[R] RGoogleDocs stopped working
Harlan and Tal have had problems. I had lots too. I spent hours getting it to work. Terrible process to go through but RGoogleDocs is so useful that the time was worth it - I think! My problems were overcome when 1. I used the latest zip file by Duncan Temple Lang see below 2. I inserted an options line that loosened the ssl security - do not know if that was a good thing or not but it got it to work Duncan said: I have put an updated version of the source of the package with these changes. It is available from http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.tar.gz There is a binary for Windows in http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.zip Here is my script that works. Does yours look like this? library(RGoogleDocs) packageDescription(RGoogleDocs) ps -readline(prompt=get the password in ) options(RCurlOptions = list(capath = system.file(CurlSSL, cacert.pem, package = RCurl), ssl.verifypeer = FALSE)) sheets.con = getGoogleDocsConnection(getGoogleAuth(fjb...@gmail.com, ps, service =wise)) ts2=getWorksheets(OnCall,sheets.con) #OnCall is just the name of a spreadsheet names(ts2) y2005-sheetAsMatrix(ts2$y2005,header=TRUE, as.data.frame=TRUE, trim=TRUE) Finally, I am willing to offer you a TeamViewer session where we can take control of one another's computers and see if the problem is code or the installation. I warn you that I am neither a programmer nor a developer, just a very enthusiastic RGoogleDocs user who probably perseveres more than is good for him. Farrel Buchinsky [[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.
[R] Rcurl giving SSL grief
Do you use RGoogleDocs? If so can you please try run a script now and tell me if you get what I am getting? Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) : SSL certificate problem, verify that the CA cert is OK. Details: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed It came after I ran this: library(RGoogleDocs) ps -readline(prompt=get the password in ) sheets.con = getGoogleDocsConnection(getGoogleAuth(fx...@gmail.com, ps, service =wise)) ts2=getWorksheets(OnCall,sheets.con) I posted the question on StackOverflow at http://stackoverflow.com/questions/3442781/rgoogledocs-or-rcurl-giving-ssl-certificate-problem Is it a breach of etiquette to cross post? Farrel Buchinsky [[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] RGoogleDocs not working for me with quot; wisequot; service
Harlan Harris harlan at harris.name writes: Hello, I'm trying to figure out how to use the RGoogleDocs package from OmegaHat, and am having a bit of trouble. I emailed Duncan Temple Lang directly, but didn't receive a response, so I thought I'd try here to see if anyone else can help. I'm using 32-bit R 2.10.1 (Mac OS X), I built RGoogleDocs 0.4-0 from source, and I'm using XML 3.1-0 and RCurl 1.2-0. Are you able to access the conversation from Fri, Dec 11, 2009 at 20:07 titled Have you used RGoogleDocs and RGoogleData? In that conversation Duncan Temple Lang referred to an updated version of hte source packages. The latest version is 0.4-1. When one goes to the omegahat site the links lead one to version 0.4-0 which is not the most recent. I was having problems with 0.4-0 and they were resolved by 0.4-1. Try it! You'll like it! Here is what Dunacan Temple Lang wrote I have put an updated version of the source of the package with these changes. It is available from http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.tar.gz There is a binary for Windows in http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.zip __ 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] RGoogleDocs not working for me with quot; wisequot; service
Dear Duncan I am not the only one who thinks RGoogleDocs is fantastic. See below. I think it would save many people a lot of time and/or disappointment if the omegahat site were updated to show/offer 0.4-1 instead of 0.4-0. Am I correct in believing that I cannot change it, only you can? If so, then sorry for asking you to do more work. However, that is the price you pay when you do something so useful. Thanks. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jun 9, 2010 at 18:17, Harlan Harris har...@harris.name wrote: It works! How fantastic a capability, and how embarrassing that I missed that version change! Thanks very much! -Harlan On Wed, Jun 9, 2010 at 5:52 PM, Farrel Buchinsky fjb...@gmail.com wrote: Harlan Harris harlan at harris.name writes: Hello, I'm trying to figure out how to use the RGoogleDocs package from OmegaHat, and am having a bit of trouble. I emailed Duncan Temple Lang directly, but didn't receive a response, so I thought I'd try here to see if anyone else can help. I'm using 32-bit R 2.10.1 (Mac OS X), I built RGoogleDocs 0.4-0 from source, and I'm using XML 3.1-0 and RCurl 1.2-0. Are you able to access the conversation from Fri, Dec 11, 2009 at 20:07 titled Have you used RGoogleDocs and RGoogleData? In that conversation Duncan Temple Lang referred to an updated version of hte source packages. The latest version is 0.4-1. When one goes to the omegahat site the links lead one to version 0.4-0 which is not the most recent. I was having problems with 0.4-0 and they were resolved by 0.4-1. Try it! You'll like it! Here is what Dunacan Temple Lang wrote I have put an updated version of the source of the package with these changes. It is available from http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.tar.gz There is a binary for Windows in http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.zip __ 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. [[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] Form using R
Tal Galili tal.galili at gmail.com writes: Hi Nilza, I just wrote a more detailed answer to your question in the following post: Google spreadsheets + google forms + R = Easily collecting and importing data for analysishttp://www.r-statistics.com/2010/03/google-spreadsheets- google-forms-r-easily-collecting-and-importing-data-for-analysis/ on Fri, Mar 12, 2010 at 4:49 PM, Nilza BARROS nilzabarros at gmail.com wrote: Hi, R users We can create a form using R? I would like to create a form where the information can be read by R. Itneeds to be updated daily because I have to tabulate the reasons for delays in the generation of numerical models products. There is also a package called RGoogleData that can import data from Google Spreadsheets (even when they are not public). It has one benefit over RGoogleDocs; RGoogleData can download a spreadsheet as a csv file to your harddrive. You can then read the csv file into R - read.csv(). Those steps can easily be written into a script so that you do not have to manually futz with them each time. The benefit of the csv download is that it is very fast. Both the RGoogleDocs and the RGoogleData are slow in reading the spreadsheet into R. I understand, but may be wrong, that Google Stores all the data as HTML and its API spits it out as xml which these r packages then need to parse out line by line. The csv treatment by comparison is instantaneous. Only one big problem. As of a few months ago, RGoogleData has stopped working for me. I think it is still working for its writer, Adrian Dragulescu. Adrian has been very generous with his time in trying to help me. He predicts that he will go back to exploring his package once Google updates their API. Try it out. I would love to hear what happens. http://r-forge.r-project.org/projects/rgoogledata/ __ 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] Have you used RGoogleDocs and RGoogleData?
