Re: [R] hash - extract key values

[Brian Smith]

Exactly. Used to work for me, but not anymore. I tried restarting session,
installing the most recent package of 'hash' etc.

Here is my sessionInfo():

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] grid  parallel  stats4stats graphics  grDevices utils
datasets  methods   base

other attached packages:
 [1] mapdata_2.2-3maps_2.3-9   org.Hs.eg.db_3.0.0
multicore_0.1-7  nlme_3.1-120 Rgraphviz_2.10.0
 [7] biomaRt_2.22.0   topGO_2.18.0 SparseM_1.6
 GO.db_3.0.0  graph_1.44.1 mouse4302.db_3.0.0
[13] org.Mm.eg.db_3.0.0   RSQLite_1.0.0DBI_0.3.1
 AnnotationDbi_1.28.1 GenomeInfoDb_1.2.4   IRanges_2.0.1
[19] S4Vectors_0.4.0  Biobase_2.26.0   BiocGenerics_0.12.1
 XML_3.98-1.1 gap_1.1-12   som_0.3-5
[25] pvclust_1.3-2foreign_0.8-63   hash_3.0.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6lattice_0.20-29 RCurl_1.95-4.5  tools_3.1.2




On Fri, Mar 27, 2015 at 9:54 PM, Boris Steipe 
wrote:

> Works for me :
>
> > library(hash)
> hash-2.2.6 provided by Decision Patterns
>
> > hx <- hash( c('a','b','c'), 1:3 )
> > class(hx)
> [1] "hash"
> attr(,"package")
> [1] "hash"
> > hx$a
> [1] 1
> > keys(hx)
> [1] "a" "b" "c"
>
>
> Maybe restart your session? Clear your workspace? Upgrade?
>
> B.
>
>
>
>
>
> On Mar 27, 2015, at 7:39 PM, Brian Smith  wrote:
>
> > Hi,
> >
> > I was trying to use hash, but can't seem to get the keys from the hash.
> > According to the hash documentation ('hash' package pdf, the following
> > should work:
> >
> >> hx <- hash( c('a','b','c'), 1:3 )
> >> class(hx)
> > [1] "hash"
> > attr(,"package")
> > [1] "hash"
> >> hx$a
> > [1] 1
> >> keys(hx)
> > Error in (function (classes, fdef, mtable)  :
> >  unable to find an inherited method for function ‘keys’ for signature
> > ‘"hash"’
> >
> > How can I get the keys for my hash?
> >
> > thanks!
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>

[[alternative HTML version deleted]]

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Re: [R] Using and abusing %>% (was Re: Why can't I access this type?)

[Hadley Wickham]

> I didn't dispute whether '%>%' may be useful -- I just pointed out that it
> is slow.  However, it is only part of the problem: 'filter()' and
> 'select()', although aesthetically pleasing, also seem to be slow:
>
>> all.states <- data.frame(state.x77, Name = rownames(state.x77))
>>
>> f1 <- function()
> + all.states[all.states$Frost > 150, c("Name", "Frost")]
>>
>> f2 <- function()
> + subset(all.states, Frost > 150, select = c("Name", "Frost"))
>>
>> f3 <- function() {
> + filt <- subset(all.states, Frost > 150)
> + subset(filt, select = c("Name", "Frost"))
> + }
>>
>> f4 <- function()
> + all.states %>% subset(Frost > 150) %>%
> + subset(select = c("Name", "Frost"))
>>
>> f5 <- function()
> + select(filter(all.states, Frost > 150), Name, Frost)
>>
>> f6 <- function()
> + all.states %>% filter(Frost > 150) %>% select(Name, Frost)
>>
>> mb <- microbenchmark(
> + f1(), f2(), f3(), f4(), f5(), f6(),
> + times = 1000L
> + )
>> print(mb, signif = 3L)
> Unit: microseconds
>  expr min   lq  mean median   uq  max neval   cld
>  f1() 115  124  134.8812129  134 1500  1000 a
>  f2() 128  141  147.4694145  151 1520  1000 a
>  f3() 303  328  344.3175338  348 1740  1000  b
>  f4() 458  494  518.0830510  523 1890  1000   c
>  f5() 806  848  887.7270875  894 3510  1000d
>  f6() 971 1010 1056.5659   1040 1060 3110  1000 e
>
> So, using '%>%', but leaving 'filter()' and 'select()' out of the equation,
> as in 'f4()' is only half as bad as the "full" 'dplyr' idiom in 'f6()'.  In
> this case, since we're talking microseconds, the speed-up is negligible but
> that *is* beside the point.

When benchmarking it's important to consider both the relative and
absolute difference and to think about how the cost scales as the data
grows - the cost of using using %>% is fixed, and 500 µs doesn't seem
like a huge performance penalty to me.

Hadley

-- 
http://had.co.nz/

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Re: [R] hash - extract key values

[Boris Steipe]

Works for me :

> library(hash)
hash-2.2.6 provided by Decision Patterns

> hx <- hash( c('a','b','c'), 1:3 )
> class(hx)
[1] "hash"
attr(,"package")
[1] "hash"
> hx$a
[1] 1
> keys(hx)
[1] "a" "b" "c"


Maybe restart your session? Clear your workspace? Upgrade?

B.





On Mar 27, 2015, at 7:39 PM, Brian Smith  wrote:

> Hi,
> 
> I was trying to use hash, but can't seem to get the keys from the hash.
> According to the hash documentation ('hash' package pdf, the following
> should work:
> 
>> hx <- hash( c('a','b','c'), 1:3 )
>> class(hx)
> [1] "hash"
> attr(,"package")
> [1] "hash"
>> hx$a
> [1] 1
>> keys(hx)
> Error in (function (classes, fdef, mtable)  :
>  unable to find an inherited method for function ‘keys’ for signature
> ‘"hash"’
> 
> How can I get the keys for my hash?
> 
> thanks!
> 
>   [[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
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] vif in package car: there are aliased coefficients in the model

[John Fox]

Dear Rodolfo,

It's apparently the case that at least one of the columns of the model
matrix for your model is perfectly collinear with others. 

There's not nearly enough information here to figure out exactly what the
problem is, and the information that you provided certainly falls short of
allowing me or anyone else to reproduce your problem and diagnose it
properly. It's not even clear from your message exactly what the structure
of the model is, although localizacao  is apparently a factor with 3 levels.


If you look at the summary() output for your model or just print it, you
should at least see which coefficients are aliased, and that might help you
understand what went wrong.

I hope this helps,
 John

---
John Fox, Professor
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/


> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Rodolfo
> Pelinson
> Sent: March-27-15 3:07 PM
> To: r-help@r-project.org
> Subject: [R] vif in package car: there are aliased coefficients in the
model
> 
> Hello. I'm trying to use the function vif from package car in a lm.
However it
> returns the following error:
> "Error in vif.default(lm(MDescores.sitescores ~ hidroperiodo + localizacao
> +  : there are aliased coefficients in the model"
> 
> When I exclude any predictor from the model, it returns this warning
> message:
> "Warning message: In cov2cor(v) : diag(.) had 0 or NA entries; non-finite
> result is doubtful"
> 
> When I exclude any other predictor from the model vif finally works. I
can't
> figure it out whats the problem. This are the results that R returns
> me:
> 
> > vif(lm(MDescores.sitescores ~ hidroperiodo + localizacao + area +
> profundidade + NTVM +  NTVI + PCs...c.1.., data = MDVIF)) Error in
> vif.default(lm(MDescores.sitescores ~ hidroperiodo + localizacao +
>  :   there are aliased coefficients in the model
> 
> > vif(lm(MDescores.sitescores ~ localizacao + area + profundidade + NTVM
> > +
>  NTVI + PCs...c.1.., data = MDVIF))
>  GVIF Df GVIF^(1/(2*Df))
> localizacao   NaN  2 NaN
> area  NaN  1 NaN
> profundidade  NaN  1 NaN
> NTVM  NaN  1 NaN
> NTVI  NaN  1 NaN
> PCs...c.1..   NaN  1 NaN
> Warning message:
> In cov2cor(v) : diag(.) had 0 or NA entries; non-finite result is doubtful
> 
> Thanks.
> --
> Rodolfo Mei Pelinson.
> 
>   [[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.


