Re: [R] Can't resolve dependency problems with package "sem"
An old version of R would be fine if that was all you wanted, but no, you want
all the latest contributed packages as well. I can't blame you for that, but
don't blame R for difficulties with contributed packages that have external
dependencies and depend on recent versions of R.
You might find
http://trestletech.com/2012/10/install-rgl-in-ubuntu/
helpful with your RGL package issue.
I very rarely configure/compile since apt is so powerful. IMHO you should
always start with apt on Debian derivatives before falling back to compiling.
--
Sent from my phone. Please excuse my brevity.
On May 4, 2016 7:06:24 PM PDT, "C&A Säger" wrote:
>Am 05.05.2016 um 01:41 schrieb Jeff Newmiller:
>> Did you follow the instructions for setting up apt to pull recent
>> versions of R, as described in CRAN? I suspect not, since your
>version
>> is old.
>> --
>
>Hello Jeff,
>
>Thank you very much for taking notice.
>
>I was hoping that any old version which used to be the best of breed 3
>years ago would be just fine for absolute beginners.
>I did not even know that CRAN exists until I actually installed the
>software. I use Ubuntu because compiling software is a major annoyance
>to me. Since 2002 I use to compile something every now and then when it
>is the only way to get something installed.
>
>Right now I try to follow the R installation guide carefully but dumb
>because I don't really understand what I'm doing. configure, make, make
>check, everything runs OK so far but sudo make install fails anyway.
>What a horrible waste of time and electricity!
>
>Actually, I'm trying to help my daughter who needs to learn some R
>basics. The installation on a Windows PC is a matter of minutes by
>following a tiny instructional PDF from her tutor. But she does not
>have
>the time nor knowledge to install R successfully on her Ubuntu PC which
>is the same as mine. While she has some real work to do, I'm trying to
>get this darn thing onto our computers. Even if I manage to compile a
>working R program on my computer, this will not be of any help for my
>daughter who does not have the compilers installed and I don't know
>which packages make it happen on my PC. I'd have to build my first
>Debian package which might take another day of reading and testing.
>
>[...]
>
>Meanwhile the installation of R out of debian packages from a CRAN
>server did the job and I managed to ...
>
>> install.packages("Rcmdr",dependencies=TRUE)
>
>... which finished with ...
>
>> ** testing if installed package can be loaded
>> * DONE (Rcmdr)
>
>... but also with warnings ...
>
>> 1: In install.packages("Rcmdr", dependencies = TRUE) :
>> Installation des Pakets ‘rgl’ hatte Exit-Status ungleich 0
>> 2: In install.packages("Rcmdr", dependencies = TRUE) :
>> Installation des Pakets ‘rglwidget’ hatte Exit-Status ungleich 0
>
>.. due to these errors:
>
>> configure: error: missing required header GL/gl.h
>> ERROR: configuration failed for package ‘rgl’
>
>> ERROR: dependency ‘rgl’ is not available for package ‘rglwidget’
>
>
>Thank you very much for the pointer to this instructive page:
>
>> http://ftp5.gwdg.de/pub/misc/cran/
>
>May be we can live without GL support for now.
>
>Greetings,
>Andreas
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Can't resolve dependency problems with package "sem"
Am 05.05.2016 um 01:41 schrieb Jeff Newmiller:
> Did you follow the instructions for setting up apt to pull recent
> versions of R, as described in CRAN? I suspect not, since your version
> is old.
> --
Hello Jeff,
Thank you very much for taking notice.
I was hoping that any old version which used to be the best of breed 3
years ago would be just fine for absolute beginners.
I did not even know that CRAN exists until I actually installed the
software. I use Ubuntu because compiling software is a major annoyance
to me. Since 2002 I use to compile something every now and then when it
is the only way to get something installed.
Right now I try to follow the R installation guide carefully but dumb
because I don't really understand what I'm doing. configure, make, make
check, everything runs OK so far but sudo make install fails anyway.
What a horrible waste of time and electricity!
Actually, I'm trying to help my daughter who needs to learn some R
basics. The installation on a Windows PC is a matter of minutes by
following a tiny instructional PDF from her tutor. But she does not have
the time nor knowledge to install R successfully on her Ubuntu PC which
is the same as mine. While she has some real work to do, I'm trying to
get this darn thing onto our computers. Even if I manage to compile a
working R program on my computer, this will not be of any help for my
daughter who does not have the compilers installed and I don't know
which packages make it happen on my PC. I'd have to build my first
Debian package which might take another day of reading and testing.
[...]
Meanwhile the installation of R out of debian packages from a CRAN
server did the job and I managed to ...
> install.packages("Rcmdr",dependencies=TRUE)
... which finished with ...
> ** testing if installed package can be loaded
> * DONE (Rcmdr)
... but also with warnings ...
> 1: In install.packages("Rcmdr", dependencies = TRUE) :
> Installation des Pakets ‘rgl’ hatte Exit-Status ungleich 0
> 2: In install.packages("Rcmdr", dependencies = TRUE) :
> Installation des Pakets ‘rglwidget’ hatte Exit-Status ungleich 0
.. due to these errors:
> configure: error: missing required header GL/gl.h
> ERROR: configuration failed for package ‘rgl’
> ERROR: dependency ‘rgl’ is not available for package ‘rglwidget’
Thank you very much for the pointer to this instructive page:
> http://ftp5.gwdg.de/pub/misc/cran/
May be we can live without GL support for now.
Greetings,
Andreas
__
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] Can't resolve dependency problems with package "sem"
Dear Andreas, As has been suggested, you're probably better off using an up-to-date version of R and corresponding up-to-date packages, but if the only issue is that sem can't be installed, the Rcmdr package should still work. The menu item for confirmatory factor analysis will be missing, and unless you tell it to suppress checking for missing packages on start-up, the Rcmdr will continue to ask you whether you want to install the sem package, but everything else should work. To suppress the start-up package check, issue the R command options(Rcmdr=list(check.packages=FALSE)) before library(Rcmdr). I hope this helps, John --- John Fox, Professor McMaster University Hamilton, Ontario, Canada http://socserv.socsci.mcmaster.ca/jfox/ > -Original Message- > From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of C&A > Säger > Sent: Wednesday, May 4, 2016 8:28 PM > To: Jim Lemon; r-help@r-project.org > Subject: Re: [R] Can't resolve dependency problems with package "sem" > > Am 05.05.2016 um 00:17 schrieb Jim Lemon: > > Hi Andreas, > > Try installing plyr, arm, scales and mi separately. If you get an > > error message about a version mismatch, that's where your problem is. > > _Sometimes_ upgrading R will fix it, if the problem is that the > > version you are downloading is too new for your R version. > > > > Jim > > > > Hello Jim, > > Indeed, this might be the problem. When I try to install plyr, I get > something like this: > "Package xxx is not availlable (not for this version 3.0.x)" > > I was hoping that any old version from the Ubuntu repositories would be > good enough for an absolute beginner. > > Thank you very much, > Andreas > __ > 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] Can't resolve dependency problems with package "sem"
Am 05.05.2016 um 00:17 schrieb Jim Lemon: > Hi Andreas, > Try installing plyr, arm, scales and mi separately. If you get an > error message about a version mismatch, that's where your problem is. > _Sometimes_ upgrading R will fix it, if the problem is that the > version you are downloading is too new for your R version. > > Jim > Hello Jim, Indeed, this might be the problem. When I try to install plyr, I get something like this: "Package xxx is not availlable (not for this version 3.0.x)" I was hoping that any old version from the Ubuntu repositories would be good enough for an absolute beginner. Thank you very much, Andreas __ 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] Can't resolve dependency problems with package "sem"
Did you follow the instructions for setting up apt to pull recent versions of
R, as described in CRAN? I suspect not, since your version is old.
--
Sent from my phone. Please excuse my brevity.
