diff options
| -rw-r--r-- | .Rbuildignore | 7 | ||||
| -rw-r--r-- | ChangeLog | 20 | ||||
| -rw-r--r-- | DESCRIPTION | 12 | ||||
| -rw-r--r-- | GNUmakefile | 46 | ||||
| -rw-r--r-- | INDEX | 18 | ||||
| -rw-r--r-- | R/checkexperiment.R | 2 | ||||
| -rw-r--r-- | R/checksubstance.R | 1 | ||||
| -rw-r--r-- | R/drdata.R | 1 | ||||
| -rw-r--r-- | R/drfit.R | 64 | ||||
| -rw-r--r-- | R/drplot.R | 1 | ||||
| -rw-r--r-- | man/drfit.Rd | 25 |
11 files changed, 163 insertions, 34 deletions
diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..6b03659 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,7 @@ +GNUmakefile +out$ +toc$ +bbl$ +blg$ +aux$ +log$ diff --git a/ChangeLog b/ChangeLog new file mode 100644 index 0000000..9163fbb --- /dev/null +++ b/ChangeLog @@ -0,0 +1,20 @@ +2014-02-03 Johannes Ranke + + * DESCRIPTION: New version 0.5-97 (leading zeros in version numbers are + deprecated), modernize author field, enable lazy loading + + * Add this ChangeLog, a GNUMakefile, and an .Rbuildignore file + + * R/*.R: Clean out unnecessary calls to library() and require() + + * R/*.R: Tell R (>2.15.1) about some undeclared global variables to avoid NOTES in + package checks + + * R/drfit.R: Add the argument showED50. If set to TRUE, drfit includes the + ED50 and its confidence interval on the original scale in the output + + * R/drfit.R: Add the possibility to calculate several EDx values for each + dose-response model + + * man/drfit.Rd: Update the documentation and use the new optional arguments + in the example diff --git a/DESCRIPTION b/DESCRIPTION index b5bfb8a..7dac5df 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,10 @@ Package: drfit -Version: 0.05-96 -Date: 2012-10-29 +Version: 0.5-97 +Date: 2014-02-03 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,MASS,RODBC +Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre"), + email = "jranke@uni-bremen.de")) +Depends: R (>= 2.1.0), 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 @@ -17,6 +17,8 @@ Description: drfit provides basic and easy-to-use functions for fitting are included. Encoding: latin1 License: GPL (>= 2) +LazyLoad: yes +LazyData: yes URL: http://www.r-project.org, http://www.uft.uni-bremen.de/chemie/ranke?page=drfit, http://kriemhild.uft.uni-bremen.de/viewcvs/?root=drfit diff --git a/GNUmakefile b/GNUmakefile new file mode 100644 index 0000000..dfc1b7b --- /dev/null +++ b/GNUmakefile @@ -0,0 +1,46 @@ +PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION) +PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION) +PKGSRC := $(shell basename $(PWD)) + +# Specify the directory holding R binaries. To use an alternate R build (say a +# pre-prelease version) use `make RBIN=/path/to/other/R/` or `export RBIN=...` +# If no alternate bin folder is specified, the default is to use the folder +# containing the first instance of R on the PATH. +RBIN ?= $(shell dirname "`which R`") + +.PHONY: help + +help: + @echo "\nExecute development tasks for $(PKGNAME)\n" + @echo "Usage: \`make <task>\` where <task> is one of:" + @echo "" + @echo "Development Tasks" + @echo "-----------------" + @echo " build Create the package" + @echo " check Invoke build and then check the package" + @echo " install Invoke build and then install the result" + @echo "" + @echo "Packaging Tasks" + @echo "---------------" + @echo " release Give some reminders" + @echo "" + @echo "Using R in: $(RBIN)" + @echo "Set the RBIN environment variable to change this." + @echo "" + + +#------------------------------------------------------------------------------ +# Development Tasks +#------------------------------------------------------------------------------ + +build: + cd ..;\ + "$(RBIN)/R" CMD build $(PKGSRC) + +install: build + cd ..;\ + "$(RBIN)/R" CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz + +check: build + cd ..;\ + "$(RBIN)/R" CMD check --as-cran $(PKGNAME)_$(PKGVERS).tar.gz @@ -1,18 +0,0 @@ -antifoul Dose-Response data for TBT and Zink Pyrithione - in IPC-81 cells -checkexperiment Check raw data from a specified experiment or - microtiter plate -drdata Get dose-response data via RODBC -drfit Fit dose-response models -drfit-package Dose-response data evaluation -drplot Plot dose-response models -IM1xIPC81 Dose-Response data for - 1-methyl-3-alkylimidazolium tetrafluoroborates - in IPC-81 cells -IM1xVibrio Dose-Response data for - 1-methyl-3-alkylimidazolium tetrafluoroborates - in V. fischeri -linlogitf Linear-logistic function -pyrithione Cytotoxicity data for different pyrithionates - and related species -XY Dose-Response data for two substances X and Y diff --git a/R/checkexperiment.R b/R/checkexperiment.R index 58fecad..2bf0ce7 100644 --- a/R/checkexperiment.R +++ b/R/checkexperiment.R @@ -1,3 +1,4 @@ +if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc")) checkexperiment <- function(id, db = "ecotox", endpoint = "%") { databases <- data.frame( @@ -8,7 +9,6 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") if (!(db %in% rownames(databases))) stop("Database is not supported") - library(RODBC) channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower") diff --git a/R/checksubstance.R b/R/checksubstance.R index 96be999..b50c3da 100644 --- a/R/checksubstance.R +++ b/R/checksubstance.R @@ -11,7 +11,6 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", if (!