Re: [R] Why aov() with Error() gives three strata?

[peter dalgaard]

At any rate: 

Error(SUBJECT/IV)

specifies two random effects: SUBJECT and SUBJECT:IV. This is most easily 
understood if you conceptually arrange your data in a SUBJECT x IV table: One 
effect is a set of random errors added to each row, the other is a set of 
effects added to each cell. 

If you have more than one observation within each cell, then you need a third 
set of errors to account for differences within cells and this is labeled 
"Within" variation. With one observation per cell, this stratum disappears (as 
far as I recall, haven't checked). 

Actually, this oversimplifies a little: What actually happens is that data gets 
split into 

1: row means
2: differences between cells within rows
3: differences between observations within cells

and if the stratum variances are decreasing, then this can be interpreted using 
random effects as above, with variances of each component proportional to the 
successive differences. (All assuming that you have a balanced data layout, 
otherwise aov() is just the wrong tool.)

-pd

> On 28 Dec 2017, at 19:36 , Jorge Fernando Saraiva de Menezes 
>  wrote:
> 
> Bert, thanks for the reply but I feel that my question is less about
> statistics and more about R interface. Specifically, because the output of
> R seems different than other programs (systat, for example, gives a between
> and a within table instead of a three level one).
> 
> I am familiar with the connection between mixed models and repeated
> measures,and how mixed models are essentially replacing the aov models due
> to their greater flexibility. But I feel that despite understanding a
> little of the logic behind the mixed models that aov error terms seem
> completely different to me than lmer randoms.
> 
> I will post in those support lists you pass to me, if nothing comes from
> here. However I had little luck in the stats exchange when I tried there.
> 
> About a local expert, I am once more in a corner. there are many people in
> my department who excel in statistics. But I none use R, drastically
> reducing their ability to explain to me the output of aov.
> 
> Em 28 de dez de 2017 20:04, "Bert Gunter"  escreveu:
> 
>> Jorge:
>> 
>> FYI, *generally speaking,* queries that are mostly statistical in
>> nature, such as yours, are off topic here -- this list is about R
>> programming help, not statistical help. Having said that, you still
>> may get a useful response here -- the r-help/statistics intersection
>> *is* nonempty. However, if not, 2.5 suggestions:
>> 
>> 1. Try posting to r-sig-mixed-models instead. Repeated measures are a
>> type of mixed/multilevel model and you may receive some useful
>> suggestions there, including alternative R approaches to fitting such
>> model (e.g. using lme() or lmer() ).
>> 
>> 2. Alternatively, try posting to a statistics site like
>> stats.stackexchange.com.
>> 
>> 2.5. Or, if you can, the best idea might be to sit down with a local
>> statistics expert.
>> 
>> Cheers,
>> Bert
>> 
>> 
>> 
>> Bert Gunter
>> 
>> "The trouble with having an open mind is that people keep coming along
>> and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>> 
>> 
>> On Thu, Dec 28, 2017 at 7:52 AM, Jorge Fernando Saraiva de Menezes
>>  wrote:
>>> Dear list users,
>>> 
>>> I am trying to learn Repeated measures ANOVA using the aov() interface,
>> but
>>> I'm struggling to understand its output.
>>> 
>>> According to tutorials on the web, formula for a repeated measures design
>>> is:
>>> 
>>> aov(Y ~ IV+ Error(SUBJECT/IV) )
>>> 
>>> This formula does work but it returns three strata (Error:SUBJECT, Error:
>>> SUBJECT:IV, Error: Within), when I would expect two strata (Within and
>>> Between subjects). I've seems some tutorials  show the exactly same
>> setup,
>>> but returning only the two first strata.
>>> 
>>> Is it possible to have two or three strata depending on the data?
>>> If there is always three strata, how this would fit the interpretation of
>>> between vs within effects?
>>> 
>>> Below a reproducible example that gives three strata:
>>> 
>>> data(beavers)
>>> data=data.frame(id =
>>> rep(c("beaver1","beaver2"),c(nrow(beaver1),nrow(beaver2))),
>> rbind(beaver1,beaver2))
>>> data$activ=factor(data$activ)
>>> #balance dataset to have 6 samples for every combination of beaver and
>>> activity.
>>> balanced = split(data,interaction(data$id,data$activ))
>>> sizes = sapply(balanced,nrow)
>>> selected = lapply(sizes,sample.int,6)
>>> balanced = mapply(function(x,y) {x[y,]}, balanced,selected,SIMPLIFY=F)
>>> balanced = do.call(rbind,balanced)
>>> aov(temp~activ+Error(id/activ),data=balanced)
>>> 
>>> Thanks,
>>> Jorge
>>> 
>>>[[alternative HTML version deleted]]
>>> 
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> 

