date:20191023

Re: [R] read.table and NaN

2019-10-23 Thread Bert Gunter

Like this?

con <- textConnection(object = 'A,B\n1,NaN\nNA,2')
> tmp <- read.table(con, header = TRUE, sep = ',', na.strings = '',
stringsAsFactors = FALSE,
+   colClasses = c("numeric", "character"))
> close.connection(con)
> tmp
   A   B
1  1 NaN
2 NA   2
> class(tmp[,1])
[1] "numeric"
> class(tmp[,2])
[1] "character"
> tmp[,2]
[1] "NaN" "2"


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 Wed, Oct 23, 2019 at 6:31 PM Sebastien Bihorel via R-help <
r-help@r-project.org> wrote:

> Hi,
>
> Is there a way to make read.table consider NaN as a string of characters
> rather than the internal NaN? Changing the na.strings argument does not
> seems to have any effect on how R interprets the NaN string (while is does
> not the the NA string)
>
> con <- textConnection(object = 'A,B\n1,NaN\nNA,2')
> tmp <- read.table(con, header = TRUE, sep = ',', na.strings = '',
> stringsAsFactors = FALSE)
> close.connection(con)
> tmp
> class(tmp[,1])
> class(tmp[,2])
>
>
> __
> 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-es] calculo porcentaje de subcategirías para individuos diferentes

2019-10-23 Thread Javier Marcuzzi

Estimada Lorena Saavedra Aracena

No alcanzo a comprender su pregunta, en R la respuesta mucha veces depende
de los datos y en la forma en que estos son accedidos, por ejemplo, si
usted tiene un data.frame que se llama datos posiblemente summay(datos)
alcanza, si no es así alguna función sobre los datos y a esta summary().
Yo llevo muchos anos con R, y la forma adecuada va cambiando con el tiempo,
simplemente porque aparecen librerías que facilitan el trabajo, pero no se
preocupe por eso, piense en lo que usted cree oportuno, es preferible que
conozca bien lo básico, y nuevamente lo básico, y la razón es sobre la
posibilidad de combinar esto básico como función dentro de otra librería,
el camino inverso la confundiría.
Aparte de summary está table y ftable, esto da el resultado en frecuencias,
no es justo porcentaje, pero es casi sinónimo.
Espero que se comprenda mi explicación, no estoy seguro de haber respondido
a su pregunta.
Javier Marcuzzi

El mié., 23 oct. 2019 a las 23:07, Lorena Saavedra Aracena (<
l.saavedra.arac...@gmail.com>) escribió:

> Buenas noches,
> Soy nueva en R y a veces me cuesta pensar los cálculos de manera más
> práctica, por los que les agradecería la ayuda.
> Tengo una matriz de datos con una dim = 35745   19, correspondientes a
> ubicaciones de 39 perros, cada perro tiene poco más o poco menos de 1000
> datos.
> Necesito saber el % de uso de hábitat natural. Es un sencillo cálculo de
> porcentaje, pero me gustaría hacerlo mas automatizado para no tomar tanto
> tiempo en correrlo manualmente.
> Entonces tengo una columna con la ID de cada perro, y otra con las
> categorías de ambiente (urbano, rural y mar).
> He calculado el promedio con este script para el perro 1:
>
> ## encontrar el numero total de zonas naturales por perro
>
> P01 <-subset(TODOS, TODOS$ID=="P01")
> ruralP01 <- subset(P01,P01$Zone=="rural")
> marP01 <- subset(P01,P01$Zone=="mar")
>
> nrow(P01)
> nrow(ruralP01)
> nrow(marP01)
>
> porcent_natP01 <- (nrow(ruralP01) + nrow(marP01))*100/ nrow(P01)
> porcent_natP01
>
> y llego a 61,35%. Es la forma más básica que se me ocurrió, podrían
> ayudarme a hacerlo más automatizado? he intentado un par de formas pero me
> es un poco complicado verlo pensando que tengo primero categorías de perros
> y luego de ambientes.
>
> Les agradezco,
>
> Saludos
>
> --
>
> *Lorena Saavedra A.**Ing. Recursos Naturales Renovables*
> *+56 9 9880 2972*
>
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>
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> https://stat.ethz.ch/mailman/listinfo/r-help-es
>

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[R-es] calculo porcentaje de subcategirías para individuos diferentes

2019-10-23 Thread Lorena Saavedra Aracena

Buenas noches,
Soy nueva en R y a veces me cuesta pensar los cálculos de manera más
práctica, por los que les agradecería la ayuda.
Tengo una matriz de datos con una dim = 35745   19, correspondientes a
ubicaciones de 39 perros, cada perro tiene poco más o poco menos de 1000
datos.
Necesito saber el % de uso de hábitat natural. Es un sencillo cálculo de
porcentaje, pero me gustaría hacerlo mas automatizado para no tomar tanto
tiempo en correrlo manualmente.
Entonces tengo una columna con la ID de cada perro, y otra con las
categorías de ambiente (urbano, rural y mar).
He calculado el promedio con este script para el perro 1:

## encontrar el numero total de zonas naturales por perro

P01 <-subset(TODOS, TODOS$ID=="P01")
ruralP01 <- subset(P01,P01$Zone=="rural")
marP01 <- subset(P01,P01$Zone=="mar")

nrow(P01)
nrow(ruralP01)
nrow(marP01)

porcent_natP01 <- (nrow(ruralP01) + nrow(marP01))*100/ nrow(P01)
porcent_natP01

y llego a 61,35%. Es la forma más básica que se me ocurrió, podrían
ayudarme a hacerlo más automatizado? he intentado un par de formas pero me
es un poco complicado verlo pensando que tengo primero categorías de perros
y luego de ambientes.

Les agradezco,

Saludos

-- 

*Lorena Saavedra A.**Ing. Recursos Naturales Renovables*
*+56 9 9880 2972*

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[R] read.table and NaN

2019-10-23 Thread Sebastien Bihorel via R-help

Hi,

Is there a way to make read.table consider NaN as a string of characters rather 
than the internal NaN? Changing the na.strings argument does not seems to have 
any effect on how R interprets the NaN string (while is does not the the NA 
string)

con <- textConnection(object = 'A,B\n1,NaN\nNA,2')
tmp <- read.table(con, header = TRUE, sep = ',', na.strings = '', 
stringsAsFactors = FALSE)
close.connection(con)
tmp
class(tmp[,1])
class(tmp[,2])


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Re: [R] negative vector length when merging data frames

2019-10-23 Thread Jeff Newmiller

Ana... contributed packages like data.table and dplyr are developed completely 
independently from R, have their own versions, and in fact both of them have 
recommendations as to how to report bugs in their package descriptions.

