Question

比方说，我正在研究两个主题（实际上是其中的20个）。由于每个主题都生成27个文件，我需要将它们合并以生成另外9个文件，因此我想使这一过程自动化！

我有一个因素在九个层面上有所不同： AA，AB，AM，BA，BB，BM，MA，MB，MM。

对于每种治疗，我都会得到三个输出文件，例如，对于AA治疗，我会得到： AA1.csv，AA1.txt和AA1log.txt。

我将需要在这些文件上运行一个脚本（我们称其为R1）；它将它们合并到一个摘要文件中。然后，我需要在生成的所有摘要文件上运行另一个脚本（我将其称为R2）。

所有主题的所有输出文件都在一个文件夹“ data”中。

（对于R示例，感谢@ManuelBickel）

# make sure you are in a safe directory!

### Generate the toy data ###

# I define the main directories I need
dir_project = "test"
dirs = list(
  dir_project = dir_project
  ,dir_data = paste0(dir_project, "/data")
  ,dir_summary = paste0(dir_project, "/summary")
  ,dir_plots= paste0(dir_project, "/plots")
)
# create dirs
lapply(dirs, dir.create)

# create some exemplary data and write it in dir
m = matrix(1:4, nrow = 2)
data = list(AA = m, AB = m, AM = m
            ,BA = m, BB = m, BM = m,
            MA = m, MB = m, MM =m)

# generate the csv files for subject 1 and 2
for (i in 1:length(data)) {
  write.csv(data[[i]], file = paste0(dirs[["dir_data"]], "/", names(data[i]), "1.csv"))  
}

for (i in 1:length(data)) {
write.csv(data[[i]], file = paste0(dirs[["dir_data"]], "/", names(data[i]), "2.csv"))  
}

# Generate the .txt files for subjects 1 and 2
for (i in
1:length(data)) {
  write.table(data[[i]], file = paste0(dirs[["dir_data"]], "/", names(data[i]), "1.txt"))  
}

for (i in 1:length(data)) {
  write.table(data[[i]], file = paste0(dirs[["dir_data"]], "/", names(data[i]), "2.txt"))  
}

 # Generate the log.txt files for subjects 1 and 2
for (i in 1:length(data)) {
  write.table(data[[i]], file = paste0(dirs[["dir_data"]], "/", names(data[i]), "1log.txt"))  
}

for (i in 1:length(data)) {
  write.table(data[[i]], file = paste0(dirs[["dir_data"]], "/", names(data[i]), "2log.txt"))  
}

以下是我的数据文件夹中的文件：

list.files(dirs[["dir_data"]])

# [1] "AA1.csv"    "AA1.txt"    "AA1log.txt" "AA2.csv"    "AA2.txt"    "AA2log.txt" "AB1.csv"    "AB1.txt"    "AB1log.txt"
# [10] "AB2.csv"    "AB2.txt"    "AB2log.txt" "AM1.csv"    "AM1.txt"    "AM1log.txt" "AM2.csv"    "AM2.txt"    "AM2log.txt"
# [19] "BA1.csv"    "BA1.txt"    "BA1log.txt" "BA2.csv"    "BA2.txt"    "BA2log.txt" "BB1.csv"    "BB1.txt"    "BB1log.txt"
# [28] "BB2.csv"    "BB2.txt"    "BB2log.txt" "BM1.csv"    "BM1.txt"    "BM1log.txt" "BM2.csv"    "BM2.txt"    "BM2log.txt"
# [37] "MA1.csv"    "MA1.txt"    "MA1log.txt" "MA2.csv"    "MA2.txt"    "MA2log.txt" "MB1.csv"    "MB1.txt"    "MB1log.txt"
# [46] "MB2.csv"    "MB2.txt"    "MB2log.txt" "MM1.csv"    "MM1.txt"    "MM1log.txt" "MM2.csv"    "MM2.txt"    "MM2log.txt"

现在，我需要我的代码来选择文件：AA1.csv，AA1.txt和AA1log.txt，并在它们上运行脚本R1。

脚本R1将生成一个csv文件作为输出，该文件将以“ summaryAA1_csv”的形式进入文件夹“ data”。它还将生成32 png。文件（AA1_1.png，AA1_2.png等），这些文件将进入文件夹“ plots”中的子文件夹“ AA1”。

然后，我将从文件夹“数据”中选择主题1的所有摘要文件，然后运行脚本R2。

基本上，首先我需要选择主题1产生的所有数据集；然后我需要选择通过相同处理生成的那些（首先是所有AA，然后是AB）。经过9种治疗后，我将转到主题2。

让我们说这就是R1在做的事情：

temp = read.csv("test/data/AA1.csv", sep=",", row.names=1)
temp1 <- as.matrix(temp) 
temp2 <- read.table("test/data/AA1.txt")
temp3 <- read.table("test/data/AA1log.txt")
summaryAA1 <- temp1 + temp2 + temp3
summaryAA1

在我编写R1代码时，它还会生成位于不同文件夹中的图（每次处理32张！）

dir.create("test/plots/AA1plots")
png(filename="test/plots//AA1plots/AA1_1_plot.png")
plot(summaryAA1)
dev.off()

我的问题是如何使我的代码两次选择文件；首先选择引用相同治疗（AA）和相同主题编号的文件；运行完所有处理后，移至引用第二个主题的相同处理的文件。

我也乐意接受有关更方便的命名系统的建议，这可能会使循环更加方便。

Answer 1

请考虑组织输入（受试者和治疗组合的列表）和过程（R1和R2）。然后适当地打电话给他们：

subjects <- c(1, 2)
treatments <- c("AA", "AB", "AM", "BA", "BB", "BM", "MA", "MB", "MM")

r1_list <- as.vector(sapply(subjects, function(x,y) paste0(y,x), treatments))
# [1] "AA1" "AB1" "AM1" "BA1" "BB1" "BM1" "MA1" "MB1" "MM1" "AA2" "AB2" "AM2" "BA2" "BB2" "BM2" "MA2" "MB2" "MM2"

r2_list <- sapply(subjects, function(x,y) paste0(y,x), treatments, simplify = FALSE)
r2_list
# [[1]]
# [1] "AA1" "AB1" "AM1" "BA1" "BB1" "BM1" "MA1" "MB1" "MM1"

# [[2]]
# [1] "AA2" "AB2" "AM2" "BA2" "BB2" "BM2" "MA2" "MB2" "MM2"

R1脚本

setwd("test")

my_func1 <- function(f){
    temp = read.csv(paste0("data/", f, ".csv"), row.names=1)
    temp1 <- as.matrix(temp) 
    temp2 <- read.table(paste0("data/", f, ".txt"))
    temp3 <- read.table(paste0("data/", f, "log.txt"))

    # SUMMARIES
    summary_all <- temp1 + temp2 + temp3
    summary_data <- read.csv(paste0("summary", f, ".csv"))

    ...

    # IMAGES
    for (i in seq(1,32)) {
        dir.create(paste0("plots/", f, "plots"))
        png(filename=paste0("plots/", f, "plots/", f, "_", i, "_plot.png"))
        plot(...)
        dev.off()
    }
}

# CREATE ALL SUMMARY AND IMAGE FILES
for (j in r1_list) my_func1(j)

R2脚本

my_func2 <- function(items){
    files <- paste0("summary", items, ".csv")

    # READ ALL SUMMARY FILES INTO A LIST OF DATA FRAMES
    df_list <- lapply(files, read.csv)

    # PROCESS LIST
    ...    
}

# PROCESS SUMMARY FILES
for (j in r2_list) my_func2(j)

如何在R

1 个答案: