Scripts for running SAVE analysis

BraveDataRun 1.R

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+library(ggplot2)
+library(sciplot)
+library(mosaic)
+library(tableone)
+library(survival)
+library(car)
+library(gridExtra)
+
+
+
+brave=read.csv("BraveModWide.csv")
+brave
+
+
+#I'm going to create a data matrix
+##(easyAndShould,DifficultAndNot,EasyAndNot,DifficultShould))
+
+dmatrix <- matrix(c(18,6,35,0),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score + or >5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+
+
+bargraph.CI(dmatrix)
+
+grid.table(dmatrix)
+
+fisher.test(dmatrix)
+
+difficult= subset(brave, Grade >="3")
+difficult
+
+
+easy= subset(brave, Grade < "3")
+easy
+
+difficult$Grade
+easy$Grade
+
+count(difficult)
+count(easy)
+
+difficult$Total.Score
+easy$Total.Score
+
+easy$Laryngoscope.used
+easy$Cricoid.Pressur
+easy$Extreme.hockey.stick
+easy$Extreme.neck.position
+easy$Bougie
+easy$Multiple.Attempts
+easy$H.O.Sifficult.Airway
+easy$Disease.associated.with
+
+easy$Mallampati
+easy$Thyromental.distance
+easy$Mouth.Opening
+easy$Neck.Mobility
+easy$Neck.Circumference
+easy$BMI.30
+easy$BMI.40
+easy$Thyro.sternal.distance
+easy$Mandibular.angle
+easy$Overbite
+easy$Absence.of.Upper.Incisors
+
+
+
+difficult$Laryngoscope.used
+difficult$Cricoid.Pressur
+difficult$Extreme.hockey.stick
+difficult$Extreme.neck.position
+difficult$Bougie
+difficult$Multiple.Attempts
+difficult$H.O.Sifficult.Airway
+difficult$Disease.associated.with
+
+difficult$Mallampati
+difficult$Thyromental.distance
+difficult$Mouth.Openingv
+difficult$Neck.Mobility
+difficult$Neck.Circumference
+difficult$BMI.30
+difficult$BMI.40
+difficult$Thyro.sternal.distance
+difficult$Mandibular.angle
+difficult$Overbite
+difficult$Absence.of.Upper.Incisors
+
+
+count(easy$Total.Score >="5")
+
+count(easy)
+
+count(easy$Total.Score<"5")
+
+amatrix <- matrix(c(50,1,3,5),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score ???5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+grid.table(amatrix)
+fisher.test(amatrix)
+
+
+bmatrix <- matrix(c(45,2,8,4),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score ???5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+grid.table(bmatrix)
+fisher.test(bmatrix)
+
+cmatrix <- matrix(c(51,2,2,4),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score ???5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+grid.table(cmatrix)
+fisher.test(cmatrix)
+
+dmatrix <- matrix(c(50,6,3,0),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score ???5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+grid.table(dmatrix)
+fisher.test(dmatrix)
+
+dmatrix <- matrix(c(18,6,35,0),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score ???5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+grid.table(dmatrix)
+fisher.test(dmatrix)
+
+dmatrix <- matrix(c(18,6,35,0),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score ???5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+grid.table(dmatrix)
+fisher.test(dmatrix)
+
+dmatrix <- matrix(c(18,6,35,0),ncol=2,byrow=TRUE,
+ dimnames = list(c("BRAVE Score < 5", "BRAVE Score ???5"), 
+ c("Easy Intubation Group", "Difficult Intubation Group")))
+grid.table(dmatrix)
+fisher.test(dmatrix)
+
+
+easyint=c("50,3")
+diffint=c("1,5")
+
+table(easyint,diffint)
+
+
+
+
+N=c(rep(50,3),rep(20,3))
+Proport=c(20,15,15,5,10,5)/N
+
+data <- data.frame(
+ Category=rep(c('Smoker','Non-smoker'), each=3),
+ Label=c('0<x<5','5<x<10','10<x<15','0<x<5','5<x<10','10<x<15'),
+ Proportion=Proport, 
+ SD=sqrt(Proport*(1-Proport)/N)
+)
+
+me1=qnorm(0.025,mean=data$Proportion,sd=data$SD)
+me2=qnorm(0.975,mean=data$Proportion,sd=data$SD)
+
+mat <- matrix(data$Proportion, nrow = 2, dimnames = list(levels(data$Category),levels(data$Label)))
+barx=barplot(mat, beside=T, col = c("blue", "orange", "blue", "orange","blue", "orange"), names.arg = toupper(colnames(mat)), legend.text=TRUE,ylim=c(0,1),xlab="Income",ylab="Proportion",main="Bar plot with 95% confidence intervals")
+box()
+arrows(barx,me2, barx, me1, angle=90, code=1)
+arrows(barx,me1, barx, me2, angle=90, code=1)
+
+
+t.test(difficult$Total.Score,easy$Total.Score)
+
+sample1=