simped {poplab} | R Documentation |
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.
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)
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. |
baseyear
, simyears
and endyear
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
fam.rel
basefamrisk
, famrisk
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).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.
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_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)