On May 4, 2016 11:51:27 AM PDT, "C&A Säger" wrote:
>Hello,
>
>First time user on Ubuntu 14.4 with Ubuntus R Commander and
>
>> $ R --version
>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>> Copyright (C) 2013 The R Foundation for Statistical Computing
>> Platform: x86_64-pc-linux-gnu (64-bit)
>
>The program icon of the commander executes
>
>> sh -c 'R_DEFAULT_PACKAGES="$R_DEFAULT_PACKAGES Rcmdr" R "$@"'
>
>On first run it started downloading, compiling and installing various
>packages. One of them fails:
>
>>
>>> install.packages("sem",dependencies=TRUE)
>> Installing package into
>‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0’
>> (as ‘lib’ is unspecified)
>> Warnung: dependencies ‘MBESS’, ‘arm’, ‘plyr’ are not available
>> also installing the dependencies ‘scales’, ‘mi’, ‘DiagrammeR’
>>
>> versuche URL
>'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/scales_0.4.0.tar.gz'
>> Content type 'application/x-gzip' length 57358 bytes (56 Kb)
>> URL geöffnet
>> ==
>> downloaded 56 Kb
>>
>> versuche URL
>'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/mi_1.0.tar.gz'
>> Content type 'application/x-gzip' length 793313 bytes (774 Kb)
>> URL geöffnet
>> ==
>> downloaded 774 Kb
>>
>> versuche URL
>'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/DiagrammeR_0.8.2.tar.gz'
>> Content type 'application/x-gzip' length 3532835 bytes (3.4 Mb)
>> URL geöffnet
>> ==
>> downloaded 3.4 Mb
>>
>> versuche URL
>'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/sem_3.1-7.tar.gz'
>> Content type 'application/x-gzip' length 154654 bytes (151 Kb)
>> URL geöffnet
>> ==
>> downloaded 151 Kb
>>
>> ERROR: dependency ‘plyr’ is not available for package ‘scales’
>> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/scales’
>> ERROR: dependency ‘arm’ is not available for package ‘mi’
>> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/mi’
>> ERROR: dependency ‘scales’ is not available for package ‘DiagrammeR’
>> * removing
>‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/DiagrammeR’
>> ERROR: dependency ‘mi’ is not available for package ‘sem’
>> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/sem’
>>
>> Die heruntergeladenen Quellpakete sind in
>> ‘/tmp/RtmplEqHDo/downloaded_packages’
>> Warnmeldungen:
>> 1: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘scales’ hatte Exit-Status ungleich 0
>> 2: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘mi’ hatte Exit-Status ungleich 0
>> 3: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘DiagrammeR’ hatte Exit-Status ungleich 0
>> 4: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘sem’ hatte Exit-Status ungleich 0
>
>How can I resolve the dependencies?
>Should I replace the Ubuntu version with something fresh?
>
>Thanks in advance,
>Andreas
>__
>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] Can't resolve dependency problems with package "sem"
Hi Andreas,
Try installing plyr, arm, scales and mi separately. If you get an
error message about a version mismatch, that's where your problem is.
_Sometimes_ upgrading R will fix it, if the problem is that the
version you are downloading is too new for your R version.
Jim
On Thu, May 5, 2016 at 4:51 AM, C&A Säger wrote:
> Hello,
>
> First time user on Ubuntu 14.4 with Ubuntus R Commander and
>
>> $ R --version
>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>> Copyright (C) 2013 The R Foundation for Statistical Computing
>> Platform: x86_64-pc-linux-gnu (64-bit)
>
> The program icon of the commander executes
>
>> sh -c 'R_DEFAULT_PACKAGES="$R_DEFAULT_PACKAGES Rcmdr" R "$@"'
>
> On first run it started downloading, compiling and installing various
> packages. One of them fails:
>
>>
>>> install.packages("sem",dependencies=TRUE)
>> Installing package into ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0’
>> (as ‘lib’ is unspecified)
>> Warnung: dependencies ‘MBESS’, ‘arm’, ‘plyr’ are not available
>> also installing the dependencies ‘scales’, ‘mi’, ‘DiagrammeR’
>>
>> versuche URL
>> 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/scales_0.4.0.tar.gz'
>> Content type 'application/x-gzip' length 57358 bytes (56 Kb)
>> URL geöffnet
>> ==
>> downloaded 56 Kb
>>
>> versuche URL 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/mi_1.0.tar.gz'
>> Content type 'application/x-gzip' length 793313 bytes (774 Kb)
>> URL geöffnet
>> ==
>> downloaded 774 Kb
>>
>> versuche URL
>> 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/DiagrammeR_0.8.2.tar.gz'
>> Content type 'application/x-gzip' length 3532835 bytes (3.4 Mb)
>> URL geöffnet
>> ==
>> downloaded 3.4 Mb
>>
>> versuche URL 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/sem_3.1-7.tar.gz'
>> Content type 'application/x-gzip' length 154654 bytes (151 Kb)
>> URL geöffnet
>> ==
>> downloaded 151 Kb
>>
>> ERROR: dependency ‘plyr’ is not available for package ‘scales’
>> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/scales’
>> ERROR: dependency ‘arm’ is not available for package ‘mi’
>> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/mi’
>> ERROR: dependency ‘scales’ is not available for package ‘DiagrammeR’
>> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/DiagrammeR’
>> ERROR: dependency ‘mi’ is not available for package ‘sem’
>> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/sem’
>>
>> Die heruntergeladenen Quellpakete sind in
>> ‘/tmp/RtmplEqHDo/downloaded_packages’
>> Warnmeldungen:
>> 1: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘scales’ hatte Exit-Status ungleich 0
>> 2: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘mi’ hatte Exit-Status ungleich 0
>> 3: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘DiagrammeR’ hatte Exit-Status ungleich 0
>> 4: In install.packages("sem", dependencies = TRUE) :
>> Installation des Pakets ‘sem’ hatte Exit-Status ungleich 0
>
> How can I resolve the dependencies?
> Should I replace the Ubuntu version with something fresh?
>
> Thanks in advance,
> Andreas
> __
> 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] Changing transformations in mi package
Thank you for providing a working example. I think you need to contact the
package maintainer:
> maintainer("mi")
[1] "Ben Goodrich "
When I run your code it appears that the c column is correctly transformed to
square roots, but the show() function is incorrectly indicating a log transform:
> data.missingdf@variables$c@raw_data # The raw data
[1] 4.2 7.9 NA 16.1 19.9 23.0
> sqrt(data.missingdf@variables$c@raw_data) # The square root of the raw data
[1] 2.049390 2.810694 NA 4.012481 4.460942 4.795832
> data.missingdf@variables$c@data # The transformed data - square roots, not
> logs
[1] 2.049390 2.810694 NA 4.012481 4.460942 4.795832
-
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Elizabeth Hensor
Sent: Wednesday, May 4, 2016 5:44 AM
To: 'r-help@r-project.org'
Subject: [R] Changing transformations in mi package
Dear all,
I am an R beginner and new to the list. In preparation for using mi to impute
missing values I am setting up the missing data frame and would like to specify
the transformation types for some of my variables, as I will be using these
transformations in my analysis models. According to the documentation the
available options are "standardize" (the default), "identity", "log",
"logshift" and "sqrt". I can successfully change the transformation types to
"log" and "logshift", but when I attempt to change to "sqrt", this changes the
type to "log" instead. I'd appreciate your help, please.
Below are details of my system and some code which replicates the issue.
> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4stats graphics grDevices utils datasets methods base
other attached packages:
[1] lmerTest_2.0-30 truncnorm_1.0-7 mi_1.0 lme4_1.1-12
Matrix_1.2-4
[6] pls_2.5-0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.4 Formula_1.2-1 cluster_2.0.3 splines_3.2.5
[5] MASS_7.3-45 munsell_0.4.3 colorspace_1.2-6arm_1.8-6
[9] lattice_0.20-33 minqa_1.2.4 plyr_1.8.3 nnet_7.3-12
[13] grid_3.2.5 nlme_3.1-126gtable_0.2.0
latticeExtra_0.6-28
[17] coda_0.18-1 abind_1.4-3 survival_2.38-3
gridExtra_2.2.1
[21] RColorBrewer_1.1-2 nloptr_1.0.4ggplot2_2.1.0
acepack_1.3-3.3
[25] rpart_4.1-10scales_0.4.0Hmisc_3.17-3foreign_0.8-66
data <-
data.frame(a=c(NA,2.1,3.3,4.5,5.9,6.2),b=c(2.2,NA,6.1,8.3,10.2,12.13),c=c(4.2,7.9,NA,16.1,19.9,23))
data
a bc
1 NA 2.20 4.2
2 2.1NA 7.9
3 3.3 6.10 NA
4 4.5 8.30 16.1
5 5.9 10.20 19.9
6 6.2 12.13 23.0
data.missingdf <- missing_data.frame(data)
show(data.missingdf)
Object of class missing_data.frame with 6 observations on 3 variables
There are 4 missing data patterns
Append '@patterns' to this missing_data.frame to access the corresponding
pattern for every observation or perhaps use table()
type missing method model
a continuous 1ppd linear
b continuous 1ppd linear
c continuous 1ppd linear
family link transformation
a gaussian identitystandardize
b gaussian identitystandardize
c gaussian identitystandardize
#Let's say I'd like to change transformation for a, b and c to "log",
"logshift" and "sqrt" respectively
data.missingdf <- change(data.missingdf, y="a", what="transformation",
to="logshift")
data.missingdf <- change(data.missingdf, y="b", what="transformation", to="log")
data.missingdf <- change(data.missingdf, y="c", what="transformation",
to="sqrt")
show(data.missingdf)
Object of class missing_data.frame with 6 observations on 3 variables
There are 4 missing data patterns
Append '@patterns' to this missing_data.frame to access the corresponding
pattern for every observation or perhaps use table()
type missing method model
a continuous 1ppd linear
b continuous 1ppd linear
c continuous 1ppd linear
family link transformation
a gaussian identity logshift
b gaussian identitylog
c gaussian identitylog
#Transformation has been successfully changed for a and b, but for c has been
changed to "log" instead of "sqrt"
Thanks in advance for your assistance,
Liz Hensor
Biostatistician
Leeds Institute of Rheumatic and Musculoskeletal Medicine &
NIHR Leeds Musculoskeletal Biomedical Research Unit
_
Re: [R] how to compute Bonferroni, Tukey's, Sheffe 95%-condence intervals for coefficients B1, B2, B3 in linear regression?