Re: [R] Help with script

[Rui Barradas]

Hello,

Just use ?aggregate.

Example <- read.table(text = "
ID   ABCDEFG
a1   0001120
a2   0101221
a2   0112021
a3   0111111
", header = TRUE)

aggregate(. ~ ID, Example , sum)


Happy holidays,

Rui Barradas

On 12/29/2017 12:03 AM, PABLO ORTIZ PINEDA wrote:

Hello there. Happy new year for everyone!

I need help with a table. This table contains 300 rows and 192 columns.
Being the first column the ID of my samples that can have several
observations.

I need to generate e NEW table that contains a single ID with the sum of
the observations by columns:
For example:

Example
ID   A    B    C    D    E    F    G 191 columns
a1   0    0    0    1    1    2    0...
a2   0    1    0    1    2    2    1...
a2   0    1    1    2    0    2    1...
a3   0    1    1    1    1    1    1
...300rows
In this case I want to make a new table in which there is only 1 ID and
the values of each columns A...G are added. I
n the example the new table would have only 3 IDs. a1, a2 and 3 and a2
has the values added by column:
a2   0   2   1   3   2   4   2..

Thank you so much and have a wonderful year!.



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Re: [R] Help with dates

[Marc Girondot via R-help]

Le 28/12/2017 à 18:13, Ramesh YAPALPARVI a écrit :

Hi all,

I’m struggling to get the dates in proper format.
I have dates as factors and is in the form 02/27/34( 34 means 1934). If I use


Try this

x <- "02/27/34"
x2 <- paste0(substr(x, 1, 6), "19", substr(x, 7, 8))
as.Date(x2, format="%m/%d/%Y")
[1] "1934-02-27"

or

x2 <- gsub("(../../)(..)", "\\119\\2", x)

Marc


as.Date with format %d%m%y it gets converted to 2034-02-27. I tried changing 
the origin in the as.Date command but nothing worked. Any help is appreciated.

Thanks,
Ramesh
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--
__
Marc Girondot, Pr

Laboratoire Ecologie, Systématique et Evolution
Equipe de Conservation des Populations et des Communautés
CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079
Bâtiment 362
91405 Orsay Cedex, France

Tel:  33 1 (0)1.69.15.72.30   Fax: 33 1 (0)1.69.15.73.53
e-mail: marc.giron...@u-psud.fr
Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
Skype: girondot

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Re: [R] Help with script

[Eric Berger]

Hi Pablo,
There are probably many ways to do this in R. This suggestion uses dplyr.
The solution is actually only one line (see the line starting with dat2).
The first section simply creates the example data.

library(dplyr)
# 1. set up the example data
m <- matrix( c(0,0,0,0,0,1,1,1,0,0,1,1,1,1,2,1,1,2,0,1,2,2,2,1,0,1,1,1),
nrow=4)
dat <- as.data.frame(m)
dat$ID <- c("a1","a2","a2","a3")
dat <- dat[,c(8,1:7)]
colnames(dat) <- c("ID",LETTERS[1:7])

#2. group the data by ID, summing the columns in each group
dat2 <- group_by(dat,ID) %>% summarise_all( sum )

