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November 20, 2017 13:23
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#install.packages(c("ggplot2","MASS","dplyr","lattice")) | |
#install.packages("plyr") | |
#install.packages("dplyr") | |
#install.packages("boot") | |
#install.packages("grphics") | |
#install.packages("lattice") | |
#install.packages("magrittr") | |
library(magrittr) | |
library(installr) | |
library(lattice) | |
library(ISLR) | |
library(plyr) | |
library(readr) | |
library(boot) | |
library(Rcpp) | |
library(reshape) | |
library(reshape2) | |
library(stringi) | |
library(MASS,readr) | |
require(graphics) | |
#load_data------ | |
for( i in 1:10 ){ | |
paste("C:/Program Files/R/Data/Loose5B/LB/PCA0102_Loose5Big_ef123/big", "\t",i, | |
"txt",sep ="\t",escape_double = FALSE, col_names = FALSE) -> aa | |
bb <- read.csv(aa) | |
list(bb) | |
#ks.test(bb) | |
} | |
#way 1 | |
big_1_ <- read_delim("C:/Program Files/R/Data/Loose5B/LB/PCA0102_Loose5Big_ef123/big (1).txt", | |
"\t", escape_double = FALSE, col_names = FALSE, | |
trim_ws = TRUE) | |
#way 2 | |
##loose 5b/LB------result_1/2/3---- | |
#LB | |
flist<- dir("C:/Program Files/R/Data/Loose5B/LB/PCA0102_Loose5Big_ef123/", "*.txt", recursive=TRUE) | |
result<-list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose5B/LB/PCA0102_Loose5Big_ef123/") | |
name <- basename(path) | |
result[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result[path]) | |
#View(result) #3057entries | |
#LB2 | |
flist<- dir("C:/Program Files/R/Data/Loose5B/LB (2)/PCA0102_Loose5Big_ef135/", "*.txt", recursive=TRUE) | |
result2<-list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose5B/LB (2)/PCA0102_Loose5Big_ef135/") | |
name <- basename(path) | |
result2[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result2[path]) | |
#View(result2)#2092 entries | |
#LB3 | |
flist<- dir("C:/Program Files/R/Data/Loose5B/LB (3)/PCA0102_Loose5Big_ef135/", "*.txt", recursive=TRUE) | |
result3<-list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose5B/LB (3)/PCA0102_Loose5Big_ef135/") | |
name <- basename(path) | |
result3[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result3[path]) | |
#View(result3) #2092 entries | |
##loose 5s--------result_4/5/6---- | |
flist<- dir("C:/Program Files/R/Data/Loose5S/LB5s_/PCA0102_Loose5Small_ef123/", "*.txt", recursive=TRUE) | |
result4 <- list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose5S/LB5s_/PCA0102_Loose5Small_ef123/") | |
name <- basename(path) | |
result4[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result4[]) | |
#View(result4) #2092 entries | |
flist<- dir("C:/Program Files/R/Data/Loose5S/LB5s_ (2)/PCA0102_Loose5Small_ef135/", "*.txt", recursive=TRUE) | |
result5 <- list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose5S/LB5s_ (2)/PCA0102_Loose5Small_ef135/") | |
name <- basename(path) | |
result5[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result5[]) | |
flist<- dir("C:/Program Files/R/Data/Loose5S/LB5s_ (3)/PCA0102_Loose5Small_ef135/", "*.txt", recursive=TRUE) | |
result6 <- list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose5S/LB5s_ (3)/PCA0102_Loose5Small_ef135/") | |
name <- basename(path) | |
