Classification Trees and Regression Trees

On this page What Are Classification Trees and Regression Trees? Example: Creating a Classification Tree Example: Creating a Regression Tree Viewing a Tree How the Fit Methods Create Trees redicting Responses With Classification Trees and Regression Trees !mpro"ing Classification Trees and Regression Trees Alternati"e: classregtree

What Are Classification Trees and Regression Trees?

Classification trees and regression trees predict responses to data# To predict a response$ follow the decisions in the tree from the root %&eginning' node down to a leaf node# The leaf node contains the response# Classification trees gi"e responses that are nominal$ s(ch as 'true' or 'false'# Regression trees gi"e n(meric responses# )tatistics Tool&ox trees are &inar*# Each step in a prediction in"ol"es chec+ing the "al(e of one predictor %"aria&le'# For example$ here is a simple classification tree:

This tree predicts classifications &ased on two predictors$ x1 and x2# To predict$ start at the top node$ represented &* a triangle %,'# The first decision is whether x1 is smaller than 0.5# !f so$ follow the left &ranch$ and see that the tree classifies the data as t*pe 0# !f$ howe"er$ x1 exceeds 0.5$ then follow the right &ranch to the lower-right triangle node# Here the tree as+s if x2 is smaller than 0.5# !f so$ then follow the left &ranch to see that the tree classifies the data as t*pe 0# !f not$ then follow the right &ranch to see that the that the tree classifies the data as t*pe 1#

To learn how to prepare *o(r data for classification or regression (sing decision trees$ see )teps in )(per"ised .earning %Machine .earning'# /ac+ to Top

Example: Creating a Classification Tree

To create a classification tree for the ionosphere data:
load ionosphere % contains X and Y variables ctree = ClassificationTree.fit X!Y" ctree = ClassificationTree# $redictor%a&es# Cate+orical$redictors# .esponse%a&e# Class%a&es# /coreTransfor&# %0bservations# '1x() cell* ,'Y' ''b' '+'* 'none' (51

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Example: Creating a Regression Tree

To create a regression tree for the cars&all data &ased on the 1orsepo2er and 3ei+ht "ectors for data$ and 4$5 "ector for response:
load cars&all % contains 1orsepo2er! 3ei+ht! 4$5 X = ,1orsepo2er 3ei+ht-6 rtree = .e+ressionTree.fit X!4$5" rtree = .e+ressionTree# $redictor%a&es# Cate+orical$redictors# .esponse%a&e# .esponseTransfor&# %0bservations# ''x1' 'x2'* ,'Y' 'none' 7)

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Viewing a Tree
There are two wa*s to "iew a tree:
vie2 tree" ret(rns a text description of the tree# vie2 tree!'&ode'!'+raph'" ret(rns a graphic description

of the tree#

Example: Creating a Classification Tree has the following two "iews:

load fisheriris ctree = ClassificationTree.fit &eas!species"6 vie2 ctree" 8ecision tree for classification 1 if x(92.)5 then node 2 elseif 2 class = setosa ( if x)91.;5 then node ) elseif ) if x(9).75 then node < elseif 5 class = vir+inica < if x)91.<5 then node = elseif ; class = vir+inica = class = versicolor 7 class = vir+inica vie2 ctree!'&ode'!'+raph'" x(:=2.)5 then node ( else setosa x):=1.;5 then node 5 else versicolor x(:=).75 then node ; else versicolor x):=1.<5 then node 7 else versicolor

)imilarl*$ Example: Creating a Regression Tree has the following two "iews:
load cars&all % contains 1orsepo2er! 3ei+ht! 4$5 X = ,1orsepo2er 3ei+ht-6 rtree = .e+ressionTree.fit X!4$5!'4in$arent'!(0"6 vie2 rtree" 8ecision tree for re+ression 1 if x29(0=5.5 then node 2 elseif x2:=(0=5.5 then node ( else 2(.;1=1 2 if x19=7 then node ) elseif x1:==7 then node 5 else 2=.;7(1 ( if x19115 then node < elseif x1:=115 then node ; else 15.5)1; ) if x2921<2 then node = elseif x2:=21<2 then node 7 else (0.7(;5 5 fit = 2).0==2 < fit = 17.<25 ; fit = 1).(;5 = fit = ((.(05< 7 fit = 27

vie2 rtree!'&ode'!'+raph'"

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How the it !ethods Create Trees

The ClassificationTree.fit and .e+ressionTree.fit methods perform the following steps to create decision trees: 0# )tart with all inp(t data$ and examine all possi&le &inar* splits on e"er* predictor# 1# )elect a split with &est optimi2ation criterion#

!f the split leads to a child node ha"ing too few o&ser"ations %less than the 4in>eaf parameter'$ select a split with the &est optimi2ation criterion s(&3ect to the 4in>eaf constraint#

4# !mpose the split# 5# Repeat rec(rsi"el* for the two child nodes# The explanation re6(ires two more items: description of the optimi2ation criterion$ and stopping r(le# "topping r#le: )top splitting when an* of the following hold:

The node is pure# o For classification$ a node is p(re if it contains onl* o&ser"ations of one class#

For regression$ a node is p(re if the mean s6(ared error %M)E' for the o&ser"ed response in this node drops &elow the M)E for the o&ser"ed response in the entire data m(ltiplied &* the tolerance on 6(adratic error per node %?etoler parameter'#

There are fewer than 4in$arent o&ser"ations in this node# An* split imposed on this node wo(ld prod(ce children with fewer than 4in>eaf o&ser"ations#

Optimi$ation criterion:

Regression: mean-s6(ared error %M)E'# Choose a split to minimi2e the M)E of predictions compared to the training data# Classification: 7ne of three meas(res$ depending on the setting of the /plitCriterion name-"al(e pair:
o o o '+di'

%8ini9s di"ersit* index$ the defa(lt'

't2oin+' 'deviance'

For details$ see ClassificationTree :efinitions# For a contin(o(s predictor$ a tree can split halfwa* &etween an* two ad3acent (ni6(e "al(es fo(nd for this predictor# For a categorical predictor with L le"els$ a classification tree needs to consider 1L;0;0 splits# To o&tain this form(la$ o&ser"e that *o( can assign L distinct "al(es to the left and right nodes in 1L wa*s# Two o(t of these 1L config(rations wo(ld lea"e either left or right node empt*$ and therefore sho(ld &e discarded# <ow di"ide &* 1 &eca(se left and right can &e swapped# A classification tree can th(s process onl* categorical predictors with a moderate n(m&er of le"els# A regression tree emplo*s a comp(tational shortc(t: it sorts the le"els &* the o&ser"ed mean response$ and considers onl* the L;0 splits &etween the sorted le"els# /ac+ to Top

%redicting Responses With Classification Trees and Regression Trees

After creating a tree$ *o( can easil* predict responses for new data# )(ppose Xne2 is new data that has the same n(m&er of col(mns as the original data X# To predict the classification or regression &ased on the tree and the new data$ enter
Yne2 = predict tree!Xne2"6

For each row of data in Xne2$ predict r(ns thro(gh the decisions in tree and gi"es the res(lting prediction in the corresponding element of Yne2# For more information for classification$ see the classification predict reference page= for regression$ see the regression predict reference page#

For example$ to find the predicted classification of a point at the mean of the ionosphere data:
load ionosphere % contains X and Y variables ctree = ClassificationTree.fit X!Y"6 Yne2 = predict ctree!&ean X"" Yne2 = '+'

To find the predicted 4$5 of a point at the mean of the cars&all data:
load cars&all % contains 1orsepo2er! 3ei+ht! 4$5 X = ,1orsepo2er 3ei+ht-6 rtree = .e+ressionTree.fit X!4$5"6 Yne2 = predict rtree!&ean X"" Yne2 = 2=.;7(1

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&mpro'ing Classification Trees and Regression Trees

