diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/checkexperiment.R | 30 | ||||
| -rw-r--r-- | R/checksubstance.R | 54 | ||||
| -rw-r--r-- | R/drcfit.R | 31 | ||||
| -rw-r--r-- | R/drdata.R | 4 | ||||
| -rw-r--r-- | R/drfit.R | 47 | ||||
| -rw-r--r-- | R/drplot.R | 36 |
6 files changed, 107 insertions, 95 deletions
diff --git a/R/checkexperiment.R b/R/checkexperiment.R index b264243..b69b81f 100644 --- a/R/checkexperiment.R +++ b/R/checkexperiment.R @@ -9,7 +9,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") if (!(db %in% rownames(databases))) stop("Database is not supported") - if (require("RODBC")) { + if (requireNamespace("RODBC")) { channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower") } else { stop("For this function, the RODBC package has to be installed and configured.") @@ -25,21 +25,21 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") " WHERE ", exptype, " = ", id) commentdata <- RODBC::sqlQuery(channel,commentquery) comment <- as.character(commentdata[[1]]) - + expquery <- paste("SELECT experimentator,substance, ", testtype, ",conc,unit,", responsename, ",performed,ok", - " FROM ",db," WHERE ",exptype,"=", id, + " FROM ",db," WHERE ",exptype,"=", id, sep = "") if (db == "ecotox") { - expquery <- paste(expquery, " AND type LIKE '", + expquery <- paste(expquery, " AND type LIKE '", endpoint, "'", sep = "") } expdata <- RODBC::sqlQuery(channel,expquery) if (db %in% c("cytotox","enzymes")) { - controlquery <- paste("SELECT type,response FROM controls + controlquery <- paste("SELECT type,response FROM controls WHERE plate=",id) controldata <- RODBC::sqlQuery(channel,controlquery) } @@ -63,7 +63,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") numberOfBlinds <- NA meanOfBlinds <- NA stdOfBlinds <- NA - + } numberOfControls <- length(controls$response) if (numberOfControls > 0) { @@ -78,7 +78,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") if (length(expdata$experimentator) < 1) { stop("There is no response data for ",exptype," ", id," in database ",db,"\n") - } + } exptypestring <- paste(toupper(substring(exptype,1,1)), substring(exptype,2),sep="") expdata$experimentator <- factor(expdata$experimentator) @@ -87,7 +87,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") expdata$substance <- factor(expdata$substance) expdata$unit <- factor(expdata$unit) expdata$ok <- factor(expdata$ok) - + cat("\n",exptypestring,id,"from database",db,":\n\n", "\tExperimentator(s):\t",levels(expdata$experimentator),"\n", "\tType(s):\t\t",levels(expdata$type),"\n", @@ -100,7 +100,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") "\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n", "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t", stdOfControls,"\t\t",percentstdOfcontrols,"\n") - + if (db == "ecotox") { boxplot(controls$response, @@ -116,22 +116,22 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%") boxwex=0.4, main=paste("Plate ",id)) } - + drdata <- expdata[c(2,4,6)] drdata$substance <- factor(drdata$substance) substances <- levels(drdata$substance) - + lld <- log10(min(subset(drdata,conc!=0)$conc)) lhd <- log10(max(drdata$conc)) plot(1,type="n", - xlim=c(lld - 0.5, lhd + 2), - ylim= c(-0.1, 2), + xlim=c(lld - 0.5, lhd + 2), + ylim= c(-0.1, 2), xlab=paste("decadic logarithm of the concentration in ",levels(expdata$unit)), ylab=responsename) - + drdatalist <- split(drdata,drdata$substance) - + for (i in 1:length(drdatalist)) { points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsename]],col=i); } diff --git a/R/checksubstance.R b/R/checksubstance.R index 790182f..06cc635 100644 --- a/R/checksubstance.R +++ b/R/checksubstance.R @@ -1,7 +1,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", - celltype = "%", enzymetype = "%", organism = "%", + celltype = "%", enzymetype = "%", organism = "%", endpoint = "%", - whereClause = "1", ok= "%") + whereClause = "1", ok= "%") { databases <- data.frame( responsename=c("viability","activity","response"), @@ -11,7 +11,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", if (!