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chjackson / flexsurv

The flexsurv R package for flexible parametric survival and multi-state modelling
http://chjackson.github.io/flexsurv/
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Enable `.` in formula for `flexsurvreg()` #144

Closed hfrick closed 1 year ago

hfrick commented 1 year ago

closes #143

I've added to the documentation of the formula argument for flexsurvreg(). Let me know if you think that this gets the point across.

I've set the default for the new data argument to NULL so it doesn't change anything for flexsurvmix(). I figured that might need some more thinking.

Are there other aspects the tests should cover?

I had the R CMD check fail when I checkout the repo, due to the vignette, but it passes with devtools::check(vignettes = FALSE). 

library(flexsurv)
#> Loading required package: survival

flexsurvreg(Surv(time, status) ~ ., data = lung, dist = "lognormal")
#> Call:
#> flexsurvreg(formula = Surv(time, status) ~ ., data = lung, dist = "lognormal")
#> 
#> Estimates: 
#>            data mean  est        L95%       U95%       se         exp(est) 
#> meanlog           NA   6.47e+00   3.52e+00   9.41e+00   1.50e+00         NA
#> sdlog             NA   9.97e-01   8.76e-01   1.13e+00   6.57e-02         NA
#> inst        1.07e+01   2.00e-02  -1.37e-03   4.14e-02   1.09e-02   1.02e+00
#> age         6.26e+01  -1.44e-02  -3.43e-02   5.41e-03   1.01e-02   9.86e-01
#> sex         1.38e+00   4.76e-01   1.20e-01   8.32e-01   1.82e-01   1.61e+00
#> ph.ecog     9.58e-01  -5.31e-01  -9.38e-01  -1.25e-01   2.08e-01   5.88e-01
#> ph.karno    8.20e+01  -1.44e-02  -3.74e-02   8.60e-03   1.17e-02   9.86e-01
#> pat.karno   7.96e+01   8.12e-03  -5.00e-03   2.12e-02   6.70e-03   1.01e+00
#> meal.cal    9.29e+02   2.37e-04  -1.66e-04   6.39e-04   2.06e-04   1.00e+00
#> wt.loss     9.72e+00   9.84e-03  -2.61e-03   2.23e-02   6.35e-03   1.01e+00
#>            L95%       U95%     
#> meanlog           NA         NA
#> sdlog             NA         NA
#> inst        9.99e-01   1.04e+00
#> age         9.66e-01   1.01e+00
#> sex         1.13e+00   2.30e+00
#> ph.ecog     3.91e-01   8.83e-01
#> ph.karno    9.63e-01   1.01e+00
#> pat.karno   9.95e-01   1.02e+00
#> meal.cal    1.00e+00   1.00e+00
#> wt.loss     9.97e-01   1.02e+00
#> 
#> N = 167,  Events: 120,  Censored: 47
#> Total time at risk: 51759
#> Log-likelihood = -837.4184, df = 10
#> AIC = 1694.837

Created on 2022-10-13 by the reprex package (v2.0.1)

chjackson commented 1 year ago

That looks good to me, thank you! I copped out of trying to implement it in flexsurvmix, but added an error message and documentation about it not being supported there.