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Ebert,Timothy Aaron

2022-Oct-13 12:03 UTC

[R] prcomp - arbitrary direction of the returned principal components

I still do not understand. However, the general approach would be to identify a
specific value to test. If the test is TRUE then do "this" otherwise
do nothing. Once the test condition is properly identified, the coding easily
follows.

 abs() is the same as
if x<0 then x = -x   (non-R code, just idea)
The R code might look something more like
for (number in 1:ncol(x)){
   if (x[3,2] < 0) {
         x[number, number] = -x[number, number] #only change the diagonal
   }
}

Depending on what values need to be changed you may need a nested for loop to go
through all values of x[number1, number2].

Your words: " I can forcefully use a NEGATIVE sign to FLIP the index when
it is LOW." Where it appeared that "low" was defined as values
that are negative. You still will have low values (close to zero) and high
values (far from zero).

You could make the condition some other value:

if x< -4 then x = -x

If you just want to rotate about zero then 
x = -x
In this case the positive values will become negative and the negative values
positive.
Add an if test to selectively rotate based on the value of a single test element
in x (as in x[3,2]).

In debugging or trouble shooting setting seed is useful. For actual data
analysis you should not set seed, or possibly better yet use set.seed(NULL).

Tim



-----Original Message-----
From: Ashim Kapoor <ashimkapoor at gmail.com> 
Sent: Thursday, October 13, 2022 12:28 AM
To: Ebert,Timothy Aaron <tebert at ufl.edu>
Cc: R Help <r-help at r-project.org>
Subject: Re: [R] prcomp - arbitrary direction of the returned principal
components

[External Email]

Dear Aaron,

Many thanks for your reply.

Please allow me to illustrate my query a bit.

I take some data, throw it to prcomp and extract the x data frame from prcomp.
>From ?prcomp:
       x: if 'retx' is true the value of the rotated data (the centred
          (and scaled if requested) data multiplied by the 'rotation'
          matrix) is returned.  Hence, 'cov(x)' is the diagonal matrix
          'diag(sdev^2)'.  For the formula method, 'napredict()'
is
          applied to handle the treatment of values omitted by the
          'na.action'.

I consider x[,1] as my index. This makes sense as x[,1] is the projection of the
data on the FIRST principal component.
Now this x[,1] can be a high +ve number or a low -ve number. I can't ignore
the sign.

If I ignore the sign by taking the absolute value, the HIGH / LOW stress values
will be indistinguishable.

Hence I do not think using absolute values of x[,1] is the solution.
Yes it will make the results REPRODUCIBLE but that will be at the cost of losing
information.

Any other idea ?

Many thanks,
Ashim

On Wed, Oct 12, 2022 at 5:23 PM Ebert,Timothy Aaron <tebert at ufl.edu>
wrote:>
> Use absolute value
>
> Tim
>
> -----Original Message-----
> From: R-help <r-help-bounces at r-project.org> On Behalf Of Ashim
Kapoor
> Sent: Wednesday, October 12, 2022 7:48 AM
> To: R Help <r-help at r-project.org>
> Subject: [R] prcomp - arbitrary direction of the returned principal 
> components
>
> [External Email]
>
> Dear R experts,
>
> From ?prcomp,
>
> ---- snip -----
> Note:
>
>      The signs of the columns of the rotation matrix are arbitrary, and
>      so may differ between different programs for PCA, and even between
>      different builds of R.
> ---- snip ------
>
> My problem is that I am building an index based on Principal Components
Analysis.
> When the index is high it should indicate stress in the market. Due to the
arbitrary sign sometimes I get an index which is HIGH when there is stress and
sometimes I get  the OPPOSITE - an index which is LOW when there is stress.
> This program is shared with other people who may have a different build of
R.
>
> I can forcefully use a NEGATIVE sign to FLIP the index when it is LOW.
> That works.
>
> Now my query is : Just like we do set.seed(1234) and force the pattern of
generation of random number and make it REPRODUCIBLE, can I do something like :
>
> set.direction.for.vector.in.pca(1234)
>
> Now each time I do prcomp it should choose the SAME ( high or low )
direction of the principle component on ANY computer having ANY version of R
installed.
>
> That's what I want. I don't want the the returned principal
component to be HIGH(LOW) on my computer and LOW(HIGH) on someone else's
computer.
> That would confuse the people the code is shared with.
>
> Is this possible ? How do people deal with this ?
>
> Many thanks,
> Ashim
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat
> .ethz.ch%2Fmailman%2Flistinfo%2Fr-help&amp;data=05%7C01%7Ctebert%40ufl
> .edu%7C60e6d6ae8645462db99b08daacd36b76%7C0d4da0f84a314d76ace60a62331e
> 1b84%7C0%7C0%7C638012321302591064%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w
> LjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C
>
&amp;sdata=AHMEDU%2BTyInvW%2FH6EZQteO1qZ%2BtW3JZfybfaveTD8Yk%3D&amp;re
> served=0 PLEASE do read the posting guide 
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r
> -project.org%2Fposting-guide.html&amp;data=05%7C01%7Ctebert%40ufl.edu%
> 7C60e6d6ae8645462db99b08daacd36b76%7C0d4da0f84a314d76ace60a62331e1b84%
> 7C0%7C0%7C638012321302591064%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM
> DAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;
> sdata=yavXAiQorhZjPTozG4Ulo8SuNmR6XFhvA%2FLX9Tfwgi0%3D&amp;reserved=0
> and provide commented, minimal, self-contained, reproducible code.

