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feature request: supporting glmmEP models #81

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IndrajeetPatil opened this issue Oct 26, 2019 · 0 comments
Open

feature request: supporting glmmEP models #81

IndrajeetPatil opened this issue Oct 26, 2019 · 0 comments

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@IndrajeetPatil
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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)

Session info 
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
@IndrajeetPatil IndrajeetPatil changed the title supporting glmmEP models feature request: supporting glmmEP models Dec 6, 2019
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