How to extract coefficients from elrm summary output

Question

I performed an exact logistic regression in my dataset using the elrm package

I compare this to the usual logistic regression.

I was able to run the bootstrap on the usual logistic regression, the statistical interest that I pulled out is the estimated coefficient and p-value.

However, I cannot start my elrm boot lot because I cannot get the coefficients that I need from the output.

With my data, the summary gives a printout:

 Results: estimate p-value p-value_se mc_size M 0.15116 0.06594 0.00443 49000 95% Confidence Intervals for Parameters lower upper M 0.00156155 0.3647232 

I want to extract the M-score and p-value so that I can pull out these statistics when I do the download. I tried a bunch of different combinations to try to pull the values ​​out and they don't work.

 summary(model)$coefficient summary(model)$Results summary(model)$estimate 

All this just spits out the resume again.

Does anyone know if elrm can be extracted from a resume?

Any help would be greatly appreciated.

Answer 1

 library(elrm) data(drugDat) drug.elrm <- elrm(formula=recovered/n~sex+treatment,interest=~sex+treatment,r=4, iter=100000,burnIn=1000,dataset=drugDat) > summary.elrm(drug.elrm) Call: [[1]] elrm(formula = recovered/n ~ sex + treatment, interest = ~sex + treatment, r = 4, iter = 1e+05, dataset = drugDat, burnIn = 1000) Results: estimate p-value p-value_se mc_size joint NA 0.14886 0.00173 99000 sex 0.27092 0.69385 0.01204 2649 treatment 0.76739 0.07226 0.00314 13160 95% Confidence Intervals for Parameters lower upper sex -0.6217756 1.212499 treatment -0.1216884 1.852346 # If you look at the summary function, it simply outputs formatted results to # the screen. So instead, we can just work with the original drug.elrm object names(drug.elrm) # shows you everything in this object # to see the p-values drug.elrm$p.values.se joint sex treatment 0.001734482 0.012039701 0.003143006 # to get the p-value for joint drug.elrm$p.values.se[[1]] # now for the CI drug.elrm$coeffs.ci lower upper sex -0.6217756 1.212499 treatment -0.1216884 1.852346 > drug.elrm$coeffs.ci[[1]] [1] -0.6217756 -0.1216884 > drug.elrm$coeffs.ci[[1]][1] [1] -0.6217756 > 

Answer 2

It appears that p values ​​and confidence intervals are stored as part of the model object itself. The summary.elrm function simply extracts and formats some of this information for you. I show the following steps that I used to figure this out, but the consolidated version is to index your model object$p.values for object$p.values and object$coeffs.ci respectively.

 #Example from help page data(utiDat) uti.elrm <- elrm(uti/n~age+current+dia+oc+pastyr+vi+vic+vicl+vis, interest=~dia,r=4,iter=5000,burnIn=1000,dataset=utiDat) #Look at summary summary(uti.elrm) #Let examine the structure of the summary object to see what in there, ie #what can we extract? str(summary(uti.elrm)) #Hmm, doesn't look like anything of interest. Let look at the source code itself summary.elrm #Looks like the p.values are stored in the actual model object iself and the summary function #just formats them for us. The relevant part of the summary code for the p-value is: #----- #inferences = as.data.frame(cbind(round(as.numeric(object$coeffs),5), # round(as.numeric(object$p.values), 5), # round(as.numeric(object$p.values.se),5), # object$mc.size) # ) #results = data.frame(row.names = names(object$coeffs), inferences) #names(results) = c("estimate", "p-value", "p-value_se", "mc_size") #So, it looks like we can grab the p.values directly from "object" > uti.elrm$p.values dia 0.02225 #And the confidence intervals are also in the object, located here in the summary code: #----- #cat(object$ci.level, "% Confidence Intervals for Parameters\n", # sep = "") #cat("\n") #print(object$coeffs.ci) #So we can extract them thusly: > uti.elrm$coeffs.ci lower upper dia 0.1256211 Inf