>o( can t(ne trees &* setting name-"al(e pairs in ClassificationTree.fit and .e+ressionTree.fit# The remainder of this section descri&es how to determine the 6(alit* of a tree$ how to decide which name-"al(e pairs to set$ and how to control the si2e of a tree:

Examining Res(&stit(tion Error Cross Validation Control :epth or ?.eafiness? r(ning

Examining Res#(stit#tion Error Resubstitution error is the difference &etween the response training data and the predictions the tree ma+es of the response &ased on the inp(t training data# !f the res(&stit(tion error is high$ *o( cannot expect the predictions of the tree to &e good# Howe"er$ ha"ing low res(&stit(tion error does not g(arantee good predictions for new data# Res(&stit(tion error is often an o"erl* optimistic estimate of the predicti"e error on new data# Example: Res#(stit#tion Error of a Classification Tree) Examine the res(&stit(tion error of a defa(lt classification tree for the Fisher iris data:
load fisheriris ctree = ClassificationTree.fit &eas!species"6 resuberror = resub>oss ctree" resuberror = 0.0200

The tree classifies nearl* all the Fisher iris data correctl*# Cross Validation To get a &etter sense of the predicti"e acc(rac* of *o(r tree for new data$ cross "alidate the tree# /* defa(lt$ cross "alidation splits the training data into 0@ parts at random# !t trains 0@ new trees$ each one on nine parts of the data# !t then examines the predicti"e acc(rac* of each new tree on the data not incl(ded in training that tree# This method gi"es a good estimate of the predicti"e acc(rac* of the res(lting tree$ since it tests the new trees on new data# Example: Cross Validating a Regression Tree) Examine the res(&stit(tion and cross"alidation acc(rac* of a regression tree for predicting mileage &ased on the cars&all data:
load cars&all X = ,@cceleration 8isplace&ent 1orsepo2er 3ei+ht-6 rtree = .e+ressionTree.fit X!4$5"6 resuberror = resub>oss rtree" resuberror = ).;1==

The res(&stit(tion loss for a regression tree is the mean-s6(ared error# The res(lting "al(e indicates that a t*pical predicti"e error for the tree is a&o(t the s6(are root of 5#A$ or a &it o"er 1# <ow calc(late the error &* cross "alidating the tree:
cvrtree = crossval rtree"6 cvloss = Afold>oss cvrtree" cvloss = 2(.)=0=

The cross-"alidated loss is almost 1B$ meaning a t*pical predicti"e error for the tree on new data is a&o(t B# This demonstrates that cross-"alidated loss is (s(all* higher than simple res(&stit(tion loss# Control *epth or +,eafiness+ When *o( grow a decision tree$ consider its simplicit* and predicti"e power# A deep tree with man* lea"es is (s(all* highl* acc(rate on the training data# Howe"er$ the tree is not g(aranteed to show a compara&le acc(rac* on an independent test set# A leaf* tree tends to o"ertrain$ and its test acc(rac* is often far less than its training %res(&stit(tion' acc(rac*# !n contrast$ a shallow tree does not attain high training acc(rac*# /(t a shallow tree can &e more ro&(st C its training acc(rac* co(ld &e close to that of a representati"e test set# Also$ a shallow tree is eas* to interpret# !f *o( do not ha"e eno(gh data for training and test$ estimate tree acc(rac* &* cross "alidation# For an alternati"e method of controlling the tree depth$ see r(ning#

Example: "electing Appropriate Tree *epth) This example shows how to control the depth of a decision tree$ and how to choose an appropriate depth#
1. .oad the ionosphere data:
load ionosphere

2. 8enerate minim(m leaf occ(pancies for classification trees from 10 to 100$ spaced

exponentiall* apart:
leafs = lo+space 1!2!10"6

3. Create cross "alidated classification trees for the ionosphere data with minim(m leaf

occ(pancies from leafs: ). % = nu&el leafs"6 5. err = Beros %!1"6 <. for n=1#% ;. t = ClassificationTree.fit X!Y!'crossval'!'on'!... =. '&inleaf'!leafs n""6 7. err n" = Afold>oss t"6 10. end 11. plot leafs!err"6 12. xlabel '4in >eaf /iBe'"6 Clabel 'crossDvalidated error'"6

The &est leaf si2e is &etween a&o(t 20 and 50 o&ser"ations per leaf#
13. Compare the near-optimal tree with at least )0 o&ser"ations per leaf with the defa(lt

tree$ which (ses 10 o&ser"ations per parent node and 1 1). 8efaultTree = ClassificationTree.fit X!Y"6 vie2 8efaultTree!'&ode'!'+raph'"

o&ser"ation per leaf#

0pti&alTree = ClassificationTree.fit X!Y!'&inleaf'!)0"6 vie2 0pti&alTree!'&ode'!'+raph'"

resub0pt = resub>oss 0pti&alTree"6 loss0pt = Afold>oss crossval 0pti&alTree""6 resub8efault = resub>oss 8efaultTree"6 loss8efault = Afold>oss crossval 8efaultTree""6 resub0pt!resub8efault!loss0pt!loss8efault resub0pt = 0.0==( resub8efault = 0.011) loss0pt = 0.105) loss8efault = 0.102<

The near-optimal tree is m(ch smaller and gi"es a m(ch higher res(&stit(tion error# >et it gi"es similar acc(rac* for cross-"alidated data# %r#ning r(ning optimi2es tree depth %leafiness' is &* merging lea"es on the same tree &ranch# Control :epth or ?.eafiness? descri&es one method for selecting the optimal depth for a tree#

Dnli+e in that section$ *o( do not need to grow a new tree for e"er* node si2e# !nstead$ grow a deep tree$ and pr(ne it to the le"el *o( choose# r(ne a tree at the command line (sing the prune method %classification' or prune method %regression'# Alternati"el*$ pr(ne a tree interacti"el* with the tree "iewer:
vie2 tree!'&ode'!'+raph'"

To pr(ne a tree$ the tree m(st contain a pr(ning se6(ence# /* defa(lt$ &oth ClassificationTree.fit and .e+ressionTree.fit calc(late a pr(ning se6(ence for a tree d(ring constr(ction# !f *o( constr(ct a tree with the '$rune' name-"al(e pair set to 'off'$ or if *o( pr(ne a tree to a smaller le"el$ the tree does not contain the f(ll pr(ning se6(ence# 8enerate the f(ll pr(ning se6(ence with the prune method %classification' or prune method %regression'# Example: %r#ning a Classification Tree) This example creates a classification tree for the ionosphere data$ and pr(nes it to a good le"el#
1. .oad the ionosphere data:
load ionosphere

1# Constr(ct a defa(lt classification tree for the data:

tree = ClassificationTree.fit X!Y"6

4# View the tree in the interacti"e "iewer:

vie2 tree!'&ode'!'+raph'"

5# Find the optimal pr(ning le"el &* minimi2ing cross-"alidated loss:

5. ,E!E!E!bestlevel- = cv>oss tree!... <. 'subtrees'!'all'!'treesiBe'!'&in'" ;. =. bestlevel = < 9. r(ne the tree to le"el < in the interacti"e "iewer:

The pr(ned tree is the same as the near-optimal tree in Example: )electing Appropriate Tree :epth#
10. )et 'treesiBe' to 'se' %defa(lt' to find the maximal pr(ning le"el for which the tree
11. ,E!E!E!bestlevel- = cv>oss tree!'subtrees'!'all'" 12. 1(. bestlevel = <

error does not exceed the error from the &est le"el pl(s one standard de"iation:

!n this case the le"el is the same for either setting of 'treesiBe'# 05# r(ne the tree to (se it for other p(rposes:
15. tree = prune tree!'>evel'!<"6 vie2 tree!'&ode'!'+raph'"