---
This email has been checked for viruses by Avast antivirus software.
http://www.avast.com

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Re: [R] Having trouble with gdata read in

[jim holtman]

pardon me it was my function which is just a call to "readWorksheetFromFile"


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 Fri, Mar 27, 2015 at 3:52 PM, Benjamin Baker  wrote:

>  Jim,
>
> I’m not seeing the command f.readXLSheet in the documentation, nor is it
> executing in my code.
>
>
> —
> Sent from Mailbox 
>
> On Thursday, Mar 26, 2015 at 5:15 AM, jim holtman ,
> wrote:
>
>> My suggestion is to use XLConnect to read the file:
>>
>>
>>  > x <-
>> "C:\\Users\\jh52822\\AppData\\Local\\Temp\\Rtmp6nVgFC\\file385c632aba3.xls"
>> > require(XLConnect)
>> Loading required package: XLConnect
>> Loading required package: XLConnectJars
>> XLConnect 0.2-10 by Mirai Solutions GmbH [aut],
>>   Martin Studer [cre],
>>   The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons
>> Codec),
>>   Stephen Colebourne [ctb, cph] (Joda-Time Java library)
>>  http://www.mirai-solutions.com ,
>> http://miraisolutions.wordpress.com
>> > input <- f.readXLSheet(x, 1)
>> >
>> > str(input)
>> 'data.frame':   2266 obs. of  51 variables:
>>  $ EIA  : num  34 59 87 97 108 118 123
>> 149 150 157 ...
>>  $ Entity.Name  : chr  "City of Abbeville" "City
>> of Abbeville" "City of Ada" "Adams Electric Cooperative" ...
>>  $ State: chr  "SC" "LA" "MN" "IL" ...
>>  $ NERC.Region  : chr  "SERC" "SPP" "MRO" "SERC"
>> ...
>>  $ Filing.Order : num  12 11 1237 392 252 ...
>>  $ Q5.MultRegion: chr  "" "" "" "" ...
>>  $ Q6.OwnMeters.: chr  "Yes" "Yes" "Yes" "Yes" ...
>>  $ Q7.ResMeters : num  3051 4253 857 8154 33670
>> ...
>>  $ Q7.ComMeters : num  531 972 132 155 1719 ...
>>  $ Q7.IntMeters : num  0 19 32 NA 626 NA 29 0 2
>> NA ...
>>  $ Q7.TransMeters   : num  0 NA NA NA NA NA NA 0 0 NA
>> ...
>>  $ Q7.OtherMeters   : num  0 NA NA 57 NA NA NA 0 0 NA
>> ...
>>  $ Q7...total.meters: num  3582 5244 1021 8366 36015
>> ...
>>  $ Q8.15Min.ResAMI  : num  0 NA NA NA NA NA NA NA NA
>> NA ...
>>  $ Q8.15Min.ComAMI  : num  0 NA NA 155 NA NA NA NA NA
>> NA ...
>>  $ Q8.15Min.IndAMI  : num  0 NA NA NA NA NA NA NA NA
>> NA ...
>>  $ Q8.15Min.TransAMI: num  0 NA NA NA NA NA NA NA NA
>> NA ...
>>  $ Q8.15Min.OtherAMI: num  0 NA NA NA NA NA NA NA NA
>> NA ...
>>  $ Q8.15Min.TotalAMI: num  0 0 0 155 0 0 0 0 0 0 ...
>>  $ Q8.Hourly.ResAMI : num  0 NA NA NA 16100 NA NA NA
>> NA NA ...
>>  $ Q8.Hourly.ComAMI : num  0 NA NA NA 1600 NA NA NA
>> NA NA ...
>>  
>>
>>
>>
>> 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 Wed, Mar 25, 2015 at 5:01 PM, Benjamin Baker  wrote:
>>
>>> Trying to read and clean up the FERC data on Advanced Metering
>>> infrastructure. Of course it is in XLS for the first two survey years and
>>> then converts to XLSX for the final two. Bad enough that it is all in
>>> excel, they had to change the survey design and data format as well. Still,
>>> I’m sorting through it. However, when I try and read in the 2008 data, I’m
>>> getting this error:
>>> ###
>>> Wide character in print at
>>> /Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdata/perl/
>>> xls2csv.pl line 270.
>>> Warning message:
>>> In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>>>   EOF within quoted string
>>> ###
>>>
>>>
>>>
>>> Here is the code I’m running to get the data:
>>> ###
>>> install.packages("gdata")
>>> library("gdata")
>>> fileUrl <- "
>>> http://www.ferc.gov/industries/electric/indus-act/demand-response/2008/survey/ami_survey_responses.xls
>>> "
>>> download.file(fileUrl, destfile="./ami.data/ami-data2008.xls")
>>> list.files("ami.data")
>>> dateDown.2008 <- date()
>>> ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1,
>>> header=TRUE)
>>> ###
>>>
>>>
>>> Reviewed the data in the XLS file, and both “” and # are present within
>>> it. Don’t know how to get the read.xls to ignore them so I can read all the
>>> data into my data frame. Tried :
>>> ###
>>> ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1,
>>> quote="", header=TRUE)
>>> ###
>>>
>>>
>>> And it spits out “More columns than column names” output.
>>>
>>>
>>> Been searching this, and I can find some “solutions” for read.table, but
>>> nothing specific to read.xls
>>>
>>>
>>> Many thanks,
>>>
>>>
>>> Benjamin Baker
>>>
>>>
>>>
>>> —
>>> Sent from Mailbox
>>> [[alternative HTML version deleted]]
>>>
>>> ___

Re: [R] Categorizing by month

[Ben Tupper]

Hi,

On Mar 27, 2015, at 12:06 PM, lychang  wrote:

> Hi everyone,
> 
> I'm trying to categorize by month in R. How can I do this if my dates are in
> date/month/year form?
> 

I'm not sure about the date form you describe, but if you have the dates as 
POSIXct you can extract the month as character and categorize with that.

x <- seq(from = as.POSIXct("2000/1/1", format="%Y/%m/%d"), to = 
as.POSIXct("2009/12/1", format="%Y/%m/%d"), by = 'month')
mon <- format(x, '%m')
xx <- split(x, mon)
str(xx)
List of 12
 $ 01: POSIXct[1:10], format: "2000-01-01" "2001-01-01" "2002-01-01" 
"2003-01-01" ...
 $ 02: POSIXct[1:10], format: "2000-02-01" "2001-02-01" "2002-02-01" 
"2003-02-01" ...
 $ 03: POSIXct[1:10], format: "2000-03-01" "2001-03-01" "2002-03-01" 
"2003-03-01" ...
 $ 04: POSIXct[1:10], format: "2000-04-01" "2001-04-01" "2002-04-01" 
"2003-04-01" ...
 $ 05: POSIXct[1:10], format: "2000-05-01" "2001-05-01" "2002-05-01" 
"2003-05-01" ...
 $ 06: POSIXct[1:10], format: "2000-06-01" "2001-06-01" "2002-06-01" 
"2003-06-01" ...
 $ 07: POSIXct[1:10], format: "2000-07-01" "2001-07-01" "2002-07-01" 
"2003-07-01" ...
 $ 08: POSIXct[1:10], format: "2000-08-01" "2001-08-01" "2002-08-01" 
"2003-08-01" ...
 $ 09: POSIXct[1:10], format: "2000-09-01" "2001-09-01" "2002-09-01" 
"2003-09-01" ...
 $ 10: POSIXct[1:10], format: "2000-10-01" "2001-10-01" "2002-10-01" 
"2003-10-01" ...
 $ 11: POSIXct[1:10], format: "2000-11-01" "2001-11-01" "2002-11-01" 
"2003-11-01" ...
 $ 12: POSIXct[1:10], format: "2000-12-01" "2001-12-01" "2002-12-01" 
"2003-12-01" ...

