Re: [MORPHMET] help us in multifactor Manova

[mahendiran mylswamy]

Mike,

That's amazing, you nailed it, finally. Great!

Yes, I didn’t have all levels of stages that match all levels of Locations,
and because of this, I am getting such error messages. Thanks a lot indeed,
for educating and enlightening me, on these aspects.

I do have some other factors with equal levels (Sex, Location). However,
the sample size may not be 147 but will have 51 observations altogether!.
Let me try this and I will let you know, probably give some more troubles
on the trajectory as well, so catch you soon.

Thanks a lot indeed, Mike

Truly

Mahen


On Fri, May 18, 2018 at 4:25 PM, Mike Collyer  wrote:

> Mahen,
>
> I think the issue is because you might not have all levels of Location
> matched with all Levels of Stages.  It appears you have 5 stages and 2
> locations.  For the model that worked, you will notice 5 rows in your ANOVA
> table.  In the one that didn’t, it was attempting to create a table with 9
> rows, which would include the 4 interactions created by your new model.
>  (Sorry I did not catch this before.)  The error implies that the the
> number of SS items and df items do not match, which suggests to me that two
> of the interactions do not work, based on your sample.
>
> You might consider the following,
>
> model.matrix( ~ Csize * ind$Stages * ind$Location)
>
> This will be a large matrix.  Check the matrix for columns of all 0s.  If
> you find that, it suggests that you are missing some factor interactions.
> If this is not the issue, then maybe you could send me your data and R
> script and I’ll try to figure out if there is a different problem.
>
> Best,
> Mike
>
> On May 18, 2018, at 2:56 AM, mahendiran mylswamy 
> wrote:
>
> My sample size is 147 not either 9 or 7 in any case. I agree that the
> computer displays these numbers! don't know why?
>
> Nevertheless, in this analysis the number of specimens (dependent shape
> variable) is 147, obviously, with the equal number of observations for each
> independent variables (here, we used two factors ind$Stages and
> ind$Location ).
>
>  It is interesting to note that I am getting good results using single
> factor Manova; dependent shape variable over, either  ind$stages or
> ind$location, at a given time,  though with/without interactions as well. 
> Even,
> it works fine with more factors if I model without any effect of
> interaction, and the results are given below
>
> > Paint<-procD.lm(coords ~ Csize + ind$Stages + ind$Location, data = 
> > Paintgeo147, iter = , RRPP = FALSE, print.progress = FALSE, int.first = 
> > FALSE)
>
> > Paint3factor
>
>
>
> Call:
>
> procD.lm(f1 = coords ~ Csize + ind$Stages + ind$Location, iter = ,
>
> RRPP = FALSE, int.first = FALSE, data = Paintgeo147, print.progress = 
> FALSE)
>
>
>
>
>
>
>
> Type I (Sequential) Sums of Squares and Cross-products
>
> Randomization of Raw Values used
>
> 1 Permutations
>
>
>
>   Df  SS   MS  Rsq   F  Z Pr(>F)
>
> Csize  1 0.04688 0.046880 0.064257 13.4431 7.9867  1e-04 ***
>
> ind$Stages 4 0.17575 0.043938 0.240899 12.5994 8.3726  1e-04 ***
>
> ind$Location   1 0.01871 0.018713 0.025650  5.3662 3.2145 0.0042 **
>
> Residuals140 0.48822 0.003487
>
> Total146 0.72956
>
> ---
>
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>
>
>
> The main issue, here, is that somehow I don’t know how to use the proper
> command to quantify effects of interaction, say for example ind$Stages:
> ind$Location, Csize: ind$Stages, Csize: ind$Locations... etc. 
>
> Thanks for spending your time and effort!
>
> Looking forward
>
> Truly
>
> Mahen
>
>
> On Fri, May 18, 2018 at 12:05 AM, Mike Collyer 
> wrote:
>
>> OK, this error is indicating you have variables of different size - one
>> with 9 and one with 7.  This does not appear to be because of the int.first
>> issue, but rather that you introduced a new variable with a different
>> number of observations.  Also, I’m not sure what kind of result you expect
>> with such a complex model and so few observations.  It might not work,
>> anyway, because the number of independent variables exceeds the number of
>> observations.  Just a warning.
>>
>> Mike
>>
>>
>> On May 17, 2018, at 2:19 PM, mahendiran mylswamy 
>> wrote:
>>
>> Hi Mike
>>
>>
>> Thanks indeed for the quick response.
>> error messages are given below
>>
>>
>> > PSfact<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data =
>> rough, iter = 99, RRPP = FALSE, int.first = TRUE, print.progress = FALSE)
>> Error in data.frame(df, SS, MS, Rsq = R2, F = Fs) :
>>   arguments imply differing number of rows: 9, 7
>> In addition: Warning message:
>> In SS/df : longer object length is not a multiple of shorter object length
>>
>>
>>
>>
>>
>>
>> On Thu, May 17, 2018 at 6:22 PM, Mike Collyer 
>> wrote:
>>
>>> Mahen,
>>>
>>> Can you be specific with the error statement?  It might 

