functions

yswutan · Jun 27, 2021 · b6cdcbd · b6cdcbd
1 parent 1c503be
commit b6cdcbd
Show file tree

Hide file tree

Showing 20 changed files with 352 additions and 1 deletion.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.Rproj.user/8CBC3624/persistent-state b/.Rproj.user/8CBC3624/persistent-state
@@ -0,0 +1,2 @@
+activeClientUrl="http://144.214.26.7:8787/"
+portToken="a801f04d248d"
diff --git a/.Rproj.user/8CBC3624/sources/s-86792e95/lock_file b/.Rproj.user/8CBC3624/sources/s-86792e95/lock_file
@@ -0,0 +1 @@
+317786
diff --git a/.Rproj.user/shared/notebooks/patch-chunk-names b/.Rproj.user/shared/notebooks/patch-chunk-names
diff --git a/ClinClean.Rproj b/ClinClean.Rproj
@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,13 @@
+Package: ClinClean
+Type: Package
+Title: convert clinical follow up to overall survival and disease-free survival
+Version: 0.1.0
+Author: person(given = "Tan", family = "Wu", email = "[email protected]", role = c("aut", "cre"))
+Maintainer: The package maintainer <[email protected]>
+Description: This package could convert clinical follow up to overall survival and disease-free survival
+License: GPL
+Encoding: UTF-8
+LazyData: true
+Imports: 
+    tcltk
+RoxygenNote: 7.1.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1 @@
+exportPattern("^[[:alpha:]]+")
diff --git a/README.md b/README.md
@@ -1 +1,35 @@
-# ClinClean
+# ClinClean
+
+## Install
+```
+devtools::install_github("yswutan/ClinClean")
+library(ClinClean)
+```
+
+
+## Step 1: read clinical raw data
+sheet0: follow up; 
+sheet1: patient information
+```
+sheet0 <- read.table("20191121-1611_follow_data_sheet0.txt", header=T, sep="\t", quote="", fileEncoding="UTF-8", fill=T, stringsAsFactors=FALSE)
+sheet1 <- read.table("20191121-1611_follow_data_sheet1_part.txt", header=T, sep="\t", quote="", fileEncoding="UTF-8", stringsAsFactors=FALSE)
+```
+## Step 2: combination
+```
+sheet <- SheetConvert(sheet0, sheet1)
+```
+## Step 3: processing
+1.OS: 死亡病人：死亡时间-入院时间 （若入院时间比手术日期晚，则选手术日期）；
+                有的病人确认死亡，但是没有死亡时间，取最后一次随访时间作为截止日期；
+      未死亡病人：最后一次随访时间-入院时间 （若入院时间比手术日期晚，则选手术日期）
+
+2.DFS: 复发病人：复发/转移时间-手术日期；
+       无复发病人：最后一次随访时间/死亡时间-手术日期；
+       无复发，死亡，但是没有死亡时间：取最后一次随访时间作为截止日期，减去手术日期
+
+3.DFS <= OS
+```
+ID1 <- unique(sheet1$'住院号')
+OS <- OSProcess(sheet, ID1, "max", Ceiling=TRUE)
+DFS <- DFSProcess(sheet, ID1, "FollowUp", Ceiling=TRUE)
+```
diff --git a/man/DFSCalculate.Rd b/man/DFSCalculate.Rd
diff --git a/man/DFSProcess.Rd b/man/DFSProcess.Rd
diff --git a/man/FollwUpRelapse.Rd b/man/FollwUpRelapse.Rd
diff --git a/man/OSCalculate.Rd b/man/OSCalculate.Rd
diff --git a/man/OSProcess.Rd b/man/OSProcess.Rd
diff --git a/man/PreRelapseRecordDateProcess.Rd b/man/PreRelapseRecordDateProcess.Rd
diff --git a/man/RelapseDate.Rd b/man/RelapseDate.Rd
diff --git a/man/RelapseDateProcess.Rd b/man/RelapseDateProcess.Rd
diff --git a/man/SheetConvert.Rd b/man/SheetConvert.Rd
diff --git a/man/preRelapseRecord.Rd b/man/preRelapseRecord.Rd
diff --git a/man/replication2.Rd b/man/replication2.Rd
diff --git a/man/timerank.Rd b/man/timerank.Rd
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		activeClientUrl="http://144.214.26.7:8787/"
		portToken="a801f04d248d"