Zelig

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631 discussions

Measures of goodness-of-fit using multiply imputed data in Zelig

by Daniel Eirikson

Dear list members, I am running a logistic regression model in R using multiply imputed data created using Amelia II, which I am then analyzing using Zelig. I would like to be able to report some measures of goodness-of-fit (e.g. likelihood ratio, pseudo R-squared, Hosmer-Lemeshow) and was wondering what options I have when using Zelig to analyze my data, as there are none that are provided in the default output. I know some packages that provide measures of goodness-of-fit, such as pscl, only work on glm objects, not MI objects created when using Amelia and Zelig. Are there any measures of goodness-of-fit that can be extracted from the zelig() object, and if so how? And if not, does anyone know if there are there any other packages that can run these tests on multiply imputed datasets? Thanks in advance for your help! Best, Daniel

9 years, 9 months

loading Zelig...

by Jennifer Boylan

Hi Zelig, I’m having trouble loading the Zelig package to my machine. My goal is to use the ei.RxC model, but I can’t get access Zelig to begin with. I installed the Zelig 4.2-1 version, but when I call library(Zelig), I get an error: Error : .onAttach failed in attachNamespace() for 'Zelig', details: call: NULL error: '.readRDS' is defunct. Use 'readRDS' instead. See help("Defunct") Error: package or namespace load failed for ‘Zelig’ I also rolled back Zelig to version 3.5 on the hopes that it would work, but no change. I have been following the installation guide ( http://zeligdev.github.io/files/zelig.pdf), among many other resources, and I am using R version 3.0.2. I have also noticed others have had this problem in the past ( http://comments.gmane.org/gmane.comp.lang.r.zelig/783) but downloading from the CRAN Network as opposed to manually with an install.packages() command made no difference in my case. Please any advice on what I am doing wrong here? Thanks, Jennifer Boylan For reference purposes, these are the packages I have loaded in my libraries: Packages in library ‘C:/Users/Jenny/Documents/R/win-library/3.0’: car Companion to Applied Regression coda Output analysis and diagnostics for MCMC colorspace Color Space Manipulation Defaults Create Global Function Defaults effects Effect Displays for Linear, Generalized Linear, Multinomial-Logit, Proportional-Odds Logit Models and Mixed-Effects Models eiPack eiPack: Ecological Inference and Higher-Dimension Data Management expm Matrix exponential gdata Various R programming tools for data manipulation gee Generalized Estimation Equation solver gmodels Various R programming tools for model fitting gtools Various R programming tools lattice Lattice Graphics lme4 Linear mixed-effects models using Eigen and S4 lmtest Testing Linear Regression Models manipulate Interactive Plots for RStudio markdown Markdown rendering for R Matrix Sparse and Dense Matrix Classes and Methods matrixcalc Collection of functions for matrix calculations MCMCpack Markov chain Monte Carlo (MCMC) Package mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation mime Map filenames to MIME types minqa Derivative-free optimization algorithms by quadratic approximation msm Multi-state Markov and hidden Markov models in continuous time mvtnorm Multivariate Normal and t Distributions nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models quantmod Quantitative Financial Modelling Framework Rcpp Seamless R and C++ Integration RcppEigen Rcpp integration for the Eigen templated linear algebra library. RMark R Code for MARK Analysis rstudio Tools and Utilities for RStudio sandwich Robust Covariance Matrix Estimators sem Structural Equation Models sfsmisc Utilities from Seminar fuer Statistik ETH Zurich snow Simple Network of Workstations snowfall Easier cluster computing (based on snow). systemfit Estimating Systems of Simultaneous Equations TTR Technical Trading Rules VGAM Vector Generalized Linear and Additive Models xts eXtensible Time Series Zelig Everyone's Statistical Software ZeligMisc A Zelig Model ZeligMultilevel Multilevel Regressions for Zelig zoo S3 Infrastructure for Regular and Irregular Time Series (Z's ordered observations) Packages in library ‘C:/Program Files/R/R-3.0.2/library’: base The R Base Package boot Bootstrap Functions (originally by Angelo Canty for S) class Functions for