syndromic_page-methods: 'syndromic_page'

In nandadorea/vetsyn: Tools for Syndromic Surveillance Implementation

syndromic_page

Description

A simple command to generate an html page that summarizes the current state of a syndromic (syndromicD or syndromicW) object. A "html" folder is created (or used if already existing) into the current working directory.

Usage

syndromic_page(x, ...)

## S4 method for signature 'syndromicD'
syndromic_page(x, tpoints.display = 7, window = 365,
  baseline = TRUE, UCL = 1, algorithms = NULL, limit = 1,
  file.name = "my.syndromic", title = "My syndromic", data.page = FALSE,
  data = NULL, date.format = "%d/%m/%Y", dates.var = NULL,
  syndromes.var = NULL, color.null = "F8F8FF", color.low = "F8FF2F",
  color.alarm = "FF0000", scale = 9, fill.colors = c("yellow2", "orange",
  "tomato"), arrow.colors = c("green", "orange", "tomato", "red"))

## S4 method for signature 'syndromicW'
syndromic_page(x, tpoints.display = 4, window = 52,
  baseline = TRUE, UCL = 1, algorithms = NULL, limit = 1,
  file.name = "my.syndromic", title = "My syndromic", data.page = FALSE,
  data = NULL, date.format = "ISOweek", dates.var = NULL,
  syndromes.var = NULL, color.null = "F8F8FF", color.low = "F8FF2F",
  color.alarm = "FF0000", scale = 9, fill.colors = c("yellow2", "orange",
  "tomato"), arrow.colors = c("green", "orange", "tomato", "red"))

Arguments

x	a syndromic (syndromicD or syndromicW) object.
...	Additional arguments to the method.
tpoints.display	This is used to choose how many days of alarms to display. The normal for daily data (syndromic object provided is form the class syndromicD ) is to show the entire last week (so 7 or 5 days, depending on whether weekends are included). For weekly data the user my choose for instance 4 weeks (one month). The user can set this number to any desired number of days to tabulate.
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 alarm 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 his 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)
file.name	an optional text to add to the date being evaluated, as the name of the file to be saved.
title	a tile for the html page. If not given the value in "file.name" is used.
data.page	the user should specify whether the plots should also provide a link to the original data, so that page viewers can inspect the original data. If using TRUE, the original data must be provided in the argument "data".
data	the original data to tabulate in case "data.page" has been set to TRUE.
date.format	the date format in the original data, if provided in the previous argument. For WEEKLY data, the original data may have been recorded daily or weekly (see rawD_to_syndromicW and rawW_to_syndromicW). If theoriginal date are recorded daily, please indicate the date.format. If the original data are recorded weekly, remember that the date format MUST be ISOweek, and for date.format please provide the value "ISOweek". See examples.
dates.var	the variable (column) in data to look for dates, in order to find the data from last week.
syndromes.var	the variable (column) in data to match to the syndromes found in the slot observed
color.null	a color for the table of alarms, used in cells giving the number of syndromic events which corresponded to NO alarm.
color.low	a color for the table of alarms, used in cells giving the number of syndromic events which generated an alarm score higher than 0, but lower than the limit for alarms.
color.alarm	a color for the table of alarms, used in cells giving the number of syndromic events which corresponded to an alarm.
scale	the maximum possible score (scale of alarms). Based on the number of detection algorithms used, and the number of detection limits set to each (3 algorithms with 5 detection limits for each, for instance, will give a scale of 15)
fill.colors	the colors to be used for the 3 degrees of alarm. By default they are yellow, orange and light red (tomato).
arrow.colors	the colors of the arrow for varying levels of alarm. By default green is used when the score is zero, and a progressive scale is used for increasing scores: orange, tomato and red.

Examples

##DAILY data
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_page (x=my.syndromicD,
                tpoints.display=5,
                file.name="SpeciesX",
                title="Lab data daily for Species X",
                data.page=TRUE,
                data=lab.daily,
                date.format="%d/%m/%Y",
                dates.var="DateofSubmission",
                syndromes.var="Syndrome",
                scale=9)        
##WEEKLY    
data(lab.weekly)
my.syndromicW <- raw_to_syndromicW (id=lab.weekly$SubmissionID,
                                  syndromes.var=lab.weekly$Syndrome,
                                  week.var=lab.weekly$DateofSubmission)
                                  
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_page (x=my.syndromicW,
                tpoints.display=4,
                file.name="SpeciesX",
                title="Lab data daily for Species X",
                data.page=TRUE,
                data=lab.weekly,
                date.format="ISOweek",
                dates.var="DateofSubmission",
                syndromes.var="Syndrome",
                scale=9)     
data(lab.daily)
my.syndromicW2 <- raw_to_syndromicW (id=SubmissionID,
                                 syndromes.var=Syndrome,
                                 dates.var=DateofSubmission,
                                 date.format="%d/%m/%Y",
                                 data=lab.daily)
my.syndromicW2 <- ewma_synd(x=my.syndromicW2,
                          evaluate.window=10,
                          limit.sd=c(2.5,3,3.5),
                          pre.process="diff",
                          diff.window=4)
syndromic_page(x=my.syndromicW2,
                tpoints.display=4,
                file.name="SpeciesX",
                title="Lab data daily for Species X",
                data.page=TRUE,
                data=lab.daily,
                date.format="%d/%m/%Y",
                dates.var="DateofSubmission",
                syndromes.var="Syndrome",
                scale=9) 

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