R/flugam.R
flugam.RdThis functions take an alternative approach to the trigonometric calculations and using spline functions and generalized additive models to fit a seasonal influenza curve.
flugam(data=NULL, outc=NULL, season, viral, time=NULL, echo=F, model_form='none', int_type="ci", alpha=0.05, ...)
| 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 | The name of a column which is a logical vector flagging a given time point as epidemic or not |
| viral | a string vector naming 1 or more viral specimens |
| time | an name of a column in data object, must be a numeric/integer class, must be unique (i.e. non-repeating) |
| echo | A logical, if T will print variables used in model. |
| 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). |
| ... | other options passed on to gam model |
an object of class data.frame, fit, upper and lower confidence bounds
Gul D, Cohen C, Tempia S, Newall AT, Muscatello DJ. Influenza-associated mortality in South Africa, 2009-2013: The importance of choices related to influenza infection proxies. Infl Oth Resp Vir 2017, 12 (1): 54-64. /urlhttps://www.ncbi.nlm.nih.gov/pubmed/29197161