(db %in% rownames(databases))) stop("Database is not supported") - if (require("RODBC")) { + if (requireNamespace("RODBC")) { channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower") } else { stop("For this function, the RODBC package has to be installed and configured.") @@ -23,13 +23,13 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", if (db == "cytotox") { type <- celltype - } + } if (db == "enzymes") { type <- enzymetype - } + } if (db == "ecotox") { type <- organism - } + } query <- paste("SELECT experimentator,substance,", testtype, ",", exptype, ",conc,unit,",responsename,",ok", @@ -41,7 +41,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", sep = "") if (db == "ecotox") { - query <- paste(query, " AND type LIKE '", + query <- paste(query, " AND type LIKE '", endpoint, "'", sep = "") } @@ -51,39 +51,39 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%", if (length(data$experimentator) < 1) { stop(paste("\nNo response data for",substance,"in database", db,"found with these parameters\n")) - } - - data$experimentator <- factor(data$experimentator) + } + + data$experimentator <- factor(data$experimentator) data$substance <- factor(data$substance) - substances <- levels(data$substance) - data$type <- factor(data[[testtype]]) - data[[exptype]] <- factor(data[[exptype]]) + substances <- levels(data$substance) + data$type <- factor(data[[testtype]]) + data[[exptype]] <- factor(data[[exptype]]) experiments <- levels(data[[exptype]]) concentrations <- split(data$conc,data$conc) concentrations <- as.numeric(names(concentrations)) - data$unit <- factor(data$unit) + data$unit <- factor(data$unit) data$ok <- factor(data$ok) if (length(experiments)>6) { - palette(rainbow(length(experiments))) + palette(rainbow(length(experiments))) } - + plot(log10(data$conc),data[[responsename]], - xlim=c(-2.5, 4.5), - ylim= c(-0.1, 2), - xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)), - ylab=responsename) - + xlim=c(-2.5, 4.5), + ylim= c(-0.1, 2), + xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)), + ylab=responsename) + explist <- split(data,data[[exptype]]) - - for (i in 1:length(explist)) { - points(log10(explist[[i]]$conc),explist[[i]][[responsename]],col=i); - } - + + for (i in 1:length(explist)) { + points(log10(explist[[i]]$conc),explist[[i]][[responsename]],col=i); + } + legend("topleft", experiments, pch=1, col=1:length(experiments), inset=0.05) title(main=paste(substance," - ",levels(data$experimentator)," - ",levels(data$type))) - exptypename <- paste(toupper(substring(exptype,1,1)), + exptypename <- paste(toupper(substring(exptype,1,1)), substring(exptype,2), sep = "") experimentators <- paste(levels(data$experimentator), collapse = " ") types <- paste(levels(data$type), collapse = " ") @@ -14,7 +14,7 @@ drcfit <- function(data, chooseone=TRUE, # model result was appended rsubstance <- array() # the substance names in the results rndl <- vector() # number of dose levels - rn <- vector() # mean number of replicates + 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 @@ -69,7 +69,8 @@ drcfit <- function(data, chooseone=TRUE, active <- FALSE if (linlogit) { - m <- try(drm(response ~ dose, data = tmp, fct = BC.4(fixed = c(NA, 1, NA, NA)))) + m <- try(drm(response ~ dose, data = tmp, fct = BC.4(fixed = c(NA, 1, NA, NA))), + silent = TRUE) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -90,10 +91,11 @@ drcfit <- function(data, chooseone=TRUE, a[[ri]] <- coef(m)[[2]] b[[ri]] <- coef(m)[[1]] c[[ri]] <- coef(m)[[3]] - ED50 <- try(ED(m, 50, interval = "delta", + ED50 <- try(ED(m, 50, interval = "delta", lower = lowestdose / 10, upper = highestdose * 10, - display = FALSE)) + display = FALSE), + silent = TRUE) if (!inherits(ED50, "try-error")) { logED50[[ri]] <- log10(ED50["1:50", "Estimate"]) logED50low[[ri]] <- log10(ED50["1:50", "Lower"]) @@ -101,14 +103,14 @@ drcfit <- function(data, chooseone=TRUE, if (logED50[[ri]] > rlhd[[ri]]) { mtype[[ri]] <- "no fit" } - } + } } } } if (probit) { - m <- try(drm(response ~ dose, data = tmp, - fct = LN.2())) + m <- try(drm(response ~ dose, data = tmp, + fct = LN.2()), silent = TRUE) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -142,7 +144,8 @@ drcfit <- function(data, chooseone=TRUE, } if (logit) { - m <- try(drm(response ~ dose, data = tmp, fct = LL.2())) + m <- try(drm(response ~ dose, data = tmp, fct = LL.2()), + silent = TRUE) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -179,7 +182,8 @@ drcfit <- function(data, chooseone=TRUE, } if (weibull) { - m <- try(drm(response ~ dose, data = tmp, fct = W1.2())) + m <- try(drm(response ~ dose, data = tmp, fct = W1.2()), + silent = TRUE) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -252,7 +256,7 @@ drcfit <- function(data, chooseone=TRUE, } } - results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, + 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 = "") @@ -275,12 +279,13 @@ drcfit <- function(data, chooseone=TRUE, mtype <- as.character(results[row.i, "mtype"]) if (mtype %in% c("probit", "logit", "weibull", "linlogit")) { for (EDi in EDx) { - EDx.drc = try(ED(m, EDi, interval = "delta", display = FALSE, level = level)) + EDx.drc = try(ED(m, EDi, interval = "delta", display = FALSE, level = level), + silent = TRUE) if (!inherits(EDx.drc, "try-error")) { results[row.i, paste0("EDx", EDi)] <- EDx.drc[paste0("1:", EDi), "Estimate"] - results[row.i, paste0("EDx", EDi, " ", lower_level_percent)] <- EDx.drc[paste0("1:", EDi), + results[row.i, paste0("EDx", EDi, " ", lower_level_percent)] <- EDx.drc[paste0("1:", EDi), "Lower"] - results[row.i, paste0("EDx", EDi, " ", upper_level_percent)] <- EDx.drc[paste0("1:", EDi), + results[row.i, paste0("EDx", EDi, " ", upper_level_percent)] <- EDx.drc[paste0("1:", EDi), "Upper"] } } @@ -3,7 +3,7 @@ drdata <- function(substances, experimentator = "%", db = "cytotox", organism = "Vibrio fischeri", endpoint = "Luminescence", whereClause = "1", ok = "'ok','no fit'") { - if (require("RODBC")) { + if (requireNamespace("RODBC")) { channel <- RODBC::odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower") slist <- paste(substances,collapse="','") if (db == "cytotox") { @@ -21,7 +21,7 @@ drdata <- function(substances, experimentator = "%", db = "cytotox", type <- organism } } - + query <- paste("SELECT conc,",responsetype,",unit,experimentator,substance,",testtype, ",ok FROM ", db, " WHERE substance IN ('", slist,"') AND experimentator LIKE '", @@ -18,7 +18,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, # model result was appended rsubstance <- array() # the substance names in the results rndl <- vector() # number of dose levels - rn <- vector() # mean number of replicates + 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 @@ -75,12 +75,13 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, active <- TRUE } else { active <- FALSE - if (linlogit && + if (linlogit && length(subset(linlogitWrong,linlogitWrong == i))==0 && length(subset(allWrong,allWrong == i))==0) { m <- try(nls(response ~ linlogitf(dose,1,f,logED50,b), - data=tmp, algorithm="port", - start=list(f=f0,logED50=startlogED50[[i]],b=b0))) + data=tmp, algorithm="port", + start=list(f=f0,logED50=startlogED50[[i]],b=b0)), + silent = TRUE) if (!inherits(m, "try-error")) { fit <- TRUE ri <- ri + 1 @@ -104,7 +105,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, c[[ri]] <- NA } else { mtype[[ri]] <- "linlogit" - logED50conf <- try(confint(m,"logED50",level=level)) + logED50conf <- try(confint(m,"logED50",level=level), + silent = TRUE) if (!inherits(logED50conf, "try-error")) { logED50low[[ri]] <- logED50conf[[1]] logED50high[[ri]] <- logED50conf[[2]] @@ -122,8 +124,9 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, if (probit && length(subset(allWrong,allWrong == i))==0) { m <- try(nls(response ~ pnorm(-log10(dose),-logED50,scale), - data=tmp, algorithm="port", - start=list(logED50=startlogED50[[i]],scale=ps0))) + data=tmp, algorithm="port", + start=list(logED50=startlogED50[[i]],scale=ps0)), + silent = TRUE) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -148,7 +151,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, b[[ri]] <- NA } else { mtype[[ri]] <- "probit" - logED50conf <- try(confint(m,"logED50",level=level)) + logED50conf <- try(confint(m,"logED50",level=level), + silent = TRUE) if (!inherits(logED50conf, "try-error")) { logED50low[[ri]] <- logED50conf[[1]] logED50high[[ri]] <- logED50conf[[2]] @@ -166,8 +170,9 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, if (logit && length(subset(allWrong,allWrong == i))==0) { m <- try(nls(response ~ plogis(-log10(dose),-logED50,scale), - data=tmp, algorithm="port", - start=list(logED50=startlogED50[[i]],scale=ls0))) + data=tmp, algorithm="port", + start=list(logED50=startlogED50[[i]],scale=ls0)), + silent = TRUE) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -193,7 +198,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, b[[ri]] <- NA } else { mtype[[ri]] <- "logit" - logED50conf <- try(confint(m,"logED50",level=level)) + logED50conf <- try(confint(m,"logED50",level=level), + silent = TRUE) if (!inherits(logED50conf, "try-error")) { logED50low[[ri]] <- logED50conf[[1]] logED50high[[ri]] <- logED50conf[[2]] @@ -209,8 +215,9 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, if (weibull && length(subset(allWrong,allWrong == i))==0) { m <- try(nls(response ~ pweibull(-log10(dose)+location,shape), - data=tmp, algorithm="port", - start=list(location=startlogED50[[i]],shape=ws0))) + data=tmp, algorithm="port", + start=list(location=startlogED50[[i]],shape=ws0)), + silent = TRUE) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { ri <- ri + 1 @@ -218,7 +225,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, a[[ri]] <- coef(m)[["location"]] b[[ri]] <- coef(m)[["shape"]] sqrdev <- function(logdose) { - (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2 + (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2 } logED50[[ri]] <- nlm(sqrdev,startlogED50[[i]])$estimate if (sqrdev(logED50[[ri]]) > 0.1) { @@ -291,7 +298,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, c[[ri]] <- NA } } - results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, + 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 = "") @@ -311,18 +318,18 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, if (mtype[[row.i]] %in% c("probit", "logit", "weibull", "linlogit")) { for (ED in EDx) { of <- function(x) { - abs(predict(models[[row.i]], data.frame(dose = 10^x)) - + abs(predict(models[[row.i]], data.frame(dose = 10^x)) - (1 - (ED/100))) - } - # Search over interval starting an order of magnitude below + } + # 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, + 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 + results[row.i, paste0("EDx", ED)] <- 10^logdose.ED } } } @@ -1,12 +1,12 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("dose", "Substance", "mtype")) -drplot <- function(drresults, data, +drplot <- function(drresults, data, dtype = "std", alpha = 0.95, ctype = "none", path = "./", fileprefix = "drplot", overlay = FALSE, xlim = c("auto","auto"), ylim = c("auto","auto"), xlab = paste("Decadic Logarithm of the dose in ", unit), ylab = "Normalized response", axes = TRUE, frame.plot = TRUE, - postscript = FALSE, pdf = FALSE, png = FALSE, + postscript = FALSE, pdf = FALSE, png = FALSE, bw = TRUE, pointsize = 12, colors = 1:8, ltys = 1:8, pchs = "auto", @@ -24,7 +24,7 @@ drplot <- function(drresults, data, if(is.data.frame(data)) { # Get rid of pseudo substance names of controls nonzerodata <- subset(data,dose!=0) - nonzerodata$substance <- factor(nonzerodata$substance) + nonzerodata$substance <- factor(nonzerodata$substance) zerodata <- subset(data,dose==0) nc <- length(zerodata$dose) # Number of control points if (nc > 0) { @@ -44,12 +44,12 @@ drplot <- function(drresults, data, hr <- max(nonzerodata$response) if (ctype == "std") hr <- max(hr,1 + sdc) if (ctype == "conf") hr <- max(hr,1 + controlconf) - dsubstances <- levels(nonzerodata$substance) + dsubstances <- levels(nonzerodata$substance) } else { lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2 lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2 if (length(subset(drresults,mtype=="linlogit")$Substance) != 0) { - hr <- 1.8 + hr <- 1.8 } else { hr <- 1.0 } @@ -70,20 +70,20 @@ drplot <- function(drresults, data, postscript(file=filename, paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (pdf) { filename = paste(path,fileprefix,".pdf",sep="") pdf(file=filename, paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (png) { filename = paste(path,fileprefix,".png",sep="") png(filename=filename, width=500, height=500, pointsize=pointsize) message("Created File: ",filename,"\n") } - + plot(0,type="n", xlim = xlim, ylim = ylim, @@ -97,7 +97,7 @@ drplot <- function(drresults, data, if (!postscript && !png && !pdf && length(dsubstances) > 1) { op <- par(ask=TRUE) on.exit(par(op)) - } + } } # nl is the overall number of fits to draw by different line types nl <- 0 @@ -123,20 +123,20 @@ drplot <- function(drresults, data, postscript(file=filename, paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (pdf) { filename = paste(path,fileprefix,sub(" ","_",i),".pdf",sep="") pdf(file=filename, paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (png) { filename = paste(path,fileprefix,sub(" ","_",i),".png",sep="") png(filename=filename, width=500, height=500, pointsize=pointsize) message("Created File: ",filename,"\n") } - + plot(0,type="n", xlim = xlim, ylim = ylim, @@ -147,7 +147,7 @@ drplot <- function(drresults, data, } if (!overlay) legend(lpos, i, lty = 1, col = color, pch = pch, inset=0.05) tmp$dosefactor <- factor(tmp$dose) # necessary because the old - # factor has all levels, not + # factor has all levels, not # only the ones tested with # this substance @@ -157,7 +157,7 @@ drplot <- function(drresults, data, abline(h = 1 + sdc, lty = 2) } if (ctype == "conf") { - abline(h = 1 - controlconf, lty = 2) + abline(h = 1 - controlconf, lty = 2) abline(h = 1 + controlconf, lty = 2) } @@ -179,7 +179,7 @@ drplot <- function(drresults, data, } if (dtype == "conf") { - confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars) + confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars) tops <- means + confidencedeltas bottoms <- means - confidencedeltas } @@ -207,13 +207,13 @@ drplot <- function(drresults, data, if (drresults[[fit.row, "mtype"]] %in% c("probit", "logit", "weibull", - "linlogit")) + "linlogit")) { m <- attr(drresults, "models")[[as.numeric(fit.row)]] of <- function(x) { predict(m, data.frame(dose = 10^x)) - } - plot(of, lld - 0.5, lhd + 2, + } + plot(of, lld - 0.5, lhd + 2, add = TRUE, col = color, lty = lty) } } |