Zelig August 2014

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ZeligMultilevel warning " | "

by Karsten Biermeier

9 years, 8 months

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, 8 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

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Zelig August 2014