As for getting help here, you really need to supply ALL of the information 
requested to make forward progress in clarifying next steps... there were 
several items that Duncan mentioned that you failed to provide.

Also, note that dplyr and data.table take very different approaches to handling 
data, and have been known to not play well with each other. At the very least I 
would suggest using as.data.frame to convert to a standardized data 
representation before switching from using functions in one of these packages 
to using functions in the other package.

[1] https://cran.r-project.org/web/packages/data.table/index.html

[2] https://cran.r-project.org/web/packages/dplyr/index.html

On October 23, 2019 5:05:44 PM PDT, Ana Marija  
wrote:
>I am using R-3.6.1
>and these libraries:
>library(data.table)
>library(dplyr)
>
>On Wed, Oct 23, 2019 at 6:54 PM Duncan Murdoch
> wrote:
>>
>> On 23/10/2019 7:04 p.m., Ana Marija wrote:
>> > I also tried left_join but I got: Error: std::bad_alloc
>> >
>> >> df3 <- left_join(l4, asign, by = c("chr","pos")
>> > Error: std::bad_alloc
>>
>> Looks like bugs in whatever package you're finding "left_join" in
>(and
>> previously "merge").  Are those from dplyr and base?  Showing us
>> str(lr), str(asign), and sessionInfo() would be helpful.
>>
>> Duncan Murdoch
>>
>> >> dim(l4)
>> > [1] 166941635 8
>> >> dim(asign)
>> > [1] 107371528 5
>> >
>> > On Wed, Oct 23, 2019 at 5:32 PM Ana Marija
> wrote:
>> >>
>> >> Hello,
>> >>
>> >> I have two data frames like this:
>> >>
>> >>> head(l4)
>> >>  X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
>> >> 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
>> >> 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
>> >> 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
>> >> 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
>> >> 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
>> >> 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
>> >>> head(asign)
>> >>gene  chrchr_pos   pos p.val.Retina
>> >> 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
>> >> 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
>> >> 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
>> >> 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
>> >> 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
>> >> 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
>> >>> m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
>> >> Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y =
>c("chr",  :
>> >>negative length vectors are not allowed
>> >>> sapply(l4,class)
>> >>X1   X2   X3   X4   X5 
> variant_id
>> >>   "character"  "character"  "character"  "character"  "character" 
>"character"
>> >> pval_nominal  gene_id.LCL
>> >> "numeric"  "character"
>> >>> sapply(asign,class)
>> >>  gene  chr  chr_pos  pos p.val.Retina
>> >>   "character"  "character"  "character"  "character"  "character"
>> >>
>> >> Please advise as to why I am getting this error when merging?
>> >>
>> >> Thanks
>> >> Ana
>> >
>> > __
>> > 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
>https://stat.ethz.ch/mailman/listinfo/r-help
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>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

-- 
Sent from my phone. Please excuse my brevity.

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Re: [R] negative vector length when merging data frames

2019-10-23 Thread Duncan Murdoch


On 23/10/2019 7:04 p.m., Ana Marija wrote:

I also tried left_join but I got: Error: std::bad_alloc


df3 <- left_join(l4, asign, by = c("chr","pos")

Error: std::bad_alloc


Looks like bugs in whatever package you're finding "left_join" in (and 
previously "merge").  Are those from dplyr and base?  Showing us 
str(lr), str(asign), and sessionInfo() would be helpful.


Duncan Murdoch


dim(l4)

[1] 166941635 8

dim(asign)

[1] 107371528 5

On Wed, Oct 23, 2019 at 5:32 PM Ana Marija  wrote:


Hello,

I have two data frames like this:


head(l4)

 X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232

head(asign)

   gene  chrchr_pos   pos p.val.Retina
1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
3: ENSG0227232 chr11:11008:C:G 11008 0.218132
4: ENSG0227232 chr11:11012:C:G 11012 0.218132
5: ENSG0227232 chr11:13110:G:A 13110 0.998262
6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572

m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))

Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr",  :
   negative length vectors are not allowed

sapply(l4,class)

   X1   X2   X3   X4   X5   variant_id
  "character"  "character"  "character"  "character"  "character"  "character"
pval_nominal  gene_id.LCL
"numeric"  "character"

sapply(asign,class)

 gene  chr  chr_pos  pos p.val.Retina
  "character"  "character"  "character"  "character"  "character"

Please advise as to why I am getting this error when merging?

Thanks
Ana


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Re: [R] negative vector length when merging data frames

2019-10-23 Thread Ana Marija

I am using R-3.6.1
and these libraries:
library(data.table)
library(dplyr)

On Wed, Oct 23, 2019 at 6:54 PM Duncan Murdoch  wrote:
>
> On 23/10/2019 7:04 p.m., Ana Marija wrote:
> > I also tried left_join but I got: Error: std::bad_alloc
> >
> >> df3 <- left_join(l4, asign, by = c("chr","pos")
> > Error: std::bad_alloc
>
> Looks like bugs in whatever package you're finding "left_join" in (and
> previously "merge").  Are those from dplyr and base?  Showing us
> str(lr), str(asign), and sessionInfo() would be helpful.
>
> Duncan Murdoch
>
> >> dim(l4)
> > [1] 166941635 8
> >> dim(asign)
> > [1] 107371528 5
> >
> > On Wed, Oct 23, 2019 at 5:32 PM Ana Marija  
> > wrote:
> >>
> >> Hello,
> >>
> >> I have two data frames like this:
> >>
> >>> head(l4)
> >>  X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> >> 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> >> 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> >> 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> >> 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> >> 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> >> 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> >>> head(asign)
> >>gene  chrchr_pos   pos p.val.Retina
> >> 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> >> 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> >> 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> >> 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> >> 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> >> 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> >>> m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> >> Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr", 
> >>  :
> >>negative length vectors are not allowed
> >>> sapply(l4,class)
> >>X1   X2   X3   X4   X5   
> >> variant_id
> >>   "character"  "character"  "character"  "character"  "character"  
> >> "character"
> >> pval_nominal  gene_id.LCL
> >> "numeric"  "character"
> >>> sapply(asign,class)
> >>  gene  chr  chr_pos  pos p.val.Retina
> >>   "character"  "character"  "character"  "character"  "character"
> >>
> >> Please advise as to why I am getting this error when merging?
> >>
> >> Thanks
> >> Ana
> >
> > __
> > 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] negative vector length when merging data frames

2019-10-23 Thread Jim Lemon

I don't have it installed - that was merely a suggestion. I notice
that both data.table and dplyr packages are mentioned as possibilities
for "merge big datasets in r". Apparently the best way to do it if you
have a database manager is to read the two datasets into tables and do
the join via SQL or whatever language is available.

