BiostatsUHNplus (version 1.0.2)

ae_timeline_plot: Outputs related adverse event timeline plots including just system organ class (AE category), or system organ class and lowest level term (AE detail). This function can fit up to 5 different attributions. Modify width, height and scale parameters in ggsave() to customize fit for large plot.

Description

Outputs related adverse event timeline plots including just system organ class (AE category), or system organ class and lowest level term (AE detail). This function can fit up to 5 different attributions. Modify width, height and scale parameters in ggsave() to customize fit for large plot.

Usage

ae_timeline_plot(
  subjID,
  subjID_ineligText = NULL,
  baseline_datasets,
  ae_dataset,
  ae_attribVars,
  ae_attribVarsName = NULL,
  ae_attribVarText = NULL,
  startDtVars,
  ae_detailVar,
  ae_categoryVar,
  ae_severityVar,
  ae_onsetDtVar,
  time_unit = c("day", "week", "month", "year"),
  include_ae_detail = TRUE,
  legendPerSpace = NULL,
  fonts = NULL,
  fontColours = NULL,
  panelColours = NULL,
  attribColours = NULL,
  attribSymbols = NULL,
  columnWidths = NULL
)

Value

ggplot object of AE timeline plot

Arguments

subjID

key identifier field for participant ID in data sets

subjID_ineligText

character text that denotes participant IDs to exclude. For example, c("New Subject") (if provided)

baseline_datasets

list of data frames that contain baseline participant characteristics. For example, list(enrollment_DF,demography_DF,ineligibility_DF)

ae_dataset

data frame that contains subject AEs

ae_attribVars

field(s) that denotes attribution to intervention under study. For example, c("CTC_AE_ATTR_SCALE","CTC_AE_ATTR_SCALE_1") (if provided)

ae_attribVarsName

character text that denotes name of interventions under study. For example, c("Drug 1", "Drug 2") (if provided)

ae_attribVarText

character text that denotes related attribution. For example c("Definite", "Probable", "Possible") (if provided)

startDtVars

field(s) that denotes participant start date (i.e. 10MAY2021). For example, it could be enrollment date or screening date. If more than one field given (unique names are required), each field is assumed to be specific start date for attribution in corresponding field order

ae_detailVar

field that denotes participant AE detail (lowest level term)

ae_categoryVar

field that denotes participant AE category (system organ class)

ae_severityVar

field that denotes participant AE severity grade (numeric)

ae_onsetDtVar

field that denotes participant AE onset date

time_unit

character text that denotes time unit for desired timeline. For example, could be one of c("day","week","month","year") (if provided)

include_ae_detail

boolean that denotes if AE detail should be included in timeline plot. Default is True

legendPerSpace

parameter at denotes proportion of vertical image space dedicated to legend at bottom. Default is 0.05 for AE detail and 0.1 for AE Category

fonts

character text that denotes font for AE category, AE detail, axis, legend and plot labels (if provided)

fontColours

character text that denotes system font colours for AE category and AE detail (if provided)

panelColours

character text that denotes panel background colours for AE category, AE detail and plot area (if provided)

attribColours

character text that denotes colours for attributions, supports up to 10 distinct colours (if provided)

attribSymbols

text that denotes median plot symbols for attributions, supports up to 10 distinct symbols (if provided)

columnWidths

text that denotes character columns widths for AE category and AE detail columns (if provided)

Examples

data("drug1_admin", "drug2_admin", "ae");
p <- ae_timeline_plot(subjID="Subject",subjID_ineligText=c("01","11"),
                      baseline_datasets=list(drug1_admin, drug2_admin),
                      ae_dataset=ae,
                      ae_attribVars=c("CTC_AE_ATTR_SCALE","CTC_AE_ATTR_SCALE_1"),
                      ae_attribVarsName=c("Drug 1","Drug 2"),
                      ae_attribVarText=c("Definite", "Probable", "Possible"),
                      startDtVars=c("TX1_DATE_INT","TX2_DATE_INT"),
                      ae_detailVar="ae_detail",
                      ae_categoryVar="ae_category",ae_severityVar="AE_SEV_GD",
                      ae_onsetDtVar="AE_ONSET_DT_INT",time_unit="month",
                      include_ae_detail=FALSE,
                      fonts=c("Calibri","Albany AMT","Gadugi","French Script MT","Forte"),
                      fontColours=c("#FFE135"),
                      panelColours=c("#E52B50",NA,"#FFE4C4"),
                      attribColours=c("#9AB973","#01796F","#FFA343","#CC7722"),   
                      attribSymbols=c(7,8,5,6),
                      columnWidths=c(23))