issues with tidiers for gamlss models
#60
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bbolker
added a commit
that referenced
this issue
Feb 21, 2019
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I think this is resolved, but it wouldn't hurt for you to check if you have a few minutes ... |
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I can confirm that all the issues mentioned have been resolved! Here is a reprex: # setup
set.seed(123)
library(gamlss)
#> Loading required package: splines
#> Loading required package: gamlss.data
#> Loading required package: gamlss.dist
#> Loading required package: MASS
#> Loading required package: nlme
#> Loading required package: parallel
#> ********** GAMLSS Version 5.1-2 **********
#> For more on GAMLSS look at http://www.gamlss.org/
#> Type gamlssNews() to see new features/changes/bug fixes.
library(broom.mixed)
#> Registered S3 methods overwritten by 'broom.mixed':
#> method from
#> augment.lme broom
#> augment.merMod broom
#> glance.lme broom
#> glance.merMod broom
#> glance.stanreg broom
#> tidy.brmsfit broom
#> tidy.gamlss broom
#> tidy.lme broom
#> tidy.merMod broom
#> tidy.rjags broom
#> tidy.stanfit broom
#> tidy.stanreg broom
# model
g <- gamlss::gamlss(
formula = y ~ pb(x),
sigma.fo = ~ pb(x),
family = BCT,
data = abdom,
method = mixed(1, 20)
)
#> GAMLSS-RS iteration 1: Global Deviance = 4771.925
#> GAMLSS-CG iteration 1: Global Deviance = 4771.013
#> GAMLSS-CG iteration 2: Global Deviance = 4770.994
#> GAMLSS-CG iteration 3: Global Deviance = 4770.994
broom.mixed::tidy(g, conf.int = TRUE)
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the mu formula.
#> Standard errors for the linear terms maybe are not appropriate
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the sigma formula.
#> Standard errors for the linear terms maybe are not appropriate
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the mu formula.
#> Standard errors for the linear terms maybe are not appropriate
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the sigma formula.
#> Standard errors for the linear terms maybe are not appropriate
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the mu formula.
#> Standard errors for the linear terms maybe are not appropriate
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the sigma formula.
#> Standard errors for the linear terms maybe are not appropriate
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the mu formula.
#> Standard errors for the linear terms maybe are not appropriate
#> Warning in vcov.gamlss(object, robust = robust): Additive terms exists in the sigma formula.
#> Standard errors for the linear terms maybe are not appropriate
#> # A tibble: 6 x 8
#> parameter term estimate std.error statistic p.value conf.low conf.high
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 mu (Int~ -64.4 1.33 -48.5 1.89e-210 -67.1 -61.8
#> 2 mu pb(x) 10.7 0.0578 185. 0. 10.6 10.8
#> 3 sigma (Int~ -2.65 0.108 -24.5 8.09e- 93 -5.26 -0.0359
#> 4 sigma pb(x) -0.0100 0.00378 -2.65 8.29e- 3 -0.123 0.103
#> 5 nu (Int~ -0.107 0.557 -0.192 8.48e- 1 -2.72 2.51
#> 6 tau (Int~ 2.49 0.301 8.28 7.77e- 16 -0.120 5.11
broom.mixed::glance(g)
#> # A tibble: 1 x 7
#> df sigma logLik AIC BIC deviance df.residual
