diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | R/drfit.R | 111 | ||||
| -rw-r--r-- | man/drdata.Rd | 3 | ||||
| -rw-r--r-- | man/drfit.Rd | 7 |
4 files changed, 69 insertions, 54 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 4069afd..95f71d7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: drfit -Version: 0.03-10 +Version: 0.03-12 Date: 2004-09-16 Title: Dose-response data evaluation Author: Johannes Ranke <jranke@uni-bremen.de> @@ -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
}
diff --git a/man/drdata.Rd b/man/drdata.Rd index dd62ff9..f46a4d3 100644 --- a/man/drdata.Rd +++ b/man/drdata.Rd @@ -13,7 +13,8 @@ A string or an array of strings with the substance names for which dose-response data is to be retrieved.} \item{experimentator}{ - The name of the experimentator whose data is to be used.} + The name of the experimentator whose data is to be used. Default is "%", which + means that data from all experimentators are retrieved.} \item{db}{ The database to be used. Currently only "cytotox" of the UFT Department of Bioorganic Chemistry is supported.} diff --git a/man/drfit.Rd b/man/drfit.Rd index f9843f5..30f3fd4 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -6,7 +6,7 @@ biometric results for (eco)toxicity evaluation } \usage{ - drfit(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE, + drfit(data, startlogEC50 = NA, chooseone = TRUE, lognorm = TRUE, logis = FALSE, linearlogis = FALSE, b0 = 2, f0 = 0) } \arguments{ @@ -32,6 +32,11 @@ \item{linearlogis}{ A boolean defining if the linear-logistic function as defined by van Ewijk and Hoekstra 1993 is fitted to the data. Default is FALSE.} + \item{chooseone}{ + If TRUE (default), the models are tried in the order linearlogis, logis and lognorm, + and the first model that produces a valid fit is used. Usually this will be the one + with the lowest residual standard deviation. If FALSE, all models that are set to TRUE + and that can be fitted will be reported.} \item{b0,f0}{ If the linearlogistic model is fitted, b0 and f0 give the possibility to adapt the starting values for the parameters b and f.} |