Re: [R] Regarding to R

[Ben Bolker]

shweta shukla  gmail.com> writes:

> 
> Dear,
> I recently started R for my analysis but still not clear concept.
> please guide me with some informative mterial to learn R.
> 
> Iam also confuse that which one I should prefer R or R studio and what
> differences in between.
> 

R and RStudio are two different types of thing; it's not a question of
"which one to use".  RStudio is a front-end (interface) for R. You
probably *should* use RStudio (rather than the standard "R console"
interface that comes with R), it's well supported and has lots of
useful features.  Most of the time when you're asking questions,
though, they will be questions about R (unless they are specific
issues about the *interface*, they won't be RStudio-specific).

  It's hard to tell you where to start with "informative material".
What is most useful will depend on your background; your field/desired
type of analyses; language; personality; etc. etc..  There are literally
thousands of R tutorials and books, many available for free on the
internet.  I'd suggest you google "learning R programming", inspect
a dozen or so of the top hits, and see which ones seem to suit you
best.

  good luck,
Ben Bolker

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Regarding to R

[Greg Snow]

Please help us help you.  Tell us what you have tried and where you
have looked (otherwise we may just point you to things you already
know about).  Also what is your focus (simple analysis, learning,
programming, ...)?

The best place to start is with "An Introduction to R" which Installs
with R.  Then there are a lot of tutorials pointed to from the main R
website.


Comparing R and Rstudio is not an either/or question.  R is the
statistical package, Rstudio is an interface to R (Rstudio by itself
is not very useful, it passes the commands to R).

Think of R as being a car with only a few options, it can take you
anywhere and for many it is good enough.  Rstudio is a nice options
package (power steering, a GPS navigation system, etc.)  Things that
make driving the car easier and more enjoyable, but would not help
much without the car to add them to.

On Tue, May 10, 2016 at 4:10 AM, shweta shukla  wrote:
> Dear,
> I recently started R for my analysis but still not clear concept.
> please guide me with some informative mterial to learn R.
>
> Iam also confuse that which one I should prefer R or R studio and what
> differences in between.
>
>
>
>
> Thank you.
>
> [[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.



-- 
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com

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

[R] Regarding to R

[shweta shukla]

Dear,
I recently started R for my analysis but still not clear concept.
please guide me with some informative mterial to learn R.

Iam also confuse that which one I should prefer R or R studio and what
differences in between.




Thank you.

[[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] Regarding accesing R- Repositories at servers

[Uwe Ligges]

On 13.07.2010 09:42, venkatesh bandaru wrote:

Dear R-help team ,
I am venkatesh, student of University of Hyderabad, India. I couldn't able to  access 
R-repositories at Your specified servers.It is giving error such as  Couldn't able 
to access media.



It would be helpful to see what you did (the function call you entered), 
what your R version is as well as your OS, how you are connected. And 
the actual error message, not one you made up


Best,
Uwe Ligges


Can you please help me Regarding this.

i am anticipating for your reply, thanking you.

wishes  regards
B.venkatesh,
University of Hyderabad,
India
9440186746



[[alternative HTML version deleted]]




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R-help@r-project.org mailing list
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
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] Regarding accesing R- Repositories at servers

[venkatesh bandaru]

Dear R-help team ,
I am venkatesh, student of University of Hyderabad, India. I couldn't able to  
access R-repositories at Your specified servers.It is giving error such as  
Couldn't able to access media. Can you please help me Regarding this.

i am anticipating for your reply, thanking you.

wishes  regards
B.venkatesh,
University of Hyderabad,
India
9440186746



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Regarding the 'R' Load Command

[Godavarthi, Murali]

Hi Gavin, Steve

Tons and tons of Thanks! This solved my problem. My sample data differed
from the original working testdata in the factor levels. Once I set the
levels using the command given by Gavin, things started working like
magic. 
Hurray!

I learned a great deal from you'll. Thank You for helping me so
promptly!



Best Regards,

Murali Godavarthi

410-585-3746 (w)

ITCD - DPSCS Data Mining


-Original Message-
From: Gavin Simpson [mailto:gavin.simp...@ucl.ac.uk] 
Sent: Wednesday, May 19, 2010 3:52 PM
To: Godavarthi, Murali
Cc: Steve Lianoglou; r-help@r-project.org
Subject: RE: [R] Regarding the 'R' Load Command

On Wed, 2010-05-19 at 14:59 -0400, Godavarthi, Murali wrote:
 Hi Gavin, Steve
 
 Sorry, please use the below dput for mytestdata. Thanks!!

No need. The issue I think issue is due to the number of levels in the
factor. IIRC correctly, I've been bitten by this before where the
newdata object contained factors with different numbers of levels and/or
a different subset of levels.

Try setting the levels on mytestdata explicitly from the levels of
testdata, e.g. something like:

mytestdata - within(mytestdata, {
 sex - factor(sex, levels = levels(testdata$sex))
 race - factor(race, levels =
levels(testdata$race))
 marstat - factor(marstat, levels =
levels(testdata$marstat))
 empac - factor(empac, levels =
levels(testdata$empac))
 })

Then check with

str(mytestdata)

that it is consistent with

str(testdata)

If it is, then try to call predict on your RF model and newdata =
testdata)

HTH

G

 
 structure(list(imurder = 0, itheft = 0, irobbery = 0, iassault = 1,
 idrug = 0, iburglary = 0, igun = 0, psych = 0, Freq = 0, priors =
 58, firstage = 19, intage = 19, sex = structure(1, .Label = 1, class
=
 factor), race = structure(1, .Label = BLACK, class = factor),
 marstat = structure(1, .Label = SINGLE, class = factor), empac
=
 structure(1, .Label = UNEMPLD, class = factor), educ = 0,
 zipcode = 21215, suspendmn = 0, drugs = 0, alco = 0, probation =
1,
 parole = 0), .Names = c(imurder, itheft, irobbery, iassault,
 idrug, iburglary, igun, psych, Freq, priors, firstage,
 intage, sex, race, marstat, empac, educ, zipcode,
 suspendmn, drugs, alco, probation, parole), class =
 data.frame, row.names = 10)
 
