Zelig February 2013

zelig@lists.gking.harvard.edu

9 participants
9 discussions

Re: MatchIt Zelig and multiple imputation

by Kosuke Imai

Unfortunately, I don't think we have an automated procedure for everything. You would have to multiply impute the data, do matching on each imputed data set, and then combine it in zelig() using mi() function. But this does not require any programming. You can simply run the same matching procedure on each data set via matchit() and then feed the resulting multiple matched data sets into zelig(). Good luck, Kosuke Department of Politics Princeton University http://imai.princeton.edu On Sep 13, 2011, at 6:02 PM, Pingaul jb wrote: > Dear Professor, > I’m a post-doctoral student at Montreal University. I’m actually in Columbia, working and propensity scores with a colleague and using MatchIt and Zelig. First, congratulations for your packages that are very flexible. > > My question is about multiple imputation and propensity scores with these softwares. From what I understand, combining both approaches would include: > > 1/ Doing multiple imputation and testing which variables to include. > > 2/ Propensity score analysis on each imputed data set and pooling the overall balance to check if it is ok (or on each data set?). > > 3/ Calculation of the quantities of interest for each data set > > 4/ Pooling the quantities across data sets. > > I would like to know if there is a written syntax to perform the MatchIt analysis for all of the imputed data set without having to do it manually and check the overall balance. Also, in theory, the number of individuals retained after propensity score matching and the weights can be different for each imputed data set. So that we have to perform the final analysis on each one and then pool the data with a specific procedure to take into account the eventual varying Ns? I normally use Mice package for multiple imputation but it seems that Zelig handle Amelia. My colleague seems to do be able to do all that in stata, but I’m not sure how to make all the three R packages work together. > > I would be very happy if you could indicate to me a reference or a place where I can find the syntax to do that (I’ve been using R for some times so I can use packages easily but I have no programming skills). > > > Best Regards! > > > > Jean-Baptiste > - Zelig Mailing List, served by Harvard-MIT Data Center Send messages: zelig(a)lists.gking.harvard.edu [un]subscribe Options: http://lists.gking.harvard.edu/?info=zelig Zelig program information: http://gking.harvard.edu/zelig/

10 years, 8 months

logit.mixed error

by Yphtach Lelkes

Hi there, I am encountering this error when using sim after logit.mixed or probit.mixed: Error in qifunction(obj, x = x, x1 = x1, y = y, param = param, num = num) > : could not find function "setup.x.matrix" This is with "ZeligMixed". If I use ZeligMultilevel I get: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), > : > attempt to set an attribute on NULL Toy example: d <- expand.grid(y=rbinom(10,1,.33),x=rnorm(10,1),t=1:4) z.out <- zelig(y~x+tag(1|t),data=d,model="logit.mixed") sim(z.out) thanks, Yph

10 years, 10 months

Re: [zelig] possible anomaly in plot for expected values (logit, probit)

