Zelig August 2011

zelig@lists.gking.harvard.edu

9 participants
10 discussions

summary with imputations bug ... any workarounds?

by Peter Flom

Good morning If I run <<< susan.lsmixed.out <- zelig(formula = unprot_vag_sex ~ married + age + TREATMENT.ARM*time + highest_grade + income + tag(1|id), data = susanMI.out$imputations, model = "ls.mixed") summary(susan.lsmixed.out) >>>> I get an error Error in x$coef : $ operator is invalid for atomic vectors Searching the archives, I see that others have had similar problems. Is there a workaround? summary(susan.lsmixed.out[[1]]) works fine; should I then average across the five imputed data sets? thanks! Peter Peter L. Flom, PhD Statistical Consultant Website: http://www DOT statisticalanalysisconsulting DOT com/ Writing; http://www.associatedcontent.com/user/582880/peter_flom.html Twitter: @peterflom - 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/

12 years, 1 month

mixed.probit, gamma specification

by Jason McMann

Hello, I am trying to run a multilevel probit model using Zelig, but keep receiving the following error message: " in .deparseTag(TT.vars[[vind]]) : wrong use of tag function!!" A simplified version of the model I am trying to run is: z.out <- zelig(formula= list(mu=investment.binary ~ edlevel + tag(1 + edlevel, gamma | country), gamma = ~ tag(GDPpc06.full| country)), data=data2006.mod1, model="probit.mixed") What I would like to do is allow the intercept and the edlevel variable listed within the first tag() to vary by country as a function of the GDPpc06.full variable, all of which are included in the same dataframe. I followed the syntax here - http://cran.r-project.org/web/packages/Zelig /vignettes/probit.mixed.pdf - but I think that I am incorrectly specifying the gamma part of the syntax, which may be causing the error. I *am* able to get the model to run when I allow the intercept and edlevel variable to vary using the following syntax: z.out <- zelig(investment.binary ~ edlevel + + tag(1 + edlevel | country), data=data2006.mod1, model="probit.mixed") However, this syntax does not allow me to specify that the intercept and edlevel variable should vary as a function of GDPpc06.full, as in the first model specified above. I have tried including multiple tags at the non-group level of the model specification - i.e. one for the intercept and one for the edlevel variable - but this does not seem to work either. Do you have any suggestions for how to fix the syntax? Sincerely, Jason -- Jason I. McMann PhD Student | Department of Politics Princeton University | jmcmann(a)princeton.edu

12 years, 5 months

Re: [zelig] mi(): Error in attach(data) : all elements of a list must be named (fwd)

