Description Usage Arguments Details Value Author(s) Examples
get.incidence
is a generic function with a method for
Date
, obkData, obkSequences and
obkContacts objects. In obkSequences and
obkContacts objects, it uses collection/occurence dates
to derive incidence data. In obkData, more options are
available as different types of information can be used. The procedure
looks for a time-stamped data with a given named field, and as an
option allows for selecting specific dates based on the values of that
field, provided as a range (numeric data), a list of retained values,
or a regular expression. This allows for defining 'positives' in a
flexible way.
In all procedures, one can specify the first and last date, as well as the time interval to be used.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | get.incidence(x, ...)
## S4 method for signature 'Date'
get.incidence(x, from=NULL, to=NULL,
interval=1, add.zero=TRUE, ...)
## S4 method for signature 'obkSequences'
get.incidence(x, from=NULL, to=NULL,
interval=1, add.zero=TRUE, ...)
## S4 method for signature 'obkContacts'
get.incidence(x, from=NULL, to=NULL,
interval=1, add.zero=TRUE, ...)
## S4 method for signature 'obkData'
get.incidence(x, data, where=NULL,
val.min=NULL, val.max=NULL, val.kept=NULL, regexp=NULL,
from=NULL, to=NULL,
interval=1, add.zero=TRUE, ...)
|
x |
an input object to seek incidence from. |
from |
the first date to be considered, in |
to |
the last date to be considered, in |
interval |
the time interval to be used to computed incidence, in number of days. |
add.zero |
a logical indicating if a zero should be added at the end of the output. |
data |
a character string indicating the name of the data field
to look for, as in |
where |
an optional character string indicating the where the
data field should be looked for, as in |
val.min |
an optional numeric value indicating the minimum value of the data to be retained in the incidence (e.g. minimum body temperature). |
val.max |
an optional numeric value indicating the maximum value of the data to be retained in the incidence (e.g. maximum CD4 counts). |
val.kept |
an optional vector containing all values to be retained in the incidence. |
regexp |
an optional character string providing a regular expression to be used to select which data are used in the incidence. |
... |
further arguments to be passed to 'grep', for the obkData procedure. |
Incidence is computed for intervals (\[D1;D2\[) which are named after the first date (D1), including the first date, and excluding the second one (D2).
A data.frame with two columns, the first one being dates in the
Date
format, and the second being integers giving the incidence
(number of new items for that date).
Thibaut Jombart t.jombart@imperial.ac.uk.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ## SIMPLE EXAMPLE ##
dates <- as.Date("2001-01-01") + c(0,1,2,1,1,4)
get.incidence(dates)
get.incidence(dates, interval=2)
get.incidence(dates, interval=2, from="2001-01-03")
## OBKDATA/OBKCONTACTS/OBKSEQUENCES OBJECTS ##
data(ToyOutbreak)
## incidence of DNA sequences collection
get.incidence(ToyOutbreak, "dna")
plot(get.incidence(ToyOutbreak, "dna"), type="s",
main="Incidence of DNA sequences collection")
## incidence of contacts
get.incidence(ToyOutbreak, "contacts")
plot(get.incidence(ToyOutbreak, "contacts"), type="s",
main="Incidence of contact occurence")
## incidence of temperature measurements
get.incidence(ToyOutbreak, "temperature")
## same, keeping temperatures above 39
get.incidence(ToyOutbreak, "temperature", val.min=39)
plot(get.incidence(ToyOutbreak, "temperature", val.min=39),
type="s", main="Incidence: temperature>=39")
## same, temperature>40, interval=2days
inc <- get.incidence(ToyOutbreak, "temperature", val.min=40, interval=2)
plot(inc, type="s", main="Incidence: temperature>=40")
|
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