Dear Adrian
Are you able to help me with problems that I am having with RGoogleData? I
would greatly appreciate it if you could give me some general trouble
shooting ideas or better yet if you could fix the problem.
I believe that I updated to the latest version of RGoogleData as evidenced
by
packageDescription(RGoogleData)
Package: RGoogleData
Type: Package
Title: An R interface to Google Data (Docs, Calendar, Contacts, Finance,
etc.)
Version: 0.2.0
Date: 2009-12-11
Depends: rJava
Author: Adrian A. Dragulescu
Maintainer: Adrian A. Dragulescu adrian.dragule...@gmail.com
Description: Provide R access to Google Data API.
License: GPL-3
Repository: R-Forge
Repository/R-Forge/Project: rgoogledata
Repository/R-Forge/Revision: 6
Date/Publication: 2009-12-13 21:43:52
Packaged: 2009-12-14 21:05:13 UTC; rforge
Built: R 2.10.1; ; 2009-12-14 23:02:39 UTC; windows
-- File: C:/PROGRA~2/R/R-210~1.1/library/RGoogleData/Meta/package.rds
But Alas
My previous script has stopped working.
library(RGoogleData)
ps -readline(prompt=get the password in )
con -googleConnect(fjb...@gmail.com,ps)
allXls - getSpreadsheets(con)
xls - allXls[[which(sapply(allXls, slot, title) == OnCall)]]
allWks - getWorksheets(xls)# get the worksheets
Error in .jcall(RJavaTools, Ljava/lang/Object;, invokeMethod, cl, :
java.lang.ClassCastException: com.google.gdata.data.TextContent cannot be
cast to com.google.gdata.data.OutOfLineContent
I also tried:
target -downloadDocument(doc=OnCall,
filepath=C:/Users/fbuchinsky/Documents/My Dropbox/OnCalltrial.csv,
fileformat=csv, sheetIndex=1)
Error in regexpr(%3A, d...@key) :
trying to get slot key from an object of a basic class (character)
with no slots
Farrel Buchinsky
Sent from Pittsburgh, Pennsylvania, United States
On Thu, Dec 10, 2009 at 10:38, Adrian Dragulescu adria...@eskimo.comwrote:
I will try to have something in place by Monday to allow you to download a
specific sheet not default to the first. I will let you know.
Adrian
On Thu, 10 Dec 2009, Farrel Buchinsky wrote:
Thank you Adrian. Your response was very informative.
?downloadDocument filled me with excitement untill I read, If you try to
download a spreadsheet with multiple worksheets into a 'csv' or 'tsv'
format, only the first worksheet will be downloaded.
So now there is a convenient fast way to read data under two circumstances
1. if the spreadsheet has been
published
http://blog.revolution-computing.com/2009/09/how-to-use-a-google-spreadsheet-as-data-in-r.html
2. if one only wants the first sheet (RGoogleData's downloadDocument()).
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
Sent from Pittsburgh, Pennsylvania, United States
On Thu, Dec 10, 2009 at 09:32, Adrian Dragulescu adria...@eskimo.com
wrote:
Farrel,
Please read the manuals. On the RGoogleData package page you can read:
The package provides R access to Google services through the Google
supported Java API.
[...]
A package with very similar functionality is maintained by Duncan Temple
Lang at \url{http://www.omegahat.org/RGoogleDocs/}. The approach taken
there is to use \code{RCurl} and \code{XML} to interact with the lower
level Google HTML protocol. You should check it out too.
Regarding the questions you have about speed. Google spreadsheets is
labeled Labs, mabye there are performance issues on Google side. The
approach for both RGoogleDocs and RGoogleData is to make requests to the
Google servers and parse the XML results. RGoogleDocs parses using a C
library, RGoogleData uses a Java library. Going through the Java
interface
is an extra step, so that might explain the speed difference.
Check ?downloadDocument if you want to download the entire document. It
should be fast. You can load it into R after that.
Best,
Adrian
On Wed, 9 Dec 2009, Farrel Buchinsky wrote:
Both of these applications fulfill a great need of mine: to read data
directly from google spreadsheets that are private to myself and one or
two
collaborators. Thanks to the authors. I had been using RGoogleDocs for
the
about 6 months (maybe more) but have had to stop using it in the past
month
since for some reason that I do not understand it no longer reads google
spreadsheets. I loved it. Its loss depresses me. I started using
RGoogleData
which works.
I have noticed that both packages read data slowly. RGoogleData is much
slower than RGoogleDocs used to be. Both seem a lot slower than if one
manually downloaded a google spreadsheet as a csv and then used read.csv
function - but then I would not be able to use scripts and execute
without
finding and futzing.
Can anyone explain in English why these packages read slower than a csv
download?