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Alternati'e: classregtree
The ClassificationTree and .e+ressionTree classes are new in MAT.A/ R1@00a# re"io(sl*$ *o( represented &oth classification trees and regression trees with a classre+tree o&3ect# The new classes pro"ide all the f(nctionalit* of the classre+tree class$ and are more con"enient when (sed in con3(nction with Ensem&le Methods# /efore the classre+tree class$ there were treefit$ treedisp$ treeval$ treeprune$ and treetest f(nctions# )tatistics Tool&ox software maintains these onl* for &ac+ward compati&ilit*# Example: Creating Classification Trees -sing classregtree This example (ses Fisher9s iris data in fisheriris.&at to create a classification tree for predicting species (sing meas(rements of sepal length$ sepal width$ petal length$ and petal width as predictors# Here$ the predictors are contin(o(s and the response is categorical#
1. .oad the data and (se the classre+tree constr(ctor of the classre+tree class to

create the classification tree:

2. load fisheriris (. ). t = classre+tree &eas!species!... 5. 'na&es'!''/>' '/3' '$>' '$3'*" <. t = ;. 8ecision tree for classification =. 1 if $>92.)5 then node 2 elseif $>:=2.)5 then node ( 7. 2 class = setosa 10. ( if $391.;5 then node ) elseif $3:=1.;5 then node versicolor 11. ) if $>9).75 then node < elseif $>:=).75 then node versicolor 12. 5 class = vir+inica 1(. < if $391.<5 then node = elseif $3:=1.<5 then node versicolor 1). ; class = vir+inica 15. = class = versicolor 7 class = vir+inica

else setosa 5 else ; else 7 else

is a classre+tree o&3ect and can &e operated on with an* class method#

16. Dse the tCpe method of the classre+tree class to show the t*pe of the tree:
1;. treetCpe = tCpe t" 1=. treetCpe = 17. classification

creates a classification tree &eca(se species is a cell arra* of strings$ and the response is ass(med to &e categorical#
classre+tree

20. To "iew the tree$ (se the vie2 method of the classre+tree class:
vie2 t"

The tree predicts the response "al(es at the circ(lar leaf nodes &ased on a series of 6(estions a&o(t the iris at the triang(lar &ranching nodes# A true answer to an* 6(estion follows the &ranch to the left# A false follows the &ranch to the right#
21. The tree does not (se sepal meas(rements for predicting species# These can go

(nmeas(red in new data$ and *o( can enter them as %a% "al(es for predictions# For example$ to (se the tree to predict the species of an iris with petal length ).= and petal width 1.<$ t*pe:
22. predicted = t ,%a% %a% ).= 1.<-" 2(. predicted = 'versicolor'

The o&3ect allows for f(nctional e"al(ation$ of the form t X"# This is a shorthand wa* of calling the eval method of the classre+tree class# The predicted species is the left leaf node at the &ottom of the tree in the pre"io(s "iew#
24. >o( can (se a "ariet* of methods of the classre+tree class$ s(ch as cutvar and

to get more information a&o(t the split at node E that ma+es the final distinction &etween versicolor and vir+inica:
cuttCpe 25. 2<. 2;. 2=. 27. (0. (1. var< = cutvar t!<" % 3hat variable deter&ines the splitF var< = '$3' tCpe< = cuttCpe t!<" % 3hat tCpe of split is itF tCpe< = 'continuous'

32. Classification trees fit the original %training' data well$ &(t can do a poor 3o& of

classif*ing new "al(es# .ower &ranches$ especiall*$ can &e strongl* affected &* o(tliers# A simpler tree often a"oids o"erfitting# >o( can (se the prune method of the classre+tree class to find the next largest tree from an optimal pr(ning se6(ence:
((. (). (5. (<. (;. (=. pruned = prune t!'level'!1" pruned = 8ecision tree for classification 1 if $>92.)5 then node 2 elseif $>:=2.)5 then node ( else setosa 2 class = setosa ( if $391.;5 then node ) elseif $3:=1.;5 then node 5 else versicolor (7. ) if $>9).75 then node < elseif $>:=).75 then node ; else versicolor )0. 5 class = vir+inica )1. < class = versicolor )2. ; class = vir+inica )(. vie2 pruned"

To find the &est classification tree$ emplo*ing the techni6(es of res(&stit(tion and cross "alidation$ (se the test method of the classre+tree class# Example: Creating Regression Trees -sing classregtree This example (ses the data on cars in cars&all.&at to create a regression tree for predicting mileage (sing meas(rements of weight and the n(m&er of c*linders as predictors# Here$ one predictor %weight' is contin(o(s and the other %c*linders' is categorical# The response %mileage' is contin(o(s#
1. .oad the data and (se the classre+tree constr(ctor of the classre+tree class to

create the regression tree:

2. load cars&all (. ). t = classre+tree ,3ei+ht! CClinders-!4$5!... 5. 'cat'!2!'split&in'!20!... <. 'na&es'!''3'!'C'*" ;. =. t = 7. 10. 8ecision tree for re+ression 11. 1 if 39(0=5.5 then node 2 elseif 3:=(0=5.5 then node ( else 2(.;1=1 12. 2 if 392(;1 then node ) elseif 3:=2(;1 then node 5 else 2=.;7(1 1(. ( if C== then node < elseif C in ') <* then node ; else 15.5)1; 1). ) if 3921<2 then node = elseif 3:=21<2 then node 7 else (2.0;)1 15. 5 if C=< then node 10 elseif C=) then node 11 else 25.7(55 1<. < if 39)(=1 then node 12 elseif 3:=)(=1 then node 1( else 1).27<( 1;. ; fit = 17.2;;=

1=. = fit = ((.(05< 17. 7 fit = 27.<111 20. 10 fit = 2(.25 21. 11 if 392=2;.5 then node 1) elseif 3:=2=2;.5 then node 15 else 2;.21)( 22. 12 if 39(5((.5 then node 1< elseif 3:=(5((.5 then node 1; else 1).=<7< 2(. 1( fit = 11 2). 1) fit = 2;.<(=7 25. 15 fit = 2).<<<; 2<. 1< fit = 1<.< 1; fit = 1).(==7

is a classre+tree o&3ect and can &e operated on with an* of the methods of the class#
t

27. Dse the tCpe method of the classre+tree class to show the t*pe of the tree:
2=. treetCpe = tCpe t" 27. treetCpe = (0. re+ression

creates a regression tree &eca(se 4$5 is a n(merical "ector$ and the response is ass(med to &e contin(o(s#
classre+tree

31. To "iew the tree$ (se the vie2 method of the classre+tree class:
vie2 t"

The tree predicts the response "al(es at the circ(lar leaf nodes &ased on a series of 6(estions a&o(t the car at the triang(lar &ranching nodes# A true answer to an* 6(estion follows the &ranch to the left= a false follows the &ranch to the right# 41# Dse the tree to predict the mileage for a 1@@@-po(nd car with either 5$ E$ or F c*linders:
((. &ilea+e2G = t ,2000 )6 2000 <6 2000 =-" (). &ilea+e2G = (5. ((.(05< (<. ((.(05< ((.(05<

The o&3ect allows for f(nctional e"al(ation$ of the form t X"# This is a shorthand wa* of calling the eval method of the classre+tree class# 4A# The predicted responses comp(ted a&o"e are all the same# This is &eca(se the* follow a series of splits in the tree that depend onl* on weight$ terminating at the left-most leaf node in the "iew a&o"e# A 5@@@-po(nd car$ following the right &ranch from the top of the tree$ leads to different predicted responses:
(=. &ilea+e)G = t ,)000 )6 )000 <6 )000 =-" (7. &ilea+e)G = )0. 17.2;;= )1. 17.2;;= 1).(==7 42. >o( can (se a "ariet* of other methods of the classre+tree class$ s(ch as cutvar$ cuttCpe$ and cutcate+ories$ to get more information a&o(t the split at node 4 that

disting(ishes the F-c*linder car:

)(. )). )5. )<. );. )=. )7. 50. 51. 52. 5(. 5). 55. 5<. 5;. 5=. 57. <0. var( = cutvar t!(" % 3hat variable deter&ines the splitF var( = 'C' tCpe( = cuttCpe t!(" % 3hat tCpe of split is itF tCpe( = 'cate+orical' c = cutcate+ories t!(" % 3hich classes are sent to the left % child node! and 2hich to the ri+htF c = ,=,1x2 doublec'1* ans = = c'2* ans = ) <

Regression trees fit the original %training' data well$ &(t ma* do a poor 3o& of predicting new "al(es# .ower &ranches$ especiall*$ ma* &e strongl* affected &* o(tliers# A simpler tree often a"oids o"er-fitting# To find the &est regression tree$ emplo*ing the techni6(es of res(&stit(tion and cross "alidation$ (se the test method of the classre+tree class#

&ntrod#ction to !A.OVA
The anal*sis of "ariance techni6(e in Example: 7ne-Wa* A<7VA ta+es a set of gro(ped data and determine whether the mean of a "aria&le differs significantl* among gro(ps# 7ften there are m(ltiple response "aria&les$ and *o( are interested in determining whether the entire set of means is different from one gro(p to the next# There is a m(lti"ariate "ersion of anal*sis of "ariance that can address the pro&lem# /ac+ to Top

A.OVA with !#ltiple Responses

The cars&all data set has meas(rements on a "ariet* of car models from the *ears 0GA@$ 0GAE$ and 0GF1# )(ppose *o( are interested in whether the characteristics of the cars ha"e changed o"er time# First$ load the data#
load cars&all 2hos %a&e @cceleration CClinders 8isplace&ent 1orsepo2er 4$5 4odel 4odelIYear 0ri+in 3ei+ht

/iBe 100x1 100x1 100x1 100x1 100x1 100x(< 100x1 100x; 100x1

HCtes =00 =00 =00 =00 =00 ;200 =00 1)00 =00

Class double arraC double arraC double arraC double arraC double arraC char arraC double arraC char arraC double arraC

Fo(r of these "aria&les %@cceleration$ 8isplace&ent$ 1orsepo2er$ and 4$5' are contin(o(s meas(rements on indi"id(al car models# The "aria&le 4odelIYear indicates the *ear in which the car was made# >o( can create a gro(ped plot matrix of these "aria&les (sing the +plot&atrix f(nction#
x = ,4$5 1orsepo2er 8isplace&ent 3ei+ht-6 +plot&atrix x!,-!4odelIYear!,-!'Jxo'"

%When the second arg(ment of +plot&atrix is empt*$ the f(nction graphs the col(mns of the x arg(ment against each other$ and places histograms along the diagonals# The empt* fo(rth arg(ment prod(ces a graph with the defa(lt colors# The fifth arg(ment controls the s*m&ols (sed to disting(ish &etween gro(ps#' !t appears the cars do differ from *ear to *ear# The (pper right plot$ for example$ is a graph of 4$5 "ers(s 3ei+ht# The 0GF1 cars appear to ha"e higher mileage than the older cars$ and the* appear to weigh less on a"erage# /(t as a gro(p$ are the three *ears significantl* different from one another? The &anova1 f(nction can answer that 6(estion#
,d!p!stats- = d = 2 p = 1.0eD00< K 0 0.11)1 stats = 3# H# T# df3# dfH# dfT# la&bda# chis?# chis?df# ei+enval# ei+envec# canon# &dist# +&dist# &anova1 x!4odelIYear"

,)x) double,)x) double,)x) double70 2 72 ,2x1 double,2x1 double,2x1 double,)x1 double,)x) double,100x) double,100x1 double,(x( double-

The &anova1 f(nction prod(ces three o(tp(ts:

The first o(tp(t$ d$ is an estimate of the dimension of the gro(p means# !f the means were all the same$ the dimension wo(ld &e @$ indicating that the means are at the same point# !f the means differed &(t fell along a line$ the dimension wo(ld &e 0# !n the example the dimension is 1$ indicating that the gro(p means fall in a plane &(t not along a line# This is the largest possi&le dimension for the means of three gro(ps# The second o(tp(t$ p$ is a "ector of p-"al(es for a se6(ence of tests# The first p "al(e tests whether the dimension is @$ the next whether the dimension is 0$ and so on# !n this case &oth p-"al(es are small# That9s wh* the estimated dimension is 1# The third o(tp(t$ stats$ is a str(ct(re containing se"eral fields$ descri&ed in the following section#

The ields of the stats "tr#ct#re The 3$ H$ and T fields are matrix analogs to the within$ &etween$ and total s(ms of s6(ares in ordinar* one-wa* anal*sis of "ariance# The next three fields are the degrees of freedom for these matrices# Fields la&bda$ chis?$ and chis?df are the ingredients of the test for the dimensionalit* of the gro(p means# %The p-"al(es for these tests are the first o(tp(t arg(ment of &anova1#' The next three fields are (sed to do a canonical anal*sis# Recall that in principal components anal*sis % rincipal Component Anal*sis % CA'' *o( loo+ for the com&ination of the original "aria&les that has the largest possi&le "ariation# !n m(lti"ariate anal*sis of "ariance$ *o( instead loo+ for the linear com&ination of the original "aria&les that has the largest separation &etween gro(ps# !t is the single "aria&le that wo(ld gi"e the most significant res(lt in a (ni"ariate one-wa* anal*sis of "ariance# Ha"ing fo(nd that com&ination$ *o( next loo+ for the com&ination with the second highest separation$ and so on# The ei+envec field is a matrix that defines the coefficients of the linear com&inations of the original "aria&les# The ei+enval field is a "ector meas(ring the ratio of the &etween-gro(p "ariance to the within-gro(p "ariance for the corresponding linear com&ination# The canon field is a matrix of the canonical "aria&le "al(es# Each col(mn is a linear com&ination of the mean-centered original "aria&les$ (sing coefficients from the ei+envec matrix# A gro(ped scatter plot of the first two canonical "aria&les shows more separation &etween gro(ps then a gro(ped scatter plot of an* pair of original "aria&les# !n this example it shows three clo(ds of points$ o"erlapping &(t with distinct centers# 7ne point in the &ottom right sits apart from the others# /* (sing the +na&e f(nction$ *o( can see that this is the 1@th point#
c1 = stats.canon #!1"6 c2 = stats.canon #!2"6 +scatter c2!c1!4odelIYear!,-!'oxs'" +na&e

Ro(ghl* spea+ing$ the first canonical "aria&le$ c1$ separates the 0GF1 cars %which ha"e high "al(es of c1' from the older cars# The second canonical "aria&le$ c2$ re"eals some separation &etween the 0GA@ and 0GAE cars# The final two fields of the stats str(ct(re are Mahalano&is distances# The &dist field meas(res the distance from each point to its gro(p mean# oints with large "al(es ma* &e o(tliers# !n this data set$ the largest o(tlier is the one in the scatter plot$ the /(ic+ Estate station wagon# %<ote that *o( co(ld ha"e s(pplied the model name to the +na&e f(nction a&o"e if *o( wanted to la&el the point with its model name rather than its row n(m&er#'
&ax stats.&dist" ans = (1.52;( find stats.&dist == ans" ans = 20 4odel 20!#" ans = buicAIestateI2a+onI s2"

The +&dist field meas(res the distances &etween each pair of gro(p means# The following commands examine the gro(p means and their distances:
+rpstats x! 4odelIYear" ans = 1.0eJ00( K 0.01;; 0.1)=7 0.2=<7 0.021< 0.1011 0.17;= 0.0(1; 0.0=15 0.12=7 stats.+&dist ans = 0 (.=2;; 11.110<

(.))1( (.0;=; 2.)5(5

(.=2;; 11.110<

0 <.1(;)