Jim

On Thu, Oct 24, 2019 at 10:17 AM Ana Marija  wrote:
>
> no can you please send me an example how the command would look like in my 
> case?
>
> On Wed, Oct 23, 2019 at 6:16 PM Jim Lemon  wrote:
> >
> > Yes. Have you tried the bigmemory package?
> >
> > Jim
> >
> > On Thu, Oct 24, 2019 at 10:08 AM Ana Marija  
> > wrote:
> > >
> > > Hi Jim,
> > >
> > > I think one of the issue is that data frames are so big,
> > > > dim(l4)
> > > [1] 166941635 8
> > > > dim(asign)
> > > [1] 107371528 5
> > >
> > > so my example would not reproduce the error
> > >
> > > On Wed, Oct 23, 2019 at 6:05 PM Jim Lemon  wrote:
> > > >
> > > > Hi Ana,
> > > > When I run this example taken from your email:
> > > >
> > > > l4<-read.table(text="X1 X2 X3 X4  X5 variant_id pval_nominal gene_id.LCL
> > > > chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > > > chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > > > chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > > > chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > > > chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > > > chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232",
> > > > header=TRUE,stringsAsFactors=FALSE)
> > > > asign<-read.table(text="gene  chr  chr_pos   pos p.val.Retina
> > > > ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > > > ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > > > ENSG0227232 chr11:11008:C:G 11008 0.218132
> > > > ENSG0227232 chr11:11012:C:G 11012 0.218132
> > > > ENSG0227232 chr11:13110:G:A 13110 0.998262
> > > > ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572",
> > > > header=TRUE,stringsAsFactors=FALSE)
> > > > merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > > >  [1] X1   X2   X3   X4   X5
> > > > [6] variant_id   pval_nominal gene_id.LCL  gene chr_pos
> > > > [11] p.val.Retina
> > > > <0 rows> (or 0-length row.names)
> > > >
> > > > It works okay, but there are no matches in the join. So I can't even
> > > > guess what the problem is.
> > > >
> > > > Jim
> > > >
> > > > On Thu, Oct 24, 2019 at 9:33 AM Ana Marija 
> > > >  wrote:
> > > > >
> > > > > Hello,
> > > > >
> > > > > I have two data frames like this:
> > > > >
> > > > > > head(l4)
> > > > > X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> > > > > 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > > > > 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > > > > 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > > > > 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > > > > 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > > > > 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > > > > > head(asign)
> > > > >   gene  chrchr_pos   pos p.val.Retina
> > > > > 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > > > > 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > > > > 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> > > > > 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> > > > > 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> > > > > 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > > > > > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > > > > Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = 
> > > > > c("chr",  :
> > > > >   negative length vectors are not allowed
> > > > > > sapply(l4,class)
> > > > >   X1   X2   X3   X4   X5   
> > > > > variant_id
> > > > >  "character"  "character"  "character"  "character"  "character"  
> > > > > "character"
> > > > > pval_nominal  gene_id.LCL
> > > > >"numeric"  "character"
> > > > > > sapply(asign,class)
> > > > > gene  chr  chr_pos  pos p.val.Retina
> > > > >  "character"  "character"  "character"  "character"  "character"
> > > > >
> > > > > Please advise as to why I am getting this error when merging?
> > > > >
> > > > > Thanks
> > > > > Ana
> > > > >
> > > > > __
> > > > > 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,

Re: [R] negative vector length when merging data frames

2019-10-23 Thread Ana Marija

no can you please send me an example how the command would look like in my case?

On Wed, Oct 23, 2019 at 6:16 PM Jim Lemon  wrote:
>
> Yes. Have you tried the bigmemory package?
>
> Jim
>
> On Thu, Oct 24, 2019 at 10:08 AM Ana Marija  
> wrote:
> >
> > Hi Jim,
> >
> > I think one of the issue is that data frames are so big,
> > > dim(l4)
> > [1] 166941635 8
> > > dim(asign)
> > [1] 107371528 5
> >
> > so my example would not reproduce the error
> >
> > On Wed, Oct 23, 2019 at 6:05 PM Jim Lemon  wrote:
> > >
> > > Hi Ana,
> > > When I run this example taken from your email:
> > >
> > > l4<-read.table(text="X1 X2 X3 X4  X5 variant_id pval_nominal gene_id.LCL
> > > chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > > chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > > chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > > chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > > chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > > chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232",
> > > header=TRUE,stringsAsFactors=FALSE)
> > > asign<-read.table(text="gene  chr  chr_pos   pos p.val.Retina
> > > ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > > ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > > ENSG0227232 chr11:11008:C:G 11008 0.218132
> > > ENSG0227232 chr11:11012:C:G 11012 0.218132
> > > ENSG0227232 chr11:13110:G:A 13110 0.998262
> > > ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572",
> > > header=TRUE,stringsAsFactors=FALSE)
> > > merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > >  [1] X1   X2   X3   X4   X5
> > > [6] variant_id   pval_nominal gene_id.LCL  gene chr_pos
> > > [11] p.val.Retina
> > > <0 rows> (or 0-length row.names)
> > >
> > > It works okay, but there are no matches in the join. So I can't even
> > > guess what the problem is.
> > >
> > > Jim
> > >
> > > On Thu, Oct 24, 2019 at 9:33 AM Ana Marija  
> > > wrote:
> > > >
> > > > Hello,
> > > >
> > > > I have two data frames like this:
> > > >
> > > > > head(l4)
> > > > X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> > > > 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > > > 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > > > 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > > > 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > > > 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > > > 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > > > > head(asign)
> > > >   gene  chrchr_pos   pos p.val.Retina
> > > > 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > > > 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > > > 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> > > > 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> > > > 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> > > > 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > > > > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > > > Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = 
> > > > c("chr",  :
> > > >   negative length vectors are not allowed
> > > > > sapply(l4,class)
> > > >   X1   X2   X3   X4   X5   
> > > > variant_id
> > > >  "character"  "character"  "character"  "character"  "character"  
> > > > "character"
> > > > pval_nominal  gene_id.LCL
> > > >"numeric"  "character"
> > > > > sapply(asign,class)
> > > > gene  chr  chr_pos  pos p.val.Retina
> > > >  "character"  "character"  "character"  "character"  "character"
> > > >
> > > > Please advise as to why I am getting this error when merging?
> > > >
> > > > Thanks
> > > > Ana
> > > >
> > > > __
> > > > 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
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] negative vector length when merging data frames

2019-10-23 Thread Jim Lemon

Yes. Have you tried the bigmemory package?