Can anyone explain what the core difference is between the two packages?
Can anyone share their experience with reading Google data straight into
R?
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
Sent from Pittsburgh, Pennsylvania, United States
Re: [R] Have you used RGoogleDocs and RGoogleData?
It Works! Thanks a lot! Its great. What were your few minor, but important, changes - in a nutshell. I will not understand unless you describe it as high level issues. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Fri, Dec 11, 2009 at 19:07, Duncan Temple Lang dun...@wald.ucdavis.eduwrote: Hi Farrel I have taken a look at the problems using RGoogleDocs to read spreadsheets and was able to reproduce the problem I believe you were having. A few minor, but important, changes and I can read spreadsheets again and apparently still other types of documents. I have put an updated version of the source of the package with these changes. It is available from http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.tar.gz There is a binary for Windows in http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.4-1.zip Hopefully this will cure the problems you have been experiencing. I'd appreciate knowing either way. Thanks, D. Farrel Buchinsky wrote: Both of these applications fulfill a great need of mine: to read data directly from google spreadsheets that are private to myself and one or two collaborators. Thanks to the authors. I had been using RGoogleDocs for the about 6 months (maybe more) but have had to stop using it in the past month since for some reason that I do not understand it no longer reads google spreadsheets. I loved it. Its loss depresses me. I started using RGoogleData which works. I have noticed that both packages read data slowly. RGoogleData is much slower than RGoogleDocs used to be. Both seem a lot slower than if one manually downloaded a google spreadsheet as a csv and then used read.csv function - but then I would not be able to use scripts and execute without finding and futzing. Can anyone explain in English why these packages read slower than a csv download? Can anyone explain what the core difference is between the two packages? Can anyone share their experience with reading Google data straight into R? Farrel Buchinsky Google Voice Tel: (412) 567-7870 Sent from Pittsburgh, Pennsylvania, United States [[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. [[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] Have you used RGoogleDocs and RGoogleData?
Thank you Adrian. Your response was very informative.
?downloadDocument filled me with excitement untill I read, If you try to
download a spreadsheet with multiple worksheets into a 'csv' or 'tsv'
format, only the first worksheet will be downloaded.
So now there is a convenient fast way to read data under two circumstances
1. if the spreadsheet has been
publishedhttp://blog.revolution-computing.com/2009/09/how-to-use-a-google-spreadsheet-as-data-in-r.html
2. if one only wants the first sheet (RGoogleData's downloadDocument()).
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
Sent from Pittsburgh, Pennsylvania, United States
On Thu, Dec 10, 2009 at 09:32, Adrian Dragulescu adria...@eskimo.comwrote:
Farrel,
Please read the manuals. On the RGoogleData package page you can read:
The package provides R access to Google services through the Google
supported Java API.
[...]
A package with very similar functionality is maintained by Duncan Temple
Lang at \url{http://www.omegahat.org/RGoogleDocs/}. The approach taken
there is to use \code{RCurl} and \code{XML} to interact with the lower
level Google HTML protocol. You should check it out too.
Regarding the questions you have about speed. Google spreadsheets is
labeled Labs, mabye there are performance issues on Google side. The
approach for both RGoogleDocs and RGoogleData is to make requests to the
Google servers and parse the XML results. RGoogleDocs parses using a C
library, RGoogleData uses a Java library. Going through the Java interface
is an extra step, so that might explain the speed difference.
Check ?downloadDocument if you want to download the entire document. It
should be fast. You can load it into R after that.
Best,
Adrian
On Wed, 9 Dec 2009, Farrel Buchinsky wrote:
Both of these applications fulfill a great need of mine: to read data
directly from google spreadsheets that are private to myself and one or
two
collaborators. Thanks to the authors. I had been using RGoogleDocs for the
about 6 months (maybe more) but have had to stop using it in the past
month
since for some reason that I do not understand it no longer reads google
spreadsheets. I loved it. Its loss depresses me. I started using
RGoogleData
which works.
I have noticed that both packages read data slowly. RGoogleData is much
slower than RGoogleDocs used to be. Both seem a lot slower than if one
manually downloaded a google spreadsheet as a csv and then used read.csv
function - but then I would not be able to use scripts and execute without
finding and futzing.
Can anyone explain in English why these packages read slower than a csv
download?
Can anyone explain what the core difference is between the two packages?
Can anyone share their experience with reading Google data straight into
R?
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
Sent from Pittsburgh, Pennsylvania, United States
[[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] Have you used RGoogleDocs and RGoogleData?
That would be fantastic. How about an option whereby all the worksheets are
downloaded and read into dataframes and appear as a a list of dataframes?
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
On Thu, Dec 10, 2009 at 10:38, Adrian Dragulescu adria...@eskimo.comwrote:
I will try to have something in place by Monday to allow you to download a
specific sheet not default to the first. I will let you know.
Adrian
On Thu, 10 Dec 2009, Farrel Buchinsky wrote:
Thank you Adrian. Your response was very informative.
?downloadDocument filled me with excitement untill I read, If you try to
download a spreadsheet with multiple worksheets into a 'csv' or 'tsv'
format, only the first worksheet will be downloaded.
So now there is a convenient fast way to read data under two circumstances
1. if the spreadsheet has been
published
http://blog.revolution-computing.com/2009/09/how-to-use-a-google-spreadsheet-as-data-in-r.html
2. if one only wants the first sheet (RGoogleData's downloadDocument()).
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
Sent from Pittsburgh, Pennsylvania, United States
On Thu, Dec 10, 2009 at 09:32, Adrian Dragulescu adria...@eskimo.com
wrote:
Farrel,
Please read the manuals. On the RGoogleData package page you can read:
The package provides R access to Google services through the Google
supported Java API.
