search for: alleffects

Dear R users, I have some trouble using the allEffects() function to compute and display effect plots for a linear model. My data is quite simple, it concerns effects of 3 treatments on the tumoral volume of mice. vTum codes for the qualitative initial volume, from small to big, temps is the time in month since beginning of treatment, and S?rie codes f...

Thanks in advance for any help. I am attempting to add points to a plot using the allEffects command in the effects package. When I try to add the points I get the following error message: Error in plot.xy(xy.coords(x, y), type = type, ...) : plot.new has not been called yet Strangely, using the code I've pasted below this has worked for me in the past however figuring out what ha...

Dear everybody! Need help with graphics. I am runnig a simple lm and then using allEffects from 'effects' package: require(effects) model<-lm(Y~A+B, data=mydataframe) I am trying to build (for each predictor - A and then B) a plot of means on Y. I was successful doing it like this - in one swoop: ml.eff<-allEffects(ml1, se=F) plot(ml.eff,ylab="Title of Y") Is...

Dear John Fox and everyone, I have been using the effects library with glms and have found it very useful. Now I'm trying it with lms and I'm not sure if the results of the allEffects() are as expected. I've got a model that looks like this: mymodel = lm(formula = A ~ B + C + D + B:D + C:D) Residuals: Min 1Q Median 3Q Max -3.80156 -0.73486 -0.09792 0.63602 4.77747 Coefficients: Estimate Std. Error t value Pr(>|t|) (In...

Dear List, I find Effects package very useful, but I believe I have found a bug in allEffects function. Please consider the following code: test <- data.frame(tries= round(runif(40, 5, 300)), tra = gl(4, 10, labels = c("V", "D", "C", "L")), prop= runif(40, 0, 1)) test$success <- round(with(test, tries*prop)) test$prop <- with(test,...

...n but don;t seem to be able to get my head around it...example based on a publicly available data set: mydata <- read.csv("https://stats.idre.ucla.edu/stat/data/binary.csv") mylogit <- glm(admit ~ gre + gpa + rank, data = mydata, family = "binomial") library(effects) plot(allEffects(mylogit) ? ? ?,axes=list(y=list(lab="Prob(xyz)")) ) axes=list(y=list(lab="Prob(xyz)")) changes the y axis labels for all 3 plots... Any thoughts on how I could change the x axis labels to let say 'black' (plot 1), 'white'?(plot 2) and 'green' (plot 3)?fo...

...he help list reply was “ ?abline: "This function adds one or more straight lines through the current plot.", i.e. the already existing *current plot*. So plot your data (e.g. with plot(x, y)) before adding a regression line.” I interpreted the above to suggest the following --- plot(allEffects(Clean.label),ask=FALSE, alternating = TRUE, ylab="Probability of Rating", xlab="City",main="Cleanliness Ratings by City", factor.names=FALSE, ticks=c(0.1,0.2,0.3,0.4,0.5,0.6)) abline(h=c(0.1,0.2,0.3,0.4,0.5,0.6)) Error in int_abline(a = a, b = b, h = h, v = v, untf...

...e the strip text, for example (16,23] in the following example, to other more informative text such as "high level" on the fly? library(effects) Cowles$ex2 <- cut(Cowles$extraversion,3) mod.cowles <- glm(volunteer ~ sex+neuroticism*ex2,data=Cowles, family=binomial) eff.cowles <- allEffects(mod.cowles) plot(eff.cowles, 'neuroticism:ex2',factor.names=F) Thank you. Ronggui -- Wincent Ronggui HUANG (Ph.D.) City University of Hong Kong http://asrr.r-forge.r-project.org/rghuang.html

...CMD check effects' >> * checking S3 generic/method consistency ... NOTE >> Found the following apparent S3 methods exported but not registered: >> all.effects and added >> The offending function, all.effects(), is deprecated in favour of >> allEffects(), but I'd rather not get rid of it for backwards compatibility. >> Is there any way to suppress the note without removing all.effects()? and I had agreed that this was a "False Positive" in this case. [.......] and then > Now I agree .. and have e-talked abo...

...the point estimates to the effects plot, can someone show me the correct syntax. I have included the "R" effects example, so you can show me the correct syntax. Thanks mod.cowles <- glm(volunteer ~ sex + neuroticism*extraversion, data=Cowles, family=binomial) eff.cowles <- allEffects(mod.cowles, xlevels=list(neuroticism=0:24, extraversion=seq(0, 24, 6)), given.values=c(sexmale=0.5)) eff.cowles plot(eff.cowles, 'neuroticism:extraversion', ylab="Prob(Volunteer)", ticks=list(at=c(.1,.25,.5,.75,.9))) Chris Anderson Data Analyst Medical Affairs wk: 925...