Jim

On Thu, Oct 24, 2019 at 10:08 AM Ana Marija  wrote:
>
> Hi Jim,
>
> I think one of the issue is that data frames are so big,
> > dim(l4)
> [1] 166941635 8
> > dim(asign)
> [1] 107371528 5
>
> so my example would not reproduce the error
>
> On Wed, Oct 23, 2019 at 6:05 PM Jim Lemon  wrote:
> >
> > Hi Ana,
> > When I run this example taken from your email:
> >
> > l4<-read.table(text="X1 X2 X3 X4  X5 variant_id pval_nominal gene_id.LCL
> > chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232",
> > header=TRUE,stringsAsFactors=FALSE)
> > asign<-read.table(text="gene  chr  chr_pos   pos p.val.Retina
> > ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > ENSG0227232 chr11:11008:C:G 11008 0.218132
> > ENSG0227232 chr11:11012:C:G 11012 0.218132
> > ENSG0227232 chr11:13110:G:A 13110 0.998262
> > ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572",
> > header=TRUE,stringsAsFactors=FALSE)
> > merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> >  [1] X1   X2   X3   X4   X5
> > [6] variant_id   pval_nominal gene_id.LCL  gene chr_pos
> > [11] p.val.Retina
> > <0 rows> (or 0-length row.names)
> >
> > It works okay, but there are no matches in the join. So I can't even
> > guess what the problem is.
> >
> > Jim
> >
> > On Thu, Oct 24, 2019 at 9:33 AM Ana Marija  
> > wrote:
> > >
> > > Hello,
> > >
> > > I have two data frames like this:
> > >
> > > > head(l4)
> > > X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> > > 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > > 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > > 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > > 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > > 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > > 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > > > head(asign)
> > >   gene  chrchr_pos   pos p.val.Retina
> > > 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > > 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > > 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> > > 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> > > 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> > > 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > > > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > > Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = 
> > > c("chr",  :
> > >   negative length vectors are not allowed
> > > > sapply(l4,class)
> > >   X1   X2   X3   X4   X5   
> > > variant_id
> > >  "character"  "character"  "character"  "character"  "character"  
> > > "character"
> > > pval_nominal  gene_id.LCL
> > >"numeric"  "character"
> > > > sapply(asign,class)
> > > gene  chr  chr_pos  pos p.val.Retina
> > >  "character"  "character"  "character"  "character"  "character"
> > >
> > > Please advise as to why I am getting this error when merging?
> > >
> > > Thanks
> > > Ana
> > >
> > > __
> > > 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
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] negative vector length when merging data frames

2019-10-23 Thread Ana Marija

thanks but I would need solution in R

On Wed, Oct 23, 2019 at 6:31 PM Jim Lemon  wrote:
>
> I don't have it installed - that was merely a suggestion. I notice
> that both data.table and dplyr packages are mentioned as possibilities
> for "merge big datasets in r". Apparently the best way to do it if you
> have a database manager is to read the two datasets into tables and do
> the join via SQL or whatever language is available.
>
> Jim
>
> On Thu, Oct 24, 2019 at 10:17 AM Ana Marija  
> wrote:
> >
> > no can you please send me an example how the command would look like in my 
> > case?
> >
> > On Wed, Oct 23, 2019 at 6:16 PM Jim Lemon  wrote:
> > >
> > > Yes. Have you tried the bigmemory package?
> > >
> > > Jim
> > >
> > > On Thu, Oct 24, 2019 at 10:08 AM Ana Marija  
> > > wrote:
> > > >
> > > > Hi Jim,
> > > >
> > > > I think one of the issue is that data frames are so big,
> > > > > dim(l4)
> > > > [1] 166941635 8
> > > > > dim(asign)
> > > > [1] 107371528 5
> > > >
> > > > so my example would not reproduce the error
> > > >
> > > > On Wed, Oct 23, 2019 at 6:05 PM Jim Lemon  wrote:
> > > > >
> > > > > Hi Ana,
> > > > > When I run this example taken from your email:
> > > > >
> > > > > l4<-read.table(text="X1 X2 X3 X4  X5 variant_id pval_nominal 
> > > > > gene_id.LCL
> > > > > chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > > > > chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > > > > chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > > > > chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > > > > chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > > > > chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232",
> > > > > header=TRUE,stringsAsFactors=FALSE)
> > > > > asign<-read.table(text="gene  chr  chr_pos   pos p.val.Retina
> > > > > ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > > > > ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > > > > ENSG0227232 chr11:11008:C:G 11008 0.218132
> > > > > ENSG0227232 chr11:11012:C:G 11012 0.218132
> > > > > ENSG0227232 chr11:13110:G:A 13110 0.998262
> > > > > ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572",
> > > > > header=TRUE,stringsAsFactors=FALSE)
> > > > > merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > > > >  [1] X1   X2   X3   X4   X5
> > > > > [6] variant_id   pval_nominal gene_id.LCL  gene chr_pos
> > > > > [11] p.val.Retina
> > > > > <0 rows> (or 0-length row.names)
> > > > >
> > > > > It works okay, but there are no matches in the join. So I can't even
> > > > > guess what the problem is.
> > > > >
> > > > > Jim
> > > > >
> > > > > On Thu, Oct 24, 2019 at 9:33 AM Ana Marija 
> > > > >  wrote:
> > > > > >
> > > > > > Hello,
> > > > > >
> > > > > > I have two data frames like this:
> > > > > >
> > > > > > > head(l4)
> > > > > > X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> > > > > > 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > > > > > 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > > > > > 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > > > > > 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > > > > > 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > > > > > 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > > > > > > head(asign)
> > > > > >   gene  chrchr_pos   pos p.val.Retina
> > > > > > 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > > > > > 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > > > > > 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> > > > > > 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> > > > > > 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> > > > > > 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > > > > > > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > > > > > Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = 
> > > > > > c("chr",  :
> > > > > >   negative length vectors are not allowed
> > > > > > > sapply(l4,class)
> > > > > >   X1   X2   X3   X4   X5   
> > > > > > variant_id
> > > > > >  "character"  "character"  "character"  "character"  "character"  
> > > > > > "character"
> > > > > > pval_nominal  gene_id.LCL
> > > > > >"numeric"  "character"
> > > > > > > sapply(asign,class)
> > > > > > gene  chr  chr_pos  pos p.val.Retina
> > > > > >  "character"  "character"  "character"  "character"  "character"
> > > > > >
> > > > > > Please advise as to why I am getting this error when merging?
> > > > > >
> > > > > > Thanks
> > > > > > Ana
> > > > > >
> > > > > >