<.1(;) 0

As might &e expected$ the m(lti"ariate distance &etween the extreme *ears 0GA@ and 0GF1 %00#0' is larger than the difference &etween more closel* spaced *ears %4#F and E#0'# This is consistent with the scatter plots$ where the points seem to follow a progression as the *ear changes from 0GA@ thro(gh 0GAE to 0GF1# !f *o( had more gro(ps$ *o( might find it instr(cti"e to (se the &anovacluster f(nction to draw a diagram that presents cl(sters of the gro(ps$ formed (sing the distances &etween their means# /ac+ to Top

Heart Rate Variability Analysis with the HRV Toolkit: Basic Time and Frequency Domain Measures
Background: Joseph E. Mietus, B.S. and Ary L. Goldberger, M.D. So t!are and related "aterial: Joseph E. Mietus, B.S. Margret and #.A. $ey %nstitute or &onlinear Dyna"ics in 'hysiology and Medicine Di(ision o %nterdisciplinary Medicine and Biotechnology and Di(ision o )ardiology Beth %srael Deaconess Medical )enter*#ar(ard Medical School, Boston, MA

&) /ac0gro#nd
Heart rate "aria&ilit* %HRV' anal*sis attempts to assess cardiac a(tonomic reg(lation thro(gh 6(antification of sin(s rh*thm "aria&ilit*# The sin(s rh*thm times series is deri"ed from the HR) to HR) %RR' inter"al se6(ence of the electrocardiogram %EC8'$ &* extracting onl* normal sin(s to normal sin(s %<<' inter&eat inter"als# Relati"el* high fre6(enc* "ariations in sin(s rh*thm reflect paras*mpathetic %"agal' mod(lation$ and slower "ariations reflect a com&ination of &oth paras*mpathetic and s*mpathetic mod(lation and non-a(tonomic factors I0-BJ# Traditional heart rate "aria&ilit* %HRV' meas(res are (s(all* di"ided into two &road categories: time domain meas(res and fre6(enc* domain meas(res I4$5J# The time domain heart rate "aria&ilit* statistics commonl* calc(lated are defined in Ta&le 0# <ote$ howe"er$ that comp(ting p<<x with x K B@ ms in &oth long- and short-term recordings ma* pro"ide a more ro&(st index of fl(ct(ations d(e to "agal tone than the standard p<<B@ statistic IEJ# Commonl* (sed fre6(enc* domain meas(res are defined in Ta&le 1# The low fre6(enc* &and %@#@5 - @#0B H2' incl(des ph*siologic oscillations associated with &aroreceptor reflexes and the high fre6(enc* &and %@#0B - @#5@ H2' encompasses respirator* sin(s arrh*thmia# The powers in these &ands has &een (sed to pro"ide indexes of a(tonomic f(nction# )(ch meas(res m(st &e interpreted with ca(tion$ howe"er# As noted$ oscillations in the ?low? fre6(enc* &ands appear to &e mediated &* paras*mpathetic and s*mpathetic components$ while the ?high? fre6(enc* power is mediated excl(si"el* &* the "ag(s# Traditionall*$ fre6(enc* domain meas(res are calc(lated &* resampling the original << inter"al series and then appl*ing the fast Fo(rier transform or a(toregressi"e spectral estimation %the maxim(m entrop* method'# This resampling$ howe"er$ can ca(se an

atten(ation in the high fre6(enc* components# !f discontin(ities exist in the << inter"al series$ either &eca(se of the presence of a&normal &eats or &eca(se of gaps or extreme noise in the original EC8 recording$ traditional approaches re6(ire either discarding the data or g(esswor+ to estimate the locations of missing normal &eats# To eliminate the need for e"enl* sampled data re6(ired &* Fo(rier or maxim(m entrop* methods$ fre6(enc* domain spectra can &e calc(lated (sing the .om& periodogram for (ne"enl* sampled data IA$FJ %the method (sed in this tool+it'# Altho(gh the long term %15-ho(r' statistics of ):A<<$ ):<<!:L and D.F power can &e calc(lated for shorter data lengths$ the* will &ecome increasingl* (nrelia&le# For short-term data %less than 0B min(tes in length'$ onl* the time domain meas(res of AV<<$ ):<<$ rM)): and p<<B@ and the fre6(enc* domain meas(res of total power$ V.F power$ HF power and .FMHF ratio sho(ld &e (sed# A n(m&er of the HRV meas(res are highl* correlated with each other# These incl(de ):<<$ ):A<<$ total power and D.F power= ):<<!:L$ V.F power and .F power= and rM)):$ p<<B@ and HF power# The .FMHF ratio does not correlate strongl* with an* other HRV meas(res I5J# Heart rate "aria&ilit* %HRV' has &een widel* applied in &asic and clinical research st(dies# !ts clinical application is "er* limited at present$ howe"er# These limitations are d(e to lac+ of standardi2ation of methodolog* and application to different non-compara&le s(&sets of s(&3ects$ as well as to the confo(nding effects of age$ gender$ dr(gs$ health stat(s$ and chrono&iologic "ariations$ among others# F(rthermore$ o(tliers d(e to ectop* and artifact can ha"e ma3or effects on comp(ted HRV "al(es# !n elderl* s(&3ects$ especiall*$ a sp(rio(sl* high "al(e of certain meas(res ma* &e d(e to the effects of ?erratic s(pra"entric(lar rh*thm? IGJ d(e to s(&tle atrial ectop*$ wandering atrial pacema+er$ or sin(s node cond(ction a&normalities# Additional information on heart rate d*namics and anal*sis techni6(es$ incl(ding non-linear and complexit* &ased meas(res$ can &e fo(nd in the HRV 1@@E co(rse notes and elsewhere on h*sio<et %see for example: :etrended Fl(ct(ation Anal*sis$ M(ltiscale Entrop* Anal*sis$ and !nformation-/ased )imilarit*$ among others'# h*sio<et9s HRV Tool+it$ a"aila&le here$ is a rigoro(sl* "alidated pac+age of open so(rce software for HRV anal*sis$ incl(ding "is(ali2ation of << inter"al time series$ a(tomated o(tlier remo"al$ and calc(lation of the &asic time- and fre6(enc*-domain HRV statistics widel* (sed in the literat(re$ incl(ding all of those listed in the ta&les &elow# )e"eral other high-6(alit*$ freel* a"aila&le HRV tool+its ma* also &e of interest to researchers= lin+s to them are pro"ided at the end of this page#

Ta(le 1: Commonl2 #sed time3domain meas#res

AVNN* SDNN* Average of all NN intervals Standard deviation of all NN intervals

SDANN

Standard deviation of the averages of NN intervals in all 5 !in"te seg!ents of a 24 ho"r re#ording &ean of the standard deviations of NN intervals in all 5 !in"te seg!ents of a 24 ho"r re#ording S'"are root of the !ean of the s'"ares of differen#es (et)een ad*a#ent NN intervals ,er#entage of differen#es (et)een ad*a#ent NN intervals that are greater than 50 !s- a !e!(er of the larger +NN. fa!il/ 061

SDNN$D %

r&SSD*

+NN50*

N )hort-term HRV statistics

Ta(le 4: Commonl2 #sed fre5#enc23domain meas#res

232,45* 89: V9:* 9:* 6:* 9:;6:* 2otal s+e#tral +o)er of all NN intervals "+ to 0.04 67 2otal s+e#tral +o)er of all NN intervals "+ to 0.003 67 2otal s+e#tral +o)er of all NN intervals (et)een 0.003 and 0.04 67 2otal s+e#tral +o)er of all NN intervals (et)een 0.04 and 0.15 67. 2otal s+e#tral +o)er of all NN intervals (et)een 0.15 and 0.4 67 5atio of lo) to high fre'"en#/ +o)er

N )hort-term HRV statistics %V.F O spectral power &etween @ and @#@5 H2#'

"elected References:
I0J Wolf MM$ Varigos 8A$ H(nt :$ )loman P8# )in(s arrh*thmia in ac(te m*ocardial infarction# Med P A(st 0GAF=1:B1-B4# I1J Qleiger RE$ Miller P $ /igger PT$ Moss AP$ and the M(lticenter ost-!nfarction Research 8ro(p# :ecreased heart rate "aria&ilit* and its association with increased mortalit* after ac(te m*ocardial infarction# Am P Cardiol 0GFA=BG:1BE-1E1#

