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authorranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2006-05-03 22:53:31 +0000
committerranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2006-05-03 22:53:31 +0000
commit2cf977cb94fcf6e68b4a75cdf33a29a5308b9457 (patch)
treec82b096ba83b4c19d5ec0b0a1012e0100ca867fb
parent8eea91d691ee60f0ce5bd3560f2e4b7e5820556a (diff)
Changed the way confidence intervals are being calculated. Now
the function confint.nls from the MASS package is being used, after stumbling across the relevant paragraph of the MASS book. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@76 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
-rw-r--r--DESCRIPTION8
-rw-r--r--R/drfit.R97
-rw-r--r--man/drfit.Rd16
-rw-r--r--tests/IM1xIPC81.Rout.save41
-rw-r--r--tests/IM1xVibrio.Rout.save45
-rw-r--r--tests/XY.Rout.save18
-rw-r--r--tests/antifoul.Rout.save15
-rw-r--r--tests/pyrithione.Rout.save76
8 files changed, 181 insertions, 135 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 5d92da7..e12b6bf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,14 +1,14 @@
Package: drfit
-Version: 0.05-75
-Date: 2006-04-28
+Version: 0.05-76
+Date: 2006-05-04
Title: Dose-response data evaluation
Author: Johannes Ranke <jranke@uni-bremen.de>
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
-Depends: R (>= 2.1.0),stats,RODBC
+Depends: R (>= 2.1.0),stats,MASS,RODBC
Description: drfit provides basic and easy-to-use functions for fitting
dose-response curves to dose-response data, calculating some
(eco)toxicological parameters and plotting the results. Functions that are
- fitted are the cumulative densitiy function of the lognormal distribution
+ fitted are the cumulative density function of the lognormal distribution
(probit fit), of the logistic distribution (logit fit), of the weibull
distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
derived from the latter, which is used to describe data showing stimulation
diff --git a/R/drfit.R b/R/drfit.R
index 1bbffa8..b33d754 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -1,27 +1,28 @@
drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
probit = TRUE, logit = FALSE, weibull = FALSE,
- linlogit = FALSE, conf = FALSE,
+ linlogit = FALSE, level = 0.95,
linlogitWrong = NA, allWrong = NA,
s0 = 0.5, b0 = 2, f0 = 0)
{
- if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data with
- # ok set to "no fit"
+ require(MASS)
+ if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data
+ # with ok set to
+ # "no fit"
substances <- levels(data$substance)
- ri <- rix <- 0 # ri is the index over the result rows
- # rix is used later to check if any
- # model result was appended
- rsubstance <- array() # the substance names in the results
- rndl <- vector() # number of dose levels
- rn <- vector() # mean number of replicates
- # in each dose level
- runit <- vector() # vector of units for each result row
- rlhd <- rlld <- vector() # highest and lowest doses tested
- mtype <- array() # the modeltypes
- sigma <- array() # the standard deviation of the residuals
+ ri <- rix <- 0 # ri is the index over the result rows
+ # rix is used later to check if any
+ # model result was appended
+ rsubstance <- array() # the substance names in the results
+ rndl <- vector() # number of dose levels
+ rn <- vector() # mean number of replicates
+ # in each dose level
+ runit <- vector() # vector of units for each result row
+ rlhd <- rlld <- vector() # highest and lowest doses tested
+ mtype <- array() # the modeltypes
+ sigma <- array() # the standard deviation of the residuals
logED50 <- vector()
- stderrlogED50 <- vector()
- conflogED50 <- vector()
+ logED50low <- logED50high <- vector()
a <- b <- c <- vector()
splitted <- split(data,data$substance)
@@ -87,15 +88,21 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
if (logED50[[ri]] > rlhd[[ri]]) {
mtype[[ri]] <- "no fit"
logED50[[ri]] <- NA
- stderrlogED50[[ri]] <- NA
- conflogED50[[ri]] <- NA
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
a[[ri]] <- NA
b[[ri]] <- NA
c[[ri]] <- NA
} else {
mtype[[ri]] <- "linlogit"
- stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"]
- conflogED50[[ri]] <- stderrlogED50[[ri]] * qt(0.975, n - 3)
+ logED50conf <- try(confint(m,"logED50",level=level))
+ if (!inherits(logED50conf, "try-error")) {