> On May 4, 2016, at 7:45 AM, super wrote: > > > Dear experts, >I have a problem in compute Bonferroni,Tukey's,Sheffe 95%-condence > intervals for coefficients B1,B2,B3 in linear regression using R? how can i > do it? I only know how to compute these three cofindence intervals in > multicomparsion by using multcomp package, and i am search a lot for how to > comupte the three CIs for linear regression coefficients but without any > useful information, so, plz help me ~ Your question does not detail where the 'confint' function in pkg:multcop is letting you down. After the first few lines of the first example I type: confint(wht) #--- And get: Simultaneous Confidence Intervals Multiple Comparisons of Means: Tukey Contrasts Fit: aov(formula = breaks ~ wool + tension, data = warpbreaks) Quantile = 2.4155 95% family-wise confidence level Linear Hypotheses: Estimate lwr upr M - L == 0 -10. -19.3536 -0.6464 H - L == 0 -14.7222 -24.0758 -5.3687 H - M == 0 -4.7222 -14.0758 4.6313 Subsequent examples on that page use linear regression models as there starting point. -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help regarding Community Detection Algorithm in R (like Propagation, Walktrap)
Please do not re-post. Search on your own. Entering "community detection" at the rseek.org R search site brought up many hits, especially from the igraph package. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, May 4, 2016 at 12:01 PM, Swagatam Basu wrote: > kindly help me ..from where do i get sample code and details about > community detection... > > Thanks > Swagatam Basu > > > On Mon, May 2, 2016 at 2:25 PM, Swagatam Basu > wrote: > >> Hi >> >> I am very new to R studio and R language. I have installed the R studio in >> my machine. >> >> I need to do a community detection of a set of message. I have a Matrix >> for that. >> >> Is there any sample code /Package/ website is present which will help me >> to understand/do this community Detection (like Propagation, Walk trap >> Algorithm) in R-language by using R-studio. >> >> Please help. >> >> Please revert back in case of any discrepencies. >> >> Thanks >> S Basu >> >> > > [[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] Can't resolve dependency problems with package "sem"
Hello,
First time user on Ubuntu 14.4 with Ubuntus R Commander and
> $ R --version
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
The program icon of the commander executes
> sh -c 'R_DEFAULT_PACKAGES="$R_DEFAULT_PACKAGES Rcmdr" R "$@"'
On first run it started downloading, compiling and installing various
packages. One of them fails:
>
>> install.packages("sem",dependencies=TRUE)
> Installing package into ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0’
> (as ‘lib’ is unspecified)
> Warnung: dependencies ‘MBESS’, ‘arm’, ‘plyr’ are not available
> also installing the dependencies ‘scales’, ‘mi’, ‘DiagrammeR’
>
> versuche URL
> 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/scales_0.4.0.tar.gz'
> Content type 'application/x-gzip' length 57358 bytes (56 Kb)
> URL geöffnet
> ==
> downloaded 56 Kb
>
> versuche URL 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/mi_1.0.tar.gz'
> Content type 'application/x-gzip' length 793313 bytes (774 Kb)
> URL geöffnet
> ==
> downloaded 774 Kb
>
> versuche URL
> 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/DiagrammeR_0.8.2.tar.gz'
> Content type 'application/x-gzip' length 3532835 bytes (3.4 Mb)
> URL geöffnet
> ==
> downloaded 3.4 Mb
>
> versuche URL 'http://ftp5.gwdg.de/pub/misc/cran/src/contrib/sem_3.1-7.tar.gz'
> Content type 'application/x-gzip' length 154654 bytes (151 Kb)
> URL geöffnet
> ==
> downloaded 151 Kb
>
> ERROR: dependency ‘plyr’ is not available for package ‘scales’
> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/scales’
> ERROR: dependency ‘arm’ is not available for package ‘mi’
> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/mi’
> ERROR: dependency ‘scales’ is not available for package ‘DiagrammeR’
> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/DiagrammeR’
> ERROR: dependency ‘mi’ is not available for package ‘sem’
> * removing ‘/home/andreas/R/x86_64-pc-linux-gnu-library/3.0/sem’
>
> Die heruntergeladenen Quellpakete sind in
> ‘/tmp/RtmplEqHDo/downloaded_packages’
> Warnmeldungen:
> 1: In install.packages("sem", dependencies = TRUE) :
> Installation des Pakets ‘scales’ hatte Exit-Status ungleich 0
> 2: In install.packages("sem", dependencies = TRUE) :
> Installation des Pakets ‘mi’ hatte Exit-Status ungleich 0
> 3: In install.packages("sem", dependencies = TRUE) :
> Installation des Pakets ‘DiagrammeR’ hatte Exit-Status ungleich 0
> 4: In install.packages("sem", dependencies = TRUE) :
> Installation des Pakets ‘sem’ hatte Exit-Status ungleich 0
How can I resolve the dependencies?
Should I replace the Ubuntu version with something fresh?
Thanks in advance,
Andreas
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Re: [R] copula package error when gumbel parameter is close to bound.
Hello > Berwin A Turlach writes: > That you don't have the package Rmpfr installed? And it seems to be > needed for the higher dimension. On my machine it works: > Thanks for the lead, Best regards, Jeremie __ 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] Help regarding Community Detection Algorithm in R (like Propagation, Walktrap)
kindly help me ..from where do i get sample code and details about community detection... Thanks Swagatam Basu On Mon, May 2, 2016 at 2:25 PM, Swagatam Basu wrote: > Hi > > I am very new to R studio and R language. I have installed the R studio in > my machine. > > I need to do a community detection of a set of message. I have a Matrix > for that. > > Is there any sample code /Package/ website is present which will help me > to understand/do this community Detection (like Propagation, Walk trap > Algorithm) in R-language by using R-studio. > > Please help. > > Please revert back in case of any discrepencies. > > Thanks > S Basu > > [[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] greek characters in Figures
> On May 4, 2016, at 10:53 AM, Alaios wrote:
>
> > install.packages("latex2exp")
> Installiere Paket nach ‘/home/apa/R/x86_64-pc-linux-gnu-library/3.2’
> (da ‘lib’ nicht spezifiziert)
> Warnung: kann nicht auf den Index für das Repository
> https://cran.cnr.Berkeley.edu/src/contrib zugreifen:
> nicht unterstütztes URL Schema
You seem to have difficulties with your Internet connection/setup:
> Warnmeldung:
> Paket ‘latex2exp’ ist nicht verfügbar (for R version 3.2.4 Revised)
> > install.packages("latex2expr")
> Installiere Paket nach ‘/home/apa/R/x86_64-pc-linux-gnu-library/3.2’
> (da ‘lib’ nicht spezifiziert)
> Warnung: kann nicht auf den Index für das Repository
> https://cran.cnr.Berkeley.edu/src/contrib zugreifen:
> nicht unterstütztes URL Schema
> Warnmeldung:
> Paket ‘latex2expr’ ist nicht verfügbar (for R version 3.2.4 Revised)
I just installed from source from that repository into an R 3.2.5 library. (I
first needed to reinstall that version since I had moved to 3.3.0. Admittedly I
was doing this on a Mac but since the package does not require any C/Fortran
level compiling, my experience should mimic that of a Linux user using a source
package.
--
David
>
>
>
> On Monday, May 2, 2016 9:39 PM, David Winsemius
> wrote:
>
>
>
> > On May 2, 2016, at 10:32 AM, Alaios via R-help wrote:
> >
> > Dear all,I am trying to write in my Figure labels short equations that
> > contain greek characters
> >
> > For example: C(h) = sigma^2 * rho(h).
> >
> > I am googling it and there are many packages available but unfortunately
> > they do not look available for my 3.2.4 latex version
> >
> > install.packages("latex2expr")
>
> My efforts found a 'latex2exp' but no 'latex2expr'. Are you sure you are not
> missplelling the package name?
>
>
>
> > Installiere Paket nach ‘/home/apa/R/x86_64-pc-linux-gnu-library/3.2’(da
> > ‘lib’ nicht spezifiziert)Warnung: kann nicht auf den Index für das
> > Repository https://cran.cnr.Berkeley.edu/src/contrib zugreifen: nicht
> > unterstütztes URL SchemaWarnmeldung:Paket ‘latex2expr’ ist nicht verfügbar
> > (for R version 3.2.4 Revised)
> >
> > Any ideas what else I can try?I would like to thank you in advance for your
> > replyRegardsAlex
> > [[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.