Does that help?

Ben

> Thanks,
> Lois
> 
> 
> 
> --
> View this message in context: 
> http://r.789695.n4.nabble.com/Categorizing-by-month-tp4705173.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> __
> 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.



Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

__
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[R] hash - extract key values

[Brian Smith]

Hi,

I was trying to use hash, but can't seem to get the keys from the hash.
According to the hash documentation ('hash' package pdf, the following
should work:

> hx <- hash( c('a','b','c'), 1:3 )
> class(hx)
[1] "hash"
attr(,"package")
[1] "hash"
> hx$a
[1] 1
> keys(hx)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘keys’ for signature
‘"hash"’

How can I get the keys for my hash?

thanks!

[[alternative HTML version deleted]]

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

Re: [R] Having trouble with gdata read in

[Benjamin Baker]

Jim,




I’m not seeing the command f.readXLSheet in the documentation, nor is it 
executing in my code.




—
Sent from Mailbox





On Thursday, Mar 26, 2015 at 5:15 AM, jim holtman , wrote:

My suggestion is to use XLConnect to read the file:






> x <- 
> "C:\\Users\\jh52822\\AppData\\Local\\Temp\\Rtmp6nVgFC\\file385c632aba3.xls"

> require(XLConnect)

Loading required package: XLConnect

Loading required package: XLConnectJars

XLConnect 0.2-10 by Mirai Solutions GmbH [aut],

  Martin Studer [cre],

  The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons

    Codec),

  Stephen Colebourne [ctb, cph] (Joda-Time Java library)


http://www.mirai-solutions.com ,

http://miraisolutions.wordpress.com

> input <- f.readXLSheet(x, 1)

> 

> str(input)

'data.frame':   2266 obs. of  51 variables:

 $ EIA                                  : num  34 59 87 97 108 118 123 149 150 
157 ...

 $ Entity.Name                          : chr  "City of Abbeville" "City of 
Abbeville" "City of Ada" "Adams Electric Cooperative" ...

 $ State                                : chr  "SC" "LA" "MN" "IL" ...

 $ NERC.Region                          : chr  "SERC" "SPP" "MRO" "SERC" ...

 $ Filing.Order                         : num  12 11 1237 392 252 ...

 $ Q5.MultRegion                        : chr  "" "" "" "" ...

 $ Q6.OwnMeters.                        : chr  "Yes" "Yes" "Yes" "Yes" ...

 $ Q7.ResMeters                         : num  3051 4253 857 8154 33670 ...

 $ Q7.ComMeters                         : num  531 972 132 155 1719 ...

 $ Q7.IntMeters                         : num  0 19 32 NA 626 NA 29 0 2 NA ...

 $ Q7.TransMeters                       : num  0 NA NA NA NA NA NA 0 0 NA ...

 $ Q7.OtherMeters                       : num  0 NA NA 57 NA NA NA 0 0 NA ...

 $ Q7...total.meters                    : num  3582 5244 1021 8366 36015 ...

 $ Q8.15Min.ResAMI                      : num  0 NA NA NA NA NA NA NA NA NA ...

 $ Q8.15Min.ComAMI                      : num  0 NA NA 155 NA NA NA NA NA NA ...

 $ Q8.15Min.IndAMI                      : num  0 NA NA NA NA NA NA NA NA NA ...

 $ Q8.15Min.TransAMI                    : num  0 NA NA NA NA NA NA NA NA NA ...

 $ Q8.15Min.OtherAMI                    : num  0 NA NA NA NA NA NA NA NA NA ...

 $ Q8.15Min.TotalAMI                    : num  0 0 0 155 0 0 0 0 0 0 ...

 $ Q8.Hourly.ResAMI                     : num  0 NA NA NA 16100 NA NA NA NA NA 
...

 $ Q8.Hourly.ComAMI                     : num  0 NA NA NA 1600 NA NA NA NA NA 
...














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 Wed, Mar 25, 2015 at 5:01 PM, Benjamin Baker  wrote:
Trying to read and clean up the FERC data on Advanced Metering infrastructure. 
Of course it is in XLS for the first two survey years and then converts to XLSX 
for the final two. Bad enough that it is all in excel, they had to change the 
survey design and data format as well. Still, I’m sorting through it. However, 
when I try and read in the 2008 data, I’m getting this error:

###

Wide character in print at 
/Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdata/perl/xls2csv.pl
 line 270.

Warning message:

In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :

  EOF within quoted string

###




Here is the code I’m running to get the data:

###

install.packages("gdata")

library("gdata")

fileUrl <- 
"http://www.ferc.gov/industries/electric/indus-act/demand-response/2008/survey/ami_survey_responses.xls";

download.file(fileUrl, destfile="./ami.data/ami-data2008.xls")

list.files("ami.data")

dateDown.2008 <- date()

ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1, header=TRUE)

###



Reviewed the data in the XLS file, and both “” and # are present within it. 
Don’t know how to get the read.xls to ignore them so I can read all the data 
into my data frame. Tried :

###

ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1, quote="", 
header=TRUE)

###



And it spits out “More columns than column names” output.



Been searching this, and I can find some “solutions” for read.table, but 
nothing specific to read.xls



Many thanks,



Benjamin Baker




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Re: [R] Using and abusing %>% (was Re: Why can't I access this type?)

[Henric Winell]

On 2015-03-26 07:48, Patrick Connolly wrote:


On Wed, 25-Mar-2015 at 03:14PM +0100, Henric Winell wrote:

...

|> Well...  Opinions may perhaps differ, but apart from '%>%' being
|> butt-ugly it's also fairly slow:

Beauty, it is said, is in the eye of the beholder.  I'm impressed by
the way using %>% reduces or eliminates complicated nested brackets.


I didn't dispute whether '%>%' may be useful -- I just pointed out that 
it is slow.  However, it is only part of the problem: 'filter()' and 
'select()', although aesthetically pleasing, also seem to be slow:


> all.states <- data.frame(state.x77, Name = rownames(state.x77))
>
> f1 <- function()
+ all.states[all.states$Frost > 150, c("Name", "Frost")]
>
> f2 <- function()
+ subset(all.states, Frost > 150, select = c("Name", "Frost"))
>
> f3 <- function() {
+ filt <- subset(all.states, Frost > 150)
+ subset(filt, select = c("Name", "Frost"))
+ }
>
> f4 <- function()
+ all.states %>% subset(Frost > 150) %>%
+ subset(select = c("Name", "Frost"))
>
> f5 <- function()
+ select(filter(all.states, Frost > 150), Name, Frost)
>
> f6 <- function()
+ all.states %>% filter(Frost > 150) %>% select(Name, Frost)
>
> mb <- microbenchmark(
+ f1(), f2(), f3(), f4(), f5(), f6(),
+ times = 1000L
+ )
> print(mb, signif = 3L)
Unit: microseconds
 expr min   lq  mean median   uq  max neval   cld
 f1() 115  124  134.8812129  134 1500  1000 a
 f2() 128  141  147.4694145  151 1520  1000 a
 f3() 303  328  344.3175338  348 1740  1000  b
 f4() 458  494  518.0830510  523 1890  1000   c
 f5() 806  848  887.7270875  894 3510  1000d
 f6() 971 1010 1056.5659   1040 1060 3110  1000 e

So, using '%>%', but leaving 'filter()' and 'select()' out of the 
equation, as in 'f4()' is only half as bad as the "full" 'dplyr' idiom 
in 'f6()'.  In this case, since we're talking microseconds, the speed-up 
is negligible but that *is* beside the point.



In this tiny example it's not obvious but it's very clear if the
objective is to sort the dataframe by three or four columns and
various lots of aggregation then returning a largish number of
consecutive columns, omitting the rest.  It's very easy to see what's
going on without the need for intermediate objects.


