### Paul Johnson 2008-05-08 ### sandwichGLM.R system("wget http://www.ats.ucla.edu/stat/stata/faq/eyestudy.dta") library(foreign) dat <-, Once again, Paul, many thanks for your thorough examination of this question! I think R should consider doing. Stack Overflow overfloweth with folks desparately trying to figure out how to get their regression tables exported to html, pdf–or, the horror, word–formats. By choosing lag = m-1 we ensure that the maximum order of autocorrelations used is \(m-1\) — just as in equation .Notice that we set the arguments prewhite = F and adjust = T to ensure that the formula is used and finite sample adjustments are made.. We find that the computed standard errors coincide. On 08-May-08 20:35:38, Paul Johnson wrote: I have the solution. This note deals with estimating cluster-robust standard errors on one and two dimensions using R (seeR Development Core Team[2007]). You can always get Huber-White (a.k.a robust) estimators of the standard errors even in non-linear models like the logistic regression. 316e-09 R reports R2 = 0. Thank you very much for your comments! So I have a little function to calculate Stata-like robust standard errors for glm: Of course this becomes trivial as $n$ gets larger. cov_HC1. On 02-Jun-04 10:52:29, Lutz Ph. {sandwich} has a ton of options for calculating heteroskedastic- and autocorrelation-robust standard errors. Let’s say we estimate the same model, but using iteratively weight least squares estimation. okay, so now the bootcov works fine. centered_tss. Heteroscedasticity robust covariance matrix. Here are two examples using hsb2.sas7bdat . residuals.lrm and residuals.coxph are examples where score residuals are computed. On Tue, 4 Jul 2006 13:14:24 -0300 Celso Barros wrote: > I am trying to get robust standard errors in a logistic regression. (5 replies) Is there a way to tell glm() that rows in the data represent a certain number of observations other than one? If you use the following approach, with the HC0 type of robust standard errors in the "sandwich" package (thanks to Achim Zeileis), you get "almost" the same numbers as that Stata output gives. This leads to R> sqrt(diag(sandwich(glm1))) (Intercept) carrot0 0.1673655 0.1971117 R> sqrt(diag(sandwich(glm1, adjust = TRUE))) (Intercept) carrot0 0.1690647 0.1991129 (Equivalently, you could youse vcovHC() with, I'd like to thank Paul Johnson and Achim Zeileis heartily for their thorough and accurate responses to my query. To get heteroskadastic-robust standard errors in R–and to replicate the standard errors as they appear in Stata–is a bit more work. Logistic regression and robust standard errors. For now I do 1 -> 2b -> 3 in R. It is sometimes the case that you might have data that falls primarily between zero and one. glm fits generalized linear models of ywith covariates x: g E(y) = x , y˘F g() is called the link function, and F is the distributional family. [*] I'm interested in the same question. For instance, if … Now, things get inteseting once we start to use generalized linear models. Example data comes from Wooldridge Introductory Econometrics: A Modern Approach. This formula fits a linear model, provides a variety ofoptions for robust standard errors, and conducts coefficient tests At 17:25 02.06.2004, Frank E Harrell Jr wrote: Sorry I didn't think of that sooner. Breitling wrote: Slight correction: robcov in the Design package, can easily be used with Design's glmD function. The method for "glm" objects always uses df = Inf (i.e., a z test). All Rcommands written in base R, unless otherwise noted. Getting Robust Standard Errors for OLS regression parameters | SAS Code Fragments One way of getting robust standard errors for OLS regression parameter estimates in SAS is via proc surveyreg . There have been several posts about computing cluster-robust standard errors in R equivalently to how Stata does it, for example (here, here and here). I was inspired by this bit of code to make a map of Brooklyn bike lanes–the lanes upon which I once biked many a mile. Cluster Robust Standard Errors for Linear Models and General Linear Models Computes cluster robust standard errors for linear models ( stats::lm ) and general linear models ( stats::glm ) using the multiwayvcov::vcovCL function in the sandwich package. On Wed, 2 Jun 2004, Lutz Ph. First, we estimate the model and then we use vcovHC() from the {sandwich} package, along with coeftest() from {lmtest} to calculate and display the robust standard errors. However, if you believe your errors do not satisfy the standard assumptions of the model, then you should not be running that model as this might lead to biased parameter estimates. > Is there any way to do it, either in car or in MASS? Robust standard errors: When robust is selected the coefficient estimates are the same as a normal logistic regression standard errors are adjusted. However, here is a simple function called ols which carries … That is indeed an excellent survey and reference! However, I have tried to trace through the thread in the R-help archives, and have failed to find anything which lays out how a solution can be formulated. Basically, if I fit a GLM to Y=0/1 response data, to obtain relative risks, as in GLM <- glm(Y ~ A + B + X + Z, family=poisson(link=log)) I can get the estimated RRs from RRs <- exp(summary(GLM)$coef[,1]) but do not see how to. Heteroscedasticity