>
>
> David Winsemius
> Alameda, CA, USA
>
>
>
David Winsemius
Alameda, CA, USA
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Re: [R] greek characters in Figures
> install.packages("latex2exp")Installiere Paket nach
> ‘/home/apa/R/x86_64-pc-linux-gnu-library/3.2’(da ‘lib’ nicht
> spezifiziert)Warnung: kann nicht auf den Index für das Repository
> https://cran.cnr.Berkeley.edu/src/contrib zugreifen: nicht unterstütztes URL
> SchemaWarnmeldung:Paket ‘latex2exp’ ist nicht verfügbar (for R version 3.2.4
> Revised) > install.packages("latex2expr")Installiere Paket nach
> ‘/home/apa/R/x86_64-pc-linux-gnu-library/3.2’(da ‘lib’ nicht
> spezifiziert)Warnung: kann nicht auf den Index für das Repository
> https://cran.cnr.Berkeley.edu/src/contrib zugreifen: nicht unterstütztes URL
> SchemaWarnmeldung:Paket ‘latex2expr’ ist nicht verfügbar (for R version 3.2.4
> Revised)
On Monday, May 2, 2016 9:39 PM, David Winsemius
wrote:
> On May 2, 2016, at 10:32 AM, Alaios via R-help wrote:
>
> Dear all,I am trying to write in my Figure labels short equations that
> contain greek characters
>
> For example: C(h) = sigma^2 * rho(h).
>
> I am googling it and there are many packages available but unfortunately they
> do not look available for my 3.2.4 latex version
>
> install.packages("latex2expr")
My efforts found a 'latex2exp' but no 'latex2expr'. Are you sure you are not
missplelling the package name?
> Installiere Paket nach ‘/home/apa/R/x86_64-pc-linux-gnu-library/3.2’(da ‘lib’
> nicht spezifiziert)Warnung: kann nicht auf den Index für das Repository
> https://cran.cnr.Berkeley.edu/src/contrib zugreifen: nicht unterstütztes URL
> SchemaWarnmeldung:Paket ‘latex2expr’ ist nicht verfügbar (for R version 3.2.4
> Revised)
>
> Any ideas what else I can try?I would like to thank you in advance for your
> replyRegardsAlex
> [[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.
David Winsemius
Alameda, CA, USA
[[alternative HTML version deleted]]
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Re: [R] Grep command
No matter how expert you are at writing regular expressions,
it is important to list which sorts of strings you want matched
and which you do not want matched. Saying you want to match
"age" but not "age2" leads to lots of possibilities. Saying how
you want to categorize each string in a vector of stirngs like
the following would narrow things down.
c("age", "ages ago", "age 60", "An aged man", "page", "Age", "age1",
"age2", "dark age", "the aGE")
>From such a list, make a good verbal description of the rule you
are thinking of and someone will be able to translate that into a regular
expression (or say that regular expressions cannot do the job).
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Wed, May 4, 2016 at 9:59 AM, David Winsemius
wrote:
>
> > On May 3, 2016, at 11:16 PM, Jeff Newmiller
> wrote:
> >
> > Yes, but the answer is likely to depend on the actual patterns of
> strings in your real data, so the sooner you go find a book or tutorial on
> regular expressions the better. This is decidedly not R specific and there
> are already lots of resources out there.
> >
> > Given the example you provide, the pattern "age$" should work. However,
> that is probably not sufficiently selective for a practical data set so
> start learning to fish (design regex patterns) yourself.
>
> @ Steven;
>
> As is almost always the case I agree with Jeff. I found that reading Rhelp
> and attempting to answer regex-questions was the best method to learn them.
> In particular I found the postings by Gabor Grothendieck very helpful in
> getting some degree of competence in this area. I see that his grep-related
> postings still exceed my grep postings and I assure you that his will be
> more sophisticated than my efforts. I recommend the MarkMail Rhelp mirror
> interface as very useful in "mining" Rhelp for knowledge:
>
> Gabor Grothendieck answers with either 'grep' pr 'regex' in their body:
>
>
> http://markmail.org/search/?q=list%3Aorg.r-project.r-help+list%3Agrep+list%3Aregex+from%3A%22Gabor+Grothendieck
>
> --
> Happy searching;
> David.
>
>
> > --
> > Sent from my phone. Please excuse my brevity.
> >
> > On May 3, 2016 10:45:42 PM PDT, Steven Yen wrote:
> >> Dear all
> >> In the grep command below, is there a way to identify only "age" and
> >> not "age2"? In other words, I like to greb "age" and "age2"
> >> separately, one at a time. Thanks.
> >>
> >> x<-c("abc","def","rst","xyz","age","age2")
> >> x
> >>
> >> [1] "abc" "def" "rst" "xyz" "age" "age2"
> >>
> >> grep("age2",x)
> >>
> >> [1] 6
> >>
> >> grep("age",x) # I need to grab "age" only, not "age2"
> >>
> >> [1] 5 6
> >>
>
> David Winsemius
> Alameda, CA, USA
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
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Re: [R] Antwort: Re: selecting columns from a data frame or data table by type, ie, numeric, integer
Hi Martin and list:
First let me thank you for thinking of me. It is probably apparent that my
programming experience is limited, and the vector aspect of R has taken some
getting used to. A very very long time ago I did some programming in Fortran
and for loops and if statements were ordinary, useful, and used frequently.
Now if I see a for loop and if statement together then it is flatly apparent
that I need to rework that code to take advantage of R's strengths using
vectoized functions on whatever object I am working on.
It has also become apparent that one should read manuals, experiment with some
code to firmly cement the knowledge, and build a solid foundation. My natural
inclination is the opposite. I am anxious to produce some code to solve a
problem or satisfy curiosity or R is not something one can learn and use
productively in a few weeks or months. It is powerful, subtle, and takes some
thinking. I started this trek into R with Jared Lander's book "R for
Everyone", progressed to Prof Norman Matloff's "The Art of R Programming"
(which was way beyond my comprehension at the beginning) and Hadley Wickham's
"ggplot2" book, and several courses with Data Camp and Couresra. One day I
will be at the point where I do know what I don't know about R and at that time
I will almost be competent with the language.
I have taken the work from Bill Dunlap and Giorgio Garziano and have applied it
to my little project and am just amazed that so little code can do so much. I
have also followed Bert Gunter's advice and taken that code and dissected it
item by item to comprehend what each element is doing.
The knowledge and help on this list is just amazing and I do appreciate the
efforts of all involved. I read the digest daily .
Carl Sutton CPA
On Wednesday, May 4, 2016 12:06 AM, Martin Maechler
wrote:
>
> on Wed, 4 May 2016 08:30:50 +0200 writes:
> Hi All,
> Hi Carl,
>
> I am not sure if this is useful to you, but I followed your conversation
> and thought of you when I read this:
>
> for (i in 1:ncol(dataset)) {
> if(class(dataset) == "character|numeric|factor|or whatsoever") {
> dataset[, i] <- as.factor(dataset[, i])
> }
> }
Ouch -- so many problems in such a short piece of R code !!!
> Source: Zumel, Nina / Mount, John: Practical Data Science with R, Manning
> Publications: Shelter Island, 2014, Chapter 2: Loading data into R, p. 25
Sorry, but after reading the above, I'd strongly recommend getting
better books about R...
{{maybe do not take those containing "data science" ;-)}}
Compared to the nice and efficient solution of Bill Dunlap,
the above is really bad-bad-bad in at least four ways :
0) They way you write it above, you cannot use it,
== "variant1|variant2|..."
is pseudocode and does not really work
1) Note the missing "[, i]" in the 2nd line: It should be
if(class(dataset[, i]) ...
2) A for loop changing each column at a time is really slow for
largish data sets
3) [last but not at all least!]
Please ... many of you readers, do learn:
Using checks such as
if ( class(x) == "numeric" )
are (almost) always wrong by design !!!
Instead you really should (almost) always use
if(inherits(x, "numeric"))
Why? Because classes in R (S3 or S4) can *extend* other classes.
Example: Many of you know that after fm <- glm(...)
class(fm) is c("glm", "lm") and so
> if(class(fm) == "lm")
+ "yes"
Warning message:
In if (class(fm) == "lm") "yes" :
the condition has length > 1 and only the first element will be used
Similarly, in your case
y <- 1:10
class(y) <- c("myNumber", "numeric")
when that 'y' is a column in your data frame,
the test for if(class(dataset[,i]) == "numeric") will *not*
work but actually produce the above warning.
However, one could als have had
Num <- setClass("Num", contains="numeric")
N <- Num(1:10)
> Num <- setClass("Num", contains="numeric")
> N <- Num(1:10)
> N
An object of class "Num"
[1] 1 2 3 4 5 6 7 8 9 10
> if(class(N) == "numeric") "yes" else "no"
[1] "no"
>
I hope that many of the readers --- including *MANY* authors of
R packages !! --- have understood the above and will fix their R
code -- and even more their books where applicable !!
Martin Maechler,
ETH Zurich & R Core Team
>
> This way you can select variables of a certain class only and do
> transformations. I found that this approach is not applicable if used with
> statistical functions like head(). Transformations worked fine for me.
>
> I found reading the above given source worthwile.
>
> Kind regards
>
> Georg
>
> PS: I am not related to the above given authors. I am just a reader
> reporting on - at least to me - a valuable ressource.
>
>
>
> Von: Carl Sutton via R-help
> An: William Dunlap ,
> Kopie: "r-help@r-project.org"
> Datum: 29.04.2016 22:08
> Betreff: Re: [R] selecting
Re: [R] Grep command
> On May 3, 2016, at 11:16 PM, Jeff Newmiller wrote:
>
> Yes, but the answer is likely to depend on the actual patterns of strings in
> your real data, so the sooner you go find a book or tutorial on regular
> expressions the better. This is decidedly not R specific and there are
> already lots of resources out there.