Why are you opposed to using intermediate objects?  In this case, as can 
be seen from 'f3()', it will also have the benefit of being faster than 
either '%>%' or the "full" 'dplyr' idiom.



|> [...]

It's no surprise that instructing a computer in something closer to
human language is an order of magnitude slower.


Certainly not true, at least for compiled languages.  In any case, 
judging from off-list correspondence, it definitely came as a surprise 
to some R users...


Given that '%>%' is so heavily marketed through 'dplyr', where the 
latter is said to provide "blazing fast performance for in-memory data 
by writing key pieces in C++" and "a fast, consistent tool for working 
with data frame like objects, both in memory and out of memory", I don't 
think it's far-fetched to expect that it should be more performant than 
base R.



I'm sure you'd get something even quicker using machine code.


Don't be ridiculous.  We're mainly discussing

all.states[all.states$Frost > 150, c("state", "Frost")]

vs.

all.states %>% filter(Frost > 150) %>% select(state, Frost)

i.e., pure R code.


I spend 3 or 4 orders of magnitude more time writing code than running it.


You and me both.  But that doesn't mean speed is of no or little importance.


It's much more important to me to be able to read and modify than

> it is to have it run at optimum speed.

Good for you.  But surely, if this is your goal, nothing beats 
intermediate objects.  And like I said, it may still be faster than the 
'dplyr' idiom.



|> Of course, this doesn't matter for interactive one-off use.  But
|> lately I've seen examples of the '%>%' operator creeping into
|> functions in packages.

That could indicate that %>% is seductively easy to use.  It's
probably true that there are places where it should be done the hard
way.


We all know how easy it is to write ugly and sluggish code in R.  But 
'foo[i,j]' is neither ugly nor sluggish and certainly not "the hard way."



|>  However, it would be nice to see a fast pipe operator as part of
|> base R.


Heck, it doesn't even have to be fast as long as it's a bit more elegant 
than '%>%'.



Henric Winell





|>
|>
|> Henric Winell
|>



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Re: [R] Why can't I access this type?

[Henric Winell]

On 2015-03-27 09:19, Patrick Connolly wrote:


[...]

On Sun, 22-Mar-2015 at 08:06AM -0800, John Kane wrote:

|> Well, first off, you have no variable called "Name".  You have lost
|> the state names as they are rownames in the matrix state.x77 and
|> not a variable.

If you did this:


all.states  <- within(as.data.frame(state.x77), Name <- rownames(state.x77))

instead of

all.states  <- within(as.data.frame(state.x77), state <- rownames(state.x77))


Alternatively, since 'data.frame()' coerces internally, one could do

all.states <- data.frame(state.x77, Name = rownames(state.x77))


Henric Winell





then this would worka;

cold.states <- all.states[all.states$Frost > 150, c("Name", "Frost")]


Modify the above to match where my guess at what you tried is in error.


HTH



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Re: [R] matrix manipulation question

[Henric Winell]

On 2015-03-27 11:41, Stéphane Adamowicz wrote:


Well, it seems to work with me.

Y <- as.matrix(airquality)
head(Y, n=8)
  Ozone Solar.R Wind Temp Month Day
[1,]41 190  7.4   67 5   1
[2,]36 118  8.0   72 5   2
[3,]12 149 12.6   74 5   3
[4,]18 313 11.5   62 5   4
[5,]NA  NA 14.3   56 5   5
[6,]28  NA 14.9   66 5   6
[7,]23 299  8.6   65 5   7
[8,]19  99 13.8   59 5   8

Z <- Y[,complete.cases(t(Y))==T]


Peter's point, I guess, is that

1. complete.cases(t(Y)) is already a vector of logicals
2. T (and F) can be redefined, so what if T <- FALSE?


Henric Winell





head(Z, n=8)
  Wind Temp Month Day
[1,]  7.4   67 5   1
[2,]  8.0   72 5   2
[3,] 12.6   74 5   3
[4,] 11.5   62 5   4
[5,] 14.3   56 5   5
[6,] 14.9   66 5   6
[7,]  8.6   65 5   7
[8,] 13.8   59 5   8

The columns that contained NA were deleted.


Le 27 mars 2015 � 10:38, peter dalgaard  a �crit :



On 27 Mar 2015, at 09:58 , St�phane Adamowicz 
 wrote:


data_no_NA <- data[, complete.cases(t(data))==T]


Ouch! logical == TRUE is bad, logical == T is worse:

data[, complete.cases(t(data))]


--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com













_
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Inra, centre de recherche Paca, unit� PSH
228, route de l'a�rodrome
CS 40509
domaine St Paul, site Agroparc
84914 Avignon, cedex 9
France

stephane.adamow...@avignon.inra.fr
tel.  +33 (0)4 32 72 24 35
fax. +33 (0)4 32 72 24 32
do not dial 0 when out of France
web PSH  : https://www6.paca.inra.fr/psh
web Inra : http://www.inra.fr/
_


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Re: [R] Having trouble with gdata read in

[Benjamin Baker]

Jim,




Thanks, XLConnect with proper syntax works great for both types of files.


—
Sent from Mailbox

On Thu, Mar 26, 2015 at 5:15 AM, jim holtman  wrote:

> My suggestion is to use XLConnect to read the file:
>> x <-
> "C:\\Users\\jh52822\\AppData\\Local\\Temp\\Rtmp6nVgFC\\file385c632aba3.xls"
>> require(XLConnect)
> Loading required package: XLConnect
> Loading required package: XLConnectJars
> XLConnect 0.2-10 by Mirai Solutions GmbH [aut],
>   Martin Studer [cre],
>   The Apache Software Foundation [ctb, cph] (Apache POI, Apache Commons
> Codec),
>   Stephen Colebourne [ctb, cph] (Joda-Time Java library)
> http://www.mirai-solutions.com ,
> http://miraisolutions.wordpress.com
>> input <- f.readXLSheet(x, 1)
>>
>> str(input)
> 'data.frame':   2266 obs. of  51 variables:
>  $ EIA  : num  34 59 87 97 108 118 123 149
> 150 157 ...
>  $ Entity.Name  : chr  "City of Abbeville" "City of
> Abbeville" "City of Ada" "Adams Electric Cooperative" ...
>  $ State: chr  "SC" "LA" "MN" "IL" ...
>  $ NERC.Region  : chr  "SERC" "SPP" "MRO" "SERC" ...
>  $ Filing.Order : num  12 11 1237 392 252 ...
>  $ Q5.MultRegion: chr  "" "" "" "" ...
>  $ Q6.OwnMeters.: chr  "Yes" "Yes" "Yes" "Yes" ...
>  $ Q7.ResMeters : num  3051 4253 857 8154 33670 ...
>  $ Q7.ComMeters : num  531 972 132 155 1719 ...
>  $ Q7.IntMeters : num  0 19 32 NA 626 NA 29 0 2 NA
> ...
>  $ Q7.TransMeters   : num  0 NA NA NA NA NA NA 0 0 NA
> ...
>  $ Q7.OtherMeters   : num  0 NA NA 57 NA NA NA 0 0 NA
> ...
>  $ Q7...total.meters: num  3582 5244 1021 8366 36015 ...
>  $ Q8.15Min.ResAMI  : num  0 NA NA NA NA NA NA NA NA NA
> ...
>  $ Q8.15Min.ComAMI  : num  0 NA NA 155 NA NA NA NA NA
> NA ...
>  $ Q8.15Min.IndAMI  : num  0 NA NA NA NA NA NA NA NA NA
> ...
>  $ Q8.15Min.TransAMI: num  0 NA NA NA NA NA NA NA NA NA
> ...
>  $ Q8.15Min.OtherAMI: num  0 NA NA NA NA NA NA NA NA NA
> ...
>  $ Q8.15Min.TotalAMI: num  0 0 0 155 0 0 0 0 0 0 ...
>  $ Q8.Hourly.ResAMI : num  0 NA NA NA 16100 NA NA NA NA
> NA ...
>  $ Q8.Hourly.ComAMI : num  0 NA NA NA 1600 NA NA NA NA
> NA ...
> 
> 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 Wed, Mar 25, 2015 at 5:01 PM, Benjamin Baker  wrote:
>> Trying to read and clean up the FERC data on Advanced Metering
>> infrastructure. Of course it is in XLS for the first two survey years and
>> then converts to XLSX for the final two. Bad enough that it is all in
>> excel, they had to change the survey design and data format as well. Still,
>> I’m sorting through it. However, when I try and read in the 2008 data, I’m
>> getting this error:
>> ###
>> Wide character in print at
>> /Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdata/perl/
>> xls2csv.pl line 270.
>> Warning message:
>> In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>>   EOF within quoted string
>> ###
>>
>>
>>
>> Here is the code I’m running to get the data:
>> ###
>> install.packages("gdata")
>> library("gdata")
>> fileUrl <- "
>> http://www.ferc.gov/industries/electric/indus-act/demand-response/2008/survey/ami_survey_responses.xls
>> "
>> download.file(fileUrl, destfile="./ami.data/ami-data2008.xls")
>> list.files("ami.data")
>> dateDown.2008 <- date()
>> ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1,
>> header=TRUE)
>> ###
>>
>>
>> Reviewed the data in the XLS file, and both “” and # are present within
>> it. Don’t know how to get the read.xls to ignore them so I can read all the
>> data into my data frame. Tried :
>> ###
>> ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1, quote="",
>> header=TRUE)
>> ###
>>
>>
>> And it spits out “More columns than column names” output.
>>
>>
>> Been searching this, and I can find some “solutions” for read.table, but
>> nothing specific to read.xls
>>
>>
>> Many thanks,
>>
>>
>> Benjamin Baker
>>
>>
>>
>> —
>> Sent from Mailbox
>> [[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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Re: [R] matrix manipulation question