Classification cluster Cluster Analysis Extended Rousseeuw et al. codetools Code Analysis Tools for R compiler The R Compiler Package datasets The R Datasets Package foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graphics MASS Support Functions and Datasets for Venables and Ripley's MASS Matrix Sparse and Dense Matrix Classes and Methods methods Formal Methods and Classes mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models parallel Support for Parallel computation in R rpart Recursive Partitioning spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes stats The R Stats Package stats4 Statistical Functions using S4 Classes survival Survival Analysis tcltk Tcl/Tk Interface tools Tools for Package Development translations The R Translations Package utils The R Utils Package Finally, some sample script: > install.packages( "Zelig", repos = "http://r.iq.harvard.edu", type = "source", lib="C:/Users/Jenny/Documents/R/win-library/3.0" ) trying URL 'http://r.iq.harvard.edu/src/contrib/Zelig_4.2-2.tar.gz' Content type 'application/x-gzip' length 3269527 bytes (3.1 Mb) opened URL downloaded 3.1 Mb * installing *source* package 'Zelig' ... ** R ** data ** demo ** inst ** preparing package for lazy loading Warning: package 'sandwich' was built under R version 3.0.3 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: package 'sandwich' was built under R version 3.0.3 * DONE (Zelig) The downloaded source packages are in ‘C:\Users\Jenny\AppData\Local\Temp\Rtmp8opSG8\downloaded_packages’ > library(Zelig) ## ## Zelig (Version 4.2-2, built: 2013-10-22) ## 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. ## Error : .onAttach failed in attachNamespace() for 'Zelig', details: call: NULL error: '.readRDS' is defunct. Use 'readRDS' instead. See help("Defunct") Error: package or namespace load failed for ‘Zelig’ > library() > help.zelig(ei.RxC) Error: could not find function "help.zelig" > ?help.zelig() Error in .helpForCall(topicExpr, parent.frame()) : no methods for ‘help.zelig’ and no documentation for it as a function > ??help.zelig() > demo(package="Zelig") > library(Zelig) ## ## Zelig (Version 4.2-2, built: 2013-10-22) ## 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. ## Error : .onAttach failed in attachNamespace() for 'Zelig', details: call: NULL error: '.readRDS' is defunct. Use 'readRDS' instead. See help("Defunct") Error: package or namespace load failed for ‘Zelig’ > install.packages( + "ZeligMisc", + repos = "http://r.iq.harvard.edu", + type = "source", lib="C:/Users/Jenny/Documents/R/win-library/3.0" + ) trying URL 'http://r.iq.harvard.edu/src/contrib/ZeligMisc_0.1-2.tar.gz' Content type 'application/x-gzip' length 10028 bytes opened URL downloaded 10028 bytes * installing *source* package 'ZeligMisc' ... ** R ** inst ** preparing package for lazy loading Warning: package 'sandwich' was built under R version 3.0.3 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: package 'sandwich' was built under R version 3.0.3 * DONE (ZeligMisc) The downloaded source packages are in ‘C:\Users\Jenny\AppData\Local\Temp\Rtmp8opSG8\downloaded_packages’ > search() [1] ".GlobalEnv" "package:sandwich" "package:boot" [4] "package:MASS" "package:gdata" "package:foreign" [7] "package:stats" "package:graphics" "package:grDevices" [10] "package:utils" "package:datasets" "package:methods" [13] "Autoloads" "package:base" > library() > STATA <- read.dta("C:/R/disaggvote2.dta", convert.factors = FALSE) > View(STATA) > z.out <- zelig(cbind(ndc04, npp04, thirdparty04, reject04, novote04) ~ agona + ahafo + ahanta + akuapem + akwamu + akyem + aowin + asante + asen + boron + chokosi + denkyira + evalue + fante + kwahu + nzema + sefwi + wasa + bawle + otherakan + allga + allewe + allguan + allgurma + allmole + allgrusi + allmande + allothers + allmissing, COVAR = NULL, model = "ei.RxC", data = STATA) Error: could not find function "zelig" > library(ZeligMisc) Loading required package: Zelig ## ## Zelig (Version 4.2-2, built: 2013-10-22) ## 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. ## Error : .onAttach failed in attachNamespace() for 'Zelig', details: call: NULL error: '.readRDS' is defunct. Use 'readRDS' instead. See help("Defunct") Error: package ‘Zelig’ could not be loaded > library() > help.zelig() Error: could not find function "help.zelig" -- PhD Candidate Department of Political Science University of Florida PO Box 117325 Gainesville, FL 32611-7325