(db %in% rownames(databases))) stop("Database is not supported") - library(RODBC) channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower") responsename = as.character(databases[db,1]) @@ -3,7 +3,6 @@ drdata <- function(substances, experimentator = "%", db = "cytotox", organism="Vibrio fischeri",endpoint="Luminescence",whereClause="1", ok="'ok','no fit'") { - library(RODBC) channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower") slist <- paste(substances,collapse="','") if (db == "cytotox") { @@ -1,11 +1,13 @@ +if(getRversion() >= '2.15.1') utils::globalVariables(c("ok", "dose")) drfit <- function(data, startlogED50 = NA, chooseone=TRUE, probit = TRUE, logit = FALSE, weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA, allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, - b0 = 2, f0 = 0) + b0 = 2, f0 = 0, + showED50 = FALSE, + EDx = NULL, EDx.tolerance = 1e-4) { - require(MASS) if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data # with ok set to # "no fit" @@ -282,14 +284,68 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, } results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, logED50, logED50low, logED50high, runit, sigma, a, b) + lower_level_percent = paste(100 * (1 - level)/2, "%", sep = "") + upper_level_percent = paste(100 * (1 + level)/2, "%", sep = "") names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50", - paste(100*(1-level)/2,"%",sep=""), - paste(100*(1+level)/2,"%",sep=""), + lower_level_percent, upper_level_percent, "unit","sigma","a","b") if (linlogit) { results$c <- c } + if (showED50) { + results[c("ED50", paste("ED50", c(lower_level_percent, upper_level_percent)))] <- + 10^results[7:9] + } + if (!is.null(EDx)) { + for (row.i in 1:ri) { + logED50 <- results[row.i, "logED50"] + mtype <- as.character(results[row.i, "mtype"]) + if (mtype == "probit") { + scale <- results[row.i, "b"] + drfunction <- function(x) pnorm(-x, -logED50, scale) + } + if (mtype == "logit") { + scale <- results[row.i, "b"] + drfunction <- function(x) plogis(-x, -logED50, scale) + } + if (mtype == "weibull") { + location <- results[row.i, "a"] + shape <- results[row.i, "b"] + drfunction <- function(x) pweibull(-x + location, shape) + } + if (mtype == "linlogit") { + drfunction <- function(x) { + r <- linlogitf(10^x, 1, + results[row.i, "c"], + results[row.i, "logED50"], + results[row.i, "b"]) + # Do not return response values above 1 to avoid trapping + # the optimization algorithm in a local minimum later on + if (r < 1) return(r) + else return(2 - 0.001 * x) # Start with 2 and decrease slowly to + # guide to the interesting part of the curve + } + } + if (mtype %in% c("probit", "logit", "weibull", "linlogit")) { + for (ED in EDx) { + of <- function(x) abs(drfunction(x) - (1 - (ED/100))) + + # Search over interval starting an order of magnitude below + # the lowest dose up to one order of magnitude above the + # highest dose + o = optimize(of, + results[row.i, c("lld", "lhd")] + c(-1, 1)) + # Only keep results within the tolerance + if ((o$objective) < EDx.tolerance) { + logdose.ED = o$minimum + results[row.i, paste0("EDx", ED)] <- 10^logdose.ED + } + } + } + } + } + rownames(results) <- 1:ri return(results) } @@ -1,3 +1,4 @@ +if(getRversion() >= '2.15.1') utils::globalVariables(c("dose", "Substance")) drplot <- function(drresults, data, dtype = "std", alpha = 0.95, ctype = "none", path = "./", fileprefix = "drplot", overlay = FALSE, diff --git a/man/drfit.Rd b/man/drfit.Rd index 6b98f36..7237404 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -8,7 +8,9 @@ \usage{ drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE, weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA, - allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0) + allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0, + showED50 = FALSE, + EDx = NULL, EDx.tolerance = 1e-4) } \arguments{ \item{data}{ @@ -68,6 +70,17 @@ \item{b0,f0}{ If the linearlogistic model is fitted, \code{b0} and \code{f0} give the possibility to adjust the starting values for the parameters b and f.} + \item{showED50}{ + If set to TRUE, the ED50 and its confidence interval on the original dose + scale (not log scale) is included in the output. + } + \item{EDx}{ + A vector of inhibition values x in percent for which the corresponding doses + EDx should be reported. + } + \item{EDx.tolerance}{ + Tolerance of the effect level, expressed on the response scale from 0 to 1. + } } \value{ \item{results}{ @@ -97,12 +110,16 @@ and in the \dQuote{weibull} fit it is the \code{shape} parameter of the fitted \code{\link{pweibull}} function. Only the \dQuote{linlogit} fit produces a third parameter \code{c} which is the variable f from the - \code{\link{linlogitf}} function.} + \code{\link{linlogitf}} function. + + If the parameter \code{showED50} was set to TRUE, the ED50 values and their + confidence intervals are also included on the original dose scale. + } } \examples{ data(antifoul) -r <- drfit(antifoul) -format(r,digits=2) +r <- drfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20)) +format(r, digits = 2) } \note{There is a demo for each dataset that can be accessed by \code{demo(dataset)}} |