search for: ymax

Hi, I want to plot grouped bars to compare 95% confidence interval estimates from two models. Each bar represents a 95% confidence interval estimate of a coefficient from one of the two models. Each group represents confidence interval estimates of the same coefficient from the two models. I think such a bar plot will nicely present whether 95% confidence interval estimates of the same

...ation of the cycle (in months). In other words, all rectangles have coordinates (start, duration) and (end, duration). rr I've spent hours trying to figure out the documentation and pouring over Google and RSeek searches and am at an impasse. The documentation refers to xmin, xmax, ymin, and ymax but doesn't say anything about them. The only example gives them both as vectors, so I assume they refer to a sequence of coordinates in which each rectangle's vertices is given by (xmin[i],ymin[i]), (xmin[i],ymax[i]), (xmax[i],ymax[i]), and (xmax[i],ymin[i]). But when I try to plot som...

...ily=poisson()) (that's why you see the "dose[-1]" term. The "first" dose in the dose vector is 0. This is really a nice fit. I can obtain a nice slope (B) and intercept (A): log(Y) = B log(x) + A I do have a biological value for dose = 0 from my "control". i/e Ymax = some number with a Poisson error again So, what I want is EC50x : Y/Ymax = 0.5 = exp(B log(EC50x) + A) / Ymax exp((log(0.5) + Log(Ymax)) - A)/B) = EC50x That's all fine, except I don't have a clue on how to calculate the confidence intervals of EC50x or even if I can model this invers...

Hello I have created a graph using the following commands: <<< startBReP3O1T <- diffs$BReP3O1T - diffs$diff_BReP3O1T endBReP3O1T <- diffs$BReP3O1T x <- seq(47,89, length = 10) ymin <- min(min(startBReP3O1T), min(endBReP3O1T)) ymax <- max(max(startBReP3O1T), max(endBReP3O1T)) y <- seq(ymin, ymax, length = 10) plot(x,y, type = 'n', xlab = 'Age', ylab = 'BReP3O1T', main = 'Age, decline and BReP3O1T') segments(x0 = startage, x1 = endage, y0 = startBReP3O1T, y1 = endBReP3O1T, col = decline)...

...within the window. I propose the fix listed below. src/main/ --- plot.c Wed Sep 17 01:03:39 2003 +++ plot.c.new Wed Sep 17 01:21:59 2003 @@ -3314,7 +3314,7 @@ SEXP do_dendwindow(SEXP call, SEXP op, SEXP args, SEXP env) { int i, imax, n; - double pin, *ll, tmp, yval, *y, ymin, ymax, yrange; + double pin, *ll, tmp, yval, *y, ymin, ymax, yrange, m; SEXP originalArgs, merge, height, llabels, str; char *vmax; DevDesc *dd; @@ -3357,8 +3357,14 @@ ll = (double*)R_alloc(n, sizeof(double)); dnd_lptr = &(INTEGER(merge)[0]); dnd_rptr = &(INTEGER...

...matrix(numeric(0),0,0) or something along those lines. Or one could change L-BFGS-B to behave the same as the other methods. cheers Ben Bolker --------------------- library(stats4) ## using example from ?mle x <- 0:10 y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) ll <- function(ymax=15, xhalf=6) -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) ## fix one parameter to get 1D profile fit2 <- mle(ll, fixed=list(xhalf=6)) profile(fit2) ## same again with method="L-BFGS-B" fit3 <- mle(ll, fixed=list(xhalf=6),method="L-BFGS-B") profile(fit3) ll...

...8B4500", "#FF7F00","#9370DB", "#800000","#104E8B","#228B22")[20:1] myagg<-aggregate(indata[invars],by=indata[datesvar],FUN=myfunction) yrange=range(pretty(as.matrix(myagg[2:length(myagg)]))) if(fixedy==0){ ymin<-yrange[1] ymax<-yrange[2]} else { ymin<-0 ymax<-yrange[2]} ydistance<-ymax-ymin if(ydistance>0.1 & ydistance<=1){mystep<-0.1} else { if(ydistance>1 & ydistance<=10){mystep<-1/2} else { if(ydistance>10 & ydistance<=100) {mystep<-10/5} else {...

