recursively.apply.leos.method: Method to generate estimates based on notification...

In Opportunity-Estimator-EpiSurveillance/leos.opportunity.estimator: Notification Opportunity Estimator

Description

Function recursively.apply.leos.method applies the following method for the estimates: Notification delay modelling by Leo Bastos

Usage

recursively.apply.leos.method(df.in, epiyearweek.list,
  quantile.target = 0.95, low.activity = NULL, generate.plots = F)

Arguments

df.in	Data frame with the FIRST THREE columns refering to [,1] location id, [,2] notification date, [,3] digitization date, unless all(c('ID_MUNICIP', 'DT_NOTIFIC', 'DT_DIGITA') %in% names(df.in)) == T
epiyearweek.list	List like object with epidemiological weeks to be estimated
quantile.target	Quantile to be used to determine Dmax from delay profile. Default: 0.95
low.activity	List of location id's not to be estimated due to low activity. Default: NULL
generate.plots	Boolean object to determine wether function should generate and save plots or not. Default: F

Details

N_t - number of notified cases at time t

Y_t,d - number of notified cases from time t with notification delay d

D - maximum acceptable time delay

N_t = Y_t,0 + sum_d=1^D Y_t,d

Y_0,t is known forall t

If T is today, Y_t,d is unknown for all (t,d) such that t+d > T

Contributtors: Claudia T Codeço and Marcelo F C Gomes

Value

Function apply.leos.method returns a list containing the following components:

estimated.data.frame	Data frame containing the weekly aggregate of df.in, plus columns with estimate mean, quantiles 2.5%, 50% and 97.5% and other relevant info
delay.cutoff	Data frame with Dmax obtained for each locality, epiyearweek used as cutoff and execution date
estimated.epiyearweek.list	List of estimated epidemiological weeks
requested.epiyearweek.list	List of epidemiological weeks requested
call	Function call

Author(s)

Marcelo F C Gomes [e-mail]

Examples

data(opportunity.example.data)
epiyearweek.list <- c('2014W30', '2014W31', '2014W32', '2014W33')
res <- recursively.apply.leos.method(opportunity.example.data,
 epiyearweek.list=epiyearweek.list, quantile.target=0.95)

Opportunity-Estimator-EpiSurveillance/leos.opportunity.estimator documentation built on Jan. 23, 2021, 6:49 p.m.