[R] (windows) opening document with particular exe file

[Jan Kacaba]

Hello dear R, I dont have specific task on mind just learning R.

1) Is it possible to open a document for example path1\myfile.pdf with
program path2\pdfviewer.exe ?
How would I do it in win? Does it differ in linux?

2)  Is it possible to run a program and supply to it some streams? The
streams are for example txt file or web address.

One specific task which comes to mid: I would like to draw in inkscape
programmatically with script. Is it somehow possible?

Thank you very much for any help in advance.

[[alternative HTML version deleted]]

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Re: [R] How to print the frequency table (produced by the command "table" to Excel

[Jim Lemon]

Hi jpm miao,
You can get CSV files that can be imported into Excel like this:

library(prettyR)
sink("excel_table1.csv")
delim.table(table(df[,c("y","z")]))
sink()
sink("excel_table2.csv")
delim.table(as.data.frame(table(df[,c("y","z")])),label="")
sink()
sink("excel_table3.csv")
delim.table(as.matrix(table(df[,c("y","z")])),label="")
sink()

Jim

On Wed, Apr 27, 2016 at 8:35 AM, jpm miao  wrote:
> Hi,
>
>How could we print the frequency table (produced by "table") to an Excel
> file?
>Is there an easy way to do so? Thanks,
>
> Miao
>
>> df <- data.frame(x = 1:3, y = 3:1, z = letters[1:3])
>
>> table(df[,c("y","z")])
>z
> y   a b c
>   1 0 0 1
>   2 0 1 0
>   3 1 0 0
>> test<-table(df[,c("y","z")])
>> as.data.frame(test)
>   y z Freq
> 1 1 a0
> 2 2 a0
> 3 3 a1
> 4 1 b0
> 5 2 b1
> 6 3 b0
> 7 1 c1
> 8 2 c0
> 9 3 c0
>> as.matrix(test)
>z
> y   a b c
>   1 0 0 1
>   2 0 1 0
>   3 1 0 0
>> testm<-as.matrix(test)
>> testm
>z
> y   a b c
>   1 0 0 1
>   2 0 1 0
>   3 1 0 0
>> typeof(testm)
> [1] "integer"
>
> [[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] How to print the frequency table (produced by the command "table" to Excel

[jpm miao]

Hi,

   How could we print the frequency table (produced by "table") to an Excel
file?
   Is there an easy way to do so? Thanks,

Miao

> df <- data.frame(x = 1:3, y = 3:1, z = letters[1:3])

> table(df[,c("y","z")])
   z
y   a b c
  1 0 0 1
  2 0 1 0
  3 1 0 0
> test<-table(df[,c("y","z")])
> as.data.frame(test)
  y z Freq
1 1 a0
2 2 a0
3 3 a1
4 1 b0
5 2 b1
6 3 b0
7 1 c1
8 2 c0
9 3 c0
> as.matrix(test)
   z
y   a b c
  1 0 0 1
  2 0 1 0
  3 1 0 0
> testm<-as.matrix(test)
> testm
   z
y   a b c
  1 0 0 1
  2 0 1 0
  3 1 0 0
> typeof(testm)
[1] "integer"

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Re: [R] From NUM to INT

[André Luis Neves]

Hi Bert:

I thought in centering Baci variable, but I wouldn`t like to draw a
conclusion based on the scaled response variable.

On the other hand, if I had to center the explanatory variable, that would
be great, but I cannot, as it is a factor.

Thanks a lot for your time. I really appreciated your help.

Best regards,

Andre



On Tue, Apr 26, 2016 at 4:11 PM, Bert Gunter  wrote:

> Inline.
>
> -- Bert
>
>
> On Tue, Apr 26, 2016 at 2:25 PM, André Luis Neves 
> wrote:
> > Ok. I`m trying to run a Poisson glmm with an observation-level random
> > intercept. But I`m getting the following error for the 'Baci' variable:
> >
> > 'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in
> > pwrssUpdate'. I  guess this message is because the baci variable is not a
> > an integer,
>
> Why would you "guess" that? Given your magnitudes, I suspect it's a
> scaling issue. Try centering and scaling your Baci variable before
> fitting.
>
> Cheers,
> Bert
>
>
>
>
>
> and cannot be transformed into an integer as R has a threshold
> > of
> > 2x10^9 even in 64 bit R.
> >
> > It runs fine for the fungii variable.
> >
> > If you guys want to run the data (attached), the full command is below.
> >
> > Thanks.
> >
> > -
> >
> > ##Import data:
> >
> > qPCR <- read.delim(file.choose(),
> >  header = TRUE,
> >  dec = ".")
> >
> > ##Load package
> >
> > library(lme4)
> >
> > ##Other steps:
> >
> > qPCR$obs <- 1:nrow(qPCR)
> > qPCR$fID<-as.factor(qPCR$ID)
> > qPCR$fDiet<-as.factor(qPCR$Diet)
> >
> > ##Run the model:
> >
> > M1 <- glmer (Baci ~ fDiet + Crossover + (1|fID:Crossover) + (1|obs),
> >  family = poisson, data=qPCR)
> >
> >
> >
> > Andre
> >
> >
> >
> > On Tue, Apr 26, 2016 at 2:36 PM, jim holtman  wrote:
> >
> >> Can you explain why you need them as 'integer',  A floating point
> >> representation can hold a value upto ~4.5e15 as an "integer" keeping the
> >> precision that you might need.
> >>
> >>
> >> Jim Holtman
> >> Data Munger Guru
> >>
> >> What is the problem that you are trying to solve?
> >> Tell me what you want to do, not how you want to do it.
> >>
> >> On Tue, Apr 26, 2016 at 1:11 PM, André Luis Neves  >
> >> wrote:
> >>
> >>> Dear all:
> >>>
> >>> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
> >>> (using excel) and then imported the data (.txt) into R. Interestingly,
> the
> >>> other three variables were loaded as INT, but the 'Baci' one continued
> as
> >>> Num.
> >>>
> >>> I imported the data using the following command line:
> >>>
> >>> X <- read.delim(file.choose(),
> >>>  header = TRUE,
> >>>  dec = ".")
> >>>
> >>> Here is the structure of X:
> >>>
> >>> > str(X)
> >>> 'data.frame': 115 obs. of  5 variables:
> >>>  $ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18
> 26 27
> >>> 29 31 32 36 ...
> >>>  $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
> >>>  $ Meti : int  352645997 334146268 767208656 171567266 462747405
> >>> 414905627 237010514 387480048 214671355 328813226 ...
> >>>  $ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156
> 13746
> >>> ...
> >>>  $ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015
> >>> 203685
> >>> 4261780 43110492 69802572 ...
> >>>
> >>>
> >>> I need Baci as an integer, and tried to convert it using as.integer
> >>> function, but was not successful.
> >>>
> >>>
> >>> Could anyone please help me to solve this problem.
> >>>
> >>> Thanks,
> >>>
> >>>
> >>>
> >>> --
> >>> Andre
> >>>
> >>> __
> >>> 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.
> >>>
> >>
> >>
> >
> >
> > --
> > Andre
> >
> > __
> > 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.
>



-- 
Andre

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] From NUM to INT

[Bert Gunter]

Inline.

-- Bert


On Tue, Apr 26, 2016 at 2:25 PM, André Luis Neves  wrote:
> Ok. I`m trying to run a Poisson glmm with an observation-level random
> intercept. But I`m getting the following error for the 'Baci' variable:
>
> 'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in
> pwrssUpdate'. I  guess this message is because the baci variable is not a
> an integer,

Why would you "guess" that? Given your magnitudes, I suspect it's a
scaling issue. Try centering and scaling your Baci variable before
fitting.

Cheers,
Bert





and cannot be transformed into an integer as R has a threshold
> of
> 2x10^9 even in 64 bit R.
>
> It runs fine for the fungii variable.
>
> If you guys want to run the data (attached), the full command is below.
>
> Thanks.
>
> -
>
> ##Import data:
>
> qPCR <- read.delim(file.choose(),
>  header = TRUE,
>  dec = ".")
>
> ##Load package
>
> library(lme4)
>
> ##Other steps:
>
> qPCR$obs <- 1:nrow(qPCR)
> qPCR$fID<-as.factor(qPCR$ID)
> qPCR$fDiet<-as.factor(qPCR$Diet)
>
> ##Run the model:
>
> M1 <- glmer (Baci ~ fDiet + Crossover + (1|fID:Crossover) + (1|obs),
>  family = poisson, data=qPCR)
>
>
>
> Andre
>
>
>
> On Tue, Apr 26, 2016 at 2:36 PM, jim holtman  wrote:
>
>> Can you explain why you need them as 'integer',  A floating point
>> representation can hold a value upto ~4.5e15 as an "integer" keeping the
>> precision that you might need.
>>
>>
>> Jim Holtman
>> Data Munger Guru
>>
>> What is the problem that you are trying to solve?
>> Tell me what you want to do, not how you want to do it.
>>
>> On Tue, Apr 26, 2016 at 1:11 PM, André Luis Neves 
>> wrote:
>>
>>> Dear all:
>>>
>>> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
>>> (using excel) and then imported the data (.txt) into R. Interestingly, the
>>> other three variables were loaded as INT, but the 'Baci' one continued as
>>> Num.
>>>
>>> I imported the data using the following command line:
>>>
>>> X <- read.delim(file.choose(),
>>>  header = TRUE,
>>>  dec = ".")
>>>
>>> Here is the structure of X:
>>>
>>> > str(X)
>>> 'data.frame': 115 obs. of  5 variables:
>>>  $ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26 27
>>> 29 31 32 36 ...
>>>  $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
>>>  $ Meti : int  352645997 334146268 767208656 171567266 462747405
>>> 414905627 237010514 387480048 214671355 328813226 ...
>>>  $ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156 13746
>>> ...
>>>  $ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015
>>> 203685
>>> 4261780 43110492 69802572 ...
>>>
>>>
>>> I need Baci as an integer, and tried to convert it using as.integer
>>> function, but was not successful.
>>>
>>>
>>> Could anyone please help me to solve this problem.
>>>
>>> Thanks,
>>>
>>>
>>>
>>> --
>>> Andre
>>>
>>> __
>>> 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.
>>>
>>
>>
>
>
> --
> Andre
>
> __
> 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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] table , exclude - count the frequency in a data frame but exclude one value

[William Dunlap via R-help]

table converts its non-factor arguments to factors using the exclude
argument that you supply.  If you want the arguments to be handled
differently, then convert them to factors
yourself, in the way you want.  E.g.,

> with(df, table(x=factor(x, exclude=1), y))
   y
x   1 2 3
  2 0 1 0
  3 1 0 0
> with(df, table(x=factor(x, exclude=1), y=factor(y, levels=3:1)))
   y
x   3 2 1
  2 0 1 0
  3 0 0 1



Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Tue, Apr 26, 2016 at 2:21 PM, jpm miao  wrote:

> Hi,
>
>I have a data frame with two variables x, y, both of which take values
> in the set {1,2,3}. I'd like to count the frequency by the command "table",
> but exclude the value "1" in variable x, but keep "1" in variable y. Is it
> possible?  When I use "exclude", value 1 in both x and y are excluded.
> Thanks,
>
>
> > df <- data.frame(x = 1:3, y = 3:1, z = letters[1:3])
> > table(df[,c("y","x")])
>x
> y   1 2 3
>   1 0 0 1
>   2 0 1 0
>   3 1 0 0
> > table(df[,c("y","x")], exclude = 1)
>x
> y   2 3
>   2 1 0
>   3 0 0
> > table(df[,c("y","x")], exclude = c(NULL, 1))
>x
> y   2 3
>   2 1 0
>   3 0 0
> > table(df[,c("y","x")], exclude = c(1, NULL))
>x
> y   2 3
>   2 1 0
>   3 0 0
> > table(df[,c("y","x")], exclude = c(1, 0))
>x
> y   2 3
>   2 1 0
>   3 0 0
> > table(df[,c("y","x")], exclude = list(1 , NULL))
> Error in as.vector(exclude, typeof(x)) :
>   (list) object cannot be coerced to type 'integer'
>
> [[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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and provide commented, minimal, self-contained, reproducible code.