...byrow=TRUE) # Read in and attach labels (names) to data rownames(test) <- c("Mount Pleasant","Jordan","Oil City","Pleasant Valley","Village of Lake Isabella","Rosebush") # Set plot limits: xmax <- nrow(test) nvec <- ncol(test) ymax <- ceiling(max(test)) yinc <- 1 # Generate Pareto order test <- test[order(test[,1],decreasing=TRUE),] # Set color palette MyCols <- rep(c("lightcyan","cornsilk","lavender"), each = xmax) # Adjust the margins par(mar = c(7, 5, 6, 3)) # Bar graph mp <...

...quence of a simulation, whereas I know that it cannot be less than (say) 0; and I want to fix the lower limit at 0 in any plot, leaving the upper limit to be assigned by plot() as a result of the computed values. I know I can do this by determining the max() of the data, and then computing a "Ymax" to put in (say) ylim = c(0,Ymax). However, for certain reasons, I would prefer not to have to do this. (And it's just a preference ... ). Whereas one can leave the whole issue of setting both plotting limits to plot(), by not specifying ylim (or xlim), or one can explcitily specify both...

....6,cex.lab=1.6,cex.axis=1.6) par(mfrow = c(3,4)) ifn <- "T.dat" trait <- read.table(ifn) i <- 1 j <- 1 for(k in 1:12) { dat <- data[i:(i+2), ] colnames(dat)<-c("SM","E","NP) Ymin <- if( min(dat$SM) < 0.0 ) (dat$SM - dat$E) else 0.0 Ymax <- if( max(dat$SM) > 0.0 ) (dat$SM + dat$E) else 0.0 Graph<-barplot(dat$SM, names.arg=dat$NP, main = trait[j:j,], xlab = data[i:i,1:1], ylim = c(Ymin,Ymax) ) segments(Graph, dat$SM + dat$E, Graph, dat$SM - dat$E) i <- i + 3 j <- j + 1 } dev.off() And the error message is: Error...

...advertise this fact, e.g., by adding one of the two examples appearing below. Best Wishes, Spencer Graves ################################ x <- 0:10 y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) # Pass data via function arguments rather than global variables ll.5 <- function(ymax=15, xhalf=6, x., y.) -sum(stats::dpois(y., lambda=ymax/(1+x./xhalf), log=TRUE)) (fit.5 <- mle(ll.5, start=list(ymax=15, xhalf=6), fixed=list(x.=x, y.=y))) ll3 <- function(lymax=log(15), lxhalf=log(6), x., y.) -sum(stats::dpois(y., lambda=exp(lymax)/(1+x./exp...

Dear All, I have this script: dat <- data.frame(Month = hstat$Date,C_avg = hstat$C.avg,C_stdev = hstat$C.stdev) ggplot(data = dat, aes(x = Month, y = C_avg, ymin = C_avg - C_stdev, ymax = C_avg + C_stdev)) + geom_point() + geom_line() + geom_errorbar() dat <- data.frame(Month = hstat$Date,K_avg = hstat$K.avg,K_stdev = hstat$K.stdev) ggplot(data = dat, aes(x = Month, y = K_avg, ymin = K_avg - K_stdev, ymax = K_avg + K_stdev)) + geom_point() + geom_line() + geom_er...

...Imedian <- quantile(meds, c(0.025, 0.5, 0.975)) CImean <- quantile(means, c(0.025, 0.5, 0.975)) hmean <- hist(means, freq = FALSE, plot = FALSE) hmeds <- hist(meds, freq = FALSE, plot = FALSE) split.screen(c(1, 2)) xlims <- range(c(hmean$breaks, hmeds$breaks)) ymax <- max(c(hmean$density, hmeds$density)) screen(1) plot(hmean, freq = FALSE, col = "red", xlim = xlims, ylim = c(0, ymax), xlab = paste("Sampling dist. of mean of ", xname), main = "") bringToTop() if (norm) { n <- length(...