[Jatin Kala]

Thanks Richard,
This works, rather obvious now that i think of it!
=)

On 27/03/2015 4:30 pm, Richard M. Heiberger wrote:

just reverse what you did before.

newdata <- data
newdata[] <- NA
newdata[,!apply(is.na(data), 2, any)] <- myfunction(data_no_NA)

On Fri, Mar 27, 2015 at 1:13 AM, Jatin Kala  wrote:

Hi,
I've got a rather large matrix of about 800 rows and 60 columns.
Each column is a time-series 800 long.

Out of these 60 time series, some have missing values (NA).
I want to strip out all columns that have one or more NA values, i.e., only
want full time series.

This should do the trick:
data_no_NA <- data[,!apply(is.na(data), 2, any)]

I now use data_no_NA as input to a function, which returns output as a
matrix of the same size as data_no_NA

The trick is that i now need to put these columns back into a new 800 by
60 empty matrix, at their original locations.
Any suggestions on how to do that? hopefully without having to use loops.
I'm using R/3.0.3

Cheers,
Jatin.

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Re: [R] Having trouble with gdata read in

[Benjamin Baker]

Anthony,




XLSX won’t read an XLS file. Additionally, the legacy Java that is required for 
the xlsx package really effs up my computer. Have to reinstall my OS to fix it.




—
Sent from Mailbox

On Wed, Mar 25, 2015 at 3:51 PM, Anthony Damico 
wrote:

> maybe
> library(xlsx)
> tf <- tempfile()
> ami <- "
> http://www.ferc.gov/industries/electric/indus-act/demand-response/2008/survey/ami_survey_responses.xls
> "
> download.file( ami , tf , mode = 'wb' )
> ami.data2008 <- read.xlsx( tf , sheetIndex = 1 )
> On Wed, Mar 25, 2015 at 5:01 PM, Benjamin Baker  wrote:
>> Trying to read and clean up the FERC data on Advanced Metering
>> infrastructure. Of course it is in XLS for the first two survey years and
>> then converts to XLSX for the final two. Bad enough that it is all in
>> excel, they had to change the survey design and data format as well. Still,
>> I’m sorting through it. However, when I try and read in the 2008 data, I’m
>> getting this error:
>> ###
>> Wide character in print at
>> /Library/Frameworks/R.framework/Versions/3.1/Resources/library/gdata/perl/
>> xls2csv.pl line 270.
>> Warning message:
>> In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>>   EOF within quoted string
>> ###
>>
>>
>>
>> Here is the code I’m running to get the data:
>> ###
>> install.packages("gdata")
>> library("gdata")
>> fileUrl <- "
>> http://www.ferc.gov/industries/electric/indus-act/demand-response/2008/survey/ami_survey_responses.xls
>> "
>> download.file(fileUrl, destfile="./ami.data/ami-data2008.xls")
>> list.files("ami.data")
>> dateDown.2008 <- date()
>> ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1,
>> header=TRUE)
>> ###
>>
>>
>> Reviewed the data in the XLS file, and both “” and # are present within
>> it. Don’t know how to get the read.xls to ignore them so I can read all the
>> data into my data frame. Tried :
>> ###
>> ami.data2008 <- read.xls("./ami.data/ami-data2008.xls", sheet=1, quote="",
>> header=TRUE)
>> ###
>>
>>
>> And it spits out “More columns than column names” output.
>>
>>
>> Been searching this, and I can find some “solutions” for read.table, but
>> nothing specific to read.xls
>>
>>
>> Many thanks,
>>
>>
>> Benjamin Baker
>>
>>
>>
>> —
>> Sent from Mailbox
>> [[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] Categorizing by month

[lychang]

Hi everyone,

I'm trying to categorize by month in R. How can I do this if my dates are in
date/month/year form?

Thanks,
Lois



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View this message in context: 
http://r.789695.n4.nabble.com/Categorizing-by-month-tp4705173.html
Sent from the R help mailing list archive at Nabble.com.

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[R] vif in package car: there are aliased coefficients in the model

[Rodolfo Pelinson]

Hello. I'm trying to use the function vif from package car in a lm. However
it returns the following error:
"Error in vif.default(lm(MDescores.sitescores ~ hidroperiodo + localizacao
+  : there are aliased coefficients in the model"

When I exclude any predictor from the model, it returns this warning
message:
"Warning message: In cov2cor(v) : diag(.) had 0 or NA entries; non-finite
result is doubtful"

When I exclude any other predictor from the model vif finally works. I
can't figure it out whats the problem. This are the results that R returns
me:

> vif(lm(MDescores.sitescores ~ hidroperiodo + localizacao + area +
profundidade + NTVM +  NTVI + PCs...c.1.., data = MDVIF))
Error in vif.default(lm(MDescores.sitescores ~ hidroperiodo + localizacao +
 :   there are aliased coefficients in the model

> vif(lm(MDescores.sitescores ~ localizacao + area + profundidade + NTVM +
 NTVI + PCs...c.1.., data = MDVIF))
 GVIF Df GVIF^(1/(2*Df))
localizacao   NaN  2 NaN
area  NaN  1 NaN
profundidade  NaN  1 NaN
NTVM  NaN  1 NaN
NTVI  NaN  1 NaN
PCs...c.1..   NaN  1 NaN
Warning message:
In cov2cor(v) : diag(.) had 0 or NA entries; non-finite result is doubtful

Thanks.
-- 
Rodolfo Mei Pelinson.

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Re: [R] Calculating area of polygons created from a spatial intersect

[MacQueen, Don]

Suggest (strongly) that you move this question to r-sig-geo. Much more
appropriate there, and more people there are more familiar with this kind
of work. But ... I suspect you want gIntersection(), not gIntersects().

