Open IndrajeetPatil opened 4 years ago
library(glmmEP) #> glmmEP 1.0 loaded. #> Copyright M.P. Wand and J.C.F. Yu 2019. #> For details on the use of glmmEP, issue the command: #> glmmEPvignette() # Simulate data corresponding to a # a simple random intercept model: set.seed(1) m <- 100 n <- 10 beta0True <- 0.37 beta1True <- 0.93 sigmaTrue <- 0.73 uTrue <- rnorm(m) * sigmaTrue x <- runif(m * n) y <- rbinom(m * n, 1, pnorm(beta0True + beta1True * x + crossprod(t(kronecker(diag(m), rep(1, n))), uTrue))) idNum <- rep(1:m, each = n) Xfixed <- cbind(1, x) Xrandom <- matrix(1, length(y), 1) colnames(Xfixed) <- c("intercept", "x") # Obtain and summarise glmmEP() fit: fit <- glmmEP(y, Xfixed, Xrandom, idNum) #> #> #> #> Starting Nelder-Mead phase: #> #> #> Nelder-Mead direct search function minimizer #> function value for initial parameters = 508.965288 #> Scaled convergence tolerance is 5.08965e-08 #> Stepsize computed as 0.064813 #> BUILD 4 509.414611 508.965288 #> LO-REDUCTION 6 509.187219 508.965288 #> LO-REDUCTION 8 509.023568 508.965288 #> LO-REDUCTION 10 509.006301 508.955954 #> HI-REDUCTION 12 508.985126 508.955954 #> LO-REDUCTION 14 508.965288 508.948869 #> HI-REDUCTION 16 508.959648 508.947793 #> HI-REDUCTION 18 508.955954 508.947081 #> LO-REDUCTION 20 508.948869 508.946220 #> LO-REDUCTION 22 508.947793 508.944610 #> LO-REDUCTION 24 508.947081 508.944610 #> HI-REDUCTION 26 508.946220 508.944567 #> HI-REDUCTION 28 508.944768 508.944039 #> HI-REDUCTION 30 508.944610 508.944039 #> LO-REDUCTION 32 508.944567 508.944017 #> LO-REDUCTION 34 508.944192 508.943909 #> HI-REDUCTION 36 508.944039 508.943909 #> HI-REDUCTION 38 508.944017 508.943872 #> HI-REDUCTION 40 508.943910 508.943872 #> HI-REDUCTION 42 508.943909 508.943863 #> LO-REDUCTION 44 508.943892 508.943863 #> LO-REDUCTION 46 508.943872 508.943851 #> HI-REDUCTION 48 508.943868 508.943851 #> HI-REDUCTION 50 508.943863 508.943851 #> LO-REDUCTION 52 508.943854 508.943851 #> HI-REDUCTION 54 508.943852 508.943849 #> REFLECTION 56 508.943851 508.943849 #> REFLECTION 58 508.943851 508.943848 #> HI-REDUCTION 60 508.943849 508.943848 #> HI-REDUCTION 62 508.943849 508.943848 #> HI-REDUCTION 64 508.943849 508.943848 #> LO-REDUCTION 66 508.943848 508.943848 #> REFLECTION 68 508.943848 508.943848 #> HI-REDUCTION 70 508.943848 508.943848 #> REFLECTION 72 508.943848 508.943848 #> LO-REDUCTION 74 508.943848 508.943848 #> Exiting from Nelder Mead minimizer #> 76 function evaluations used #> #> #> #> Finished Nelder-Mead phase. #> #> #> #> Starting Broyden-Fletcher-Goldfarb-Shanno phase: #> #> #> initial value 508.943848 #> iter 1 value 508.943847 #> final value 508.943847 #> converged #> #> #> #> Finished Broyden-Fletcher-Goldfarb-Shanno phase. #> #> #> #> #> Starting Hessian computation phase: #> #> #> initial value 508.943847 #> iter 1 value 508.943847 #> final value 508.943847 #> converged #> #> #> #> Finished Hessian computation phase. class(fit) #> [1] "glmmEP" summary(fit) #> 95% C.I low estimate 95% C.I upp #> intercept 0.3109579 0.5347597 0.7585803 #> x 0.3091558 0.6417042 0.9742694 #> sigma 0.5077951 0.6491995 0.8299789 broom.mixed::tidy(fit) #> Registered S3 method overwritten by 'broom.mixed': #> method from #> tidy.gamlss broom #> Error: No tidy method for objects of class glmmEP
Created on 2019-10-26 by the reprex package (v0.3.0)
