USER'S GUIDE - Biosignal Analysis and Medical Imaging Group
USER'S GUIDE - Biosignal Analysis and Medical Imaging Group USER'S GUIDE - Biosignal Analysis and Medical Imaging Group
3.3. Nonlinear methods 280−0.5−1log C m (r)−1.5−2D 2−2.5−3−1.4 −1.2 −1 −0.8 −0.6 −0.4log rFigure 3.3: Approximation of the correlation dimension D 2 from the (log r, log C m (r)) plot.which is the so-called correlation integral. The correlation dimension D 2 is defined as thelimit valuelog C m (r)D 2 (m) = lim lim. (3.21)r→0 N→∞ log rIn practice this limit value is approximated by the slope of the regression curve(log r, log C m (r)) [17]. The slope is calculated from the linear part of the log-log plot,see Fig. 3.3. The slope of the regression curves tend to saturate on the finite value of D 2when m is increased. In the software, a value of m = 10 was selected for the embedding.3.3.6 Recurrence plot analysisYet another approach, included in the software, for analyzing the complexity of the timeseries is the so-called recurrence plot (RP) analysis. In this approach, vectorsu j =(RR j , RR j+τ ,...,RR j+(m−1)τ ), j =1, 2,...,N − (m − 1)τ (3.22)where m is the embedding dimension and τ the embedding lag. The vectors u j then representthe RR interval time series as a trajectory in m dimensional space. A recurrence plot is asymmetrical [N − (m − 1)τ] × [N − (m − 1)τ] matrix of zeros and ones. The element inthe j’th row and k’th column of the RP matrix, i.e. RP(j,k), is 1 if the point u j on thetrajectory is close to point u k .ThatisRP(j, k) ={1, d(uj − u k ) ≤ r0, otherwise(3.23)where d(u j ,u k ) is the Euclidean distance given in (3.19) andr is a fixed threshold. Thestructure of the RP matrix usually shows short line segments of ones parallel to the maindiagonal. The lengths of these diagonal lines describe the duration of which the two pointsare close to each other. An example RP for HRV time series is presented in Fig. 3.4.Kubios HRV Analysisversion 2.0 betaBiosignal Analysis and Medical Imaging GroupDepartment of PhysicsUniversity of Kuopio, FINLAND
3.3. Nonlinear methods 29987Time (min)6543211 2 3 4 5 6 7 8 9Time (min)Figure 3.4: Recurrence plot matrix for HRV time series (black = 1 and white = 0).Methods for quantifying recurrence plots were proposed in [47]. The methods included inthis software are introduced below.In the software the following selections were made. The embedding dimension and lagwere selected to be m =10andτ = 1, respectively. The threshold distance r was selectedto be √ m SD, where SD is the standard deviation of the RR time series. The selection aresimilar to those made in [7].The first quantitative measure of RP is the recurrence rate (REC) which is simply theratio of ones and zeros in the RP matrix. The number of elements in the RP matrix forτ =1isequaltoN − m + 1 and the recurrence rate is simply given asN−m+11 ∑REC =(N − m +1) 2 RP(j, k). (3.24)The recurrence rate can also be calculated separately for each diagonal parallel to the lineof-identity(main diagonal). The trend of REC as a function of the time distance betweenthese diagonals and the line-of-identity describes the fading of the recurrences for pointsfurther away.The rest of the RP measures consider the lengths of the diagonal lines. A thresholdl min = 2 is used for excluding the diagonal lines formed by tangential motion of the trajectory.The maximum line length is denoted l max and its inverse, the divergence,DIV = 1(3.25)l maxhas been shown to correlate with the largest positive Lyapunov exponent [46]. The averagej,k=1diagonal line length, on the other hand, is obtained asl mean =∑ lmaxl=l minlN l∑ lmaxl=l minN l(3.26)Kubios HRV Analysisversion 2.0 betaBiosignal Analysis and Medical Imaging GroupDepartment of PhysicsUniversity of Kuopio, FINLAND
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3.3. Nonlinear methods 280−0.5−1log C m (r)−1.5−2D 2−2.5−3−1.4 −1.2 −1 −0.8 −0.6 −0.4log rFigure 3.3: Approximation of the correlation dimension D 2 from the (log r, log C m (r)) plot.which is the so-called correlation integral. The correlation dimension D 2 is defined as thelimit valuelog C m (r)D 2 (m) = lim lim. (3.21)r→0 N→∞ log rIn practice this limit value is approximated by the slope of the regression curve(log r, log C m (r)) [17]. The slope is calculated from the linear part of the log-log plot,see Fig. 3.3. The slope of the regression curves tend to saturate on the finite value of D 2when m is increased. In the software, a value of m = 10 was selected for the embedding.3.3.6 Recurrence plot analysisYet another approach, included in the software, for analyzing the complexity of the timeseries is the so-called recurrence plot (RP) analysis. In this approach, vectorsu j =(RR j , RR j+τ ,...,RR j+(m−1)τ ), j =1, 2,...,N − (m − 1)τ (3.22)where m is the embedding dimension <strong>and</strong> τ the embedding lag. The vectors u j then representthe RR interval time series as a trajectory in m dimensional space. A recurrence plot is asymmetrical [N − (m − 1)τ] × [N − (m − 1)τ] matrix of zeros <strong>and</strong> ones. The element inthe j’th row <strong>and</strong> k’th column of the RP matrix, i.e. RP(j,k), is 1 if the point u j on thetrajectory is close to point u k .ThatisRP(j, k) ={1, d(uj − u k ) ≤ r0, otherwise(3.23)where d(u j ,u k ) is the Euclidean distance given in (3.19) <strong>and</strong>r is a fixed threshold. Thestructure of the RP matrix usually shows short line segments of ones parallel to the maindiagonal. The lengths of these diagonal lines describe the duration of which the two pointsare close to each other. An example RP for HRV time series is presented in Fig. 3.4.Kubios HRV <strong>Analysis</strong>version 2.0 beta<strong>Biosignal</strong> <strong>Analysis</strong> <strong>and</strong> <strong>Medical</strong> <strong>Imaging</strong> <strong>Group</strong>Department of PhysicsUniversity of Kuopio, FINLAND