syndromicW: Create an object of the class 'syndromicW' from pre-cleaned...

In nandadorea/vetsyn: Tools for Syndromic Surveillance Implementation

Create an object of the class syndromicW from pre-cleaned data.

Description

Syndromic is the main class of the package. Two versions are available, syndromicD, which is intended for use when data are to be monitored daily, and syndromicW, which is to be used when data are monitored weekly.

Usage

syndromicW(observed, dates = data.frame(), min.week = NULL,
  max.week = NULL, min.year = NULL, max.year = NULL,
  baseline = matrix(nrow = 0, ncol = 0), alarms = array(dim = 0),
  UCL = array(dim = 0), LCL = array(dim = 0), formula = list())

Arguments

observed	A matrix with the observed data
dates	A data.frame with the complete ISOweeks of of each time point in the first column (each row in the matrix provided in observed).
min.week	Alternative to providing dates: the user can specify the minimum week-year, and the maximum week-year, and the function will generate a complete sequence of weeks between them. This is the recommended use of the function because then additional date variables will also be created and assigned to the slot dates, such as ISOweek, year and numerical weeks. Note that the sequence must match the number of rows in the matrix observed.
max.week	see min.week above
min.year	see min.week above
max.year	see min.week above
baseline	Optional argument. A matrix of same dimensions as observed, containing observed data that has been pre-processed to remove excessive noise and outbreak signals retrospectively, generating an "outbreak-free baseline". Normally syndromic objects are created without this slot, receiving by default an empty matrix. Methods within this package are then used to create this slot from data on observed.
alarms	Optional argument. An array with the same number of rows and columns as observed, with an additional dimension to store the alarm output of multiple detection algorithms used. Normally syndromic objects are created without this slot, receiving by default an empty array. Methods within this package are then used to create this slot from data on observed.
UCL	Optional argument. An array with the same number of rows and columns as observed, with an additional dimension to store the upper control limit output of multiple detection algorithms used. Normally syndromic objects are created without this slot, receiving by default an empty array. Methods within this package are then used to create this slot from data on observed.
LCL	Lower control limit. See UCL above.
formula	A formula, or list of formulas, specifying the regression formula to be used when removing temporal patterns from each of the syndromes in @observed. For instance formula=list(y~dow+mon) for a single syndrome, where regression must take into account the variables dow (day-of-week) and month; or formula=c(y~dow, y~dow+mon) specifying two different formulas for two syndromes. The names of the variables given should exist in the columns of the slot @dates. Make sure that formulas' index match the columns in observed (for instance the second formula should correspond to the second syndrome, or second column in the observed matrix).You can provide NA for syndromes which should not be associated with any formula. This parameter is often only filled after some analysis in the data, not at the time of object creation.

Details

The observed data are assumed to be formatted as a matrix, in which each row corresponds to an observation time point (here, WEEKS), columns correspond to each syndromic group to be monitored, and the numbers refer to the number of observatiosn per group per time point. For an example of data formatted this way use date(observedW). For data not formatted use directly the function raw_to_syndromicW.

The dates are expected to be a data.frame with the first column in the ISOweek format, though the function will also accept a minimum and maximum week, and take care of constructing the appropriate data frame (this is the recommended use).

Value

an object of the class syndromicW with the slots corresponding to the parameters described. See class-syndromic for more details.

Examples

data(observedW)
my.syndromicW <- syndromicW(observed,min.week=1, min.year=2011, 
                              max.week=22, max.year=2013)

nandadorea/vetsyn documentation built on April 30, 2022, 1:15 a.m.