#3. show the results
dat2

# # A tibble: 3 x 8
#  ID A B C D E F G
#  
# 1a1 0 0 0 1 1 2 0
# 2a2 0 2 1 3 2 4 2
# 3a3 0 1 1 1 1 1 1

HTH,
Eric


On Fri, Dec 29, 2017 at 2:03 AM, PABLO ORTIZ PINEDA 
wrote:

> Hello there. Happy new year for everyone!
>
> I need help with a table. This table contains 300 rows and 192 columns.
> Being the first column the ID of my samples that can have several
> observations.
>
> I need to generate e NEW table that contains a single ID with the sum of
> the observations by columns:
> For example:
>
> Example
> ID   ABCDEFG 191 columns
> a1   0001120...
> a2   0101221...
> a2   0112021...
> a3   0111111
> ...300rows
> In this case I want to make a new table in which there is only 1 ID and
> the values of each columns A...G are added. I
> n the example the new table would have only 3 IDs. a1, a2 and 3 and a2
> has the values added by column:
> a2   0   2   1   3   2   4   2..
>
> Thank you so much and have a wonderful year!.
>
> --
> Pablo A. Ortiz-Pineda (Ph.D.)
> Molecular Biology & Bioinformatics
> Yale University. School of Medicine.
> Pediatrics Department.
> New Haven, CT 06510
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

[[alternative HTML version deleted]]

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Re: [R] RQuantLib

[Joshua Ulrich]

On Thu, Dec 28, 2017 at 6:02 PM, rsherry8  wrote:
>
> I have recently installed R on my new computer. I also want to install the
> package RQuantLib. So I run the following command and get the following
> output:
>
>>  install.packages("RQuantLib")
> Installing package into ‘C:/Users/rsher/Documents/R/win-library/3.2’
> (as ‘lib’ is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> Warning message:
> package ‘RQuantLib’ is not available (for R version 3.2.4 Revised)
>
> The package did not install. Am I doing something wrong. Is the package
> going to be updated for the latest version of R?
>
Windows binary packages are only built for the most current (major)
version of R.  You need to upgrade to at least R-3.4.0, or you will
have to install RQuantLib (and therefore QuantLib itself) from source.

> Thanks,
> Bob
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



-- 
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com
R/Finance 2018 | www.rinfinance.com

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[R] Help with script

[PABLO ORTIZ PINEDA]

Hello there. Happy new year for everyone!

I need help with a table. This table contains 300 rows and 192 columns. 
Being the first column the ID of my samples that can have several 
observations.

I need to generate e NEW table that contains a single ID with the sum of 
the observations by columns:
For example:

Example
ID   A    B    C    D    E    F    G 191 columns
a1   0    0    0    1    1    2    0...
a2   0    1    0    1    2    2    1...
a2   0    1    1    2    0    2    1...
a3   0    1    1    1    1    1    1
...300rows
In this case I want to make a new table in which there is only 1 ID and 
the values of each columns A...G are added. I
n the example the new table would have only 3 IDs. a1, a2 and 3 and a2 
has the values added by column:
a2   0   2   1   3   2   4   2..

Thank you so much and have a wonderful year!.

-- 
Pablo A. Ortiz-Pineda (Ph.D.)
Molecular Biology & Bioinformatics
Yale University. School of Medicine.
Pediatrics Department.
New Haven, CT 06510


[[alternative HTML version deleted]]

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[R] RQuantLib

[rsherry8]

I have recently installed R on my new computer. I also want to install 
the package RQuantLib. So I run the following command and get the 
following output:


>  install.packages("RQuantLib")
Installing package into ‘C:/Users/rsher/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Warning message:
package ‘RQuantLib’ is not available (for R version 3.2.4 Revised)

The package did not install. Am I doing something wrong. Is the package 
going to be updated for the latest version of R?


Thanks,
Bob

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Re: [R] Help with dates

[Simmering, Jacob E]

Your dates have an incomplete year information with 34. R assumes that 00-68 
are 2000 to 2068 and 69 to 99 are 1969 to 1999. See ?strptime and the details 
for %y. 