I4J Tas+ Force of the E(ropean )ociet* of Cardiolog* and the <orth American )ociet* of acing and Electroph*siolog*# Heart rate "aria&ilit*: )tandards of meas(rement$ ph*siological interpretation$ and clinical (se# Circ(lation 0GGE= G4:0@54-0@EB# I5J Miet(s PE# Time domain meas(res: from "ariance to p<<x# http:MMph*sionet#orgMe"entsMhr"-1@@EMmiet(s-0#pdf IBJ arati 8$ Mancia 8$ :i Rien2o M$ Castiglioni $ Ta*lor PA$ )t(dinger # ointCo(nterpoint: Cardio"asc(lar "aria&ilit* isMis not an index of a(tonomic control of circ(lation# P Appl h*siol 1@@E= 0@0: EAE - EF1# IEJ Miet(s PE$ eng C-Q$ Henr* !$ 8oldsmith R.$ 8old&erger A.# The p<<x-files: Reexamining a widel*-(sed heart rate "aria&ilit* meas(re# Heart 1@@1=FF:4AF-4F@# IAJ ress WH$ Te(+ols+* )A$ Vetterling WT$ Flanner* / # <(merical Recipes in C: The Art of )cientific Comp(ting$ 1nd ed# Cam&ridge Dni"# ress$ 0GG1$ pp# BAB-BF5# IFJ Mood* 8/# )pectral anal*sis of heart rate witho(t resampling# Comp(ters in Cardiolog* 0GG4= A0B-A0F# IGJ )tein Q$ >ane2 :$ :omitro"ich $ 8ottdiener P$ Cha"es $ Qronmal R$ Ra(tahar3( # Heart rate "aria&ilit* is confo(nded &* the presence of erratic sin(s rh*thm# Comp(ters in Cardiolog* 1@@1= EEG-A1#

&&) O(taining the HRV Tool0it

The HRV Tool0it: Contents
The HRV Tool+it consists of a Lsa+es file$ a 4aAefile$ and the following programs:
pltIrrs

a shell s#ri+t for +lotting 55;NN interval series a shell s#ri+t for #al#"lating ti!e and fre'"en#/ do!ain 65V statisti#s

+etIhrv

Scripts above use the programs below, and others from the WFDB and plt packages
rrlist.c

< #ode for e.tra#ting an 55 interval list fro! an annotation file < #ode for filtering 55;NN intervals < #ode for filtering 55;NN intervals < #ode for #al#"lating ti!e do!ain statisti#s

filt.c

filtnn.c

statnn.c

p2r.c

< #ode for #al#"lating +o)er in "+ to 10 fre'"en#/ (ands fro! a +o)er s+e#tr"! < #ode for #onverting hh=!!=ss to se#onds < #ode for #onverting se#onds to hh=!!=ss

seconds.c

hours.c

and +etIhrv are the main scripts (sed in calc(lating HRV as ill(strated &elow# These two scripts call the "ario(s C programs to accomplish their calc(lations# The C programs can &e (sed separatel* and their (sage and "ario(s options can &e fo(nd in Dsages$ or &* r(nning an* of these programs with the Dh option#
pltIrrs

*ownloading and &nstalling the HRV Tool0it

!nstalling the HRV tool+it is eas*:
1. 3n 4indo)s> install the free </g)in soft)are first- see o"r t"torial for details. </g)in in#l"des the +cc < #o!+iler and all other "tilities needed to ("ild and r"n the #o!+onents of the 65V 2ool?it on 4indo)s. Start a </g)in @ter!inal e!"latorA )indo) and "se it for all of the re!aining ste+s. 2. $nstall the free 4:DB and +lt soft)are +a#?ages. 3. 2he 65V tool?it is availa(le as a tar(all of so"r#es @for all +latfor!sA or as tar(alls of +re("ilt (inaries for CN8;9in". @.D6A> &a# 3S % @.D6A> Solaris @S,A5<A> or 4indo)s;</g)in. Do)nload the version of /o"r #hoi#e. 4. 8n+a#? the 65V tool?it tar(all /o" do)nloaded. @See the ,h/sioNet :AE for infor!ation on "n+a#?ing tar(alls.A 5. $f /o" do)nloaded the so"r#es> enter the so"r#e dire#tor/ @1.M.srcA and #o!+ile and install the tool?it (/ t/+ing=
<. &aAe install

$f /o" do)nloaded the (inaries> !ove the #ontents of the 1.M dire#tor/ into so!e dire#tor/ in /o"r $@T1 @or add the 1.M dire#tor/ to /o"r $@T1A. 2he (inaries re'"ire the sa!e additional +a#?ages as the so"r#e distri("tion @3N8H> plt> and @on 4indo)sA </g)inA.

&&&) -sing the HRV tool0it

-ser interface
2he 65V tool?it does not in#l"de a gra+hi#al "ser interfa#e. $ts #o!+onents are #o!!and line tools that !"st (e r"n fro! a ter!inal )indo) @"nder &S 4indo)s> a </g)in )indo)A or (/ a shell s#ri+t. @Fven pltIrrs !"st (e started fro! the #o!!and line or a s#ri+t> altho"gh it +rod"#es gra+hi#al o"t+"t.A

&np#t data format

/oth pltIrrs %for plotting the RRM<< inter"al series' and +etIhrv %for calc(lating the HRV statistics' can ta+e as inp(t either a h*sio/an+-compati&le &eat annotation file or a text file containing an RR inter"al list# RR inter"al lists can &e in an* of fo(r formats:

3 #ol"!ns @2> 55> AA 2 #ol"!ns @55> AA 2 #ol"!ns @2> 55A 1 #ol"!n @55A

)here 2 is the ti!e of o##"rren#e of the (eginning of the 55 interval> 55 is the d"ration of the 55 interval> and A is a (eat la(el. Nor!al sin"s (eats are la(eled %.

Altho(gh T is ass(med to &e expressed in seconds &* defa(lt$ the DO option of pltIrrs and +etIhrv %see &elow' can &e (sed if the RR inter"al list contains T "al(es expressed as cloc+ time %hh:mm:ss#xxx'$ ho(rs %hh#xxxxxxx' or min(tes %mm#xxxxx'# )imilarl*$ altho(gh RR is ass(med to &e expressed in seconds$ inter"als in milliseconds can &e inp(t &* (sing the R-m9 option# %)ee details &elow or in Dsages'# /eat annotation files are a"aila&le for most of the h*sio/an+ records that incl(de EC8s# For information a&o(t record and annotation con"entions see the h*sio<et FAH# !f *o( wish to st(d* a recording for which no &eat annotation file or RR inter"al listing is a"aila&le$ *o( ma* &e a&le to create an annotation file (sing software from the WF:/ software pac+age# Additional information on RR inter"als$ heart rate$ and HRV can &e fo(nd at the RRMHRMHRV Howto# &np#t #sed in this t#torial The examples &elow read the ec+ annotations from record chf0( of the /!:MC Congesti"e Heart Fail(re :ata&ase# To reprod(ce the res(lts shown &elow$ it is not necessar* to download this annotation file$ &eca(se applications that (se the WF:/ li&rar* %incl(ding those in the HRV Tool+it that read annotation files' can locate and read the cop* from the h*sio<et we& ser"er if no local cop* exists# !n order to do so s(ccessf(ll*$ it is necessar* to specif* the path to the record from the h*sio/an+ archi"e director* within the record name$ as shown in these examples %(se chfdbPchf0( rather than simpl* chf0('# Examples that ill(strate inp(t from RR inter"al lists ass(me that the inp(t file is named chf0(.rr$ and that it is in the c(rrent %local' director*#
plt_rrs:

plotting the RR6.. inter'al time series

<< inter"al o(tliers d(e to missed or false &eat detections can serio(sl* corr(pt HRV statistics# Most fre6(enc* domain meas(res are especiall* s(scepti&le to o(tliers$ partic(larl* .F and HF power which can &e in error &* greater than 0@@@S# Most time domain meas(res are less affected &* o(tliers$ &(t still can gi"e errors in excess of 0@@S# AV<<$ p<<B@ and D.F power are least affected$ generall* with errors less than 0@S %see Time domain Meas(res: From Variance to p<<x'#