Re: [R] From NUM to INT

[André Luis Neves]

Ok. I`m trying to run a Poisson glmm with an observation-level random
intercept. But I`m getting the following error for the 'Baci' variable:

'Error: (maxstephalfit) PIRLS step-halvings failed to reduce deviance in
pwrssUpdate'. I  guess this message is because the baci variable is not a
an integer, and cannot be transformed into an integer as R has a threshold
of
2x10^9 even in 64 bit R.

It runs fine for the fungii variable.

If you guys want to run the data (attached), the full command is below.

Thanks.

-

##Import data:

qPCR <- read.delim(file.choose(),
 header = TRUE,
 dec = ".")

##Load package

library(lme4)

##Other steps:

qPCR$obs <- 1:nrow(qPCR)
qPCR$fID<-as.factor(qPCR$ID)
qPCR$fDiet<-as.factor(qPCR$Diet)

##Run the model:

M1 <- glmer (Baci ~ fDiet + Crossover + (1|fID:Crossover) + (1|obs),
 family = poisson, data=qPCR)



Andre



On Tue, Apr 26, 2016 at 2:36 PM, jim holtman  wrote:

> Can you explain why you need them as 'integer',  A floating point
> representation can hold a value upto ~4.5e15 as an "integer" keeping the
> precision that you might need.
>
>
> Jim Holtman
> Data Munger Guru
>
> What is the problem that you are trying to solve?
> Tell me what you want to do, not how you want to do it.
>
> On Tue, Apr 26, 2016 at 1:11 PM, André Luis Neves 
> wrote:
>
>> Dear all:
>>
>> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
>> (using excel) and then imported the data (.txt) into R. Interestingly, the
>> other three variables were loaded as INT, but the 'Baci' one continued as
>> Num.
>>
>> I imported the data using the following command line:
>>
>> X <- read.delim(file.choose(),
>>  header = TRUE,
>>  dec = ".")
>>
>> Here is the structure of X:
>>
>> > str(X)
>> 'data.frame': 115 obs. of  5 variables:
>>  $ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26 27
>> 29 31 32 36 ...
>>  $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
>>  $ Meti : int  352645997 334146268 767208656 171567266 462747405
>> 414905627 237010514 387480048 214671355 328813226 ...
>>  $ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156 13746
>> ...
>>  $ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015
>> 203685
>> 4261780 43110492 69802572 ...
>>
>>
>> I need Baci as an integer, and tried to convert it using as.integer
>> function, but was not successful.
>>
>>
>> Could anyone please help me to solve this problem.
>>
>> Thanks,
>>
>>
>> ​
>> --
>> Andre
>>
>> __
>> 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.
>>
>
>


-- 
Andre
ID  Crossover   Period  DietPen TimeBaciFungii  fNDF
Starch
126BLK  1   1   Forage  1   End12.90E+1243645   
3.87056104  1.443771827
13ZBLK  1   1   Forage  1   End15.55E+1119009   
3.970286296 1.480970702
157BLK  1   1   Forage  1   End19.46E+1115998   
4.114130366 1.534626493
162ZRED 1   1   Forage  1   End18.13E+112189
3.600760128 1.343132423
17ZBLKY 1   1   Forage  1   End14.06E+118972
3.79087129  1.414046468
184ZBLK 1   1   Forage  1   End15.75E+118240
3.815881751 1.42337571
1ZBLKW  1   1   Forage  1   End134490836164 3133
3.295433507 1.229241447
2094ZBLK1   1   Forage  1   End13.49E+1117922   
3.737865394 1.394274549
20LZBLK 1   1   Forage  1   End11.63E+116156
4.007824601 1.494972999
29ZBLK  1   1   Forage  1   End13.37E+1113746   
3.59031272  1.339235398
2ZBLKG  1   1   Forage  1   End13.13E+114003
3.964994752 1.478996884
60ZRED  1   1   Forage  1   End13.76E+1112473   
3.477652579 1.297211636
77BLK   1   1   Forage  1   End12.92E+1113328   
4.546906317 1.696057799
8ZBLK   1   1   Forage  1   End12.45E+112900
4.447927304 1.659137284
91ZRED  1   1   Forage  1   End15.62E+118584
4.118042491 1.536085769
112BLKW 2   1   Forage  2   End170249927920 192654  
4.024558544 1.501214987
1226BLK 2   1   Forage  2   End118390770816 65524   
3.933087193 1.467094931
12ZBLK  2   1   Forage  2   End164465242768 286966  
3.678844325 1.372258889
134BLK  2   1   Forage  2   End19652868358  47474   
3.902242465 

[R] table , exclude - count the frequency in a data frame but exclude one value

[jpm miao]

Hi,

   I have a data frame with two variables x, y, both of which take values
in the set {1,2,3}. I'd like to count the frequency by the command "table",
but exclude the value "1" in variable x, but keep "1" in variable y. Is it
possible?  When I use "exclude", value 1 in both x and y are excluded.
Thanks,


> df <- data.frame(x = 1:3, y = 3:1, z = letters[1:3])
> table(df[,c("y","x")])
   x
y   1 2 3
  1 0 0 1
  2 0 1 0
  3 1 0 0
> table(df[,c("y","x")], exclude = 1)
   x
y   2 3
  2 1 0
  3 0 0
> table(df[,c("y","x")], exclude = c(NULL, 1))
   x
y   2 3
  2 1 0
  3 0 0
> table(df[,c("y","x")], exclude = c(1, NULL))
   x
y   2 3
  2 1 0
  3 0 0
> table(df[,c("y","x")], exclude = c(1, 0))
   x
y   2 3
  2 1 0
  3 0 0
> table(df[,c("y","x")], exclude = list(1 , NULL))
Error in as.vector(exclude, typeof(x)) :
  (list) object cannot be coerced to type 'integer'

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[R] Predicting probabilities in ordinal probit analysis in R

[Faradj Koliev]

Dear all, 

I have two questions that are almost completely related to how to do things in 
R.

I am running an ordinal probit regression analysis in R. The dependent variable 
has three levels (0=no action; 1=warning; 2=sanction).

I use the lrm command in the rms package:

print( res1<- lrm(Y ~ x1+x2+x3+x4+x5+x6, y=TRUE, x=TRUE, data=mydata))
I simply couldn't make any sense of the information generated my ?predict.lrm. 
What I want to do is to calculate the marginal effects of all explanatory 
variables for each level of the dependent variable. In Stata, this is very 
simple: mfx compute, predict (outcome(#0)); mfx compute, predict (outcome(#2)) 
and mfx compute, predict (outcome(#3)).

So my first question is: how do I generate marginal effects for each outcome in 
R? 

The second question is related to interaction effects, which I need to include 
in the same model:

print( res1<- lrm(Y ~ x1+x2+x3+x4+x5+x6+x5*x6, y=TRUE, x=TRUE, data=mydata))
If I knew the answer to the first question, I would have ran marginal effects 
with the interaction term included. Then, I would have plotted the predicted 
values of the interaction term.

So the second question is: how do I plot the effects (predicted values) of 
variables in the interaction term?

Many thanks!

Small sample from my dataset (only one country)

dput(mydatasample)

structure(list(year = 1989:2014, country = structure(c(1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = "Canada", class = "factor"), 
id = structure(1:26, .Label = c("CAN 1989", "CAN 1990", "CAN 1991", 
"CAN 1992", "CAN 1993", "CAN 1994", "CAN 1995", "CAN 1996", 
"CAN 1997", "CAN 1998", "CAN 1999", "CAN 2000", "CAN 2001", 
"CAN 2002", "CAN 2003", "CAN 2004", "CAN 2005", "CAN 2006", 
"CAN 2007", "CAN 2008", "CAN 2009", "CAN 2010", "CAN 2011", 
"CAN 2012", "CAN 2013", "CAN 2014"), class = "factor"), stage1 = c(1L, 
1L, 0L, 0L, 0L, 0L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 0L, 0L, 0L, 
0L, 2L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L), x1 = c(1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L), x2 = c(1L, 2L, 1L, 2L, 2L, 
2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 
2L, 1L, 2L, 2L, 2L, 2L), x3 = c(9L, 9L, 9L, 9L, 9L, 9L, 9L, 
9L, 9L, 9L, 9L, 8L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 
10L, 10L, 10L, 10L, 10L, 10L), x4 = c(31L, 31L, 31L, 31L, 
31L, 30L, 30L, 30L, 31L, 30L, 29L, 30L, 28L, 28L, 28L, 27L, 
29L, 29L, 29L, 28L, 25L, 24L, 23L, NA, NA, NA), x5 = structure(1:26, .Label 
= c("17,12528685", 
"17,14022279", "17,15382785", "17,16610202", "17,17704534", 
"17,18665779", "17,19493938", "17,20571103", "17,21628118", 
"17,22493732", "17,23321101", "17,242041", "17,25213621", 
"17,26110753", "17,27106985", "17,2810902", "17,29094924", 
"17,29891768", "17,30861622", "17,31943819", "17,33088659", 
"17,34202619", "17,35190237", "17,36381421", "17,37537139", 
"17,38618117"), class = "factor"), x5.1 = c(0L, 0L, 0L, 0L, 
1L, 0L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 
0L, 0L, 0L, 0L, 1L, 1L, 0L)), .Names = c("year", "country", 
"id", "stage1", "x1", "x2", "x3", "x4", "x5", "x5.1"), class = "data.frame", 
row.names = c(NA, 
-26L))




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Re: [R] From NUM to INT

[jim holtman]

Can you explain why you need them as 'integer',  A floating point
representation can hold a value upto ~4.5e15 as an "integer" keeping the
precision that you might need.


Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

On Tue, Apr 26, 2016 at 1:11 PM, André Luis Neves 
wrote:

> Dear all:
>
> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
> (using excel) and then imported the data (.txt) into R. Interestingly, the
> other three variables were loaded as INT, but the 'Baci' one continued as
> Num.
>
> I imported the data using the following command line:
>
> X <- read.delim(file.choose(),
>  header = TRUE,
>  dec = ".")
>
> Here is the structure of X:
>
> > str(X)
> 'data.frame': 115 obs. of  5 variables:
>  $ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26 27
> 29 31 32 36 ...
>  $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
>  $ Meti : int  352645997 334146268 767208656 171567266 462747405
> 414905627 237010514 387480048 214671355 328813226 ...
>  $ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156 13746
> ...
>  $ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015 203685
> 4261780 43110492 69802572 ...
>
>
> I need Baci as an integer, and tried to convert it using as.integer
> function, but was not successful.
>
>
> Could anyone please help me to solve this problem.
>
> Thanks,
>
>
> ​
> --
> Andre
>
> __
> 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] vectors of equations in ode / desolve

[Frank B.]

Hello,

I have a syntactic problem with ode. How do I specify vectors of
equations in ordinary differential equation systems. (i.e. in my case I
want to simulate an a priory undefined number of species that have
different  parameters but the same behaviour)

I demonstrate this using the Lotka Volterra example. The code below does
not work and I have not a good idea how to specify this right. 


