Hi Jarrod, hi all,
I am still struggling with that MCMCglmm function:
First, in the course notes I have read that for some reason which should come clearer later on in the text the IJ matrix is used for the prior of the residuals and the random effects in the multinomial model. Why especially this matrix?
Second, probably a very stupid questions: if the model did not converge, you have to run it longer, so increase the number of iterations, right? However, when I am increasing the number of iterations (increased from 12,000 to 100,000, there are still trends in the times series plots. What can I do then? what else might be the problem here? And also related to that, in the last email you wrote that there might be a problem du to my small effect sizes, however, it also seems that those do not increase with increasing number of iterations.
I am very thankful for some help.
Cheers,
Sereina
Gesendet: Freitag, 02. August 2013 um 14:54 Uhr
Von: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk>
An: "Sereina Graber" <sereina.gra...@gmx.ch>
Cc: r-sig-phylo@r-project.org
Betreff: Re: Aw: Re: [R-sig-phylo] WG: Re: Re: MCMCglmm for categorical data with more than 2 levels - prior specification?
Von: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk>
An: "Sereina Graber" <sereina.gra...@gmx.ch>
Cc: r-sig-phylo@r-project.org
Betreff: Re: Aw: Re: [R-sig-phylo] WG: Re: Re: MCMCglmm for categorical data with more than 2 levels - prior specification?
Hi,
They are the effect of the covariates on the probability of being in
the categories 2,3,4 versus category 1. Note that your effective
sample sizes are very small which means mixing is a problem and you
need to run it for longer. Numerical/Inferential problems can also
occur if the joint distribution of the predictors and the outcomes
results in `extreme categorical problems'. You then might want to
follow Gelman's advice on priors for fixed effects. See the function
gelman.prior.
Cheers,
Jarrod
Quoting Sereina Graber <sereina.gra...@gmx.ch> on Fri, 2 Aug 2013
14:48:44 +0200 (CEST):
Great, thanks a lot! Then I have one last question: How do I have to
interpret the following output of the location effects? the first
three lines I guess represent the intercepts of categories 2 to 4, but
how I should I interpret the rest having the two covariates lnBrain
(continuous) and binary (binary).
With the following model...
myMCMC.phyl<- MCMCglmm(nominal ~ trait-1+ trait:lnBrain +
trait:binary, random=~us(trait):species, rcov = ~us(trait):units,
pedigree=bird.tree,
+ data = "" family="categorical",
+ prior=Prior.phyl6)
...I got the following location effects:
Location effects: nominal ~ trait - 1 + trait:lnBrain + trait:binary
post.mean l-95% CI u-95% CI eff.samp pMCMC
traitnominal.2 5.59844 4.49565 6.90609 9.676 <0.001
***
traitnominal.3 -4.12383 -5.58366 -2.65665 7.794 <0.001
***
traitnominal.4 -1.70863 -2.86831 -0.38491 12.770 0.006
**
traitnominal.2:lnBrain -0.08244 -2.10570 1.57463 3.228 0.880
traitnominal.3:lnBrain -1.29069 -3.36790 1.08456 3.790 0.376
traitnominal.4:lnBrain -0.53814 -2.76265 1.67985 3.859 0.762
traitnominal.2:binary2 -9.59263 -16.21345 -3.88906 3.403 <0.001
***
traitnominal.3:binary2 13.37745 9.26769 19.93064 4.247 <0.001
***
traitnominal.4:binary2 8.61585 3.82747 15.54171 3.446 <0.001
***
---
Best & thank you so much for your help!
GESENDET: Freitag, 02. August 2013 um 13:55 Uhr
VON: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk>
AN: "sereina.graber" <sereina.gra...@gmx.ch>
CC: r-sig-phylo@r-project.org
BETREFF: Re: [R-sig-phylo] WG: Re: Aw: Re: MCMCglmm for categorical
data with more than 2 levels - prior specification?
Hi,
1.) There is no difference between the arguments pedigree=bird.tree
and "ginverse = list(species=Ainv)" where Ainv is defined by
"Ainv=inverseA(bird.tree)$Ainv". The latter argument was added after
the first version in order to provide more flexibility (for example if
multiple phylogenies are to be fitted).