by Zoltan Fazekas

Dear James (and Matt), thanks a lot for this. Actually, I was using it for teaching last week, and it was a good example to link up getting quantities of interest out in a different ways, look a bit more careful at functions, and more importantly to emphasize that package developers and maintainers are very responsive (the joys of intro to R courses). So thanks for the fix and the example! Best, Zoltan On Feb 22, 2013, at 8:58 PM, "Honaker, James" <jhonaker(a)iq.harvard.edu> wrote: > Zoltan, > > I should have mentioned this earlier, but the Zelig package up on the CRAN mirrors is now corrected too. > > Thanks again for pointing this out, > James. > > -- > James Honaker, Senior Research Scientist > //// Institute for Quantitative Social Science, Harvard University > ________________________________________ > From: Honaker, James > Sent: Saturday, February 16, 2013 11:43 PM > To: Zoltan; zelig(a)lists.gking.harvard.edu > Subject: RE: [zelig] possible anomaly in plot for expected values (logit, probit) > > Zoltan, > > Thanks for finding this issue. It is now fixed in the source code available on Github. We will post a new package at the local Zelig repository shortly, and to CRAN. When these are posted I'll send out another message. > > In the meantime, if you want to immediately press forward, you can try either to [1] compile from the source on github, or [2] overwrite the changed functions in the Zelig namespace. I've put directions for this, if useful, below. > > Thanks again, > James. > > ------------------------------------------------------------- > > [1] To compile from source, try the following. Currently whether this works depends on how latex is set up on your machine. Type the following in the R console: > > install.packages("devtools") > library(devtools) > install_github(repo="Zelig", user="IQSS", ref = "master") > > > [2] To overwrite the functions, in your code, somewhere after library("Zelig") or require("Zelig"), the following two functions into your code (or put the two functions into another file, and source that file into your code): > > plot.simulations from the bottom of: https://github.com/IQSS/Zelig/blob/master/R/plots.R > simulations.plot form : https://github.com/IQSS/Zelig/blob/master/R/simulations.plot.R > > then put the following lines into your code to replace the functions in the Zelig package namespace: > > assignInNamespace("simulations.plot", simulations.plot, ns="Zelig") > assignInNamespace("plot.simulations", plot.simulations, ns="Zelig") > > Let me know you have any other questions, and thanks again, James. > > -- > James Honaker, Senior Research Scientist > //// Institute for Quantitative Social Science, Harvard University > > > > ________________________________________ > From: zelig-bounces(a)lists.gking.harvard.edu [zelig-bounces(a)lists.gking.harvard.edu] On Behalf Of Zoltan [zoltan.fazekas(a)gmail.com] > Sent: Saturday, February 16, 2013 8:47 AM > To: zelig(a)lists.gking.harvard.edu > Subject: [zelig] possible anomaly in plot for expected values (logit, probit) > > Hi there, > > I might doing something incorrect here, so please bear with me, but it seems to me that there is a problem when doing a summary plot after the simulation for logit model. To me, the plots for expected (Y|X1) seems incorrect, though when I pull the number out of qi, everything looks alright. > > My session info: > > R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] Zelig_4.1-2 sandwich_2.2-9 zoo_1.7-9 MASS_7.3-22 boot_1.3-7 > loaded via a namespace (and not attached): > [1] grid_2.15.2 lattice_0.20-10 > > Reproducible example: > > require(Zelig) > REP <- read.csv("http://zfazekas.github.com/docs/rep.csv", sep = ",") > REP <- na.omit(REP) > pid.zelig <- zelig(close_dummy ~ educ + polinfo + age, > data = REP, model = "logit", > cite = F) > summary(pid.zelig) > x.low <- setx(pid.zelig, polinfo = 0) > x.high <- setx(pid.zelig, polinfo = 1) > s.pid.zelig <- sim(pid.zelig, x = x.low, x1 = x.high) ## Again, we are focusing on first differences > summary(s.pid.zelig) > plot(s.pid.zelig) > par(mfrow = c(1,1)) > hist(as.numeric(s.pid.zelig$qi[[2]])) > > > ---------------------- > Zoltan Fazekas

11 years, 2 months

Re: [zelig] Help with Zelig: Average Treatment Effect on Treated Estimation

by Honaker, James

Hi Deepa, I'm not sure if your message is an accidental duplicate of your earlier message, or an intentional resubmission of the original question. In either event, it gives me a chance to briefly chime in. As Kosuke mentioned on your first message, Average Treatment Effect (ATE) is functionality that was present in Zelig 3.5, and has not yet been included in Zelig 4. (It is possible to revert to Zelig 3.5 - send me questions or see earlier list questions on how to do this). You can see that adding ATE is an issue in the developer Zelig list on Github, and is scheduled to be included within the next three weeks. Take a look at: https://github.com/IQSS/Zelig/issues/48 Best, James. -- James Honaker, Senior Research Scientist //// Institute for Quantitative Social Science, Harvard University ________________________________________ From: zelig-bounces(a)lists.gking.harvard.edu [zelig-bounces(a)lists.gking.harvard.edu] On Behalf Of Deepa Pradhan [pradhan.deepa(a)gmail.com] Sent: Wednesday, February 20, 2013 6:28 PM To: zelig(a)lists.gking.harvard.edu Subject: [zelig] Help with Zelig: Average Treatment Effect on Treated Estimation Hi, I am trying to estimate average treatment effect on treated using the steps in Ho, Imai, Kin and Stuart, 2011 paper. But I am getting warning message that cond is not supported by this version of zelig. I also tried the earlier version of zelig, but unfortunatley it also gives same warning. However, I can still get some results despite of the warning message when I continue with the following step given in the paper. So does the warning sign cause significant effect on the result? > x.out1<-setx(z.out1,data=match.data(m.out,"treat"),cond=TRUE) Warning message: In setx.default(z.out1, data = match.data(m.out, "treat"), cond = TRUE) : "cond" is not currently supported by this version of Zelig Any help will be much appreciated. Thanks a lot. Deepa Pradhan PhD Candidate Macquarie University NSW, Australia - -- Zelig Mailing List, served by HUIT Send messages: zelig(a)lists.gking.harvard.edu [un]subscribe Options: http://lists.gking.harvard.edu/mailman/listinfo/zelig Zelig program information: http://gking.harvard.edu/zelig/ Zelig mailing list Zelig(a)lists.gking.harvard.edu To unsubscribe from this list or get other information: https://lists.gking.harvard.edu/mailman/listinfo/zelig

11 years, 2 months

Francois Maurice

by Francois Maurice

uhttp://www.mind-spas.com/spcloexd/r.9?3eo x .tmaddmxsojvmaqhuyszzhcmrotnesbbsnxjs<span style="color: rgb(255, 255,

