Bastos2019
Gabriel M N Guimaraes e Helga B G Silva
22 de junho de 2019
knitr::opts_chunk$set(echo = TRUE)
library(openxlsx)
library(BayesFactor)## Loading required package: coda## Loading required package: Matrix## ************
## Welcome to BayesFactor 0.9.12-4.2. If you have questions, please contact Richard Morey (richarddmorey@gmail.com).
##
## Type BFManual() to open the manual.
## ************read.xlsx2 = function(bdata){
bdata=read.xlsx(bdata)
nv=length(bdata)
ischar=rep(FALSE,nv)
for(i in c(1:nv)){
if(is.character(bdata[,i][0])){
bdata[,i]=factor(bdata[,i])
}
}
bdata
}
TwoByTwoBFc = function (x,y){
a=sum(x & y,na.rm=TRUE)
b=sum(x & !y,na.rm=TRUE)
c=sum(!x & y,na.rm=TRUE)
d=sum(!x & !y,na.rm=TRUE)
table=as.matrix(data.frame(yes=c(a,c),no=c(b,d)))
bf=extractBF(contingencyTableBF(table, sampleType = "indepMulti", fixedMargin = "cols"))[1]$bf
rownames(table)=c("Intervention","Control")
r1=a/(a+c)
r2=b/(b+d)
print(paste("Risco no grupo sim",r1))
print(paste("Risco no grupo não",r2))
print(paste("Risco relativo",r1/r2))
print("Fator bayesiano:")
print(bf)
print("p-valor, teste exato de Fisher:")
print(fisher.test(table)[1]$`p.value`)
print(substitute(y))
table
}Summary
This is a MARKDOWN file describing the data analysis of an experimental trial. Pigs were randomly allocated in two groups:
- Intervention group received an arterial tourniquet, with no initial ventilation, followed by conventional CPR.
- Controu group received no tourniquet, only conventional CPR.
Bayes factors were calculated also for the main study hypothesis. Data Analysis contact information: gabriel@gabriel.med.br
Raw data
datafile="D:\\DataAnalysis\\Bastos2019\\Bastos2019.xlsx";
data=read.xlsx2(datafile)
data$weight=as.numeric(as.character(data$weight))
data## id male weight Intervention return.circulation cpr.minutes
## 1 1 FALSE 24.45 TRUE FALSE 28
## 2 2 TRUE 24.80 FALSE TRUE 13
## 3 3 FALSE 26.00 FALSE TRUE 14
## 4 4 TRUE 22.80 TRUE TRUE 18
## 5 5 FALSE 28.20 TRUE FALSE 30
## 6 6 FALSE 27.45 FALSE TRUE 16
## 7 7 TRUE 28.00 TRUE FALSE 30
## 8 8 TRUE 28.00 FALSE FALSE 30
## 9 9 FALSE 31.10 TRUE FALSE 30
## 10 10 FALSE 27.80 FALSE TRUE 14
## 11 11 TRUE 26.00 FALSE TRUE 16
## 12 12 TRUE 28.00 TRUE FALSE 30
## 13 13 FALSE 31.00 FALSE FALSE 30
## 14 14 FALSE 29.85 TRUE FALSE 30
## 15 15 TRUE 32.00 FALSE TRUE 19
## 16 16 TRUE 30.00 TRUE TRUE 21
## 17 17 FALSE 27.00 FALSE TRUE 17
## 18 18 FALSE 26.15 TRUE TRUE 15
## 19 19 TRUE 29.00 FALSE FALSE 30
## 20 20 TRUE 28.15 TRUE FALSE 30
## 21 21 FALSE 25.60 FALSE FALSE 30
## 22 22 FALSE 27.10 TRUE FALSE 30
## 23 23 TRUE 27.85 FALSE FALSE 30
## 24 24 TRUE 27.60 TRUE FALSE 30
## 25 25 FALSE 24.00 TRUE FALSE 30
## 26 26 FALSE 25.00 FALSE FALSE 30
## 27 27 TRUE 24.30 FALSE FALSE 30
## 28 28 TRUE 24.65 TRUE FALSE 30
## 29 29 FALSE 27.35 FALSE FALSE 30
## 30 30 FALSE 23.45 TRUE FALSE 30
## 31 31 TRUE 27.05 TRUE FALSE 30
## 32 32 TRUE 25.75 FALSE FALSE 30
## 33 33 FALSE 28.00 TRUE FALSE 30
## epinephrine.doses survival.30d
## 1 3 FALSE
## 2 0 TRUE
## 3 0 TRUE
## 4 1 FALSE
## 5 3 FALSE
## 6 1 TRUE
## 7 3 FALSE
## 8 3 FALSE
## 9 3 FALSE
## 10 1 TRUE
## 11 1 TRUE
## 12 3 FALSE
## 13 3 FALSE
## 14 3 FALSE
## 15 2 FALSE
## 16 3 FALSE
## 17 1 FALSE
## 18 0 FALSE
## 19 3 FALSE
## 20 3 FALSE
## 21 3 FALSE
## 22 3 FALSE
## 23 3 FALSE
## 24 3 FALSE
## 25 3 FALSE
## 26 3 FALSE
## 27 3 FALSE
## 28 3 FALSE
## 29 3 FALSE
## 30 3 FALSE
## 31 3 FALSE
## 32 3 FALSE
## 33 3 FALSEData summary
summary(data)## id male weight Intervention