Ashim Kapoor

2022-Oct-13 14:05 UTC

head link

[R] prcomp - arbitrary direction of the returned principal components

Dear All,

Many thanks for your replies.

My PC1 loading turns out to be :

1/sqrt(2) , -1/sqrt(2)

In simple words : I had 2 variables and I ran prcomp on them. I got my
PC1 as :  .7071068 var1 - .7071068 var2

PC2 turned out to be the same as PC1 with a PLUS replacing the minus,
ie. .7071068 var1 + .7071068 var2

But forget PC2 for the time being.

Now my question is : I am not able to use the rule that : choose the
variable with a bigger magnitude of loading and multiply PC1 by -1 if
needed (to flip the PC1 since any vector x and it's flipped version -x
 are the same vector but with opposite direction) if the variable with
bigger magnitude is of negative sign.

I have an alternative measure of stress which is trending UP and has 2
peaks during 2 recessions and I can see that PC1 is trending DOWN and
has 2 TROUGHS during the same recessions. That's how I wish to FLIP
PC1 with a negative sign.

The data is not mine and I am not at liberty to share it. I can
construct an artificial example but I would need time to do that.

That's what's happening.

Best Regards and
Many thanks.
Ashim









On Thu, Oct 13, 2022 at 5:38 PM Ebert,Timothy Aaron <tebert at ufl.edu>
wrote:>
> I still do not understand. However, the general approach would be to
identify a specific value to test. If the test is TRUE then do "this"
otherwise do nothing. Once the test condition is properly identified, the coding
easily follows.
>
>  abs() is the same as
> if x<0 then x = -x   (non-R code, just idea)
> The R code might look something more like
> for (number in 1:ncol(x)){
>    if (x[3,2] < 0) {
>          x[number, number] = -x[number, number] #only change the diagonal
>    }
> }
>
> Depending on what values need to be changed you may need a nested for loop
to go through all values of x[number1, number2].
>
> Your words: " I can forcefully use a NEGATIVE sign to FLIP the index
when it is LOW." Where it appeared that "low" was defined as
values that are negative. You still will have low values (close to zero) and
high values (far from zero).
>
> You could make the condition some other value:
>
> if x< -4 then x = -x
>
> If you just want to rotate about zero then
> x = -x
> In this case the positive values will become negative and the negative
values positive.
> Add an if test to selectively rotate based on the value of a single test
element in x (as in x[3,2]).
>
> In debugging or trouble shooting setting seed is useful. For actual data
analysis you should not set seed, or possibly better yet use set.seed(NULL).
>
> Tim
>
>
>
> -----Original Message-----
> From: Ashim Kapoor <ashimkapoor at gmail.com>
> Sent: Thursday, October 13, 2022 12:28 AM
> To: Ebert,Timothy Aaron <tebert at ufl.edu>
> Cc: R Help <r-help at r-project.org>
> Subject: Re: [R] prcomp - arbitrary direction of the returned principal
components
>
> [External Email]
>
> Dear Aaron,
>
> Many thanks for your reply.
>
> Please allow me to illustrate my query a bit.
>
> I take some data, throw it to prcomp and extract the x data frame from
prcomp.
>
> From ?prcomp:
>
>        x: if 'retx' is true the value of the rotated data (the
centred
>           (and scaled if requested) data multiplied by the
'rotation'
>           matrix) is returned.  Hence, 'cov(x)' is the diagonal
matrix
>           'diag(sdev^2)'.  For the formula method,
'napredict()' is
>           applied to handle the treatment of values omitted by the
>           'na.action'.
>
> I consider x[,1] as my index. This makes sense as x[,1] is the projection
