ezcox: Easy Group Cox Analysis and
Visualization
library(survival)
lung$ph.ecog <- factor(lung$ph.ecog)
ezcox_group(lung, grp_var = "sex", covariate = "ph.ecog")
#> => Processing variable 1
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable 2
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> covariates=NULL but drop_controls=TRUE, detecting controls...
#> No. Skipping...
#> Done.
#> Returns a list containing data and ggplot.
#> $data
#> $stats
#> # A tibble: 6 × 13
#> Group Variable is_control contrast_level ref_level n_contrast n_ref beta
#> <chr> <chr> <lgl> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 1 ph.ecog FALSE 1 0 71 36 0.364
#> 2 1 ph.ecog FALSE 2 0 29 36 0.819
#> 3 1 ph.ecog FALSE 3 0 1 36 1.9
#> 4 2 ph.ecog FALSE 1 0 42 27 0.416
#> 5 2 ph.ecog FALSE 2 0 21 27 1.22
#> 6 2 ph.ecog FALSE 3 0 0 27 NA
#> # ℹ 5 more variables: HR <dbl>, lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>,
#> # global.pval <dbl>
#>
#> $models
#> # A tibble: 2 × 6
#> Group Variable control model_file model status
#> <chr> <chr> <chr> <chr> <list> <lgl>
#> 1 1 ph.ecog <NA> /tmp/RtmpZC94kt/ezcox/ezcox_120676011708 <coxph> TRUE
#> 2 2 ph.ecog <NA> /tmp/RtmpZC94kt/ezcox/ezcox_120653da7fe0 <coxph> TRUE
#>
#> attr(,"class")
#> [1] "ezcox"
#>
#> $plot
ezcox_group(lung, grp_var = "sex", covariate = "ph.ecog", controls = "age")
#> => Processing variable 1
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable 2
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> covariates=NULL but drop_controls=TRUE, detecting controls...
#> Yes. Setting variables to keep...
#> Done.
#> Returns a list containing data and ggplot.
#> $data
#> $stats
#> # A tibble: 8 × 13
#> Group Variable is_control contrast_level ref_level n_contrast n_ref beta
#> <chr> <chr> <lgl> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 1 ph.ecog FALSE 1 0 71 36 0.353
#> 2 1 ph.ecog FALSE 2 0 29 36 0.809
#> 3 1 ph.ecog FALSE 3 0 1 36 1.77
#> 4 1 ph.ecog TRUE age age 138 138 0.0182
#> 5 2 ph.ecog FALSE 1 0 42 27 0.439
#> 6 2 ph.ecog FALSE 2 0 21 27 1.41
#> 7 2 ph.ecog FALSE 3 0 0 27 NA
#> 8 2 ph.ecog TRUE age age 90 90 -0.0153
#> # ℹ 5 more variables: HR <dbl>, lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>,
#> # global.pval <dbl>
#>
#> $models
#> # A tibble: 2 × 6
#> Group Variable control model_file model status
#> <chr> <chr> <chr> <chr> <list> <lgl>
#> 1 1 ph.ecog age /tmp/RtmpZC94kt/ezcox/ezcox_12066ea4cbdf <coxph> TRUE
#> 2 2 ph.ecog age /tmp/RtmpZC94kt/ezcox/ezcox_12065072c5b6 <coxph> TRUE
#>
#> attr(,"class")
#> [1] "ezcox"
#>
#> $plot
ezcox_group(lung, grp_var = "sex", covariate = "ph.ecog", controls = "age", add_all = TRUE)
#> => Processing variable 1
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable 2
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable ALL
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> covariates=NULL but drop_controls=TRUE, detecting controls...
#> Yes. Setting variables to keep...
#> Done.
#> Returns a list containing data and ggplot.
#> $data
#> $stats
#> # A tibble: 12 × 13
#> Group Variable is_control contrast_level ref_level n_contrast n_ref beta
#> <chr> <chr> <lgl> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 1 ph.ecog FALSE 1 0 71 36 0.353
#> 2 1 ph.ecog FALSE 2 0 29 36 0.809
#> 3 1 ph.ecog FALSE 3 0 1 36 1.77
#> 4 1 ph.ecog TRUE age age 138 138 0.0182
#> 5 2 ph.ecog FALSE 1 0 42 27 0.439
#> 6 2 ph.ecog FALSE 2 0 21 27 1.41
#> 7 2 ph.ecog FALSE 3 0 0 27 NA
#> 8 2 ph.ecog TRUE age age 90 90 -0.0153
#> 9 ALL ph.ecog FALSE 1 0 113 63 0.359
#> 10 ALL ph.ecog FALSE 2 0 50 63 0.857
#> 11 ALL ph.ecog FALSE 3 0 1 63 2.11
#> 12 ALL ph.ecog TRUE age age 228 228 0.0108
#> # ℹ 5 more variables: HR <dbl>, lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>,
#> # global.pval <dbl>
#>
#> $models
#> # A tibble: 3 × 6
#> Group Variable control model_file model status
#> <chr> <chr> <chr> <chr> <list> <lgl>
#> 1 1 ph.ecog age /tmp/RtmpZC94kt/ezcox/ezcox_12065ce888a9 <coxph> TRUE
#> 2 2 ph.ecog age /tmp/RtmpZC94kt/ezcox/ezcox_12064b1b34bb <coxph> TRUE
#> 3 ALL ph.ecog age /tmp/RtmpZC94kt/ezcox/ezcox_120648af1937 <coxph> TRUE
#>
#> attr(,"class")
#> [1] "ezcox"
#>
#> $plot