Re: [R] negative vector length when merging data frames

2019-10-23 Thread Ana Marija

Hi Jim,

I think one of the issue is that data frames are so big,
> dim(l4)
[1] 166941635 8
> dim(asign)
[1] 107371528 5

so my example would not reproduce the error

On Wed, Oct 23, 2019 at 6:05 PM Jim Lemon  wrote:
>
> Hi Ana,
> When I run this example taken from your email:
>
> l4<-read.table(text="X1 X2 X3 X4  X5 variant_id pval_nominal gene_id.LCL
> chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232",
> header=TRUE,stringsAsFactors=FALSE)
> asign<-read.table(text="gene  chr  chr_pos   pos p.val.Retina
> ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> ENSG0227232 chr11:11008:C:G 11008 0.218132
> ENSG0227232 chr11:11012:C:G 11012 0.218132
> ENSG0227232 chr11:13110:G:A 13110 0.998262
> ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572",
> header=TRUE,stringsAsFactors=FALSE)
> merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
>  [1] X1   X2   X3   X4   X5
> [6] variant_id   pval_nominal gene_id.LCL  gene chr_pos
> [11] p.val.Retina
> <0 rows> (or 0-length row.names)
>
> It works okay, but there are no matches in the join. So I can't even
> guess what the problem is.
>
> Jim
>
> On Thu, Oct 24, 2019 at 9:33 AM Ana Marija  
> wrote:
> >
> > Hello,
> >
> > I have two data frames like this:
> >
> > > head(l4)
> > X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> > 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > > head(asign)
> >   gene  chrchr_pos   pos p.val.Retina
> > 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> > 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> > 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> > 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr",  
> > :
> >   negative length vectors are not allowed
> > > sapply(l4,class)
> >   X1   X2   X3   X4   X5   
> > variant_id
> >  "character"  "character"  "character"  "character"  "character"  
> > "character"
> > pval_nominal  gene_id.LCL
> >"numeric"  "character"
> > > sapply(asign,class)
> > gene  chr  chr_pos  pos p.val.Retina
> >  "character"  "character"  "character"  "character"  "character"
> >
> > Please advise as to why I am getting this error when merging?
> >
> > Thanks
> > Ana
> >
> > __
> > 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] negative vector length when merging data frames

2019-10-23 Thread Jim Lemon

Ah, it looks like a memory allocation problem.

Jim

On Thu, Oct 24, 2019 at 10:05 AM Ana Marija  wrote:
>
> I also tried left_join but I got: Error: std::bad_alloc
>
> > df3 <- left_join(l4, asign, by = c("chr","pos"))
> Error: std::bad_alloc
> > dim(l4)
> [1] 166941635 8
> > dim(asign)
> [1] 107371528 5
>
> On Wed, Oct 23, 2019 at 5:32 PM Ana Marija  
> wrote:
> >
> > Hello,
> >
> > I have two data frames like this:
> >
> > > head(l4)
> > X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> > 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> > 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> > 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> > 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> > 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> > 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > > head(asign)
> >   gene  chrchr_pos   pos p.val.Retina
> > 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> > 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> > 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> > 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> > 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> > 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> > Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr",  
> > :
> >   negative length vectors are not allowed
> > > sapply(l4,class)
> >   X1   X2   X3   X4   X5   
> > variant_id
> >  "character"  "character"  "character"  "character"  "character"  
> > "character"
> > pval_nominal  gene_id.LCL
> >"numeric"  "character"
> > > sapply(asign,class)
> > gene  chr  chr_pos  pos p.val.Retina
> >  "character"  "character"  "character"  "character"  "character"
> >
> > Please advise as to why I am getting this error when merging?
> >
> > Thanks
> > Ana
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] negative vector length when merging data frames

2019-10-23 Thread Jim Lemon

Hi Ana,
When I run this example taken from your email:

l4<-read.table(text="X1 X2 X3 X4  X5 variant_id pval_nominal gene_id.LCL
chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232",
header=TRUE,stringsAsFactors=FALSE)
asign<-read.table(text="gene  chr  chr_pos   pos p.val.Retina
ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
ENSG0227232 chr11:11008:C:G 11008 0.218132
ENSG0227232 chr11:11012:C:G 11012 0.218132
ENSG0227232 chr11:13110:G:A 13110 0.998262
ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572",
header=TRUE,stringsAsFactors=FALSE)
merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
 [1] X1   X2   X3   X4   X5
[6] variant_id   pval_nominal gene_id.LCL  gene chr_pos
[11] p.val.Retina
<0 rows> (or 0-length row.names)

It works okay, but there are no matches in the join. So I can't even
guess what the problem is.

Jim

On Thu, Oct 24, 2019 at 9:33 AM Ana Marija  wrote:
>
> Hello,
>
> I have two data frames like this:
>
> > head(l4)
> X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > head(asign)
>   gene  chrchr_pos   pos p.val.Retina
> 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr",  :
>   negative length vectors are not allowed
> > sapply(l4,class)
>   X1   X2   X3   X4   X5   variant_id
>  "character"  "character"  "character"  "character"  "character"  "character"
> pval_nominal  gene_id.LCL
>"numeric"  "character"
> > sapply(asign,class)
> gene  chr  chr_pos  pos p.val.Retina
>  "character"  "character"  "character"  "character"  "character"
>
> Please advise as to why I am getting this error when merging?
>
> Thanks
> Ana
>
> __
> 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] negative vector length when merging data frames

2019-10-23 Thread Ana Marija

I also tried left_join but I got: Error: std::bad_alloc

> df3 <- left_join(l4, asign, by = c("chr","pos"))
Error: std::bad_alloc
> dim(l4)
[1] 166941635 8
> dim(asign)
[1] 107371528 5

