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DoseResponse
Error with `estfun` with R version 4.0.x
Calculation of robust standard errors using the sandwich package appears to fail under R 4.0.x but not under earlier versions (3.6.0).
I see this issue has already be raised and closed, and am just noting that it is reproducible on versions of R > 4.
suppressPackageStartupMessages({
library(drc)
library(lmtest)
library(sandwich)
})
ryegrass.m1<-drm(rootl ~ conc, data = ryegrass, fct = LL.4())
coeftest(ryegrass.m1, vcov = sandwich)
#> Error in UseMethod("estfun"): no applicable method for 'estfun' applied to an object of class "drc"
sessionInfo()
#> R version 4.0.2 (2020-06-22)
#> Platform: i386-w64-mingw32/i386 (32-bit)
#> Running under: Windows 10 x64 (build 17134)
#>
#> Matrix products: default
#>
#> locale:
#> [1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New Zealand.1252
#> [3] LC_MONETARY=English_New Zealand.1252 LC_NUMERIC=C
#> [5] LC_TIME=English_New Zealand.1252
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] sandwich_2.5-1 lmtest_0.9-37 zoo_1.8-8 drc_3.0-1 MASS_7.3-51.6
#>
#> loaded via a namespace (and not attached):
#> [1] zip_2.1.1 Rcpp_1.0.5 compiler_4.0.2 pillar_1.4.6
#> [5] cellranger_1.1.0 highr_0.8 forcats_0.5.0 tools_4.0.2
#> [9] digest_0.6.25 evaluate_0.14 tibble_3.0.3 lifecycle_0.2.0
#> [13] lattice_0.20-41 pkgconfig_2.0.3 rlang_0.4.7 Matrix_1.2-18
#> [17] openxlsx_4.1.5 curl_4.3 yaml_2.2.1 mvtnorm_1.1-1
#> [21] haven_2.3.1 xfun_0.16 rio_0.5.16 stringr_1.4.0
#> [25] knitr_1.29 vctrs_0.3.3 gtools_3.8.2 hms_0.5.3
#> [29] grid_4.0.2 data.table_1.13.0 R6_2.4.1 plotrix_3.7-8
#> [33] survival_3.1-12 readxl_1.3.1 foreign_0.8-80 rmarkdown_2.3
#> [37] multcomp_1.4-13 TH.data_1.0-10 carData_3.0-4 car_3.0-9
#> [41] magrittr_1.5 scales_1.1.1 codetools_0.2-16 splines_4.0.2
#> [45] ellipsis_0.3.1 htmltools_0.5.0 abind_1.4-5 colorspace_1.4-1
#> [49] stringi_1.4.6 munsell_0.5.0 crayon_1.3.4
Created on 2020-10-19 by the reprex package (v0.3.0)
But works at https://rdrr.io/snippets/ which uses R 3.4.4, but same version of drc and sandwich.
t test of coefficients:
Estimate Std. Error t value Pr(>|t|)
b:(Intercept) 2.98222 0.47438 6.2865 3.882e-06 ***
c:(Intercept) 0.48141 0.12779 3.7672 0.001212 **
d:(Intercept) 7.79296 0.15311 50.8976 < 2.2e-16 ***
e:(Intercept) 3.05795 0.26741 11.4355 3.170e-10 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
sh: 1: cannot create /dev/null: Permission denied
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sandwich_2.5-1 lmtest_0.9-37 zoo_1.8-5 drc_3.0-1 MASS_7.3-51.4
loaded via a namespace (and not attached):
[1] zip_2.0.1 Rcpp_1.0.1 cellranger_1.1.0 pillar_1.3.1
[5] compiler_3.4.4 forcats_0.4.0 tools_3.4.4 tibble_2.1.1
[9] lattice_0.20-38 pkgconfig_2.0.2 rlang_0.3.4 openxlsx_4.1.0
[13] Matrix_1.2-17 curl_3.3 mvtnorm_1.0-8 haven_2.1.0
[17] rio_0.5.16 gtools_3.8.1 hms_0.4.2 grid_3.4.4
[21] data.table_1.12.2 plotrix_3.7-5 readxl_1.3.1 survival_2.44-1.1
[25] foreign_0.8-71 multcomp_1.4-8 TH.data_1.0-10 carData_3.0-2
[29] car_3.0-2 magrittr_1.5 scales_1.0.0 codetools_0.2-16
[33] splines_3.4.4 abind_1.4-5 colorspace_1.4-1 munsell_0.5.0
[37] crayon_1.3.4
Hi @jwilliman ,
I just tried your example with an up to date package drc, reinstalled via install_github, now at version 3.2.0:
library(devtools)
install_github("DoseResponse/drc")
As far as I can say, it works as expected now:
> coeftest(ryegrass.m1, vcov = sandwich)
t test of coefficients:
Estimate Std. Error t value Pr(>|t|)
b:(Intercept) 2.98222 0.47438 6.2865 3.882e-06 ***
c:(Intercept) 0.48141 0.12779 3.7672 0.001212 **
d:(Intercept) 7.79296 0.15311 50.8976 < 2.2e-16 ***
e:(Intercept) 3.05795 0.26741 11.4355 3.170e-10 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
I am on R-4.2.0 (devel), but before updating drc via github this R version gave the exact same error. Here is my sessionInfo:
> sessionInfo()
R Under development (unstable) (2021-08-27 r80829)
Platform: amd64-portbld-freebsd14.0 (64-bit)
Running under: FreeBSD xxx.xxx.xxx 14.0-CURRENT FreeBSD 14.0-CURRENT #0 main-n249159-bb61ccd530b: Sun Sep 5 18:50:40 CEST 2021 [email protected]:/usr/obj/usr/src/amd64.amd64/sys/RHURLIN amd64
Matrix products: default
LAPACK: /usr/local/lib/R/lib/libRlapack.so.4.2.0
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] C/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sandwich_3.0-1 lmtest_0.9-38 zoo_1.8-9 drc_3.2-0 drcData_1.1-3 MASS_7.3-54
loaded via a namespace (and not attached):
[1] zip_2.2.0 Rcpp_1.0.7 pillar_1.6.2 compiler_4.2.0 cellranger_1.1.0
[6] forcats_0.5.1 tools_4.2.0 lifecycle_1.0.0 tibble_3.1.4 lattice_0.20-44
[11] pkgconfig_2.0.3 rlang_0.4.11 Matrix_1.3-4 openxlsx_4.2.4 curl_4.3.2
[16] mvtnorm_1.1-2 haven_2.4.3 rio_0.5.27 vctrs_0.3.8 gtools_3.9.2
[21] hms_1.1.0 grid_4.2.0 data.table_1.14.0 R6_2.5.1 plotrix_3.8-2
[26] fansi_0.5.0 survival_3.2-13 readxl_1.3.1 foreign_0.8-81 multcomp_1.4-17
[31] TH.data_1.0-10 carData_3.0-4 car_3.0-11 magrittr_2.0.1 scales_1.1.1
[36] codetools_0.2-18 splines_4.2.0 ellipsis_0.3.2 abind_1.4-5 colorspace_2.0-2
[41] utf8_1.2.2 stringi_1.7.4 munsell_0.5.0 crayon_1.4.1
HTH, Rainer
