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Add treatment data to a chronogram

cg_add_treatment.Rd

Add treatment data to a chronogram

Usage

cg_add_treatment(cg, treatment)

Arguments

cg

a chronogram object (class cg_tbl)

treatment

a tibble::tibble() containing treatment data. The dates and IDs columns in cg must be present in experiment.

Value

A chronogram

See also

cg_add_experiment()

Examples

## Example 1: A small study ##-------------------------------------
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
data(built_smallstudy)

## Setup ##
cg <- built_smallstudy$chronogram

# Create a tibble of exemplar treatment data
# Here, we have treated ID=1 with B cell depletion
# therapy, rituximab (RTX).

treatments_to_add <-
  tibble::tribble(
    ~elig_study_id, ~calendar_date, ~treatment,
    1, "01/02/2021", "RTX"
  )
  
## Make calendar_date a date class ##
treatments_to_add <- treatments_to_add %>%
  mutate(across(contains("date"), ~ lubridate::dmy(.x)))
  
## Add this new treatment data ##
cg_added <- cg_add_experiment(cg, treatments_to_add)

## Example 2: Incorrect column names ##----------------------------

## Setup as for Example 1 ##
treatments_to_add_renamed <- treatments_to_add %>%
dplyr::rename(ID = elig_study_id)

## this fails ##
try(
cg_added_2 <- cg_add_experiment(cg, 
treatments_to_add_renamed)
)
#> Error in check_experiment(x = experiment, cg = cg) : 
#>   Invalid experiment: provided ids_column_name is not present

##------------------------------------------------------------------