On Wed, Oct 23, 2019 at 5:32 PM Ana Marija  wrote:
>
> Hello,
>
> I have two data frames like this:
>
> > head(l4)
> X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
> 1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
> 2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
> 3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
> 4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
> 5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
> 6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> > head(asign)
>   gene  chrchr_pos   pos p.val.Retina
> 1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
> 2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
> 3: ENSG0227232 chr11:11008:C:G 11008 0.218132
> 4: ENSG0227232 chr11:11012:C:G 11012 0.218132
> 5: ENSG0227232 chr11:13110:G:A 13110 0.998262
> 6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> > m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
> Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr",  :
>   negative length vectors are not allowed
> > sapply(l4,class)
>   X1   X2   X3   X4   X5   variant_id
>  "character"  "character"  "character"  "character"  "character"  "character"
> pval_nominal  gene_id.LCL
>"numeric"  "character"
> > sapply(asign,class)
> gene  chr  chr_pos  pos p.val.Retina
>  "character"  "character"  "character"  "character"  "character"
>
> Please advise as to why I am getting this error when merging?
>
> Thanks
> Ana

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[R] negative vector length when merging data frames

2019-10-23 Thread Ana Marija

Hello,

I have two data frames like this:

> head(l4)
X1X2 X3 X4  X5  variant_id pval_nominal gene_id.LCL
1 chr1 13550  G  A b38 1:13550:G:A 0.375614 ENSG0227232
2 chr1 14671  G  C b38 1:14671:G:C 0.474708 ENSG0227232
3 chr1 14677  G  A b38 1:14677:G:A 0.699887 ENSG0227232
4 chr1 16841  G  T b38 1:16841:G:T 0.127895 ENSG0227232
5 chr1 16856  A  G b38 1:16856:A:G 0.627822 ENSG0227232
6 chr1 17005  A  G b38 1:17005:A:G 0.802803 ENSG0227232
> head(asign)
  gene  chrchr_pos   pos p.val.Retina
1: ENSG0227232 chr1   1:10177:A:AC 10177 0.381708
2: ENSG0227232 chr1 rs145072688:10352:T:TA 10352 0.959523
3: ENSG0227232 chr11:11008:C:G 11008 0.218132
4: ENSG0227232 chr11:11012:C:G 11012 0.218132
5: ENSG0227232 chr11:13110:G:A 13110 0.998262
6: ENSG0227232 chr1  rs201725126:13116:T:G 13116 0.438572
> m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr",  :
  negative length vectors are not allowed
> sapply(l4,class)
  X1   X2   X3   X4   X5   variant_id
 "character"  "character"  "character"  "character"  "character"  "character"
pval_nominal  gene_id.LCL
   "numeric"  "character"
> sapply(asign,class)
gene  chr  chr_pos  pos p.val.Retina
 "character"  "character"  "character"  "character"  "character"

Please advise as to why I am getting this error when merging?

Thanks
Ana

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Re: [R] Change colour ggiNEXT plot package iNEXT

2019-10-23 Thread William Michels via R-help

Apparently, the iNEXT package was first described in an academic paper
published in 2016, although CRAN archives go back to 2015.
http://chao.stat.nthu.edu.tw/wordpress/paper/120_pdf_appendix.pdf
https://cran.r-project.org/src/contrib/Archive/iNEXT/

The vignette below has a section entitled "General Customization"
which talks about color. See the four lines of code I've added to the
vignette's code to get a general idea what to do.
https://cran.r-project.org/web/packages/iNEXT/vignettes/Introduction.html

library(iNEXT)
library(ggplot2)
library(gridExtra)
library(grid)
data("spider")
out <- iNEXT(spider, q=0, datatype="abundance")
g <- ggiNEXT(out, type=1, color.var = "site")
print(g)
g1 <- g + scale_colour_manual(values=c("yellow", "green"))
print(g1)
g2 <- g1 + scale_fill_manual(values=c("yellow", "green"))
print(g2)

HTH, Bill.

W. Michels, Ph.D.




On Wed, Oct 23, 2019 at 11:13 AM David Winsemius  wrote:
>
>
> On 10/22/19 12:48 PM, Luigi Marongiu wrote:
> > I thought it was a major package for ecological analysis.
>
>
> Yours is the first question in 20 years of Rhelp about the package iNEXT.
>
>
> --
>
> David
>
> > Anyway,
> > thank you for the tips. I'll dip from there.
> >
> > On Tue, Oct 22, 2019 at 5:29 PM Jeff Newmiller  
> > wrote:
> >> Probably, assuming that function returns a ggplot object. You will need to 
> >> identify the levels of the factor used for distinguishing groups, and add 
> >> a scale_colour_manual() to the ggplot object with colors specified in the 
> >> same order as those levels.
> >>
> >> Support for obscure packages is technically off-topic here ... if you need 
> >> a more specific answer you may need to correspond with the package authors 
> >> or use their suggested support resources.
> >>
> >> On October 22, 2019 2:18:49 AM PDT, Luigi Marongiu 
> >>  wrote:
> >>> Dear all,
> >>> is it possible to provide custom color to the rarefaction curve of the
> >>> package iNEXT (ggiNEXT)?
> >>> If I have these data:
> >>> ```
> >>> library(iNEXT)
> >>> library(ggplot2)
> >>> data(spider)
> >>> out <- iNEXT(spider, q=0, datatype="abundance")
> >>> ggiNEXT(out, type=1)
> >>> ```
> >>> can i colour the lines with, let's say, yellow and green?
> >>> Thank you
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >
> >
>
> __
> 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] Conditions in R (Help Post)

2019-10-23 Thread David Winsemius




On 10/22/19 10:19 PM, Yeasmin Alea wrote:

Thank you. Can you please have a look the below data sets, script and
question?

*Dataset-1: Pen*

*YEAR   DAY  X Y   Sig phase  *

*  *

*1  1981 9 -0.213 1.08   1.10 Phase-7*

*2  198110  0.065 1.05   1.05 Phase-6*



*Dataset-2: Book*

*YEAR Time *

*1  1981 1981-12-03 06:00:00 *

*2  19811981-12-04 00:00:00*



I want the output table as

*YEAR Time   phase*

*1  1981 1981-12-03 06:00:00 Phase-7*

*2  19811981-12-04 00:00:00 Phase-4*



You are posting in HTML. R help is a plain text mailing list. It is easy 
to send plain text using gmail. You should start over by configuring 
your mail client for this purpose and send the output of dput(head(Pen)) 
and dput(head(Book)) rather than the versions above which do not lend 
themselves to simple input strategies.



--

David.





