earsC: Surveillance for a count data time series using the EARS C1,...

In surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Surveillance for a count data time series using the EARS C1, C2 or C3 method and its extensions

Description

The function takes range values of the surveillance time series sts and for each time point computes a threshold for the number of counts based on values from the recent past. This is then compared to the observed number of counts. If the observation is above a specific quantile of the prediction interval, then an alarm is raised. This method is especially useful for data without many historic values, since it only needs counts from the recent past.

Usage

earsC(sts, control = list(range = NULL, method = "C1",
                          baseline = 7, minSigma = 0,
                          alpha = 0.001))

Arguments

sts

object of class sts (including the observed and the state time series) , which is to be monitored.

control

Control object range Specifies the index in the sts object of all the timepoints which should be monitored. If range is NULL the maximum number of possible timepoints is used (this number depends on the method chosen): C1 all timepoints from the observation with index baseline + 1 can be monitored, C2 timepoints from index baseline + 3 can be monitored, C3 timepoints starting from the index baseline + 5 can be monitored. method String indicating which method to use: "C1" for EARS C1-MILD method (Default), "C2" for EARS C2-MEDIUM method, "C3" for EARS C3-HIGH method. See Details for further information about the methods. baseline how many time points to use for calculating the baseline, see details minSigma By default 0. If minSigma is higher than 0, for C1 and C2, the quantity zAlpha * minSigma is then the alerting threshold if the baseline is zero. Howard Burkom suggests using a value of 0.5 or 1 for sparse data. alpha An approximate (two-sided) (1-\alpha)\cdot 100\% prediction interval is calculated. By default if alpha is NULL the value 0.001 is assumed for C1 and C2 whereas 0.025 is assumed for C3. These different choices are the one made at the CDC.

Details

The three methods are different in terms of baseline used for calculation of the expected value and in terms of method for calculating the expected value:

• in C1 and C2 the expected value is the moving average of counts over the sliding window of the baseline and the prediction interval depends on the standard derivation of the observed counts in this window. They can be considered as Shewhart control charts with a small sample used for calculations.

• in C3 the expected value is based on the sum over 3 timepoints (assessed timepoints and the two previous timepoints) of the discrepancy between observations and predictions, predictions being calculated with the C2 method. This method has similarities with a CUSUM method due to it adding discrepancies between predictions and observations over several timepoints, but is not a CUSUM (sum over 3 timepoints, not accumulation over a whole range), even if it sometimes is presented as such.

Here is what the function does for each method, see the literature sources for further details:

1. For C1 the baseline are the baseline (default 7) timepoints before the assessed timepoint t, t-baseline to t-1. The expected value is the mean of the baseline. An approximate (two-sided) (1-\alpha)\cdot 100\% prediction interval is calculated based on the assumption that the difference between the expected value and the observed value divided by the standard derivation of counts over the sliding window, called C_1(t), follows a standard normal distribution in the absence of outbreaks:

   C_1(t)= \frac{Y(t)-\bar{Y}_1(t)}{S_1(t)},

   where

   \bar{Y}_1(t)= \frac{1}{\code{baseline}} \sum_{i=t-1}^{t-\code{baseline}} Y(i)

   and

   S^2_1(t)= \frac{1}{6} \sum_{i=t-1}^{t-\code{baseline}} [Y(i) - \bar{Y}_1(i)]^2.

   Then under the null hypothesis of no outbreak,

   C_1(t) \mathcal \> \sim \> {N}(0,1)

   An alarm is raised if

   C_1(t)\ge z_{1-\alpha}

   with z_{1-\alpha} the (1-\alpha)^{th} quantile of the standard normal distribution.
   

   The upperbound U_1(t) is then defined by:

   U_1(t)= \bar{Y}_1(t) + z_{1-\alpha}S_1(t).

2. C2 is very similar to C1 apart from a 2-day lag in the baseline definition. In other words the baseline for C2 is baseline (Default: 7) timepoints with a 2-day lag before the monitored timepoint t, i.e. (t-\code{baseline}-2) to t-3. The expected value is the mean of the baseline. An approximate (two-sided) (1-\alpha)\cdot 100\% prediction interval is calculated based on the assumption that the difference between the expected value and the observed value divided by the standard derivation of counts over the sliding window, called C_2(t), follows a standard normal distribution in the absence of outbreaks:

   C_2(t)= \frac{Y(t)-\bar{Y}_2(t)}{S_2(t)},

   where

   \bar{Y}_2(t)= \frac{1}{\code{baseline}} \sum_{i=t-3}^{t-\code{baseline}-2} Y(i)

   and

   S^2_2(t)= \frac{1}{\code{baseline}-1} \sum_{i=t-3}^{t-\code{baseline}-2} [Y(i) - \bar{Y}_2(i)]^2.

   Then under the null hypothesis of no outbreak,

   C_2(t) \mathcal \sim {N}(0,1)

   An alarm is raised if

   C_2(t)\ge z_{1-\alpha},

   with z_{1-\alpha} the (1-\alpha)^{th} quantile of the standard normal distribution.
   

   The upperbound U_{2}(t) is then defined by:

   U_{2}(t)= \bar{Y}_{2}(t) + z_{1-\alpha}S_{2}(t).

3. C3 is quite different from the two other methods, but it is based on C2. Indeed it uses C_2(t) from timepoint t and the two previous timepoints. This means the baseline consists of the timepoints t-(\code{baseline}+4) to t-3. The statistic C_3(t) is the sum of discrepancies between observations and predictions.

   C_3(t)= \sum_{i=t}^{t-2} \max(0,C_2(i)-1)

   Then under the null hypothesis of no outbreak,

   C_3(t) \mathcal \sim {N}(0,1)

   An alarm is raised if

   C_3(t)\ge z_{1-\alpha},

   with z_{1-\alpha} the (1-\alpha)^{th} quantile of the standard normal distribution.
   

   The upperbound U_3(t) is then defined by:

   U_3(t)= \bar{Y}_2(t) + S_2(t)\left(z_{1-\alpha}-\sum_{i=t-1}^{t-2} \max(0,C_2(i)-1)\right).

Value

An object of class sts with the slots upperbound and alarm filled by the chosen method.

Author(s)

M. Salmon, H. Burkom

Source

Fricker, R.D., Hegler, B.L, and Dunfee, D.A. (2008). Comparing syndromic surveillance detection methods: EARS versus a CUSUM-based methodology, 27:3407-3429, Statistics in medicine.

Salmon, M., Schumacher, D. and Höhle, M. (2016): Monitoring count time series in R: Aberration detection in public health surveillance. Journal of Statistical Software, 70 (10), 1-35. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.18637/jss.v070.i10")}

Examples

#Sim data and convert to sts object
disProgObj <- sim.pointSource(p = 0.99, r = 0.5, length = 208, A = 1,
                              alpha = 1, beta = 0, phi = 0,
                              frequency = 1, state = NULL, K = 1.7)
stsObj <- disProg2sts( disProgObj)


# Call earsC function and show result
res1 <- earsC(stsObj, control = list(range = 20:208, method="C1"))
plot(res1, legend.opts=list(horiz=TRUE, x="topright"))


# Compare C3 upperbounds depending on alpha
res3 <- earsC(stsObj, control = list(range = 20:208,method="C3",alpha = 0.001))
plot(upperbound(res3), type='l')
res3 <- earsC(stsObj, control = list(range = 20:208,method="C3"))
lines(upperbound(res3), col='red')

surveillance documentation built on Nov. 4, 2024, 3 a.m.