[...]
A package with very similar functionality is maintained by Duncan Temple
Lang at \url{http://www.omegahat.org/RGoogleDocs/}. The approach taken
there is to use \code{RCurl} and \code{XML} to interact with the lower
level Google HTML protocol. You should check it out too.
Regarding the questions you have about speed. Google spreadsheets is
labeled Labs, mabye there are performance issues on Google side. The
approach for both RGoogleDocs and RGoogleData is to make requests to the
Google servers and parse the XML results. RGoogleDocs parses using a C
library, RGoogleData uses a Java library. Going through the Java
interface
is an extra step, so that might explain the speed difference.
Check ?downloadDocument if you want to download the entire document. It
should be fast. You can load it into R after that.
Best,
Adrian
On Wed, 9 Dec 2009, Farrel Buchinsky wrote:
Both of these applications fulfill a great need of mine: to read data
directly from google spreadsheets that are private to myself and one or
two
collaborators. Thanks to the authors. I had been using RGoogleDocs for
the
about 6 months (maybe more) but have had to stop using it in the past
month
since for some reason that I do not understand it no longer reads google
spreadsheets. I loved it. Its loss depresses me. I started using
RGoogleData
which works.
I have noticed that both packages read data slowly. RGoogleData is much
slower than RGoogleDocs used to be. Both seem a lot slower than if one
manually downloaded a google spreadsheet as a csv and then used read.csv
function - but then I would not be able to use scripts and execute
without
finding and futzing.
Can anyone explain in English why these packages read slower than a csv
download?
Can anyone explain what the core difference is between the two packages?
Can anyone share their experience with reading Google data straight into
R?
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
Sent from Pittsburgh, Pennsylvania, United States
[[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.
[R] Have you used RGoogleDocs and RGoogleData?
Both of these applications fulfill a great need of mine: to read data directly from google spreadsheets that are private to myself and one or two collaborators. Thanks to the authors. I had been using RGoogleDocs for the about 6 months (maybe more) but have had to stop using it in the past month since for some reason that I do not understand it no longer reads google spreadsheets. I loved it. Its loss depresses me. I started using RGoogleData which works. I have noticed that both packages read data slowly. RGoogleData is much slower than RGoogleDocs used to be. Both seem a lot slower than if one manually downloaded a google spreadsheet as a csv and then used read.csv function - but then I would not be able to use scripts and execute without finding and futzing. Can anyone explain in English why these packages read slower than a csv download? Can anyone explain what the core difference is between the two packages? Can anyone share their experience with reading Google data straight into R? Farrel Buchinsky Google Voice Tel: (412) 567-7870 Sent from Pittsburgh, Pennsylvania, United States [[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] Reading from Google Docs
Is anyone using RGoogleDocs? If so have you used it in the last few weeks
and is it working as it used to. Look at the problem I have run into.
Farrel Buchinsky
On Sat, Nov 28, 2009 at 14:25, Farrel Buchinsky fjb...@gmail.com wrote:
Thank you for the interest in my problem.
I have been using the same script (see below) successfully for the past 5
months and now all of a sudden I have problems. Could R be
functioning differently under 2.10? Could Google have changed their
authentication procedures? In other words are you currently able to read
spreadsheets into R the way you used to?
library(RGoogleDocs)
ps -readline(prompt=get the password in )
sheets.con = getGoogleDocsConnection(getGoogleAuth(fjb...@gmail.com, ps,
service =wise))
ts2=getWorksheets(OnCall,sheets.con)
Error in getDocs(con) : problems connecting to get the list of documents
I used options(error = recover) to troubleshoot but alas I am none the
wiser (no pun intended). I am pasting the output here. Can you see where the
problem is coming from? [By the way, I changed my script temporarily to
service=writely and the getDocs command worked. If I remember correctly
RGoogleDocs had a problem about 6 months ago whereby one could list the
documents but not the spreadsheets and then you fixed it. ]
Enter a frame number, or 0 to exit
1: getWorksheets(OnCall, sheets.con)
2: getDocs(con)
Selection: 2
Called from: eval(expr, envir, enclos)
Browse[1] objects()
[1] as.data.frame auth curl folders h
statuswhat x
Browse[1] body()
{
if (what %in% names(GoogleURLs))
what = GoogleURLs[what]
else if (is(curl, GoogleSpreadsheetsConnection))
what = GoogleURLs[spreadsheets]
curlSetOpt(customrequest = GET, curl = curl)
h = basicTextGatherer()
if (folders)
what = paste(what, showfolders=true, sep = ?)
x = getURL(what, curl = curl, headerfunction = h$update,
followlocation = TRUE, ...)
status = parseHTTPHeader(h$value())
if (floor(as.numeric(status[[status]])/100) != 2)
stop(problems connecting to get the list of documents)
doc = xmlParse(x, asText = TRUE)
if (toupper(xmlName(xmlRoot(doc))) == HTML)
stop(Can't get document list. Is the connection still valid?
Perhaps initialize a new connection.)
convertDocList(doc, curl, as.data.frame)
}
Browse[1] status
WWW-Authenticate
Content-Type
GoogleLogin realm=\http://www.google.com/accounts/ClientLogin\;,
service=\writely\
text/html; charset=UTF-8
Date
Expires
Sat, 28 Nov 2009
19:04:22 GMT Sat,
28 Nov 2009 19:04:22 GMT
Cache-Control
X-Content-Type-Options
private, max-age=0
nosniff
X-XSS-Protection
X-Frame-Options
0
SAMEORIGIN
Server
Transfer-Encoding
GFE/2.0
chunked
status
statusMessage
401
Token invalid
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
On Sat, Nov 28, 2009 at 12:45, Duncan Temple Lang dun...@wald.ucdavis.edu
wrote:
Farrel Buchinsky wrote:
Please oh please could someone help me or at least confirm that they are
having the same problem.
