library(car) 
library(ggplot2) 
library(pastecs)  
library(ppcor) 
 
 
pro <- read.csv("C:/Users/mehdi/Desktop/Projects/PPMI dataset/Lumbar_Puncture.csv") 
pro <- subset(pro, EVENT_ID == "V04") 
pro <- pro[ , c(2 , 35 , 37)] 
pro <- na.omit(pro) 
pro <- subset(pro, PATNO < 10000) 
 
mds <- read.csv("C:/Users/mehdi/Desktop/Projects/Reyhaneh/mds.csv") 
mds <- subset(mds, EVENT_ID == "V04") 
mds <- mds[ , c(2 , 13)] 
mds <- subset(mds, PATNO < 10000) 
 
final <- merge(pro, mds, by = "PATNO") 
 
test <- cor.test(final$TOPRRSLT, final$NP1RTOT, conf.level = 0.99) 
test 
 
plot1 <- ggplot(final, aes(final$NP1RTOT)) + 
  geom_histogram(aes(y = ..density..), color = "red", fill = "white") + 
  stat_function(fun = dnorm , args = list(mean = mean(final$NP1RTOT, na.rm = TRUE), 
                                          sd = sd(final$NP1RTOT, na.rm = TRUE))) 
plot1 
 
plot2 <- qplot(sample = final$NP1RTOT) 
plot2 
 
plot(final$NP1RTOT, final$TOPRRSLT) 
 
test.s <- shapiro.test(final$NP1RTOT) 
test.s 
 
test <- cor.test(final$TOPRRSLT, final$NP1RTOT, method = "kendall") 
test 
 
 
x = (1:100) 
y = 2^x 
plot(x  , y) 
 
cor.test(x, y, method = "spearman") 
 
 
cor.test(final$TGLCRSLT, final$TOPRRSLT) 
cor.test 
 
age <- read.csv("C:/Users/mehdi/Desktop/Projects/Reyhaneh/status.csv") 
age <- age[ , 1:2] 
age <- subset(age , COHORT != "3") 
age <- subset(age, PATNO <10000) 
final <- merge(final, age, by = "PATNO") 
 
demo <- read.csv("C:/Users/mehdi/Desktop/Projects/Reyhaneh/Age.csv") 
demo <- subset(demo, EVENT_ID == "V04") 
demo <- demo[ , -2] 
final <- merge(final, demo, by = "PATNO") 
 
help("pcor") 
 
final2 <- final[ , -1] 
 
pc <- pcor(final2) 
pc