2.)and 4.) You have also fixed the phylogenetic covariance matrix in
the prior (by using fix=1). You should remove the fix=1 if you want to
actually estimate it rather than fix it. You should also add trait as
a main effect to allow the traits to have different intercepts. Its
hard to know what to recommend regarding prior information, but you
could start perhaps with V=IJ and nu low (see CourseNotes).
3.) The number of traits is one less than the number of categories, so
for a binary response there is only one trait. This is because if yuo
know the probability of being in one state (Pr(A)), you already know
the probability of being in the other state (1-Pr(A)). The covariance
matrix specification in the prior should therefore be 1x1 not 2x2. You
should also drop trait from the models and just have ~species, ~units
etc.
Cheers,
Jarrod
Quoting "sereina.graber" <sereina.gra...@gmx.ch> on Fri, 02 Aug 2013
12:54:00 +0200:
>
>
>
> -------- Ursprüngliche Nachricht --------
> Betreff: Re: Aw: Re: [R-sig-phylo] MCMCglmm for categorical data
> with more than 2 levels - prior specification?
> Von: Jarrod Hadfield <j.hadfi...@ed.ac.uk>
> An: Sereina Graber <sereina.gra...@gmx.ch>
> CC:
>
>
>
> Quoting Sereina Graber <sereina.gra...@gmx.ch> on Fri, 2 Aug 2013
> 12:12:41 +0200 (CEST):
>
>
>
> Hi Jarrod,
>
> Thanks a lot for those helpful tips. However, now I ran into some
> further problems:
>
> 1.) What is the difference between the arguments pedigree=bird.tree
> and "ginverse = list(species=Ainv)" where Ainv is defined by
> "Ainv=inverseA(bird.tree)$Ainv"?
>
> 2.) Now the nominal model seems to work with the following code, did
I
> implement it right like that?
>
> Prior.phyl3 = list(R = list(V = diag(3), fix=1),G = list( G1 =
list(V
> = diag(3) ,fix=1)))
> myMCMC.phyl<- MCMCglmm(nominal ~ trait:lnBrain,
> random=~us(trait):species, rcov = ~us(trait):units, ginverse =
> list(species=Ainv), data = "" family="categorical",
> prior=Prior.phyl3)
>
> However, if I try the same code with an adjusted prior specification
> for a binary response variable
>
> Prior.phyl31 = list(R = list(V = diag(2), fix=1),G = list( G1 =
list(V
> = diag(2),fix=1)))
> myMCMC.phyl<- MCMCglmm(binary ~ trait:lnBrain,
> random=~us(trait):species, rcov = ~us(trait):units,
> pedigree=bird.tree,
> data = "" family="categorical",
> prior=Prior.phyl31)
>
> Then I always get the error:
> Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
> contrasts can be applied only to factors with 2 or more levels
>
> What is the problem here?
>
> 3.) And about prior specifications: I found out that depending on
what
> prior you specifiy, the results are completely different. So for the
> example above, I used a identity matrix for the variance-covariance
> matrix, so the covariances are equal to zero. In my case now having
4
> levels in my nominal response variable should I put some covariances
> or not, and if yes, how do I choose them? What kind of prior would
you
> take?
> And for G: G is the covariance structure of the random effects, but
> aren`t actually the (co)variances of the random effects specified by
> the vcv of the tree? so why is that a 3times3 matrix? For the
> (co)variance structure of B: if I have two covariates, and I
simulated
> them to be correlated with r=0.5, what covariances in B can I take?
> would 0.5 be appropriate assuming SD=1?
>
> Thanks a lot & Best,
> Sereina
>
> GESENDET: Freitag, 02. August 2013 um 11:03 Uhr
> VON: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk>
> AN: "Sereina Graber" <sereina.gra...@gmx.ch>
> CC: r-sig-phylo@r-project.org
> BETREFF: Re: [R-sig-phylo] MCMCglmm for categorical data with more
> than 2 levels - prior specification?