 
 Best Regards,
 
 Murali Godavarthi
 
 410-585-3746 (w)
 
 ITCD - DPSCS Data Mining
 
 
 -Original Message-
 From: Godavarthi, Murali 
 Sent: Wednesday, May 19, 2010 2:43 PM
 To: 'gavin.simp...@ucl.ac.uk'; Steve Lianoglou
 Cc: r-help@r-project.org
 Subject: RE: [R] Regarding the 'R' Load Command
 
 Hi Steve, Gavin
 
 This is being really helpful. I've pasted the working data, and my
test
 data below after running the str command on both of those variables.
The
 working sample actually contains about 300 records, hence I am not
able
 to paste the whole data here. However my sample test data which I am
 trying to get working, is only 1 record, and I've pasted the dput
result
 below. Datatypes  seem to match in both variables for me in terms of
 being num/factor. Please suggest where it could be wrong. Thank You!
 
 
 
 mytestdata
 
 structure(list(imurder = 0, itheft = 0, irobbery = 0, iassault = 1L,
 idrug = 0L, iburglary = 0L, igun = 0L, psych = 0L, Freq = 0L,
priors
 = 58L, firstage = 19L, intage = 19L, sex = structure(1L, .Label = 1,
 class = factor), race = structure(1L, .Label = BLACK, class =
 factor), marstat = structure(1L, .Label = SINGLE, class =
 factor), empac = structure(1L, .Label = UNEMPLD, class =
 factor), educ = 0L, zipcode = 21215L, suspendmn = 0L, drugs =
0L,
 alco = 0L, probation = 1L, parole = 0L), .Names = c(imurder,
itheft,
 irobbery, iassault, idrug, iburglary, igun, psych, Freq,
 priors, firstage, intage, sex, race, marstat, empac,
 educ, zipcode, suspendmn, drugs, alco, probation,
parole),
 class = data.frame, row.names = 10)
 
 
  str(testdata)
 'data.frame':   291 obs. of  23 variables:
  $ imurder  : num  0 0 0 0 0 0 0 0 0 0 ...
  $ itheft   : num  0 0 0 0 0 1 0 0 0 0 ...
  $ irobbery : num  0 0 0 0 0 0 0 0 0 0 ...
  $ iassault : num  1 0 1 0 0 0 0 0 0 0 ...
  $ idrug: num  0 1 0 1 1 0 0 1 1 1 ...
  $ iburglary: num  0 0 0 0 0 0 0 0 0 0 ...
  $ igun : num  0 0 0 0 0 0 0 0 0 0 ...
  $ psych: num  0 0 0 0 0 0 0 0 0 0 ...
  $ Freq : num  0 0 0 0 0 0 0 0 0 0 ...
  $ priors   : num  58 4 2 0 6 22 0 36 0 0 ...
  $ firstage : num  19 39 28 0 49 32 0 24 0 55 ...
  $ intage   : num  19 39 28 25 49 32 32 24 30 55 ...
  $ sex  : Factor w/ 2 levels 1,2: 1 2 1 2 2 1 1 1 1 1 ...
  $ race : Factor w/ 5 levels WHITE,BLACK,..: 2 2 1 1 2 1 1 2 2
2
 ...
  $ marstat  : Factor w/ 7 levels SINGLE,MARRIED,..: 1 2 2 1 2 4 7
1
 7 3 ...
  $ empac: Factor w/ 6 levels EMPLD FT,EMPLD PT,..: 3 4 3 3 3 3
6
 3 6 3 ...
  $ educ : num  0 0 0 1 0 0 0 0 0 1 ...
  $ zipcode  : num  21215 21217 21223 21223 21217 ...
  $ suspendmn

Re: [R] Regarding the 'R' Load Command

[Steve Lianoglou]

Hi Murali,

I'm sorry, but you're making this too difficult to provide any help.
Describing what your data structures are and contain is too tedious to
follow, and end up being rather ambiguous anyway.

My first guess: by your error message, perhaps the columns of the data
to predict on are different than the training.

If you want to get help, please provide your data in a form that we
can test against. Look at this post by Hadley Wickham to help you do
that:
http://gist.github.com/270442

In particular, not the use of dput that you should use so we can
paste the result in our workspace and get the data objects you try to
describe. So, to be clear: send us a chunk of text we can paste into R
that will recreate a workspace that can reproduce your problem. Please
trim your data files to be only as large as necessary (eg. provide 3
observations instead of 300)

Thanks,
-steve

On Wed, May 19, 2010 at 11:40 AM, Godavarthi, Murali
mgodavar...@dpscs.state.md.us wrote:
 Hi Steve,

 Thanks so much for your inputs! I was actually trying to implement your
 suggestions, I get the below error (please see the results of predict
 command below).

 What we are trying to do is to feed in values for about 23
 characteristics of an individual, and use the randomForest() function to
 determine if the individual is a violent offender. Expected output is 0
 or 1, indicating yes/no.

 Am I going wrong again? Here is what I was doing:

 1) Created a text file with following data:
 imurder itheft irobbery iassault idrug iburglary igun
 psych Freq priors firstage intage sex race marstat
 empac educ zipcode suspendmn drugs alco probation parole
 10 0 0 0 1 0 0 0 0 0 58 19 19 1 BLACK SINGLE UNEMPLD 0 21215 0
 0 0 1 0

 The above format in which the text file was created is in the same
 format as the one which is already working, but has characteristics of
 about 290 individuals fed-in instead of just one individual as above.
 Not sure why this doesn't work!


 2) Executed the below command sequence:


 library(randomForest)
 randomForest 4.5-34
 Type rfNews() to see new features/changes/bug fixes.

 load(C://Program Files//R//R-2.10.1//bin//rfoutput)

 testmurali-read.table(ex.data,T)

 load(testmurali)
 Error in load(testmurali) : bad 'file' argument

 load(testmurali)

 names(testmurali)
  [1] imurder   itheft    irobbery  iassault  idrug
 iburglary igun      psych     Freq      priors
 [11] firstage  intage    sex       race      marstat   empac
 educ      zipcode   suspendmn drugs
 [21] alco      probation parole

 predict(rfoutput,newdata=testmurali,type=response)
 Error in predict.randomForest(rfoutput, newdata = testmurali, type =
 response) :
  Type of predictors in new data do not match that of the training data.