robust covariance matrix. glm2 <- glm(lenses~carrot0 +gender1 +latitude, data=dat, I'd like to thank Paul Johnson and Achim Zeileis heartily, No, no. For further detail on when robust standard errors are smaller than OLS standard errors, see Jorn-Steffen Pische’s response on Mostly Harmless Econometrics’ Q&A blog. You need to estimate with glm and then get standard errors that are adjusted for heteroskedasticity. Postdoctoral scholar at LRDC at the University of Pittsburgh. You can, to some extent, pass objects back and forth between the R and Python environments. First, we estimate the model and then we use vcovHC() from the {sandwich} package, along with coeftest() from {lmtest} to calculate and display the robust standard errors. Since the presence of heteroskedasticity makes the lest-squares standard errors incorrect, there is a need for another method to calculate them. below some code to demonstrate. robcov needs the residuals method for the fitter to allow a type="score" or type="hscore" (for Efron's method) argument. the following approach, with the HC0 type of robust standard errors in the "sandwich" package (thanks to Achim Zeileis), you get "almost" the same numbers as that Stata output gives. Similarly, if you had a bin… Download Stata data sets here. For example, these may be proportions, grades from 0-100 that can be transformed as such, reported percentile values, and similar. The number of persons killed by mule or horse kicks in thePrussian army per year. I was lead down this rabbithole by a (now deleted) post to Stack Overflow. And, just to confirm, it all worked perfectly for me in the end. Best wishes, Ted, There is an article available online (by a frequent contributor to this list) which addresses the topic of estimating relative risk in multivariable models. Creating tables in R inevitably entails harm–harm to your self-confidence, your sense of wellbeing, your very sanity. The number of people in line in front of you at the grocery store.Predictors may include the number of items currently offered at a specialdiscount… cov_HC2. Some folks work in R. Some work in Python. Perhaps even fractional values? however, i still do not get it right. That is why the standard errors are so important: they are crucial in determining how many stars your table gets. ### Paul Johnson 2008-05-08 ### sandwichGLM.R In R, estimating “non-Stata” robust standard errors: I wrote this up a few years back and updated it to include {ggraph} and {tidygraph}, my go-tos now for network manipulation and visualization. I conduct my analyses and write up my research in R, but typically I need to use word to share with colleagues or to submit to journals, conferences, etc. For instance, if yis distributed as Gaussian (normal) and … Description. The \(R\) function that does this job is hccm(), which is part of the car package and I find this especially cool in Rmarkdown, since you can knit R and Python chucks in the same document! In "sandwich" I have implemented two scaling strategies: divide by "n" (number of observations) or by "n-k" (residual degrees of freedom). Be able to specify ex-post the standard errors I need, save it either to the object that is directly exported by GLM or have it in another vector. On 13-May-08 14:25:37, Michael Dewey wrote: http://www.ats.ucla.edu/stat/stata/faq/relative_risk.htm, https://www.stat.math.ethz.ch/mailman/listinfo/r-help, http://www.R-project.org/posting-guide.html, http://www.ats.ucla.edu/stat/stata/faq/eyestudy.dta"), http://www.bepress.com/uwbiostat/paper293/, https://stat.ethz.ch/mailman/listinfo/r-help, [R] Glm and user defined variance functions, [R] lme: model variance and error by group, [R] effective sample size in logistic regression w/spat autocorr, [R] external regressors in garch variance, [R] ar.ols() behaviour when time series variance is zero, [R] Problem with NA data when computing standard error, [R] Fixing error variance in a path analysis to model measurement error in scales using sem package, [R] fwdmsa package: Error in search.normal(X[samp, ], verbose = FALSE) : At least one item has no variance. 6glm— Generalized linear models General use glm fits generalized linear models of ywith covariates x: g E(y) = x , y˘F g() is called the link function, and F is the distributional family. what am i still doing wrong? To get heteroskadastic-robust standard errors in R–and to replicate the standard errors as they appear in Stata–is a bit more work. Dear all, I use ”polr” command (library: MASS) to estimate an ordered logistic regression. But note that inference using these standard errors is only valid for sufficiently large sample sizes (asymptotically normally distributed t-tests). Robust Standard Errors in R Stata makes the calculation of robust standard errors easy via the vce (robust) option. Stata is unusual in providing these covariance matrix estimates for just about every regression estimator. You can easily calculate the standard error of the mean using functions contained within the base R package. cov_HC0. That’s because Stata implements a specific estimator. A common question when users of Stata switch to R is how to replicate the vce(robust) option when running linear models to correct for heteroskedasticity. et al. Using the Ames Housing Prices data from Kaggle, we can see this. The same applies to clustering and this paper. I