+ logED50low[[ri]] <- logED50conf[[1]]
+ logED50high[[ri]] <- logED50conf[[2]]
+ } else {
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
+ }
a[[ri]] <- coef(m)[["logED50"]]
b[[ri]] <- coef(m)[["b"]]
c[[ri]] <- coef(m)[["f"]]
@@ -125,14 +132,20 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
if (logED50[[ri]] > rlhd[[ri]]) {
mtype[[ri]] <- "no fit"
logED50[[ri]] <- NA
- stderrlogED50[[ri]] <- NA
- conflogED50[[ri]] <- NA
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
a[[ri]] <- NA
b[[ri]] <- NA
} else {
mtype[[ri]] <- "probit"
- stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"]
- conflogED50[[ri]] <- stderrlogED50[[ri]] * qt(0.975, n - 2)
+ logED50conf <- try(confint(m,"logED50",level=level))
+ if (!inherits(logED50conf, "try-error")) {
+ logED50low[[ri]] <- logED50conf[[1]]
+ logED50high[[ri]] <- logED50conf[[2]]
+ } else {
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
+ }
a[[ri]] <- coef(m)[["logED50"]]
b[[ri]] <- coef(m)[["scale"]]
}
@@ -163,14 +176,20 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
if (logED50[[ri]] > rlhd[[ri]]) {
mtype[[ri]] <- "no fit"
logED50[[ri]] <- NA
- stderrlogED50[[ri]] <- NA
- conflogED50[[ri]] <- NA
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
a[[ri]] <- NA
b[[ri]] <- NA
} else {
mtype[[ri]] <- "logit"
- stderrlogED50[[ri]] <- s$parameters["logED50","Std. Error"]
- conflogED50[[ri]] <- stderrlogED50[[ri]] * qt(0.975, n - 2)
+ logED50conf <- try(confint(m,"logED50",level=level))
+ if (!inherits(logED50conf, "try-error")) {
+ logED50low[[ri]] <- logED50conf[[1]]
+ logED50high[[ri]] <- logED50conf[[2]]
+ } else {
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
+ }
}
}
}
@@ -200,17 +219,15 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
}
logED50[[ri]] <- nlm(sqrdev,startlogED50[[i]])$estimate
c[[ri]] <- NA
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
if (logED50[[ri]] > rlhd[[ri]]) {
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)
}
}
}
@@ -247,21 +264,17 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
}
sigma[[ri]] <- NA
logED50[[ri]] <- NA
- stderrlogED50[[ri]] <- NA
- conflogED50[[ri]] <- NA
+ logED50low[[ri]] <- NA
+ logED50high[[ri]] <- NA
a[[ri]] <- NA
b[[ri]] <- NA
c[[ri]] <- NA
}
}
- 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")
- }
+ results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype,
+ logED50, logED50low, logED50high, runit, sigma, a, b)
+ names(results) <- c("Substance","ndl","n","lld","lhd","mtype",
+ "logED50",names(logED50conf)[[1]],names(logED50conf)[[2]],"unit","sigma","a","b")
if (linlogit) {
results$c <- c
diff --git a/man/drfit.Rd b/man/drfit.Rd
index a89b5dd..453c0f8 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -7,7 +7,7 @@
}
\usage{
drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
- weibull = FALSE, linlogit = FALSE, conf = FALSE, linlogitWrong = NA,
+ weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA,
allWrong = NA, s0 = 0.5, b0 = 2, f0 = 0)
}
\arguments{
@@ -43,10 +43,8 @@
A boolean defining if the linear-logistic function
\code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is
fitted to the data. Default is FALSE.}
- \item{conf}{
- A boolean defining if a confidence interval of the log ED50 is to be
- listed for alpha = 5 \% (two-sided). If FALSE (default), the standard
- deviation is listed in the output of drfit.}
+ \item{level}{
+ The level for the confidence interval listed for the log ED50.}
\item{linlogitWrong}{
An optional vector containing the names of the substances for which the
linlogit function produces a wrong fit.}
@@ -81,10 +79,10 @@
\code{lhd} is the decadic logarithm of the highest dose. For the
\dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
parameter \code{a} that is reported coincides with the logED50, i.e the
- logED50 is one of the model parameters that is being fitted, and
- therefore, depending on the argument \code{conf}, a standard deviation
- \code{std} or a confidence interval \code{conf} is reported for the
- logED50. In the case of the \dQuote{weibull} model, \code{a} is a
+ logED50 is one of the model parameters that is being fitted. Therefore,
+ a confidence interval for the confidence level \code{level} is calculated
+ using the \code{\link[MASS:confint]{confint.nls}} function and listed.