 The model rfoutput used in the above predict command is also based on a
 working example with similar data.


 Also, does load command accept a data string input directly (without
 storing it into a file and then providing path of the file as a string)?

 Please suggest. Thanks in advance!


 Best Regards,
 Murali Godavarthi
 410-585-3746 (w)

 ITCD - DPSCS Data Mining






 -Original Message-
 From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com]
 Sent: Tuesday, May 18, 2010 4:13 PM
 To: Godavarthi, Murali
 Cc: r-help@r-project.org
 Subject: Re: [R] Regarding the 'R' Load Command

 Hi,

 On Tue, May 18, 2010 at 2:49 PM, Godavarthi, Murali
 mgodavar...@dpscs.state.md.us wrote:
 Hi,

 I'm new to 'R' and need some help on the Load command. Any responses
 will be highly appreciated. Thanks in advance!

 As per manuals, the Load command expects a binary file input that is
 saved using a save command.

 Or a path to the file ...

 However it is required that we need to
 call the 'R' program from

 Java web application using RJava, and pass a string to the 'R program
 instead of a binary file. Is it possible?

 Yes, pay closer attention to the description for the file argument
 in the load function (see ?load):

 a (readable binary) connection **or a character string** giving the
 name of the file to load

 (emphasis mine)

 I was exploring the options of using TextConnections, file connections
 and other types of connections in order to read a stream of input
 (either from a file, stdin etc). I am able to read the string, but the
 Save and Load commands are not accepting the string input. Here is the
 sequence of commands I tried running, and the error received. There is
 no clue on this error, especially when trying to use the eval function
 in randomForest package, even on the internet. Can anyone help please!

 library(randomForest)

 randomForest 4.5-34

 Type rfNews() to see new features/changes/bug fixes.



 load(C://Program Files//R//R-2.10.1//bin//rfoutput)



 zz - file(ex.data, w)



 cat(\imurder\ \itheft\ \irobbery\ \iassault\ \idrug\
 \iburglary\ \igun\ \psych\ \Freq\ \priors\ \firstage\
 \intage\ \sex\ \race\ \marstat\ \empac\

 \educ\ \zipcode\ \suspendmn\ \drugs\ \alco\ \probation

Re: [R] Regarding the 'R' Load Command

[Gavin Simpson]

I think the answer is clear from the error: R thinks the type of data in
the components of 'testmurali' do not match those of the data used to
fit the original randomForest.

The OP should go back to his model fitting code and do

str(obj)

where 'obj' is the name of his original data object used to fit the
randomForest and compare it with

str(testmurali)

to see why the types of data are different. Look for variables that were
factors or characters in one data set and numeric/integer in the other.
This smells like a data import issue...

If revelation still doesn't occur Murali, *please* follow Steve's
suggestions and post and message that shows exactly (i.e. the R code
executed) along side a data set *we* can load into R without jumping
through hoops or having to divine what your data look like using a
crystal ball or ESP.

HTH

G

On Wed, 2010-05-19 at 12:24 -0400, Steve Lianoglou wrote:
 Hi Murali,
 
 I'm sorry, but you're making this too difficult to provide any help.
 Describing what your data structures are and contain is too tedious to
 follow, and end up being rather ambiguous anyway.
 
 My first guess: by your error message, perhaps the columns of the data
 to predict on are different than the training.
 
 If you want to get help, please provide your data in a form that we
 can test against. Look at this post by Hadley Wickham to help you do
 that:
 http://gist.github.com/270442
 
 In particular, not the use of dput that you should use so we can
 paste the result in our workspace and get the data objects you try to
 describe. So, to be clear: send us a chunk of text we can paste into R
 that will recreate a workspace that can reproduce your problem. Please
 trim your data files to be only as large as necessary (eg. provide 3
 observations instead of 300)
 
 Thanks,
 -steve
 
 On Wed, May 19, 2010 at 11:40 AM, Godavarthi, Murali
 mgodavar...@dpscs.state.md.us wrote:
  Hi Steve,
 
  Thanks so much for your inputs! I was actually trying to implement your
  suggestions, I get the below error (please see the results of predict
  command below).
 
  What we are trying to do is to feed in values for about 23
  characteristics of an individual, and use the randomForest() function to
  determine if the individual is a violent offender. Expected output is 0
  or 1, indicating yes/no.
 
  Am I going wrong again? Here is what I was doing:
 
  1) Created a text file with following data:
  imurder itheft irobbery iassault idrug iburglary igun
  psych Freq priors firstage intage sex race marstat
  empac educ zipcode suspendmn drugs alco probation parole
  10 0 0 0 1 0 0 0 0 0 58 19 19 1 BLACK SINGLE UNEMPLD 0 21215 0
  0 0 1 0
 
  The above format in which the text file was created is in the same
  format as the one which is already working, but has characteristics of
  about 290 individuals fed-in instead of just one individual as above.
  Not sure why this doesn't work!
 
 
  2) Executed the below command sequence:
 
 
  library(randomForest)
  randomForest 4.5-34
  Type rfNews() to see new features/changes/bug fixes.
 
  load(C://Program Files//R//R-2.10.1//bin//rfoutput)
 
  testmurali-read.table(ex.data,T)
 
  load(testmurali)
  Error in load(testmurali) : bad 'file' argument
 
  load(testmurali)
 
  names(testmurali)
   [1] imurder   itheftirobbery  iassault  idrug
  iburglary igun  psych Freq  priors
  [11] firstage  intagesex   race  marstat   empac
  educ  zipcode   suspendmn drugs
  [21] alco  probation parole
 
  predict(rfoutput,newdata=testmurali,type=response)
  Error in predict.randomForest(rfoutput, newdata = testmurali, type =
  response) :
   Type of predictors in new data do not match that of the training data.
 