> Hi Sereina,
>
> You should not get that error message when you do not specify a
prior
> - but if you do can you let me know.
>
> For the prior you specified you get the error message because
> us(trait):units is specifying a 3x3 covariance matrix, and yet your
> prior, R=list(V=1,nu=0.002), is specifying a 1x1 matrix. V should be
a
> 3x3 matrix, but note that the residual covariance matrix with
> categorical data cannot be estimated from the data. For this reason
> most people would not fit a weak prior (i.e. nu=0.002) but fit a
very
> strong prior (fixing it at some value a priori using fix=1 in the
> prior specification). The choice of residual covariance matrix is
> arbitrary - the results can always be expressed in a way that do not
> depend on the choice of residual covariance matrix (See the
> CourseNotes).
>
> The fixed and random effect formulae are also a bit odd. This type
of
> model is essentially equivalent to a trivariate model where the
three
> traits (on the latent scale) are the differences on a log scale
> between the probability of being in categories 2,3 or 4 compared to
> category 1:
>
> log(Pr(nominal[2]))-log(Pr(nominal[1]))
> log(Pr(nominal[3]))-log(Pr(nominal[1]))
> log(Pr(nominal[4]))-log(Pr(nominal[1]))
>
> where nominal[1] is called the baseline category. You can change the
> baseline category by reordering the factor levels in nominal.
>
> By having ~animal in the random formula you are assuming that a) the
> phylogenetic variance for each contrast is equal and b) that the
> correlation between the phylogenetic effects is one. This may make
> sense in some models and with some types of base-line category, but
> not generally I think. us(trait):animal allows the phylogenetic
> variances to differ over the traits and for each pair of traits to
> have a unique phylogenetic correlation. There are also other
variance
> structures that can be fitted that are somewhere between these two
> extremes.
>
> For the same reason you probably want to have trait specific
> intercepts and trait specific regression coefficients for the
> covariates. This can be achieved by having:
>
> ~ trait-1+trait:lnBrain + trait:binary.x
>
> I remove the global intercept (-1) because I find the model output
> easier to interpret, but it is not necessary.
>
> You need to be careful with this type of model on these type of
data,
> because generally there is not much information from data on extant
> taxa about the parameters of comparative analyses, particularly when
> the data are categorical. This means that priors, even ones that
> appear innocuous such as flat priors, may have a substantial
influence
> on the posterior. In addition, numerical problems may exist in
> categorical models when the posterior distribution for the
> phylogenetic intra-class correlations has support in regions close
to
> one (either because the true value is close to one, or because the
> posterior distribution is very wide because the data are not very
> informative). This can be checked by saving the latent variables
> (pL=TRUE in the call to MCMCglmm) and making sure that the absolute
> values of the latent variables do not regularly exceed 20. Lastly,
> mixing may be (very) poor so you may have to wait an inordinate
amount
> of time to completely sample the posterior.
>
> Cheers,
>
> Jarrod
>
> Doing this is fine: you can always rescale the model parameters post
> analysis
>
> Quoting Sereina Graber <sereina.gra...@gmx.ch> on Fri, 2 Aug 2013
> 10:17:58 +0200 (CEST):
>
> Hi all,
>
> I am doing a phylogenetic analysis using the MCMCglmm package with
the
> phylogenetic tree as the pedigree (Hadfield & Nakagawa 2010). I have
a
> categorical response variable ("nominal") with more than 2
categories
> (4 categories in total) and a continuous and a binary explanatory
> variable. My model:
>
> mod<-MCMCglmm(nominal ~ lnBrain + binary.x, random= ~animal,
> family="categorical",rcov=~us(trait):units, prior=prior4,
> data="" pedigree=bird.tree)
>
> Now there is always the following error message appearing if I do
not
> specify any priors, thus, using the default:
>
> Error in priorformat(if (NOpriorG) { :
> V is the wrong dimension for some prior$G/prior$R elements
>
> However, I then tried different priors which didn`t work, because I
> would have the wrong dimensions in the prior...can any one help me
> with how I have to specifiy the priors correctly, what dimensions do
I
> need? My priors:
>
> var2<-cbind(c(1e+08,0.1,0.1), c(0.1,1e+08,0.1),c(0.1,0.1,1e+08))
> prior4<-list(R=list(V=1,nu=0.002), G=list(G1=list(V=1,
> nu=0.002)),B=list(mu=rep(0,3), V=var2))
>
> These priors lead to the error:
>
> Error in priorformat(if (NOpriorG) { :
> V is the wrong dimension for some prior$G/prior$R elements
>
> For any help I am very grateful.