...rary(effects) Loading required package: lattice Loading required package: grid Loading required package: MASS Loading required package: nnet Loading required package: colorspace Attaching package: ?effects? The following object(s) are masked from ?package:datasets?: Titanic HTML> summary(allEffects(resin1.aov) + ) model: resp ~ trt + block trt effect trt A B C D 92.81667 91.68333 88.91667 85.76667 Lower 95 Percent Confidence Limits trt A B C D 90.46148 89.32815 86.56148 83.41148 Upper 95 Percent Confidence Limits trt A...

...set with no problems (i.e., nothing is wrong with the created glm object). However, when I try to use the "effects" package to plot the effects I get the error message shown below. I get the same message if I try to plot a single effect. Any idea what could be wrong here? glm.eff <- allEffects(glm1) plot(glm.eff) Error in apply(mod.matrix[, components], 1, prod) : subscript out of bounds In addition: Warning messages: 1: In `[<-.factor`(`*tmp*`, ri, value = c(1, 1, 1, 1, 1, 1, 1, 1, 1, : invalid factor level, NAs generated 2: In matrix(apply(as.matrix(X.mod[, facs]), 2, mean),...

...ng S3 generic/method consistency ... NOTE >> >> Found the following apparent S3 methods exported but not registered: >> >> all.effects >> >> and added >> >> >> The offending function, all.effects(), is deprecated in favour of >> >> allEffects(), but I'd rather not get rid of it for backwards compatibility. >> >> Is there any way to suppress the note without removing all.effects()? >> >> and I had agreed that this was a "False Positive" in this case. >> >> [.......] >> >>...

...NOTE >>>>> Found the following apparent S3 methods exported but not registered: >>>>> all.effects >>>> >>>> and added >>>> >>>>> The offending function, all.effects(), is deprecated in favour of >>>>> allEffects(), but I'd rather not get rid of it for backwards compatibility. >>>>> Is there any way to suppress the note without removing all.effects()? >>>> >>>> and I had agreed that this was a "False Positive" in this case. >>>> >>&gt...

...apparent S3 methods exported but not registered: >>>>>>> all.effects >>>>>> >>>>>> and added >>>>>> >>>>>>> The offending function, all.effects(), is deprecated in favour of >>>>>>> allEffects(), but I'd rather not get rid of it for backwards compatibility. >>>>>>> Is there any way to suppress the note without removing all.effects()? >>>>>> >>>>>> and I had agreed that this was a "False Positive" in this case. >&gt...

...gt; * checking S3 generic/method consistency ... NOTE > >> Found the following apparent S3 methods exported but not registered: > >> all.effects > > and added > > >> The offending function, all.effects(), is deprecated in favour of > >> allEffects(), but I'd rather not get rid of it for backwards compatibility. > >> Is there any way to suppress the note without removing all.effects()? > > and I had agreed that this was a "False Positive" in this case. > > [.......] > > and then > >...

...gt; * checking S3 generic/method consistency ... NOTE > >> Found the following apparent S3 methods exported but not registered: > >> all.effects > > and added > > >> The offending function, all.effects(), is deprecated in favour of > >> allEffects(), but I'd rather not get rid of it for backwards compatibility. > >> Is there any way to suppress the note without removing all.effects()? > > and I had agreed that this was a "False Positive" in this case. > > [.......] > > and then > >...

I can't figure out how to customize the order of the panels for effects plots. Any help would be appreciated. Here's my code: library(effects) lm.hour3eff<-allEffects(lm.hour3, xlevels=list(road=c(0, 1000, 2000, 3000), trail=c(0, 1000, 2000, 3000))) plot(lm.hour3eff,"road:trail", xlab="Trail Distance (m)", ylab="Step Length (m)", main=NULL) Thanks, McCrea -- View this message in context: http://www.nabble.com/order-of-effects-...

Dear Colleagues, John Mandel ( Chain block designs with two-way elimination of heterogeneity. Biometrics 10, 251-272 ,1954). extended the class of chain block designs (Youden & Conner (1953) to elimination of both row and column (blocks) effects. These experimental designs can be useful in engineering and other fields. I am having difficulty obtaining his adjusted treatment means in his

Can anyone show me how to test for significant simple slopes of a 3-way interaction, with covariates. my equation tmod<-(glm(PCL~ rank.f + gender.f + MONTHS + CEXPOSE.M + bf.m + MONTHS*CEXPOSE.M*bf.m, data=mhatv, family=gaussian ,na.action=na.omit)) Thank you Mike [[alternative HTML version deleted]]