 
  The model rfoutput used in the above predict command is also based on a
  working example with similar data.
 
 
  Also, does load command accept a data string input directly (without
  storing it into a file and then providing path of the file as a string)?
 
  Please suggest. Thanks in advance!
 
 
  Best Regards,
  Murali Godavarthi
  410-585-3746 (w)
 
  ITCD - DPSCS Data Mining
 
 
 
 
 
 
  -Original Message-
  From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com]
  Sent: Tuesday, May 18, 2010 4:13 PM
  To: Godavarthi, Murali
  Cc: r-help@r-project.org
  Subject: Re: [R] Regarding the 'R' Load Command
 
  Hi,
 
  On Tue, May 18, 2010 at 2:49 PM, Godavarthi, Murali
  mgodavar...@dpscs.state.md.us wrote:
  Hi,
 
  I'm new to 'R' and need some help on the Load command. Any responses
  will be highly appreciated. Thanks in advance!
 
  As per manuals, the Load command expects a binary file input that is
  saved using a save command.
 
  Or a path to the file ...
 
  However it is required that we need to
  call the 'R' program from
 
  Java web application using RJava, and pass a string to the 'R program
  instead of a binary file. Is it possible?
 
  Yes, pay closer attention to the description for the file argument

Re: [R] Regarding the 'R' Load Command

[Godavarthi, Murali]

Hi Steve, Gavin

This is being really helpful. I've pasted the working data, and my test
data below after running the str command on both of those variables. The
working sample actually contains about 300 records, hence I am not able
to paste the whole data here. However my sample test data which I am
trying to get working, is only 1 record, and I've pasted the dput result
below. Datatypes  seem to match in both variables for me in terms of
being num/factor. Please suggest where it could be wrong. Thank You!



mytestdata

structure(list(imurder = 0, itheft = 0, irobbery = 0, iassault = 1L,
idrug = 0L, iburglary = 0L, igun = 0L, psych = 0L, Freq = 0L, priors
= 58L, firstage = 19L, intage = 19L, sex = structure(1L, .Label = 1,
class = factor), race = structure(1L, .Label = BLACK, class =
factor), marstat = structure(1L, .Label = SINGLE, class =
factor), empac = structure(1L, .Label = UNEMPLD, class =
factor), educ = 0L, zipcode = 21215L, suspendmn = 0L, drugs = 0L,
alco = 0L, probation = 1L, parole = 0L), .Names = c(imurder, itheft,
irobbery, iassault, idrug, iburglary, igun, psych, Freq,
priors, firstage, intage, sex, race, marstat, empac,
educ, zipcode, suspendmn, drugs, alco, probation, parole),
class = data.frame, row.names = 10)


 str(testdata)
'data.frame':   291 obs. of  23 variables:
 $ imurder  : num  0 0 0 0 0 0 0 0 0 0 ...
 $ itheft   : num  0 0 0 0 0 1 0 0 0 0 ...
 $ irobbery : num  0 0 0 0 0 0 0 0 0 0 ...
 $ iassault : num  1 0 1 0 0 0 0 0 0 0 ...
 $ idrug: num  0 1 0 1 1 0 0 1 1 1 ...
 $ iburglary: num  0 0 0 0 0 0 0 0 0 0 ...
 $ igun : num  0 0 0 0 0 0 0 0 0 0 ...
 $ psych: num  0 0 0 0 0 0 0 0 0 0 ...
 $ Freq : num  0 0 0 0 0 0 0 0 0 0 ...
 $ priors   : num  58 4 2 0 6 22 0 36 0 0 ...
 $ firstage : num  19 39 28 0 49 32 0 24 0 55 ...
 $ intage   : num  19 39 28 25 49 32 32 24 30 55 ...
 $ sex  : Factor w/ 2 levels 1,2: 1 2 1 2 2 1 1 1 1 1 ...
 $ race : Factor w/ 5 levels WHITE,BLACK,..: 2 2 1 1 2 1 1 2 2 2
...
 $ marstat  : Factor w/ 7 levels SINGLE,MARRIED,..: 1 2 2 1 2 4 7 1
7 3 ...
 $ empac: Factor w/ 6 levels EMPLD FT,EMPLD PT,..: 3 4 3 3 3 3 6
3 6 3 ...
 $ educ : num  0 0 0 1 0 0 0 0 0 1 ...
 $ zipcode  : num  21215 21217 21223 21223 21217 ...
 $ suspendmn: num  0 600 0 0 60 3 2 479 0 3 ...
 $ drugs: num  0 1 0 0 0 1 0 0 0 1 ...
 $ alco : num  0 0 0 0 0 1 0 0 0 1 ...
 $ probation: num  1 1 0 0 1 1 1 1 0 1 ...
 $ parole   : num  0 0 0 0 0 0 0 0 0 0 ...
 
 
 
 
 str(mytestdata)
'data.frame':   1 obs. of  23 variables:
 $ imurder  : num 0
 $ itheft   : num 0
 $ irobbery : num 0
 $ iassault : num 1
 $ idrug: num 0
 $ iburglary: num 0
 $ igun : num 0
 $ psych: num 0
 $ Freq : num 0
 $ priors   : num 58
 $ firstage : num 19
 $ intage   : num 19
 $ sex  : Factor w/ 1 level 1: 1
 $ race : Factor w/ 1 level BLACK: 1
 $ marstat  : Factor w/ 1 level SINGLE: 1
 $ empac: Factor w/ 1 level UNEMPLD: 1
 $ educ : num 0
 $ zipcode  : num 21215
 $ suspendmn: num 0
 $ drugs: num 0
 $ alco : num 0
 $ probation: num 1
 $ parole   : num 0




Best Regards,

Murali Godavarthi

410-585-3746 (w)

ITCD - DPSCS Data Mining


-Original Message-
From: Gavin Simpson [mailto:gavin.simp...@ucl.ac.uk] 
Sent: Wednesday, May 19, 2010 12:58 PM
To: Steve Lianoglou
Cc: Godavarthi, Murali; r-help@r-project.org
Subject: Re: [R] Regarding the 'R' Load Command

I think the answer is clear from the error: R thinks the type of data in
the components of 'testmurali' do not match those of the data used to
fit the original randomForest.

