Group Cox Analysis and Visualization

Group Cox Analysis and Visualization

ezcox_group(
  data,
  grp_var,
  covariate,
  controls = NULL,
  time = "time",
  status = "status",
  sort = FALSE,
  decreasing = TRUE,
  add_all = FALSE,
  add_caption = TRUE,
  verbose = TRUE,
  headings = list(variable = "Group", n = "N", measure = "Hazard ratio", ci = NULL, p =
    "p"),
  ...
)

Arguments

data

a data.frame containing variables, time and os status.

grp_var

a group column.

covariate

a covariable for cox analysis.

controls

column names specifying controls. The names with pattern "*:|()" will be treated as interaction/combination term, please make sure all column names in data are valid R variable names.

time

column name specifying time, default is 'time'.

status

column name specifying event status, default is 'status'.

sort

if TRUE, sort the models by the HR values.

decreasing

logical, should the sort order be increasing or decreasing?

add_all

if TRUE, add a group for all data rows.

add_caption

if TRUE, add caption to the plot.

verbose

if TRUE, print extra info.

headings

a list for setting the heading text.

...

other arguments passing to forestmodel::forest_model().

Value

a list.

Examples

library(survival)
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.
#> Resized limits to included dashed line in forest panel
#> Returns a list containing data and ggplot.
#> $data
#> $stats
#> # A tibble: 2 × 13
#>   Group Variable is_control contrast…¹ ref_l…² n_con…³ n_ref  beta    HR lower…⁴
#>   <chr> <chr>    <lgl>      <chr>      <chr>     <int> <int> <dbl> <dbl>   <dbl>
#> 1 1     ph.ecog  FALSE      1          1           137   137 0.426  1.53    1.18
#> 2 2     ph.ecog  FALSE      2          2            90    90 0.637  1.89    1.23
#> # … 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.
#> Resized limits to included dashed line in forest panel
#> Returns a list containing data and ggplot.
#> $data
#> $stats
#> # A tibble: 4 × 13
#>   Group Variable is_control contra…¹ ref_l…² n_con…³ n_ref    beta    HR lower…⁴
#>   <chr> <chr>    <lgl>      <chr>    <chr>     <int> <int>   <dbl> <dbl>   <dbl>
#> 1 1     ph.ecog  FALSE      1        1           137   137  0.419  1.52    1.17 
#> 2 1     ph.ecog  TRUE       age      age         138   138  0.0184 1.02    0.996
#> 3 2     ph.ecog  FALSE      2        2            90    90  0.714  2.04    1.25 
#> 4 2     ph.ecog  TRUE       age      age          90    90 -0.0112 0.989   0.957
#> # … 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

#> 
p <- 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.
#> Resized limits to included dashed line in forest panel
#> Returns a list containing data and ggplot.