From 27a255ea7e95c1924f34a5d3aa0bcd39ad902b98 Mon Sep 17 00:00:00 2001 From: ranke Date: Sat, 1 Apr 2006 04:41:28 +0000 Subject: Corrected the split of the drift.R file. Added example data IM1xIPC81. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@61 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc --- R/linlogitf.R | 254 ---------------------------------------------------------- 1 file changed, 254 deletions(-) (limited to 'R/linlogitf.R') diff --git a/R/linlogitf.R b/R/linlogitf.R index 2af8b7e..2d69256 100644 --- a/R/linlogitf.R +++ b/R/linlogitf.R @@ -2,257 +2,3 @@ linlogitf <- function(x,k,f,mu,b) { k*(1 + f*x) / (1 + ((2*f*(10^mu) + 1) * ((x/(10^mu))^b))) } - -drfit <- function(data, startlogED50 = NA, chooseone=TRUE, - probit = TRUE, logit = FALSE, weibull = FALSE, - linlogit = FALSE, linlogitWrong = NA, allWrong = NA, - s0 = 0.5, b0 = 2, f0 = 0) -{ - if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data with - # ok set to "no fit" - substances <- levels(data$substance) - - ri <- rix <- 0 # ri is the index over the result rows - # rix is used later to check if any - # model result was appended - rsubstance <- array() # the substance names in the results - rndl <- vector() # number of dose levels - rn <- vector() # mean number of replicates - # in each dose level - runit <- vector() # vector of units for each result row - rlhd <- rlld <- vector() # highest and lowest doses tested - mtype <- array() # the modeltypes - sigma <- array() # the standard deviation of the residuals - logED50 <- vector() - stderrlogED50 <- vector() - a <- b <- c <- vector() - - splitted <- split(data,data$substance) - for (i in substances) { - tmp <- splitted[[i]] - fit <- FALSE - if (length(tmp) != 0) { - unit <- levels(as.factor(as.vector(tmp$unit))) - cat("\n",i,": Fitting data...\n",sep="") - } else { - unit <- "" - cat("\n",i,": No data\n",sep="") - } - if (length(unit) > 1) { - cat("More than one unit for substance ",i,", halting\n\n",sep="") - break - } - if (length(tmp$response) == 0) { - nodata = TRUE - } else { - nodata = FALSE - } - rix <- ri - if (nodata) { - n <- ndl <- 0 - } else { - ndl <- length(levels(factor(tmp$dose))) - n <- round(length(tmp$response)/ndl) - if (is.na(startlogED50[i])){ - w <- 1/abs(tmp$response - 0.3) - startlogED50[[i]] <- sum(w * log10(tmp$dose))/sum(w) - } - highestdose <- max(tmp$dose) - lowestdose <- min(tmp$dose) - lhd <- log10(highestdose) - lld <- log10(lowestdose) - responseathighestdose <- mean(subset(tmp,dose==highestdose)$response) - responseatlowestdose <- mean(subset(tmp,dose==lowestdose)$response) - if (responseathighestdose < 0.5) { - inactive <- FALSE - if (responseatlowestdose < 0.5) { - active <- TRUE - } else { - active <- FALSE - if (linlogit && - length(subset(linlogitWrong,linlogitWrong == i))==0 && - length(subset(allWrong,allWrong == i))==0) { - m <- try(nls(response ~ linlogitf(dose,1,f,logED50,b), - data=tmp, - start=list(f=f0,logED50=startlogED50[[i]],b=b0))) - if (!inherits(m, "try-error")) { - fit <- TRUE - ri <- ri + 1 - s <- summary(m) - sigma[[ri]] <- s$sigma - rsubstance[[ri]] <- i - rndl[[ri]] <- ndl - rn[[ri]] <- n - runit[[ri]] <- unit - rlld[[ri]] <- log10(lowestdose) - rlhd[[ri]] <- log10(highestdose) - logED50[[ri]] <- coef(m)[["logED50"]] - if (logED50[[ri]] > rlhd[[ri]]) { - mtype[[ri]] <- "no fit" - logED50[[ri]] <- NA - stderrlogED50[[ri]] <- NA - a[[ri]] <- NA - b[[ri]] <- NA - c[[ri]] <- NA - } else { - mtype[[ri]] <- "linlogit" - stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"] - a[[ri]] <- coef(m)[["logED50"]] - b[[ri]] <- coef(m)[["b"]] - c[[ri]] <- coef(m)[["f"]] - } - } - } - - if (probit && - length(subset(allWrong,allWrong == i))==0) { - m <- try(nls(response ~ pnorm(-log10(dose),-logED50,scale), - data=tmp, - start=list(logED50=startlogED50[[i]],scale=1))) - if (chooseone==FALSE || fit==FALSE) { - if (!inherits(m, "try-error")) { - fit <- TRUE - ri <- ri + 1 - s <- summary(m) - sigma[[ri]] <- s$sigma - rsubstance[[ri]] <- i - rndl[[ri]] <- ndl - rn[[ri]] <- n - runit[[ri]] <- unit - rlld[[ri]] <- log10(lowestdose) - rlhd[[ri]] <- log10(highestdose) - logED50[[ri]] <- coef(m)[["logED50"]] - c[[ri]] <- NA - if (logED50[[ri]] > rlhd[[ri]]) { - mtype[[ri]] <- "no fit" - logED50[[ri]] <- NA - stderrlogED50[[ri]] <- NA - a[[ri]] <- NA - b[[ri]] <- NA - } else { - mtype[[ri]] <- "probit" - stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"] - a[[ri]] <- coef(m)[["logED50"]] - b[[ri]] <- coef(m)[["scale"]] - } - } - } - } - - if (logit && - length(subset(allWrong,allWrong == i))==0) { - m <- try(nls(response ~ plogis(-log10(dose),-logED50,scale), - data=tmp, - start=list(logED50=startlogED50[[i]],scale=1))) - if (chooseone==FALSE || fit==FALSE) { - if (!inherits(m, "try-error")) { - fit <- TRUE - ri <- ri + 1 - s <- summary(m) - sigma[[ri]] <- s$sigma - rsubstance[[ri]] <- i - rndl[[ri]] <- ndl - rn[[ri]] <- n - runit[[ri]] <- unit - rlld[[ri]] <- log10(lowestdose) - rlhd[[ri]] <- log10(highestdose) - logED50[[ri]] <- a[[ri]] <- coef(m)[["logED50"]] - b[[ri]] <- coef(m)[["scale"]] - c[[ri]] <- NA - if (logED50[[ri]] > rlhd[[ri]]) { - mtype[[ri]] <- "no fit" - logED50[[ri]] <- NA - stderrlogED50[[ri]] <- NA - a[[ri]] <- NA - b[[ri]] <- NA - } else { - mtype[[ri]] <- "logit" - stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"] - } - } - } - } - - if (weibull && - length(subset(allWrong,allWrong == i))==0) { - m <- try(nls(response ~ pweibull(-log10(dose)+location,shape), - data=tmp, - start=list(location=startlogED50[[i]],shape=s0))) - if (chooseone==FALSE || fit==FALSE) { - if (!inherits(m, "try-error")) { - fit <- TRUE - ri <- ri + 1 - s <- summary(m) - sigma[[ri]] <- s$sigma - rsubstance[[ri]] <- i - rndl[[ri]] <- ndl - rn[[ri]] <- n - runit[[ri]] <- unit - rlld[[ri]] <- log10(lowestdose) - rlhd[[ri]] <- log10(highestdose) - a[[ri]] <- coef(m)[["location"]] - b[[ri]] <- coef(m)[["shape"]] - sqrdev <- function(logdose) { - (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2 - } - logED50[[ri]] <- nlm(sqrdev,startlogED50[[i]])$estimate - c[[ri]] <- NA - if (logED50[[ri]] > rlhd[[ri]]) { - mtype[[ri]] <- "no fit" - logED50[[ri]] <- NA - stderrlogED50[[ri]] <- NA - a[[ri]] <- NA - b[[ri]] <- NA - } else { - mtype[[ri]] <- "weibull" - stderrlogED50[[ri]] <- NA - } - } - } - } - - } - - } else { - inactive <- TRUE - } - } - if (ri == rix) { # if no entry was appended for this substance - ri <- ri + 1 - rsubstance[[ri]] <- i - rndl[[ri]] <- ndl - rn[[ri]] <- n - if (nodata) { - rlld[[ri]] <- rlhd[[i]] <- NA - mtype[[ri]] <- "no data" - runit[[ri]] <- NA - } else { - rlld[[ri]] <- log10(lowestdose) - rlhd[[i]] <- log10(highestdose) - runit[[ri]] <- unit - if (inactive) { - mtype[[ri]] <- "inactive" - } else { - if (active) { - mtype[[ri]] <- "active" - } else { - mtype[[ri]] <- "no fit" - } - } - } - sigma[[ri]] <- NA - logED50[[ri]] <- NA - stderrlogED50[[ri]] <- NA - a[[ri]] <- NA - b[[ri]] <- NA - c[[ri]] <- NA - } - } - results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, logED50, stderrlogED50, runit, sigma, a, b) - names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50","std","unit","sigma","a","b") - if (linlogit) { - results$c <- c - } - rownames(results) <- 1:ri - return(results) -} -- cgit v1.2.1