problem with jtools::summ and MASS::glm.nb() #142
Description
I have encountered a problem when using jtools::summ() with MASS::glm.nb(). There seems to be some parameter mismatch in the glm.control() function.
The reprex is from Francis L Huang
articles <- rio::import("https://raw.githubusercontent.com/flh3/pubdata/main/miscdata/articles.csv")
negb <- MASS::glm.nb(art ~ fem + ment + phd + mar + kid5, data = articles) #negative binomial
jtools::summ(negb, exp = T)In the code outlined in the example, jtools::summ runs perfectly fine with the given data. When I run the command, I encounter a problem with glm.control(), and I do not get any values for R squared. All other values in the table are correct.
I therefore suppose that it is a conflict with any of the packages that I have loaded, or an issue caused by an update of jtools or MASS since the tutorial was written.
Output:
Error in glm.control(...) :
unused argument (family = list("Negative Binomial(2.2644)", "log", function (mu)
log(mu), function (eta)
pmax(exp(eta), .Machine$double.eps), function (mu)
mu + mu^2/.Theta, function (y, mu, wt)
2 * wt * (y * log(pmax(1, y)/mu) - (y + .Theta) * log((y + .Theta)/(mu + .Theta))), function (y, n, mu, wt, dev)
{
term <- (y + .Theta) * log(mu + .Theta) - y * log(mu) + lgamma(y + 1) - .Theta * log(.Theta) + lgamma(.Theta) - lgamma(.Theta + y)
2 * sum(term * wt)
}, function (eta)
pmax(exp(eta), .Machine$double.eps), expression({
if (any(y < 0)) stop("negative values not allowed for the negative binomial family")
n <- rep(1, nobs)
mustart <- y + (y == 0)/6
}), function (mu)
all(mu > 0), function (eta)
TRUE, function (object, nsim)
{
ftd <- fitted(object)
rnegbin(nsim * length(ftd), ftd, .Theta)
}))
MODEL INFO:
Observations: 915
Dependent Variable: art
Type: Generalized linear model
Family: Negative Binomial(2.2644)
Link function: log
MODEL FIT:
χ²(NA) = NA, p = NA
Pseudo-R² (Cragg-Uhler) = NA
Pseudo-R² (McFadden) = NA
AIC = 3135.92, BIC = 3169.65
Standard errors: MLE
------------------------------------------------------------
exp(Est.) 2.5% 97.5% z val. p
----------------- ----------- ------ ------- -------- ------
(Intercept) 1.29 0.99 1.69 1.86 0.06
fem 0.81 0.70 0.93 -2.98 0.00
ment 1.03 1.02 1.04 9.05 0.00
phd 1.02 0.95 1.09 0.43 0.67
mar 1.16 0.99 1.37 1.83 0.07
kid5 0.84 0.76 0.93 -3.34 0.00
------------------------------------------------------------
Warning message:
Something went wrong when calculating the pseudo R-squared. Returning NA instead. >sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2019 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=German_Austria.1252 LC_CTYPE=German_Austria.1252 LC_MONETARY=German_Austria.1252 LC_NUMERIC=C LC_TIME=German_Austria.1252
time zone: Europe/Vienna
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] jtools_2.2.2 rio_0.5.29 reshape2_1.4.4 summarytools_1.0.1 pscl_1.5.5.1 ggplot2_3.4.3 MASS_7.3-60 fstcore_0.9.14 readxl_1.4.3 eurostat_3.8.2 beepr_1.3 odbc_1.3.5 comorbidity_1.0.7
[14] magrittr_2.0.3 tsibble_1.1.3 tidyr_1.3.0 purrr_1.0.2 fst_0.9.8 dplyr_1.1.2 ztools_0.6.0
loaded via a namespace (and not attached):
[1] DBI_1.1.3 tcltk_4.3.1 sandwich_3.0-2 rlang_1.1.1 tidytable_0.10.1 matrixStats_1.0.0 e1071_1.7-13 compiler_4.3.1 vctrs_0.6.3 stringr_1.5.0 pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.1.1
[14] backports_1.4.1 dbplyr_2.3.3 magick_2.7.5 ellipsis_0.3.2 ISOweek_0.6-2 pander_0.6.5 utf8_1.2.3 tzdb_0.4.0 haven_2.5.3 anytime_0.3.9 bit_4.0.5 jsonlite_1.8.7 RefManageR_1.4.0
[27] covtools_0.6.0 blob_1.2.4 pryr_0.1.6 broom_1.0.5 parallel_4.3.1 R6_2.5.1 stringi_1.7.12 lubridate_1.9.2 cellranger_1.1.0 Rcpp_1.0.11 assertthat_0.2.1 zoo_1.8-12 audio_0.1-11
[40] fortunes_1.5-4 base64enc_0.1-3 pacman_0.5.1 readr_2.1.4 timechange_0.2.0 tidyselect_1.2.0 codetools_0.2-19 curl_5.0.2 lattice_0.21-8 tibble_3.2.1 plyr_1.8.8 withr_2.5.0 foreign_0.8-84
[53] proxy_0.4-27 zip_2.3.0 xml2_1.3.5 pillar_1.9.0 KernSmooth_2.23-21 checkmate_2.2.0 generics_0.1.3 rprojroot_2.0.3 hms_1.1.3 munsell_0.5.0 regions_0.1.8 scales_1.2.1 class_7.3-22
[66] glue_1.6.2 tools_4.3.1 data.table_1.14.8 openxlsx_4.2.5.2 forcats_1.0.0 rapportools_1.1 grid_4.3.1 bibtex_0.5.1 colorspace_2.1-0 nlme_3.1-162 cli_3.6.1 fansi_1.0.4 rematch_1.0.1
[79] countrycode_1.5.0 gtable_0.3.4 rmsfact_0.0.3 digest_0.6.33 cowsay_0.8.2 classInt_0.4-9 librarian_1.8.1 htmltools_0.5.6 lifecycle_1.0.3 httr_1.4.7 here_1.0.1 bit64_4.0.5