Why am I getting the error message from RGoogleDocs
getDocs(sheets.con)
Error in getDocs(sheets.con) :
problems connecting to get the list of documents
You are using a connection to the wise service (for worksheets)
to get the list of documents from the document service.
If you call getDocs() with an connection to writely, I
imagine it will succeed.
So you have a token, but it is for the wrong thing.
How do I troubleshoot?
The first thing is to learn about debugging in R.
For example,
options(error = recover)
getDocs(sheets.con)
The error occurs and you are presented with a menu prompt that allows you
to select the call frame of interest. There is only one - getDocs().
Enter 1 Return. Now you have an R prompt that allows you to explore
the call frame.
objects()
body()
Take a look at status
status
WWW-Authenticate
GoogleLogin realm=\http://www.google.com/accounts/ClientLogin\;,
service=\writely\
Content-Type
text/html;
charset=UTF-8
Date
Sat, 28 Nov 2009
17:36:16 GMT
Expires
Sat, 28 Nov 2009
17:36:16 GMT
Cache-Control
private, max-age=0
X-Content-Type-Options
nosniff
X-XSS-Protection
0
X-Frame-Options
SAMEORIGIN
Server
GFE/2.0
Transfer-Encoding
chunked
status
401
statusMessage
Token invalid
This is the parsed
Re: [R] Reading from Google Docs
Please oh please could someone help me or at least confirm that they are having the same problem. Why am I getting the error message from RGoogleDocs getDocs(sheets.con) Error in getDocs(sheets.con) : problems connecting to get the list of documents How do I troubleshoot? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Nov 25, 2009 at 17:08, Farrel Buchinsky fjb...@gmail.com wrote: Oh OH! Could you please help with a problem that I never used to get. library(RGoogleDocs) ps -readline(prompt=get the password in ) sheets.con = getGoogleDocsConnection(getGoogleAuth(fjb...@gmail.com, ps, service =wise)) ts2=getWorksheets(OnCall,sheets.con) Those opening lines of script used to work flawlesly. Now I get. Error in getDocs(con) : problems connecting to get the list of documents Yet I got it to work earlier while I had been toying with RGoogleData package in another session. Could RGoogleData have opened something for RGoogleDocs to use? Farrel Buchinsky Google Voice Tel: (412) 567-7870 Sent from Pittsburgh, Pennsylvania, United States On Wed, Nov 25, 2009 at 16:34, Farrel Buchinsky fjb...@gmail.com wrote: That was painless. I had already installed Rtools and had already put it on my path. Your line worked very well. [Thanks for telling me. However I did it last time was worse than sticking daggers in my eyes. ] install.packages( RGoogleDocs, repos=http://www.omegahat.org/R;, type=source ) I now have Package: RGoogleDocs Version: 0.4-0 Title: Maintainer: Duncan Temple Lang dun...@wald.ucdavis.edu Packaged: 2009-10-27 22:10:22 UTC; duncan Built: R 2.10.0; ; 2009-11-25 20:59:03 UTC; windows I am providing the following link to a copy of my RGoogleDocs zipped directory. It is for people who run R in windows and do not want to go through the pain of setting things up so that they can install source. http://dl.dropbox.com/u/23200/RGoogleDocs/RGoogleDocs.zip I BELIEVE that if one downloads the zip and extracts it to an empty directory called RGoogleDocs in one's Library directory then everything will work. Please let me know. Farrel Buchinsky Google Voice Tel: (412) 567-7870 [[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] Reading from Google Docs
Thank you for the interest in my problem.
I have been using the same script (see below) successfully for the past 5
months and now all of a sudden I have problems. Could R be
functioning differently under 2.10? Could Google have changed their
authentication procedures? In other words are you currently able to read
spreadsheets into R the way you used to?
library(RGoogleDocs)
ps -readline(prompt=get the password in )
sheets.con = getGoogleDocsConnection(getGoogleAuth(fjb...@gmail.com, ps,
service =wise))
ts2=getWorksheets(OnCall,sheets.con)
Error in getDocs(con) : problems connecting to get the list of documents
I used options(error = recover) to troubleshoot but alas I am none the wiser
(no pun intended). I am pasting the output here. Can you see where the
problem is coming from? [By the way, I changed my script temporarily to
service=writely and the getDocs command worked. If I remember correctly
RGoogleDocs had a problem about 6 months ago whereby one could list the
documents but not the spreadsheets and then you fixed it. ]
Enter a frame number, or 0 to exit
1: getWorksheets(OnCall, sheets.con)
2: getDocs(con)
Selection: 2
Called from: eval(expr, envir, enclos)
Browse[1] objects()
[1] as.data.frame auth curl folders h
statuswhat x
Browse[1] body()
{
if (what %in% names(GoogleURLs))
what = GoogleURLs[what]
else if (is(curl, GoogleSpreadsheetsConnection))
what = GoogleURLs[spreadsheets]
curlSetOpt(customrequest = GET, curl = curl)
h = basicTextGatherer()
if (folders)
what = paste(what, showfolders=true, sep = ?)
x = getURL(what, curl = curl, headerfunction = h$update,
followlocation = TRUE, ...)
status = parseHTTPHeader(h$value())
if (floor(as.numeric(status[[status]])/100) != 2)
stop(problems connecting to get the list of documents)
doc = xmlParse(x, asText = TRUE)
if (toupper(xmlName(xmlRoot(doc))) == HTML)
stop(Can't get document list. Is the connection still valid?