result6[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result6[]) | |
##loose 6b--------result_7/8---- | |
flist<- dir("C:/Program Files/R/Data/Loose6B/L6B/PCA0102_Loose6Big_ef123/", "*.txt", recursive=TRUE) | |
result7 <- list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose6B/L6B/PCA0102_Loose6Big_ef123/") | |
name <- basename(path) | |
result7[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result7[]) | |
flist<- dir("C:/Program Files/R/Data/Loose6B/L6B (2)/PCA0102_Loose6Big_ef135/", "*.txt", recursive=TRUE) | |
result8 <- list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose6B/L6B (2)/PCA0102_Loose6Big_ef135/") | |
name <- basename(path) | |
result8[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result8[]) | |
##loose 6s--------result_9/10----- | |
flist<- dir("C:/Program Files/R/Data/Loose6S/L6s/PCA0102_Loose6Small_ef123/", "*.txt", recursive=TRUE) | |
result9 <- list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose6S/L6s/PCA0102_Loose6Small_ef123/") | |
name <- basename(path) | |
result9[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result9[]) | |
flist<- dir("C:/Program Files/R/Data/Loose6S/L6s (2)/PCA0102_Loose6Small_ef135/", "*.txt", recursive=TRUE) | |
result10 <- list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Loose6S/L6s (2)/PCA0102_Loose6Small_ef135/") | |
name <- basename(path) | |
result10[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result10[]) | |
##normal-----result_N%PCA----- | |
#normal 123 | |
flist<- dir("C:/Program Files/R/Data/Normal123/normal/PCA01", "*.txt", recursive=TRUE) | |
result_N1p1<-list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Normal123/normal/PCA01") | |
name <- basename(path) | |
result_N1p1[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result_N1p1[path]) | |
View(result_N1p1) #3057 entries | |
flist<- dir("C:/Program Files/R/Data/Normal123/normal/PCA02", "*.txt", recursive=TRUE) | |
result_N1p2<-list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Normal123/normal/PCA02") | |
name <- basename(path) | |
result_N1p2[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result_N1p2[path]) | |
View(result_N1p2) #3057 entries | |
#normal 135 | |
flist<- dir("C:/Program Files/R/Data/Normal135/normal/PCA01", "*.txt", recursive=TRUE) | |
result_N2p1<-list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Normal135/normal/PCA01") | |
name <- basename(path) | |
result_N2p1[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result_N2p1[path]) | |
View(result_N2p1) #2092 entries | |
flist<- dir("C:/Program Files/R/Data/Normal135/normal/PCA02", "*.txt", recursive=TRUE) | |
result_N2p2<-list() | |
for(path in flist) { | |
setwd(dir = "C:/Program Files/R/Data/Normal135/normal/PCA02") | |
name <- basename(path) | |
result_N2p2[[path]]<-read_csv(path, col_names = FALSE) | |
} | |
View(result_N2p2[path]) | |
View(result_N2p2) #2092 entries | |
-------------------------- | |
# manipulate -------------------------------------------------------------- | |
#result1 | |
mean(result2$`3b_3P13PCA01_Normal01~06ef1Loose5Big01_1.txt`$X1) | |
par(mfcol = c(3,3)) | |
plot(result$`big (10).txt`$x1.1) | |
lb1_1 <- result | |