>
> Given the example you provide, the pattern "age$" should work. However, that
> is probably not sufficiently selective for a practical data set so start
> learning to fish (design regex patterns) yourself.
@ Steven;
As is almost always the case I agree with Jeff. I found that reading Rhelp and
attempting to answer regex-questions was the best method to learn them. In
particular I found the postings by Gabor Grothendieck very helpful in getting
some degree of competence in this area. I see that his grep-related postings
still exceed my grep postings and I assure you that his will be more
sophisticated than my efforts. I recommend the MarkMail Rhelp mirror interface
as very useful in "mining" Rhelp for knowledge:
Gabor Grothendieck answers with either 'grep' pr 'regex' in their body:
http://markmail.org/search/?q=list%3Aorg.r-project.r-help+list%3Agrep+list%3Aregex+from%3A%22Gabor+Grothendieck
--
Happy searching;
David.
> --
> Sent from my phone. Please excuse my brevity.
>
> On May 3, 2016 10:45:42 PM PDT, Steven Yen wrote:
>> Dear all
>> In the grep command below, is there a way to identify only "age" and
>> not "age2"? In other words, I like to greb "age" and "age2"
>> separately, one at a time. Thanks.
>>
>> x<-c("abc","def","rst","xyz","age","age2")
>> x
>>
>> [1] "abc" "def" "rst" "xyz" "age" "age2"
>>
>> grep("age2",x)
>>
>> [1] 6
>>
>> grep("age",x) # I need to grab "age" only, not "age2"
>>
>> [1] 5 6
>>
David Winsemius
Alameda, CA, USA
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[R] Robust MARS regression with R ?
Dear R-helpers, I would like to know if it is possible using R (earth packages or another one) to realize robust MARS regression RMARS or RCMARS (C mean "conic"). Some authors have done it using MOSEK combined with Salford-MARS and special MATLAB programs. Best Regards, Sacha __ 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] Grep command
You asked this question yesterday, and received responses on this same
response. Is there a reason this is reposted?
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Steven Yen
Sent: Wednesday, May 04, 2016 1:46 AM
To: r-help
Subject: [R] Grep command
Dear all
In the grep command below, is there a way to identify only "age" and not
"age2"? In other words, I like to greb "age" and "age2"
separately, one at a time. Thanks.
x<-c("abc","def","rst","xyz","age","age2")
x
[1] "abc" "def" "rst" "xyz" "age" "age2"
grep("age2",x)
[1] 6
grep("age",x) # I need to grab "age" only, not "age2"
[1] 5 6
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[R] how to compute Bonferroni, Tukey's, Sheffe 95%-condence intervals for coefficients B1, B2, B3 in linear regression?
Dear experts, I have a problem in compute Bonferroni,Tukey's,Sheffe 95%-condence intervals for coefficients B1,B2,B3 in linear regression using R? how can i do it? I only know how to compute these three cofindence intervals in multicomparsion by using multcomp package, and i am search a lot for how to comupte the three CIs for linear regression coefficients but without any useful information, so, plz help me ~ __ 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] copula package error when gumbel parameter is close to bound.
Hello,
In a situation where the dimension is high and the parameter is close to
the bound computing the density of the gumbel copula throws the following
error.
library(copula)
dCopula(rep(0.5,127),gumbelCopula(1.19,127),log=TRUE)
Loading required namespace: Rmpfr
Failed with error: ‘there is no package called ‘Rmpfr’’
Error: requireNamespace("Rmpfr") is not TRUE
It does not seem to be a ploblem with lower dimension though
dCopula(rep(0.5,17),gumbelCopula(1.19,17),log=TRUE)
[1] 2.402906
I'm I missing something about the computation?
Best regards
--
Jeremie Juste
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] Changing transformations in mi package
Dear all, I am an R beginner and new to the list. In preparation for using mi to impute missing values I am setting up the missing data frame and would like to specify the transformation types for some of my variables, as I will be using these transformations in my analysis models. According to the documentation the available options are "standardize" (the default), "identity", "log", "logshift" and "sqrt". I can successfully change the transformation types to "log" and "logshift", but when I attempt to change to "sqrt", this changes the type to "log" instead. I'd appreciate your help, please. Below are details of my system and some code which replicates the issue. > sessionInfo() R version 3.2.5 (2016-04-14) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats4stats graphics grDevices utils datasets methods base other attached packages: [1] lmerTest_2.0-30 truncnorm_1.0-7 mi_1.0 lme4_1.1-12 Matrix_1.2-4 [6] pls_2.5-0 loaded via a namespace (and not attached): [1] Rcpp_0.12.4 Formula_1.2-1 cluster_2.0.3 splines_3.2.5 [5] MASS_7.3-45 munsell_0.4.3 colorspace_1.2-6arm_1.8-6 [9] lattice_0.20-33 minqa_1.2.4 plyr_1.8.3 nnet_7.3-12 [13] grid_3.2.5 nlme_3.1-126gtable_0.2.0 latticeExtra_0.6-28 [17] coda_0.18-1 abind_1.4-3 survival_2.38-3 gridExtra_2.2.1 [21] RColorBrewer_1.1-2 nloptr_1.0.4ggplot2_2.1.0 acepack_1.3-3.3 [25] rpart_4.1-10scales_0.4.0Hmisc_3.17-3foreign_0.8-66 data <- data.frame(a=c(NA,2.1,3.3,4.5,5.9,6.2),b=c(2.2,NA,6.1,8.3,10.2,12.13),c=c(4.2,7.9,NA,16.1,19.9,23)) data a bc 1 NA 2.20 4.2 2 2.1NA 7.9 3 3.3 6.10 NA 4 4.5 8.30 16.1 5 5.9 10.20 19.9 6 6.2 12.13 23.0 data.missingdf <- missing_data.frame(data) show(data.missingdf) Object of class missing_data.frame with 6 observations on 3 variables There are 4 missing data patterns Append '@patterns' to this missing_data.frame to access the corresponding pattern for every observation or perhaps use table() type missing method model a continuous 1ppd linear b continuous 1ppd linear c continuous 1ppd linear family link transformation a gaussian identitystandardize b gaussian identitystandardize c gaussian identitystandardize #Let's say I'd like to change transformation for a, b and c to "log", "logshift" and "sqrt" respectively data.missingdf <- change(data.missingdf, y="a", what="transformation", to="logshift") data.missingdf <- change(data.missingdf, y="b", what="transformation", to="log") data.missingdf <- change(data.missingdf, y="c", what="transformation", to="sqrt") show(data.missingdf) Object of class missing_data.frame with 6 observations on 3 variables There are 4 missing data patterns Append '@patterns' to this missing_data.frame to access the corresponding pattern for every observation or perhaps use table() type missing method model a continuous 1ppd linear b continuous 1ppd linear c continuous 1ppd linear family link transformation a gaussian identity logshift b gaussian identitylog c gaussian identitylog #Transformation has been successfully changed for a and b, but for c has been changed to "log" instead of "sqrt" Thanks in advance for your assistance, Liz Hensor Biostatistician Leeds Institute of Rheumatic and Musculoskeletal Medicine & NIHR Leeds Musculoskeletal Biomedical Research Unit __ 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] undefined columns selected!
First, type names(msub) and then type cn and compare the output. Probably, you will find a name in cn that is not among the names of msub. To maybe make it easier to see the missing column(s), you can type setdiff(cn, names(msub)) The expression msub[,cn] is intended to select columns from msub. That error message means that you are trying to select one or more columns that are not there. Or perhaps Bert Gunter is correct, and it should be msub[,'cn'] but I believe that if that were the case the error message would likely be different. Without more information we can't be sure. -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 5/4/16, 6:05 AM, "R-help on behalf of ch.elahe via R-help" wrote: > >Hi all, >I know it seems simple but I am trying to copy a code and I don't know >what is the problem with this command! > >msubsub=msub[,cn] > >the error I get is : error in '[.data.frame '(msub, ,cn) : undefined >columns selected > >Thanks for any help, >Elahe > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://secure-web.cisco.com/17LbfsJ6l1TxAGGDaZPJaqSjzCIWn5E9CwPSSMrKL6TmF >nzxq4NMk2_I5ZoRND9U7-DVdKRI4gQq-ksFm42c_Y4YLWER6RjmX7KA43TlJE090H6BW03h2ch >R-AjcGVBd7OkbsupK4ILVvkOhZEs4oearHg3fxw5eGd1HheF2ZmV23Gk8iUz73qq3xABMYDqRs >MimloONz77mr0nVciORpjobMGuDvIH69DttdwbXnkLyVgrlscdiOjTp_LjcdJMSFKqMjepMDxH >iQGQfThQ4q3l5ZjSUts8soTR8Bg5R722f-4WJkevdYYreIEU3i0aH64_AdN7Hhn9lHL1MUOm0K >Mg0IV4twClhcRjs7Bf5Qf9M/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2F >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] undefined columns selected!