Perhaps initialize a new connection.)
convertDocList(doc, curl, as.data.frame)
}
Browse[1] status
WWW-Authenticate
Content-Type
GoogleLogin realm=\http://www.google.com/accounts/ClientLogin\;,
service=\writely\
text/html; charset=UTF-8
Date
Expires
Sat, 28 Nov 2009
19:04:22 GMT Sat,
28 Nov 2009 19:04:22 GMT
Cache-Control
X-Content-Type-Options
private,
max-age=0
nosniff
X-XSS-Protection
X-Frame-Options
0
SAMEORIGIN
Server
Transfer-Encoding
GFE/2.0
chunked
status
statusMessage
401
Token invalid
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
On Sat, Nov 28, 2009 at 12:45, Duncan Temple Lang
dun...@wald.ucdavis.eduwrote:
Farrel Buchinsky wrote:
Please oh please could someone help me or at least confirm that they are
having the same problem.
Why am I getting the error message from RGoogleDocs
getDocs(sheets.con)
Error in getDocs(sheets.con) :
problems connecting to get the list of documents
You are using a connection to the wise service (for worksheets)
to get the list of documents from the document service.
If you call getDocs() with an connection to writely, I
imagine it will succeed.
So you have a token, but it is for the wrong thing.
How do I troubleshoot?
The first thing is to learn about debugging in R.
For example,
options(error = recover)
getDocs(sheets.con)
The error occurs and you are presented with a menu prompt that allows you
to select the call frame of interest. There is only one - getDocs().
Enter 1 Return. Now you have an R prompt that allows you to explore
the call frame.
objects()
body()
Take a look at status
status
WWW-Authenticate
GoogleLogin realm=\http://www.google.com/accounts/ClientLogin\;,
service=\writely\
Content-Type
text/html;
charset=UTF-8
Date
Sat, 28 Nov 2009
17:36:16 GMT
Expires
Sat, 28 Nov 2009
17:36:16 GMT
Cache-Control
private,
max-age=0
X-Content-Type-Options
nosniff
X-XSS-Protection
0
X-Frame-Options
SAMEORIGIN
Server
GFE/2.0
Transfer-Encoding
chunked
status
401
statusMessage
Token invalid
This is the parsed header of the reply from the GoogleDocs server.
x contains the result of the query and it is an HTML document with the
(same) error message.
Farrel Buchinsky
Google Voice Tel: (412) 567-7870
On Wed, Nov 25, 2009 at 17
Re: [R] Reading from Google Docs
I recently installed R 2.10 Now I get library(RGoogleDocs) Loading required package: RCurl Loading required package: bitops Loading required package: XML Attaching package: 'RGoogleDocs' The following object(s) are masked from package:methods : getAccess Warning message: package 'RGoogleDocs' was built under R version 2.9.1 and help will not work correctly Please re-install it But alas reinstalling it does not take away the error message. Farrel Buchinsky Google Voice Tel: (412) 567-7870 Sent from Pittsburgh, Pennsylvania, United States On Thu, Jul 9, 2009 at 08:15, Duncan Temple Lang dun...@wald.ucdavis.eduwrote: Thanks for pointing that out. Yes, the link on the package web site was for 0.2-1 and that was the one used to build the binary for Windows. Now updated in both places and the binary repository will give 0.2-2. How to find the version of an installed package? packageDescription(RGoogleDocs) D. Farrel Buchinsky wrote: Dear Duncan On my home computer I was able to use install.packages(RGoogleDocs, repos = http://www.omegahat.org/R;) But, alas it would not read the data in the spreadsheet. It went back to its nasty ways Error in !includeEmpty : invalid argument type That is what I was getting with version 0.2-1.You then sent me link to 0.2-2 (in source code) which is what worked. Is it possible that that the windows binary version you put in omegahat was 0.2-1 and not 0.2-2? I did not know how to tell what version had been installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 22:53, Duncan Temple Lang dun...@wald.ucdavis.edumailto: dun...@wald.ucdavis.edu wrote: Farrel Buchinsky wrote: Boy oh boy that process of getting source to binary was super painful. Now that I have the package as binary I can share the whole folder with my coworker and she is able to use RGoogleDocs. I intend to use the same process for the other two windows machines that I use. I really do not want to go through the same installation and path hassles all over again. Should I post my directory containing the binary files somewhere so that others do not have to experience pain. Does etiquette dictate that I should post the directory to help other or does etiquette dictate that it is Duncan Temple Lang's code and thus it his prerogative to distribute his work as he wishes? Etiquette is one thing and the license another. Both encourage you to help others and make the binary available to others. And indeed, I hope that Windows users do build binaries for others and remove the additional work from those who provide the software in the first place. Having seen this thread today, I did put a binary version of RGoogleDocs on the Omegahat repository so install.packages(RGoogleDocs, repos = http://www.omegahat.org/R;) should install it and, if I had had time earlier, saved you the hardship of building the binary. Sorry to do it so soon after. D. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:59, Farrel Buchinsky fjb...@gmail.com mailto:fjb...@gmail.com wrote: Does changing the path in Windows work in real time or does one need to restart the computer for the changes to take effect. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:04, Gabor Grothendieck ggrothendi...@gmail.com mailto:ggrothendi...@gmail.com wrote: Its safer just to temporarily add it to your path. Unfortunately Rtools has a find command that conflicts with the find command in Windows so if you add the Rtools bin directory to your path permanently then you could find other programs stop working. That actually happened to me once and it took the longest time until I discovered that Rtools was the culprit. If you follow the advice I gave you normally won't have that problem. On Wed, Jul 8, 2009 at 11:21 AM, Duncan Murdochmurd...@stats.uwo.ca mailto:murd...@stats.uwo.ca wrote: On 08/07/2009 10:13 AM, Farrel Buchinsky wrote: Forgive my naivte, but how do I make windows find tar. In other words from where do I issue the command and what is the command. You need to install the toolset, and let the installer set your path. Duncan Murdoch Farrel