+ In the case of the \dQuote{weibull} model, \code{a} is a
location parameter. Parameter \code{b} in the case of the
\dQuote{linlogit} fit is the variable b from the \code{\link{linlogitf}}
function. In the case of \dQuote{probit} fit it is the standard deviation
diff --git a/tests/IM1xIPC81.Rout.save b/tests/IM1xIPC81.Rout.save
index b67ed2a..b56b8c9 100644
--- a/tests/IM1xIPC81.Rout.save
+++ b/tests/IM1xIPC81.Rout.save
@@ -16,6 +16,7 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
Type 'q()' to quit R.
> library(drfit)
+Loading required package: MASS
Loading required package: RODBC
> data(IM1xIPC81)
> rIM1xIPC81 <- drfit(IM1xIPC81,linlogit=TRUE)
@@ -35,41 +36,45 @@ IM15 BF4: Fitting data...
IM16 BF4: Fitting data...
IM17 BF4: Fitting data...
+Waiting for profiling to be done...
Error in numericDeriv(form[[3]], names(ind), env) :
Missing value or an infinity produced when evaluating the model
In addition: Warning message:
NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
IM18 BF4: Fitting data...
+Waiting for profiling to be done...
Error in numericDeriv(form[[3]], names(ind), env) :
Missing value or an infinity produced when evaluating the model
In addition: Warning message:
NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
IM19 BF4: Fitting data...
+Waiting for profiling to be done...
Error in numericDeriv(form[[3]], names(ind), env) :
Missing value or an infinity produced when evaluating the model
In addition: Warning message:
NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
IM1-10 BF4: Fitting data...
+Waiting for profiling to be done...
> rIM1xIPC81
- Substance ndl n lld lhd mtype logED50 std unit
-1 IM13 BF4 9 81 0.59176003 3.000000 inactive NA NA 然
-2 IM14 BF4 20 216 -0.01030017 3.176091 no fit NA NA 然
-3 IM15 BF4 9 135 0.59176003 3.000000 inactive NA NA 然
-4 IM16 BF4 9 108 0.59176003 3.000000 inactive NA NA 然
-5 IM17 BF4 9 81 0.59176003 3.000000 linlogit 2.5785719 0.03819482 然
-6 IM18 BF4 9 135 0.59176003 3.000000 linlogit 1.6806040 0.02982682 然
-7 IM19 BF4 9 81 0.59176003 3.000000 linlogit 1.6496121 0.02636274 然
-8 IM1-10 BF4 11 162 -0.01030017 3.000000 linlogit 0.7696961 0.04165397 然
- sigma a b c
-1 NA NA NA NA
-2 NA NA NA NA
-3 NA NA NA NA
-4 NA NA NA NA
-5 0.2375857 2.5785719 2.300216 0.01468034
-6 0.2324871 1.6806040 2.237338 0.05719295
-7 0.1452716 1.6496121 1.976976 0.10956088
-8 0.2987708 0.7696961 1.936253 0.45808611
+ Substance ndl n lld lhd mtype logED50 2.5%
+1 IM13 BF4 9 81 0.59176003 3.000000 inactive NA NA
+2 IM14 BF4 20 216 -0.01030017 3.176091 no fit NA NA
+3 IM15 BF4 9 135 0.59176003 3.000000 inactive NA NA
+4 IM16 BF4 9 108 0.59176003 3.000000 inactive NA NA
+5 IM17 BF4 9 81 0.59176003 3.000000 linlogit 2.5785719 2.5057219
+6 IM18 BF4 9 135 0.59176003 3.000000 linlogit 1.6806040 1.6229756
+7 IM19 BF4 9 81 0.59176003 3.000000 linlogit 1.6496121 1.5984793
+8 IM1-10 BF4 11 162 -0.01030017 3.000000 linlogit 0.7696961 0.6870081
+ 97.5% unit sigma a b c
+1 NA 然 NA NA NA NA
+2 NA 然 NA NA NA NA
+3 NA 然 NA NA NA NA
+4 NA 然 NA NA NA NA
+5 2.6617385 然 0.2375857 2.5785719 2.300216 0.01468034
+6 1.7418917 然 0.2324871 1.6806040 2.237338 0.05719295
+7 1.7031463 然 0.1452716 1.6496121 1.976976 0.10956088
+8 0.8544213 然 0.2987708 0.7696961 1.936253 0.45808612
>
diff --git a/tests/IM1xVibrio.Rout.save b/tests/IM1xVibrio.Rout.save
index 5d37703..bebdcea 100644
--- a/tests/IM1xVibrio.Rout.save
+++ b/tests/IM1xVibrio.Rout.save
@@ -16,42 +16,51 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
Type 'q()' to quit R.