9 years, 9 months

Cannot load Zelig

by Elinor

Hello, I cannot seem to load the Zelig package. I get the following error message when trying to load it: library(Zelig) Loading required package: boot Loading required package: MASS Loading required package: sandwich Error : .onAttach failed in attachNamespace() for 'Zelig', details: call: packageDescription(package.name, lib.loc = mylib)$Version error: $ operator is invalid for atomic vectors In addition: Warning message: In packageDescription(package.name, lib.loc = mylib) : no package 'Zelig' was found Error: package or namespace load failed for ‘Zelig’ Any idea how I can get it to work? I am using R version 3.1.1. Thanks, Elinor

9 years, 9 months

Zelig 5?

by Ryan Turner

Dear Zelig List: Can anybody comment on the status of Zelig 5? The Zelig website indicates a "Spring - Summer 2014" release, though it looks like it hasn't been updated in a while (Documentation page says Zelig Documentation will be updated summer 2013). I found the Zelig 5 github repository, and it looks like there has been a lot of work done. Is the dev version considered stable and safe or is it still alpha/early beta? For reasons I don't perfectly recall, I had to downgrade from Zelig 4.2.1 to 3.5.4. On a recent rebuild of my R library I thought it was time to look back into this issue. Thanks, Ryan -- Ryan J. Turner, M.S. <rjturner(a)cmu.edu> Ph.D. Candidate, Dept. of Engineering and Public Policy Carnegie Mellon University & Instituto Superior Técnico +1-412-304-5014 (C) | +1-484-483-3244 (GV)

9 years, 9 months

Re: [zelig] Question regarding "plot(z.out)"

by Héctor Bahamonde

Hello, I think I figured it out… thanks. ############################## # match.data <- matchit(...) # model.1 <- zelig(...match.data...) treat.r <- c(0, 1) model.treat <- setx(model.1, treat = treat.r) model.treat.s <- sim(model.1, x = Model.treat) model.treat.e <- data.frame(simulation.matrix(model.treat.s, "Expected Values: Y|X")) X1 <- model.treat.e$X1 X2 <- model.treat.e$X2 density.plot <- ggplot() + geom_density(aes(x=X1), data= model.treat.e, fill="grey", alpha = .5) + geom_density(aes(x=X2), data=model.treat.e, fill="dark grey", alpha = .5) ############################## On 18Jul, 2014, at 12:00 PM, zelig-request(a)lists.gking.harvard.edu wrote: Send Zelig mailing list submissions to zelig(a)lists.gking.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://lists.gking.harvard.edu/mailman/listinfo/zelig or, via email, send a message with subject or body 'help' to zelig-request(a)lists.gking.harvard.edu You can reach the person managing the list at zelig-owner(a)lists.gking.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Zelig digest..." Today's Topics: 1. Question regarding "plot(z.out)" (Hector Bahamonde) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jul 2014 10:17:52 -0400 From: Hector Bahamonde <hib6(a)scarletmail.rutgers.edu> To: zelig(a)lists.gking.harvard.edu Subject: [zelig] Question regarding "plot(z.out)" Message-ID: <CAOXA_80sDPRCr31j+FNBno_QBqXnP0E33t0gw7v3Oq+PGW_QBA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear all, I am very new to R and I am trying to plot the simulations Zelig performs. I know about the "plot(z.out)" syntax, but I am only interested in plotting the ?Comparison of E(Y|X) and E(Y|X1)? plot. Is that possible? My final goal is to plot it using the ggplot2 library. Thanks, Hector -- *H?ctor Bahamonde N.* PhD Student Political Science Department - Rutgers University Hickman Hall, 89 George street, room 602.

