fluglm: fluglm: Generate fitted prediction values with generalized...

In kmcconeghy/flumodelr: An R Package for Estimating Attributable Influenza Morbidity and Mortality

Description

Similar to serflm, but allows for more specifications.

Usage

fluglm(data=NULL, outc=NULL, season, viral, 
              time=NULL, period=52, echo=F, poly=T, 
              model_form='none', int_type="ci", alpha=0.05, offset,
              glmnb=F, ...)

Arguments

data	A dataframe class object, must contain time variable, epidemic indicator, and measure of influenza morbidity
outc	an unquoted name of a column in data which corresponds to the outcome variable of interest
season	Either 'T', where the epidemic baseline model will be created assuming time variable is a date, and Oct-May is epidemic season, or the name of a column which is a logical vector flagging a given week as epidemic or not
viral	a string vector naming 1 or more viral specimens
time	an unquoted name of a column in data object, must be a numeric/integer class variable in dataframe which corresponds to a unit of time, must be unique (i.e. non-repeating)
period	a numeric vector indicating period length, i.e. 52 weeks in year
echo	A logical, if T will print variables used in model.
poly	A logical, if T will include a quadratic, cubic, quartic and quintic term.
model_form	An object of type formula, allowing for user-specified model to be passed on to glm(). Default missing.
int_type	Specifies type of upper interval to be output, currently only allows for confidence intervals. Prediction intervals to be added, but are only approximate for Poisson families.
alpha	The threshold for CI interval, default is 0.05 (one-sided).
offset	Specify if offset term to be used, must specify log(object)
glmnb	Logical, if True will run a negative binomial model using MASS::nb.glm
...	other options passed on to glm model (e.g. family=poisson, see ?glm)

Value

an object of class data.frame, fit, upper and lower confidence bounds

References

Thompson WW1, Weintraub E, Dhankhar P, Cheng PY, Brammer L, Meltzer MI, Bresee JS, Shay DK. Estimates of US influenza-associated deaths made using four different methods. Influenza Other Respir Viruses. 2009 Jan;3(1):37-49. /urlhttps://www.ncbi.nlm.nih.gov/pubmed/19453440

Examples

require(flumodelr)
fludta <- flumodelr::fludta
flu_fit <- fluglm(fludta, outc = fludeaths, time = week_in_order, season=epi)  
              
head(flu_fit)

kmcconeghy/flumodelr documentation built on June 7, 2019, 8:47 p.m.