> library(drfit)
+Loading required package: MASS
Loading required package: RODBC
> data(IM1xVibrio)
> rIM1xVibrio <- drfit(IM1xVibrio)
IM13 BF4: Fitting data...
+Waiting for profiling to be done...
IM14 BF4: Fitting data...
+Waiting for profiling to be done...
IM15 BF4: Fitting data...
+Waiting for profiling to be done...
IM16 BF4: Fitting data...
+Waiting for profiling to be done...
IM17 BF4: Fitting data...
+Waiting for profiling to be done...
IM18 BF4: Fitting data...
+Waiting for profiling to be done...
IM19 BF4: Fitting data...
+Waiting for profiling to be done...
IM1-10 BF4: Fitting data...
+Waiting for profiling to be done...
> rIM1xVibrio
- Substance ndl n lld lhd mtype logED50 std unit
-1 IM13 BF4 13 22 -5.30103 4.69897 probit 3.9399128 0.03658457 然
-2 IM14 BF4 12 57 -4.30103 4.69897 probit 3.5442110 0.02060194 然
-3 IM15 BF4 7 20 -0.30103 4.69897 probit 3.1398488 0.01254468 然
-4 IM16 BF4 13 30 -4.30103 4.69897 probit 3.1804247 0.01801591 然
-5 IM17 BF4 10 20 -1.30103 4.69897 probit 2.4317301 0.03015341 然
-6 IM18 BF4 10 17 -2.30103 2.69897 probit 1.4015187 0.04053083 然
-7 IM19 BF4 13 22 -5.30103 2.69897 probit 0.7157942 0.02085130 然
-8 IM1-10 BF4 11 20 -6.30103 2.69897 probit -0.1790307 0.03623821 然
- sigma a b
-1 0.06302893 3.9399128 0.5763074
-2 0.05905375 3.5442110 0.6561300
-3 0.02695476 3.1398488 0.5526675
-4 0.04514079 3.1804247 0.4881559
-5 0.04773317 2.4317301 0.6386547
-6 0.05611347 1.4015187 0.8008513
-7 0.02956284 0.7157942 0.6969275
-8 0.04098662 -0.1790307 0.8019351
+ Substance ndl n lld lhd mtype logED50 2.5% 97.5%
+1 IM13 BF4 13 22 -5.30103 4.69897 probit 3.9399128 3.8636215 4.0160099
+2 IM14 BF4 12 57 -4.30103 4.69897 probit 3.5442110 3.5030166 3.5855474
+3 IM15 BF4 7 20 -0.30103 4.69897 probit 3.1398488 3.1135935 3.1662394
+4 IM16 BF4 13 30 -4.30103 4.69897 probit 3.1804247 3.1435815 3.2176152
+5 IM17 BF4 10 20 -1.30103 4.69897 probit 2.4317301 2.3680656 2.4951179
+6 IM18 BF4 10 17 -2.30103 2.69897 probit 1.4015187 1.3146736 1.4880647
+7 IM19 BF4 13 22 -5.30103 2.69897 probit 0.7157942 0.6703743 0.7592458
+8 IM1-10 BF4 11 20 -6.30103 2.69897 probit -0.1790307 -0.2569430 -0.1037183
+ unit sigma a b
+1 然 0.06302893 3.9399128 0.5763074
+2 然 0.05905375 3.5442110 0.6561300
+3 然 0.02695476 3.1398488 0.5526675
+4 然 0.04514079 3.1804247 0.4881559
+5 然 0.04773317 2.4317301 0.6386547
+6 然 0.05611347 1.4015187 0.8008513
+7 然 0.02956284 0.7157942 0.6969275
+8 然 0.04098662 -0.1790307 0.8019351
>
diff --git a/tests/XY.Rout.save b/tests/XY.Rout.save
index 7bcc0df..d8098ae 100644
--- a/tests/XY.Rout.save
+++ b/tests/XY.Rout.save
@@ -16,6 +16,7 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
Type 'q()' to quit R.
> library(drfit)
+Loading required package: MASS
Loading required package: RODBC
> data(XY)
> rXY <- drfit(XY)
@@ -23,15 +24,16 @@ Loading required package: RODBC
Control: Fitting data...
Substance X: Fitting data...
+Waiting for profiling to be done...
Substance Y: Fitting data...
