simped {poplab}R Documentation

Simulate the evolution of a population of related individuals over a calendar period

Description

Simulate the evolution of a baseline population of related individuals over a specified calendar period. Requires the period-specific fertility, mortality and disease incidence rates, and the real population age profile for the first simulated year.

The function looks in the folder specified in its call for 6 input data files: age-specific population counts for males and females separately, female fertility, mortality rates for males and females separately, and disease (e.g. breast cancer) incidence rates.

Usage

simped (baseyear, basehealth, basefamrisk, sex.a, basetotal,
warmuptime, simyears, endyear, healthy, famrisk, mortratio, 
d.mod, fam.rel, print.option, population.fem, population.male, 
mortality.fem, mortality.male, fertility, incidence, seed, 
folder, name.base)

Arguments

baseyear first calendar year to be simulated (the year for which to create a baseline population - see create.baseline.complete help for more details).
basehealth 0/1 values - disease incidence simulated/not simulated during the creation of the baseline population (see create.baseline.complete help). The default is 1 (i.e. disease incidence not simulated).
basefamrisk parameter for familial aggregation of disease applied in the creation of the baseline population; used only if the basehealth is set to 0 (see create.baseline.complete help). The default is 1 (i.e. no familial aggregation). See Details below.
sex.a 1/2 values - gender specification (1 = males, 2 = females) for familial aggregation of disease; used only if healthy or basehealth is set to 0. The default is 2 (mother/daughter or sister/sister disease aggregation).
basetotal this factor multiplied by 100 is the sex-specific number of individuals in the starting population (see create.baseline.complete help). The default is 500.
warmuptime number of years the baseyear real population age profile is set back in time (see create.baseline.complete help). The default is 100.
simyears number of years to be simulated.
endyear last calendar year to be simulated.
healthy 0/1 values - disease incidence simulated/not simulated during the evolution of the population. The default is 1.
famrisk parameter for familial aggregation of disease; used only if healthy is set to 0. The default is 1 (i.e. no familial aggregation). See Details below.
mortratio mortality ratio for cases compared to disease free individuals. The default is 1 (i.e. cases have the same risk of death as disease free individuals).
d.mod familial model of disease aggregation to choose from (see Details below); used only if healthy is set to 0.
fam.rel familial relationship of disease aggregation to choose from (see Details below); used only if healthy is set to 0.
print.option TRUE/FALSE values - option for saving the simulated pedigree to file. The default is FALSE.
population.fem name (quoted) of the tab-separated file storing age-specific counts from the real female population (e.g. "populationfem.txt").
population.male name (quoted) of the tab-separated file storing age-specific counts from the real male population (e.g. "populationmale.txt").
mortality.fem name (quoted) of the tab-separated file storing age-specific female mortality rates (e.g. "mortalityfem.txt").
mortality.male name (quoted) of the tab-separated file storing age-specific male mortality rates (e.g. "mortalitymale.txt").
fertility name (quoted) of the tab-separated file storing female fertility rates (e.g. "fertility.txt").
incidence name (quoted) of the tab-separated file storing incidence rates (e.g. "incidence.txt").
seed seed used in the creation of the population. The default is NULL. Useful when the user wants to reproduce the exact same simulation results (population).
folder folder (quoted) where the function looks for input files such as population counts, mortality, fertility and incidence rates. For example, it might be your R_HOME/library/poplab/data/ directory, where R_HOME is the location where R is installed on your computer (see Examples below).
name.base Ending string of the file name storing the baseline population. The default is "". See Details below.

Details

baseyear, simyears and endyear
give the calendar interval to be simulated; the user may specify any combination of 2 out of these 3 arguments and omit the other argument.

The function will first identify if a virtual baseline population has been created and saved to file, by searching into the specified folder for a file named, for example, 'base_pop_1955.txt' if baseyear is 1955. base_pop_yyyy.txt, where yyyy is a baseyear, is the name format that the print.poplab function uses to save to file virtual baseline populations, after their creation with the create.baseline.complete function. This name format should not be used for other purposes. If the baseline population is found, the simped function reads in this population and simulates further its evolution. If it is not found, a call to the create.baseline.complete function is implicitly made by the simped function, as follows:

create.baseline.complete (baseyear, healthy = basehealth, 
    risk = basefamrisk, sex.a = sex.a, mortratio = mortratio,
    print.option = print.option, base.scale = basetotal, 
    runintime = warmuptime, population.fem = population.fem, 
    population.male = population.male, mortality.fem = mortality.fem,
    mortality.male = mortality.male, fertility = fertility,
    incidence = incidence, seed = seed, folder = folder)
Immediately after creating or reading in the baseline population, a plot of the simulated baseline age profile versus the real population age profile for the baseyear year is displayed and the function starts simulating the evolution of this population over the specified calendar period.