*How can I combine and match the Dataset-1 DAY (365 days*35 years) +YEAR
with Dataset-2 YEAR+Time? Dataset 1 has 5,551 rows and dataset 2 has 22,210*

d$Pen<-Pen[cbind(match(Book$Time,Pen$DAY)]
Kind regards
Alea Yeasmin


On Wed, Oct 23, 2019 at 2:20 AM jim holtman  wrote:


Here is one way of doing it; I think the output you show is wrong:

library(tidyverse)
input <- read_delim(" YEAR   DAY  X Y   Sig
   1981 9 -0.213 1.08   1.10
   198110  0.065 1.05   1.05", delim = ' ', trim_ws = TRUE)

input <- mutate(input,
   phase = case_when(X < 0 & Y < 0 & Y < X ~ 'phase=1',
 X < 0 & Y > 0 & Y < X ~ 'phase=2',
 X < 0 & Y > 0 & Y < X ~ 'phase=7',
 X < 0 & Y > 0 & Y > X ~ 'phase=8',
 X > 0 & Y < 0 & Y < X ~ 'phase=3',
 X > 0 & Y < 0 & Y > X ~ 'phase=4',
 X > 0 & Y > 0 & Y > X ~ 'phase=6',
 X > 0 & Y > 0 & Y < X ~ 'phase=5',
 TRUE ~ 'unknown'
   )
)


input

# A tibble: 2 x 6
YEAR   DAY  X Y   Sig phase
 
1  1981 9 -0.213  1.08  1.1  phase=8
2  198110  0.065  1.05  1.05 phase=6

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, Oct 22, 2019 at 9:43 AM Yeasmin Alea 
wrote:


Hello Team
I would like to add a new column (for example-Phase) from the below data
set based on the conditions
YEAR   DAY  X Y   Sig
  1  1981 9 -0.213 1.08   1.10
  2  198110  0.065 1.05   1.05
*Conditions*

D$Phase=sapply(D,function(a,b) {
  a <-D$X
  b<-D$Y
  if (a<0 && b<0 && ba)
 {phase=2} else if (a<0 && b>0 && b0 && b>a)
 {phase=8} else if (a>0 && b<0 && b0 && b<0 && b>a)
 {phase=4} else if (a>0 && b>0 && b>a)
 {phase=6} else (a>0 && b>0 && bhttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


[[alternative HTML version deleted]]

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Re: [R] Change colour ggiNEXT plot package iNEXT

2019-10-23 Thread David Winsemius




On 10/22/19 12:48 PM, Luigi Marongiu wrote:

I thought it was a major package for ecological analysis.



Yours is the first question in 20 years of Rhelp about the package iNEXT.


--

David


Anyway,
thank you for the tips. I'll dip from there.

On Tue, Oct 22, 2019 at 5:29 PM Jeff Newmiller  wrote:

Probably, assuming that function returns a ggplot object. You will need to 
identify the levels of the factor used for distinguishing groups, and add a 
scale_colour_manual() to the ggplot object with colors specified in the same 
order as those levels.

Support for obscure packages is technically off-topic here ... if you need a 
more specific answer you may need to correspond with the package authors or use 
their suggested support resources.

On October 22, 2019 2:18:49 AM PDT, Luigi Marongiu  
wrote:

Dear all,
is it possible to provide custom color to the rarefaction curve of the
package iNEXT (ggiNEXT)?
If I have these data:
```
library(iNEXT)
library(ggplot2)
data(spider)
out <- iNEXT(spider, q=0, datatype="abundance")
ggiNEXT(out, type=1)
```
can i colour the lines with, let's say, yellow and green?
Thank you

--
Sent from my phone. Please excuse my brevity.





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[R] problem in drawing relative potency curve

2019-10-23 Thread Ahmad Rahbari

Dear
I investigated herbicide affect on weeds growth (dose-response). I used drc
package and fitted data to best model by mselect function and parameters of
models. For some data, Logistic model was the best and for others, Weibull.
But when I wanted to draw relative potency curve, the R-program displayed
error massage just for Weibull model (attachment files).
could you please help me?
thanks a lot.
your sincerely, Ahmad Rahbari
> mydata<- read.csv ("D:\\MY Data\\R\\Tri-set.csv" , sep=",", dec=".", 
> header=TRUE)
> mydata1 <- drm (Survival ~ Dose, Herbicide, fct = W1.3(), data=mydata)
> summary(mydata1)

Model fitted: Weibull (type 1) with lower limit at 0 (3 parms)

Parameter estimates:

   Estimate Std. Error t-value   p-value
b:EC   1.440454   0.239782  6.0073 3.346e-06 ***
b:MC   1.915474   0.320034  5.9852 3.533e-06 ***
d:EC 100.489083   5.303133 18.9490 6.368e-16 ***
d:MC 100.356215   5.257064 19.0898 4.791e-16 ***
e:EC   0.711835   0.054866 12.9740 2.444e-12 ***
e:MC   0.637447   0.042248 15.0882 9.551e-14 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error:

 9.398498 (24 degrees of freedom)
> EDcomp(mydata1, c(10,10), interval = "delta")

Estimated ratios of effect doses

Estimate   Lower   Upper
EC/MC:10/10  0.75802 0.18863 1.32740
> EDcomp(mydata1, c(50,50), interval = "delta") 

Estimated ratios of effect doses

Estimate   Lower   Upper
EC/MC:50/50  1.04841 0.77686 1.31997
> EDcomp(mydata1, c(90,90), interval = "delta")

Estimated ratios of effect doses

Estimate  Lower  Upper
EC/MC:90/90   1.2891 0.9224 1.6559

> relpot(mydata1, plotit = TRUE, compMatch = NULL, percVec = NULL, interval = 
> "none", type="relative")
Error in match.fun(FUN) : 
  'object$fct$lowerAs' is not a function, character or symbol
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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] Conditions in R (Help Post)

2019-10-23 Thread Yeasmin Alea

Thank you. Can you please have a look the below data sets, script and
question?