> rXY
- Substance ndl n lld lhd mtype logED50 std unit sigma
-1 Control 1 6 -Inf -Inf inactive NA NA mg/L NA
-2 Substance X 4 12 1 3 probit 2.161905 0.02425144 mg/L 0.04131746
-3 Substance Y 4 12 1 3 active NA NA mg/L NA
- a b
-1 NA NA
-2 2.161905 0.5061306
-3 NA NA
+ Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit
+1 Control 1 6 -Inf -Inf inactive NA NA NA mg/L
+2 Substance X 4 12 1 3 probit 2.161905 2.105861 2.214359 mg/L
+3 Substance Y 4 12 1 3 active NA NA NA mg/L
+ sigma a b
+1 NA NA NA
+2 0.04131746 2.161905 0.5061306
+3 NA NA NA
>
diff --git a/tests/antifoul.Rout.save b/tests/antifoul.Rout.save
index 5bc166c..9967240 100644
--- a/tests/antifoul.Rout.save
+++ b/tests/antifoul.Rout.save
@@ -16,18 +16,21 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
Type 'q()' to quit R.
> library(drfit)
+Loading required package: MASS
Loading required package: RODBC
> data(antifoul)
> rantifoul <- drfit(antifoul)
TBT: Fitting data...
+Waiting for profiling to be done...
Zn Pyrithion: Fitting data...
+Waiting for profiling to be done...
> rantifoul
- Substance ndl n lld lhd mtype logED50 std unit
-1 TBT 38 135 -2.709271 2.39794 probit -0.1643560 0.05349216 然
-2 Zn Pyrithion 27 81 -2.107210 2.00000 probit -0.3979222 0.05393693 然
- sigma a b
-1 0.1928611 -0.1643560 0.6763882
-2 0.2286560 -0.3979222 0.4169632
+ Substance ndl n lld lhd mtype logED50 2.5%
+1 TBT 38 135 -2.709271 2.39794 probit -0.1643560 -0.2650411
+2 Zn Pyrithion 27 81 -2.107210 2.00000 probit -0.3979222 -0.5078291
+ 97.5% unit sigma a b
+1 -0.05648615 然 0.1928611 -0.1643560 0.6763882
+2 -0.29156056 然 0.2286560 -0.3979222 0.4169632
>
diff --git a/tests/pyrithione.Rout.save b/tests/pyrithione.Rout.save
index fb11ca9..2a05dd8 100644
--- a/tests/pyrithione.Rout.save
+++ b/tests/pyrithione.Rout.save
@@ -16,70 +16,86 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
Type 'q()' to quit R.
> library(drfit)
+Loading required package: MASS
Loading required package: RODBC
> data(pyrithione)
> rpyr <- drfit(pyrithione,linlogit=TRUE,linlogitWrong=c("MSPT","MSPHI"))
Na Pyrithion: Fitting data...
+Waiting for profiling to be done...
+Error in prof$getProfile() : number of iterations exceeded maximum of 50
Pyridin: Fitting data...
PyNO: Fitting data...
(PT)2: Fitting data...
+Waiting for profiling to be done...
MSO2P: Fitting data...
MSPHI: Fitting data...
+Waiting for profiling to be done...
PyS: Fitting data...
Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp, :
step factor 0.000488281 reduced below 'minFactor' of 0.000976562
+Waiting for profiling to be done...
+Error in numericDeriv(form[[3]], names(ind), env) :
+ Missing value or an infinity produced when evaluating the model
+In addition: Warning message:
+NaNs produced in: pnorm(q, mean, sd, lower.tail, log.p)
Zn Pyrithion: Fitting data...
+Waiting for profiling to be done...
Cu Pyrithion: Fitting data...
+Waiting for profiling to be done...
Fe Pyrithion: Fitting data...
+Waiting for profiling to be done...
(PyS)2: Fitting data...
Error in nls(response ~ linlogitf(dose, 1, f, logED50, b), data = tmp, :
singular gradient
+Waiting for profiling to be done...
MSPT: Fitting data...
+Waiting for profiling to be done...
TBT: Fitting data...
+Waiting for profiling to be done...
NaJ: Fitting data...