-Don

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 3/27/15, 7:16 AM, "Walter Anderson"  wrote:

>-BEGIN PGP SIGNED MESSAGE-
>Hash: SHA1
>
>Hello all,
>
>I am attempting to automate an analysis that I developed with ArcInfo
>using R and the gdal and geos packages (or any other) if possible.
>
>Here is the basic process
>
>I have a shape file (lines) that defines the limits of all of the
>projects with each project having a unique identifier.
>
>I have another shape file (polys) that contains total population and
>low income population and represent Census block groups.  This shape
>file has an area field which has the acreage of the total block group.
>
>Process
>
>Step 1.
>I then buffer these project lines to create a second shape file that
>represents the 'footprint' of the project. (Creates polys).
>
>Step 2.
>In ArcInfo, I perform an intersection of the two shape files
>(footprint and census blocks) and this creates a third shape file
>which has a unique polygon for every project/census block intersection.
>
>Step 3.
>I then perform an area calculation (acres) on this new poly shape file
>and use this calculated area divided by the original area of the
>associated census block group to apportion the two population datum to
>this new polygon.
>
>Step 4.
>Finally, I sum the two population datums for each of the projects from
>the attribute table of this final shape file.
>
>When I try to replicate the above procedure I run into a problem with
>Step 2 when I use what I think is the appropriate command:
>
>gIntersects(buffered_projects, census_blocks, byID=TRUE)
>
>This command is producing a matrix of each project/census block
>combination and only providing me a true/false indication.  Is there
>any way to replicate the process from ArcInfo that I outlined above
>within R?
>
>Walter Anderson
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Re: [R] matrix manipulation question

[David Winsemius]

On Mar 27, 2015, at 3:41 AM, Stéphane Adamowicz wrote:

> Well, it seems to work with me.
> 

No one is doubting that it worked for you in this instance. What Peter D. was 
criticizing was the construction :

complete.cases(t(Y))==T

... and it was on two bases that it is "wrong". The first is that `T` is not 
guaranteed to be TRUE. The second is that the test ==T (or similarly ==TRUE) is 
completely unnecessary because `complete.cases` returns a logical vector and so 
that expression is a waste of time.

(The issue of matrix versus dataframe was raised by someone else.)

-- 
David.


> Y <- as.matrix(airquality)
> head(Y, n=8)
> Ozone Solar.R Wind Temp Month Day
> [1,]41 190  7.4   67 5   1
> [2,]36 118  8.0   72 5   2
> [3,]12 149 12.6   74 5   3
> [4,]18 313 11.5   62 5   4
> [5,]NA  NA 14.3   56 5   5
> [6,]28  NA 14.9   66 5   6
> [7,]23 299  8.6   65 5   7
> [8,]19  99 13.8   59 5   8
> 
> Z <- Y[,complete.cases(t(Y))==T]
> 
> head(Z, n=8)
> Wind Temp Month Day
> [1,]  7.4   67 5   1
> [2,]  8.0   72 5   2
> [3,] 12.6   74 5   3
> [4,] 11.5   62 5   4
> [5,] 14.3   56 5   5
> [6,] 14.9   66 5   6
> [7,]  8.6   65 5   7
> [8,] 13.8   59 5   8
> 
> The columns that contained NA were deleted.
> 
> 
> Le 27 mars 2015 à 10:38, peter dalgaard  a écrit :
> 
>> 
>> On 27 Mar 2015, at 09:58 , Stéphane Adamowicz 
>>  wrote:
>> 
>>> data_no_NA <- data[, complete.cases(t(data))==T]
>> 
>> Ouch! logical == TRUE is bad, logical == T is worse:
>> 
>> data[, complete.cases(t(data))]
>> 
>> 
>> -- 
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> 
> 
> _
> Stéphane Adamowicz
> Inra, centre de recherche Paca, unité PSH
> 228, route de l'aérodrome
> CS 40509
> domaine St Paul, site Agroparc
> 84914 Avignon, cedex 9
> France
> 
> stephane.adamow...@avignon.inra.fr
> tel.  +33 (0)4 32 72 24 35
> fax. +33 (0)4 32 72 24 32
> do not dial 0 when out of France
> web PSH  : https://www6.paca.inra.fr/psh
> web Inra : http://www.inra.fr/
> _
> 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

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Re: [R] Problem with download.file ?

[William Dunlap]

Add the argument mode="wb" to your call to download.file().  On Windows
this means to use 'binary' format - do not change line endings.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Fri, Mar 27, 2015 at 7:25 AM, Giles Crane  wrote:

>
> # download.file() Seems to put the xlsx file onto hard drive.
>
> >download.file("
> http://www.udel.edu/johnmack/data_library/zipcode_centroids.xlsx";,
> "zipcode_centroids.xlsx")
> trying URL '
> http://www.udel.edu/johnmack/data_library/zipcode_centroids.xlsx'
> Content type
> 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length
> 2785832 bytes (2.7 Mb)
> opened URL
> downloaded 2.7 Mb
>
>
> # Trouble reading file with xlsx.
>
> library(xlsx)
> Loading required package: rJava
> Loading required package: xlsxjars
> Warning messages:
> 1: package ‘xlsx’ was built under R version 3.1.3
> 2: package ‘rJava’ was built under R version 3.1.3
>
> >df <- read.xlsx2("zipcode_centroids.xlsx", sheetIndex=1)
> Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :
>java.util.zip.ZipException: invalid entry size (expected 1168 but got
> 1173 bytes)
>
>
> # I downloaded the file manually (same name) from the web page and tried
> again.
> # Then I read the file into R with xlsx successfully.
>
>
> >df <- read.xlsx2("/zipdist/zipcode_centroids.xlsx", sheetIndex=1)
> >str(df)
> 'data.frame':   42961 obs. of  8 variables:
>   $ ZIPCODE  : Factor w/ 42961 levels "01001","01002",..: 1 2 3 4 5 6 7 8
> 9 10 ...
>   $ TOWN.: Factor w/ 18955 levels "Aaronsburg","Abbeville",..: 85 333
> 333 333 898 1089 1459 1620 1899 2929 ...
>   $ STATE: Factor w/ 52 levels "AK","AL","AR",..: 21 21 21 21 21 21 21
> 21 21 21 ...
>   $ LATITUDE : Factor w/ 37352 levels "-7.209975","19.101978",..: 28020
> 28948 28916 28971 29047 28624 28326 28418 28197 28603 ...
>   $ LONGITUDE: Factor w/ 37241 levels "-100.00991","-100.02632",..: 8799
> 8706 8811 8715 8470 8639 9019 8608 8531 9065 ...
>   $ STFIPS   : Factor w/ 51 levels "01","02","04",..: 22 22 22 22 22 22 22
> 22 22 22 ...
>   $ CD   : Factor w/ 55 levels "00","01","02",..: 3 2 2 2 2 2 2 3 3 2
> ...
>   $ CONG_DIST: Factor w/ 436 levels "01_01","01_02",..: 191 190 190 190
> 190 190 190 191 191 190 ...
>
> # Is there a problem with download.file() when file is an Excel file or
> this particular Excel file?
>
> --
> Giles L Crane, MPH, ASA, NJPHA
> Statistical Consultant and R Instructor
> 621 Lake Drive
> Princeton, NJ  08540
> Phone: 609 924-0971
> Email: gilescr...@verizon.net
>
>
> [[alternative HTML version deleted]]
>
> __
> 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.

[[alternative HTML version deleted]]

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[R] Problem with download.file ?

[Giles Crane]

# download.file() Seems to put the xlsx file onto hard drive.

>download.file("http://www.udel.edu/johnmack/data_library/zipcode_centroids.xlsx";,
> "zipcode_centroids.xlsx")
trying URL 'http://www.udel.edu/johnmack/data_library/zipcode_centroids.xlsx'
Content type 
'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet' length 
2785832 bytes (2.7 Mb)
opened URL
downloaded 2.7 Mb


# Trouble reading file with xlsx.

library(xlsx)
Loading required package: rJava
Loading required package: xlsxjars
Warning messages:
1: package ‘xlsx’ was built under R version 3.1.3
2: package ‘rJava’ was built under R version 3.1.3

>df <- read.xlsx2("zipcode_centroids.xlsx", sheetIndex=1)
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :
   java.util.zip.ZipException: invalid entry size (expected 1168 but got 1173 
bytes)


# I downloaded the file manually (same name) from the web page and tried again.
# Then I read the file into R with xlsx successfully.