Re: [MORPHMET] help us in multifactor Manova

[Mike Collyer]

Mahen,

I think the issue is because you might not have all levels of Location matched 
with all Levels of Stages.  It appears you have 5 stages and 2 locations.  For 
the model that worked, you will notice 5 rows in your ANOVA table.  In the one 
that didn’t, it was attempting to create a table with 9 rows, which would 
include the 4 interactions created by your new model.  (Sorry I did not catch 
this before.)  The error implies that the the number of SS items and df items 
do not match, which suggests to me that two of the interactions do not work, 
based on your sample.

You might consider the following,

model.matrix( ~ Csize * ind$Stages * ind$Location)

This will be a large matrix.  Check the matrix for columns of all 0s.  If you 
find that, it suggests that you are missing some factor interactions.  If this 
is not the issue, then maybe you could send me your data and R script and I’ll 
try to figure out if there is a different problem.

Best,
Mike

> On May 18, 2018, at 2:56 AM, mahendiran mylswamy  wrote:
> 
> My sample size is 147 not either 9 or 7 in any case. I agree that the 
> computer displays these numbers! don't know why?
> 
> Nevertheless, in this analysis the number of specimens (dependent shape 
> variable) is 147, obviously, with the equal number of observations for each 
> independent variables (here, we used two factors ind$Stages and ind$Location 
> ).
> 
>  It is interesting to note that I am getting good results using single factor 
> Manova; dependent shape variable over, either  ind$stages or ind$location, at 
> a given time,  though with/without interactions as well. Even, it works fine 
> with more factors if I model without any effect of interaction, and the 
> results are given below  
> 
> > Paint<-procD.lm(coords ~ Csize + ind$Stages + ind$Location, data = 
> > Paintgeo147, iter = , RRPP = FALSE, print.progress = FALSE, int.first = 
> > FALSE)
> > Paint3factor
>  
> Call:
> procD.lm(f1 = coords ~ Csize + ind$Stages + ind$Location, iter = ,  
> RRPP = FALSE, int.first = FALSE, data = Paintgeo147, print.progress = 
> FALSE) 
>  
>  
>  
> Type I (Sequential) Sums of Squares and Cross-products
> Randomization of Raw Values used
> 1 Permutations
>  
>   Df  SS   MS  Rsq   F  Z Pr(>F)
> Csize  1 0.04688 0.046880 0.064257 13.4431 7.9867  1e-04 ***
> ind$Stages 4 0.17575 0.043938 0.240899 12.5994 8.3726  1e-04 ***
> ind$Location   1 0.01871 0.018713 0.025650  5.3662 3.2145 0.0042 ** 
> Residuals140 0.48822 0.003487   
> Total146 0.72956
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>  
>  
> The main issue, here, is that somehow I don’t know how to use the proper 
> command to quantify effects of interaction, say for example ind$Stages: 
> ind$Location, Csize: ind$Stages, Csize: ind$Locations... etc. 
> 
> Thanks for spending your time and effort!
> 
> Looking forward
> 
> Truly
> 
> Mahen
> 
> 
> 
> On Fri, May 18, 2018 at 12:05 AM, Mike Collyer  > wrote:
> OK, this error is indicating you have variables of different size - one with 
> 9 and one with 7.  This does not appear to be because of the int.first issue, 
> but rather that you introduced a new variable with a different number of 
> observations.  Also, I’m not sure what kind of result you expect with such a 
> complex model and so few observations.  It might not work, anyway, because 
> the number of independent variables exceeds the number of observations.  Just 
> a warning.
> 
> Mike
> 
> 
>> On May 17, 2018, at 2:19 PM, mahendiran mylswamy > > wrote:
>> 
>> Hi Mike
>>  
>> Thanks indeed for the quick response.
>> error messages are given below 
>>  
>> > PSfact<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data = rough, 
>> > iter = 99, RRPP = FALSE, int.first = TRUE, print.progress = FALSE)
>> Error in data.frame(df, SS, MS, Rsq = R2, F = Fs) :
>>   arguments imply differing number of rows: 9, 7
>> In addition: Warning message:
>> In SS/df : longer object length is not a multiple of shorter object length
>> 
>> 
>>  
>> 
>> 
>> 
>> On Thu, May 17, 2018 at 6:22 PM, Mike Collyer > > wrote:
>> Mahen,
>> 
>> Can you be specific with the error statement?  It might not me related to 
>> the int.first use but more so how you set up your formula.  If ind$Stages 
>> and ind$Location are in the data frame, you are asking R to create a model 
>> matrix from dat in an environment within another environment.  This might 
>> cause some problems.
>> 
>> Please let us know what the error says, and we can see if it is obvious.
>> 
>> Cheers!
>> Mike
>> 
>>> On May 17, 2018, at 8:22 AM, mahendiran mylswamy >> > wrote:
>>> 

