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PrepareDataforLinearMixedEffectsModelsMATLAB&Simulink
PrepareDataforLinearMixedEffectsModels
TablesandDatasetArrays
Tofitalinearmixedeffectsmodel,youmuststoreyourdatainatableordatasetarray.Inyourtableordataset
array,youmusthaveacolumnforeachvariableincludingtheresponsevariable.Morespecifically,thetableor
datasetarray,saytbl,mustcontainthefollowing:
Aresponsevariabley
PredictivevariablesXjwhichcanbecontinuousorgroupingvariables
Groupingvariablesg1,g2,...,gR,
wherethegroupingvariablesinXjandgrcanbecategorical,logical,characterarrays,oracellarraysof
strings,r=1,2,...,R.
Youmustorganizeyourdatasothateachrowrepresentsanobservation.Andeachrowshouldcontainthe
valueofvariablesandthelevelsofgroupingvariablescorrespondingtothatobservation.Forexample,ifyou
havedatafromanexperimentwithfourtreatmentoptions,onfivedifferenttypesofindividualschosen
randomlyfromapopulationofindividuals(blocks),thetableordatasetarraymustlooklikethis.
Block
Treatment
Response
y11
y12
y13
y14
...
...
...
y51
y52
y53
y54
Now,considerasplitplotexperiment,wheretheeffectoffourdifferenttypesoffertilizersontheyieldof
tomatoplantsisstudied.Thesoilwherethetomatoplantsareplantedisdividedintothreeblocksbasedonthe
soiltype:sandy,silty,andloamy.Eachblockisdividedintofiveplots,wherefivetypesoftomatoplants,
(cherry,heirloom,grape,vine,andplum)arerandomlyassignedtotheseplots.Then,thetomatoplantsinthe
plotsaredividedintosubplots,whereeachsubplotistreatedbyoneofthefourfertilizers.Thedatafromthis
experimentlookslike:
Soil
Tomato
Fertilizer
Yield
'Sandy'
'Plum'
104
'Sandy'
'Plum'
136
'Sandy'
'Plum'
158
'Sandy'
'Plum'
174
'Sandy'
'Cherry'
57
'Sandy'
'Cherry'
86
...
...
...
...
'Sandy'
'Vine'
99
'Sandy'
'Vine'
117
http://www.mathworks.com/help/stats/preparedataforlinearmixedeffectsmodels.html
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PrepareDataforLinearMixedEffectsModelsMATLAB&Simulink
'Silty'
'Plum'
120
'Silty'
'Plum'
115
...
...
...
...
'Loamy'
'Vine'
111
'Loamy'
'Vine'
105
Youmustspecifythemodelyouwanttofitusingtheformulainputargumenttofitlme.
Ingeneral,aformulaformodelspecificationisastringoftheterm'y~terms'.Forlinearmixedeffects
models,thisformulaisintheform'y~fixed+(random1|grouping1)+...+(randomR|groupingR)',
wherefixedcontainsthefixedeffectstermsandrandom1,...,randomRcontaintherandomeffectsterms.
Forexample,forthepreviousfertilizerexperiment,considerthefollowingmixedeffectsmodel
yimjk = 0 +
m=2
[ ]
[ ]
1mI F im +
2jI T ij + b0k Sk + b0jk (S T ) jk + imjk ,
j=2
wherei=1,2,...,60,theindexmcorrespondstothefertilizertypes,jcorrespondstothetomatotypes,andk
=1,2,3correspondstotheblocks(soil).Skrepresentsthekthsoiltype,andI[F]imisthedummyvariable
representinglevelmofthefertilizer.Similarly,I[T]ijisthedummyvariablerepresentingtheleveljofthetomato
type.
Youcanfitthismodelusingtheformula'Yield~1+Fertilizer+Tomato+(1|Soil)+
(1|Soil:Tomato)'.
Fordetailedinformationonhowtospecifyyourmodelusingformula,seeRelationshipBetweenFormulaand
DesignMatrices.
DesignMatrices
Ifyoucannoteasilydescribeyourmodelusingaformula,youcancreatedesignmatricestodefinethefixed
andrandomeffects,andfitthemodelusingfitlmematrix(X,y,Z,G).Youmustcreateyourdesignmatrices
asfollows.
FixedeffectsandrandomeffectsdesignmatricesXandZ:
Enteracolumnof1sfortheinterceptusingones(n,1),wherenisthetotalnumberofobservations.
IfX1isacontinuousvariable,thenenterX1asitisinaseparatecolumn.
IfX1isacategoricalvariablewithmlevels,thentheremustbem1dummyvariablesform1levelsof
X1inX.