by Matt Blackwell

Hi Audrey, Ah, sorry, I read your example too quickly. The imputations from amelia() now follow the new Zelig requirements for named lists, but this example does not. Here's a updated example that should work: z.out <- zelig(as.factor(ipip) ~ wage1992 + prtyid + ideol, + model = "ologit", + data = mi(imp1=immi1, imp2=immi2, imp3=immi3, imp4=immi4, imp5=immi5)) Thus, you simply need to add names to each item of the mi() list. I'm not sure if the mi() class should require names, but this code should work either way. Cheers, matt. 2011/8/21 Audrey Sacks <sacks(a)u.washington.edu> > Dear Matt, > > Thanks for your response. The same error still shows up after I install > the newer version of Amelia as you suggest below. > > Here's my sessioninfo and codes > > Thanks, > Audrey > > > R version 2.13.1 (2011-07-08) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > Platform: i386-pc-mingw32/i386 (32-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > install.packages("Amelia", repos = "http://r.iq.harvard.edu", type = >> "source") >> > Installing package(s) into ‘C:/Users/Audrey/Desktop/** > Documents/R/win-library/2.13’ > (as ‘lib’ is unspecified) > trying URL 'http://r.iq.harvard.edu/src/**contrib/Amelia_1.5-4.tar.gz<http://r.iq.harvard.edu/src/contrib/Amelia_1.5-4.tar.gz> > ' > Content type 'application/x-gzip' length 1078553 bytes (1.0 Mb) > opened URL > downloaded 1.0 Mb > > * installing *source* package 'Amelia' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > ## ## Amelia II: Multiple Imputation > ## (Version 1.5-4, built: 2011-08-21) > > ## Copyright (C) 2005-2011 James Honaker, Gary King and Matthew Blackwell > ## Refer to http://gking.harvard.edu/**amelia/<http://gking.harvard.edu/amelia/>for more information > ## > > * DONE (Amelia) > > The downloaded packages are in > ‘C:\Users\Audrey\AppData\**Local\Temp\RtmpRzvM0Y\** > downloaded_packages’ > > >> library(Zelig) >> > Loading required package: MASS > Loading required package: boot > Loading required package: MNP > MNP: R Package for Fitting the Multinomial Probit Model > Version: 2.6-2 > ## ## Zelig (Version 3.5-1, built: 2011-03-25) > ## Please refer to http://gking.harvard.edu/zelig for full > ## documentation or help.zelig() for help with commands and > ## models supported by Zelig. > ## > > ## Zelig project citations: > ## Kosuke Imai, Gary King, and Olivia Lau. (2009). > ## ``Zelig: Everyone's Statistical Software,'' > ## http://gking.harvard.edu/zelig**. > ## and > ## Kosuke Imai, Gary King, and Olivia Lau. (2008). > ## ``Toward A Common Framework for Statistical Analysis > ## and Development,'' Journal of Computational and > ## Graphical Statistics, Vol. 17, No. 4 (December) > ## pp. 892-913. > > ## To cite individual Zelig models, please use the citation format printed > with > ## each model run and in the documentation. > ## > Warning message: > '.readRDS' is deprecated. > Use 'readRDS' instead. > See help("Deprecated") > >> library(Amelia) >> > Loading required package: foreign > ## ## Amelia II: Multiple Imputation > ## (Version 1.5-4, built: 2011-08-21) > > ## Copyright (C) 2005-2011 James Honaker, Gary King and Matthew Blackwell > ## Refer to http://gking.harvard.edu/**amelia/<http://gking.harvard.edu/amelia/>for more information > ## > >> data(turnout) >> >> data(immi1, immi2, immi3, immi4, immi5) >> z.out <- zelig(as.factor(ipip) ~ wage1992 + prtyid + ideol, >> > + model = "ologit", > + data = mi(immi1, immi2, immi3, immi4, immi5)) > Error in attach(data) : all elements of a list must be named > > > >

12 years, 8 months

mi(): Error in attach(data) : all elements of a list must be named (fwd)

by Audrey Sacks

Hi, After updating to R 2.13.1 and updating Zelig to 3.5-1, the following error appears when I try to use the mi() command in Zelig. I ran the exact same code in R 2.8 and it worked fine. Error in attach(data) : all elements of a list must be named Any ideas? Complete code and SessionInfo is below: Thank you, Audrey library(Zelig) Loading required package: MASS Loading required package: boot Loading required package: MNP MNP: R Package for Fitting the Multinomial Probit Model Version: 2.6-2 ## ## Zelig (Version 3.5-1, built: 2011-03-25) ## Please refer to http://gking.harvard.edu/zelig for full ## documentation or help.zelig() for help with commands and ## models supported by Zelig. ## ## Zelig project citations: ## Kosuke Imai, Gary King, and Olivia Lau. (2009). ## ``Zelig: Everyone's Statistical Software,'' ## http://gking.harvard.edu/zelig. ## and ## Kosuke Imai, Gary King, and Olivia Lau. (2008). ## ``Toward A Common Framework for Statistical Analysis ## and Development,'' Journal of Computational and ## Graphical Statistics, Vol. 17, No. 4 (December) ## pp. 892-913. ## To cite individual Zelig models, please use the citation format printed with ## each model run and in the documentation. ## Warning message: '.readRDS' is deprecated. Use 'readRDS' instead. See help("Deprecated") > library(Amelia) Loading required package: foreign ## ## Amelia II: Multiple Imputation ## (Version 1.2-18, built: 2010-11-04) ## Copyright (C) 2005-2011 James Honaker, Gary King and Matthew Blackwell ## Refer to http://gking.harvard.edu/amelia/ for more information ## > sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Amelia_1.2-18 foreign_0.8-45 Zelig_3.5-1 MNP_2.6-2 boot_1.3-2 [6] MASS_7.3-14 > data(turnout) > data(immi1, immi2, immi3, immi4, immi5) > z.out <- zelig(as.factor(ipip) ~ wage1992 + prtyid + ideol, + model = "ologit", + data = mi(immi1, immi2, immi3, immi4, immi5)) Error in attach(data) : all elements of a list must be named - 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/