>
> Best
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
> [[alternative HTML version deleted]]
>
>
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
They are the effect of the covariates on the probability of being in
the categories 2,3,4 versus category 1. Note that your effective
sample sizes are very small which means mixing is a problem and you
need to run it for longer. Numerical/Inferential problems can also
occur if the joint distribution of the predictors and the outcomes
results in `extreme categorical problems'. You then might want to
follow Gelman's advice on priors for fixed effects. See the function
gelman.prior.
Cheers,
Jarrod
Quoting Sereina Graber <sereina.gra...@gmx.ch> on Fri, 2 Aug 2013
14:48:44 +0200 (CEST):
Great, thanks a lot! Then I have one last question: How do I have to
interpret the following output of the location effects? the first
three lines I guess represent the intercepts of categories 2 to 4, but
how I should I interpret the rest having the two covariates lnBrain
(continuous) and binary (binary).
With the following model...
myMCMC.phyl<- MCMCglmm(nominal ~ trait-1+ trait:lnBrain +
trait:binary, random=~us(trait):species, rcov = ~us(trait):units,
pedigree=bird.tree,
+ data = "" family="categorical",
+ prior=Prior.phyl6)
...I got the following location effects:
Location effects: nominal ~ trait - 1 + trait:lnBrain + trait:binary
post.mean l-95% CI u-95% CI eff.samp pMCMC
traitnominal.2 5.59844 4.49565 6.90609 9.676 <0.001
***
traitnominal.3 -4.12383 -5.58366 -2.65665 7.794 <0.001
***
traitnominal.4 -1.70863 -2.86831 -0.38491 12.770 0.006
**
traitnominal.2:lnBrain -0.08244 -2.10570 1.57463 3.228 0.880
traitnominal.3:lnBrain -1.29069 -3.36790 1.08456 3.790 0.376
traitnominal.4:lnBrain -0.53814 -2.76265 1.67985 3.859 0.762
traitnominal.2:binary2 -9.59263 -16.21345 -3.88906 3.403 <0.001
***
traitnominal.3:binary2 13.37745 9.26769 19.93064 4.247 <0.001
***
traitnominal.4:binary2 8.61585 3.82747 15.54171 3.446 <0.001
***
---
Best & thank you so much for your help!
GESENDET: Freitag, 02. August 2013 um 13:55 Uhr
VON: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk>
AN: "sereina.graber" <sereina.gra...@gmx.ch>
CC: r-sig-phylo@r-project.org
BETREFF: Re: [R-sig-phylo] WG: Re: Aw: Re: MCMCglmm for categorical
data with more than 2 levels - prior specification?
Hi,
1.) There is no difference between the arguments pedigree=bird.tree
and "ginverse = list(species=Ainv)" where Ainv is defined by
"Ainv=inverseA(bird.tree)$Ainv". The latter argument was added after
the first version in order to provide more flexibility (for example if
multiple phylogenies are to be fitted).
2.)and 4.) You have also fixed the phylogenetic covariance matrix in
the prior (by using fix=1). You should remove the fix=1 if you want to
actually estimate it rather than fix it. You should also add trait as
a main effect to allow the traits to have different intercepts. Its
hard to know what to recommend regarding prior information, but you
could start perhaps with V=IJ and nu low (see CourseNotes).