Re: [MORPHMET] help us in multifactor Manova

[mahendiran mylswamy]

My sample size is 147 not either 9 or 7 in any case. I agree that the
computer displays these numbers! don't know why?

Nevertheless, in this analysis the number of specimens (dependent shape
variable) is 147, obviously, with the equal number of observations for each
independent variables (here, we used two factors ind$Stages and ind$Location
).

 It is interesting to note that I am getting good results using single
factor Manova; dependent shape variable over, either  ind$stages or
ind$location, at a given time,  though with/without interactions as well. Even,
it works fine with more factors if I model without any effect of
interaction, and the results are given below

> Paint<-procD.lm(coords ~ Csize + ind$Stages + ind$Location, data = 
> Paintgeo147, iter = , RRPP = FALSE, print.progress = FALSE, int.first = 
> FALSE)

> Paint3factor



Call:

procD.lm(f1 = coords ~ Csize + ind$Stages + ind$Location, iter = ,

RRPP = FALSE, int.first = FALSE, data = Paintgeo147,
print.progress = FALSE)







Type I (Sequential) Sums of Squares and Cross-products

Randomization of Raw Values used

1 Permutations



  Df  SS   MS  Rsq   F  Z Pr(>F)

Csize  1 0.04688 0.046880 0.064257 13.4431 7.9867  1e-04 ***

ind$Stages 4 0.17575 0.043938 0.240899 12.5994 8.3726  1e-04 ***

ind$Location   1 0.01871 0.018713 0.025650  5.3662 3.2145 0.0042 **

Residuals140 0.48822 0.003487

Total146 0.72956

---

Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1





The main issue, here, is that somehow I don’t know how to use the proper
command to quantify effects of interaction, say for example ind$Stages:
ind$Location, Csize: ind$Stages, Csize: ind$Locations... etc. 

Thanks for spending your time and effort!

Looking forward

Truly

Mahen


On Fri, May 18, 2018 at 12:05 AM, Mike Collyer  wrote:

> OK, this error is indicating you have variables of different size - one
> with 9 and one with 7.  This does not appear to be because of the int.first
> issue, but rather that you introduced a new variable with a different
> number of observations.  Also, I’m not sure what kind of result you expect
> with such a complex model and so few observations.  It might not work,
> anyway, because the number of independent variables exceeds the number of
> observations.  Just a warning.
>
> Mike
>
>
> On May 17, 2018, at 2:19 PM, mahendiran mylswamy 
> wrote:
>
> Hi Mike
>
>
> Thanks indeed for the quick response.
> error messages are given below
>
>
> > PSfact<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data =
> rough, iter = 99, RRPP = FALSE, int.first = TRUE, print.progress = FALSE)
> Error in data.frame(df, SS, MS, Rsq = R2, F = Fs) :
>   arguments imply differing number of rows: 9, 7
> In addition: Warning message:
> In SS/df : longer object length is not a multiple of shorter object length
>
>
>
>
>
>
> On Thu, May 17, 2018 at 6:22 PM, Mike Collyer  wrote:
>
>> Mahen,
>>
>> Can you be specific with the error statement?  It might not me related to
>> the int.first use but more so how you set up your formula.  If ind$Stages
>> and ind$Location are in the data frame, you are asking R to create a model
>> matrix from dat in an environment within another environment.  This might
>> cause some problems.
>>
>> Please let us know what the error says, and we can see if it is obvious.
>>
>> Cheers!
>> Mike
>>
>> On May 17, 2018, at 8:22 AM, mahendiran mylswamy 
>> wrote:
>>
>> Dear All.
>>
>> I did a single and multi-factor Manova, through Geomorph package in R,
>> using the following commands given below, it is working fine!
>>
>> *Paint1factor <-procD.lm (coords ~ Csize*indep1$Stages, data =
>> Paintgeo147, iter = , RRPP = FALSE, print.progress = FALSE)*
>>
>> *Paint3factor<-procD.lm(coords ~ Csize + ind$Stages + ind$Location, data
>> = Paintgeo3fac, iter = 99, RRPP = FALSE, print.progress = FALSE, int.first
>> = FALSE)*
>>
>> HOWEVER,  when I did the multifactor Manova  to check the interaction
>> effects, using the command, though i inserted int.first = false,  somehow
>> it’s not working often shows error
>>
>> *Paint3factor<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data
>> = Paintgeo3fac, iter = 99, RRPP = FALSE, print.progress = FALSE, int.first
>> = FALSE)*
>>
>>
>> apart from changing, + to *, inserting int.first, any other stuff to be
>> added?
>>
>> Please help me :(
>>
>> Thanks in Advance!
>>
>> Truly
>>
>> Mahen
>>
>>
>> --
>> ***
>> M Mahendiran, Ph D
>> Scientist - Division of Wetland Ecology
>> Salim Ali Centre for Ornithology and Natural History (SACON)
>> Anaikatti (PO), Coimbatore - 641108, TamilNadu, India
>> Tel: 0422-2203100 (Ext. 122), 2203122 (Direct), Mob: 09787320901
>> Fax: 0422-2657088
>> http://www.sacon.in/staff/dr-m-mahendiran/
>>
>> P Please consider the environment before printing this 

Re: [MORPHMET] help us in multifactor Manova

[Mike Collyer]

Mahen,

Can you be specific with the error statement?  It might not me related to the 
int.first use but more so how you set up your formula.  If ind$Stages and 
ind$Location are in the data frame, you are asking R to create a model matrix 
from dat in an environment within another environment.  This might cause some 
problems.

Please let us know what the error says, and we can see if it is obvious.

Cheers!
Mike

> On May 17, 2018, at 8:22 AM, mahendiran mylswamy  wrote:
> 
> Dear All.
> 
> I did a single and multi-factor Manova, through Geomorph package in R, using 
> the following commands given below, it is working fine!
> 
> Paint1factor <-procD.lm (coords ~ Csize*indep1$Stages, data = Paintgeo147, 
> iter = , RRPP = FALSE, print.progress = FALSE)
> 
> Paint3factor<-procD.lm(coords ~ Csize + ind$Stages + ind$Location, data = 
> Paintgeo3fac, iter = 99, RRPP = FALSE, print.progress = FALSE, int.first = 
> FALSE)   
> 
> HOWEVER,  when I did the multifactor Manova  to check the interaction 
> effects, using the command, though i inserted int.first = false,  somehow 
> it’s not working often shows error
> 
> Paint3factor<-procD.lm(coords ~ Csize * ind$Stages * ind$Location, data = 
> Paintgeo3fac, iter = 99, RRPP = FALSE, print.progress = FALSE, int.first = 
> FALSE)
> 
> 
> 
> apart from changing, + to *, inserting int.first, any other stuff to be added?
> 
> Please help me :(
> 
> Thanks in Advance!
> 
> Truly
> 
> Mahen
> 
> 
> 
> -- 
> ***
> M Mahendiran, Ph D
> Scientist - Division of Wetland Ecology
> Salim Ali Centre for Ornithology and Natural History (SACON)
> Anaikatti (PO), Coimbatore - 641108, TamilNadu, India
> Tel: 0422-2203100 (Ext. 122), 2203122 (Direct), Mob: 09787320901
> Fax: 0422-2657088
> http://www.sacon.in/staff/dr-m-mahendiran/ 
> 
> 
> P Please consider the environment before printing this email
> 
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org 
> 
> --- 
> You received this message because you are subscribed to the Google Groups 
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to morphmet+unsubscr...@morphometrics.org 
> .

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
You received this message because you are subscribed to the Google Groups 
"MORPHMET" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to morphmet+unsubscr...@morphometrics.org.