*Dataset-1: Pen*

*YEAR   DAY  X Y   Sig phase  *

*  *

*1  1981 9 -0.213 1.08   1.10 Phase-7*

*2  198110  0.065 1.05   1.05 Phase-6*



*Dataset-2: Book*

*YEAR Time *

*1  1981 1981-12-03 06:00:00 *

*2  19811981-12-04 00:00:00*



I want the output table as

*YEAR Time   phase*

*1  1981 1981-12-03 06:00:00 Phase-7*

*2  19811981-12-04 00:00:00 Phase-4*



*How can I combine and match the Dataset-1 DAY (365 days*35 years) +YEAR
with Dataset-2 YEAR+Time? Dataset 1 has 5,551 rows and dataset 2 has 22,210*

d$Pen<-Pen[cbind(match(Book$Time,Pen$DAY)]
Kind regards
Alea Yeasmin


On Wed, Oct 23, 2019 at 2:20 AM jim holtman  wrote:

> Here is one way of doing it; I think the output you show is wrong:
>
> library(tidyverse)
> input <- read_delim(" YEAR   DAY  X Y   Sig
>   1981 9 -0.213 1.08   1.10
>   198110  0.065 1.05   1.05", delim = ' ', trim_ws = TRUE)
>
> input <- mutate(input,
>   phase = case_when(X < 0 & Y < 0 & Y < X ~ 'phase=1',
> X < 0 & Y > 0 & Y < X ~ 'phase=2',
> X < 0 & Y > 0 & Y < X ~ 'phase=7',
> X < 0 & Y > 0 & Y > X ~ 'phase=8',
> X > 0 & Y < 0 & Y < X ~ 'phase=3',
> X > 0 & Y < 0 & Y > X ~ 'phase=4',
> X > 0 & Y > 0 & Y > X ~ 'phase=6',
> X > 0 & Y > 0 & Y < X ~ 'phase=5',
> TRUE ~ 'unknown'
>   )
> )
>
> > input
> # A tibble: 2 x 6
>YEAR   DAY  X Y   Sig phase
> 
> 1  1981 9 -0.213  1.08  1.1  phase=8
> 2  198110  0.065  1.05  1.05 phase=6
>
> 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, Oct 22, 2019 at 9:43 AM Yeasmin Alea 
> wrote:
>
>> Hello Team
>> I would like to add a new column (for example-Phase) from the below data
>> set based on the conditions
>>YEAR   DAY  X Y   Sig
>>  1  1981 9 -0.213 1.08   1.10
>>  2  198110  0.065 1.05   1.05
>> *Conditions*
>>
>> D$Phase=sapply(D,function(a,b) {
>>  a <-D$X
>>  b<-D$Y
>>  if (a<0 && b<0 && b> {phase=1} else if (a<0 && b<0 && b>a)
>> {phase=2} else if (a<0 && b>0 && b> {phase=7} else if (a<0 && b>0 && b>a)
>> {phase=8} else if (a>0 && b<0 && b> {phase=3} else if (a>0 && b<0 && b>a)
>> {phase=4} else if (a>0 && b>0 && b>a)
>> {phase=6} else (a>0 && b>0 && b> {phase=5}
>> })
>>
>> Can anyone help to fix the script to get a Phase column based on the
>> conditions. The table will be like the below
>>YEAR   DAY  X Y   Sig  Phase
>>  1  1981 9 -0.213 1.08   1.10   phase=7
>>  2  198110  0.065 1.05   1.05   phase=6
>>
>> Many thanks
>> Alea
>>
>> [[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]]

__
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] If Loop I Think

2019-10-23 Thread PIKAL Petr

Hi

***do not think in if or if loops in R***.

to elaborate Jim's solution further

With simple function based on logical expression
fff <- function(x) (x!="")+0

you could use apply

t(apply(phdf[,3:5], 1, fff))

and add results to your data frame columns
phdf[, 6:8] <- t(apply(phdf[,3:5], 1, fff))

Regarding some tutorial

Basic stuff is in R-intro, there is excellent documentation to each function.

And as R users pool is huge, you could simply ask Google
e.g.
r change values based on condition

Cheers
Petr

> -Original Message-
> From: R-help  On Behalf Of Jim Lemon
> Sent: Wednesday, October 23, 2019 12:26 AM
> To: Phillip Heinrich 
> Cc: r-help 
> Subject: Re: [R] If Loop I Think
> 
> Hi Philip,
> Try this:
> 
> phdf<-read.table(
> text="Row Outs RunnerFirst RunnerSecond RunnerThird R1 R2 R3
> 1 0
> 2 1
> 3 1
> 4 1 arenn001
> 5 2 arenn001
> 6 0
> 7 0 perad001
> 8 0 polla001 perad001
> 9 0 goldp001 polla001 perad001
> 10 0  lambj001 goldp001
> 11 1  lambj001 goldp001
> 12 2   lambj001
> 13 0
> 14 1   ",
> header=TRUE,stringsAsFactors=FALSE,fill=TRUE)
> phdf$R1<-ifelse(nchar(phdf$RunnerFirst) > 0,1,0)
> phdf$R2<-ifelse(nchar(phdf$RunnerSecond) > 0,1,0)
> phdf$R3<-ifelse(nchar(phdf$RunnerThird) > 0,1,0)
> 
> Jim
> 
> On Wed, Oct 23, 2019 at 7:54 AM Phillip Heinrich 
> wrote:
> >
> >   Row Outs RunnerFirst RunnerSecond RunnerThird R1 R2 R3
> >   1 0
> >   2 1
> >   3 1
> >   4 1 arenn001
> >   5 2 arenn001
> >   6 0
> >   7 0 perad001
> >   8 0 polla001 perad001
> >   9 0 goldp001 polla001 perad001
> >   10 0  lambj001 goldp001
> >   11 1  lambj001 goldp001
> >   12 2   lambj001
> >   13 0
> >   14 1
> >
> >
> >
> > With the above data, Arizona Diamondbacks baseball, I’m trying to put
> zeros into the R1 column is the RunnerFirst column is blank and a one if the
> column has a coded entry such as rows 4,5,7,8,& 9.  Similarly I want zeros in
> R2 and R3 if RunnerSecond and RunnerThird respectively are blank and ones
> if there is an entry.
> >
> > I’ve tried everything I know how to do such as “If Loops”, “If-Then loops”,
> “apply”, “sapply”, etc.  I wrote function below and it ran without errors but 
> I
> have no idea what to do with it to accomplish my goal:
> >
> > R1 <- function(x) {
> >   if (ari18.test3$RunnerFirst == " "){
> >ari18.test3$R1 <- 0
> >return(R1)
> >  }else{
> >R1 <- ari18.test3$R1 <- 1
> >return(R1)
> >  }
> >}
> >
> > The name of the data frame is ari18.test3
> >
> > On a more philosophical note, data handling in R seems to be made up of
> thousands of details with no over-riding principles.  I’ve read two books on R
> and a number of tutorial and watched several videos but I don’t seem to be
> making any progress.  Can anyone suggest videos, or tutorials, or books that
> might help?  Database stuff has never been my strong point but I’m
> determined to learn.
> >
> > Thanks,
> > Philip Heinrich
> > [[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.
> 
> __
> 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
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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