library(ezcox)
#> Welcome to 'ezcox' package!
#> =======================================================================
#> You are using ezcox version 1.0.4
#> 
#> Project home : https://github.com/ShixiangWang/ezcox
#> Documentation: https://shixiangwang.github.io/ezcox
#> Cite as      : arXiv:2110.14232
#> =======================================================================
#> 
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 contras…¹ ref_l…² n_con…³ n_ref   beta    HR lower…⁴
#>   <chr> <chr>    <lgl>      <chr>     <chr>     <dbl> <dbl>  <dbl> <dbl>   <dbl>
#> 1 1     ph.ecog  FALSE      1         0            71    36  0.364  1.44   0.907
#> 2 1     ph.ecog  FALSE      2         0            29    36  0.819  2.27   1.34 
#> 3 1     ph.ecog  FALSE      3         0             1    36  1.9    6.66   0.877
#> 4 2     ph.ecog  FALSE      1         0            42    27  0.416  1.52   0.711
#> 5 2     ph.ecog  FALSE      2         0            21    27  1.22   3.38   1.48 
#> 6 2     ph.ecog  FALSE      3         0             0    27 NA     NA     NA    
#> # … with 3 more variables: upper_95 <dbl>, p.value <dbl>, global.pval <dbl>,
#> #   and abbreviated variable names ¹​contrast_level, ²​ref_level, ³​n_contrast,
#> #   ⁴​lower_95
#> 
#> $models
#> # A tibble: 2 × 6
#>   Group Variable control model_file                               model   status
#>   <chr> <chr>    <chr>   <chr>                                    <list>  <lgl> 
#> 1 1     ph.ecog  NA      /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh… <coxph> TRUE  
#> 2 2     ph.ecog  NA      /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh… <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 contr…¹ ref_l…² n_con…³ n_ref    beta     HR lower…⁴
#>   <chr> <chr>    <lgl>      <chr>   <chr>     <dbl> <dbl>   <dbl>  <dbl>   <dbl>
#> 1 1     ph.ecog  FALSE      1       0            71    36  0.353   1.42    0.897
#> 2 1     ph.ecog  FALSE      2       0            29    36  0.809   2.24    1.32 
#> 3 1     ph.ecog  FALSE      3       0             1    36  1.77    5.86    0.767
#> 4 1     ph.ecog  TRUE       age     age         138   138  0.0182  1.02    0.996
#> 5 2     ph.ecog  FALSE      1       0            42    27  0.439   1.55    0.726
#> 6 2     ph.ecog  FALSE      2       0            21    27  1.41    4.09    1.62 
#> 7 2     ph.ecog  FALSE      3       0             0    27 NA      NA      NA    
#> 8 2     ph.ecog  TRUE       age     age          90    90 -0.0153  0.985   0.952
#> # … with 3 more variables: upper_95 <dbl>, p.value <dbl>, global.pval <dbl>,
#> #   and abbreviated variable names ¹​contrast_level, ²​ref_level, ³​n_contrast,
#> #   ⁴​lower_95
#> 
#> $models
#> # A tibble: 2 × 6
#>   Group Variable control model_file                               model   status
#>   <chr> <chr>    <chr>   <chr>                                    <list>  <lgl> 
#> 1 1     ph.ecog  age     /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh… <coxph> TRUE  
#> 2 2     ph.ecog  age     /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh… <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_cont…¹ contr…² ref_l…³ n_con…⁴ n_ref    beta     HR lower…⁵
#>    <chr> <chr>    <lgl>     <chr>   <chr>     <dbl> <dbl>   <dbl>  <dbl>   <dbl>
#>  1 1     ph.ecog  FALSE     1       0            71    36  0.353   1.42    0.897
#>  2 1     ph.ecog  FALSE     2       0            29    36  0.809   2.24    1.32 
#>  3 1     ph.ecog  FALSE     3       0             1    36  1.77    5.86    0.767
#>  4 1     ph.ecog  TRUE      age     age         138   138  0.0182  1.02    0.996
#>  5 2     ph.ecog  FALSE     1       0            42    27  0.439   1.55    0.726
#>  6 2     ph.ecog  FALSE     2       0            21    27  1.41    4.09    1.62 
#>  7 2     ph.ecog  FALSE     3       0             0    27 NA      NA      NA    
#>  8 2     ph.ecog  TRUE      age     age          90    90 -0.0153  0.985   0.952
#>  9 ALL   ph.ecog  FALSE     1       0           113    63  0.359   1.43    0.969
#> 10 ALL   ph.ecog  FALSE     2       0            50    63  0.857   2.36    1.5  
#> 11 ALL   ph.ecog  FALSE     3       0             1    63  2.11    8.23    1.09 
#> 12 ALL   ph.ecog  TRUE      age     age         228   228  0.0108  1.01    0.992
#> # … with 3 more variables: upper_95 <dbl>, p.value <dbl>, global.pval <dbl>,
#> #   and abbreviated variable names ¹​is_control, ²​contrast_level, ³​ref_level,
#> #   ⁴​n_contrast, ⁵​lower_95
#> 
#> $models
#> # A tibble: 3 × 6
#>   Group Variable control model_file                               model   status
#>   <chr> <chr>    <chr>   <chr>                                    <list>  <lgl> 
#> 1 1     ph.ecog  age     /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh… <coxph> TRUE  
#> 2 2     ph.ecog  age     /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh… <coxph> TRUE  
#> 3 ALL   ph.ecog  age     /var/folders/bj/nw1w4g1j37ddpgb6zmh3sfh… <coxph> TRUE  
#> 
#> attr(,"class")
#> [1] "ezcox"
#> 
#> $plot