syndromic_alarm-methods: 'syndromic_alarm'

In nandadorea/vetsyn: Tools for Syndromic Surveillance Implementation

syndromic_alarm

Description

A simple command to generate an alarm around a syndromic (syndromicD or syndromicW) object - the user can generate automated e-mails and also generate a pdf report of all syndromes in a syndromic object, or only those for which an alarm was generated.

Usage

syndromic_alarm(x, ...)

## S4 method for signature 'syndromicD'
syndromic_alarm(x, pdf.report = TRUE,
  email.alarm.to = NULL, email.noalarm.to = NULL, date = NULL,
  plot.all = FALSE, window = 365, baseline = TRUE, UCL = 1,
  algorithms = NULL, limit = 1, email.from = NULL, smtpServer = NULL,
  subject = paste((Sys.Date()), "ALARM: There are alarms today", sep = ","),
  message = NULL, height = 7.5, width = 10.5, pdf.dir = TRUE,
  file.name = NULL)

## S4 method for signature 'syndromicW'
syndromic_alarm(x, pdf.report = TRUE,
  email.alarm.to = NULL, email.noalarm.to = NULL, date = NULL,
  plot.all = FALSE, window = 52, baseline = TRUE, UCL = 1,
  algorithms = NULL, limit = 1, email.from = NULL, smtpServer = NULL,
  subject = paste((Sys.Date()), "ALARM: There are alarms today", sep = ","),
  message = NULL, height = 7.5, width = 10.5, pdf.dir = TRUE,
  file.name = NULL)

Arguments

x	a syndromic (syndromicD or syndromicW) object.
...	Additional arguments to the method.
pdf.report	default is TRUE, that is, a pdf report will be generated.
email.alarm.to	email recipient(s) for when an alarm is detected. If a pdf report has been generated, it will be attached to the email. See examples for e-mail formats. Multiple e-mails should be separated by commas. If set to NULL, no e-mail will be generated.
email.noalarm.to	email recipient(s) for when NO alarm is detected. This is used so that a recipient can be warned that the calculations were performed and finished successfully, but no alarm was generated (for control that the system actuall ran with no problems). See examples for e-mail formats. Multiple e-mails should be separated by commas. If set to NULL, no e-mail will be generated.
date	by default (NULL) it looks up alarms in the last date saved in the syndromic object, but the user can set past dates in order to plot historical alarms. Dates must be provided in the same format as they are stored in dates, that is, for syndromicD objects, in the format "yyyy-mm-dd" (for instance "2013-12-31"); and for syndromicW in the ISOweek format (for instance "2014-W01-2")
plot.all	by default, only syndromes associated with an alarm are plotted (plot.all=FALSE), but the user can set plot.all=TRUE to plot all syndromes found in the syndromic object.
window	the number of time points to plot, always finishing at the last time point recorded, or the date specified in the parameter "date" above.
baseline	whether to plot the baseline, by default equal to TRUE.
UCL	the dimension of the slot UCL, from the syndromic object, from which the user wants to plot the UCL. Set to NULL or to 0 if it is not desired to plot the UCL.
algorithms	an optional parameter specifying which dimensions of the alarms slot to plot and sum for a final alarm score. If not specified (NULL), all are plotted. If set to zero, none are plotted.
limit	the parameter specifying the limit above which alarms are considered meaningful. Only important if the user has specified that only syndromes with an alarm are to be plotted. Remember that this is not a statistical value, but the sum of the scores of each individual detection algorithm. If for instance the syndromic object has been subjected to detection using a holt_winters_synd algorithm with 3 alarm detection limits, and an ewma_synd algorithm with 3 alarm detection limits, than the maximum alarm score is 6. The limit parameter establishes the minimum value (in this 0-6 scale) that in considered an alarm. By default 1 is used. It can be provided as a single value (if all syndromes are to have the same limit) or as a vector with length equal to the number of syndromes in use (number of columns in the slot observed)
email.from	e-mail client to use when sending alarms, if left as NULL, the default email in the package mail will be used, but it doesn't support attachments (email will be sent without a pdf report attachment). For emails with attachment, please install and load the package "sendmailR", and see smtpServer set up below.
smtpServer	to be used as control prameter in the mail sending function. The smtpServer for the email client provided as the "email.from" above. If left as NULL, the default email in the package mail will be used, but it doesn't support attachments (email will be sent without a pdf report attachment).
subject	the subject in the email in case of alarms. By default it's the system date, plus the text "ALARM: There are alarms today"
message	any message that the user wants to add to the body of the email generated in case of alarm. This will be added to the default message, which is the name of the syndromes which generated an alarm.
height	in inches, for the pdf page. The default (7.5) fits well a letter or A4 page.
width	the width, in inches, if a pdf file is to be generated.
pdf.dir	whether to create (or use) a directory called "PDF_reports" within the current working directory, to save the files. If set to FALSE, the current working directory is used. The current working directory is not changed by using the function.
file.name	an optional text to add to the date being evaluated, as the name of the file to be saved.
height	in inches, for the pdf page. The default (10.5) fits well a letter or A4 page.
height	the height, in inches, if a pdf file is to be generated.

Details

Emails can be sent from the R interface (without attachments). For email attachments, the package "sendmailR" should be installed and loaded.

Examples

data(lab.daily)
my.syndromicD <- raw_to_syndromicD (id=SubmissionID,
                                 syndromes.var=Syndrome,
                                 dates.var=DateofSubmission,
                                 date.format="%d/%m/%Y",
                                 remove.dow=c(6,0),
                                 add.to=c(2,1),
                                 data=lab.daily)
my.syndromicD <- holt_winters_synd(x=my.syndromicD,
                                evaluate.window=30,
                                frequency=5,
                                baseline.window=260)
                                
syndromic_alarm(x=my.syndromicD,
               plot.all=TRUE,
               email.alarm.to="<[e-mail]>",
               email.noalarm.to="<[e-mail]>")

## WEEKLY
data(lab.daily)
my.syndromicW <- raw_to_syndromicW (id=SubmissionID,
                                 syndromes.var=Syndrome,
                                 dates.var=DateofSubmission,
                                 date.format="%d/%m/%Y",
                                 data=lab.daily)
my.syndromicW <- ewma_synd(x=my.syndromicW,
                          evaluate.window=10,
                          limit.sd=c(2.5,3,3.5),
                          pre.process="diff",
                          diff.window=4)
                          
syndromic_alarm(x=my.syndromicW,
               plot.all=TRUE,
               email.alarm.to="<[e-mail]>",
               email.noalarm.to="<[e-mail]>")
                              

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