The OP should go back to his model fitting code and do

str(obj)

where 'obj' is the name of his original data object used to fit the
randomForest and compare it with

str(testmurali)

to see why the types of data are different. Look for variables that were
factors or characters in one data set and numeric/integer in the other.
This smells like a data import issue...

If revelation still doesn't occur Murali, *please* follow Steve's
suggestions and post and message that shows exactly (i.e. the R code
executed) along side a data set *we* can load into R without jumping
through hoops or having to divine what your data look like using a
crystal ball or ESP.

HTH

G

On Wed, 2010-05-19 at 12:24 -0400, Steve Lianoglou wrote:
 Hi Murali,
 
 I'm sorry, but you're making this too difficult to provide any help.
 Describing what your data structures are and contain is too tedious to
 follow, and end up being rather ambiguous anyway.
 
 My first guess: by your error message, perhaps the columns of the data
 to predict on are different than the training.
 
 If you want to get help, please provide your data in a form that we
 can test against. Look at this post by Hadley Wickham to help you do
 that:
 http://gist.github.com/270442
 
 In particular, not the use of dput that you should use so we can
 paste the result in our workspace and get the data objects you try to
 describe. So, to be clear: send us

Re: [R] Regarding the 'R' Load Command

[Godavarthi, Murali]

Hi Steve,

Thanks so much for your inputs! I was actually trying to implement your
suggestions, I get the below error (please see the results of predict
command below). 

What we are trying to do is to feed in values for about 23
characteristics of an individual, and use the randomForest() function to
determine if the individual is a violent offender. Expected output is 0
or 1, indicating yes/no. 

Am I going wrong again? Here is what I was doing:

1) Created a text file with following data:
imurder itheft irobbery iassault idrug iburglary igun
psych Freq priors firstage intage sex race marstat
empac educ zipcode suspendmn drugs alco probation parole
10 0 0 0 1 0 0 0 0 0 58 19 19 1 BLACK SINGLE UNEMPLD 0 21215 0
0 0 1 0

The above format in which the text file was created is in the same
format as the one which is already working, but has characteristics of
about 290 individuals fed-in instead of just one individual as above.
Not sure why this doesn't work!


2) Executed the below command sequence:


 library(randomForest)
randomForest 4.5-34
Type rfNews() to see new features/changes/bug fixes.

 load(C://Program Files//R//R-2.10.1//bin//rfoutput)

 testmurali-read.table(ex.data,T)

 load(testmurali)
Error in load(testmurali) : bad 'file' argument

 load(testmurali)

 names(testmurali)
 [1] imurder   itheftirobbery  iassault  idrug
iburglary igun  psych Freq  priors   
[11] firstage  intagesex   race  marstat   empac
educ  zipcode   suspendmn drugs
[21] alco  probation parole   

 predict(rfoutput,newdata=testmurali,type=response)
Error in predict.randomForest(rfoutput, newdata = testmurali, type =
response) : 
  Type of predictors in new data do not match that of the training data.
 

The model rfoutput used in the above predict command is also based on a
working example with similar data. 


Also, does load command accept a data string input directly (without
storing it into a file and then providing path of the file as a string)?

Please suggest. Thanks in advance!


Best Regards,
Murali Godavarthi
410-585-3746 (w)

ITCD - DPSCS Data Mining






-Original Message-
From: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com] 
Sent: Tuesday, May 18, 2010 4:13 PM
To: Godavarthi, Murali
Cc: r-help@r-project.org
Subject: Re: [R] Regarding the 'R' Load Command

Hi,

On Tue, May 18, 2010 at 2:49 PM, Godavarthi, Murali
mgodavar...@dpscs.state.md.us wrote:
 Hi,

 I'm new to 'R' and need some help on the Load command. Any responses
 will be highly appreciated. Thanks in advance!

 As per manuals, the Load command expects a binary file input that is
 saved using a save command.

Or a path to the file ...

 However it is required that we need to
 call the 'R' program from

 Java web application using RJava, and pass a string to the 'R program
 instead of a binary file. Is it possible?

Yes, pay closer attention to the description for the file argument
in the load function (see ?load):

a (readable binary) connection **or a character string** giving the
name of the file to load

(emphasis mine)

 I was exploring the options of using TextConnections, file connections
 and other types of connections in order to read a stream of input
 (either from a file, stdin etc). I am able to read the string, but the
 Save and Load commands are not accepting the string input. Here is the
 sequence of commands I tried running, and the error received. There is
 no clue on this error, especially when trying to use the eval function
 in randomForest package, even on the internet. Can anyone help please!

 library(randomForest)

 randomForest 4.5-34

 Type rfNews() to see new features/changes/bug fixes.



 load(C://Program Files//R//R-2.10.1//bin//rfoutput)



 zz - file(ex.data, w)



 cat(\imurder\ \itheft\ \irobbery\ \iassault\ \idrug\
 \iburglary\ \igun\ \psych\ \Freq\ \priors\ \firstage\
 \intage\ \sex\ \race\ \marstat\ \empac\

 \educ\ \zipcode\ \suspendmn\ \drugs\ \alco\ \probation\
 \parole\,file = zz, sep = \n, fill = TRUE)



 cat(\10\ 0 0 0 1 0 0 0 0 0 58 19 19 \1\ \BLACK\ \SINGLE\
 \UNEMPLD\ 0 21215 0 0 0 1 0,file = zz, sep = \n, fill = TRUE)

What are you trying to do here?
It looks like you want to save a table of sorts. First create your
data into a data.frame, then save that data.frame to a file using
write.table (or write.csv, etc).

 save(zz, file = testmurali, version = 2)

You're saving a file object here, not the contents of the file.
Once you successfully serialize your data into a text file, just load
it from like normal using read.table (or similar).