To red(ce the errors d(e to o(tliers$ the first step in HRV anal*sis is to "is(all* examine the RRM<< inter"al data and determine the necessit* of o(tlier filtering# This can &e done (sing pltIrrs# can &e (sed with either an annotation file or an RR inter"al listing %see &elow' and has the following options:
pltIrrs pltIrrs ,options- D. rrfile Q record annotator ,start ,end-$lot .. intervals or .. interval heart rates options # ,D$ 2Q)Q=Q1<Q2)Q(2- # plot 2! )! =! 1<! 2) or (2 hours per pa+e default# scale pa+e len+th to data len+th" ,D. rrfile- # .. interval file # ti&e sec"! interval ,D%- # plot %% intervals instead of .. intervals ,D1- # plot ..P%% interval heart rate ,DN Rfilt h2inR- # filter intervals! plot filtered data ,Df Rfilt h2inR- # filter intervals ,Dp- # plot points ,DO cQhQ&- # input ti&e for&at# hh##&&#ss! hours! &inutes default# seconds" ,D&- # .. intervals in &sec ,DC RC&in C&axR- # C axis li&its ,Do- # output postscript B/ defa"lt> pltIrrs )ill o+en a plt )indo) and dis+la/ the +lot on the ter!inal s#reen. 2o

o"t+"t the +lot as a +osts#ri+t file "se the Do o+tion. 2o +rint the +lot to a +osts#ri+t +rinter "se
pltIrrs Do other arguments Q lpr

Dsing an annotation file$ li+e this:

pltIrrs chfdbPchf0( ec+

)ill +lot the entire 55 interval series for the #ongestive heart fail"re re#ord #hfd(;#hf03 "sing the ec+ annotator. B/ defa"lt> pltIrrs s#ales the +lot so that the entire 55 interval series is +lotted on one +age> )ith a !a.i!"! of D lines +er +age. 2o +lot a s+e#ified n"!(er of ho"rs +er +age> "se the D$ o+tion. :or e.a!+le> D$ ) )ill +rint 4 ho"rs +er +age @15 !in"tes +er lineA> D$ 1< )ill +rint 16 ho"rs +er +age @2 ho"rs +er lineA> et#.

To plot selected portions of the data$ specif* a start time and optionall* an end time# For example$
pltIrrs D$ = chfdbPchf0( ec+ 00#00#00 01#00#00

+lots the first ho"r of the 55 interval se'"en#e=

With the Dp option$ as in

pltIrrs D$ = Dp chfdbPchf0( ec+ 00#00#00 01#00#00 pltIrrs +lots the 55 interval se'"en#e as individ"al +oints=

With the D% option$ as in

pltIrrs D$ = D% chfdbPchf0( ec+ 00#00#00 01#00#00 pltIrrs +lots NN intervals onl/> o!itting intervals that are not (o"nded (/ nor!al sin"s

(eats at (oth ends=

The ?%% # .. = (=2( # )20( = 0.710 ,(=0 nonD%%-? in the title indicates the total n(m&er of << inter"als$ the total n(m&er of RR inter"als$ the fraction of RR inter"als that are << inter"als and the n(m&er of non-<< inter"als# To filter o(tliers$ (se the DN or Df options$ as in

pltIrrs D$ = D% DN R0.2 20 Dx 0.) 2.0R chfdbPchf0( ec+ 00#00#00 01#00#00

2his +ro#ed"re )ill +lot the first ho"r of the filtered NN intervals se'"en#e. 6ere the GDN 0.2 20 Dx 0.) 2.0G s+e#ifies the filtering +ara!eters as follo)s. :irst> an/ intervals less than 0.4 se# or greater than 2.0 se# are e.#l"ded. Ne.t> "sing a )indo) of 41 intervals @20 intervals on either side of the #entral +ointA> the average over the )indo) is #al#"lated e.#l"ding the #entral interval. $f the #entral interval lies o"tside 20H @0.2A of the )indo) average this interval is flagged as an o"tlier and e.#l"ded. 2hen the )indo) is advan#ed to the ne.t interval. 2hese +ara!eters #an (e ad*"sted as a++ro+riate for different data sets.

Dsing DN allows pltIrrs to plot the excl(ded inter"als as small filled circles:

The Df option s(ppresses o(tp(t of excl(ded inter"als:

The RNilt # %% # .. = (;<2 # (=2( # )20( = 7=) # 0.710 = 0.=75 ,<1 Niltered! (=0 nonD%%-R in the title of the two plots a&o"e gi"es the total n(m&er of << inter"als remaining after filtering$ the total n(m&er of << inter"als &efore filtering$ the total n(m&er of RR inter"als$ the fraction of << inter"als remaining after filtering$ the fraction of RR inter"als that are << inter"als$ the fraction of the total n(m&er of RR inter"als that are << inter"als remaining after filtering$ and the n(m&er of << inter"als filtered o(t together with the n(m&er of non-<< inter"als# Filtering the << inter"al data ma* not &e necessar* if there are no extreme o(tliers# To plot the RR inter"al series of an RR inter"al file containing three col(mns of data : time in seconds$ inter"al in seconds and &eat la&el$ (se the D. option followed &* the name of the

file$ rather than specif*ing the record and annotator names# For example$ if the file chf0(.rr contains:
1.(5< 0.752 % 2.(12 0.75< % (.252 0.7)0 % ).212 0.7<0 % 5.15< 0.7)) % <.112 0.75< % ;.0)= 0.7(< % ;.77< 0.7)= % =.7<0 0.7<) % 7.700 0.7)0 % . . . "se pltIrrs D. chf0(.rr )ith an/ of the a(ove o+tions to +lot its #ontents.

The a&o"e RR inter"al list was generated (sing the command

rrlist ec+ chfdbPchf0( Ds :chf0(.rr

@Noti#e that the re#ord and annotator arg"!ents a++ear in reverse order in rrlist #o!!ands.A 2he vario"s other o+tions availa(le for rrlist are given in 8sages.

!f an RR inter"al listing contains onl* time in seconds and inter"al in seconds$ e#g#$
1.(5< 2.(12 (.252 ).212 5.15< <.112 ;.0)= ;.77< =.7<0 7.700 . . . 0.752 0.75< 0.7)0 0.7<0 0.7)) 0.75< 0.7(< 0.7)= 0.7<) 0.7)0

then a #o!!and s"#h as pltIrrs D. chf0(.rr +lots the 55 interval se'"en#e #orre#tl/> ("t )ill not (e a(le to +lot the NN interval se'"en#e "sing the D% o+tion> sin#e the (eat la(els are !issing.

To plot an RR inter"al listing containing onl* RR inter"als in seconds and &eat la&els$ e#g#$
0.752 0.75< 0.7)0 0.7<0 0.7)) 0.75< 0.7(< 0.7)= 0.7<) 0.7)0 . % % % % % % % % % %

. .

the #o!!and pltIrrs D. chf0(.rr #al#"lates the ti!e of ea#h 55 interval fro! the 55 interval se'"en#e> !a?ing the ass"!+tion that the intervals are #onse#"tive.

Finall*$ if the RR inter"al listing contains onl* RR inter"als in seconds$ e#g#$

0.752 0.75< 0.7)0 0.7<0 0.7)) 0.75< 0.7(< 0.7)= 0.7<) 0.7)0 . . . then pltIrrs D. chf0(.rr #al#"lates the ti!e of the ti!e of the 55 interval fro! the 55

interval se'"en#e> ("t as in a +revio"s e.a!+le )ill not (e a(le to +lot the NN interval se'"en#e "sing the D% o+tion.

