S3 method for extracting information regarding Hazard Ratios. The function allows the survival object's formula to be updated. No default method is available at the moment.
Arguments
- x
An object of class
survfit- ...
other arguments passed on to the method survival::coxph
- update_formula
Template which specifies how to update the formula of the survfit object
update.formula
Examples
## treatment effect
survfit_object_trt <- visR::estimate_KM(data = adtte, strata = c("TRTP"))
visR::get_COX_HR(survfit_object_trt)
#> tidyme S3 default method (broom::tidy) used.
#> term estimate std.error statistic p.value
#> 1 TRTPXanomeline High Dose 1.614618 0.2332605 6.921953 4.454580e-12
#> 2 TRTPXanomeline Low Dose 1.422555 0.2295098 6.198232 5.710099e-10
## treatment and gender effect
survfit_object_trt_sex <- visR::estimate_KM(data = adtte, strata = c("TRTP", "SEX"))
visR::get_COX_HR(survfit_object_trt_sex)
#> tidyme S3 default method (broom::tidy) used.
#> term estimate std.error statistic p.value
#> 1 TRTPXanomeline High Dose 1.6159986 0.2339757 6.906695 4.960732e-12
#> 2 TRTPXanomeline Low Dose 1.4755033 0.2317331 6.367252 1.924446e-10
#> 3 SEXM 0.3745729 0.1651854 2.267591 2.335412e-02
## update formula of KM estimates by treatment to include "SEX" for HR estimation
visR::get_COX_HR(survfit_object_trt, update_formula = ". ~ . + SEX")
#> tidyme S3 default method (broom::tidy) used.
#> term estimate std.error statistic p.value
#> 1 TRTPXanomeline High Dose 1.6159986 0.2339757 6.906695 4.960732e-12
#> 2 TRTPXanomeline Low Dose 1.4755033 0.2317331 6.367252 1.924446e-10
#> 3 SEXM 0.3745729 0.1651854 2.267591 2.335412e-02
## update formula of KM estimates by treatment to include "AGE" for
## HR estimation with ties considered via the efron method
visR::get_COX_HR(survfit_object_trt,
update_formula = ". ~ . + survival::strata(AGE)", ties = "efron"
)
#> Warning: Loglik converged before variable 3,7,18,36,37 ; coefficient may be infinite.
#> tidyme S3 default method (broom::tidy) used.
#> term estimate std.error statistic
#> 1 TRTPXanomeline High Dose 1.5676387 2.555278e-01 6.1349054151
#> 2 TRTPXanomeline Low Dose 1.3216405 2.530283e-01 5.2232906436
#> 3 survival::strata(AGE)AGE=52 -18.1640265 5.298844e+03 -0.0034279227
#> 4 survival::strata(AGE)AGE=54 -0.2090228 1.415797e+00 -0.1476361992
#> 5 survival::strata(AGE)AGE=56 -1.6206873 1.097690e+00 -1.4764526121
#> 6 survival::strata(AGE)AGE=57 -1.1398148 1.166518e+00 -0.9771082854
#> 7 survival::strata(AGE)AGE=59 -18.1578569 3.767502e+03 -0.0048196009
#> 8 survival::strata(AGE)AGE=60 -1.3242727 1.241054e+00 -1.0670547450
#> 9 survival::strata(AGE)AGE=61 -1.4515246 1.133242e+00 -1.2808598926
#> 10 survival::strata(AGE)AGE=62 -1.4077265 1.428274e+00 -0.9856138035
#> 11 survival::strata(AGE)AGE=63 -1.7199741 1.245995e+00 -1.3804019425
#> 12 survival::strata(AGE)AGE=64 -1.4654615 1.256398e+00 -1.1663993068
#> 13 survival::strata(AGE)AGE=65 -1.8714042 1.236610e+00 -1.5133340637
#> 14 survival::strata(AGE)AGE=66 -0.7392248 1.443026e+00 -0.5122740113
#> 15 survival::strata(AGE)AGE=67 -1.7065320 1.132933e+00 -1.5062959259
#> 16 survival::strata(AGE)AGE=68 -1.5389556 1.104752e+00 -1.3930331338
#> 17 survival::strata(AGE)AGE=69 -1.1214615 1.136235e+00 -0.9869979981
#> 18 survival::strata(AGE)AGE=70 -18.2495027 2.607234e+03 -0.0069995634
#> 19 survival::strata(AGE)AGE=71 -1.3835479 1.085266e+00 -1.2748469333
#> 20 survival::strata(AGE)AGE=72 -1.5861528 1.109620e+00 -1.4294562988
#> 21 survival::strata(AGE)AGE=73 -1.3311583 1.078529e+00 -1.2342349648
#> 22 survival::strata(AGE)AGE=74 -1.8664225 1.086626e+00 -1.7176312590
#> 23 survival::strata(AGE)AGE=75 -1.0701874 1.094268e+00 -0.9779939016
#> 24 survival::strata(AGE)AGE=76 -1.5673346 1.094736e+00 -1.4317009758
#> 25 survival::strata(AGE)AGE=77 -1.6854602 1.064611e+00 -1.5831705057
#> 26 survival::strata(AGE)AGE=78 -1.3770729 1.070742e+00 -1.2860927604
#> 27 survival::strata(AGE)AGE=79 -1.4209295 1.057330e+00 -1.3438841443
#> 28 survival::strata(AGE)AGE=80 -1.0569092 1.073982e+00 -0.9841035589
#> 29 survival::strata(AGE)AGE=81 -2.4638433 1.083968e+00 -2.2729862787
#> 30 survival::strata(AGE)AGE=82 -1.9384962 1.095070e+00 -1.7702034739
#> 31 survival::strata(AGE)AGE=83 -0.9201888 1.089830e+00 -0.8443416072
#> 32 survival::strata(AGE)AGE=84 -1.4853330 1.059185e+00 -1.4023361544
#> 33 survival::strata(AGE)AGE=85 -1.5477944 1.140473e+00 -1.3571508894
#> 34 survival::strata(AGE)AGE=86 -2.2322079 1.172337e+00 -1.9040670529
#> 35 survival::strata(AGE)AGE=87 -2.6816908 1.423263e+00 -1.8841844010
#> 36 survival::strata(AGE)AGE=88 -18.7682740 2.704813e+03 -0.0069388434
#> 37 survival::strata(AGE)AGE=89 -18.1983764 1.889752e+04 -0.0009630034
#> p.value
#> 1 8.520988e-10
#> 2 1.757712e-07
#> 3 9.972649e-01
#> 4 8.826299e-01
#> 5 1.398224e-01
#> 6 3.285155e-01
#> 7 9.961545e-01
#> 8 2.859471e-01
#> 9 2.002429e-01
#> 10 3.243227e-01
#> 11 1.674629e-01
#> 12 2.434530e-01
#> 13 1.301948e-01
#> 14 6.084593e-01
#> 15 1.319912e-01
#> 16 1.636098e-01
#> 17 3.236436e-01
#> 18 9.944152e-01
#> 19 2.023634e-01
#> 20 1.528731e-01
#> 21 2.171154e-01
#> 22 8.586389e-02
#> 23 3.280773e-01
#> 24 1.522294e-01
#> 25 1.133826e-01
#> 26 1.984107e-01
#> 27 1.789859e-01
#> 28 3.250646e-01
#> 29 2.302701e-02
#> 30 7.669325e-02
#> 31 3.984785e-01
#> 32 1.608149e-01
#> 33 1.747333e-01
#> 34 5.690145e-02
#> 35 5.954004e-02
#> 36 9.944636e-01
#> 37 9.992316e-01