csu_trendCohortPeriod: csu_trendCohortPeriod

In Rcan: Cancer Registry Data Analysis and Visualisation

Description

csu_trendCohortPeriod plot cohort period age specific graph.

Usage

csu_trendCohortPeriod(
  df_data,
  var_age = "age",
  var_cases="cases",
  var_py="py",
  var_year = "year",
  type = "Cohort",
  missing_age = NULL,
  logscale = TRUE,
  db_rate = 100000,
  first_age = 6,
  last_age = 16,
  year_group = 5,
  age_dropped=FALSE,
  plot_title = "csu_title",
  format_export = NULL,
  graph_dev =FALSE) 

Arguments

df_data	Data (need to be R data.frame format, see example to import csv file).
var_age	Age variable. Several format are accepted 1 "0-4" 0 2 "5-9" 5 3 "10-14" 10 ... ... ... 17 "80-84" 80 18 "85+" 85 Missing age value must be precise in the option missing_age. Last age group will always be considere without size (ie: 80+,85+, etc..).
var_cases	Number of event (cases, deaths, ...) variable.
var_py	Population year variable.
var_year	Time variable.
type	Type of the plot: "Cohort" Cohort graph. "Period" Period graph. "Both" Cohort Period graph.
missing_age	Age value representing the missing age cases.
logscale	Logical value: if TRUE Y-axis use logscale.
db_rate	The denominator population. Default is 100000.
first_age	First age group included, must be between 1 and 17. 1 represents 0-4, 2 represents 5-9, ... 5 represents 20-24 etc. Default is 6 (25-29 years).
last_age	Last age group included, must be between 2 and 18. 2 represents 5-9, ... 5 represents 20-24, ... 18 represents 85+ etc. Default is 16 (75-79 years). To plot the age group from 15-19 years until 65-69 years, use: first_age(4), last_age(14)
year_group	Usually, data are regrouped in 5 years period. . The numerical parameter controls the size of the group.
age_dropped	Only if some age grouped are missing in the data. Logical value: if TRUE, assume the age group not used are already dropped from the data. First_age and last_age option must still be filled.
plot_title	Title of the plot.
format_export	export the graph in different format: NULL Plot in R studio windows. "pdf" Export in PDF format. "tiff" Export in TIFF 300dpi format. "png" Export in PNG 200dpi format. "svg" Export in SVG format. Can be edit with https://inkscape.org/fr/. The filename is the plot_title option.
graph_dev	If the plot is embedded in a graphics Device function (such as pdf()), the graph_dev option should be set to TRUE for the first graph to avoid a blank page.

Details

This function is design the plot a the age-specific cohort and period plot. The type option allow to choose between the 3 different graphics: "Cohort", "Period", or "Both". Please note than the cohort plot and the period plot can be superimposed if the first_age is too low.

Value

Return a plot.

Author(s)

Mathieu Laversanne

See Also

csu_group_cases csu_merge_cases_pop csu_asr csu_cumrisk csu_eapc csu_ageSpecific csu_ageSpecific_top csu_bar_top csu_time_trend

Examples

	data(csu_registry_data_2)

	# you can import your data from csv file using read.csv:
	# mydata <-  read.csv("mydata.csv", sep=",")
	
	# to select only 1 population 
	test <- subset(csu_registry_data_2,registry == 84020 & sex == 1)


	
	# plot cohort graph from 25-29 years until 75-79 years.
	csu_trendCohortPeriod(df_data=test,
                        missing_age =99,
                        plot_title = "USA, Liver, males")
						
	# plot Period graph from 0-5 until 85+.
	csu_trendCohortPeriod(df_data=test,
                        missing_age =99,
                        plot_title = "USA, Liver, males",
						type="Period",
						first_age=1,
						last_age=18)
						
	# plot Cohort-Period graph from 30-34 years until 70-74 years.
	csu_trendCohortPeriod(df_data=test,
                        missing_age =99,
                        plot_title = "USA, Liver, males",
						type="Both",
						first_age=7,
						last_age=15)

	# plot Cohort-Period graph from 30-34 years until 70-74 years with Y axis normal scale.
	csu_trendCohortPeriod(df_data=test,
                        missing_age =99,
                        plot_title = "USA, Liver, males",
						type="Both",
						first_age=7,
						last_age=15,
						logscale=FALSE)

					
	# plot Cohort graph from 25-29 years until 75-79 years, with data grouped in 2 years period.
	csu_trendCohortPeriod(df_data=test,
						  missing_age =99,
						  plot_title = "USA, Liver, males",
						  type="Cohort",
						  year_group = 2)
						  
	# Plot embedded in a graphic device
	pdf("example_test.pdf")
	csu_trendCohortPeriod(df_data=test,
                        missing_age =99,
                        plot_title = "USA, Liver, males",
						type="Both",
						first_age=7,
						last_age=15,
						graph_dev=TRUE)
			  
	csu_trendCohortPeriod(df_data=test,
                        missing_age =99,
                        plot_title = "USA, Liver, males",
						type="Both",
						first_age=7,
						last_age=15,
						logscale=FALSE)
				
	dev.off()
		

Rcan documentation built on July 1, 2020, 10:20 p.m.