1. MiPP
  2. R
  3. logistic.R
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MiPP@13527 bc3139a8-67e5-0310-9ffc-ced21a209358

HyungJun Cho authored on 10/08/2005 18:32:37
Showing 1 changed files
R/logistic.R
History View file @ dfe8a46
... ... 
@@ -1,27 +1,24 @@
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-get.mipp.logistic <- function(x.train, y.train, x.test, y.test){
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-
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-	y.train <- factor(y.train)
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-	levels(y.train) <- c("1","0")
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-	y.test <- factor(y.test)
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-	levels(y.test) <- c("1","0")
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-
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-        if(is.data.frame(x.train)) x.train <- as.matrix(x.train)
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-        if(is.data.frame(x.test))  x.test  <- as.matrix(x.test)
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-
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-	fit <- glm(y.train ~ x.train, family="binomial")
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-
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-	predx <- cbind(1, x.test)%*%t(matrix(fit$coef, nrow=1))
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-	prob <- 1/(1+exp(-predx))
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-
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-	postdf <- data.frame(prob, y.test)
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-	post.prob <- ifelse(postdf$y.test=="1", 1-postdf$prob, postdf$prob)
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-	ind <- ifelse(post.prob > .5, 1, 0)
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-
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-	N <- length(y.test)
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-	nMiss <- N - sum(ind)
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-	Er <- nMiss/N
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-	MiPP <- sum(post.prob)-nMiss
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-	sMiPP <- MiPP/N
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-
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-	return(list(N.Miss=nMiss, ErrorRate=Er, MiPP=MiPP, sMiPP=sMiPP))
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-}
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+get.mipp.logistic <- function(x.train, y.train, x.test, y.test){
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+
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+	y.train <- factor(y.train); levels(y.train) <- c("1","0")
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+	y.test <- factor(y.test); levels(y.test) <- c("1","0")
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+      if(is.data.frame(x.train)) x.train <- as.matrix(x.train)
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+      if(is.data.frame(x.test))  x.test  <- as.matrix(x.test)
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+
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+	fit <- glm(y.train ~ x.train, family="binomial")
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+
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+	predx <- cbind(1, x.test)%*%t(matrix(fit$coef, nrow=1))
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+	prob <- 1/(1+exp(-predx))
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+
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+	postdf <- data.frame(prob, y.test)
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+	post.prob <- ifelse(postdf$y.test=="1", 1-postdf$prob, postdf$prob)
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+	ind <- ifelse(post.prob > .5, 1, 0)
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+
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+	N <- length(y.test)
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+	nMiss <- N - sum(ind)
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+	Er <- nMiss/N
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+	MiPP <- sum(post.prob)-nMiss
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+	sMiPP <- MiPP/N
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+
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+	return(list(N.Miss=nMiss, ErrorRate=Er, MiPP=MiPP, sMiPP=sMiPP))
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+}
Browse code

Add MiPP package. Initial version.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MiPP@11863 bc3139a8-67e5-0310-9ffc-ced21a209358

Seth Falcon authored on 18/04/2005 17:05:11
Showing 1 changed files
R/logistic.R
History View file @ 52b033c
1 1 
new file mode 100644
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@@ -0,0 +1,27 @@
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+get.mipp.logistic <- function(x.train, y.train, x.test, y.test){
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+
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+	y.train <- factor(y.train)
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+	levels(y.train) <- c("1","0")
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+	y.test <- factor(y.test)
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+	levels(y.test) <- c("1","0")
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+
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+        if(is.data.frame(x.train)) x.train <- as.matrix(x.train)
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+        if(is.data.frame(x.test))  x.test  <- as.matrix(x.test)
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+
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+	fit <- glm(y.train ~ x.train, family="binomial")
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+
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+	predx <- cbind(1, x.test)%*%t(matrix(fit$coef, nrow=1))
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+	prob <- 1/(1+exp(-predx))
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+
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+	postdf <- data.frame(prob, y.test)
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+	post.prob <- ifelse(postdf$y.test=="1", 1-postdf$prob, postdf$prob)
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+	ind <- ifelse(post.prob > .5, 1, 0)
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+
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+	N <- length(y.test)
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+	nMiss <- N - sum(ind)
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+	Er <- nMiss/N
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+	MiPP <- sum(post.prob)-nMiss
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+	sMiPP <- MiPP/N
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+
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+	return(list(N.Miss=nMiss, ErrorRate=Er, MiPP=MiPP, sMiPP=sMiPP))
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+}