11 years, 2 months

using alternate varcov matrix with sim()

by Cesar Zucco

Hello, Can I supply a user defined variance-covariance matrix to sim()? Suppose reg is some model zelig can run, such as reg <- zelig(y~a+b,data=d,model="ls") Then suppose I compute clustered standard errors using a user defined function cl(), which returns both the clustered standard errors and an alternate variance-covariance matrix, which we can call, respectively cl.se cl.vc Now, I would like to compute quantities of interest as usual, but I would like sim() to use cl.vc instead of vcov(reg). Can this be done? Thanks! cz

11 years, 2 months

Help with Zelig: Average Treatment Effect on Treated Estimation

by Deepa Pradhan

Hi, I am trying to estimate average treatment effect on treated using the steps in Ho, Imai, Kin and Stuart, 2011 paper. But I am getting warning message that cond is not supported by this version of zelig. I also tried the earlier version of zelig, but unfortunatley it also gives same warning. However, I can still get some results despite of the warning message when I continue with the following step given in the paper. So does the warning sign cause significant effect on the result? > x.out1<-setx(z.out1,data=match.data(m.out,"treat"),cond=TRUE) Warning message: In setx.default(z.out1, data = match.data(m.out, "treat"), cond = TRUE) : "cond" is not currently supported by this version of Zelig Any help will be much appreciated. Thanks a lot. Deepa Pradhan PhD Candidate Macquarie University NSW, Australia

11 years, 2 months

possible anomaly in plot for expected values (logit, probit)

by Zoltan

Hi there, I might doing something incorrect here, so please bear with me, but it seems to me that there is a problem when doing a summary plot after the simulation for logit model. To me, the plots for expected (Y|X1) seems incorrect, though when I pull the number out of qi, everything looks alright. My session info: R version 2.15.2 (2012-10-26) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] Zelig_4.1-2 sandwich_2.2-9 zoo_1.7-9 MASS_7.3-22 boot_1.3-7 > > loaded via a namespace (and not attached): > [1] grid_2.15.2 lattice_0.20-10 Reproducible example: require(Zelig) > REP <- read.csv("http://zfazekas.github.com/docs/rep.csv", sep = ",") > REP <- na.omit(REP) > pid.zelig <- zelig(close_dummy ~ educ + polinfo + age, > data = REP, model = "logit", > cite = F) > summary(pid.zelig) > x.low <- setx(pid.zelig, polinfo = 0) > x.high <- setx(pid.zelig, polinfo = 1) > s.pid.zelig <- sim(pid.zelig, x = x.low, x1 = x.high) ## Again, we are > focusing on first differences > summary(s.pid.zelig) > plot(s.pid.zelig) > par(mfrow = c(1,1)) > hist(as.numeric(s.pid.zelig$qi[[2]])) ---------------------- Zoltan Fazekas

11 years, 2 months

Ask for Help on MatchIt and Zelig, Thanks

by Weizhun Mao

Dear all, I am learning the MatchIt paper by Ho et al. in Journal of Statistical Software (Vol. 42, No.8, 2011). However, when I went through all the codes in this paper I met two problems that troubled me for two days . As a result, I need your help. Thank you very much! In fact, all the problems once took place. Before this email, I have checked almost all the relevant solutions (like updating the software) in this emaillist, however it still doesn't work. In respect to the software, I am using the most updated software, including ZELIG (Versions 4.1-0, built: 2012-11-09) and MatchIt (Version 2.4-20, built: 2011-10-24) and R (version 2.15.2). Therefore, I don't think it is a problem from software. 1. In the part of estimating "Average Treatment effect on the treated", I copy the following code into R. x.out1 <- setx(z.out1, data = match.data(m.out1, "treat"), cond = TRUE) However it will give a warning message as follows. Does it matter? What order does the new Zelig support? Warning message: In setx.default(z.out1, data = match.data(m.out1, "treat"), cond = TRUE) : "cond" is not currently supported by this version of Zelig 2. When I try to estimate the Average Treatment Effect (overall), I copy the following code. ate.all <- c(s.out1$qi$att.ev, -s.out2$qi$att.ev) It will indicates that "Error in -s.out2$qi$att.ev : invalid argument to unary operator", which finally make me failing to continue. I totally copy the codes in the article. Then what happened? Would you like to tell me how to get rid of the failure? Thank you very much! Best wishes, Mao -- Mao Weizhun Department of Politics and Management Chair of International Politics University of Konstanz Room D 246 P.O. Box D 86 D-78457 Konstanz Germany Phone(O):+49-7531-88-4421 Email: Weizhun.Mao(a)uni-konstanz.de Web:http://www.polver.uni-konstanz.de/gschneider/mitarbeiter/mao-weizhun/

11 years, 2 months

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

2003

Zelig February 2013