lm method for plot generic not being used
Closed this issue · 1 comments
sahirbhatnagar commented
This was one of the issues brought up by the reviewer (see #136). Here I reproduce what I believe to be the issue. Basically, the lm method isn't being used, i.e., it's overridden by plot.singleEventCB. This likely suggests that we somehow need to use NextMethod. Also see https://sloop.r-lib.org/reference/s3_dispatch.html for details on what the symbols for s3_dispatch mean.
# devtools::install_github("r-lib/sloop")
library(sloop)
library(casebase)
#> See example usage at http://sahirbhatnagar.com/casebase/
library(splines)
data("eprchd")
eprchd <- transform(eprchd,
treatment = factor(treatment, levels = c("placebo","estPro")))
fit_mason <- fitSmoothHazard(status ~ treatment*ns(time),
data = eprchd,
time = "time")
sloop::s3_dispatch(plot(fit_mason))
#> => plot.singleEventCB
#> plot.glm
#> * plot.lm
#> * plot.defaultCreated on 2021-02-02 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.2 (2020-06-22)
#> os Pop!_OS 20.04 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Toronto
#> date 2021-02-02
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
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#> casebase * 0.9.0 2020-07-03 [1] CRAN (R 4.0.2)
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#> ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.2)
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#> nlme 3.1-149 2020-08-23 [4] CRAN (R 4.0.2)
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#> pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
#> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
#> processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
#> ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.2)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
#> R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
#> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
#> rlang 0.4.9 2020-11-26 [1] CRAN (R 4.0.2)
#> rmarkdown 2.5.3 2020-10-31 [1] Github (rstudio/rmarkdown@62d9b6b)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
#> scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
#> sloop * 1.0.1.9000 2021-02-02 [1] Github (r-lib/sloop@0838334)
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#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
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#> usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
#> vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
#> VGAM 1.1-3 2020-04-28 [1] CRAN (R 4.0.2)
#> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
#> xfun 0.19 2020-10-30 [1] CRAN (R 4.0.2)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
#>
#> [1] /home/sahir/R/x86_64-pc-linux-gnu-library/4.0
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/libraryturgeonmaxime commented
Yeah, I looked at that one yesterday, but I couldn't really understand what the reviewer meant. Of course we override the plot method, that was intentional. A user who insists on using plot.lm can call it directly, e.g. plot.lm(fit_mason).
My best guess of what the reviewing was saying is that the print method looked like the user called glm, which may be confusing:
> fitDF
Call: glm(formula = formula, family = binomial, data = sampleData)
Coefficients:
(Intercept) Z
0.1350 0.9446
Degrees of Freedom: 7877 Total (i.e. Null); 7876 Residual
Null Deviance: 875.2
Residual Deviance: 858.6 AIC: 862.6
So I changed the code a bit to capture the call to fitSmoothHazard:
> fitDF
Call: fitSmoothHazard(formula = event ~ Z, data = DF, time = "ftime")
Coefficients:
(Intercept) Z
0.1350 0.9446
Degrees of Freedom: 7877 Total (i.e. Null); 7876 Residual
Null Deviance: 875.2
Residual Deviance: 858.6 AIC: 862.6
That's the best interpretation I have for that comment. Other methods like summary and anova are inherited from glm, which is fine. The plot method for glm is inherited from lm, without using NextMethod.