> rpyr
- Substance ndl n lld lhd mtype logED50 std unit
-1 Na Pyrithion 20 108 -2.107210 2.00000 linlogit -0.3461318 0.04237833 然
-2 Pyridin 19 161 0.591760 3.69897 inactive NA NA 然
-3 PyNO 19 81 0.591760 3.69897 no fit NA NA 然
-4 (PT)2 19 81 -2.408240 2.00000 linlogit -0.4197031 0.05030460 然
-5 MSO2P 28 108 -1.709271 3.69897 inactive NA NA 然
-6 MSPHI 19 81 0.591760 3.69897 probit 3.6625025 0.06724673 然
-7 PyS 18 80 -0.408240 3.00000 probit 2.6817944 0.02031252 然
-8 Zn Pyrithion 27 81 -2.107210 2.00000 linlogit -0.4132885 0.06234927 然
-9 Cu Pyrithion 19 79 -2.408240 2.00000 linlogit -0.3074717 0.07918130 然
-10 Fe Pyrithion 19 81 -2.408240 2.00000 linlogit -0.3534572 0.07263386 然
-11 (PyS)2 20 81 -0.408240 3.00000 probit 1.7840499 0.05230663 然
-12 MSPT 18 108 -0.408240 3.00000 probit 2.1384811 0.03379904 然
-13 TBT 38 135 -2.709271 2.39794 linlogit -0.1580954 0.05474371 然
-14 NaJ 10 108 0.591760 3.30103 inactive NA NA 然
- sigma a b c
-1 0.20857751 -0.3461318 2.1188272 -0.26698979
-2 NA NA NA NA
-3 0.09188853 NA NA NA
-4 0.20509070 -0.4197031 1.8466994 -0.51508088
-5 NA NA NA NA
-6 0.12943273 3.6625025 0.4387540 NA
-7 0.13401920 2.6817944 0.1250523 NA
-8 0.22877916 -0.4132885 1.7424846 0.61078660
-9 0.24494451 -0.3074717 1.0150649 -0.04897422
-10 0.23383185 -0.3534572 1.1823558 0.02510613
-11 0.23298721 1.7840499 0.4098018 NA
-12 0.22881257 2.1384811 0.2112625 NA
-13 0.19264079 -0.1580954 1.0406576 -0.02416104
-14 NA NA NA NA
+ Substance ndl n lld lhd mtype logED50 2.5%
+1 Na Pyrithion 20 108 -2.107210 2.00000 linlogit -0.3461318 NA
+2 Pyridin 19 161 0.591760 3.69897 inactive NA NA
+3 PyNO 19 81 0.591760 3.69897 no fit NA NA
+4 (PT)2 19 81 -2.408240 2.00000 linlogit -0.4197042 -0.5326102
+5 MSO2P 28 108 -1.709271 3.69897 inactive NA NA
+6 MSPHI 19 81 0.591760 3.69897 probit 3.6625025 3.5548278
+7 PyS 18 80 -0.408240 3.00000 probit 2.6817944 NA
+8 Zn Pyrithion 27 81 -2.107210 2.00000 linlogit -0.4132886 -0.5293327
+9 Cu Pyrithion 19 79 -2.408240 2.00000 linlogit -0.3074717 -0.4753489
+10 Fe Pyrithion 19 81 -2.408240 2.00000 linlogit -0.3534573 -0.5003829
+11 (PyS)2 20 81 -0.408240 3.00000 probit 1.7840499 1.6726792
+12 MSPT 18 108 -0.408240 3.00000 probit 2.1384811 2.0709306
+13 TBT 38 135 -2.709271 2.39794 linlogit -0.1580954 -0.2602139
+14 NaJ 10 108 0.591760 3.30103 inactive NA NA
+ 97.5% unit sigma a b c
+1 NA 然 0.20857751 -0.3461318 2.1188275 -0.26698926
+2 NA 然 NA NA NA NA
+3 NA 然 0.09188853 NA NA NA
+4 NA 然 0.20509070 -0.4197042 1.8467290 -0.51505615
+5 NA 然 NA NA NA NA
+6 3.88053203 然 0.12943273 3.6625025 0.4387540 NA
+7 NA 然 0.13401920 2.6817944 0.1250523 NA
+8 -0.29979846 然 0.22877916 -0.4132886 1.7424848 0.61079006
+9 -0.15442805 然 0.24494451 -0.3074717 1.0150650 -0.04897413
+10 -0.21459555 然 0.23383185 -0.3534573 1.1823561 0.02510663
+11 1.88824519 然 0.23298721 1.7840499 0.4098018 NA
+12 2.20511512 然 0.22881257 2.1384811 0.2112625 NA
+13 -0.05045493 然 0.19264079 -0.1580954 1.0406577 -0.02416082
+14 NA 然 NA NA NA NA
>

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