Re: [R] Reading from Google Docs
That was painless. I had already installed Rtools and had already put it on my path. Your line worked very well. [Thanks for telling me. However I did it last time was worse than sticking daggers in my eyes. ] install.packages( RGoogleDocs, repos=http://www.omegahat.org/R;, type=source ) I now have Package: RGoogleDocs Version: 0.4-0 Title: Maintainer: Duncan Temple Lang dun...@wald.ucdavis.edu Packaged: 2009-10-27 22:10:22 UTC; duncan Built: R 2.10.0; ; 2009-11-25 20:59:03 UTC; windows I am providing the following link to a copy of my RGoogleDocs zipped directory. It is for people who run R in windows and do not want to go through the pain of setting things up so that they can install source. http://dl.dropbox.com/u/23200/RGoogleDocs/RGoogleDocs.zip I BELIEVE that if one downloads the zip and extracts it to an empty directory called RGoogleDocs in one's Library directory then everything will work. Please let me know. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Nov 25, 2009 at 15:15, Charlie Sharpsteen ch...@sharpsteen.netwrote: On Wed, Nov 25, 2009 at 12:02 PM, Farrel Buchinsky fjb...@gmail.com wrote: I reinstalled from a binary that Duncan Temple Lang placed in omegahat. I see that omegahat has a subdirectory for each version of R. There is not a directory for 2.10. I took the liberty of taking it from the 2.9 directory. That explains the warning message. Who knows what crime I committed. Is that first or third degree murder. Well, it's just a warning-- so it shouldn't be a show-stopper. And from what I see the warning is only referring to the package help pages, which are available online. It looks like the functionality of the package should still work just fine if you don't want to bother with a reinstall. I saw however that there is a far more recent version of RGoogleDocs (Last Release: 0.4-0 (27 Oct 2009)). But it is in tar.gz. I assume that it is in source. Once before I spent about 27000 hours getting a source to become a binary. I don't know how I finally got it right and am reluctant to wander into that swamp again. Farrel Buchinsky This shouldn't be extraordinarily difficult-- unfortunately Murphy's Law does come into play sometimes. But it should just be a matter of: install.packages( RGoogleDocs, repos=http://www.omegahat.org/R;, type=source ) And that's it for Linux, Mac OS or other UNIX-based system. With Windows you will first have to install the toolset available at: http://www.murdoch-sutherland.com/Rtools/ Grab the Rtools210 installer as you are using R 2.10.x. Install using the Package Authoring option and make sure you check any options that ask about modifying your PATH. Good luck! -Charlie [[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] Reading from Google Docs
Oh OH! Could you please help with a problem that I never used to get. library(RGoogleDocs) ps -readline(prompt=get the password in ) sheets.con = getGoogleDocsConnection(getGoogleAuth(fjb...@gmail.com, ps, service =wise)) ts2=getWorksheets(OnCall,sheets.con) Those opening lines of script used to work flawlesly. Now I get. Error in getDocs(con) : problems connecting to get the list of documents Yet I got it to work earlier while I had been toying with RGoogleData package in another session. Could RGoogleData have opened something for RGoogleDocs to use? Farrel Buchinsky Google Voice Tel: (412) 567-7870 Sent from Pittsburgh, Pennsylvania, United States On Wed, Nov 25, 2009 at 16:34, Farrel Buchinsky fjb...@gmail.com wrote: That was painless. I had already installed Rtools and had already put it on my path. Your line worked very well. [Thanks for telling me. However I did it last time was worse than sticking daggers in my eyes. ] install.packages( RGoogleDocs, repos=http://www.omegahat.org/R;, type=source ) I now have Package: RGoogleDocs Version: 0.4-0 Title: Maintainer: Duncan Temple Lang dun...@wald.ucdavis.edu Packaged: 2009-10-27 22:10:22 UTC; duncan Built: R 2.10.0; ; 2009-11-25 20:59:03 UTC; windows I am providing the following link to a copy of my RGoogleDocs zipped directory. It is for people who run R in windows and do not want to go through the pain of setting things up so that they can install source. http://dl.dropbox.com/u/23200/RGoogleDocs/RGoogleDocs.zip I BELIEVE that if one downloads the zip and extracts it to an empty directory called RGoogleDocs in one's Library directory then everything will work. Please let me know. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Nov 25, 2009 at 15:15, Charlie Sharpsteen ch...@sharpsteen.netwrote: On Wed, Nov 25, 2009 at 12:02 PM, Farrel Buchinsky fjb...@gmail.com wrote: I reinstalled from a binary that Duncan Temple Lang placed in omegahat. I see that omegahat has a subdirectory for each version of R. There is not a directory for 2.10. I took the liberty of taking it from the 2.9 directory. That explains the warning message. Who knows what crime I committed. Is that first or third degree murder. Well, it's just a warning-- so it shouldn't be a show-stopper. And from what I see the warning is only referring to the package help pages, which are available online. It looks like the functionality of the package should still work just fine if you don't want to bother with a reinstall. I saw however that there is a far more recent version of RGoogleDocs (Last Release: 0.4-0 (27 Oct 2009)). But it is in tar.gz. I assume that it is in source. Once before I spent about 27000 hours getting a source to become a binary. I don't know how I finally got it right and am reluctant to wander into that swamp again. Farrel Buchinsky This shouldn't be extraordinarily difficult-- unfortunately Murphy's Law does come into play sometimes. But it should just be a matter of: install.packages( RGoogleDocs, repos=http://www.omegahat.org/R;, type=source ) And that's it for Linux, Mac OS or other UNIX-based system. With Windows you will first have to install the toolset available at: http://www.murdoch-sutherland.com/Rtools/ Grab the Rtools210 installer as you are using R 2.10.x. Install using the Package Authoring option and make sure you check any options that ask about modifying your PATH. Good luck! -Charlie [[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] RGoogleDocs: getDocs() - problems connecting to get the list of documents