...coding="UTF-8" ?> - <layout> <name>Layout 2</name> <pagesByX>1</pagesByX> <pagesByY>1</pagesByY> - <elements> <legend refParent="r3" xmax="0.54156171284634758" xmin="0.020151133501259435" ymax="0.31480598161051165" ymin="0.042461931948864044" /> <component background="auto" border="none" borderDegMinSec="false" borderEachPage="true" borderFont="Tahoma, 8" borderFore="#000000" borderMargin="12&q...

Hi, How can we set the environment for the minuslog function in mle()? The call in this code fails because the "ll" function cannot find the object 'y'. Modifying from the example in ?mle: library(stats4) ll <- function(ymax=15, xhalf=6) { -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) } fit.mle <- function(FUN, x, y) { loglik.fun <- match.fun(FUN) mle(loglik.fun, method="L-BFGS-B", lower=c(0, 0)) } fit.mle("ll", x=0:10, y=c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)) How sh...

...PopStd <- 90468 beta <- Beta DIs <- Dls MnmN <- Nmin OptN <- Nopt1 # define model function Y.model <- function(gN, MnmN, OptN, DIs, beta, eta1, eta2, Popn, Dmax, AWC, SumEp, PotYield3, Nsupply) { Ymax<- 1-ifelse(Popn<=PopStd, eta1, eta2)*log(Popn/PopStd) Ymax <- Ymax*PotYield3*Popn/1000 Ymax <- Ymax*ifelse(Dmax<=DIs*AWC, 1, 1 - beta*(Dmax -DIs*AWC)/SumEp) Nstar <- (Nsupply- MnmN*Ymax) / (OptN*Ymax - MnmN*Ymax) Nsta...

...ing and installing the GDD package under my FreeBSD 6.1 box after eliminating ifdef DEBUG ? ?PKG_CFLAGS+=-DJGD_DEBUG endif in Makevars.in Now, with the following code .............................................. grafico1<- function() { plot(1:length(tabella[,1]),tabella[,2],ylim=c(Ymin,Ymax),type="h", lwd=6,col="red",main=paste("TEMPERATURE MEDIE GIORNALIERE\nMESE DI", toupper(format(ierid,"%B")),sep=" "), col.main="dark blue", xlab="Giorni del mese",ylab="?C", col.lab="blue",axes=FALS...

The mle2 function (bbmle library) gives an example something like the following in its help page. How do I access the coefficients, standard errors, etc in the summary of "a"? > x <- 0:10 > y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8) > LL <- function(ymax=15, xhalf=6) + -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) > a <- mle2(LL, fixed=list(xhalf=6)) > summary(a) Maximum likelihood estimation Call: mle2(minuslogl = LL, fixed = list(xhalf = 6)) Coefficients: Estimate Std. Error z value Pr(z) ymax 19.2881 1.7...

Dear List, I am having trouble setting the transparency of a ribbon in ggplot2 and was wondering if anybody had any suggestions so far i have a plot exactly as i want it and i want to add a ribbon connecting the ymax and ymin, whci i do with the following command m10 + stat_summary(geom="ribbon", fun.ymin="min", fun.ymax="max") However the ribbon is a dark grey and i want to make it much lighter or change the colour. I was wondering if anybody had any ideas? I have kept the code...

...growth over time. The specific model giving me problems at the moment is only one of a whole class of such models which I need to work with. I specify it here to illustrate that it is not always obvious what the bounds on the parameters are. SSbaranyiBR94<-selfStart( model=function(Time, y0, ymax, mu, lambda, m = 1, v = mu) { #+ # From the paper Baranyi J. & Roberts T. A. (1994). A dynamic approach to predicting bacterial growth in food. Int J. of Fd. Micro. 23. 277-294 # Papers equations (6), (5b), (4b) # eq 4b: y(Time) = y0 + mu' * A(Time) - ln(1+(exp(m' * mu' * A(Tim...