went and read that UCLA website on the RR eye study and the Zou article that uses a glm with robust standard errors. This method allowed us to estimate valid standard errors for our coefficients in linear regression, without requiring the usual assumption that the residual errors have constant variance. Oddly in your example I am finding that the bootstrap variances are lower than. Substituting various definitions for g() and F results in a surprising array of models. Some work in both. 2b. Most importantly then. The percentage differences (vcovHC relative to STATA) for the two cases you analyse above are vcovHC "HC0": 0.1673655 0.1971117 STATA : 0.1682086 0.1981048 ------------------------------------- %. In Stata, this is trivially easy: reg y x, vce(robust). The estimated b's from the glm match exactly, but the robust standard errors are a bit off. Here's my best guess. For discussion of robust inference under within groups correlated errors, see Ladislaus Bortkiewicz collected data from 20 volumes ofPreussischen Statistik. You want glm() and then a function to compute the robust covariance matrix (there's robcov() in the Hmisc package), or use gee() from the "gee" package or geese() from "geepack" with independence working correlation. Ted. However, the bloggers make the issue a bit more complicated than it really is. The estimated b's from the glm match exactly, but the robust standard errors are a bit off. I found it very helpful. The standard errors are not quite the same. http://www.bepress.com/uwbiostat/paper293/ Michael Dewey http://www.aghmed.fsnet.co.uk, Thanks, Michael. The total (weighted) sum of squares centered about the mean. I have adopted a workflow using {huxtable} and {flextable} to export tables to word format. I think that the details og how to use the procedure, and of its variants, which they have sent to the list should be definitive -- and very helpfully usable -- for folks like myself who may in future grope in the archives concerning this question. I've only one comment -- see at end. Breitling wrote: There have been several questions about getting robust standard errors in glm lately. The corresponding Wald confidence intervals can be computed either by applying coefci to the original model or confint to the output of coeftest. On Thu, May 8, 2008 at 8:38 AM, Ted Harding wrote: Thanks for the link to the data. Packages abound for creating nicely formatted tables, and they have strengths and drawbacks. I don't think "rlm" is the right way to go because that gives different parameter estimates. Tables are pretty complicated objects with lots of bells, whistles, and various points of customization. Now you can calculate robust t-tests by using the estimated coefficients and the new standard errors (square roots of the diagonal elements on vcv). If you had the raw counts where you also knew the denominator or total value that created the proportion, you would be able to just use standard logistic regression with the binomial distribution. In practice, heteroskedasticity-robust and clustered standard errors are usually larger than standard errors from regular OLS — however, this is not always the case. View source: R/lm.cluster.R. An Introduction to Robust and Clustered Standard Errors Outline 1 An Introduction to Robust and Clustered Standard Errors Linear Regression with Non-constant Variance GLM’s and Non-constant Variance Cluster-Robust Standard Errors 2 Replicating in R Molly Roberts Robust and Clustered Standard Errors March 6, 2013 3 / 35. I thought it would be fun, as an exercise, to do a side-by-side, nose-to-tail analysis in both R and Python, taking advantage of the wonderful {reticulate} package in R. {reticulate} allows one to access Python through the R interface. And like in any business, in economics, the stars matter a lot. The above differences look somewhat systematic (though very small). Replicating Stata’s robust standard errors is not so simple now. You can get robust variance-covariance estimates with the bootstrap using bootcov for glmD fits. In a previous post we looked at the (robust) sandwich variance estimator for linear regression. To replicate the standard errors we see in Stata, we need to use type = HC1. (2019), Econometrics with R, and Wickham and Grolemund (2017), R for Data Science. Therefore, it aects the hypothesis testing. And for spelling out your approach!!! On SO, you see lots of people using {stargazer}. White robust standard errors is such a method. A … They are different. Network range: An R function for network analysis, Regression tables in R: An only slightly harmful approach, Using R and Python to Predict Housing Prices. An Introduction to Robust and Clustered Standard Errors Linear Regression with Non-constant Variance Review: Errors and Residuals Errorsare the vertical distances between observations and the unknownConditional Expectation Function. At 13:46 05.06.2004, Frank E Harrell Jr wrote: The below is an old thread: It seems it may have led to a solution. Using the weights argument has no effect on the standard errors. Until someone adds score residuals to residuals.glm robcov will not work for you. (Karla Lindquist, Senior Statistician in the Division of Geriatrics at UCSF) but one more question: so i cannot get SANDWICH estimates of the standard error for a [R] glm or glmD? Package sandwich offers various types of