!f the RR inter"als in an* of the a&o"e formats are listed in milliseconds rather than seconds$ (se pltIrrs with the D& option#
get_hrv:

calc#lating the HRV statistics

To calc(late the time and fre6(enc* domain HRV statistics (se +etIhrv$ where the options are:
+etIhrv ,options- D. rrfile Q record annotator ,start ,end-5et 1.M statistics # .SC # %%P.. @M%% /8%% /8@%% /8%%O%8X .4//8 $%% # T0T$3. L>N M>N >N 1N >NP1N options # ,D. rrfile- # .. interval file # ti&e sec"! interval ,Df Rfilt h2inR- # filter outliers ,Dp Rnndiff ...R- # nn difference for pnn default# 50 &sec" ,D$ Rlo1 hi1 lo2 hi2 lo( hi( lo) hi)R- # po2er bands default # 0 0.00(( 0.00(( 0.0) 0.0) 0.15 0.15 0.)" ,Ds- # short ter& stats of .SC # %%P.. @M%% /8%% .4//8 $%% # T0T$3. M>N >N 1N >NP1N ,DO cQhQ&- # input ti&e for&at# hh##&&#ss! hours! &inutes default# seconds" ,D&- # .. intervals in &sec ,D4- # output statistics in &sec rather than sec ,D>- # output statistics on one line ,D/- # plot 1.M results on screen plottin+ options # ,DN Rfilt h2inR- # filter outliers! plot filtered data ,DC RC&in C&axR- # ti&e series CDaxis li&its RD DR for selfD scalin+" ,DX &axfre?- # fft &axi&u& fre?uencC default # 0.) 1B"

,DY fft&ax- # fft &axi&u& RDR for selfDscalin+" ,Do- # output plot in postscript +etIhrv "ses statnn to #al#"late the ti!e do!ain statisti#s> and lo&b @fro! the 4:DB

soft)are +a#?ageA and p2r to #al#"late the fre'"en#/ do!ain statisti#s. NN;55 is the fra#tion of total 55 intervals that are #lassified as nor!al to nor!al @NNA intervals and in#l"ded in the #al#"lation of 65V statisti#s. 2his ratio #an (e "sed as a !eas"re of data relia(ilit/. :or e.a!+le> if the NN;55 ratio is less than 0.D> fe)er than D0H of the 55 intervals are #lassified as NN intervals> and the res"lts )ill (e so!e)hat "nrelia(le.

The command
+etIhrv Df R0.2 20 Dx 0.) 2.0R Dp R20 50R chfdbPchf0( ec+

sho"ld give the follo)ing o"t+"t=

chfdbPchf0( # %%P.. = 0.7)2=77 @M%% = 0.=7220< /8%% = 0.05);12 /8@%% = 0.0)<<;;( /8%%O8X = 0.02)112) r4//8 = 0.01;;<7) p%%20 = 0.0<==<7= p%%50 = 0.0252(=7 T0T $3. = 0.00((==2 L>N $3. = 0.002;0)=7 M>N $3. = 0.000(701= >N $3. = 0.00012)10) 1N $3. = 0.0001<702; >NP1N = 0.;()22<

$n this #ase AVNN> SDNN> SDANN> SDNN$D% are r&SSD are given in se#onds> +NN val"es as ratios and ,45 val"es in se#onds s'"ared. Note that the e.a#t val"es o(tained on different +latfor!s !a/ var/ (/ a++ro.i!atel/ 10 6 d"e to ro"nd off errors.

/* defa(lt$ +etIhrv o(tp(ts the HRV statistics in seconds# To o(tp(t res(lts in milliseconds (se the D4 option$ as in
+etIhrv D4 Df R0.2 20 Dx 0.) 2.0R Dp R20 50R chfdbPchf0( ec+

2his sho"ld give the follo)ing o"t+"t=

chfdbPchf0( # %%P.. = 0.7)2=77 @M%% = =72.20< /8%% = 5).;12 /8@%% = )<.<;;( /8%%O8X = 2).112) r4//8 = 1;.;<7) p%%20 = <.==<7= p%%50 = 2.52(=7 T0T $3. = ((==.<5 L>N $3. = 2;05.17 M>N $3. = (70.25 >N $3. = 12).15< 1N $3. = 1<7.05; >NP1N = 0.;())0(

$n this #ase AVNN> SDNN> SDANN> SDNN$D% are r&SSD are given in !illise#onds> +NN val"es as +er#entages and ,45 val"es in !illise#onds s'"ared.

To o(tp(t the HRV statistics all on one line$ (se the D> option:
+etIhrv D> D4 Df R0.2 20 Dx 0.) 2.0R Dp R20 50R chfdbPchf0( ec+

2his )ill o"t+"t

chfdbPchf0( # 0.7)2=77 =72.20< 5).;12 )<.<;;( 2).112) 1;.;<7) <.==<7= 2.52(=7 # ((==.<5 2;05.17 (70.25 12).15< 1<7.05; 0.;())0(

)here the !eas"res are

.SC # %%P.. @M%% /8%% /8@%% /8%%O%8X .4//8 $%%20 $%%50 # T0T$3. L>N M>N >N 1N >NP1N

To limit the o(tp(t to the statistics named as short-term HRV statistics in ta&les 0 and 1 a&o"e$ (se the Ds option$ as in
+etIhrv Ds D4 Df R0.2 20 Dx 0.) 2.0R Dp R20 50R chfdbPchf0( ec+ 0#00#00 1#00#00

2his sho"ld give the follo)ing o"t+"t=

chfdbPchf0( # %%P.. = 0.701;( @M%% = =<;.75= /8%% = (7.;171 r4//8 = 20.=<57 p%%20 = <.2<55( p%%50 = 2.20=11 T0T $3. = 1;02.7< M>N $3. = 1)2(.01 >N $3. = 10(.7)1 1N $3. = 1;<.00= >NP1N = 0.5705);

To o(tp(t the short-term HRV statistics all on one line$ (se &oth the Ds and the D> options:
+etIhrv D> Ds D4 Df R0.2 20 Dx 0.) 2.0R Dp R20 50R chfdbPchf0( ec+ 0#00#00 1#00#00

2his )ill o"t+"t

chfdbPchf0( # 0.701;( =<;.75= (7.;171 20.=<57 <.2<55( 2.20=11 # 1;02.7< 1)2(.01 10(.7)1 1;<.00= 0.5705);

)here the !eas"res are

.SC # %%P.. @M%% /8%% .4//8 $%%20 $%%50 # T0T$3. M>N >N 1N >NP1N

As with pltIrrs$ +etIhrv with the D. option can accept a text file containing an RR inter"al listing in an* of the formats descri&ed a&o"e# !f the inter"al times are not listed$ +etIhrv will calc(late the time of the RR inter"al from the RR inter"al se6(ence$ and if there are no &eat la&els$ +etIhrv D. will treat all inter"als as normal# !f the RR inter"als are listed in milliseconds rather than seconds$ (se +etIhrv with the D& option# To plot the HRV res(lts in a window incl(ding the << inter"al time series$ the << inter"al histogram and the << inter"al power spectr(m (se the D/ option to +etIhrv# As with pltIrrs the Do will o(tp(t ost)cript$ and the DN filtering option will plot the excl(ded

inter"als of the << inter"al time series: the non-normal &eats as small open circles and o(tliers as small filled circles# For example
+etIhrv D/ Ds D4 DN R0.2 20 Dx 0.) 2.0R Dp R20 50R chf0( ec+ 0#00#00 1#00#00

)ill generate the follo)ing +lot=

<ote that plots made this wa* show the calc(lated HRV statistics with red(ced precision# Additional +etIhrv plotting options incl(de DC for scaling the time series *-axis limits$ the DX option for scaling the po