The the column name must be quoted in the index: msubsub=msub[,"cn"] Please go through a basic R tutorial or two if you want to learn to use R. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, May 4, 2016 at 6:05 AM, ch.elahe via R-help wrote: > > Hi all, > I know it seems simple but I am trying to copy a code and I don't know what > is the problem with this command! > > msubsub=msub[,cn] > > the error I get is : error in '[.data.frame '(msub, ,cn) : undefined columns > selected > > Thanks for any help, > Elahe > > __ > 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] undefined columns selected!
On Wed, May 4, 2016 at 8:05 AM, ch.elahe via R-help wrote: > > Hi all, > I know it seems simple but I am trying to copy a code and I don't know > what is the problem with this command! > > msubsub=msub[,cn] > > the error I get is : error in '[.data.frame '(msub, ,cn) : undefined > columns selected > First - very important - please change from HTML posting to plain text. This forum doesn't handle HTML well and its use very often results in unreadable and thus unusable messages. TLI (Too Little Information). I would probably help if you would post the information from things like: dput(head(msub)) dput(head(cn)) Most want "dput(msub)" and "dput(cn)", but I use the "head()" to subset that to examples which are usually easier to post. It depends on the problem and the size of the data involved. Oh, please don't just cut'n'paste the output from simply listing "msub" or "cn", that produces output which cannot be cut and pasted easily into an R session. Thanks. > > Thanks for any help, > Elahe > > -- The unfacts, did we have them, are too imprecisely few to warrant our certitude. Maranatha! <>< John McKown [[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] undefined columns selected!
Hi all, I know it seems simple but I am trying to copy a code and I don't know what is the problem with this command! msubsub=msub[,cn] the error I get is : error in '[.data.frame '(msub, ,cn) : undefined columns selected Thanks for any help, Elahe __ 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] Install on Xenial
Pick different mirror. -- Sent from my phone. Please excuse my brevity. On May 4, 2016 5:22:43 AM PDT, Erich Neuwirth wrote: >I am trying to install R-3.3.0 on Xenial. >I followed the instructions on the corresponding CRAN page, and I added >the GPG key. >But after adding >deb https://cran.at.r-project.org//bin/linux/ubuntu xenial/ >to /etc/apt/sources.list >and >sudo apt-get update >I get the following error: > >Err:7 https://cran.at.r-project.org//bin/linux/ubuntu xenial/ Packages >SSL: certificate subject name (*.r-project.org) does not match target >host name 'cran.at.r-project.org’ > >What do I need to do to get rid of this error > > > > > > >__ >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.
[R] Install on Xenial
I am trying to install R-3.3.0 on Xenial. I followed the instructions on the corresponding CRAN page, and I added the GPG key. But after adding deb https://cran.at.r-project.org//bin/linux/ubuntu xenial/ to /etc/apt/sources.list and sudo apt-get update I get the following error: Err:7 https://cran.at.r-project.org//bin/linux/ubuntu xenial/ Packages SSL: certificate subject name (*.r-project.org) does not match target host name 'cran.at.r-project.org’ What do I need to do to get rid of this error signature.asc Description: Message signed with OpenPGP using GPGMail __ 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] expression input to a function
On 04/05/2016 7:11 AM, Naresh Gurbuxani wrote:
I am trying to write a function, which can be made very general if one of the
inputs can be an expression. How can this be done?
For example, to find root of a function, I would like to say
my.func <- function(x) {x^3 + 2 * (x^2) - 7}
x.left <- 0
x.right <- 2
n.iterations <- 0
find.root <- function(my.func, x.left, x.right) {
# code here
return(c(x.mid, n.iterations))
}
The above method clearly does not work.
You are taking the right approach. You can pass functions as arguments
to other functions; they are "first class objects". For example:
evaluate <- function(f, x) f(x)
evaluate(my.func, 3)
would give the same result as my.func(3).
For your find.root function, just write the search in find.root using
the name of the argument (which for didactic purposes I'd recommend be
different from the actual function name, but it'll be fine in practice).
It is also possible to pass expressions that aren't in functions, but it
gets tricky, and you shouldn't do that in your first attempt.
Duncan Murdoch
__
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Re: [R] R column assignment fails for lists
Dear Jim and David,
Thank you very much for your reply. I guess my question is whether it is
legal to store vectors in the elements of a data.frame. These are useful
for storing things like neighbors of a graph vertex, orthologs of a gene
etc. I have been using data frames of this sort and they are very useful,
so I am hoping this is a feature, rather than a bug. The weird code in my
email to form a was just one quick way of making such an object for a toy
example. These sort of data frames were doing fine for a number of analysis
pipelines until I used a function on them that had code of the sort
df[, j] <- sapply(df[, j], fun)
The interesting thing is that while
a[,3] <- a[,3] changes the object and gives the warning
a$c <- a$c works "correctly". leaving a to what it was and doesn't give a
warning.
If elements of a data frame are supposed to be able to store vectors, then
shouldn't
a[,3] <- a[,3] work?
Best regards,
yasir
On Tue, May 3, 2016 at 9:48 PM, David Winsemius
wrote:
>
> > On May 3, 2016, at 4:13 PM, Yasir Suhail wrote:
> >
> > Dear R developers and users,
> >
> > Consider the object :
> >
> >> a <- data.frame(a=c(1,2), b=c(2,3), c=c("a,b","c,d"), stringsAsFactors
> = F)
> >> a$c <- strsplit(a$c, ",")
>
> You are the one who should "consider the object". Look at what
> strsplit(a$c, ",") returns and then perhaps re-consider trying to assign it
> to a single column.
>
> >
> > Re-assignment works fine for columns 1 and 2, but fails for column 3. If
> a
> > is a valid object, the assignment should work.
> >
> >> a[,1] <- a[,1]
> >> a[,2] <- a[,2]
> >> a[,3] <- a[,3]
> > Warning message:
> > In `[<-.data.frame`(`*tmp*`, , 3, value = list(c("a", "b"), c("c", :
> > provided 2 variables to replace 1 variables
> >
> > [[alternative HTML version deleted]]
>
> And please reconsider also the format of your postings.
>
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
>
[[alternative HTML version deleted]]
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Re: [R] Grep command
> x <- c("abc","def","rst","xyz","age","age2")
> grep("^age$", x)
[1] 5
> grep("^age2$", x)
[1] 6
>
>
-Oprindelig meddelelse-
Fra: R-help [mailto:r-help-boun...@r-project.org] På vegne af Steven Yen
Sendt: 4. maj 2016 07:46
Til: r-help
Emne: [R] Grep command
Dear all
In the grep command below, is there a way to identify only "age" and not
"age2"? In other words, I like to greb "age" and "age2"
separately, one at a time. Thanks.
x<-c("abc","def","rst","xyz","age","age2")
x
[1] "abc" "def" "rst" "xyz" "age" "age2"
grep("age2",x)
[1] 6
grep("age",x) # I need to grab "age" only, not "age2"
[1] 5 6
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Antwort: Antwort: Re: selecting columns from a data frame or data table by type, ie, numeric, integer
Hi
> -Original Message-
> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
> g.maub...@weinwolf.de
> Sent: Wednesday, May 4, 2016 10:06 AM
> To: Martin Maechler
> Cc: r-help@r-project.org
> Subject: [R] Antwort: Antwort: Re: selecting columns from a data frame or
> data table by type, ie, numeric, integer
>
> Hi Martin,
>
> many thanks for your answer and your broad explanation.
>
> I am a newbie to "R" and got help on this list and thought I could give
> something back what looked OK to me.
>
> regarding 0)
> You're right, it's pseudo code. I assumed that anybody on the list would be
> able to adapt the code to their needs so that it worked. Next time I will post
> runnable code.
>
> regarding 1)
> Your right: "[, i]" is missing. My fault. Sorry.
>
> regarding 3)
> I got your point and will do better in the future.
>
> One question: What books do you recommend to read to get to know "R"
> better?
Freely available from CRAN
These I can recommend as I went through them
“A Guide for the Unwilling S User” by Patrick Burns
“Using R for Data Analysis and Graphics - Introduction, Examples and
Commentary” by John Maindonald (PDF, data sets and scripts are available at
JM's homepage).
“Practical Regression and Anova using R” by Julian Faraway (PDF, data sets and
scripts are available at the book homepage).
There are also some German books but I do not have experience with them.
Books from bookstores
Modern Applied Statistics with S. Fourth Edition, by W. N. Venables and B. D.
Ripley
Introductory Statistics with R, Authors: Dalgaard, Peter
Cheers
Petr
>
> Kind regards
>
> Georg
>
>
>
>
> Von:Martin Maechler
> An: ,
> Kopie: Carl Sutton , "r-help@r-project.org"
>
> Datum: 04.05.2016 09:05
> Betreff:[R] Antwort: Re: selecting columns from a data frame or
> data table by type, ie, numeric, integer
>
>
>
> >
> > on Wed, 4 May 2016 08:30:50 +0200 writes:
>
> > Hi All,
> > Hi Carl,
> >
> > I am not sure if this is useful to you, but I followed your
> > conversation
>
> > and thought of you when I read this:
> >
> > for (i in 1:ncol(dataset)) {
> > if(class(dataset) == "character|numeric|factor|or whatsoever") {
> > dataset[, i] <- as.factor(dataset[, i])
> > }
> > }
>
> Ouch -- so many problems in such a short piece of R code !!!