Created on 2019-10-26 by the reprex package (v0.3.0)
Session info
``` r devtools::session_info() #> - Session info ---------------------------------------------------------- #> setting value #> version R version 3.6.1 (2019-07-05) #> os Windows 10 x64 #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.1252 #> ctype English_United States.1252 #> tz Europe/Berlin #> date 2019-10-26 #> #> - Packages -------------------------------------------------------------- #> package * version date lib #> assertthat 0.2.1 2019-03-21 [1] #> backports 1.1.5 2019-10-02 [1] #> boot 1.3-23 2019-07-05 [1] #> broom 0.5.2.9002 2019-10-14 [1] #> broom.mixed 0.2.4.9000 2019-08-07 [1] #> callr 3.3.2 2019-09-22 [1] #> cli 1.1.0 2019-03-19 [1] #> coda 0.19-3 2019-07-05 [1] #> crayon 1.3.4 2017-09-16 [1] #> desc 1.2.0 2019-04-03 [1] #> devtools 2.2.1 2019-09-24 [1] #> digest 0.6.22 2019-10-21 [1] #> dplyr 0.8.3.9000 2019-10-10 [1] #> ellipsis 0.3.0 2019-09-20 [1] #> evaluate 0.14 2019-05-28 [1] #> fs 1.3.1 2019-05-06 [1] #> generics 0.0.2 2019-03-05 [1] #> glmmEP * 1.0-3.1 2019-10-15 [1] #> glue 1.3.1 2019-03-12 [1] #> highr 0.8 2019-03-20 [1] #> htmltools 0.4.0 2019-10-04 [1] #> knitr 1.25 2019-09-18 [1] #> lattice 0.20-38 2018-11-04 [2] #> lifecycle 0.1.0 2019-08-01 [1] #> lme4 1.1-21 2019-03-05 [1] #> magrittr 1.5 2014-11-22 [1] #> MASS 7.3-51.4 2019-03-31 [1] #> Matrix 1.2-17 2019-03-22 [1] #> matrixcalc 1.0-3 2012-09-15 [1] #> memoise 1.1.0 2017-04-21 [1] #> minqa 1.2.4 2014-10-09 [1] #> nlme 3.1-140 2019-05-12 [2] #> nloptr 1.2.1 2018-10-03 [1] #> pillar 1.4.2 2019-06-29 [1] #> pkgbuild 1.0.6 2019-10-09 [1] #> pkgconfig 2.0.3 2019-09-22 [1] #> pkgload 1.0.2 2018-10-29 [1] #> plyr 1.8.4 2016-06-08 [1] #> prettyunits 1.0.2 2015-07-13 [1] #> processx 3.4.1 2019-07-18 [1] #> ps 1.3.0 2018-12-21 [1] #> purrr 0.3.3 2019-10-18 [1] #> R6 2.4.0 2019-02-14 [1] #> Rcpp 1.0.2 2019-07-25 [1] #> remotes 2.1.0 2019-06-24 [1] #> reshape2 1.4.3 2017-12-11 [1] #> rlang 0.4.1 2019-10-24 [1] #> rmarkdown 1.16 2019-10-01 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> stringi 1.4.3 2019-03-12 [1] #> stringr 1.4.0 2019-02-10 [1] #> testthat 2.2.1 2019-07-25 [1] #> tibble 2.1.3 2019-06-06 [1] #> tidyr 1.0.0 2019-09-11 [1] #> tidyselect 0.2.5 2018-10-11 [1] #> TMB 1.7.15 2018-11-09 [1] #> usethis 1.5.1.9000 2019-10-18 [1] #> vctrs 0.2.0 2019-07-05 [1] #> withr 2.1.2 2018-03-15 [1] #> xfun 0.10 2019-10-01 [1] #> yaml 2.2.0 2018-07-25 [1] #> zeallot 0.1.0 2018-01-28 [1] #> source #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> local #> Github (bbolker/broom.mixed@46f79ec) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> Github (r-lib/desc@c860e7b) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> Github (tidyverse/dplyr@dcfc1d1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> Github (r-lib/generics@c15ac43) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.0) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> Github (r-lib/rlang@30feeac) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.6.0) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> Github (r-lib/usethis@55cff6e) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.6.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> #> [1] C:/Users/inp099/Documents/R/win-library/3.6 #> [2] C:/Program Files/R/R-3.6.1/library ```