## Min. : 1 Mode :logical Min. :22.80 Mode :logical
## 1st Qu.: 9 FALSE:17 1st Qu.:25.60 FALSE:16
## Median :17 TRUE :16 Median :27.35 TRUE :17
## Mean :17 Mean :27.07
## 3rd Qu.:25 3rd Qu.:28.00
## Max. :33 Max. :32.00
## return.circulation cpr.minutes epinephrine.doses survival.30d
## Mode :logical Min. :13.00 Min. :0.000 Mode :logical
## FALSE:23 1st Qu.:19.00 1st Qu.:2.000 FALSE:28
## TRUE :10 Median :30.00 Median :3.000 TRUE :5
## Mean :25.79 Mean :2.394
## 3rd Qu.:30.00 3rd Qu.:3.000
## Max. :30.00 Max. :3.000Hypothesis testing
TwoByTwoBFc(data$return.circulation,data$Intervention)## [1] "Risco no grupo sim 0.176470588235294"
## [1] "Risco no grupo não 0.4375"
## [1] "Risco relativo 0.403361344537815"
## [1] "Fator bayesiano:"
## [1] 1.322059
## [1] "p-valor, teste exato de Fisher:"
## [1] 0.1410703
## data$Intervention## yes no
## Intervention 3 7
## Control 14 9TwoByTwoBFc(data$survival.30d,data$Intervention)## [1] "Risco no grupo sim 0"
## [1] "Risco no grupo não 0.3125"
## [1] "Risco relativo 0"
## [1] "Fator bayesiano:"
## [1] 6.037241
## [1] "p-valor, teste exato de Fisher:"
## [1] 0.01840429
## data$Intervention## yes no
## Intervention 0 5
## Control 17 11TwoByTwoBFc(data$survival.30d,data$male)## [1] "Risco no grupo sim 0.125"
## [1] "Risco no grupo não 0.176470588235294"
## [1] "Risco relativo 0.708333333333333"
## [1] "Fator bayesiano:"
## [1] 0.3231699
## [1] "p-valor, teste exato de Fisher:"
## [1] 1
## data$male## yes no
## Intervention 2 3
## Control 14 14wilcox.test(data$weight~data$survival.30d)## Warning in wilcox.test.default(x = c(24.45, 22.8, 28.2, 28, 28, 31.1, 28, :
## cannot compute exact p-value with ties##
## Wilcoxon rank sum test with continuity correction
##
## data: data$weight by data$survival.30d
## W = 87, p-value = 0.407
## alternative hypothesis: true location shift is not equal to 0CPR minutes
boxplot(data$cpr.minutes~data$survival.30d)
boxplot(data$cpr.minutes~data$return.circulation)
Epidephrine doses
table(data$epinephrine.doses,data$return.circulation)##
## FALSE TRUE
## 0 0 3
## 1 0 5
## 2 0 1
## 3 23 1wilcox.test(data$epinephrine.doses~data$return.circulation)## Warning in wilcox.test.default(x = c(3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, :
## cannot compute exact p-value with ties##
## Wilcoxon rank sum test with continuity correction
##
## data: data$epinephrine.doses by data$return.circulation
## W = 218.5, p-value = 2.48e-07
## alternative hypothesis: true location shift is not equal to 0table(data$epinephrine.doses,data$survival.30d)##
## FALSE TRUE
## 0 1 2
## 1 2 3
## 2 1 0
## 3 24 0wilcox.test(data$epinephrine.doses~data$survival.30d)## Warning in wilcox.test.default(x = c(3, 1, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, :
## cannot compute exact p-value with ties##
## Wilcoxon rank sum test with continuity correction
##
## data: data$epinephrine.doses by data$survival.30d
## W = 133, p-value = 6.006e-05
## alternative hypothesis: true location shift is not equal to 0If no return of spontaneous circulation before third dose, there was a remote (4%) chance of survival (p=0.0000024) and no chance of 30-day survival (p=0.00006).
30-Day survival proportion by number of needed epinephrine doses from 0 to 3: 66.6%, 60%, 0, 0.