9 years, 10 months

Question regarding "plot(z.out)"

by Hector Bahamonde

Dear all, I am very new to R and I am trying to plot the simulations Zelig performs. I know about the "plot(z.out)" syntax, but I am only interested in plotting the “Comparison of E(Y|X) and E(Y|X1)” plot. Is that possible? My final goal is to plot it using the ggplot2 library. Thanks, Hector -- *Héctor Bahamonde N.* PhD Student Political Science Department - Rutgers University Hickman Hall, 89 George street, room 602.

9 years, 10 months

Quantile regression

by Korom, Philipp

Dear all, I am currently trying to conduct quantile regression in Zelig and it does not work out. In the net I can find two vignettes: Rq: Quantile Regression for Continuous Dependent Variables http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.205.1968 quantile: Quantile Regression for Continuous Dependent Variables http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.205.3837 Independent of which specification I use (model="rq"; model="quantile"), I get the following message: ** The model "rq" is not available with the currently loaded packages, ** and is not an official Zelig package. ** The model's name may be a typo. I greatly appreciate any help Best regards, Philipp Philipp Korom ____________________________________ Senior Researcher Max Planck Institute for the Study of Societies Institut Max Planck pour l'étude des sociétés Paulstr. 3 | 50676 Cologne | Germany kr(a)mpifg.de | www.mpifg.de Phone +49 221 2767-274 | Fax +49 221 2767-555

9 years, 10 months

Cannot retrieve summary() of combined datasets in gamma.mixed

by David Hill

Greetings, I am attempting to run a gamma.mixed model on five imputed datasets from Amelia II. I used mi() to combine the datasets in the zelig run. As with some others, when I call the summary () , I receive the error *Error in object[[1]]$result$call : $ operator not defined for this S4 class* I can get the summaries for each individual dataset,but I cannot retrieve the summary of the combined datasets. I can combine the datasets using Rubin's rules, but given this analysis will use several different models and plots, having the combined results would be far simpler. Thanks, David David Hill Associate Professor of Political Science Stetson University DeLand, FL 32723 (386) 822-7579

9 years, 10 months

Model Residual Help

by Whitney

> LU2010 -> zelig(Result~ Wetland + Developed+ Grasses+Crops, model="logit.gee", id="Location",corstr="exchangeable", data=y2010) > LU2010$residuals NULL I am running Zelig 4.2-1 and using the "logit.gee" model link to fit a model. I am trying to get a print out of the model residuals to use to test for spatial autocorrelation; however, when I try to get the print out it says null. My model is. I do not get any errors when I run the model and I get coefficients and cun run Wald test. Any help or ideas would be greatly appreciated.

9 years, 11 months

Help with sim()

by Laura Lazarus Frankel

Hi All, I think I'm having an issue either with setx() or sim()--not sure which one. The zelig() command runs fine and summary(z.out) output has the correct results--the same I get from lm(). Setx() and Sim() also both run without a problem, but summary(s.out) prints without any actual results and when I try to plot(s.out) I get an error saying there are no y values. The output and my code are below. I feel like I'm missing something pretty obvious here, but am about out of ideas. Thanks in advance for any help! Cheers, Laura > masculinityscorewhole<-zelig(qual~masculinityscore+female+age+education+black+latino+republican+working+homemaker+partnered+kids+homemaker*kids+partnered*kids+polinterest+vote12b, weights=cces3$postweight, model="normal", data=cces3) > x.high<- setx(masculinityscorewhole, female=1) > x.low <- setx(masculinityscorewhole, female=0) > exp.out2<- sim(masculinityscorewhole, x = x.low, x1 = x.high) > summary(exp.out2) Model: normal Number of simulations: 1000 Values of X (Intercept) masculinityscore female age education black latino republican working homemaker partnered kids polinterest vote12b homemaker:kids partnered:kids attr(,"assign") [1] 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Values of X1 (Intercept) masculinityscore female age education black latino republican working homemaker partnered kids polinterest vote12b homemaker:kids partnered:kids attr(,"assign") [1] 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

9 years, 11 months

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