3.) The number of traits is one less than the number of categories, so
for a binary response there is only one trait. This is because if yuo
know the probability of being in one state (Pr(A)), you already know
the probability of being in the other state (1-Pr(A)). The covariance
matrix specification in the prior should therefore be 1x1 not 2x2. You
should also drop trait from the models and just have ~species, ~units
etc.
Cheers,
Jarrod
Quoting "sereina.graber" <sereina.gra...@gmx.ch> on Fri, 02 Aug 2013
12:54:00 +0200:
>
>
>
> -------- Ursprüngliche Nachricht --------
> Betreff: Re: Aw: Re: [R-sig-phylo] MCMCglmm for categorical data
> with more than 2 levels - prior specification?
> Von: Jarrod Hadfield <j.hadfi...@ed.ac.uk>
> An: Sereina Graber <sereina.gra...@gmx.ch>
> CC:
>
>
>
> Quoting Sereina Graber <sereina.gra...@gmx.ch> on Fri, 2 Aug 2013
> 12:12:41 +0200 (CEST):
>
>
>
> Hi Jarrod,
>
> Thanks a lot for those helpful tips. However, now I ran into some
> further problems:
>
> 1.) What is the difference between the arguments pedigree=bird.tree
> and "ginverse = list(species=Ainv)" where Ainv is defined by
> "Ainv=inverseA(bird.tree)$Ainv"?
>
> 2.) Now the nominal model seems to work with the following code, did
I
> implement it right like that?
>
> Prior.phyl3 = list(R = list(V = diag(3), fix=1),G = list( G1 =
list(V
> = diag(3) ,fix=1)))
> myMCMC.phyl<- MCMCglmm(nominal ~ trait:lnBrain,
> random=~us(trait):species, rcov = ~us(trait):units, ginverse =
> list(species=Ainv), data = "" family="categorical",
> prior=Prior.phyl3)
>
> However, if I try the same code with an adjusted prior specification
> for a binary response variable
>
> Prior.phyl31 = list(R = list(V = diag(2), fix=1),G = list( G1 =
list(V
> = diag(2),fix=1)))
> myMCMC.phyl<- MCMCglmm(binary ~ trait:lnBrain,
> random=~us(trait):species, rcov = ~us(trait):units,
> pedigree=bird.tree,
> data = "" family="categorical",
> prior=Prior.phyl31)
>
> Then I always get the error:
> Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
> contrasts can be applied only to factors with 2 or more levels
>
> What is the problem here?
>
> 3.) And about prior specifications: I found out that depending on
what
> prior you specifiy, the results are completely different. So for the
> example above, I used a identity matrix for the variance-covariance
> matrix, so the covariances are equal to zero. In my case now having
4
> levels in my nominal response variable should I put some covariances
> or not, and if yes, how do I choose them? What kind of prior would
you
> take?
> And for G: G is the covariance structure of the random effects, but
> aren`t actually the (co)variances of the random effects specified by
> the vcv of the tree? so why is that a 3times3 matrix? For the
> (co)variance structure of B: if I have two covariates, and I
simulated
> them to be correlated with r=0.5, what covariances in B can I take?
> would 0.5 be appropriate assuming SD=1?
>
> Thanks a lot & Best,
> Sereina
>
> GESENDET: Freitag, 02. August 2013 um 11:03 Uhr
> VON: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk>
> AN: "Sereina Graber" <sereina.gra...@gmx.ch>
> CC: r-sig-phylo@r-project.org
> BETREFF: Re: [R-sig-phylo] MCMCglmm for categorical data with more
> than 2 levels - prior specification?
> Hi Sereina,
>
> You should not get that error message when you do not specify a
prior
> - but if you do can you let me know.
>
> For the prior you specified you get the error message because
> us(trait):units is specifying a 3x3 covariance matrix, and yet your
> prior, R=list(V=1,nu=0.002), is specifying a 1x1 matrix. V should be
a
> 3x3 matrix, but note that the residual covariance matrix with
> categorical data cannot be estimated from the data. For this reason
> most people would not fit a weak prior (i.e. nu=0.002) but fit a
very
> strong prior (fixing it at some value a priori using fix=1 in the
> prior specification). The choice of residual covariance matrix is
> arbitrary - the results can always be expressed in a way that do not
> depend on the choice of residual covariance matrix (See the
> CourseNotes).