## ===
## Example1: Predator-Prey Lotka-Volterra model (with logistic prey)
## ===

LVmod <- function(Time, State, Pars) {
  with(as.list(c(State, Pars)), {
# Now there are different species of Prey so Prey is a one dimensional
vector,
#Ingestion is also a one-dimensional vector.  The number of species is
not defined a priory
Ingestion<- rIng  * Prey * Predator
GrowthPrey   <- rGrow * Prey * (1 - Prey/K)
MortPredator <- rMort * Predator

dPrey<- GrowthPrey - Ingestion
# thegrowth of predator would depend on the ingestion of all prays
regardless of species
sumIngestion<-sum(Ingestion)
dPredator<- sumIngestion * assEff - MortPredator
 # returning an array of preys does produce an error
return(list(c(dPrey, dPredator)))
  })
}


# Example is made for  three different species of prey
pars  <- c(rIng   = 0.2,# /day, rate of ingestion
# I do not know how to pass on these parameters as a vector this
productes and error
   rGrow  = c(1.0, 1.3, 1.7)# /day, growth rate of prey
   rMort  = 0.2 ,   # /day, mortality rate of predator
   assEff = 0.5,# -, assimilation efficiency
   K  = 10) # mmol/m3, carrying capacity

yini  <- c(Prey = c(1, 2,3), Predator = 2)
times <- seq(0, 200, by = 1)
out   <- ode(yini, times, LVmod, pars)
summary(out)


Thanks

Frank

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Re: [R] Linear Regressions with constraint coefficients

[charles rockson via R-help]

Any help with exporting anova output in R to csv or xlsx?

  From: "Aleksandrovic, Aljosa (Pfaeffikon)" 
 To: Bert Gunter  
Cc: "r-help@r-project.org" 
 Sent: Tuesday, April 26, 2016 8:29 AM
 Subject: Re: [R] Linear Regressions with constraint coefficients
   
Ok, and if I would just like to force my slope coefficients to be inside an 
interval, let's say, between 0 and 1? Is there a way in R to formulate such a 
constraint regression?

Thanks in advance and kind regards,
Aljosa



Aljosa Aleksandrovic, FRM, CAIA
Quantitative Analyst - Convertibles
aljosa.aleksandro...@man.com
Tel +41 55 417 7603

Man Investments (CH) AG
Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland


-Original Message-
From: Bert Gunter [mailto:bgunter.4...@gmail.com] 
Sent: Dienstag, 26. April 2016 16:51
To: Aleksandrovic, Aljosa (Pfaeffikon)
Cc: r-help@r-project.org
Subject: Re: [R] Linear Regressions with constraint coefficients

If the slope coefficients sum to a constant, the regressors are dependent and 
so a unique solution is impossible (an infinity of solutions would result). So 
I think you have something going on that you don't understand and should 
consult a local statistician to help you formulate your problem appropriately.

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 Tue, Apr 26, 2016 at 5:39 AM, Aleksandrovic, Aljosa (Pfaeffikon) 
 wrote:
> Hi all,
>
> I hope you are doing well?
>
> I’m currently using the lm() function from the package stats to fit linear 
> multifactor regressions.
>
> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
> with constraint coefficients? I would like the slope coefficients to be all 
> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
> slope coefficients should add up to 1.
>
> Is there an elegant and not too complicated way to do such a constraint 
> regression estimation in R?
>
> I would very much appreciate if you could help me with my issue?
>
> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
> Sent: Dienstag, 26. April 2016 14:35
> To: Aleksandrovic, Aljosa (Pfaeffikon)
> Subject: Re: Linear Regressions with constraint coefficients
>
> You need to send it to r-help@r-project.org however.
>
> Kevin
>
> On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>> Ok, will do! Thx a lot!
>>
>> Please find below my request:
>>
>> Hi all,
>>
>> I hope you are doing well?
>>
>> I’m currently using the lm() function from the package stats to fit linear 
>> multifactor regressions.
>>
>> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
>> with constraint coefficients? I would like the slope coefficients to be all 
>> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
>> slope coefficients should add up to 1.
>>
>> Is there an elegant and not too complicated way to do such a constraint 
>> regression estimation in R?
>>
>> I would very much appreciate if you could help me with my issue?
>>
>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>>
>> -Original Message-
>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>> Sent: Dienstag, 26. April 2016 14:28
>> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
>> Subject: Re: Linear Regressions with constraint coefficients
>>
>> I believe I approved a message with such a subject. Perhaps there was 
>> another layer that subsequently rejected it after that. I didn't notice any 
>> unusual content. Try again, making sure you send the message in plain text 
>> only.
>>
>> Kevin
>>
>> On 04/26/2016 08:16 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>>> Do you know where I get help for my issue?
>>>
>>> Thanks in advance and kind regards,
>>> Aljosa
>>>
>>>
>>> Aljosa Aleksandrovic, FRM, CAIA
>>> Quantitative Analyst - Convertibles
>>> aljosa.aleksandro...@man.com
>>> Tel +41 55 417 7603
>>>
>>> Man Investments (CH) AG
>>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>>
>>> -Original Message-
>>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>>> r-help-ow...@r-project.org
>>> Sent: Dienstag, 26. April 2016 14:10
>>> To: Aleksandrovic, Aljosa (Pfaeffikon)
>>> 

[R] survival::clogit, how to extract residuals for GOF assessment

[Joe Ceradini]

Hi Folks,

Hopefully this question has enough R and not too much stats to be
appropriate for this list. Based on,* Hosmer et al. 2013. Logistic
regression for matched case-control studies. Applied Logistic
Regression *(eqtn.
7.8)*, *I am assessing GOF of conditional (or matched) logistic regression
models with the *standardized Pearson residuals*. The authors define
“large” as delta chi-squared values > 4.

For a 1:1 study, I can fit a conditional logistic model via an
unconditional routine by making the response variable all 1’s, taking the
difference of the covariate values for each pair, and removing the
intercept. I can then extract the standardized residuals from the model
(see code at bottom for example). However, if I want to fit a 1:many model,
I need to use survival::clogit, which is where my question comes in:

How can I apply this same "test" to a clogit model? Which residuals should
I be extracting? Or, is this not an option for a clogit model?

## The default residuals of coxph in R are the martingale residuals.

## resid(fit1,type=c("martingale", "deviance", "score", "schoenfeld",

##   "dfbeta", "dfbetas", "scaledsch","partial"))



R code below shows equivalence between clogit and binomial GLM fit on the
differences (note: these would not be equivalent if used a "cluster"
argument in clogit), and GOF "test" for binomial GLM fit on the
differences. I would like to assess GOF of the fit.clogit model but do not
know how.


require(survival)

require(plyr)


# Dataframe

dat.full <- structure(list(resp = c(1L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, 1L, 0L,

0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L,

0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 0L, 1L, 0L,

0L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,

1L, 0L), x1 = c(3.92, 2.04, 2.27, 9.25, 6.13, 10.44, 5.09, 1.27,

5.9, 2.88, 3.79, 1.46, 3.35, 3.82, 4.28, 6.52, 3.54, 3.46, 0.46,

1.68, 3.22, 1.64, -0.12, 2.78, 2.58, 2, 2.83, 3.58, 1.45, 1.64,

2.89, 3.12, 5.6, 8.29, 3.42, 4.8, 3.04, 4.33, 5.31, 1.78, 8.18,

4.56, 4.85, 7.99, 7.52, 6.85, 7.64, 3.33, 5.17, 4.62, 1.24, 2.54,

3.08, 8.2, 1.81, 2.78, 2.16, 2.76, 3.45, 3.43), ID = c(10L, 10L,

11L, 11L, 13L, 13L, 17L, 17L, 18L, 18L, 23L, 23L, 25L, 25L, 29L,

29L, 31L, 31L, 33L, 33L, 35L, 35L, 38L, 38L, 39L, 39L, 4L, 4L,

41L, 41L, 43L, 43L, 45L, 45L, 46L, 46L, 49L, 49L, 50L, 50L, 54L,

54L, 55L, 55L, 56L, 56L, 57L, 57L, 59L, 59L, 6L, 6L, 60L, 60L,

7L, 7L, 8L, 8L, 9L, 9L)), .Names = c("resp", "x1", "ID"), row.names = c(1L,

2L, 3L, 4L, 7L, 8L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 21L,

22L, 23L, 24L, 25L, 26L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L,

37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 49L, 50L, 55L,

56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L, 67L, 68L,

71L, 72L, 73L, 74L, 75L, 76L), class = "data.frame")


# fit clogit

fit.clogit <- clogit(resp ~ x1 + strata(ID), method = "efron", data =
dat.full)

summary(fit.clogit)


# Make dataframe so can fit on differences with unconditional routine.

# x1 where resp = 1 minus x1 where resp = 0, grouped by ID

dat.diff <- ddply(dat.full, .(ID), summarise,

  x1.diff = x1[resp == 1] - x1[resp == 0])

dat.diff$resp <- 1 # response variable is all 1's


# Fit on differences and 1's, remove intercept

fit.diff <- glm(resp ~ -1 + x1.diff, family = binomial, data = dat.diff)

summary(fit.diff)

summary(fit.clogit)$coefficients


# GOF: delta chi-squared

plot(fit.diff$fitted.values, rstandard(fit.diff)^2)

round(sort(rstandard(fit.diff)^2), 4)

Thanks!
Joe

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Re: [R] From NUM to INT

[Bert Gunter]

Please respond to the list. It will be obvious why in a second.

That's not my threshhold! -- it's R's. Your numeric integers cannot be
exactly represented as integers in R. Period. Maybe there are special
packages for extended arithmetic that can do this. but someone else
would have to help you there.  See here for a discussion that might be
helpful:

http://www.r-bloggers.com/r-in-a-64-bit-world/


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 Tue, Apr 26, 2016 at 10:46 AM, André Luis Neves  wrote:
> So, How could I implement this, Bert?
>
> I really need that the variable be converted unto an integer, and it seems
> that my numbers are much higher than that threshold you stated.
>
> Thanks,
>
> Andre
>
> On Tue, Apr 26, 2016 at 11:42 AM, Bert Gunter 
> wrote:
>>
>> No.
>>
>> From ?as.integer:
>>
>> "Note that current implementations of R use 32-bit integers for
>> integer vectors, so the range of representable integers is restricted
>> to about +/-2*10^9: doubles can hold much larger integers exactly. "
>>
>> 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 Tue, Apr 26, 2016 at 10:11 AM, André Luis Neves 
>> wrote:
>> > Dear all:
>> >
>> > I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
>> > (using excel) and then imported the data (.txt) into R. Interestingly,
>> > the
>> > other three variables were loaded as INT, but the 'Baci' one continued
>> > as
>> > Num.
>> >
>> > I imported the data using the following command line:
>> >
>> > X <- read.delim(file.choose(),
>> >  header = TRUE,
>> >  dec = ".")
>> >
>> > Here is the structure of X:
>> >
>> >> str(X)
>> > 'data.frame': 115 obs. of  5 variables:
>> >  $ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26
>> > 27
>> > 29 31 32 36 ...
>> >  $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
>> >  $ Meti : int  352645997 334146268 767208656 171567266 462747405
>> > 414905627 237010514 387480048 214671355 328813226 ...
>> >  $ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156
>> > 13746
>> > ...
>> >  $ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015
>> > 203685
>> > 4261780 43110492 69802572 ...
>> >
>> >
>> > I need Baci as an integer, and tried to convert it using as.integer
>> > function, but was not successful.
>> >
>> >
>> > Could anyone please help me to solve this problem.
>> >
>> > Thanks,
>> >
>> >
>> >
>> > --
>> > Andre
>> >
>> > __
>> > 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.
>
>
>
>
> --
> Andre

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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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.

Re: [R] From NUM to INT

[Jeff Newmiller]

That is the "impossible" case, since R integers are 32 bit signed (~2×10^9) 
even in 64 bit R. You can Google for "R arbitrary precision" and look for 
packages like Ryacas, bit64 or gmp. However, having such large integers stored 
as integers would not be necessary for most statistical analyses so you should 
confirm that your analysis cannot be performed using floating point numbers 
before resorting to that.
-- 
Sent from my phone. Please excuse my brevity.