Anyway, I'm not sure what we're talking about here, but in short:

1. You need to make sure that you are correctly saving what you think
you're saving.
2. You can pass a character string to the `load` function, so you can
send it through (over from) java as  you wich.
3. I don't think you really want to deal with load/save here, because
it looks like you are dealing with some tab delimited file -- in which
case use

Re: [R] Regarding the 'R' Load Command

[Godavarthi, Murali]

Hi Gavin, Steve

Sorry, please use the below dput for mytestdata. Thanks!!

structure(list(imurder = 0, itheft = 0, irobbery = 0, iassault = 1,
idrug = 0, iburglary = 0, igun = 0, psych = 0, Freq = 0, priors =
58, firstage = 19, intage = 19, sex = structure(1, .Label = 1, class =
factor), race = structure(1, .Label = BLACK, class = factor),
marstat = structure(1, .Label = SINGLE, class = factor), empac =
structure(1, .Label = UNEMPLD, class = factor), educ = 0,
zipcode = 21215, suspendmn = 0, drugs = 0, alco = 0, probation = 1,
parole = 0), .Names = c(imurder, itheft, irobbery, iassault,
idrug, iburglary, igun, psych, Freq, priors, firstage,
intage, sex, race, marstat, empac, educ, zipcode,
suspendmn, drugs, alco, probation, parole), class =
data.frame, row.names = 10)


Best Regards,

Murali Godavarthi

410-585-3746 (w)

ITCD - DPSCS Data Mining


-Original Message-
From: Godavarthi, Murali 
Sent: Wednesday, May 19, 2010 2:43 PM
To: 'gavin.simp...@ucl.ac.uk'; Steve Lianoglou
Cc: r-help@r-project.org
Subject: RE: [R] Regarding the 'R' Load Command

Hi Steve, Gavin

This is being really helpful. I've pasted the working data, and my test
data below after running the str command on both of those variables. The
working sample actually contains about 300 records, hence I am not able
to paste the whole data here. However my sample test data which I am
trying to get working, is only 1 record, and I've pasted the dput result
below. Datatypes  seem to match in both variables for me in terms of
being num/factor. Please suggest where it could be wrong. Thank You!



mytestdata

structure(list(imurder = 0, itheft = 0, irobbery = 0, iassault = 1L,
idrug = 0L, iburglary = 0L, igun = 0L, psych = 0L, Freq = 0L, priors
= 58L, firstage = 19L, intage = 19L, sex = structure(1L, .Label = 1,
class = factor), race = structure(1L, .Label = BLACK, class =
factor), marstat = structure(1L, .Label = SINGLE, class =
factor), empac = structure(1L, .Label = UNEMPLD, class =
factor), educ = 0L, zipcode = 21215L, suspendmn = 0L, drugs = 0L,
alco = 0L, probation = 1L, parole = 0L), .Names = c(imurder, itheft,
irobbery, iassault, idrug, iburglary, igun, psych, Freq,
priors, firstage, intage, sex, race, marstat, empac,
educ, zipcode, suspendmn, drugs, alco, probation, parole),
class = data.frame, row.names = 10)


 str(testdata)
'data.frame':   291 obs. of  23 variables:
 $ imurder  : num  0 0 0 0 0 0 0 0 0 0 ...
 $ itheft   : num  0 0 0 0 0 1 0 0 0 0 ...
 $ irobbery : num  0 0 0 0 0 0 0 0 0 0 ...
 $ iassault : num  1 0 1 0 0 0 0 0 0 0 ...
 $ idrug: num  0 1 0 1 1 0 0 1 1 1 ...
 $ iburglary: num  0 0 0 0 0 0 0 0 0 0 ...
 $ igun : num  0 0 0 0 0 0 0 0 0 0 ...
 $ psych: num  0 0 0 0 0 0 0 0 0 0 ...
 $ Freq : num  0 0 0 0 0 0 0 0 0 0 ...
 $ priors   : num  58 4 2 0 6 22 0 36 0 0 ...
 $ firstage : num  19 39 28 0 49 32 0 24 0 55 ...
 $ intage   : num  19 39 28 25 49 32 32 24 30 55 ...
 $ sex  : Factor w/ 2 levels 1,2: 1 2 1 2 2 1 1 1 1 1 ...
 $ race : Factor w/ 5 levels WHITE,BLACK,..: 2 2 1 1 2 1 1 2 2 2
...
 $ marstat  : Factor w/ 7 levels SINGLE,MARRIED,..: 1 2 2 1 2 4 7 1
7 3 ...
 $ empac: Factor w/ 6 levels EMPLD FT,EMPLD PT,..: 3 4 3 3 3 3 6
3 6 3 ...
 $ educ : num  0 0 0 1 0 0 0 0 0 1 ...
 $ zipcode  : num  21215 21217 21223 21223 21217 ...
 $ suspendmn: num  0 600 0 0 60 3 2 479 0 3 ...
 $ drugs: num  0 1 0 0 0 1 0 0 0 1 ...
 $ alco : num  0 0 0 0 0 1 0 0 0 1 ...
 $ probation: num  1 1 0 0 1 1 1 1 0 1 ...
 $ parole   : num  0 0 0 0 0 0 0 0 0 0 ...
 
 
 
 
 str(mytestdata)
'data.frame':   1 obs. of  23 variables:
 $ imurder  : num 0
 $ itheft   : num 0
 $ irobbery : num 0
 $ iassault : num 1
 $ idrug: num 0
 $ iburglary: num 0
 $ igun : num 0
 $ psych: num 0
 $ Freq : num 0
 $ priors   : num 58
 $ firstage : num 19
 $ intage   : num 19
 $ sex  : Factor w/ 1 level 1: 1
 $ race : Factor w/ 1 level BLACK: 1
 $ marstat  : Factor w/ 1 level SINGLE: 1
 $ empac: Factor w/ 1 level UNEMPLD: 1
 $ educ : num 0
 $ zipcode  : num 21215
 $ suspendmn: num 0
 $ drugs: num 0
 $ alco : num 0
 $ probation: num 1
 $ parole   : num 0




Best Regards,

Murali Godavarthi

410-585-3746 (w)

ITCD - DPSCS Data Mining


-Original Message-
From: Gavin Simpson [mailto:gavin.simp...@ucl.ac.uk] 
Sent: Wednesday, May 19, 2010 12:58 PM
To: Steve Lianoglou
Cc: Godavarthi, Murali; r-help@r-project.org
Subject: Re: [R] Regarding the 'R' Load Command

I think the answer is clear from the error: R thinks the type of data in
the components of 'testmurali' do not match those of the data used to
fit the original randomForest.

