# Plotting the probability curve from a logit model with 10 predictors

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## Plotting the probability curve from a logit model with 10 predictors

 I have a logit model with about 10 predictors and I am trying to plot the probability curve for the model. Y=1 = 1 / 1+e^-z  where  z=B0 + B1X1 + ... + BnXi If the model had only one predictor, I know to do something like below. mod1 = glm(factor(won) ~ as.numeric(bid), data=mydat, family=binomial(link="logit")) all.x <- expand.grid(won=unique(won), bid=unique(bid)) y.hat.new <- predict(mod1, newdata=all.x, type="response") plot(bid<-000:250,predict(mod1,newdata=data.frame(bid<-c(000:250)),type="response"), lwd=5, col="blue", type="l") I'm not sure how to proceed when I have 10 or so predictors in the logit model. Do I simply expand the expand.grid() function to include all the variables? So my question is how do I form a plot of a logit probability curve when I have 10 predictors? would be nice to do this in ggplot2. Thanks! -- *Abraham Mathew Statistical Analyst www.amathew.com 720-648-0108 @abmathewks*         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: Plotting the probability curve from a logit model with 10 predictors

 You have an about 11-D response surface, not a curve! -- Bert On Thu, Jul 5, 2012 at 2:39 PM, Abraham Mathew <[hidden email]> wrote: > I have a logit model with about 10 predictors and I am trying to plot the > probability curve for the model. > > Y=1 = 1 / 1+e^-z  where  z=B0 + B1X1 + ... + BnXi > > If the model had only one predictor, I know to do something like below. > > mod1 = glm(factor(won) ~ as.numeric(bid), data=mydat, > family=binomial(link="logit")) > > all.x <- expand.grid(won=unique(won), bid=unique(bid)) > y.hat.new <- predict(mod1, newdata=all.x, type="response") > > plot(bid<-000:250,predict(mod1,newdata=data.frame(bid<-c(000:250)),type="response"), > lwd=5, col="blue", type="l") > > > I'm not sure how to proceed when I have 10 or so predictors in the logit > model. Do I simply expand the > expand.grid() function to include all the variables? > > So my question is how do I form a plot of a logit probability curve when I > have 10 predictors? > > would be nice to do this in ggplot2. > > Thanks! > > > -- > *Abraham Mathew > Statistical Analyst > www.amathew.com > 720-648-0108 > @abmathewks* > >         [[alternative HTML version deleted]] > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help> PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code. > -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm        [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: Plotting the probability curve from a logit model with 10 predictors

 Ok, so let's say I have a logit equation outlined as Y= 2.5 + 3X1 + 2.3X2 + 4X3 + 3.6X4 + 2.2X5 So a one unit increase in X2 is associated with a 2.3 increase in Y, regardless of what the other predictor values are. So I guess instead of trying to plot of curve with all the predictors accounted for, I should plot each curve by itself. I'm still not sure how to do that with so many predictors. Any help would be appreciated. On Thu, Jul 5, 2012 at 4:23 PM, Bert Gunter <[hidden email]> wrote: > You have an about 11-D response surface, not a curve! > > -- Bert > > On Thu, Jul 5, 2012 at 2:39 PM, Abraham Mathew <[hidden email]>wrote: > >> I have a logit model with about 10 predictors and I am trying to plot the >> probability curve for the model. >> >> Y=1 = 1 / 1+e^-z  where  z=B0 + B1X1 + ... + BnXi >> >> If the model had only one predictor, I know to do something like below. >> >> mod1 = glm(factor(won) ~ as.numeric(bid), data=mydat, >> family=binomial(link="logit")) >> >> all.x <- expand.grid(won=unique(won), bid=unique(bid)) >> y.hat.new <- predict(mod1, newdata=all.x, type="response") >> >> plot(bid<-000:250,predict(mod1,newdata=data.frame(bid<-c(000:250)),type="response"), >> lwd=5, col="blue", type="l") >> >> >> I'm not sure how to proceed when I have 10 or so predictors in the logit >> model. Do I simply expand the >> expand.grid() function to include all the variables? >> >> So my question is how do I form a plot of a logit probability curve when I >> have 10 predictors? >> >> would be nice to do this in ggplot2. >> >> Thanks! >> >> >> -- >> *Abraham Mathew >> Statistical Analyst >> www.amathew.com >> 720-648-0108 >> @abmathewks* >> >>         [[alternative HTML version deleted]] >> >> ______________________________________________ >> [hidden email] mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help>> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html>> and provide commented, minimal, self-contained, reproducible code. >> > > > > -- > > Bert Gunter > Genentech Nonclinical Biostatistics > > Internal Contact Info: > Phone: 467-7374 > Website: > > http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm> > > -- *Abraham Mathew Statistical Analyst www.amathew.com 720-648-0108 @abmathewks*         [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: Plotting the probability curve from a logit model with 10 predictors