On April 26, 2016 10:11:38 AM PDT, "André Luis Neves"  
wrote:
>Dear all:
>
>I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
>(using excel) and then imported the data (.txt) into R. Interestingly,
>the
>other three variables were loaded as INT, but the 'Baci' one continued
>as
>Num.
>
>I imported the data using the following command line:
>
>X <- read.delim(file.choose(),
> header = TRUE,
> dec = ".")
>
>Here is the structure of X:
>
>> str(X)
>'data.frame': 115 obs. of  5 variables:
>$ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26
>27
>29 31 32 36 ...
> $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
> $ Meti : int  352645997 334146268 767208656 171567266 462747405
>414905627 237010514 387480048 214671355 328813226 ...
>$ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156
>13746
>...
>$ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015
>203685
>4261780 43110492 69802572 ...
>
>
>I need Baci as an integer, and tried to convert it using as.integer
>function, but was not successful.
>
>
>Could anyone please help me to solve this problem.
>
>Thanks,
>
>
>​
>-- 
>Andre
>
>
>
>
>__
>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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] From NUM to INT

[Bert Gunter]

No.

>From ?as.integer:

"Note that current implementations of R use 32-bit integers for
integer vectors, so the range of representable integers is restricted
to about +/-2*10^9: doubles can hold much larger integers exactly. "

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 Tue, Apr 26, 2016 at 10:11 AM, André Luis Neves  wrote:
> Dear all:
>
> I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
> (using excel) and then imported the data (.txt) into R. Interestingly, the
> other three variables were loaded as INT, but the 'Baci' one continued as
> Num.
>
> I imported the data using the following command line:
>
> X <- read.delim(file.choose(),
>  header = TRUE,
>  dec = ".")
>
> Here is the structure of X:
>
>> str(X)
> 'data.frame': 115 obs. of  5 variables:
>  $ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26 27
> 29 31 32 36 ...
>  $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
>  $ Meti : int  352645997 334146268 767208656 171567266 462747405
> 414905627 237010514 387480048 214671355 328813226 ...
>  $ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156 13746
> ...
>  $ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015 203685
> 4261780 43110492 69802572 ...
>
>
> I need Baci as an integer, and tried to convert it using as.integer
> function, but was not successful.
>
>
> Could anyone please help me to solve this problem.
>
> Thanks,
>
>
>
> --
> Andre
>
> __
> 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.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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.

[R] From NUM to INT

[André Luis Neves]

Dear all:

I converted the columns (Baci, Meti, Fungii, Protozoai) into integers
(using excel) and then imported the data (.txt) into R. Interestingly, the
other three variables were loaded as INT, but the 'Baci' one continued as
Num.

I imported the data using the following command line:

X <- read.delim(file.choose(),
 header = TRUE,
 dec = ".")

Here is the structure of X:

> str(X)
'data.frame': 115 obs. of  5 variables:
 $ ID   : Factor w/ 61 levels "107ZRED","112BLKW",..: 8 12 15 18 26 27
29 31 32 36 ...
 $ Baci : num  2.90e+12 5.55e+11 9.46e+11 8.13e+11 4.06e+11 ...
 $ Meti : int  352645997 334146268 767208656 171567266 462747405
414905627 237010514 387480048 214671355 328813226 ...
 $ Fungii   : int  43645 19009 15998 2189 8972 8240 3133 17922 6156 13746
...
 $ Protozoai: int  3220523 1851891 3252462 1665675 34123768 23175015 203685
4261780 43110492 69802572 ...


I need Baci as an integer, and tried to convert it using as.integer
function, but was not successful.


Could anyone please help me to solve this problem.

Thanks,


​
-- 
Andre
ID  BaciMetiFungii  Protozoai
126BLK  2.90E+12352645997   43645   3220523
13ZBLK  5.55E+11334146268   19009   1851891
157BLK  9.46E+11767208656   15998   3252462
162ZRED 8.13E+11171567266   21891665675
17ZBLKY 4.06E+11462747405   897234123768
184ZBLK 5.75E+11414905627   824023175015
1ZBLKW  3.45E+10237010514   3133203685
2094ZBLK3.49E+11387480048   17922   4261780
20LZBLK 1.63E+11214671355   615643110492
29ZBLK  3.37E+11328813226   13746   69802572
2ZBLKG  3.13E+11564519908   400393195958
60ZRED  3.76E+11145383281   12473   33141411
77BLK   2.92E+11227643897   13328   306363850
8ZBLK   2.45E+11565298547   290029939862
91ZRED  5.62E+11472996887   858473402283
112BLKW 7.02E+10475554339   192654  37844605
1226BLK 1.84E+10239034620   65524   3994847
12ZBLK  6.45E+10296646742   286966  45244390
134BLK  9.65E+09201168840   47474   2756770
160ZRED 5.96E+10193983600   155040  79660710
166ZRED 8.14E+10315417009   26056   85856558
17ZBLK G1.88E+11626249880   74214   17763633
226ZBLK 3.88E+10181768548   291862  128256576
3ZBLK   2.38E+10175939117   46015   8351259
58BLK   5.37E+10304530782   50342   7718372
60ZBLK  4.23E+10375725507   146473  58960339
72ZRED  9.58E+10373650117   73205   171268872
7ZBLK   4.78E+10146490232   17068   171268872
95BLK   4.18E+10210377292   71368   31213851
9PZRED  7.12E+10278312630   178204  392574732
107ZRED 1.18E+11497812799   70745212968
129BLK  1.01E+10172557004   565 373103
150ZRED 1.48E+11343107486   786965118676
168BLK  9.45E+10298332033   528117428719
174ZBLK 6.29E+10269735103   24635   42532632
185ZRED 7.81E+10647775276   197348855746
2ZBLKY  4.93E+0935698451318328935576
4089ZBLK1.94E+10326852779   1329520051
438XZRED7.20E+09113153909   630 127811
4ZBLK   5.30E+10248877230   1469827989
706ZBLK 3.12E+10151072339   24074885127
86BLK   9.39E+10526984044   417 1034021
86ZRED  5.71E+10385701592   783492440481
89BLK   3.80E+10297806285   631462159379
112XZBLKG   9.56E+11603355806   5205199868382
1191ZBLK4.59E+11403738704   35115   93137246
122ZRED 2.93E+11266699375   930 68471595
14ZBLK  8.03E+11607043335   557075196835
15ZBLK  3.99E+11185346266   171626429018
163BLK  7.18E+11598193580   20475   419543828
175ZRED 2.08E+11660223375   442135481033
1ZBLKY  6.84E+11472986697   43059   137129730
20SXZBLK3.16E+112611953820297   8031502
22ZBLK  7.70E+11823508297   154975  264859084
63ZBLK  2.10E+111601226529  13317   44878482
6ZBLK   1.31E+11110772471   139540830068
82ZBLK  1.10E+12839550736   536868087375
92ZBLK  4.32E+11829679134   14981   98201518
94BLK   1.54E+11197873442   16806800437
126BLK  2.22E+11209765315   13000   92754991
13ZBLK  6.75E+11366018180   18291   60965929
157BLK  2.88E+11227660122   890420595699
162ZRED 1.85E+11372912115   3124516219
17ZBLKY 1.02E+11170028711   42881391174
184ZBLK 4.28E+11385951078   18173   142041693
1ZBLKW  1.26E+11258658827   39741096335
2094ZBLK2.80E+11299019239   

Re: [R] Issue while building xtable on R on Ubuntu 15.04

[David Winsemius]

> On Apr 26, 2016, at 4:08 AM, Zaid Golwala  wrote:
> 
> Please help in the below mentioned issue.
> 
> Regards
> Zaid Golwala
> 
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Zaid Golwala
> Sent: Wednesday, April 06, 2016 1:35 PM
> To: r-help@R-project.org
> Subject: [R] Issue while building xtable on R on Ubuntu 15.04
> 
> Hi,
> 
> I am trying to build xtable on R  on Ubuntu 15.04 but I get following error :
> 
> 
> + R CMD check --no-vignettes --timings xtable_1.8-2.tar.gz
> 
> * using log directory 
> '/home/jenkins/workspace/Rlang_xtable_Ubuntu15.04/xtable.Rcheck'
> 
> * using R version 3.2.3 (2015-12-10)
> 
> * using platform: powerpc64le-unknown-linux-gnu (64-bit)
> 
> * using session charset: UTF-8
> 
> * using option '--no-vignettes
> 
> '* checking for file 'xtable/DESCRIPTION' ... OK
> 
> * this is package 'xtable' version '1.8-2'
> 
> * checking package namespace information ... OK
> 
> * checking package dependencies ...Error in .build_vignette_index(vigns) :   
> In 'inst' vignettes 'xtableGallery.Rnw' and 'xtableGallery.snw' have the same 
> vignette name

Why not change one of the names?

-- 
David.
> 
> Can someone please help me regarding the same.
> 
> Regards
> Zaid Golwala
> 
> DISCLAIMER\ ==\ This e-mail ...{{dropped:18}}
> 
> __
> 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.

David Winsemius
Alameda, CA, USA

__
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.

Re: [R] Linear Regressions with constraint coefficients

[Aleksandrovic, Aljosa (Pfaeffikon)]

Hi Gabor,

Thanks a lot for your input!

Kind regards,
Aljosa



Aljosa Aleksandrovic, FRM, CAIA
Quantitative Analyst - Convertibles
aljosa.aleksandro...@man.com
Tel +41 55 417 76 03

Man Investments (CH) AG
Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland


-Original Message-
From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com] 
Sent: Dienstag, 26. April 2016 17:59
To: Aleksandrovic, Aljosa (Pfaeffikon)
Cc: r-help@r-project.org
Subject: Re: [R] Linear Regressions with constraint coefficients

This is a quadratic programming problem that you can solve using either a 
quadratic programming solver with constraints or a general nonlinear solver 
with constraints.  See https://cran.r-project.org/web/views/Optimization.html
for more info on what is available.

Here is an example using a nonlinear least squares solver and non-negative 
bound constraints. The constraint that the coefficients sum to 1 is implied by 
dividing them by their sum and then dividing the coefficients found by their 
sum at the end:

# test data
set.seed(123)
n <- 1000
X1 <- rnorm(n)
X2 <- rnorm(n)
X3 <- rnorm(n)
Y <- .2 * X1 + .3 * X2 + .5 * X3 + rnorm(n)

# fit
library(nlmrt)
fm <- nlxb(Y ~ (b1 * X1 + b2 * X2 + b3 * X3)/(b1 + b2 + b3),
 data = list(Y = Y, X1 = X1, X2 = X2, X3 = X3),
 lower = numeric(3),
 start = list(b1 = 1, b2 = 2, b3 = 3))

giving the following non-negative coefficients which sum to 1 that are 
reasonably close to the true values of 0.2, 0.3 and 0.5:

> fm$coefficients / sum(fm$coefficients)
 b1  b2  b3
0.18463 0.27887 0.53650


On Tue, Apr 26, 2016 at 8:39 AM, Aleksandrovic, Aljosa (Pfaeffikon) 
 wrote:
> Hi all,
>
> I hope you are doing well?
>
> I’m currently using the lm() function from the package stats to fit linear 
> multifactor regressions.
>
> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
> with constraint coefficients? I would like the slope coefficients to be all 
> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
> slope coefficients should add up to 1.
>
> Is there an elegant and not too complicated way to do such a constraint 
> regression estimation in R?
>
> I would very much appreciate if you could help me with my issue?
>
> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
> Sent: Dienstag, 26. April 2016 14:35
> To: Aleksandrovic, Aljosa (Pfaeffikon)
> Subject: Re: Linear Regressions with constraint coefficients
>
> You need to send it to r-help@r-project.org however.
>
> Kevin
>
> On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>> Ok, will do! Thx a lot!
>>
>> Please find below my request:
>>
>> Hi all,
>>
>> I hope you are doing well?
>>
>> I’m currently using the lm() function from the package stats to fit linear 
>> multifactor regressions.
>>
>> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
>> with constraint coefficients? I would like the slope coefficients to be all 
>> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
>> slope coefficients should add up to 1.
>>
>> Is there an elegant and not too complicated way to do such a constraint 
>> regression estimation in R?
>>
>> I would very much appreciate if you could help me with my issue?
>>
>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>>
>> -Original Message-
>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>> Sent: Dienstag, 26. April 2016 14:28
>> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
>> Subject: Re: Linear Regressions with constraint coefficients
>>
>> I believe I approved a message with such a subject. Perhaps there was 
>> another layer that subsequently rejected it after that. I didn't notice any 
>> unusual content. Try again, making sure you send the message in plain text 
>> only.
>>
>> Kevin
>>
>> On 04/26/2016 08:16 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>>> Do you know where I get help for my issue?
>>>
>>> Thanks in advance and kind regards,
>>> Aljosa
>>>
>>>
>>> Aljosa Aleksandrovic, FRM, CAIA
>>> Quantitative Analyst - Convertibles
>>> aljosa.aleksandro...@man.com
>>> Tel +41 55 417 7603
>>>
>>> Man Investments (CH) AG
>>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>>
>>> -Original Message-
>>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>>> r-help-ow...@r-project.org
>>> Sent: Dienstag, 26. April 

Re: [R] ylim in barplot()

[Ivan Calandra]

Dear useRs,

It seems that my last e-mail went quite unnoticed...
Has anyone an idea about ylim doesn't work in barplot (see details below)?