>df <- read.xlsx2("/zipdist/zipcode_centroids.xlsx", sheetIndex=1)
>str(df)
'data.frame':   42961 obs. of  8 variables:
  $ ZIPCODE  : Factor w/ 42961 levels "01001","01002",..: 1 2 3 4 5 6 7 8 9 10 
...
  $ TOWN.: Factor w/ 18955 levels "Aaronsburg","Abbeville",..: 85 333 333 
333 898 1089 1459 1620 1899 2929 ...
  $ STATE: Factor w/ 52 levels "AK","AL","AR",..: 21 21 21 21 21 21 21 21 
21 21 ...
  $ LATITUDE : Factor w/ 37352 levels "-7.209975","19.101978",..: 28020 28948 
28916 28971 29047 28624 28326 28418 28197 28603 ...
  $ LONGITUDE: Factor w/ 37241 levels "-100.00991","-100.02632",..: 8799 8706 
8811 8715 8470 8639 9019 8608 8531 9065 ...
  $ STFIPS   : Factor w/ 51 levels "01","02","04",..: 22 22 22 22 22 22 22 22 
22 22 ...
  $ CD   : Factor w/ 55 levels "00","01","02",..: 3 2 2 2 2 2 2 3 3 2 ...
  $ CONG_DIST: Factor w/ 436 levels "01_01","01_02",..: 191 190 190 190 190 190 
190 191 191 190 ...

# Is there a problem with download.file() when file is an Excel file or this 
particular Excel file?

-- 
Giles L Crane, MPH, ASA, NJPHA
Statistical Consultant and R Instructor
621 Lake Drive
Princeton, NJ  08540
Phone: 609 924-0971
Email: gilescr...@verizon.net


[[alternative HTML version deleted]]

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[R] Calculating area of polygons created from a spatial intersect

[Walter Anderson]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello all,

I am attempting to automate an analysis that I developed with ArcInfo
using R and the gdal and geos packages (or any other) if possible.

Here is the basic process

I have a shape file (lines) that defines the limits of all of the
projects with each project having a unique identifier.

I have another shape file (polys) that contains total population and
low income population and represent Census block groups.  This shape
file has an area field which has the acreage of the total block group.

Process

Step 1.
I then buffer these project lines to create a second shape file that
represents the 'footprint' of the project. (Creates polys).

Step 2.
In ArcInfo, I perform an intersection of the two shape files
(footprint and census blocks) and this creates a third shape file
which has a unique polygon for every project/census block intersection.

Step 3.
I then perform an area calculation (acres) on this new poly shape file
and use this calculated area divided by the original area of the
associated census block group to apportion the two population datum to
this new polygon.

Step 4.
Finally, I sum the two population datums for each of the projects from
the attribute table of this final shape file.

When I try to replicate the above procedure I run into a problem with
Step 2 when I use what I think is the appropriate command:

gIntersects(buffered_projects, census_blocks, byID=TRUE)

This command is producing a matrix of each project/census block
combination and only providing me a true/false indication.  Is there
any way to replicate the process from ArcInfo that I outlined above
within R?

Walter Anderson
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Re: [R] matrix manipulation question

[Stéphane Adamowicz]

> 
>> example. Furthermore in my example no unwanted format occurred. You can
> 
> Yes because data.frame was (luckily) numeric.
> 

Luck has nothing to do with this. I Chose this example on purpose …

Stéphane

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Re: [R] matrix manipulation question

[PIKAL Petr]

Hi

> -Original Message-
> From: Stéphane Adamowicz [mailto:stephane.adamow...@avignon.inra.fr]
> Sent: Friday, March 27, 2015 1:26 PM
> To: PIKAL Petr
> Cc: peter dalgaard; r-help@r-project.org
> Subject: Re: [R] matrix manipulation question
>
>
> Le 27 mars 2015 à 12:34, PIKAL Petr  a écrit :
>
> > Very, very, very bad solution.
> >
> > as.matrix can change silently your data to unwanted format,
> complete.cases()==T is silly as Peter already pointed out.
> >
> >
>
> Perhaps, but it happens that in the original message, the question

I do not have original message.

> dealt with a matrix not a dataframe, and thus I needed a matrix

But you made matrix from data frame. If one column was not numeric all 
resulting matrix would chnge to nonnumeric format.

> example. Furthermore in my example no unwanted format occurred. You can

Yes because data.frame was (luckily) numeric.

> check easily that the final matrix contains only « numeric » data as in
> the original data frame.

You want matrix? Here it is.

> head(as.matrix(airquality)[ ,colSums(is.na(airquality))==0])
 Wind Temp Month Day
[1,]  7.4   67 5   1
[2,]  8.0   72 5   2
[3,] 12.6   74 5   3
[4,] 11.5   62 5   4
[5,] 14.3   56 5   5
[6,] 14.9   66 5   6

Works same with matrix as with data frame without need to transform it.

Cheers
Petr

>
> Stéphane
> > >
> > >
> > >
> > >
> > >
> >
> >
> >
> > _
> > St phane Adamowicz
> > Inra, centre de recherche Paca, unit  PSH 228, route de l'a rodrome
> CS
> > 40509 domaine St Paul, site Agroparc
> > 84914 Avignon, cedex 9
> > France
> >
> > stephane.adamow...@avignon.inra.fr
> > tel.  +33 (0)4 32 72 24 35
> > fax. +33 (0)4 32 72 24 32
> > do not dial 0 when out of France
> > web PSH  : https://www6.paca.inra.fr/psh web Inra :
> > http://www.inra.fr/ _
> >
> >
> > [[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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Re: [R] matrix manipulation question

[Stéphane Adamowicz]

Le 27 mars 2015 à 12:34, PIKAL Petr  a écrit :

> Very, very, very bad solution.
>  
> as.matrix can change silently your data to unwanted format, 
> complete.cases()==T is silly as Peter already pointed out.
>  
> 

Perhaps, but it happens that in the original message, the question dealt with a 
matrix not a dataframe, and thus I needed a matrix example. Furthermore in my 
example no unwanted format occurred. You can check easily that the final matrix 
contains only « numeric » data as in the original data frame.

Stéphane
> > 
> > 
> > 
> > 
> > 
> 
> 
> 
> _
> St�phane Adamowicz
> Inra, centre de recherche Paca, unit� PSH
> 228, route de l'a�rodrome
> CS 40509
> domaine St Paul, site Agroparc
> 84914 Avignon, cedex 9
> France
> 
> stephane.adamow...@avignon.inra.fr
> tel.  +33 (0)4 32 72 24 35
> fax. +33 (0)4 32 72 24 32
> do not dial 0 when out of France
> web PSH  : https://www6.paca.inra.fr/psh
> web Inra : http://www.inra.fr/
> _
> 
> 
> [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.
> 
> Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou 
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Re: [R] matrix manipulation question

[PIKAL Petr]

Very, very, very bad solution.

as.matrix can change silently your data to unwanted format, complete.cases()==T 
is silly as Peter already pointed out.

I use

head(airquality[ ,colSums(is.na(airquality))==0])
  Wind Temp Month Day
1  7.4   67 5   1
2  8.0   72 5   2
3 12.6   74 5   3
4 11.5   62 5   4
5 14.3   56 5   5
6 14.9   66 5   6

if I want to get rid of columns with NA.

Cheers
Petr


From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Stéphane 
Adamowicz
Sent: Friday, March 27, 2015 11:42 AM
To: peter dalgaard
Cc: r-help@r-project.org
Subject: Re: [R] matrix manipulation question

Well, it seems to work with me.