Forexample,consideranexperimentwhereyouwanttostudytheimpactofqualityofrawmaterialsfrom
fourdifferentprovidersontheproductivityofaproductionline.Ifyoufitalinearmixedeffectsmodelwith
interceptandproviderasthefixedeffectsterms,interceptistherandomeffectsterm,andyouuse
referencecontrastscoding,thenyoumustconstructyourfixedandrandomeffectsdesignmatricesas
follows.
D=dummyvar(provider);%Createdummyvariables
X=[ones(n,1)D(:,2)D(:,3)D(:,4)];
Z=[ones(n,1)];
Becausereferencecontrastcodingusesthefirstproviderasthereference,andthemodelhasanintercept,
youmustusethedummyvariablesforonlythelastthreeproviders.
IfthereisaninteractiontermofpredictorvariablesX1andX2,thenyoumustenteracolumnthatyouform
byelementwiseproductofthevectorsX1andX2.
Forexample,ifyouwanttofitamodel,wherethereisanintercept,acontinuoustreatmentfactor,a
continuoustimefactor,andtheirinteractionasthefixedeffectsinalongitudinalstudy,andtimeisthe
randomeffectsterm,thenyourfixedandrandomeffectsdesignmatricesshouldlooklike
http://www.mathworks.com/help/stats/preparedataforlinearmixedeffectsmodels.html
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PrepareDataforLinearMixedEffectsModelsMATLAB&Simulink
X=[ones(n,1),treatment,time,treatment.*time];
y=response;
Z=[time];
GroupingvariablesG:
Thereisonecolumnforeachgroupingvariableandacolumnofelementwiseproductofthegroupingvariables
incaseofanesting.
Forexample,ifyouwanttogroupplots(plot)withinblocks(block),thenyoumustaddacolumnof
elementwiseproductofplotbyblock.Morespecifically,ifyouwanttofitamodelwherethereisintercept
andacontinuoustreatmentfactorasthefixedeffectsinasplitblockexperiment,andtheinterceptand
treatmentaregroupedbytheplotsnestedwithinblocks,thenthedesignmatricesshouldlooklikethis.
X=[ones(n,1),treatment];
y=response;
Z=[ones(n,1),treatment];
G=[block.*plot];
Supposeintheearlierqualityofrawmaterialsexample,therawmaterialsarriveinbulks,andthebulksare
nestedwithinproviders.Ifyouwanttofitalinearmixedeffectsmodel,whereinterceptisgroupedbythebulks
withinproviders,thenyourdesignmatricesshouldlooklikethis.
D=dummyvar(provider);
X=[ones(n,1)D(:,2)D(:,3)D(:,4)];
y=response;
Z=ones(n,1);
G=[provider.*bulks];
Intheearlierlongitudinalstudyexample,ifyouwanttoaddrandomeffectsforinterceptandtimegroupedby
subjectsthatparticipatedinthestudy,thenyourdesignmatricesshouldlooklike
X=[ones(n,1),treatment,time,treatment.*time];
y=response;
Z=[ones(n,1),time];
G=subject;
RelationofMatrixFormtoTablesandDatasetArrays
fitlme(tbl,formula)andfitlmematrix(X,y,Z,G)areequivalentinfunctionality,suchthat
yisthenby1responsevector.
Xisannbypfixedeffectsdesignmatrix.fitlmeconstructsthisfromtheexpressionfixedinformula.
ZisanRby1cellarraywithZ{r}beingannbyq(r)randomeffectsdesignmatrixconstructedfromtherth
expressioninrandominformula,r=1,2,...,R.
GisanRby1cellarraywithG{r}beingannby1groupingvariable,gr,informulawithM(r)levelsor
groups.
Forexample,iftblisatableordatasetarraycontainingtheresponsevariabley,thecontinuousvariablesX1
andX2,andthegroupingvariableg,thentofitalinearmixedeffectsmodelthatcorrespondstotheformula
expression'y~X1+X2+(X1*X2|g)'usingfitlmematrix(X,y,Z,G)theinputargumentsmustcorrespond
tothefollowing:
y=tbl.y
X=[ones(n,1),tbl.X1,tbl.X2]
Z=[ones(n,1),tbl.X1,tbl.X2,tbl.X1.*tbl.X2]
G=tbl.g
http://www.mathworks.com/help/stats/preparedataforlinearmixedeffectsmodels.html
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PrepareDataforLinearMixedEffectsModelsMATLAB&Simulink
SeeAlso
fitlme|fitlmematrix|LinearMixedModel
MoreAbout
LinearMixedEffectsModels
RelationshipBetweenFormulaandDesignMatrices
http://www.mathworks.com/help/stats/preparedataforlinearmixedeffectsmodels.html
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