Thank you in advance,
Ivan (on behalf of Stéphanie)

--
Ivan Calandra, PhD
Scientific Mediator
University of Reims Champagne-Ardenne
GEGENAA - EA 3795
CREA - 2 esplanade Roland Garros
51100 Reims, France
+33(0)3 26 77 36 89
ivan.calan...@univ-reims.fr
--
https://www.researchgate.net/profile/Ivan_Calandra
https://publons.com/author/705639/

Le 26/04/2016 à 08:41, Ivan Calandra a écrit :

Thank you David,

That's a nice workaround using plotrix::barp(), but that doesn't 
explain why ylim doesn't work as intended (or at least, as I expect it 
to work), or why xpd has no influence when using devEMF::emf()...


The problem with saving directly in RStudio is that it requires to 
manually save the plot, and this becomes troublesome when there are a 
lot of plot commands in a single script.


Bests,
Ivan (on behalf of Stéphanie)

--
Ivan Calandra, PhD
Scientific Mediator
University of Reims Champagne-Ardenne
GEGENAA - EA 3795
CREA - 2 esplanade Roland Garros
51100 Reims, France
+33(0)3 26 77 36 89
ivan.calan...@univ-reims.fr
--
https://www.researchgate.net/profile/Ivan_Calandra
https://publons.com/author/705639/

Le 25/04/2016 21:16, David L Carlson a écrit :
If you are using a Windows system, you can Export the plot from 
RStudio and save it as a metafile without using package devEMF and it 
will crop the bars with xpd=FALSE. When I used devEMF on a Windows 
machine, the bars were not cropped with barplot() as you indicated, 
but when I switched to plotrix::barp() they were cropped. The 
arguments are a bit different, but I did not need xpd=FALSE:


emf("TestPlot.emf")
barp(t(mydata), col=c("orange", "green", "yellow", "purple"),
ylim=c(50,70), legend.lab=colnames(mydata), legend.pos="topright")
dev.off()

-
David L Carlson
Department of Anthropology
Texas A University
College Station, TX 77840-4352


-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of 
EYSSAUTIER Stéphanie

Sent: Monday, April 25, 2016 9:53 AM
To: r-help@r-project.org
Subject: [R] ylim in barplot()

Dear useRs,

I'm having troubles with using ylim in barplot(): even though I reduce
the y-scale using ylim, the bars still extend down to 0into the 
x-labels.

The sample data is below, and here is the code.

#This works fine but I would like to plot only from 50 to 70:
barplot(t(mydata), beside=TRUE, col=c("orange", "green", "yellow",
"purple"), legend=TRUE, las=2, axis.lty=1)

#This is the ylim version with the bar problem:
barplot(t(mydata), beside=TRUE, col=c("orange", "green", "yellow",
"purple"), ylim=c(50,70), legend=TRUE, las=2, axis.lty=1)

#I have tried using xpd=FALSE and this works fine withinRguior Rstudio
but not when I plot within devEMF::emf()
barplot(t(mydata), beside=TRUE, col=c("orange", "green", "yellow",
"purple"), ylim=c(50,70), legend=TRUE, las=2, axis.lty=1, xpd=FALSE)

I need the emf file to edit the plot.

Why isn't it working with ylim alone? And why doesn't xpd work with 
emf()?


Thanks in advance for your help,
Stéphanie


mydata <- structure(c(68.1799689328282, 68.2164021637813,
68.3243626415103, 61.7899567386469, 59.5182501049449, 63.9916220705152,
64.1442535260522, 64.2585746423512, 62.5653571705887, 61.631969055001,
61.3991475513249, 63.2401411727188, 65.0488808306348, 63.43022364909,
64.8425577471775, 65.4986231824992, 64.7798619682232, 64.4174790601806,
65.5696701695485, 65.0253962620178, 63.2476885701954, 63.2473647791827,
62.5000542212819, 63.1742307643225, 62.1560658393146, 62.5810636272476,
64.0935149828315, 65.5432025084893, 66.7535104579705, 59.6500997601308,
59.4641686257122, 59.8891527196501, 60.0117050975523, 64.3309521324969,
62.0079305659785, 57.0665210362419, 57.5202118193362, 61.3280531011031,
62.6326634763289, 60.2094259175778, 65.5923786551105, 65.6946445059829,
65.2498254841218, 65.3468620859567, 67.024437492438, 65.8533801964148,
65.0047369761726, 65.0310208374089, 64.3121920326177, 64.8038153143374,
63.7306643056964, 64.2579190762784, 67.5745906026732, 67.0351170775703,
66.4053872920113, 59.9302305698358, 60.368722602391, 60.3572311841096,
60.0960412312049, 63.7886894551889, 62.24708719601, 59.3334729073243,
59.9537485303794, 63.1828096654404, 63.5352778562394, 60.621828397375,
65.8889763819732, 66.2059756115814, 66.4567010911873, 65.8796623180062,
67.5552743734229, 66.504738660398, 66.2085036370622, 66.4230781907321,
65.5130180297911, 65.9051623923225, 64.8408013974267, 65.5175045910169,
68.0760225106606, 66.8615536135711, 65.0390748892256, 59.2940092440695,
60.7061368898884, 59.7345965097738, 59.6019925755588, 63.6011933836225,
62.1134684942427, 60.4227073441121, 60.7834352002706, 63.4539745079728,
63.6329498376672, 58.8034486099638, 65.2910772858539, 65.5952764758513,
65.8371262481454, 66.1191053038481, 67.5230043279325, 66.8569714429862,
66.1045642986574, 66.8499631633452, 

Re: [R] Linear Regressions with constraint coefficients

[Gabor Grothendieck]

This is a quadratic programming problem that you can solve using
either a quadratic programming solver with constraints or a general
nonlinear solver with constraints.  See
https://cran.r-project.org/web/views/Optimization.html
for more info on what is available.

Here is an example using a nonlinear least squares solver and
non-negative bound constraints. The constraint that the coefficients
sum to 1 is implied by dividing them by their sum and then dividing
the coefficients found by their sum at the end:

# test data
set.seed(123)
n <- 1000
X1 <- rnorm(n)
X2 <- rnorm(n)
X3 <- rnorm(n)
Y <- .2 * X1 + .3 * X2 + .5 * X3 + rnorm(n)

# fit
library(nlmrt)
fm <- nlxb(Y ~ (b1 * X1 + b2 * X2 + b3 * X3)/(b1 + b2 + b3),
 data = list(Y = Y, X1 = X1, X2 = X2, X3 = X3),
 lower = numeric(3),
 start = list(b1 = 1, b2 = 2, b3 = 3))

giving the following non-negative coefficients which sum to 1 that are
reasonably close to the true values of 0.2, 0.3 and 0.5:

> fm$coefficients / sum(fm$coefficients)
 b1  b2  b3
0.18463 0.27887 0.53650


On Tue, Apr 26, 2016 at 8:39 AM, Aleksandrovic, Aljosa (Pfaeffikon)
 wrote:
> Hi all,
>
> I hope you are doing well?
>
> I’m currently using the lm() function from the package stats to fit linear 
> multifactor regressions.
>
> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
> with constraint coefficients? I would like the slope coefficients to be all 
> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
> slope coefficients should add up to 1.
>
> Is there an elegant and not too complicated way to do such a constraint 
> regression estimation in R?
>
> I would very much appreciate if you could help me with my issue?
>
> Thanks a lot in advance and kind regards,
> Aljosa Aleksandrovic
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
> Sent: Dienstag, 26. April 2016 14:35
> To: Aleksandrovic, Aljosa (Pfaeffikon)
> Subject: Re: Linear Regressions with constraint coefficients
>
> You need to send it to r-help@r-project.org however.
>
> Kevin
>
> On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>> Ok, will do! Thx a lot!
>>
>> Please find below my request:
>>
>> Hi all,
>>
>> I hope you are doing well?
>>
>> I’m currently using the lm() function from the package stats to fit linear 
>> multifactor regressions.
>>
>> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
>> with constraint coefficients? I would like the slope coefficients to be all 
>> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
>> slope coefficients should add up to 1.
>>
>> Is there an elegant and not too complicated way to do such a constraint 
>> regression estimation in R?
>>
>> I would very much appreciate if you could help me with my issue?
>>
>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>>
>> -Original Message-
>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>> Sent: Dienstag, 26. April 2016 14:28
>> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
>> Subject: Re: Linear Regressions with constraint coefficients
>>
>> I believe I approved a message with such a subject. Perhaps there was 
>> another layer that subsequently rejected it after that. I didn't notice any 
>> unusual content. Try again, making sure you send the message in plain text 
>> only.
>>
>> Kevin
>>
>> On 04/26/2016 08:16 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>>> Do you know where I get help for my issue?
>>>
>>> Thanks in advance and kind regards,
>>> Aljosa
>>>
>>>
>>> Aljosa Aleksandrovic, FRM, CAIA
>>> Quantitative Analyst - Convertibles
>>> aljosa.aleksandro...@man.com
>>> Tel +41 55 417 7603
>>>
>>> Man Investments (CH) AG
>>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>>
>>> -Original Message-
>>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>>> r-help-ow...@r-project.org
>>> Sent: Dienstag, 26. April 2016 14:10
>>> To: Aleksandrovic, Aljosa (Pfaeffikon)
>>> Subject: Linear Regressions with constraint coefficients
>>>
>>> The message's content type was not explicitly allowed
>>>
>
>
> --
> Kevin E. Thorpe
> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's Hospital
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>
> This email has been sent 

Re: [R] Linear Regressions with constraint coefficients

[Aleksandrovic, Aljosa (Pfaeffikon)]

Ok, will try!

Thanks a kind regards,
Aljosa


Aljosa Aleksandrovic, FRM, CAIA
Quantitative Analyst - Convertibles
aljosa.aleksandro...@man.com
Tel +41 55 417 76 03

Man Investments (CH) AG
Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland


-Original Message-
From: Bert Gunter [mailto:bgunter.4...@gmail.com] 
Sent: Dienstag, 26. April 2016 17:49
To: Aleksandrovic, Aljosa (Pfaeffikon)
Cc: r-help@r-project.org
Subject: Re: [R] Linear Regressions with constraint coefficients

Have you tried web searching on " R constrained linear regression" or similar. 
There seemed to be resources related to your issues when I looked. You might 
also search on rseek.org  . There are apparently several packages that do 
regression with constraints, but I don't know if they fit your situation.