sandwich estimators that can also be applied to objects of class "glm", in particular sandwich() which computes the standard Eicker-Huber-White estimate. For calculating robust standard errors in R, both with more goodies and in (probably) a more efficient way, look at the sandwich package. It certainly looks as though you're very close to target (or even spot-on). aren't the lower bootstrap variances just what Karla is talking about when she writes on the website describing the eyestudy that i was trying to redo in the first place: "Using a Poisson model without robust error variances will result in a confidence interval that is too wide." Usage -Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University. I’m not getting in the weeds here, but according to this document, robust standard errors are calculated thus for linear models (see page 6): And for generalized linear models using maximum likelihood estimation (see page 16): If we make this adjustment in R, we get the same standard errors. I’m more on the R side, which has served my needs as a Phd student, but I also use Python on occasion. ... associated standard errors, test statistics and p values. The standard errors determine how accurate is your estimation. HAC-robust standard errors/p-values/stars. Five different methods are available for the robust covariance matrix estimation. Return condition number of exogenous matrix. But, the API is very unclear and it is not customizable or extensible. Robust standard errors The regression line above was derived from the model savi = β0 + β1inci + ϵi, for which the following code produces the standard R output: # Estimate the model model <- lm (sav ~ inc, data = saving) # Print estimates and standard test statistics summary (model) Now, I’m not going to harsh on someone’s hardwork and {stargazer} is a servicable packages that pretty easily creates nice looking regression tables. condition_number. thx for your efforts- lutz id<-1:500 outcome<-sample(c(0,1), 500, replace=T, prob=c(.6, .4)) exposed<-sample(c(0,1), 500, replace=T, prob=c(.5, .5)) my.data<-data.frame(id=id, ou=outcome, ex=exposed) model1<-glmD(ou~ex. Wow. Be able to automatically export a regression table to latex with the e.g. Well, you may wish to use rlm for other reasons, but to replicate that eyestudy project, you need to. Hence, obtaining the correct SE, is critical See below for examples. Example 1. These are not outlier-resistant estimates of the regression coefficients, they are model-agnostic estimates of the standard errors. Computes cluster robust standard errors for linear models (stats::lm) and general linear models (stats::glm) using the multiwayvcov::vcovCL function in the sandwich package. Parameter estimates with robust standard errors displays a table of parameter estimates, along with robust or heteroskedasticity-consistent (HC) standard errors; and t statistics, significance values, and confidence intervals that use the robust standard errors. As a follow-up to an earlier post, I was pleasantly surprised to discover that the code to handle two-way cluster-robust standard errors in R that I blogged about earlier worked out of the box with the IV regression routine available in the AER package … Cluster-robust stan-dard errors are an issue when the errors are correlated within groups of observa-tions. ing robust standard errors for real applications is nevertheless available: If your robust and classical standard errors differ, follow venerable best practices by using well-known model diagnostics 2 The term “consistent standard errors” is technically a misnomer because as … These are not outlier-resistant estimates of the regression coefficients, These are not outlier-resistant estimates of the regression, Once again, Paul, many thanks for your thorough examination. Not too different, but different enough to make a difference. -------------------------------------------------------------------- E-Mail: (Ted Harding) Fax-to-email: +44 (0)870 094 0861 Date: 13-May-08 Time: 17:43:10 ------------------------------ XFMail ------------------------------. Replicating the results in R is not exactly trivial, but Stack Exchange provides a solution, see replicating Stata’s robust option in R. So here’s our final model for the program effort data using the robust option in Stata HC0 Therefore, they are unknown. This adjustment is used by default when probability weights are specified in estimation. Note that the ratio of both standard errors to those from sandwich is almost constant which suggests a scaling difference. That’s because (as best I can figure), when calculating the robust standard errors for a glm fit, Stata is using $n / (n - 1)$ rather than $n / (n = k)$, where $n$ is the number of observations and k is the number of parameters. robcov() accepts fit objects like lrm or ols objects as arguments, but obviously not the glmD objects (or at least not as simple as that). These data were collected on 10 corps ofthe Prussian army in the late 1800s over the course of 20 years.Example 2. Yes, word documents are still the standard format in the academic world. The standard errors of the parameter estimates. Substituting various definitions for g() and F results in a surprising array of models. Rdata sets can be accessed by installing the `wooldridge` package from CRAN.
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