lb2_1 <- result2$`3b_3P13PCA01_Normal01~06ef1Loose5Big01_1.txt`$X1 | |
mean(lb2_1) | |
#result2 | |
lbb_1 <- result2$`3b_3P13PCA01_Normal01~06ef1Loose5Big01_1.txt`$X1 | |
View(result2[]) | |
for(i in 1:100){ | |
x = rnorm(200) | |
#data.frame(as.numeric(result2[])) | |
hist(x, main ="") | |
} | |
boxplot(result2$`3b_3P13PCA01_Normal01~06ef1Loose5Big01_1.txt`$X1) | |
layout(matrix(0.5,0.5,0.5,0.5)) | |
for(i in 1:10){ | |
i <- sample(result2[[]],10,replace = TRUE) | |
View(i) | |
} | |
# data_bind --------------------------------------------------------------- | |
r1 = as.data.frame(result) | |
r2 = as.data.frame(result2) | |
r3 = as.data.frame(result3) | |
r4 = as.data.frame(result4) | |
r5 = as.data.frame(result5) | |
r6 = as.data.frame(result6) | |
r7 = as.data.frame(result7) | |
r8 = as.data.frame(result8) | |
r9 = as.data.frame(result9) | |
r10 = as.data.frame(result10) | |
rN1p1 = as.data.frame(result_N1p1) | |
rN1p2 = as.data.frame(result_N1p2) | |
rN2p1 = as.data.frame(result_N2p1) | |
rN2p2 = as.data.frame(result_N2p2) | |
#?do.call() | |
A <- 2 | |
f <- function(x) print(x^2) | |
env <- new.env() | |
assign("A", 10, envir = env) | |
assign("f", f, envir = env) | |
f <- function(x) print(x) | |
f() | |
#````````{ | |
#你要從result,result1,result2,... 就開始改了 | |
#寫一個 result <- list() | |
#然後把原本的result放到result[[1]], result2放到result[[2]],... | |
#最後寫do.call(what = rbind, result)即可 | |
#``````````} | |
View(r2[sample(nrow(r2),30),]) | |
rr1<-r1[sample(nrow(r1),30),] | |
rr2<-r2[sample(nrow(r2),30),] | |
rr3<-r3[sample(nrow(r3),30),] | |
rr4<-r4[sample(nrow(r4),30),] | |
rr5<-r5[sample(nrow(r5),30),] | |
rr6<-r6[sample(nrow(r6),30),] | |
rr7<-r7[sample(nrow(r7),30),] | |
rr8<-r8[sample(nrow(r8),30),] | |
rr9<-r9[sample(nrow(r9),30),] | |
rr10<-r10[sample(nrow(r10),30),] | |
spc_all <- cbind(rr1,rr2,rr3,rr4,rr5,rr6,rr7,rr8,rr9,rr10) #numers ROW NOT MATCH | |
qqnorm(spc_all[6,]) | |
View(spc_all[2,]) | |
View(t(spc_all)) | |
#visualization-------------30graphics----- | |
#result2 | |
r2 = as.data.frame(result2) | |
par(mar = c(1,1,1,1),mfrow = c(6,5),mfcol = c(5,6)) | |
for(i in 1:30){ | |
x = r2[i,] | |
qqnorm(x);qqline(x,col = 2,xlab = "Z value") | |
} | |
layout(matrix(1,1,1)) #?T?w?e??1;1;1 <reconstruct graph | |
#result3 | |
r3 = as.data.frame(result3) | |
par(mar = c(1,1,1,1),mfrow = c(6,5),mfcol = c(5,6)) | |
for(i in 1:30){ | |
x = r3[i,] | |
qqnorm(x);qqline(x,col = 1,xlab = "Z value") | |
} | |
layout(matrix(1,1,1)) #?T?w?e??1;1;1 <reconstruct graph | |
#result4 | |
r4 = as.data.frame(result4) | |
par(mar = c(1,1,1,1),mfrow = c(6,5),mfcol = c(5,6)) | |
for(i in 1:30){ | |
x = r4[i,] | |
qqnorm(x);qqline(x,col = 3,xlab = "Z value") | |
} | |
layout(matrix(1,1,1)) #?T?w?e??1;1;1 <reconstruct graph | |
#result5 | |
r5 = as.data.frame(result5) | |
par(mar = c(1,1,1,1),mfrow = c(6,5),mfcol = c(5,6)) | |
for(i in 1:30){ | |
x = r5[i,] | |
qqnorm(x);qqline(x,col = 6,xlab = "Z value" ) | |
} | |
layout(matrix(1,1,1)) #adjust draftmap to 1;1;1 <reconstruct graph | |
------------------------------ | |
#result2 | |
r2 = as.data.frame(result2) | |
par(mar = c(1,1,1,1),mfrow = c(2,2)) | |
for(i in 1:6){ | |
y = r2[i,] | |
x = r2[,i] | |
z = seq(-10,10,0.01) | |
