Safety Results Over Time plot

Source: R/safety_results_over_time.R

Safety Results Over Time plot

safety_results_over_time(data, settings)

Arguments

data

labs data structured as one record per person per visit per measurement. See details for column requirements.
settings

named list of settings with the parameters specified below.

Value

returns a chart object

Details

The settings object provides details the columns in the data set.

  • "value_col"Value column

  • "measure_col"Measure column

  • "measure_values"Measure values

  • "visit_col"Study Visit

  • "visitn_col"Study Number

  • "group_col"Grouping column

  • "violins"Show Violin plots?

  • "boxplots"Show Box Plots?

  • "axis"set to "log" to use a log transformed axis, linear otherwise

  • "drop_visit_string"Drop visits that contain this string. e.g. "unscheduled"

Examples

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
lb <- safetyData::sdtm_lb
sub_ids <- unique(lb$USUBJID)[1:100]
lb<-lb %>% filter(USUBJID %in% sub_ids)
settings <- list(
    value_col = "LBORRES",
    measure_col = "LBTEST",
    measure_values = c("Chloride"),
    visit_col = "VISIT",
    visitn_col = "VISITNUM",
    axis = "log"
)
safety_results_over_time(lb, settings)

#> Warning: `fun.y` is deprecated. Use `fun` instead.

# remove unscheduled visits, add violin plot and 2nd panel
settings$drop_visit_string <- "unscheduled"
settings$violins <- TRUE
settings$measure_values <- c("Albumin")
safety_results_over_time(lb, settings)

#> Warning: `fun.y` is deprecated. Use `fun` instead.
#> Warning: Groups with fewer than two data points have been dropped.

# add grouping by treatment
dm_sub <- safetyData::sdtm_dm %>% select(USUBJID, ARM)
dm_lb <- dm_sub %>% left_join(lb)

#> Joining, by = "USUBJID"
settings$group_col <- "ARM"
safety_results_over_time(dm_lb, settings)

#> Warning: `fun.y` is deprecated. Use `fun` instead.
#> Warning: Groups with fewer than two data points have been dropped.