simped: Simulate the evolution of a population of related individuals...
In poplab: Population Lab

Description Usage Arguments Details Value Note See Also Examples

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 8 input data files: age-specific population counts for males and females separately, female fertility, mortality rates for males and females separately, disease (e.g. acute appendicitis) incidence rates for males and females separately and the simulated baseline population (see create.baseline.complete, print.poplab). For diseases or conditions which affect only one gender (e.g., breast cancer), 7 files are sufficient, that is, there is only one incidence file for sex.a = 1 (males) or sex.a = 2 (females).

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

`baseyear`	the baseline year, needed to load the baseline population
`simyears`	number of years to be simulated.
`endyear`	last calendar year to be simulated.
`population.male`	name (quoted) of the tab-separated file containing age-specific counts from the real male population (e.g. "populationmale.txt").
`population.fem`	name (quoted) of the tab-separated file containing age-specific counts from the real female population (e.g. "populationfem.txt").
`fertility`	name (quoted) of the tab-separated file containing age-specific female fertility rates (e.g. "fertility.txt").
`incidence.male`	name (quoted) of the tab-separated file containing age-specific male incidence rates (e.g. "incidence.male.txt").
`incidence.fem`	name (quoted) of the tab-separated file containing age-specific female incidence rates (e.g. "incidence.fem.txt").
`mortality.male`	name (quoted) of the tab-separated file containing age-specific male mortality rates (e.g. "mortalitymale.txt").
`mortality.fem`	name (quoted) of the tab-separated file containing age-specific female mortality rates (e.g. "mortalityfem.txt").
`healthy`	0/1 values - disease incidence simulated/not simulated during the evolution of the population. The default is 1.
`sex.a`	1/2/3 values - gender specification (1 = males, 2 = females, 3 = for both males and females) for familial aggregation of disease; used only if `healthy` is set to 0. The default is 2 (mother/daughter or sister/sister disease aggregation).
`fam.rel`	familial relationship of disease aggregation to choose from (see Details below); used only if `healthy` is set to 0.
`d.mod`	familial model of disease aggregation to choose from (see Details below); used only if `healthy` is set to 0.
`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).
`print.option`	TRUE/FALSE values - option for saving the simulated pedigree to file. The default is TRUE.
`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/extdata/ 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.

baseyear, simyears and endyear gives 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\_yyyy.txt where yyyy is the baseyear. base\_pop\_yyyy.txt is the name format that the print.poplab function uses to save a virtual baseline population to file, after its 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 error message is printed i.e., object basepop not found. There is a need to evoke the create.baseline.complete function prior to running simped.

Immediately after 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").

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.

A 2-component list. The first component (matrix) is the baseline population. The second component (matrix) is the evolved population.

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.

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

## Not run: 
The syntax below will search into the specified folder for a file called 
'base_pop_1954.txt' (see Details). If the file is found, it is read-in as the 
baseline population otherwise an error message will be printed.

Next the evolution of the baseline population is simulated over the calendar 
period 1954 - 2007 ([baseyear, endyear]). Incident acute appendicitis is 
assigned (healthy=0) to the entire population (sex.a=3) via a model of familial 
relative risk (d.mod="rr"), where the risk ratio for people with an affected parents 
compared to those with both unaffected parents is 2 (fam.rel="p", famrisk=2). 
The mortality ratio for cases is 1 (mortratio=1). The resulting pedigree is saved to 
file (print.option+TRUE). 

## End(Not run)


simpop <- 
simped (baseyear = 1954, endyear = 2007, population.male = "populationmale.txt",
population.fem = "populationfem.txt", fertility = "fertility.txt",
incidence.male = "incidence.male.txt", incidence.fem = "incidence.fem.txt",
mortality.male  = "mortalitymale.txt", mortality.fem = "mortalityfem.txt",
healthy = 0, sex.a = 3, fam.rel = "p", d.mod = "rr", famrisk = 2, 
mortratio = 1, print.option = TRUE, seed =19780720, 
folder = system.file("extdata", package = "poplab")) 

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

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