From f92cc2ed89ea77d206866231247cc5fa28e564ed Mon Sep 17 00:00:00 2001 From: ranke Date: Thu, 24 Feb 2005 14:53:32 +0000 Subject: I added the possibility to select one from the possible fits in the drfit function, so only one fit is reported per substance. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@12 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc --- R/drfit.R | 111 +++++++++++++++++++++++++++++++++----------------------------- 1 file changed, 60 insertions(+), 51 deletions(-) (limited to 'R/drfit.R') diff --git a/R/drfit.R b/R/drfit.R index 20f4426..70e05df 100644 --- a/R/drfit.R +++ b/R/drfit.R @@ -51,6 +51,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, splitted <- split(data,data$substance) for (i in substances) { tmp <- splitted[[i]] + fit <- FALSE if (length(tmp$response) == 0) { nodata = TRUE } else { @@ -73,29 +74,31 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, if (responseathighestdose < 0.5) { inactive <- FALSE - if (lognorm) { - m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,slope), - data=tmp, - start=list(logEC50=startlogEC50[[i]],slope=1))) + if (linearlogis) { + m <- try(nls(response ~ linearlogisf(dose,1,f,logEC50,b), + data=tmp, + start=list(f=f0,logEC50=startlogEC50[[i]],b=b0))) if (!inherits(m, "try-error")) { - s <- summary(m) + fit <- TRUE ri <- ri + 1 + s <- summary(m) sigma[[ri]] <- s$sigma rsubstance[[ri]] <- i rn[[ri]] <- n rlld[[ri]] <- log10(lowestdose) rlhd[[ri]] <- log10(highestdose) - mtype[[ri]] <- "lognorm" + mtype[[ri]] <- "linearlogis" logEC50[[ri]] <- coef(m)[["logEC50"]] - b[[ri]] <- NA - f[[ri]] <- NA + slope[[ri]] <- NA if (logEC50[[ri]] > rlhd[[ri]]) { logEC50[[ri]] <- NA - slope[[ri]] <- NA stderrlogEC50[[ri]] <- NA + b[[ri]] <- NA + f[[ri]] <- NA } else { - slope[[ri]] <- coef(m)[["slope"]] stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"] + b[[ri]] <- coef(m)[["b"]] + f[[ri]] <- coef(m)[["f"]] } } } @@ -106,56 +109,62 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, m <- try(nls(response ~ plogis(-log10(dose),-logEC50,slope), data=tmp, start=list(logEC50=startlogEC50[[i]],slope=1))) - if (!inherits(m, "try-error")) { - s <- summary(m) - ri <- ri + 1 - rsubstance[[ri]] <- i - rn[[ri]] <- n - rlld[[ri]] <- log10(lowestdose) - rlhd[[ri]] <- log10(highestdose) - mtype[[ri]] <- "logis" - sigma[[ri]] <- s$sigma - logEC50[[ri]] <- coef(m)[["logEC50"]] - b[[ri]] <- NA - f[[ri]] <- NA - if (logEC50[[ri]] > rlhd[[ri]]) { - logEC50[[ri]] <- NA - slope[[ri]] <- NA - stderrlogEC50[[ri]] <- NA - } else { - slope[[ri]] <- coef(m)[["slope"]] - stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"] + if (chooseone==FALSE || fit==FALSE) { + if (!inherits(m, "try-error")) { + fit <- TRUE + ri <- ri + 1 + s <- summary(m) + sigma[[ri]] <- s$sigma + rsubstance[[ri]] <- i + rn[[ri]] <- n + rlld[[ri]] <- log10(lowestdose) + rlhd[[ri]] <- log10(highestdose) + mtype[[ri]] <- "logis" + logEC50[[ri]] <- coef(m)[["logEC50"]] + b[[ri]] <- NA + f[[ri]] <- NA + if (logEC50[[ri]] > rlhd[[ri]]) { + logEC50[[ri]] <- NA + slope[[ri]] <- NA + stderrlogEC50[[ri]] <- NA + } else { + slope[[ri]] <- coef(m)[["slope"]] + stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"] + } } } } - if (linearlogis) { - m <- try(nls(response ~ linearlogisf(dose,1,f,logEC50,b), - data=tmp, - start=list(f=f0,logEC50=startlogEC50[[i]],b=b0))) - if (!inherits(m, "try-error")) { - s <- summary(m) - ri <- ri + 1 - rsubstance[[ri]] <- i - rn[[ri]] <- n - rlld[[ri]] <- log10(lowestdose) - rlhd[[ri]] <- log10(highestdose) - mtype[[ri]] <- "linearlogis" - sigma[[ri]] <- s$sigma - logEC50[[ri]] <- coef(m)[["logEC50"]] - slope[[ri]] <- NA - if (logEC50[[ri]] > rlhd[[ri]]) { - logEC50[[ri]] <- NA - stderrlogEC50[[ri]] <- NA + if (lognorm) { + m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,slope), + data=tmp, + start=list(logEC50=startlogEC50[[i]],slope=1))) + if (chooseone==FALSE || fit==FALSE) { + if (!inherits(m, "try-error")) { + fit <- TRUE + ri <- ri + 1 + s <- summary(m) + sigma[[ri]] <- s$sigma + rsubstance[[ri]] <- i + rn[[ri]] <- n + rlld[[ri]] <- log10(lowestdose) + rlhd[[ri]] <- log10(highestdose) + mtype[[ri]] <- "lognorm" + logEC50[[ri]] <- coef(m)[["logEC50"]] b[[ri]] <- NA f[[ri]] <- NA - } else { - stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"] - b[[ri]] <- coef(m)[["b"]] - f[[ri]] <- coef(m)[["f"]] + if (logEC50[[ri]] > rlhd[[ri]]) { + logEC50[[ri]] <- NA + slope[[ri]] <- NA + stderrlogEC50[[ri]] <- NA + } else { + slope[[ri]] <- coef(m)[["slope"]] + stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"] + } } } } + } else { inactive <- TRUE } -- cgit v1.2.1