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bbolker / broom.mixed

tidy methods for mixed models in R
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mcmc tidier doesn't work with `ess = TRUE` #56

Closed IndrajeetPatil closed 5 years ago

IndrajeetPatil commented 5 years ago 
# loading the data
set.seed(123)
library(coda)
data(line)

# select first chain
x1 <- line[[1]]

# with default arguments (works)
broom.mixed::tidy(x = x1,
                  conf.int = TRUE)

#> # A tibble: 3 x 5
#>   term  estimate std.error conf.low conf.high
#>   <chr>    <dbl>     <dbl>    <dbl>     <dbl>
#> 1 alpha    2.97      0.531    2.09       3.84
#> 2 beta     0.792     0.341    0.141      1.38
#> 3 sigma    0.778     0.889    0.425      2.36

# additional arguments (doesn't work)
broom.mixed::tidy(
  x = x1,
  conf.int = TRUE,
  robust = TRUE,
  rhat = TRUE,
  index = TRUE,
  ess = TRUE
)

#> Warning in tidy.mcmc(x = x1, conf.int = TRUE, robust = TRUE, rhat = TRUE, :
#> ignoring 'rhat' and 'ess' (only available for stanfit objects)
#> Error in round(summ[, "n_eff"]): non-numeric argument to mathematical function

# works again if `ess` argument is commented out
broom.mixed::tidy(
  x = x1,
  conf.int = TRUE,
  robust = TRUE,
  rhat = TRUE,
  index = TRUE,
  #ess = TRUE
)

#> Warning in tidy.mcmc(x = x1, conf.int = TRUE, robust = TRUE, rhat = TRUE, :
#> ignoring 'rhat' and 'ess' (only available for stanfit objects)
#> # A tibble: 3 x 6
#>   term  index estimate std.error conf.low conf.high
#>   <chr> <int>    <dbl>     <dbl>    <dbl>     <dbl>
#> 1 alpha    NA    2.98      0.378    2.09       3.84
#> 2 beta     NA    0.787     0.264    0.141      1.38
#> 3 sigma    NA    0.954     0.289    0.425      2.36

Here is traceback for the instance when the function fails-

traceback()
2: tidy.mcmc(x = x1, conf.int = TRUE, robust = TRUE, rhat = TRUE, 
       index = TRUE, ess = TRUE)
1: broom.mixed::tidy(x = x1, conf.int = TRUE, robust = TRUE, rhat = TRUE, 
       index = TRUE, ess = TRUE)
Session info ``` r devtools::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 2019-02-05 #> #> - 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 0.2.3.9000 2019-01-23 [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] #> colorspace 1.4-0 2019-01-13 [1] #> crayon 1.3.4 2017-09-16 [1] #> desc 1.2.0 2019-01-21 [1] #> devtools 2.0.1.9000 2019-01-29 [1] #> digest 0.6.18 2018-10-10 [1] #> dplyr 0.8.0 2019-01-31 [1] #> evaluate 0.12 2018-10-09 [1] #> fansi 0.4.0 2018-11-05 [1] #> fs 1.2.6 2018-08-23 [1] #> generics 0.0.2 2019-01-20 [1] #> ggplot2 3.1.0.9000 2019-01-31 [1] #> glue 1.3.0 2018-07-17 [1] #> gridExtra 2.3 2017-09-09 [1] #> gtable 0.2.0 2016-02-26 [1] #> highr 0.7 2018-06-09 [1] #> htmltools 0.3.6 2017-04-28 [1] #> inline 0.3.15 2018-05-18 [1] #> knitr 1.21 2018-12-10 [1] #> lattice 0.20-38 2018-11-04 [2] #> lazyeval 0.2.1 2017-10-29 [1] #> loo 2.0.0 2018-04-11 [1] #> magrittr 1.5 2014-11-22 [1] #> Matrix 1.2-15 2018-11-01 [1] #> matrixStats 0.54.0 2018-07-23 [1] #> memoise 1.1.0 2017-04-21 [1] #> munsell 0.5.0 2018-06-12 [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 2019-01-25 [1] #> R6 2.3.0 2018-10-04 [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 2018-12-08 [1] #> rprojroot 1.3-2 2018-01-03 [1] #> rstan 2.18.2 2018-11-07 [1] #> scales 1.0.0 2018-08-09 [1] #> sessioninfo 1.1.1 2018-11-05 [1] #> StanHeaders 2.18.1 2019-01-28 [1] #> stringi 1.2.4 2018-07-20 [1] #> stringr 1.3.1 2018-05-10 [1] #> 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 2019-01-29 [1] #> utf8 1.1.4 2018-05-24 [1] #> withr 2.1.2 2018-03-15 [1] #> xfun 0.4 2018-10-23 [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@fbe9597) #> CRAN (R 3.6.0) #> Github (r-lib/cli@94e2fc5) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.1) #> Github (r-lib/desc@42b9578) #> Github (r-lib/devtools@e4e57aa) #> CRAN (R 3.5.1) #> Github (tidyverse/dplyr@67b9f4f) #> CRAN (R 3.5.1) #> Github (brodieG/fansi@ab11e9c) #> CRAN (R 3.5.1) #> Github (r-lib/generics@d59e6b4) #> Github (tidyverse/ggplot2@54e773b) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> 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 3.5.1) #> CRAN (R 3.5.1) #> CRAN (R 3.5.1) #> 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 3.5.1) #> 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) #> Github (tidyverse/purrr@240f7b2) #> 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 3.6.0) #> CRAN (R 3.5.1) #> CRAN (R 3.5.2) #> CRAN (R 3.5.1) #> CRAN (R 3.6.0) #> CRAN (R 3.5.2) #> 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 3.6.0) #> Github (r-lib/usethis@5a0680b) #> 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 ```