The OP should go back to his model fitting code and do

str(obj)

where 'obj' is the name of his original data object used to fit the
randomForest and compare it with

str(testmurali)

to see why the types of data are different. Look for variables that were
factors or characters in one data set and numeric/integer in the other

Re: [R] Regarding the 'R' Load Command

[Gavin Simpson]

On Wed, 2010-05-19 at 14:59 -0400, Godavarthi, Murali wrote:
 Hi Gavin, Steve
 
 Sorry, please use the below dput for mytestdata. Thanks!!

No need. The issue I think issue is due to the number of levels in the
factor. IIRC correctly, I've been bitten by this before where the
newdata object contained factors with different numbers of levels and/or
a different subset of levels.

Try setting the levels on mytestdata explicitly from the levels of
testdata, e.g. something like:

mytestdata - within(mytestdata, {
 sex - factor(sex, levels = levels(testdata$sex))
 race - factor(race, levels = levels(testdata$race))
 marstat - factor(marstat, levels = 
levels(testdata$marstat))
 empac - factor(empac, levels = levels(testdata$empac))
 })

Then check with

str(mytestdata)

that it is consistent with

str(testdata)

If it is, then try to call predict on your RF model and newdata = testdata)

HTH

G

 
 structure(list(imurder = 0, itheft = 0, irobbery = 0, iassault = 1,
 idrug = 0, iburglary = 0, igun = 0, psych = 0, Freq = 0, priors =
 58, firstage = 19, intage = 19, sex = structure(1, .Label = 1, class =
 factor), race = structure(1, .Label = BLACK, class = factor),
 marstat = structure(1, .Label = SINGLE, class = factor), empac =
 structure(1, .Label = UNEMPLD, class = factor), educ = 0,
 zipcode = 21215, suspendmn = 0, drugs = 0, alco = 0, probation = 1,
 parole = 0), .Names = c(imurder, itheft, irobbery, iassault,
 idrug, iburglary, igun, psych, Freq, priors, firstage,
 intage, sex, race, marstat, empac, educ, zipcode,
 suspendmn, drugs, alco, probation, parole), class =
 data.frame, row.names = 10)
 
 
 Best Regards,
 
 Murali Godavarthi
 
 410-585-3746 (w)
 
 ITCD - DPSCS Data Mining
 
 
 -Original Message-
 From: Godavarthi, Murali 
 Sent: Wednesday, May 19, 2010 2:43 PM
 To: 'gavin.simp...@ucl.ac.uk'; Steve Lianoglou
 Cc: r-help@r-project.org
 Subject: RE: [R] Regarding the 'R' Load Command
 
 Hi Steve, Gavin
 
 This is being really helpful. I've pasted the working data, and my test
 data below after running the str command on both of those variables. The
 working sample actually contains about 300 records, hence I am not able
 to paste the whole data here. However my sample test data which I am
 trying to get working, is only 1 record, and I've pasted the dput result
 below. Datatypes  seem to match in both variables for me in terms of
 being num/factor. Please suggest where it could be wrong. Thank You!
 
 
 
 mytestdata
 
 structure(list(imurder = 0, itheft = 0, irobbery = 0, iassault = 1L,
 idrug = 0L, iburglary = 0L, igun = 0L, psych = 0L, Freq = 0L, priors
 = 58L, firstage = 19L, intage = 19L, sex = structure(1L, .Label = 1,
 class = factor), race = structure(1L, .Label = BLACK, class =
 factor), marstat = structure(1L, .Label = SINGLE, class =
 factor), empac = structure(1L, .Label = UNEMPLD, class =
 factor), educ = 0L, zipcode = 21215L, suspendmn = 0L, drugs = 0L,
 alco = 0L, probation = 1L, parole = 0L), .Names = c(imurder, itheft,
 irobbery, iassault, idrug, iburglary, igun, psych, Freq,
 priors, firstage, intage, sex, race, marstat, empac,
 educ, zipcode, suspendmn, drugs, alco, probation, parole),
 class = data.frame, row.names = 10)
 
 
  str(testdata)
 'data.frame':   291 obs. of  23 variables:
  $ imurder  : num  0 0 0 0 0 0 0 0 0 0 ...
  $ itheft   : num  0 0 0 0 0 1 0 0 0 0 ...
  $ irobbery : num  0 0 0 0 0 0 0 0 0 0 ...
  $ iassault : num  1 0 1 0 0 0 0 0 0 0 ...
  $ idrug: num  0 1 0 1 1 0 0 1 1 1 ...
  $ iburglary: num  0 0 0 0 0 0 0 0 0 0 ...
  $ igun : num  0 0 0 0 0 0 0 0 0 0 ...
  $ psych: num  0 0 0 0 0 0 0 0 0 0 ...
  $ Freq : num  0 0 0 0 0 0 0 0 0 0 ...
  $ priors   : num  58 4 2 0 6 22 0 36 0 0 ...
  $ firstage : num  19 39 28 0 49 32 0 24 0 55 ...
  $ intage   : num  19 39 28 25 49 32 32 24 30 55 ...
  $ sex  : Factor w/ 2 levels 1,2: 1 2 1 2 2 1 1 1 1 1 ...
  $ race : Factor w/ 5 levels WHITE,BLACK,..: 2 2 1 1 2 1 1 2 2 2
 ...
  $ marstat  : Factor w/ 7 levels SINGLE,MARRIED,..: 1 2 2 1 2 4 7 1
 7 3 ...
  $ empac: Factor w/ 6 levels EMPLD FT,EMPLD PT,..: 3 4 3 3 3 3 6
 3 6 3 ...
  $ educ : num  0 0 0 1 0 0 0 0 0 1 ...
  $ zipcode  : num  21215 21217 21223 21223 21217 ...
  $ suspendmn: num  0 600 0 0 60 3 2 479 0 3 ...
  $ drugs: num  0 1 0 0 0 1 0 0 0 1 ...
  $ alco : num  0 0 0 0 0 1 0 0 0 1 ...
  $ probation: num  1 1 0 0 1 1 1 1 0 1 ...
  $ parole   : num  0 0 0 0 0 0 0 0 0 0 ...
  