12 years, 8 months

sim () command error

by Zsófia Ignácz

Dear Everyone, I have attempted to run some multinomial logit models with mixed results with the Zelig package. I very much baffled with the fact that what ran about two weeks ago on the same computer, is not working any longer. Neither are course examples that also ran on the computer. The only alteration that happened was I downloaded R Studio, although was NOT using it to run my models in the end. I would appreciate if anyone has an idea what went wrong...! Thank you and kind regards, Zsofia Ignacz Complete syntax: baseyear <- zelig(as.factor(chair) ~ v5+v8+v67+fHU+fCZ+fEG+fw32+fw33, model="mlogit", data=isjp2) summary (baseyear) hypHU91 <- setx(baseyear, v5=1, v8=50, v67=4, fHU=1, fCZ=0, fEG=0, fw32=1, fw33=0) hypCZ91 <- setx(baseyear, v5=1, v8=50, v67=4, fHU=0, fCZ=1, fEG=0, fw32=0, fw33=0) hypEG91 <- setx(baseyear, v5=1, v8=50, v67=4, fHU=0, fCZ=0, fEG=1, fw32=0, fw33=0) hypWG91 <- setx(baseyear, v5=1, v8=50, v67=4, fHU=0, fCZ=0, fEG=0, fw32=0, fw33=0) hypprobHU91 <- sim(baseyear, x=hypHU91 , num=1500) ###Error message: "Error in UseMethod("cov") : no applicable method for 'vcov' applied to an object of class "c('vglm', 'vlm', 'vlmsmall')" -- Zsófia Ignácz PhD Student Berlin Graduate School of Social Sciences European PhD for Social-economic and Social Statistics Institut für Sozialwissenschaften Humboldt Universität zu Berlin Unter den Linden 6 D 10099 Berlin Office: Luisenstrasse 56, Room 208, 10177 Berlin zsofia.ignacz(a)sowi.hu-berlin.de - 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/

12 years, 8 months

confidence intervals for multiply imputed data

by Lloyd Balbuena

Dear all, I ran a poisson model on 5 multiply imputed datasets produced by amelia: z.out <- zelig(months ~ netsize, model="poisson", data=a.out$imputations) I can get the 95% CI of each imputation's coefficients using confint(z.out[[n]]$coefficients), where n is the imputed dataset index. What I want however is the 95% CI of the combined results. Sorry, I couldn't find an answer in the documentation. Lloyd

12 years, 8 months

Error in sim() for a logistic model

by Mattia Guidi

Hi everyone, I am trying to simulate expected probabilities for a logistic model, but I get a strange error message when running sim(). Since I am using a data frame from the 'car' package by J. Fox, the code can be easily reproduced by everyone. Here is the code I am running: library(car) library(Zelig) data(Chile) Chile$vote.d <- recode(Chile$vote, "'N'=0; 'Y'=1; else=NA") model3.z <- zelig(vote.d ~ region + sex + population + age + education + income + statusquo, model="logit", data=Chile) summary(model3.z) x.out1 <- setx(model3.z, sex="M", education="PS") summary(x.out1) s.out1 <- sim(x.out1, x = x.out1) The last command returns the following error message: Error in UseMethod("vcov") : no applicable method for 'vcov' applied to an object of class "data.frame" I have tried to google this message, but I found only a few results, and none of them was useful for understanding where the problem is. Note that, until the last command, I do not get errors or warnings from any of the previous functions. demo(logit) does not return any errors. Thanks in advance for your help. Mattia -------------------------- (Mr.) Mattia Guidi Ph.D Candidate European University Institute Department of Political and Social Sciences Badia Fiesolana Via dei Roccettini 9 I-50014 San Domenico di Fiesole (FI) ITALY