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 Tue, Apr 26, 2016 at 8:29 AM, Aleksandrovic, Aljosa (Pfaeffikon) 
 wrote:
> Ok, and if I would just like to force my slope coefficients to be inside an 
> interval, let's say, between 0 and 1? Is there a way in R to formulate such a 
> constraint regression?
>
> Thanks in advance and kind regards,
> Aljosa
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Bert Gunter [mailto:bgunter.4...@gmail.com]
> Sent: Dienstag, 26. April 2016 16:51
> To: Aleksandrovic, Aljosa (Pfaeffikon)
> Cc: r-help@r-project.org
> Subject: Re: [R] Linear Regressions with constraint coefficients
>
> If the slope coefficients sum to a constant, the regressors are dependent and 
> so a unique solution is impossible (an infinity of solutions would result). 
> So I think you have something going on that you don't understand and should 
> consult a local statistician to help you formulate your problem appropriately.
>
> 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 Tue, Apr 26, 2016 at 5:39 AM, Aleksandrovic, Aljosa (Pfaeffikon) 
>  wrote:
>> Hi all,
>>
>> I hope you are doing well?
>>
>> I’m currently using the lm() function from the package stats to fit linear 
>> multifactor regressions.
>>
>> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
>> with constraint coefficients? I would like the slope coefficients to be all 
>> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
>> slope coefficients should add up to 1.
>>
>> Is there an elegant and not too complicated way to do such a constraint 
>> regression estimation in R?
>>
>> I would very much appreciate if you could help me with my issue?
>>
>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>>
>> -Original Message-
>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>> Sent: Dienstag, 26. April 2016 14:35
>> To: Aleksandrovic, Aljosa (Pfaeffikon)
>> Subject: Re: Linear Regressions with constraint coefficients
>>
>> You need to send it to r-help@r-project.org however.
>>
>> Kevin
>>
>> On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>>> Ok, will do! Thx a lot!
>>>
>>> Please find below my request:
>>>
>>> Hi all,
>>>
>>> I hope you are doing well?
>>>
>>> I’m currently using the lm() function from the package stats to fit linear 
>>> multifactor regressions.
>>>
>>> Unfortunately, I didn’t yet find a way to fit linear multifactor 
>>> regressions with constraint coefficients? I would like the slope 
>>> coefficients to be all inside an interval, let’s say, between 0 and 1. 
>>> Further, if possible, the slope coefficients should add up to 1.
>>>
>>> Is there an elegant and not too complicated way to do such a constraint 
>>> regression estimation in R?
>>>
>>> I would very much appreciate if you could help me with my issue?
>>>
>>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>>
>>>
>>>
>>> Aljosa Aleksandrovic, FRM, CAIA
>>> Quantitative Analyst - Convertibles
>>> aljosa.aleksandro...@man.com
>>> Tel +41 55 417 7603
>>>
>>> Man Investments (CH) AG
>>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>>
>>>
>>> -Original Message-
>>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>>> Sent: Dienstag, 26. April 2016 14:28
>>> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
>>> Subject: Re: Linear Regressions 

Re: [R] Linear Regressions with constraint coefficients

[Bert Gunter]

Have you tried web searching on " R constrained linear regression" or
similar. There seemed to be resources related to your issues when I
looked. You might also search on rseek.org  . There are apparently
several packages that do regression with constraints, but I don't know
if they fit your situation.

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 Tue, Apr 26, 2016 at 8:29 AM, Aleksandrovic, Aljosa (Pfaeffikon)
 wrote:
> Ok, and if I would just like to force my slope coefficients to be inside an 
> interval, let's say, between 0 and 1? Is there a way in R to formulate such a 
> constraint regression?
>
> Thanks in advance and kind regards,
> Aljosa
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Bert Gunter [mailto:bgunter.4...@gmail.com]
> Sent: Dienstag, 26. April 2016 16:51
> To: Aleksandrovic, Aljosa (Pfaeffikon)
> Cc: r-help@r-project.org
> Subject: Re: [R] Linear Regressions with constraint coefficients
>
> If the slope coefficients sum to a constant, the regressors are dependent and 
> so a unique solution is impossible (an infinity of solutions would result). 
> So I think you have something going on that you don't understand and should 
> consult a local statistician to help you formulate your problem appropriately.
>
> 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 Tue, Apr 26, 2016 at 5:39 AM, Aleksandrovic, Aljosa (Pfaeffikon) 
>  wrote:
>> Hi all,
>>
>> I hope you are doing well?
>>
>> I’m currently using the lm() function from the package stats to fit linear 
>> multifactor regressions.
>>
>> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
>> with constraint coefficients? I would like the slope coefficients to be all 
>> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
>> slope coefficients should add up to 1.
>>
>> Is there an elegant and not too complicated way to do such a constraint 
>> regression estimation in R?
>>
>> I would very much appreciate if you could help me with my issue?
>>
>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>>
>> -Original Message-
>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>> Sent: Dienstag, 26. April 2016 14:35
>> To: Aleksandrovic, Aljosa (Pfaeffikon)
>> Subject: Re: Linear Regressions with constraint coefficients
>>
>> You need to send it to r-help@r-project.org however.
>>
>> Kevin
>>
>> On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>>> Ok, will do! Thx a lot!
>>>
>>> Please find below my request:
>>>
>>> Hi all,
>>>
>>> I hope you are doing well?
>>>
>>> I’m currently using the lm() function from the package stats to fit linear 
>>> multifactor regressions.
>>>
>>> Unfortunately, I didn’t yet find a way to fit linear multifactor 
>>> regressions with constraint coefficients? I would like the slope 
>>> coefficients to be all inside an interval, let’s say, between 0 and 1. 
>>> Further, if possible, the slope coefficients should add up to 1.
>>>
>>> Is there an elegant and not too complicated way to do such a constraint 
>>> regression estimation in R?
>>>
>>> I would very much appreciate if you could help me with my issue?
>>>
>>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>>
>>>
>>>
>>> Aljosa Aleksandrovic, FRM, CAIA
>>> Quantitative Analyst - Convertibles
>>> aljosa.aleksandro...@man.com
>>> Tel +41 55 417 7603
>>>
>>> Man Investments (CH) AG
>>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>>
>>>
>>> -Original Message-
>>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>>> Sent: Dienstag, 26. April 2016 14:28
>>> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
>>> Subject: Re: Linear Regressions with constraint coefficients
>>>
>>> I believe I approved a message with such a subject. Perhaps there was 
>>> another layer that subsequently rejected it after that. I didn't notice any 
>>> unusual content. Try again, making sure you send the message in plain text 
>>> only.
>>>
>>> Kevin
>>>
>>> On 04/26/2016 08:16 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
 Do you know where I get help for my issue?

 Thanks in advance and kind regards,
 Aljosa


 

Re: [R] Linear Regressions with constraint coefficients

[Aleksandrovic, Aljosa (Pfaeffikon)]

Ok, and if I would just like to force my slope coefficients to be inside an 
interval, let's say, between 0 and 1? Is there a way in R to formulate such a 
constraint regression?

Thanks in advance and kind regards,
Aljosa



Aljosa Aleksandrovic, FRM, CAIA
Quantitative Analyst - Convertibles
aljosa.aleksandro...@man.com
Tel +41 55 417 7603

Man Investments (CH) AG
Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland


-Original Message-
From: Bert Gunter [mailto:bgunter.4...@gmail.com] 
Sent: Dienstag, 26. April 2016 16:51
To: Aleksandrovic, Aljosa (Pfaeffikon)
Cc: r-help@r-project.org
Subject: Re: [R] Linear Regressions with constraint coefficients

If the slope coefficients sum to a constant, the regressors are dependent and 
so a unique solution is impossible (an infinity of solutions would result). So 
I think you have something going on that you don't understand and should 
consult a local statistician to help you formulate your problem appropriately.

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 Tue, Apr 26, 2016 at 5:39 AM, Aleksandrovic, Aljosa (Pfaeffikon) 
 wrote:
> Hi all,
>
> I hope you are doing well?
>
> I’m currently using the lm() function from the package stats to fit linear 
> multifactor regressions.
>
> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
> with constraint coefficients? I would like the slope coefficients to be all 
> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
> slope coefficients should add up to 1.
>
> Is there an elegant and not too complicated way to do such a constraint 
> regression estimation in R?
>
> I would very much appreciate if you could help me with my issue?
>
> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
> Sent: Dienstag, 26. April 2016 14:35
> To: Aleksandrovic, Aljosa (Pfaeffikon)
> Subject: Re: Linear Regressions with constraint coefficients
>
> You need to send it to r-help@r-project.org however.
>
> Kevin
>
> On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>> Ok, will do! Thx a lot!
>>
>> Please find below my request:
>>
>> Hi all,
>>
>> I hope you are doing well?
>>
>> I’m currently using the lm() function from the package stats to fit linear 
>> multifactor regressions.
>>
>> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
>> with constraint coefficients? I would like the slope coefficients to be all 
>> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
>> slope coefficients should add up to 1.
>>
>> Is there an elegant and not too complicated way to do such a constraint 
>> regression estimation in R?
>>
>> I would very much appreciate if you could help me with my issue?
>>
>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>>
>> -Original Message-
>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>> Sent: Dienstag, 26. April 2016 14:28
>> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
>> Subject: Re: Linear Regressions with constraint coefficients
>>
>> I believe I approved a message with such a subject. Perhaps there was 
>> another layer that subsequently rejected it after that. I didn't notice any 
>> unusual content. Try again, making sure you send the message in plain text 
>> only.
>>
>> Kevin
>>
>> On 04/26/2016 08:16 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>>> Do you know where I get help for my issue?
>>>
>>> Thanks in advance and kind regards,
>>> Aljosa
>>>
>>>
>>> Aljosa Aleksandrovic, FRM, CAIA
>>> Quantitative Analyst - Convertibles
>>> aljosa.aleksandro...@man.com
>>> Tel +41 55 417 7603
>>>
>>> Man Investments (CH) AG
>>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>>
>>> -Original Message-
>>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>>> r-help-ow...@r-project.org
>>> Sent: Dienstag, 26. April 2016 14:10
>>> To: Aleksandrovic, Aljosa (Pfaeffikon)
>>> Subject: Linear Regressions with constraint coefficients
>>>
>>> The message's content type was not explicitly allowed
>>>
>
>
> --
> Kevin E. Thorpe
> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's Hospital
> Assistant Professor, Dalla Lana School of Public Health
> University 

Re: [R] Linear Regressions with constraint coefficients

[Bert Gunter]

If the slope coefficients sum to a constant, the regressors are
dependent and so a unique solution is impossible (an infinity of
solutions would result). So I think you have something going on that
you don't understand and should consult a local statistician to help
you formulate your problem appropriately.

