diff options
| author | ranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc> | 2005-07-07 12:19:33 +0000 |
|---|---|---|
| committer | ranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc> | 2005-07-07 12:19:33 +0000 |
| commit | 3e1ab23d4c457386882473a4de3b76b4c327f3b3 (patch) | |
| tree | 0c108c820951022f73f3751000909ba622934e41 | |
| parent | 9b08a42e6eb2c35818f904b309da5632fa3eff1c (diff) | |
Added the possibility to simultaneously fit dose-response curves with different
units in drfit. Added cat output from drfit to keep track of which substance is currently
being worked on.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@26 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/drfit.R | 22 |
2 files changed, 21 insertions, 5 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index d082ff6..d8b55a7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drfit -Version: 0.03-25 -Date: 2005-05-19 +Version: 0.03-26 +Date: 2005-07-07 Title: Dose-response data evaluation Author: Johannes Ranke <jranke@uni-bremen.de> Maintainer: Johannes Ranke <jranke@uni-bremen.de> @@ -41,15 +41,16 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, linearlogis = FALSE, linearlogisWrong = NA, allWrong = NA, b0 = 2, f0 = 0) { - if(!is.null(data$ok)) data <- subset(data,ok!="no fit") + if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data where ok + # was set to "no fit" substances <- levels(data$substance) - unit <- levels(as.factor(data$unit)) 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 rn <- vector() # number of dose-response curves + 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 @@ -63,6 +64,17 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, for (i in substances) { tmp <- splitted[[i]] fit <- FALSE + if (length(tmp) != 0) { + unit <- levels(as.factor(as.vector(tmp$unit))) + cat("\n",i,": Fitting data...\n",sep="") + } else { + unit <- "" + cat("\n",i,": No data\n",sep="") + } + if (length(unit) > 1) { + cat("More than one unit for substance ",i,", halting\n\n",sep="") + break + } n <- round(length(tmp$response)/9) if (length(tmp$response) == 0) { nodata = TRUE @@ -96,6 +108,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, sigma[[ri]] <- s$sigma rsubstance[[ri]] <- i rn[[ri]] <- n + runit[[ri]] <- unit rlld[[ri]] <- log10(lowestdose) rlhd[[ri]] <- log10(highestdose) mtype[[ri]] <- "linearlogis" @@ -158,6 +171,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, sigma[[ri]] <- s$sigma rsubstance[[ri]] <- i rn[[ri]] <- n + runit[[ri]] <- unit rlld[[ri]] <- log10(lowestdose) rlhd[[ri]] <- log10(highestdose) mtype[[ri]] <- "lognorm" @@ -187,9 +201,11 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, if (nodata) { rlld[[ri]] <- rlhd[[i]] <- NA mtype[[ri]] <- "no data" + runit[[ri]] <- NA } else { rlld[[ri]] <- log10(lowestdose) rlhd[[i]] <- log10(highestdose) + runit[[ri]] <- unit if (inactive) { mtype[[ri]] <- "inactive" } else { @@ -204,7 +220,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, f[[ri]] <- NA } } - results <- data.frame(rsubstance, rn, rlld, rlhd, mtype, logEC50, stderrlogEC50, unit, sigma) + results <- data.frame(rsubstance, rn, rlld, rlhd, mtype, logEC50, stderrlogEC50, runit, sigma) names(results) <- c("Substance","n","lld","lhd","mtype","logEC50","std","unit","sigma") if (lognorm || logis) { results$slope <- slope |