>
> > Source: Zumel, Nina / Mount, John: Practical Data Science with R,
> Manning
> > Publications: Shelter Island, 2014, Chapter 2: Loading data into R, p.
> 25
>
> Sorry, but after reading the above, I'd strongly recommend getting better
> books about R...
>{{maybe do not take those containing "data science" ;-)}}
>
> Compared to the nice and efficient solution of Bill Dunlap, the above is
> really
> bad-bad-bad in at least four ways :
>
> 0) They way you write it above, you cannot use it,
> == "variant1|variant2|..."
>is pseudocode and does not really work
>
> 1) Note the missing "[, i]" in the 2nd line: It should be
> if(class(dataset[, i]) ...
>
> 2) A for loop changing each column at a time is really slow for
>largish data sets
>
> 3) [last but not at all least!]
>Please ... many of you readers, do learn:
>
> Using checks such as
>if ( class(x) == "numeric" )
> are (almost) always wrong by design !!!
>
> Instead you really should (almost) always use
>
> if(inherits(x, "numeric"))
>
> Why? Because classes in R (S3 or S4) can *extend* other classes.
> Example: Many of you know that after fm <- glm(...)
> class(fm) is c("glm", "lm") and so
>
> > if(class(fm) == "lm")
> + "yes"
> Warning message:
> In if (class(fm) == "lm") "yes" :
> the condition has length > 1 and only the first element will be used
>
> Similarly, in your case
>
> y <- 1:10
> class(y) <- c("myNumber", "numeric")
>
> when that 'y' is a column in your data frame, the test for
> if(class(dataset[,i])
> == "numeric") will *not* work but actually produce the above warning.
>
> However, one could als have had
>
> Num <- setClass("Num", contains="numeric") N <- Num(1:10)
>
> > Num <- setClass("Num", contains="numeric")
> > N <- Num(1:10)
> > N
> An object of class "Num"
> [1] 1 2 3 4 5 6 7 8 9 10
> > if(class(N) == "numeric") "yes" else "no"
> [1] "no"
> >
>
> I hope that many of the readers --- including *MANY* authors of R packages
> !! --- have understood the above and will fix their R code -- and even more
> their books where applicable !!
>
> Martin Maechler,
> ETH Zurich & R Core Team
>
> >
>
>
> > This way you can select variables of a certain class only and do
> > transformations. I found that this approach is not applicable if used
> with
> > statistical functions like head(). Transformations worked fine for me.
> >
> > I found reading the above given source worthwile.
> >
> > Kind regards
> >
> > Georg
> >
> > PS: I am not related to the above given authors. I am just a reader
> > reporting on -
[R] Antwort: Antwort: Re: selecting columns from a data frame or data table by type, ie, numeric, integer
Hi Martin,
many thanks for your answer and your broad explanation.
I am a newbie to "R" and got help on this list and thought I could give
something back what looked OK to me.
regarding 0)
You're right, it's pseudo code. I assumed that anybody on the list would
be able to adapt the code to their needs so that it worked. Next time I
will post runnable code.
regarding 1)
Your right: "[, i]" is missing. My fault. Sorry.
regarding 3)
I got your point and will do better in the future.
One question: What books do you recommend to read to get to know "R"
better?
Kind regards
Georg
Von:Martin Maechler
An: ,
Kopie: Carl Sutton , "r-help@r-project.org"
Datum: 04.05.2016 09:05
Betreff:[R] Antwort: Re: selecting columns from a data frame or
data table by type, ie, numeric, integer
>
> on Wed, 4 May 2016 08:30:50 +0200 writes:
> Hi All,
> Hi Carl,
>
> I am not sure if this is useful to you, but I followed your conversation
> and thought of you when I read this:
>
> for (i in 1:ncol(dataset)) {
> if(class(dataset) == "character|numeric|factor|or whatsoever") {
> dataset[, i] <- as.factor(dataset[, i])
> }
> }
Ouch -- so many problems in such a short piece of R code !!!
> Source: Zumel, Nina / Mount, John: Practical Data Science with R,
Manning
> Publications: Shelter Island, 2014, Chapter 2: Loading data into R, p.
25
Sorry, but after reading the above, I'd strongly recommend getting
better books about R...
{{maybe do not take those containing "data science" ;-)}}
Compared to the nice and efficient solution of Bill Dunlap,
the above is really bad-bad-bad in at least four ways :
0) They way you write it above, you cannot use it,
== "variant1|variant2|..."
is pseudocode and does not really work
1) Note the missing "[, i]" in the 2nd line: It should be
if(class(dataset[, i]) ...
2) A for loop changing each column at a time is really slow for
largish data sets
3) [last but not at all least!]
Please ... many of you readers, do learn:
Using checks such as
if ( class(x) == "numeric" )
are (almost) always wrong by design !!!
Instead you really should (almost) always use
if(inherits(x, "numeric"))
Why? Because classes in R (S3 or S4) can *extend* other classes.
Example: Many of you know that after fm <- glm(...)
class(fm) is c("glm", "lm") and so
> if(class(fm) == "lm")
+ "yes"
Warning message:
In if (class(fm) == "lm") "yes" :
the condition has length > 1 and only the first element will be used
Similarly, in your case
y <- 1:10
class(y) <- c("myNumber", "numeric")
when that 'y' is a column in your data frame,
the test for if(class(dataset[,i]) == "numeric") will *not*
work but actually produce the above warning.
However, one could als have had
Num <- setClass("Num", contains="numeric")
N <- Num(1:10)
> Num <- setClass("Num", contains="numeric")
> N <- Num(1:10)
> N
An object of class "Num"
[1] 1 2 3 4 5 6 7 8 9 10
> if(class(N) == "numeric") "yes" else "no"
[1] "no"
>
I hope that many of the readers --- including *MANY* authors of
R packages !! --- have understood the above and will fix their R
code -- and even more their books where applicable !!
Martin Maechler,
ETH Zurich & R Core Team
>
> This way you can select variables of a certain class only and do
> transformations. I found that this approach is not applicable if used
with
> statistical functions like head(). Transformations worked fine for me.
>
> I found reading the above given source worthwile.
>
> Kind regards
>
> Georg
>
> PS: I am not related to the above given authors. I am just a reader
> reporting on - at least to me - a valuable ressource.
>
>
>
> Von:Carl Sutton via R-help
> An: William Dunlap ,
> Kopie: "r-help@r-project.org"
> Datum: 29.04.2016 22:08
> Betreff:Re: [R] selecting columns from a data frame or data
table
> by type, ie, numeric, integer
> Gesendet von: "R-help"
>
>
>
> Thank you Bill Dunlap. So simple I never tried that approach. Tried
> dozens of others though, read manuals till I was getting headaches, and
of
> course the answer was simple when one is competent. Learning, its a
> struggle, but slowly getting there.
> Thanks again
> Carl Sutton CPA
>
>
> On Friday, April 29, 2016 10:50 AM, William Dunlap
> wrote:
>
>
>
> > dt1[ vapply(dt1, FUN=is.numeric, FUN.VALUE=NA) ]a c1 1 1.12 2
> 1.0...10 10 0.2
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
> On Fri, Apr 29, 2016 at 9:19 AM, Carl Sutton via R-help
> wrote:
>
> Good morning RGuru's
> I have a data frame of 575 columns. I want to extract only those
columns
> that are numeric(double) or integer to do some machine learning with. I
> have searched the web for a couple of days (off and on) and have not
found
> anything that shows how to do this. Lots of ways
Re: [R] Grep command
Yes, but the answer is likely to depend on the actual patterns of strings in
your real data, so the sooner you go find a book or tutorial on regular
expressions the better. This is decidedly not R specific and there are already
lots of resources out there.
Given the example you provide, the pattern "age$" should work. However, that
is probably not sufficiently selective for a practical data set so start
learning to fish (design regex patterns) yourself.
--
Sent from my phone. Please excuse my brevity.
On May 3, 2016 10:45:42 PM PDT, Steven Yen wrote:
>Dear all
>In the grep command below, is there a way to identify only "age" and
>not "age2"? In other words, I like to greb "age" and "age2"
>separately, one at a time. Thanks.
>
>x<-c("abc","def","rst","xyz","age","age2")
>x
>
>[1] "abc" "def" "rst" "xyz" "age" "age2"
>
>grep("age2",x)
>
>[1] 6
>
>grep("age",x) # I need to grab "age" only, not "age2"
>
>[1] 5 6
>
>__
>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] Custom data structures inside of a hash function
It is impolite to put such a minor code fragment on a transient website. Also,
this is a plain text mailing list... html usually gets stripped, damaging any
advantage the HTML might have had and creating confusion for people reading
your message, so please learn how to send plain text.
You wrote:
--
keys <- c('AB', 'AC')
values <- c(c('hello', 0), c('world', 0))
names(values) <- keys
cat(length(values))
-
You seem to think this is Perl. The c function concatenates... it does not make
tuples, it makes vectors, which must have all elements of the same type (unless
the vector is of list type). And while vectors can have named elements, those
names are not hashes. And since this is R, not Perl, you should use data
structures that can be operated on in vectorized fashion, or you will have
horrible performance.