 In reply to this post by Abraham Mathew Look at the Predict.Plot and TkPredict functions in the TeachingDemos package.  These will not plot all 11 dimensions at once, but will plot 2 of the dimensions conditioned on the others.  You can then change the conditioning to see relationships. These use base rather than ggplot graphics. On Thu, Jul 5, 2012 at 3:39 PM, Abraham Mathew <[hidden email]> wrote: > I have a logit model with about 10 predictors and I am trying to plot the > probability curve for the model. > > Y=1 = 1 / 1+e^-z  where  z=B0 + B1X1 + ... + BnXi > > If the model had only one predictor, I know to do something like below. > > mod1 = glm(factor(won) ~ as.numeric(bid), data=mydat, > family=binomial(link="logit")) > > all.x <- expand.grid(won=unique(won), bid=unique(bid)) > y.hat.new <- predict(mod1, newdata=all.x, type="response") > plot(bid<-000:250,predict(mod1,newdata=data.frame(bid<-c(000:250)),type="response"), > lwd=5, col="blue", type="l") > > > I'm not sure how to proceed when I have 10 or so predictors in the logit > model. Do I simply expand the > expand.grid() function to include all the variables? > > So my question is how do I form a plot of a logit probability curve when I > have 10 predictors? > > would be nice to do this in ggplot2. > > Thanks! > > > -- > *Abraham Mathew > Statistical Analyst > www.amathew.com > 720-648-0108 > @abmathewks* > >         [[alternative HTML version deleted]] > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. [hidden email] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.
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## Re: Plotting the probability curve from a logit model with 10 predictors

 In reply to this post by Abraham Mathew On Jul 6, 2012, at 4:30 PM, Abraham Mathew wrote: > Ok, so let's say I have a logit equation outlined as Y= 2.5 + 3X1 +   > 2.3X2 + > 4X3 + 3.6X4 + 2.2X5 > > So a one unit increase in X2 is associated with a 2.3 increase in Y, Assuming, that is, you also understand what Y is. From you comments so   far, I have some nagging worries regarding your understanding of that   point. -- David. > regardless of what the other > predictor values are. So I guess instead of trying to plot of curve   > with > all the predictors accounted > for, I should plot each curve by itself. > > I'm still not sure how to do that with so many predictors. > > Any help would be appreciated. > > > > > On Thu, Jul 5, 2012 at 4:23 PM, Bert Gunter <[hidden email]>   > wrote: > >> You have an about 11-D response surface, not a curve! >> >> -- Bert >> >> On Thu, Jul 5, 2012 at 2:39 PM, Abraham Mathew   >> <[hidden email]>wrote: >> >>> I have a logit model with about 10 predictors and I am trying to   >>> plot the >>> probability curve for the model. >>> >>> Y=1 = 1 / 1+e^-z  where  z=B0 + B1X1 + ... + BnXi >>> >>> If the model had only one predictor, I know to do something like   >>> below. >>> >>> mod1 = glm(factor(won) ~ as.numeric(bid), data=mydat, >>> family=binomial(link="logit")) >>> >>> all.x <- expand.grid(won=unique(won), bid=unique(bid)) >>> y.hat.new <- predict(mod1, newdata=all.x, type="response") >>> >>> plot(bid<-000:250,predict(mod1,newdata=data.frame(bid<- >>> c(000:250)),type="response"), >>> lwd=5, col="blue", type="l") >>> >>> >>> I'm not sure how to proceed when I have 10 or so predictors in the   >>> logit >>> model. Do I simply expand the >>> expand.grid() function to include all the variables? >>> >>> So my question is how do I form a plot of a logit probability   >>> curve when I >>> have 10 predictors? >>> >>> would be nice to do this in ggplot2. >>> >>> Thanks! >>> >>> >>> -- >>> *Abraham Mathew >>> Statistical Analyst >>> www.amathew.com >>> 720-648-0108 >>> @abmathewks* >>> David Winsemius, MD West Hartford, CT ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code.