d.mod
The options to choose from are: familial relative risk ("rr"), familial odds-ratio ("or"), familial relative risk depending on the age at incidence of the affected relative ("agesprr") and familial odds-ratio depending on age at incidence of the affected relative ("agespor").
fam.rel
The options to choose from are: familial aggregation occurs through a parent ("p") and familial aggregation occurs thorugh a sibling ("s").
basefamrisk, famrisk
If this is a single value, it is expected that the value for d.mod is either "rr" or "or". For the familial models of disease where the risk and the odds, respectively, depend on the age at incidence of the affected relative, a numerical array is specified. The first part of the array represents the upper limit of the age categories and the last part are the actual coefficients of increase. The age-intervals are open to the left (see also Examples).
name.base
When reading in the simulated baseline population the default of the file name is base_pop_yyyy.txt (where yyyy is the baseline year). Other specifications (e.g., "fam_risk2") should be included in this parameter.

Value

A 2-component list. The first component (matrix) is the baseline population (either read-in from the specified folder or just created). The second component (matrix) is the evolved population.

Note

If a call to this function is made without assigning its value to a variable, the result will be printed on the screen (most probably, a very large matrix)! Thus it is advisable to always assign the object returned by this function to a variable.

See Also

create.baseline.complete, plot.poplab, print.poplab

Examples


## Not run: 
The syntax below will search into the specified folder for a
file called 'base_pop_1955.txt' (see Details). If the file
is found, it is read-in as the baseline population. If it is
not found, an implicit call to the create.baseline.complete
function is made as follows:

create.baseline.complete(baseyear = 1955, healthy = 0, risk =
2, sex.a = 2, base.scale = 50, runintime = 70, d.mod = 
"rr", fam.rel = "p", print.option = FALSE, population.fem = 
"populationfem.txt", population.male = "populationmale.txt", 
mortality.fem = "mortalityfem.txt", mortality.male = 
"mortalitymale.txt", fertility = "fertility.txt", incidence = 
"incidence.txt", seed = 52482337, folder =
system.file("data", package = "poplab"))

Next the evolution of this baseline population is simulated
over the calendar period 1955 - 1985 ([baseyear, endyear]).
Incident cancer is assigned (healthy) to the female population
(sex.a) via a model of familial relative risk (d.mod), where the 
risk ratio for women with an affected mother (fam.rel) is 2 (famrisk). 
The mortality ratio for cases is 2 (mortratio). The resulting 
pedigree is not saved to file (print.option). The input files 
are "populationfem.txt", "populationmale.txt", "mortalityfem.txt", 
"mortalitymale.txt", "fertility.txt" and "incidence.txt" from the "data"
folder of the poplab package.
## End(Not run)

simpop <- 
simped(baseyear = 1955, basehealth = 0, basefamrisk = 2,
sex.a = 2, basetotal = 50, warmuptime = 70, endyear = 1985,
healthy = 0, famrisk = 2, mortratio = 2, d.mod = "rr", 
fam.rel = "p", print.option = FALSE, population.fem = 
"populationfem.txt",  population.male = "populationmale.txt", 
mortality.fem = "mortalityfem.txt", mortality.male = 
"mortalitymale.txt", fertility = "fertility.txt", incidence = 
"incidence.txt", seed = 52482337,
folder = system.file("data", package = "poplab"))

## resulting baseline population
base <- simpop[[1]]

## resulting evolved population
evolved <- simpop[[2]]

## Not run: 
In the syntax below the familial relative risk (d.mod) depends
on maternal (fam.rel) age at incidence: the risk of disease (risk) 
is increased by factor of 4 for women whose mothers where strictly 
younger than 50 years of age at diagnosis compared to daughters 
of unaffected mothers, and by a factor of 2 for daughters of 
women diagnosed between the age of 50 to 100 years.

simpop <- 
simped(baseyear = 1955, basehealth = 0, basefamrisk = 
c(50, 101, 4, 2), sex.a = 2, basetotal = 50, warmuptime = 
70, endyear = 1985, healthy = 0, famrisk = c(50, 101, 4, 2), 
mortratio = 2, d.mod = "agesprr", fam.rel = "p", print.option = 
FALSE, population.fem = "populationfem.txt", population.male = 
"populationmale.txt", mortality.fem = "mortalityfem.txt", 
mortality.male = "mortalitymale.txt", fertility = 
"fertility.txt", incidence = "incidence.txt", 
seed = 52482337,
folder = system.file("data", package = "poplab"))
## End(Not run)


[Package poplab version 1.0.2 Index]