So, the unhelpful but literal answer to your question is
-
values <- list( list( 'hello', 0 ), list( 'world', 0 ))
names( values ) <- c( "AB", "AC" )
values[[ "AC" ]]
values[[ "AC" ]][[ 2 ]] <- 1
-
but if you want a scalable solution then you need something like
-
values <- data.frame( string=c( "hello", "world" ), num=c( 0, 0 ) )
rownames( values ) <- c( "AB", "AC" )
values[ "AC", ]
values[ "AC", 2 ] <- 1
though often as not the names get stuffed into another column in the data frame
and rows are simply accessed using integer or logical vector indexing.
Note that data frames are column oriented. This is fundamental to the way R
works... embrace it.
If you absolutely must have a hash then you need environments, but they are
tricky animals and are remarkably (if you come from a Perl background) rarely
needed.
A long time ago I came to R with similar thoughts of writing Perl in R... but
eventually I read the actual words in the Introduction to R document instead of
trying to reframe them in the Perl mind set and only then did I start to make
progress with R.
--
Sent from my phone. Please excuse my brevity.
On May 3, 2016 6:55:09 PM PDT, "Yves S. Garret"
wrote:
>Hello,
>
>I have the following code:
>http://pastebin.ca/3590201
>
>What I'm trying to do is to create a hash map where the key is two
>characters and
>that maps to a structure of some information. The problem with the
>above
>example
>is that the first two keys match to the first instance of c('hello',
>0),
>but the second is
>completely ignored. Ideally, I'd like to retrieve the structure with
>my
>values based on
>the key at hand and modify it as I see fit.
>
>How can I achieve this?
>
> [[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.
[R] Antwort: Re: selecting columns from a data frame or data table by type, ie, numeric, integer
>
> on Wed, 4 May 2016 08:30:50 +0200 writes:
> Hi All,
> Hi Carl,
>
> I am not sure if this is useful to you, but I followed your conversation
> and thought of you when I read this:
>
> for (i in 1:ncol(dataset)) {
> if(class(dataset) == "character|numeric|factor|or whatsoever") {
> dataset[, i] <- as.factor(dataset[, i])
> }
> }
Ouch -- so many problems in such a short piece of R code !!!
> Source: Zumel, Nina / Mount, John: Practical Data Science with R, Manning
> Publications: Shelter Island, 2014, Chapter 2: Loading data into R, p. 25
Sorry, but after reading the above, I'd strongly recommend getting
better books about R...
{{maybe do not take those containing "data science" ;-)}}
Compared to the nice and efficient solution of Bill Dunlap,
the above is really bad-bad-bad in at least four ways :
0) They way you write it above, you cannot use it,
== "variant1|variant2|..."
is pseudocode and does not really work
1) Note the missing "[, i]" in the 2nd line: It should be
if(class(dataset[, i]) ...
2) A for loop changing each column at a time is really slow for
largish data sets
3) [last but not at all least!]
Please ... many of you readers, do learn:
Using checks such as
if ( class(x) == "numeric" )
are (almost) always wrong by design !!!
Instead you really should (almost) always use
if(inherits(x, "numeric"))
Why? Because classes in R (S3 or S4) can *extend* other classes.
Example: Many of you know that after fm <- glm(...)
class(fm) is c("glm", "lm") and so
> if(class(fm) == "lm")
+ "yes"
Warning message:
In if (class(fm) == "lm") "yes" :
the condition has length > 1 and only the first element will be used
Similarly, in your case
y <- 1:10
class(y) <- c("myNumber", "numeric")
when that 'y' is a column in your data frame,
the test for if(class(dataset[,i]) == "numeric") will *not*
work but actually produce the above warning.
However, one could als have had
Num <- setClass("Num", contains="numeric")
N <- Num(1:10)
> Num <- setClass("Num", contains="numeric")
> N <- Num(1:10)
> N
An object of class "Num"
[1] 1 2 3 4 5 6 7 8 9 10
> if(class(N) == "numeric") "yes" else "no"
[1] "no"
>
I hope that many of the readers --- including *MANY* authors of
R packages !! --- have understood the above and will fix their R
code -- and even more their books where applicable !!
Martin Maechler,
ETH Zurich & R Core Team
>
> This way you can select variables of a certain class only and do
> transformations. I found that this approach is not applicable if used with
> statistical functions like head(). Transformations worked fine for me.
>
> I found reading the above given source worthwile.
>
> Kind regards
>
> Georg
>
> PS: I am not related to the above given authors. I am just a reader
> reporting on - at least to me - a valuable ressource.
>
>
>
> Von:Carl Sutton via R-help
> An: William Dunlap ,
> Kopie: "r-help@r-project.org"
> Datum: 29.04.2016 22:08
> Betreff:Re: [R] selecting columns from a data frame or data table
> by type, ie, numeric, integer
> Gesendet von: "R-help"
>
>
>
> Thank you Bill Dunlap. So simple I never tried that approach. Tried
> dozens of others though, read manuals till I was getting headaches, and of
> course the answer was simple when one is competent. Learning, its a
> struggle, but slowly getting there.
> Thanks again
> Carl Sutton CPA
>
>
> On Friday, April 29, 2016 10:50 AM, William Dunlap
> wrote:
>
>
>
> > dt1[ vapply(dt1, FUN=is.numeric, FUN.VALUE=NA) ]a c1 1 1.12 2
> 1.0...10 10 0.2
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
> On Fri, Apr 29, 2016 at 9:19 AM, Carl Sutton via R-help
> wrote:
>
> Good morning RGuru's
> I have a data frame of 575 columns. I want to extract only those columns
> that are numeric(double) or integer to do some machine learning with. I
> have searched the web for a couple of days (off and on) and have not found
> anything that shows how to do this. Lots of ways to extract rows, but
> not columns. I have attempted to use "(x == y)" indices extraction method
> but that threw error that == was for atomic vectors and lists, and I was
> doing this on a data frame.
>
> My test code is below
>
> # a technique to get column classes
> library(data.table)
> a <- 1:10
> b <- c("a","b","c","d","e","f","g","h","i","j")
> c <- seq(1.1, .2, length = 10)
> dt1 <- data.table(a,b,c)
> str(dt1)
> col.classes <- sapply(dt1, class)
> head(col.classes)
> dt2 <- subset(dt1, typeof = "double" | "numeric")
> str(dt2)
> dt2 # not subset
> dt2 <- dt1[, list(typeof = "double")]
> str(dt2)
> class_data <- dt1[,sapply(dt1,is.integer) | sapply(dt1, is.numeric)]
> class_data
> sum(class_data)
> typeof(class_data)
> names(class_data)
> str(class_data)
> Any help is appreciated
> Carl Sutton CPA
Re: [R] Reading multiple tables from one .txt doc
Mark Fingerle writes: > Dear all, > I have a .txt file which contains multiple tables and I would like to > read these tables separately in order to create graphs for each one. > The tables are separated by a blank line, have a variable number of > lines, fixed nr. Of rows, have a header and a comment above the header > (#) which contains a specific word that identifies each table. (see > example below). It would be possible to change the layout of the .txt > data a bit (Add a word, remove comment etc..) > I would be extremely grateful if anyone could help me with this daunting task > :-) > Example: > # CoordA > ImageX Y Z MeasuredMove MachineMove > vf_36.png-114.345475 -89.043448 556.073402 > 0 0 > vf_37.png-111.118715 -89.978534 606.040764 > 50.080172 50.00 > vf_38.png-107.911209 -90.901958 656.025557 > 50.096111 50.00 > vf_39.png-104.693931 -91.814392 705.982620 > 50.068868 50.00 > vf_40.png-101.459549 -92.730113 755.983835 > 50.114082 50.00 > > # CoordB > ImageX Y Z MeasuredMove MachineMove > vf_36.png-115.345475 -89.043448 556.073402 > 0 0 > vf_37.png-115.118715 -89.978534 606.040764 > 50.080172 50.00 > vf_38.png-134.911209 -90.901958 656.025557 > 50.096111 50.00 > vf_39.png-164.693931 -91.814392 705.982620 > 50.068868 50.00 > vf_40.png-134.459549 -92.730113 755.983835 > 50.114082 50.00 > > # CoordC > ImageX Y Z MeasuredMove MachineMove > vf_36.png-168.345475 -89.043448 556.073402 > 0 0 > vf_37.png-115.118715 -89.978534 606.040764 > 50.080172 50.00 > vf_38.png-146.911209 -90.901958 656.025557 > 50.096111 50.00 > vf_39.png-187.693931 -91.814392 705.982620 > 50.068868 50.00 > vf_40.png-185.459549 -92.730113 755.983835 > 50.114082 50.00 > > [[alternative HTML version deleted]] > This is not a solution if you really want separate graphs of the individual tables, but you could add column "Coord", roll everything into a single table and then create one or more facet plots from that. Cheers, Loris -- This signature is currently under construction. __ 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.