Y <- as.matrix(airquality)
head(Y, n=8)
 Ozone Solar.R Wind Temp Month Day
[1,]41 190  7.4   67 5   1
[2,]36 118  8.0   72 5   2
[3,]12 149 12.6   74 5   3
[4,]18 313 11.5   62 5   4
[5,]NA  NA 14.3   56 5   5
[6,]28  NA 14.9   66 5   6
[7,]23 299  8.6   65 5   7
[8,]19  99 13.8   59 5   8

Z <- Y[,complete.cases(t(Y))==T]

head(Z, n=8)
 Wind Temp Month Day
[1,]  7.4   67 5   1
[2,]  8.0   72 5   2
[3,] 12.6   74 5   3
[4,] 11.5   62 5   4
[5,] 14.3   56 5   5
[6,] 14.9   66 5   6
[7,]  8.6   65 5   7
[8,] 13.8   59 5   8

The columns that contained NA were deleted.


Le 27 mars 2015 � 10:38, peter dalgaard 
mailto:pda...@gmail.com>> a �crit :

>
> On 27 Mar 2015, at 09:58 , St�phane Adamowicz 
> mailto:stephane.adamow...@avignon.inra.fr>>
>  wrote:
>
>> data_no_NA <- data[, complete.cases(t(data))==T]
>
> Ouch! logical == TRUE is bad, logical == T is worse:
>
> data[, complete.cases(t(data))]
>
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: 
> pda...@gmail.com
>
>
>
>
>
>
>
>
>



_
St�phane Adamowicz
Inra, centre de recherche Paca, unit� PSH
228, route de l'a�rodrome
CS 40509
domaine St Paul, site Agroparc
84914 Avignon, cedex 9
France

stephane.adamow...@avignon.inra.fr
tel.  +33 (0)4 32 72 24 35
fax. +33 (0)4 32 72 24 32
do not dial 0 when out of France
web PSH  : https://www6.paca.inra.fr/psh
web Inra : http://www.inra.fr/
_


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Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny 
pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně 
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svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email 
jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či 
zpožděním přenosu e-mailu.

V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a 
to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; 
Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce 
s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným 
dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost 
žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně 
pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně 
osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi 
či osobě jím zastoupené známá.

This e-mail and any documents attached to it may be confidential and are 
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If you received this e-mail by mistake, please immediately inform its sender. 
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If you are not the intended recipient of this e-mail, you are not authorized to 
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The sender of this e-mail shall not be liable for any possible damage caused by 
modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a 
contract in any time, for any reason, and without statin

Re: [R] matrix manipulation question

[Stéphane Adamowicz]

Well, it seems to work with me.

Y <- as.matrix(airquality)
head(Y, n=8)
 Ozone Solar.R Wind Temp Month Day
[1,]41 190  7.4   67 5   1
[2,]36 118  8.0   72 5   2
[3,]12 149 12.6   74 5   3
[4,]18 313 11.5   62 5   4
[5,]NA  NA 14.3   56 5   5
[6,]28  NA 14.9   66 5   6
[7,]23 299  8.6   65 5   7
[8,]19  99 13.8   59 5   8

Z <- Y[,complete.cases(t(Y))==T]

head(Z, n=8)
 Wind Temp Month Day
[1,]  7.4   67 5   1
[2,]  8.0   72 5   2
[3,] 12.6   74 5   3
[4,] 11.5   62 5   4
[5,] 14.3   56 5   5
[6,] 14.9   66 5   6
[7,]  8.6   65 5   7
[8,] 13.8   59 5   8

The columns that contained NA were deleted.


Le 27 mars 2015 � 10:38, peter dalgaard  a �crit :

> 
> On 27 Mar 2015, at 09:58 , St�phane Adamowicz 
>  wrote:
> 
>> data_no_NA <- data[, complete.cases(t(data))==T]
> 
> Ouch! logical == TRUE is bad, logical == T is worse:
> 
> data[, complete.cases(t(data))]
> 
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> 
> 
> 
> 
> 
> 
> 
> 



_
St�phane Adamowicz
Inra, centre de recherche Paca, unit� PSH
228, route de l'a�rodrome
CS 40509
domaine St Paul, site Agroparc
84914 Avignon, cedex 9
France

stephane.adamow...@avignon.inra.fr
tel.  +33 (0)4 32 72 24 35
fax. +33 (0)4 32 72 24 32
do not dial 0 when out of France
web PSH  : https://www6.paca.inra.fr/psh
web Inra : http://www.inra.fr/
_


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Re: [R] Vennerable Plots for Publications

[Jim Lemon]

HI Dario,
Have you tried creating a larger PNG image and then shrinking the result
with an image manipulation program (e.g. GIMP)?

Jim


On Fri, Mar 27, 2015 at 4:00 PM, Dario Strbenac 
wrote:

> Does anyone make Venn diagrams for publication using Vennerable ? I found
> that the font size is too big when the plot is created at 300 DPI, and
> there's no option to change it, even when the point size argument to the
> device is changed.
>
> aVenn <- Venn(Sets = list(A = 1:5, B = 3:6))
> png("forPublication.png", units = "in", h = 2.55, w = 2.4, res = 300) #
> Changing pointsize to a smaller number has no effect on size of the text.
> plot(aVenn)
> dev.off()
>
> --
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
> __
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>

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Re: [R] matrix manipulation question

[peter dalgaard]

On 27 Mar 2015, at 09:58 , Stéphane Adamowicz 
 wrote:

> data_no_NA <- data[, complete.cases(t(data))==T]

Ouch! logical == TRUE is bad, logical == T is worse:

data[, complete.cases(t(data))]


-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] matrix manipulation question

[Stéphane Adamowicz]

Why not use complete.cases() ?

data_no_NA <- data[, complete.cases(t(data))==T]


Le 27 mars 2015 à 06:13, Jatin Kala  a écrit :

> Hi,
> I've got a rather large matrix of about 800 rows and 60 columns.
> Each column is a time-series 800 long.
> 
> Out of these 60 time series, some have missing values (NA).
> I want to strip out all columns that have one or more NA values, i.e., only 
> want full time series.
> 
> This should do the trick:
> data_no_NA <- data[,!apply(is.na(data), 2, any)]
> 
> I now use data_no_NA as input to a function, which returns output as a matrix 
> of the same size as data_no_NA
> 
> The trick is that i now need to put these columns back into a new 800 by 
> 60 empty matrix, at their original locations.
> Any suggestions on how to do that? hopefully without having to use loops.
> I'm using R/3.0.3
> 
> Cheers,
> Jatin.
> 
> __
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Re: [R] Why can't I access this type?

[Patrick Connolly]

On Thu, 26-Mar-2015 at 04:58PM -0400, yoursurrogate...@gmail.com wrote:

[...]
|>  I agree with you on the indexing approach.  But even after using
|> within, I still get the same error.  >

You leave us to guess just what you tried, but if you did this:

> all.states  <- within(as.data.frame(state.x77), state <- rownames(state.x77))
and then again did this:

> cold.states <- all.states[all.states$Frost > 150, c("Name", "Frost")]

of course it will give the same error, because as you haven't
addressed the problem as you've been told

On Sun, 22-Mar-2015 at 08:06AM -0800, John Kane wrote:

|> Well, first off, you have no variable called "Name".  You have lost
|> the state names as they are rownames in the matrix state.x77 and
|> not a variable.

If you did this:

> all.states  <- within(as.data.frame(state.x77), Name <- rownames(state.x77))
instead of
> all.states  <- within(as.data.frame(state.x77), state <- rownames(state.x77))

then this would worka;
> cold.states <- all.states[all.states$Frost > 150, c("Name", "Frost")]

Modify the above to match where my guess at what you tried is in error.


HTH

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___Patrick Connolly   
 {~._.~}   Great minds discuss ideas
 _( Y )_ Average minds discuss events 
(:_~*~_:)  Small minds discuss people  
 (_)-(_)  . Eleanor Roosevelt
  
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