  
  
  
  str(mytestdata)
 'data.frame':   1 obs. of  23 variables:
  $ imurder  : num 0
  $ itheft   : num 0
  $ irobbery : num 0
  $ iassault : num 1
  $ idrug: num 0
  $ iburglary: num 0
  $ igun : num 0
  $ psych: num 0
  $ Freq : num 0
  $ priors   : num 58
  $ firstage : num 19
  $ intage   : num 19
  $ sex  : Factor w/ 1 level 1: 1
  $ race : Factor w/ 1 level BLACK: 1
  $ marstat

[R] Regarding the 'R' Load Command

[Godavarthi, Murali]

Hi,

 

I'm new to 'R' and need some help on the Load command. Any responses
will be highly appreciated. Thanks in advance!

 

As per manuals, the Load command expects a binary file input that is
saved using a save command. However it is required that we need to
call the 'R' program from 

Java web application using RJava, and pass a string to the 'R program
instead of a binary file. Is it possible?

 

I was exploring the options of using TextConnections, file connections
and other types of connections in order to read a stream of input
(either from a file, stdin etc). I am able to read the string, but the
Save and Load commands are not accepting the string input. Here is the
sequence of commands I tried running, and the error received. There is
no clue on this error, especially when trying to use the eval function
in randomForest package, even on the internet. Can anyone help please!

 

 

 

 library(randomForest)

randomForest 4.5-34

Type rfNews() to see new features/changes/bug fixes.

 

 load(C://Program Files//R//R-2.10.1//bin//rfoutput)

 

 zz - file(ex.data, w)

 

 cat(\imurder\ \itheft\ \irobbery\ \iassault\ \idrug\
\iburglary\ \igun\ \psych\ \Freq\ \priors\ \firstage\
\intage\ \sex\ \race\ \marstat\ \empac\ 

\educ\ \zipcode\ \suspendmn\ \drugs\ \alco\ \probation\
\parole\,file = zz, sep = \n, fill = TRUE)

 

 cat(\10\ 0 0 0 1 0 0 0 0 0 58 19 19 \1\ \BLACK\ \SINGLE\
\UNEMPLD\ 0 21215 0 0 0 1 0,file = zz, sep = \n, fill = TRUE)

 

 save(zz, file = testmurali, version = 2)

 

 predict(rfoutput,newdata=testmurali,type=response)

Error in eval(expr, envir, enclos) : object 'imurder' not found

 

  

 

Best Regards,

Murali Godavarthi

mgodavar...@dpscs.state.md.us

 

 

 

 

 


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Regarding the 'R' Load Command

[Steve Lianoglou]

Hi,

On Tue, May 18, 2010 at 2:49 PM, Godavarthi, Murali
mgodavar...@dpscs.state.md.us wrote:
 Hi,

 I'm new to 'R' and need some help on the Load command. Any responses
 will be highly appreciated. Thanks in advance!

 As per manuals, the Load command expects a binary file input that is
 saved using a save command.

Or a path to the file ...

 However it is required that we need to
 call the 'R' program from

 Java web application using RJava, and pass a string to the 'R program
 instead of a binary file. Is it possible?

Yes, pay closer attention to the description for the file argument
in the load function (see ?load):

a (readable binary) connection **or a character string** giving the
name of the file to load

(emphasis mine)

 I was exploring the options of using TextConnections, file connections
 and other types of connections in order to read a stream of input
 (either from a file, stdin etc). I am able to read the string, but the
 Save and Load commands are not accepting the string input. Here is the
 sequence of commands I tried running, and the error received. There is
 no clue on this error, especially when trying to use the eval function
 in randomForest package, even on the internet. Can anyone help please!

 library(randomForest)

 randomForest 4.5-34

 Type rfNews() to see new features/changes/bug fixes.



 load(C://Program Files//R//R-2.10.1//bin//rfoutput)



 zz - file(ex.data, w)



 cat(\imurder\ \itheft\ \irobbery\ \iassault\ \idrug\
 \iburglary\ \igun\ \psych\ \Freq\ \priors\ \firstage\
 \intage\ \sex\ \race\ \marstat\ \empac\

 \educ\ \zipcode\ \suspendmn\ \drugs\ \alco\ \probation\
 \parole\,file = zz, sep = \n, fill = TRUE)



 cat(\10\ 0 0 0 1 0 0 0 0 0 58 19 19 \1\ \BLACK\ \SINGLE\
 \UNEMPLD\ 0 21215 0 0 0 1 0,file = zz, sep = \n, fill = TRUE)

What are you trying to do here?
It looks like you want to save a table of sorts. First create your
data into a data.frame, then save that data.frame to a file using
write.table (or write.csv, etc).

 save(zz, file = testmurali, version = 2)

You're saving a file object here, not the contents of the file.
Once you successfully serialize your data into a text file, just load
it from like normal using read.table (or similar).

Anyway, I'm not sure what we're talking about here, but in short:

1. You need to make sure that you are correctly saving what you think
you're saving.
2. You can pass a character string to the `load` function, so you can
send it through (over from) java as  you wich.
3. I don't think you really want to deal with load/save here, because
it looks like you are dealing with some tab delimited file -- in which
case use read.table (or similar) and load it that way. You can, of
course, still use save/load, but make sure you save/load the right
thing (not a file object like you're doing here).

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

__
R-help@r-project.org mailing list
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.