of the data on the FIRST principal component.
> Now this x[,1] can be a high +ve number or a low -ve number. I can't
ignore the sign.
>
> If I ignore the sign by taking the absolute value, the HIGH / LOW stress
values will be indistinguishable.
>
> Hence I do not think using absolute values of x[,1] is the solution.
> Yes it will make the results REPRODUCIBLE but that will be at the cost of
losing information.
>
> Any other idea ?
>
> Many thanks,
> Ashim
>
> On Wed, Oct 12, 2022 at 5:23 PM Ebert,Timothy Aaron <tebert at
ufl.edu> wrote:
> >
> > Use absolute value
> >
> > Tim
> >
> > -----Original Message-----
> > From: R-help <r-help-bounces at r-project.org> On Behalf Of
Ashim Kapoor
> > Sent: Wednesday, October 12, 2022 7:48 AM
> > To: R Help <r-help at r-project.org>
> > Subject: [R] prcomp - arbitrary direction of the returned principal
> > components
> >
> > [External Email]
> >
> > Dear R experts,
> >
> > From ?prcomp,
> >
> > ---- snip -----
> > Note:
> >
> >      The signs of the columns of the rotation matrix are arbitrary,
and
> >      so may differ between different programs for PCA, and even
between
> >      different builds of R.
> > ---- snip ------
> >
> > My problem is that I am building an index based on Principal
Components Analysis.
> > When the index is high it should indicate stress in the market. Due to
the arbitrary sign sometimes I get an index which is HIGH when there is stress
and sometimes I get  the OPPOSITE - an index which is LOW when there is stress.
> > This program is shared with other people who may have a different
build of R.
> >
> > I can forcefully use a NEGATIVE sign to FLIP the index when it is LOW.
> > That works.
> >
> > Now my query is : Just like we do set.seed(1234) and force the pattern
of generation of random number and make it REPRODUCIBLE, can I do something like
:
> >
> > set.direction.for.vector.in.pca(1234)
> >
> > Now each time I do prcomp it should choose the SAME ( high or low )
direction of the principle component on ANY computer having ANY version of R
installed.
> >
> > That's what I want. I don't want the the returned principal
component to be HIGH(LOW) on my computer and LOW(HIGH) on someone else's
computer.
> > That would confuse the people the code is shared with.
> >
> > Is this possible ? How do people deal with this ?
> >
> > Many thanks,
> > Ashim
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat
> >
.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&amp;data=05%7C01%7Ctebert%40ufl
> > .edu%7C60e6d6ae8645462db99b08daacd36b76%7C0d4da0f84a314d76ace60a62331e
> > 1b84%7C0%7C0%7C638012321302591064%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4w
> > LjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C
> >
&amp;sdata=AHMEDU%2BTyInvW%2FH6EZQteO1qZ%2BtW3JZfybfaveTD8Yk%3D&amp;re
> > served=0 PLEASE do read the posting guide
> > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r
> >
-project.org%2Fposting-guide.html&amp;data=05%7C01%7Ctebert%40ufl.edu%
> > 7C60e6d6ae8645462db99b08daacd36b76%7C0d4da0f84a314d76ace60a62331e1b84%
> > 7C0%7C0%7C638012321302591064%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwM
> >
DAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;
> >
sdata=yavXAiQorhZjPTozG4Ulo8SuNmR6XFhvA%2FLX9Tfwgi0%3D&amp;reserved=0
> > and provide commented, minimal, self-contained, reproducible code.

R help - Oct 2022 - prcomp - arbitrary direction of the returned principal components

[R] prcomp - arbitrary direction of the returned principal components

[R] prcomp - arbitrary direction of the returned principal components