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 Tue, Apr 26, 2016 at 5:39 AM, Aleksandrovic, Aljosa (Pfaeffikon)
 wrote:
> Hi all,
>
> I hope you are doing well?
>
> I’m currently using the lm() function from the package stats to fit linear 
> multifactor regressions.
>
> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
> with constraint coefficients? I would like the slope coefficients to be all 
> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
> slope coefficients should add up to 1.
>
> Is there an elegant and not too complicated way to do such a constraint 
> regression estimation in R?
>
> I would very much appreciate if you could help me with my issue?
>
> Thanks a lot in advance and kind regards,
> Aljosa Aleksandrovic
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
> Sent: Dienstag, 26. April 2016 14:35
> To: Aleksandrovic, Aljosa (Pfaeffikon)
> Subject: Re: Linear Regressions with constraint coefficients
>
> You need to send it to r-help@r-project.org however.
>
> Kevin
>
> On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>> Ok, will do! Thx a lot!
>>
>> Please find below my request:
>>
>> Hi all,
>>
>> I hope you are doing well?
>>
>> I’m currently using the lm() function from the package stats to fit linear 
>> multifactor regressions.
>>
>> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
>> with constraint coefficients? I would like the slope coefficients to be all 
>> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
>> slope coefficients should add up to 1.
>>
>> Is there an elegant and not too complicated way to do such a constraint 
>> regression estimation in R?
>>
>> I would very much appreciate if you could help me with my issue?
>>
>> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>>
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>>
>> -Original Message-
>> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
>> Sent: Dienstag, 26. April 2016 14:28
>> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
>> Subject: Re: Linear Regressions with constraint coefficients
>>
>> I believe I approved a message with such a subject. Perhaps there was 
>> another layer that subsequently rejected it after that. I didn't notice any 
>> unusual content. Try again, making sure you send the message in plain text 
>> only.
>>
>> Kevin
>>
>> On 04/26/2016 08:16 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>>> Do you know where I get help for my issue?
>>>
>>> Thanks in advance and kind regards,
>>> Aljosa
>>>
>>>
>>> Aljosa Aleksandrovic, FRM, CAIA
>>> Quantitative Analyst - Convertibles
>>> aljosa.aleksandro...@man.com
>>> Tel +41 55 417 7603
>>>
>>> Man Investments (CH) AG
>>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>>
>>> -Original Message-
>>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>>> r-help-ow...@r-project.org
>>> Sent: Dienstag, 26. April 2016 14:10
>>> To: Aleksandrovic, Aljosa (Pfaeffikon)
>>> Subject: Linear Regressions with constraint coefficients
>>>
>>> The message's content type was not explicitly allowed
>>>
>
>
> --
> Kevin E. Thorpe
> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's Hospital
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016
>
> This email has been sent by a member of the Man group (“Man”). Man’s parent 
> company, Man Group plc, is registered in England and Wales (company number 
> 08172396) at Riverbank House, 2 Swan  Lane, London, EC4R 3AD.
> The contents of this email are for the named addressee(s) only. It contains 
> information which may be confidential and privileged. If you are not the 
> intended recipient, please notify the sender immediately, destroy this email 
> and any attachments and do not otherwise disclose or use them. Email 
> transmission is not a secure method of communication 

Re: [R] Linear Regressions with constraint coefficients

[Aleksandrovic, Aljosa (Pfaeffikon)]

Hi all,

I hope you are doing well?

I’m currently using the lm() function from the package stats to fit linear 
multifactor regressions.

Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
with constraint coefficients? I would like the slope coefficients to be all 
inside an interval, let’s say, between 0 and 1. Further, if possible, the slope 
coefficients should add up to 1.

Is there an elegant and not too complicated way to do such a constraint 
regression estimation in R?

I would very much appreciate if you could help me with my issue?

Thanks a lot in advance and kind regards, 
Aljosa Aleksandrovic



Aljosa Aleksandrovic, FRM, CAIA
Quantitative Analyst - Convertibles
aljosa.aleksandro...@man.com
Tel +41 55 417 7603

Man Investments (CH) AG
Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland


-Original Message-
From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca] 
Sent: Dienstag, 26. April 2016 14:35
To: Aleksandrovic, Aljosa (Pfaeffikon)
Subject: Re: Linear Regressions with constraint coefficients

You need to send it to r-help@r-project.org however.

Kevin

On 04/26/2016 08:32 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
> Ok, will do! Thx a lot!
>
> Please find below my request:
>
> Hi all,
>
> I hope you are doing well?
>
> I’m currently using the lm() function from the package stats to fit linear 
> multifactor regressions.
>
> Unfortunately, I didn’t yet find a way to fit linear multifactor regressions 
> with constraint coefficients? I would like the slope coefficients to be all 
> inside an interval, let’s say, between 0 and 1. Further, if possible, the 
> slope coefficients should add up to 1.
>
> Is there an elegant and not too complicated way to do such a constraint 
> regression estimation in R?
>
> I would very much appreciate if you could help me with my issue?
>
> Thanks a lot in advance and kind regards, Aljosa Aleksandrovic
>
>
>
> Aljosa Aleksandrovic, FRM, CAIA
> Quantitative Analyst - Convertibles
> aljosa.aleksandro...@man.com
> Tel +41 55 417 7603
>
> Man Investments (CH) AG
> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>
>
> -Original Message-
> From: Kevin E. Thorpe [mailto:kevin.tho...@utoronto.ca]
> Sent: Dienstag, 26. April 2016 14:28
> To: Aleksandrovic, Aljosa (Pfaeffikon); r-help-ow...@r-project.org
> Subject: Re: Linear Regressions with constraint coefficients
>
> I believe I approved a message with such a subject. Perhaps there was another 
> layer that subsequently rejected it after that. I didn't notice any unusual 
> content. Try again, making sure you send the message in plain text only.
>
> Kevin
>
> On 04/26/2016 08:16 AM, Aleksandrovic, Aljosa (Pfaeffikon) wrote:
>> Do you know where I get help for my issue?
>>
>> Thanks in advance and kind regards,
>> Aljosa
>>
>>
>> Aljosa Aleksandrovic, FRM, CAIA
>> Quantitative Analyst - Convertibles
>> aljosa.aleksandro...@man.com
>> Tel +41 55 417 7603
>>
>> Man Investments (CH) AG
>> Huobstrasse 3 | 8808 Pfäffikon SZ | Switzerland
>>
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>> r-help-ow...@r-project.org
>> Sent: Dienstag, 26. April 2016 14:10
>> To: Aleksandrovic, Aljosa (Pfaeffikon)
>> Subject: Linear Regressions with constraint coefficients
>>
>> The message's content type was not explicitly allowed
>>


-- 
Kevin E. Thorpe
Head of Biostatistics,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael's Hospital
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: kevin.tho...@utoronto.ca  Tel: 416.864.5776  Fax: 416.864.3016

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[R] Penalised spline regression

[David Mcnulty]

Good Afternoon Everyone,

I am looking for advice fitting a linear mixed model where the random 
components do not seem to fit within the model formulae for lmer. The columns 
of Z are not stratified and have the notional random formula (z1 | 1) + ... + 
(zk | 1). 

Context
I am fitting a penalised thin plate spline with knots k1 to kn. The basis 
functions Zk are |x-ki|^3 and the penalty matrix has elements |ki-kj|^3. Rather 
than fit basis functions Zk I have transformed the basis to Z = Zk %*% 
penalty^(-1/2).

Full details are in section 2: Bayesian analysis for penalised spline 
regression using winBUGS. 
https://www.jstatsoft.org/article/view/v014i14/v14i14.pdf

I am specifically looking for an alternative to the function spm() in package 
semipar.

Thank you for any help or advice.

Dave.

David Mcnulty
Medical Statistician
 
 
Tel: +44 (0) 121 371 2448  
Internal: 12448 
Email: david.mcnu...@uhb.nhs.uk 
Web: http://www.uhb.nhs.uk  


Health Informatics - University Hospitals Birmingham NHS Foundation Trust
Yardley Court, 11-13 Frederick Road, Edgbaston
Birmingham, B15 1JD


The Health Informatics Department is a team of specialist NHS information 
analysts who work together to provide analysis solutions. The Team filters, 
analyses and presents comprehensive information that empowers NHS professionals 
to make informed decisions. 

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[R] Issue while building xtable on R on Ubuntu 15.04

[Zaid Golwala]

Please help in the below mentioned issue.

Regards
Zaid Golwala

-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Zaid Golwala
Sent: Wednesday, April 06, 2016 1:35 PM
To: r-help@R-project.org
Subject: [R] Issue while building xtable on R on Ubuntu 15.04

Hi,

I am trying to build xtable on R  on Ubuntu 15.04 but I get following error :


+ R CMD check --no-vignettes --timings xtable_1.8-2.tar.gz

* using log directory 
'/home/jenkins/workspace/Rlang_xtable_Ubuntu15.04/xtable.Rcheck'

* using R version 3.2.3 (2015-12-10)

* using platform: powerpc64le-unknown-linux-gnu (64-bit)

* using session charset: UTF-8

* using option '--no-vignettes

'* checking for file 'xtable/DESCRIPTION' ... OK

* this is package 'xtable' version '1.8-2'

* checking package namespace information ... OK

* checking package dependencies ...Error in .build_vignette_index(vigns) :   In 
'inst' vignettes 'xtableGallery.Rnw' and 'xtableGallery.snw' have the same 
vignette name

Can someone please help me regarding the same.

Regards
Zaid Golwala

DISCLAIMER\ ==\ This e-mail ...{{dropped:18}}

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[R] Haplotype network appearance

[NURIA BLASCO LAVILLA]

Hi,

I'm doing haplotype networks with the package pegas and the script from
Jimmy O'Donell's blog. The networks which I obtain are a little ugly and
I'd like to change some aspects of their appearance, but I'm just starting
with R and I don't know how to do it. I have the following problems:

-Some nodes overlap. I increase the scale.ratio but then I get a tiny
legend. So I need to increase the legend or the links in the graphic. I
haven't found any way to increase only the links and, as to the legend, I
haven't seen a way to adjust its size without creating it apart from the
graphic. Is there another way to solve this problem?

-Some nodes are very small and labels hide them. As their size is already
small, I'd like to know if there is a way of changing its position and put
them outside the nodes.

-Finally, I get a lot of gray and discontinous lines which I don't
understand and I don't know how to remove them.

Thanks in advance,

Nuria.

[[alternative HTML version deleted]]

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Re: [R] Missing Values in Logical Expressions

[PIKAL Petr]

Hm

Based on Jim's data your construction gives me correct result.

> Umsatz_2011<-c(1,2,3,4,5,NA,7,8,NA,10)
> Kunde_2011<-rep(0:1,5)
> Check_Kunde_2011 <- ifelse(is.na(Umsatz_2011) == TRUE & Kunde_2011 == 1, 1, 0)
> Check_Kunde_2011 <- factor(Check_Kunde_2011, levels = c(1,0), labels = 
> c("Check", "OK"))
> table(Check_Kunde_2011)
Check_Kunde_2011
CheckOK
1 9

So I presume that the problem lies in your data.
You should provide some sample of your data either by posting result of

str(yourdata)
or
dput(head(yourdata))

if you want some advice why with correct code you did not get appropriate 
result.

Instead ifelse you can also use

Check_Kunde_2011 <- (is.na(Umsatz_2011)&(Kunde_2011==1))*1

to get desired 0/1 vector.

Cheers
Petr

> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
> g.maub...@weinwolf.de
> Sent: Tuesday, April 26, 2016 10:10 AM
> To: r-help@r-project.org
> Subject: [R] Missing Values in Logical Expressions
>
> Hi All,
>
> I need to evaluate missing values in my data. I am able to filter these values
> and do simple statistics on it. But I do need new variables based on variables
> with missing values in my dataset:
>
> Check_Kunde_2011 <- ifelse(is.na(Umsatz_2011) == TRUE & Kunde_2011 ==
> 1, 1, 0)
> Check_Kunde_2011 <- factor(Check_Kunde_2011, levels = c(1,0), labels =
> c("Check", "OK"))
>
> The new variable is not correctly created. It contains no values:
>
> table(Check_Kunde_2011)
> < table of extent 0 >
>
> I searched the web but could not find a solution.
>
> How can I work with variables and missing values in logical expressions?
>
> Where could I find something about this?
>
> Kind regards
>
> Georg
>
> __
> 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] Missing Values in Logical Expressions

[Jim Lemon]

Hi Georg,
You could just use this:

Umsatz_2011<-c(1,2,3,4,5,NA,7,8,NA,10)
Kunde_2011<-rep(0:1,5)
Check_Kunde_2011<-
 c("OK","Check")[as.numeric(is.na(Umsatz_2011) & Kunde_2011 == 1)+1]

Check_Kunde_2011 will be a vector of strings.

