From c5315525c80a6822eef2311e6b0733ee5018db60 Mon Sep 17 00:00:00 2001 From: ranke Date: Mon, 3 Apr 2006 16:28:19 +0000 Subject: - The drplot function now accepts custom xlim and ylim values - Confidence intervals for the EC50 can now (again) be generated by drfit by giving the argument conf=TRUE - Update of the INDEX git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@62 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc --- R/drfit.R | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) (limited to 'R/drfit.R') diff --git a/R/drfit.R b/R/drfit.R index ff03d90..1bbffa8 100644 --- a/R/drfit.R +++ b/R/drfit.R @@ -1,6 +1,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, probit = TRUE, logit = FALSE, weibull = FALSE, - linlogit = FALSE, linlogitWrong = NA, allWrong = NA, + linlogit = FALSE, conf = FALSE, + linlogitWrong = NA, allWrong = NA, s0 = 0.5, b0 = 2, f0 = 0) { if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data with @@ -20,6 +21,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, sigma <- array() # the standard deviation of the residuals logED50 <- vector() stderrlogED50 <- vector() + conflogED50 <- vector() a <- b <- c <- vector() splitted <- split(data,data$substance) @@ -47,7 +49,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, n <- ndl <- 0 } else { ndl <- length(levels(factor(tmp$dose))) - n <- round(length(tmp$response)/ndl) + n <- length(tmp$response) if (is.na(startlogED50[i])){ w <- 1/abs(tmp$response - 0.3) startlogED50[[i]] <- sum(w * log10(tmp$dose))/sum(w) @@ -86,12 +88,14 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, mtype[[ri]] <- "no fit" logED50[[ri]] <- NA stderrlogED50[[ri]] <- NA + conflogED50[[ri]] <- NA a[[ri]] <- NA b[[ri]] <- NA c[[ri]] <- NA } else { mtype[[ri]] <- "linlogit" stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"] + conflogED50[[ri]] <- stderrlogED50[[ri]] * qt(0.975, n - 3) a[[ri]] <- coef(m)[["logED50"]] b[[ri]] <- coef(m)[["b"]] c[[ri]] <- coef(m)[["f"]] @@ -122,11 +126,13 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, mtype[[ri]] <- "no fit" logED50[[ri]] <- NA stderrlogED50[[ri]] <- NA + conflogED50[[ri]] <- NA a[[ri]] <- NA b[[ri]] <- NA } else { mtype[[ri]] <- "probit" stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"] + conflogED50[[ri]] <- stderrlogED50[[ri]] * qt(0.975, n - 2) a[[ri]] <- coef(m)[["logED50"]] b[[ri]] <- coef(m)[["scale"]] } @@ -158,11 +164,13 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, mtype[[ri]] <- "no fit" logED50[[ri]] <- NA stderrlogED50[[ri]] <- NA + conflogED50[[ri]] <- NA a[[ri]] <- NA b[[ri]] <- NA } else { mtype[[ri]] <- "logit" stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"] + conflogED50[[ri]] <- stderrlogED50[[ri]] * qt(0.975, n - 2) } } } @@ -196,11 +204,13 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, mtype[[ri]] <- "no fit" logED50[[ri]] <- NA stderrlogED50[[ri]] <- NA + conflogED50[[ri]] <- NA a[[ri]] <- NA b[[ri]] <- NA } else { mtype[[ri]] <- "weibull" stderrlogED50[[ri]] <- NA + conflogED50[[ri]] <- stderrlogED50[[ri]] * qt(0.975, n - 2) } } } @@ -238,13 +248,21 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, sigma[[ri]] <- NA logED50[[ri]] <- NA stderrlogED50[[ri]] <- NA + conflogED50[[ri]] <- NA a[[ri]] <- NA b[[ri]] <- NA c[[ri]] <- NA } } - results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, logED50, stderrlogED50, runit, sigma, a, b) - names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50","std","unit","sigma","a","b") + if (conf) + { + results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, logED50, conflogED50, runit, sigma, a, b) + names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50","conf","unit","sigma","a","b") + } else { + results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, logED50, stderrlogED50, runit, sigma, a, b) + names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50","std","unit","sigma","a","b") + } + if (linlogit) { results$c <- c } -- cgit v1.2.1