>
> The fixed and random effect formulae are also a bit odd. This type
of
> model is essentially equivalent to a trivariate model where the
three
> traits (on the latent scale) are the differences on a log scale
> between the probability of being in categories 2,3 or 4 compared to
> category 1:
>
> log(Pr(nominal[2]))-log(Pr(nominal[1]))
> log(Pr(nominal[3]))-log(Pr(nominal[1]))
> log(Pr(nominal[4]))-log(Pr(nominal[1]))
>
> where nominal[1] is called the baseline category. You can change the
> baseline category by reordering the factor levels in nominal.
>
> By having ~animal in the random formula you are assuming that a) the
> phylogenetic variance for each contrast is equal and b) that the
> correlation between the phylogenetic effects is one. This may make
> sense in some models and with some types of base-line category, but
> not generally I think. us(trait):animal allows the phylogenetic
> variances to differ over the traits and for each pair of traits to
> have a unique phylogenetic correlation. There are also other
variance
> structures that can be fitted that are somewhere between these two
> extremes.
>
> For the same reason you probably want to have trait specific
> intercepts and trait specific regression coefficients for the
> covariates. This can be achieved by having:
>
> ~ trait-1+trait:lnBrain + trait:binary.x
>
> I remove the global intercept (-1) because I find the model output
> easier to interpret, but it is not necessary.
>
> You need to be careful with this type of model on these type of
data,
> because generally there is not much information from data on extant
> taxa about the parameters of comparative analyses, particularly when
> the data are categorical. This means that priors, even ones that
> appear innocuous such as flat priors, may have a substantial
influence
> on the posterior. In addition, numerical problems may exist in
> categorical models when the posterior distribution for the
> phylogenetic intra-class correlations has support in regions close
to
> one (either because the true value is close to one, or because the
> posterior distribution is very wide because the data are not very
> informative). This can be checked by saving the latent variables
> (pL=TRUE in the call to MCMCglmm) and making sure that the absolute
> values of the latent variables do not regularly exceed 20. Lastly,
> mixing may be (very) poor so you may have to wait an inordinate
amount
> of time to completely sample the posterior.
>
> Cheers,
>
> Jarrod
>
> Doing this is fine: you can always rescale the model parameters post
> analysis
>
> Quoting Sereina Graber <sereina.gra...@gmx.ch> on Fri, 2 Aug 2013
> 10:17:58 +0200 (CEST):
>
> Hi all,
>
> I am doing a phylogenetic analysis using the MCMCglmm package with
the
> phylogenetic tree as the pedigree (Hadfield & Nakagawa 2010). I have
a
> categorical response variable ("nominal") with more than 2
categories
> (4 categories in total) and a continuous and a binary explanatory
> variable. My model:
>
> mod<-MCMCglmm(nominal ~ lnBrain + binary.x, random= ~animal,
> family="categorical",rcov=~us(trait):units, prior=prior4,
> data="" pedigree=bird.tree)
>
> Now there is always the following error message appearing if I do
not
> specify any priors, thus, using the default:
>
> Error in priorformat(if (NOpriorG) { :
> V is the wrong dimension for some prior$G/prior$R elements
>
> However, I then tried different priors which didn`t work, because I
> would have the wrong dimensions in the prior...can any one help me
> with how I have to specifiy the priors correctly, what dimensions do
I
> need? My priors:
>
> var2<-cbind(c(1e+08,0.1,0.1), c(0.1,1e+08,0.1),c(0.1,0.1,1e+08))
> prior4<-list(R=list(V=1,nu=0.002), G=list(G1=list(V=1,
> nu=0.002)),B=list(mu=rep(0,3), V=var2))
>
> These priors lead to the error:
>
> Error in priorformat(if (NOpriorG) { :
> V is the wrong dimension for some prior$G/prior$R elements
>
> For any help I am very grateful.
>
> Best
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
> [[alternative HTML version deleted]]
>
>
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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