You can either append “19” to the start of your year variable to make it 
completely express the year or check if the date is in the future (assuming all 
dates should be in the past) and subtract 100 years from the date. 


> On Dec 28, 2017, at 11:13 AM, Ramesh YAPALPARVI 
>  wrote:
> 
> Hi all,
> 
> I’m struggling to get the dates in proper format.
> I have dates as factors and is in the form 02/27/34( 34 means 1934). If I use
> 
> as.Date with format %d%m%y it gets converted to 2034-02-27. I tried changing 
> the origin in the as.Date command but nothing worked. Any help is appreciated.
> 
> Thanks,
> Ramesh
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Why aov() with Error() gives three strata?

[Jorge Fernando Saraiva de Menezes]

Bert, thanks for the reply but I feel that my question is less about
statistics and more about R interface. Specifically, because the output of
R seems different than other programs (systat, for example, gives a between
and a within table instead of a three level one).

I am familiar with the connection between mixed models and repeated
measures,and how mixed models are essentially replacing the aov models due
to their greater flexibility. But I feel that despite understanding a
little of the logic behind the mixed models that aov error terms seem
completely different to me than lmer randoms.

 I will post in those support lists you pass to me, if nothing comes from
here. However I had little luck in the stats exchange when I tried there.

About a local expert, I am once more in a corner. there are many people in
my department who excel in statistics. But I none use R, drastically
reducing their ability to explain to me the output of aov.

Em 28 de dez de 2017 20:04, "Bert Gunter"  escreveu:

> Jorge:
>
> FYI, *generally speaking,* queries that are mostly statistical in
> nature, such as yours, are off topic here -- this list is about R
> programming help, not statistical help. Having said that, you still
> may get a useful response here -- the r-help/statistics intersection
> *is* nonempty. However, if not, 2.5 suggestions:
>
> 1. Try posting to r-sig-mixed-models instead. Repeated measures are a
> type of mixed/multilevel model and you may receive some useful
> suggestions there, including alternative R approaches to fitting such
> model (e.g. using lme() or lmer() ).
>
> 2. Alternatively, try posting to a statistics site like
> stats.stackexchange.com.
>
> 2.5. Or, if you can, the best idea might be to sit down with a local
> statistics expert.
>
> Cheers,
> Bert
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Thu, Dec 28, 2017 at 7:52 AM, Jorge Fernando Saraiva de Menezes
>  wrote:
> > Dear list users,
> >
> > I am trying to learn Repeated measures ANOVA using the aov() interface,
> but
> > I'm struggling to understand its output.
> >
> > According to tutorials on the web, formula for a repeated measures design
> > is:
> >
> > aov(Y ~ IV+ Error(SUBJECT/IV) )
> >
> > This formula does work but it returns three strata (Error:SUBJECT, Error:
> > SUBJECT:IV, Error: Within), when I would expect two strata (Within and
> > Between subjects). I've seems some tutorials  show the exactly same
> setup,
> > but returning only the two first strata.
> >
> > Is it possible to have two or three strata depending on the data?
> > If there is always three strata, how this would fit the interpretation of
> > between vs within effects?
> >
> > Below a reproducible example that gives three strata:
> >
> > data(beavers)
> > data=data.frame(id =
> > rep(c("beaver1","beaver2"),c(nrow(beaver1),nrow(beaver2))),
> rbind(beaver1,beaver2))
> > data$activ=factor(data$activ)
> > #balance dataset to have 6 samples for every combination of beaver and
> > activity.
> > balanced = split(data,interaction(data$id,data$activ))
> > sizes = sapply(balanced,nrow)
> > selected = lapply(sizes,sample.int,6)
> > balanced = mapply(function(x,y) {x[y,]}, balanced,selected,SIMPLIFY=F)
> > balanced = do.call(rbind,balanced)
> > aov(temp~activ+Error(id/activ),data=balanced)
> >
> > Thanks,
> > Jorge
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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[R] Help with dates

[Ramesh YAPALPARVI]

Hi all,

I’m struggling to get the dates in proper format.
I have dates as factors and is in the form 02/27/34( 34 means 1934). If I use

as.Date with format %d%m%y it gets converted to 2034-02-27. I tried changing 
the origin in the as.Date command but nothing worked. Any help is appreciated.