Jim


On Tue, Apr 26, 2016 at 6:09 PM,   wrote:
> Hi All,
>
> I need to evaluate missing values in my data. I am able to filter these
> values and do simple statistics on it. But I do need new variables based
> on variables with missing values in my dataset:
>
> Check_Kunde_2011 <- ifelse(is.na(Umsatz_2011) == TRUE & Kunde_2011 == 1,
> 1, 0)
> Check_Kunde_2011 <- factor(Check_Kunde_2011, levels = c(1,0), labels =
> c("Check", "OK"))
>
> The new variable is not correctly created. It contains no values:
>
> table(Check_Kunde_2011)
> < table of extent 0 >
>
> I searched the web but could not find a solution.
>
> How can I work with variables and missing values in logical expressions?
>
> Where could I find something about this?
>
> Kind regards
>
> Georg
>
> __
> 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] Vegemite Function is Cowardly refusing

[Jari Oksanen]

Ansley Silva  gmail.com> writes:

> 
> R version 3.2.2.
> library(vegan)
> 
> I was to look at community tables from my dendrograms and am trying out the
> vegemite command.  This is the error I get:
> 
> Error in vegemite(apst, apst.clusters) :
>   Cowardly refusing to use longer than 1 char symbols:
> Use scale
> 
> I thought the problem was that I was using the log transformed data, but I
> tried it on the raw (which is single digit numbers), and still no luck.
> Any suggestions would be appreciated.
> 
I imagined that the error message is clear: vegemite only uses one-character
symbols (because the result is so compact). The example data you had with
this message had numbers up to 55 -- and that is a two-digit number. The
message also suggest that you use 'scale' which is an argument of 
vegemite() to transform numbers to one-charactar symbols. You can also
transform your data to to one-digit width yourself, and vegemite() will be 
happy.

cheers, Jari Oksanen

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[R] Missing Values in Logical Expressions

[G . Maubach]

Hi All,

I need to evaluate missing values in my data. I am able to filter these 
values and do simple statistics on it. But I do need new variables based 
on variables with missing values in my dataset:

Check_Kunde_2011 <- ifelse(is.na(Umsatz_2011) == TRUE & Kunde_2011 == 1, 
1, 0)
Check_Kunde_2011 <- factor(Check_Kunde_2011, levels = c(1,0), labels = 
c("Check", "OK"))

The new variable is not correctly created. It contains no values:

table(Check_Kunde_2011)
< table of extent 0 >

I searched the web but could not find a solution.

How can I work with variables and missing values in logical expressions?

Where could I find something about this?

Kind regards

Georg

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[R] Antwort: Fw: Re: Creating variables on the fly (SOLVED)

[G . Maubach]

Hi Don,
Hi to all readers,

many thanks for all your answers and all your help.

I adapted Don's code to my data and Don's code does the trick:

str(Kunden01)

for (year in 2011:2015) {
  Reeller_Kunde <- paste0("Reeller_Kunde_", year)
  Umsatz <- paste0("Umsatz_", year)
  cat('Creating', Reeller_Kunde,'from', Umsatz,'\n')
  Kunden01[[ Reeller_Kunde ]] <- ifelse( Kunden01[[ Umsatz ]] >= 0, 1, 2)
  Kunden01[[ Reeller_Kunde ]] <- factor( Kunden01[[ Reeller_Kunde ]],
 levels=c(1,2),
 labels= c("NICHT kaufend", 
"kaufend")
  )
}

str(Kunden01)

This way a new variable is created by building it from a string 
concatenation.

I also like the cat() function to document the process within the loop 
while running the program.

Many thanks for your help.

Kind regards

Georg




Von:g.maub...@gmx.de
An: g.maub...@weinwolf.de, 
Datum:  25.04.2016 21:37
Betreff:Fw: Re: [R] Creating variables on the fly





> Gesendet: Montag, 25. April 2016 um 19:35 Uhr
> Von: "MacQueen, Don" 
> An: "g.maub...@gmx.de" , "r-help@r-project.org" 

> Betreff: Re: [R] Creating variables on the fly
>
> I'm going to assume that Kunden is a data frame, and it has columns
> (variables) with names like
>   Umstatz_2011
> and that you want to create new columns with names like
>   Kunde_real_2011
> 
> If that is so, then try this (not tested):
> 
> for (year in 2011:2015) {
>   nmK <- paste0("Kunde_real_", year)
>   nmU <- paste0("Umsatz_", year)
>   cat('Creating',nmK,'from',nmU,'\n')
>   Kunden[[ nmK ]] <- ifelse( Kunden[[ nmU ]] <= 0, 1, 2)
>   Kunden[[ nmK ]] <- factor( Kunden[[ nmK ]],
>levels=c(1,2),
>labels= c("NICHT kaufend", "kaufend")
>)
> 
> }
> 
> This little example should illustrate the method:
> 
> 
> > foo <- data.frame(a=1:4)
> > foo
>   a
> 1 1
> 2 2
> 3 3
> 4 4
> > foo[['b']] <- foo[['a']]*3
> > foo
>   a  b
> 1 1  3
> 2 2  6
> 3 3  9
> 4 4 12
> 
> 
> 
> -- 
> Don MacQueen
> 
> Lawrence Livermore National Laboratory
> 7000 East Ave., L-627
> Livermore, CA 94550
> 925-423-1062
> 
> 
> 
> 
> 
> On 4/22/16, 8:52 AM, "R-help on behalf of g.maub...@gmx.de"
>  wrote:
> 
> >Hi all,
> >
> >I would like to use a loop for tasks that occurs repeatedly:
> >
> ># Groups 
> ># Umsatz <= 0: 1 (NICHT kaufend)
> ># Umsatz > 0: 2  (kaufend)
> >for (year in c("2011", "2012", "2013", "2014", "2015")) {
> >  paste0("Kunden$Kunde_real_", year) <- (paste0("Kunden$Umsatz_", year)
> ><= 0) * 1 + 
> >(paste0("Kunden$Umsatz_", year) 
>
> > 0) * 2 
> >  paste0("Kunden$Kunde_real_", year) <- factor(paste0("Kunden$Umsatz_",
> >year), 
> >   levels = c(1, 2),
> >   labels = c("NICHT
> >kaufend", "kaufend"))
> >  } 
> >
> >This actually does not work due to the fact that the expression
> >"paste0("Kunden$Kunde_real_", year)" ist not interpreted as a variable
> >name by the R script language interpreter.
> >
> >Is there a way to assembly variable names on the fly in R?
> >
> >Regards
> >
> >Georg
> >
> >__
> >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] ylim in barplot()

[Ivan Calandra]

Thank you David,

That's a nice workaround using plotrix::barp(), but that doesn't explain 
why ylim doesn't work as intended (or at least, as I expect it to work), 
or why xpd has no influence when using devEMF::emf()...


The problem with saving directly in RStudio is that it requires to 
manually save the plot, and this becomes troublesome when there are a 
lot of plot commands in a single script.


Bests,
Ivan (on behalf of Stéphanie)

--
Ivan Calandra, PhD
Scientific Mediator
University of Reims Champagne-Ardenne
GEGENAA - EA 3795
CREA - 2 esplanade Roland Garros
51100 Reims, France
+33(0)3 26 77 36 89
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--
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https://publons.com/author/705639/

Le 25/04/2016 21:16, David L Carlson a écrit :

If you are using a Windows system, you can Export the plot from RStudio and 
save it as a metafile without using package devEMF and it will crop the bars 
with xpd=FALSE. When I used devEMF on a Windows machine, the bars were not 
cropped with barplot() as you indicated, but when I switched to plotrix::barp() 
they were cropped. The arguments are a bit different, but I did not need 
xpd=FALSE:

emf("TestPlot.emf")
barp(t(mydata), col=c("orange", "green", "yellow", "purple"),
ylim=c(50,70), legend.lab=colnames(mydata), legend.pos="topright")
dev.off()

-
David L Carlson
Department of Anthropology
Texas A University
College Station, TX 77840-4352


-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of EYSSAUTIER 
Stéphanie
Sent: Monday, April 25, 2016 9:53 AM
To: r-help@r-project.org
Subject: [R] ylim in barplot()

Dear useRs,

I'm having troubles with using ylim in barplot(): even though I reduce
the y-scale using ylim, the bars still extend down to 0into the x-labels.
The sample data is below, and here is the code.

#This works fine but I would like to plot only from 50 to 70:
barplot(t(mydata), beside=TRUE, col=c("orange", "green", "yellow",
"purple"), legend=TRUE, las=2, axis.lty=1)

#This is the ylim version with the bar problem:
barplot(t(mydata), beside=TRUE, col=c("orange", "green", "yellow",
"purple"), ylim=c(50,70), legend=TRUE, las=2, axis.lty=1)

#I have tried using xpd=FALSE and this works fine withinRguior Rstudio
but not when I plot within devEMF::emf()
barplot(t(mydata), beside=TRUE, col=c("orange", "green", "yellow",
"purple"), ylim=c(50,70), legend=TRUE, las=2, axis.lty=1, xpd=FALSE)

I need the emf file to edit the plot.

Why isn't it working with ylim alone? And why doesn't xpd work with emf()?

Thanks in advance for your help,
Stéphanie


mydata <- structure(c(68.1799689328282, 68.2164021637813,
68.3243626415103, 61.7899567386469, 59.5182501049449, 63.9916220705152,
64.1442535260522, 64.2585746423512, 62.5653571705887, 61.631969055001,
61.3991475513249, 63.2401411727188, 65.0488808306348, 63.43022364909,
64.8425577471775, 65.4986231824992, 64.7798619682232, 64.4174790601806,
65.5696701695485, 65.0253962620178, 63.2476885701954, 63.2473647791827,
62.5000542212819, 63.1742307643225, 62.1560658393146, 62.5810636272476,
64.0935149828315, 65.5432025084893, 66.7535104579705, 59.6500997601308,
59.4641686257122, 59.8891527196501, 60.0117050975523, 64.3309521324969,
62.0079305659785, 57.0665210362419, 57.5202118193362, 61.3280531011031,
62.6326634763289, 60.2094259175778, 65.5923786551105, 65.6946445059829,
65.2498254841218, 65.3468620859567, 67.024437492438, 65.8533801964148,
65.0047369761726, 65.0310208374089, 64.3121920326177, 64.8038153143374,
63.7306643056964, 64.2579190762784, 67.5745906026732, 67.0351170775703,
66.4053872920113, 59.9302305698358, 60.368722602391, 60.3572311841096,
60.0960412312049, 63.7886894551889, 62.24708719601, 59.3334729073243,
59.9537485303794, 63.1828096654404, 63.5352778562394, 60.621828397375,
65.8889763819732, 66.2059756115814, 66.4567010911873, 65.8796623180062,
67.5552743734229, 66.504738660398, 66.2085036370622, 66.4230781907321,
65.5130180297911, 65.9051623923225, 64.8408013974267, 65.5175045910169,
68.0760225106606, 66.8615536135711, 65.0390748892256, 59.2940092440695,
60.7061368898884, 59.7345965097738, 59.6019925755588, 63.6011933836225,
62.1134684942427, 60.4227073441121, 60.7834352002706, 63.4539745079728,
63.6329498376672, 58.8034486099638, 65.2910772858539, 65.5952764758513,
65.8371262481454, 66.1191053038481, 67.5230043279325, 66.8569714429862,
66.1045642986574, 66.8499631633452, 66.0121950308609, 66.2593339018511,
65.4397264829666, 65.8389305084859), .Dim = c(26L, 4L), .Dimnames =
list(c("T40", "T41", "T42", "306iv01", "306iv02", "306iv19", "306iv13",
"306iv04", "306iv05", "402iv01", "402iv02", "402iv03", "306iv16",
"306iv10", "TG1", "TG2", "TG3", "TG4", "TG5", "TG6", "TG7", "TG8",
"TG9", "TG10", "TG11", "TG12"), c("L.mean", "L.mean_T1", "L.mean_T2",
"L.mean_T3")))




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