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 11.8 2.80 -2385. 4795. 4846. 4771. 598.Created on 2019-02-21 by the reprex package (v0.2.1.9000) Session infodevtools::session_info()
#> - Session info ----------------------------------------------------------
#> setting value
#> version R Under development (unstable) (2018-11-30 r75724)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/New_York
#> date 2019-02-21
#>
#> - Packages --------------------------------------------------------------
#> package * version date lib
#> assertthat 0.2.0 2017-04-11 [1]
#> backports 1.1.3 2018-12-14 [1]
#> broom 0.5.1.9000 2019-01-20 [1]
#> broom.mixed * 0.2.4 2019-02-21 [1]
#> callr 3.1.1 2018-12-21 [1]
#> cli 1.0.1.9000 2019-01-20 [1]
#> coda 0.19-2 2018-10-08 [1]
#> crayon 1.3.4 2017-09-16 [1]
#> desc 1.2.0 2019-01-21 [1]
#> devtools 2.0.1.9000 2019-02-18 [1]
#> digest 0.6.18 2018-10-10 [1]
#> dplyr 0.8.0.9000 2019-02-15 [1]
#> evaluate 0.13 2019-02-12 [1]
#> fansi 0.4.0 2018-11-05 [1]
#> fs 1.2.6 2018-08-23 [1]
#> gamlss * 5.1-2 2018-10-06 [1]
#> gamlss.data * 5.1-0 2018-10-06 [1]
#> gamlss.dist * 5.1-1 2018-12-08 [1]
#> generics 0.0.2 2019-01-20 [1]
#> glue 1.3.0 2018-07-17 [1]
#> highr 0.7 2018-06-09 [1]
#> htmltools 0.3.6 2017-04-28 [1]
#> knitr 1.21 2018-12-10 [1]
#> lattice 0.20-38 2018-11-04 [2]
#> magrittr 1.5 2014-11-22 [1]
#> MASS * 7.3-51.1 2018-11-01 [2]
#> Matrix 1.2-15 2018-11-01 [1]
#> memoise 1.1.0 2017-04-21 [1]
#> nlme * 3.1-137 2018-04-07 [2]
#> pillar 1.3.1 2018-12-15 [1]
#> pkgbuild 1.0.2 2018-10-16 [1]
#> pkgconfig 2.0.2 2018-08-16 [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 3.2.1 2018-12-05 [1]
#> ps 1.3.0 2018-12-21 [1]
#> purrr 0.3.0 2019-01-27 [1]
#> R6 2.4.0 2019-02-14 [1]
#> Rcpp 1.0.0 2018-11-07 [1]
#> remotes 2.0.2 2018-10-30 [1]
#> reshape2 1.4.3 2017-12-11 [1]
#> rlang 0.3.1 2019-01-08 [1]
#> rmarkdown 1.11.6 2019-02-14 [1]
#> rprojroot 1.3-2 2018-01-03 [1]
#> sessioninfo 1.1.1 2018-11-05 [1]
#> stringi 1.3.1 2019-02-13 [1]
#> stringr 1.4.0 2019-02-10 [1]
#> survival 2.43-3 2018-11-26 [2]
#> testthat 2.0.1 2018-10-13 [1]
#> tibble 2.0.1 2019-01-12 [1]
#> tidyr 0.8.2 2018-10-28 [1]
#> tidyselect 0.2.5 2018-10-11 [1]
#> TMB 1.7.15 2018-11-09 [1]
#> usethis 1.4.0.9000 2019-02-18 [1]
#> utf8 1.1.4 2018-05-24 [1]
#> withr 2.1.2 2018-03-15 [1]
#> xfun 0.5 2019-02-20 [1]
#> yaml 2.2.0 2018-07-25 [1]
#> source
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> Github (tidymodels/broom@66411c4)
#> Github (bbolker/broom.mixed@1db56ce)
#> CRAN (R 3.6.0)
#> Github (r-lib/cli@94e2fc5)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> Github (r-lib/desc@42b9578)
#> Github (r-lib/devtools@188a613)
#> CRAN (R 3.5.1)
#> Github (tidyverse/dplyr@b541182)
#> CRAN (R 3.6.0)
#> Github (brodieG/fansi@ab11e9c)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> Github (r-lib/generics@d59e6b4)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.2)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> Github (rstudio/rmarkdown@bbd0786)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> Github (r-lib/usethis@ed9ae17)
#> CRAN (R 3.5.1)
#> CRAN (R 3.5.1)
#> CRAN (R 3.6.0)
#> CRAN (R 3.5.1)
#>
#> [1] C:/Users/inp099/Documents/R/win-library/3.6
#> [2] C:/Program Files/R/R-devel/library |
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tidymodels/broom#507
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