / Row Total |
## | N / Col Total |
## | N / Table Total |
## |-------------------------|
##
##
## Total Observations in Table: 200
##
##
## | tem_gene
## drug | gene absent | gene present | Row Total |
## ----------------------------|--------------|--------------|--------------|
## Amoxycillin/Clavulinic acid | 30 | 10 | 40 |
## | 0.000 | 0.000 | |
## | 0.750 | 0.250 | 0.200 |
## | 0.200 | 0.200 | |
## | 0.150 | 0.050 | |
## ----------------------------|--------------|--------------|--------------|
## Ampicillin | 30 | 10 | 40 |
## | 0.000 | 0.000 | |
## | 0.750 | 0.250 | 0.200 |
## | 0.200 | 0.200 | |
## | 0.150 | 0.050 | |
## ----------------------------|--------------|--------------|--------------|
## Cefotaxime | 30 | 10 | 40 |
## | 0.000 | 0.000 | |
## | 0.750 | 0.250 | 0.200 |
## | 0.200 | 0.200 | |
## | 0.150 | 0.050 | |
## ----------------------------|--------------|--------------|--------------|
## Ceftazidime. | 30 | 10 | 40 |
## | 0.000 | 0.000 | |
## | 0.750 | 0.250 | 0.200 |
## | 0.200 | 0.200 | |
## | 0.150 | 0.050 | |
## ----------------------------|--------------|--------------|--------------|
## Imipenem | 30 | 10 | 40 |
## | 0.000 | 0.000 | |
## | 0.750 | 0.250 | 0.200 |
## | 0.200 | 0.200 | |
## | 0.150 | 0.050 | |
## ----------------------------|--------------|--------------|--------------|
## Column Total | 150 | 50 | 200 |
## | 0.750 | 0.250 | |
## ----------------------------|--------------|--------------|--------------|
##
##
CrossTable(drug,status)
##
##
## Cell Contents
## |-------------------------|
## | N |
## | Chi-square contribution |
## | N / Row Total |
## | N / Col Total |
## | N / Table Total |
## |-------------------------|
##
##
## Total Observations in Table: 200
##
##
## | status
## drug | resistance | susceptibility | Row Total |
## ----------------------------|----------------|----------------|----------------|
## Amoxycillin/Clavulinic acid | 6 | 34 | 40 |
## | 0.094 | 0.019 | |
## | 0.150 | 0.850 | 0.200 |
## | 0.176 | 0.205 | |
## | 0.030 | 0.170 | |
## ----------------------------|----------------|----------------|----------------|
## Ampicillin | 20 | 20 | 40 |
## | 25.624 | 5.248 | |
## | 0.500 | 0.500 | 0.200 |
## | 0.588 | 0.120 | |
## | 0.100 | 0.100 | |
## ----------------------------|----------------|----------------|----------------|
## Cefotaxime | 8 | 32 | 40 |
## | 0.212 | 0.043 | |
## | 0.200 | 0.800 | 0.200 |
## | 0.235 | 0.193 | |
## | 0.040 | 0.160 | |
## ----------------------------|----------------|----------------|----------------|
## Ceftazidime. | 0 | 40 | 40 |
## | 6.800 | 1.393 | |
## | 0.000 | 1.000 | 0.200 |
## | 0.000 | 0.241 | |
## | 0.000 | 0.200 | |
## ----------------------------|----------------|----------------|----------------|
## Imipenem | 0 | 40 | 40 |
## | 6.800 | 1.393 | |
## | 0.000 | 1.000 | 0.200 |
## | 0.000 | 0.241 | |
## | 0.000 | 0.200 | |
## ----------------------------|----------------|----------------|----------------|
## Column Total | 34 | 166 | 200 |
## | 0.170 | 0.830 | |
## ----------------------------|----------------|----------------|----------------|
##
##