syndromicD-function | R Documentation |
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.The observed data are assumed to be formatted as a matrix
, in
which each row corresponds to an observation time point (DAYS),
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(observed). For data
not formatted use directly the function "raw_to_syndromicD".
syndromicD(observed, dates = data.frame(), min.date = NULL, max.date = NULL, date.format = "%d/%m/%Y", weekends = TRUE, baseline = matrix(nrow = 0, ncol = 0), alarms = array(dim = 0), UCL = array(dim = 0), LCL = array(dim = 0), formula = list())
observed |
A |
dates |
A |
min.date |
Alternative to providing dates: the user can specify the
minimum date, and the maximum date, and the function will generate
a complete sequence of days 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 day of the week, month, year,
is.weekend, etc. Note that the sequence must match the number of rows
in the matrix |
max.date |
see min.date above |
date.format |
The date.format of the min.date and max.date provided. Default is d/m/Y. See strptime() for format specifications. |
weekends |
An optional argument, by default set to TRUE, meaning weekends will be included in the sequence of dates generated. If observed data refers to weekdays only, then weekends should be set to FALSE, and weekends wil be removed. |
baseline |
Optional argument. A |
alarms |
Optional argument. An |
UCL |
Optional argument. An |
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. |
The dates are expected to be a data.frame
with the first column
in the dates
format, though the function will also accept a
minimum and maximum date, and take care of constructing the appropriate
data frame (this is the recommended use).
an object of the class syndromicD
with the slots
corresponding to the parameters described. See class-syndromicD
for more details.
## Load data data(observed) my.syndromicD <- syndromicD(observed[1:5,]) my.syndromicD <- syndromicD(observed[1:5,],min.date="01/01/2010",max.date="05/01/2010") my.syndromicD <- syndromicD(observed[1:6,],min.date="01/01/2010",max.date="08/01/2010", weekends=FALSE) dates = seq(from=as.Date("01/01/2010",format ="%d/%m/%Y" ), to=as.Date("05/01/2010",format ="%d/%m/%Y" ), by="days") my.syndromicD <- syndromicD(observed[1:5,],dates=dates)
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