# boxplot(x) | |
contour(x,y,z) | |
} | |
layout(matrix(1,1,1)) #djust draftmap to 1;1;1 <reconstruct graph | |
plot(x=rN1[1,],y=rN1[2,],data = rN1) | |
##conclusion----- | |
for(i in 1:10){ | |
AAA <- print(shapiro.test(t(spc_all)[i,])) | |
shapiro.test(t(spc_all)[i,]) | |
if( AAA$p.value < 0.1){ | |
yyy <- print("Reject") | |
}else{ | |
print("Accept");break} | |
qqnorm(t(spc_all)[i,]);qqline(t(spc_all),col = 3); | |
} | |
#rN1p1 | |
count_Reject = 0 | |
for(i in 1:30) { | |
BBB <- print(shapiro.test(t(rN1p1[i,]))) | |
shapiro.test(t(rN1p1[i,])) | |
if( BBB$p.value < 0.1){ | |
yyy <- print("Reject") | |
count_Reject = count_Reject + 1 | |
}else{ | |
print("Accept"); | |
qqnorm(t(rN1p1[i,]));qqline(t(rN1p1[i,]),col = 10); | |
abline(h = -1:5, v = -2:3, col = "blue", lty = 3, lwd =1.5) | |
} | |
# aggregate(count_Reject) | |
} | |
print(count_Reject) | |
View(t(rN1p1[i,])) | |
View(t(rN1p1)) | |
?which() | |
BBB | |
#rN1p2 | |
count_Reject = 0 | |
for(i in 1:30) { | |
BBB <- print(shapiro.test(t(rN1p2[i,]))) | |
shapiro.test(t(rN1p2[i,])) | |
if( BBB$p.value < 0.1){ | |
yyy <- print("Reject") | |
count_Reject = count_Reject + 1 | |
}else{ | |
print("Accept"); | |
qqnorm(t(rN1p2[i,]));qqline(t(rN1p2[i,]),col = 10); | |
abline(h = -1:5, v = -2:3, col = "blue", lty = 3, lwd =1.5) | |
} | |
# aggregate(count_Reject) | |
} | |
print(count_Reject) | |
View(t(rN1p2[,1])) | |
#rN2p1 | |
count_Reject = 0 | |
for(i in 1:2092) { | |
BBB <- print(shapiro.test(t(rN2p1[i,]))) | |
shapiro.test(t(rN2p1[i,])) | |
if( BBB$p.value < 0.1){ | |
yyy <- print("Reject") | |
count_Reject = count_Reject + 1 | |
}else{ | |
print("Accept"); | |
qqnorm(t(rN2p1[i,]));qqline(t(rN2p1[i,]),col = 10); | |
abline(h = -1:5, v = -2:3, col = "blue", lty = 3, lwd =1.5) | |
} | |
# aggregate(count_Reject) | |
} | |
print(count_Reject) | |
#rN2p2 | |
count_Reject = 0 | |
for(i in 1:2092) { | |
BBB <- print(shapiro.test(t(rN2p2[i,]))) | |
shapiro.test(t(rN2p2[i,])) | |
if( BBB$p.value < 0.1){ | |
yyy <- print("Reject") | |
count_Reject = count_Reject + 1 | |
}else{ | |
print("Accept"); | |
qqnorm(t(rN2p2[i,]));qqline(t(rN2p2[i,]),col = 10); | |
abline(h = -1:5, v = -2:3, col = "blue", lty = 3, lwd =1.5) | |
} | |
# aggregate(count_Reject) | |
} | |
print(count_Reject) | |
shapiro_test_df <- function(df, bonf= TRUE, alpha= 0.05) { | |
l <- lapply(df, shapiro.test) | |
s <- do.call("c", lapply(l, "[[", 1)) | |
p <- do.call("c", lapply(l, "[[", 2)) | |
if (bonf == TRUE) { | |
sig <- ifelse(p > alpha / length(l), "H0", "Ha") | |
} else { | |
sig <- ifelse(p < alpha, "H0", "Ha") | |
} | |
return(list(statistic= s, | |
p.value= p, | |
significance= sig, | |
method= ifelse(bonf == TRUE, "Shapiro-Wilks test with Bonferroni Correction", | |
"Shapiro-Wilks test without Bonferroni Correction"))) | |
} | |
shapiro_test_df(spc_all[,1]) | |
for( i in 1:10 ){ | |
temp <- paste("rr",i,sep = "") | |
#RBdata = temp[sample(nrow(temp),30),] | |
} | |
temp <- paste("rr",1:10,sep = "") | |
f3 <- function(n){ | |
df <- data.frame(x = numeric(n), y = character(n), stringsAsFactors = FALSE) | |
for(i in 1:n){ | |
df$x[i] <- i | |
df$y[i] <- toString(i) | |
} | |
df | |
} |
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