Refers to section 6.1.2.
Usage
farrington_model(
age,
start,
pos = NULL,
tot = NULL,
status = NULL,
fixed = list()
)Arguments
- age
the age vector.
- start
Named list of vectors or single vector. Initial values for optimizer.
- pos
the positive count vector (optional if status is provided).
- tot
the total count vector (optional if status is provided).
- status
the serostatus vector (optional if pos & tot are provided).
- fixed
Named list of vectors or single vector. Parameter values to keep fixed during optimization.
Value
a list of class farrington_model with 5 items
- datatype
type of datatype used for model fitting (aggregated or linelisting)
- df
the dataframe used for fitting the model
- info
fitted "glm" object
- sp
seroprevalence
- foi
force of infection
Examples
df <- rubella_uk_1986_1987
model <- farrington_model(
df$age, pos = df$pos, tot = df$tot,
start=list(alpha=0.07,beta=0.1,gamma=0.03)
)
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
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#> Warning: NaNs produced
#> Warning: NaNs produced
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#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
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#> Warning: NaNs produced
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#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
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#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
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#> Warning: NaNs produced
plot(model)
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