Thanks,
Ramesh
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Re: [R] Why aov() with Error() gives three strata?

[Bert Gunter]

Jorge:

FYI, *generally speaking,* queries that are mostly statistical in
nature, such as yours, are off topic here -- this list is about R
programming help, not statistical help. Having said that, you still
may get a useful response here -- the r-help/statistics intersection
*is* nonempty. However, if not, 2.5 suggestions:

1. Try posting to r-sig-mixed-models instead. Repeated measures are a
type of mixed/multilevel model and you may receive some useful
suggestions there, including alternative R approaches to fitting such
model (e.g. using lme() or lmer() ).

2. Alternatively, try posting to a statistics site like stats.stackexchange.com.

2.5. Or, if you can, the best idea might be to sit down with a local
statistics expert.

Cheers,
Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Dec 28, 2017 at 7:52 AM, Jorge Fernando Saraiva de Menezes
 wrote:
> Dear list users,
>
> I am trying to learn Repeated measures ANOVA using the aov() interface, but
> I'm struggling to understand its output.
>
> According to tutorials on the web, formula for a repeated measures design
> is:
>
> aov(Y ~ IV+ Error(SUBJECT/IV) )
>
> This formula does work but it returns three strata (Error:SUBJECT, Error:
> SUBJECT:IV, Error: Within), when I would expect two strata (Within and
> Between subjects). I've seems some tutorials  show the exactly same setup,
> but returning only the two first strata.
>
> Is it possible to have two or three strata depending on the data?
> If there is always three strata, how this would fit the interpretation of
> between vs within effects?
>
> Below a reproducible example that gives three strata:
>
> data(beavers)
> data=data.frame(id =
> rep(c("beaver1","beaver2"),c(nrow(beaver1),nrow(beaver2))),rbind(beaver1,beaver2))
> data$activ=factor(data$activ)
> #balance dataset to have 6 samples for every combination of beaver and
> activity.
> balanced = split(data,interaction(data$id,data$activ))
> sizes = sapply(balanced,nrow)
> selected = lapply(sizes,sample.int,6)
> balanced = mapply(function(x,y) {x[y,]}, balanced,selected,SIMPLIFY=F)
> balanced = do.call(rbind,balanced)
> aov(temp~activ+Error(id/activ),data=balanced)
>
> Thanks,
> Jorge
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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[R] Why aov() with Error() gives three strata?

[Jorge Fernando Saraiva de Menezes]

Dear list users,

I am trying to learn Repeated measures ANOVA using the aov() interface, but
I'm struggling to understand its output.

According to tutorials on the web, formula for a repeated measures design
is:

aov(Y ~ IV+ Error(SUBJECT/IV) )

This formula does work but it returns three strata (Error:SUBJECT, Error:
SUBJECT:IV, Error: Within), when I would expect two strata (Within and
Between subjects). I've seems some tutorials  show the exactly same setup,
but returning only the two first strata.

Is it possible to have two or three strata depending on the data?
If there is always three strata, how this would fit the interpretation of
between vs within effects?

Below a reproducible example that gives three strata:

data(beavers)
data=data.frame(id =
rep(c("beaver1","beaver2"),c(nrow(beaver1),nrow(beaver2))),rbind(beaver1,beaver2))
data$activ=factor(data$activ)
#balance dataset to have 6 samples for every combination of beaver and
activity.
balanced = split(data,interaction(data$id,data$activ))
sizes = sapply(balanced,nrow)
selected = lapply(sizes,sample.int,6)
balanced = mapply(function(x,y) {x[y,]}, balanced,selected,SIMPLIFY=F)
balanced = do.call(rbind,balanced)
aov(temp~activ+Error(id/activ),data=balanced)

Thanks,
Jorge

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.