12 years, 9 months

Issue with loading data into R

by Sera Onalan

Hi, I'm trying to load my data into R. This is the command I'm using: FinalData2.data <- read.csv('FinalData2.csv') attach(FinalData2.data) this is the error I get: FinalData2.data <- read.csv('FinalData2.csv') Error in type.convert(data[[i]], as.is = as.is[i], dec = dec, na.strings = character(0L)) : invalid multibyte string at '<ff>' > attach(FinalData2.data) Error in attach(FinalData2.data) : object 'FinalData2.data' not found My working directory is set as this: setwd("/Users/Sera/Desktop/R Work") I don't understand why I'm getting this error. I also tried this, but I still get errors: FinalData2.csv <- read.csv(Users/Sera/Desktop/R Work/FinalData2.csv) Error: unexpected symbol in "FinalData2.csv <- read.csv(Users/Sera/Desktop/R Work" > + attach(FinalData2.data) Error in attach(FinalData2.data) : object 'FinalData2.data' not found Sorry to bug you guys. Thanks for your help. Sera

12 years, 9 months

Zelig Library Issue

by Sera Onalan

Hi, I just downloaded R onto my Mac. I was able to successfully download Amelia, but not successful with downloading Zelig. I think I have to create a library. I followed the commands to create one, but I keep getting errors.. I only want to run R commands. here is the first error I got: > install.packages("Zelig", repos="http://r.iq.harvard.edu/", type="source") Installing package(s) into ‘/Users/Sera/Library/R/2.13/library’ (as ‘lib’ is unspecified) Warning: dependency ‘MNP’ is not available trying URL 'http://r.iq.harvard.edu/src/contrib/Zelig_3.5-1.tar.gz' Content type 'application/x-gzip' length 14407206 bytes (13.7 Mb) opened URL ================================================== downloaded 13.7 Mb ERROR: dependency ‘MNP’ is not available for package ‘Zelig’ * removing ‘/Users/Sera/Library/R/2.13/library/Zelig’ The downloaded packages are in ‘/private/var/folders/na/nal9eab8GYO6s7zuPcRYMk+++TI/-Tmp-/RtmpWFnWZW/downloaded_packages’ Warning message: In install.packages("Zelig", repos = "http://r.iq.harvard.edu/", : installation of package 'Zelig' had non-zero exit status library(Zelig) > library(Zelig) Error in library(Zelig) : there is no package called 'Zelig' Please help... Thank you, Sera

12 years, 9 months

Some questions on simulations and why they are better than the computation of predicted values/probabilities

by Mattia Guidi

Dear all, I have a general question on the simulation technique developed in Zelig, and available for estimating first differences and expected values of the dependent variable for different quantities of interest of the independent variables. It is not completely clear to me to what extent simulation techniques are more suitable for this purpose than the simple computation of predicted values (or probabilities). I understand the *logical* difference between algebraic computation of effects, and the simulation of them. But expected and predicted values are practically the same for the same model, although derived with different methods. My question, then, is: is it only a question of *methodological elegance* or are there strong theoretical reasons for which we should prefer simulations over the computation of predicted values/probabilities? And, are there statistical models for which only simulations can be meaningfully used? Thanks a lot in advance for your answers. Mattia -------------------------- (Mr.) Mattia Guidi Ph.D Candidate European University Institute Department of Political and Social Sciences Badia Fiesolana Via dei Roccettini 9 I-50014 San Domenico di Fiesole (FI) ITALY

12 years, 9 months

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Zelig August 2011