It is working for me. Are you using the latest version as in Version: 0.2-2? Blackett, Matthew wrote: Hi I have been using RGoogleDocs successfully for some time now but something seems to have happened which is preventing me from accessing my data in google spreadsheets. I get the message: problems connecting to get the list of documents when I use getDocs, despite being logged in e.g. sheets.con = getGoogleDocsConnection(getGoogleAuth(username, password, service = wise)) ts = getWorksheets(formname, sheets.con) รจ Error in getDocs(con) : problems connecting to get the list of documents Does anyone know what might be causing this? Is it maybe a problem at the google end? Matthew Blackett Researcher King's College London http://geography.kcl.ac.uk/micromet/MBlackett/ [[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. -- View this message in context: http://www.nabble.com/RGoogleDocs%3A-getDocs%28%29---%22problems-connecting-to-get-the-list-of-documents%22-tp24969136p24970787.html Sent from the R help mailing list archive at Nabble.com. __ 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] space in column name
I read a table from Microsoft Access using RODBC. Some of the variables had a name with a space in it. R has no problem with it but I do. I cannot find out how to specify the space names(alltime) [1] IDLVL7 Ref Pv No Ref Pv Name DOS Pt Last Name Pt First Name MRN CPT CPT Desc DxCd1 DxCd2 DxCd3 DxCd4 [15] DOE But what do I do if I want to do something such as this alltime[grep(MIDDLE EAR EXPLORE,alltime$CPT Desc,] Error: unexpected symbol in alltime[grep(MIDDLE EAR EXPLORE,alltime$CPT Desc Farrel Buchinsky Sent from Pittsburgh, Pennsylvania, United States [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] space in column name
I sifted some more and read about a workaround for the problem. I could simply rename the columns so that there were no more spaces names(alltime) -gsub( ,., names(alltime)) names(alltime) [1] IDLVL7 Ref.Pv.No Ref.Pv.Name DOS Pt.Last.Name Pt.First.Name MRN CPT CPT.Desc DxCd1 DxCd2 DxCd3 DxCd4 [15] DOE Farrel Buchinsky Google Voice Tel: (412) 567-7870 Sent from Pittsburgh, Pennsylvania, United States On Sun, Jul 19, 2009 at 14:32, Farrel Buchinsky fjb...@gmail.com wrote: I read a table from Microsoft Access using RODBC. Some of the variables had a name with a space in it. R has no problem with it but I do. I cannot find out how to specify the space names(alltime) [1] IDLVL7 Ref Pv No Ref Pv Name DOS Pt Last Name Pt First Name MRN CPT CPT Desc DxCd1 DxCd2 DxCd3 DxCd4 [15] DOE But what do I do if I want to do something such as this alltime[grep(MIDDLE EAR EXPLORE,alltime$CPT Desc,] Error: unexpected symbol in alltime[grep(MIDDLE EAR EXPLORE,alltime$CPT Desc Farrel Buchinsky Sent from Pittsburgh, Pennsylvania, United States [[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] Reading from Google Docs
I have previously read R Installation and Administration. I read it again. It does not help me The relevant paragraph is below. But I need lower level instructions. Where can I find them. R CMD INSTALL works in Windows to install source packages if you have the source-code package files (option ยSource Package Installation Filesย in the installer) and toolset (see The Windows toolsetfile:///C:/Program%20Files/R/R-2.9.1/doc/manual/R-admin.html#The-Windows-toolset) installed. Installation of binary packages must be done by install.packages . R CMD INSTALL --help will tell you the current options under Windows (which differ from those on a Unix-alike): in particular there is a choice of the types of documentation to be installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 2009/6/19 Uwe Ligges lig...@statistik.tu-dortmund.de See the manual R Installation and Administration for information on how to install source packages on Windows. Uwe Ligges Farrel Buchinsky wrote: After issuing tar xvfz RgoogleDocs_0.2.2-src.tar.gzI am getting an error message 'tar' is not recongnized as an internal or external command, operable program or batch file. Should I use my 7-zip to open up the archive? Where should I be doing this? For instance can I do it all in my download directory or should I do it in C:\Program Files\R\R-2.9.0\library or should I manually create C:\Program Files\R\R-2.9.0\library\RGoogleDocs and do it all there or will the Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz command do that for me. Yes, you assumed correctly. I am using Windows XP. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Thu, Jun 18, 2009 at 20:17, Gabor Grothendieck ggrothendi...@gmail.comwrote: I have haven't neen following this thread but: 1. if RGoogleDocs_0.2-2.tar.gz is a source distribution (as opposed to built source) then the first line renames it so that its not the same name as the built file about to be created. The second line detars it into the RGoogleDocs directory. The third builds the built source file, RGoogleDocs_0.2-2.tar.gz. The fourth installs the built source file into R. I've assumed Windows. If you are on Linux replace rename with mv. rename RGoogleDocs_0.2-2.tar.gz RgoogleDocs_0.2.2-src.tar.gz tar xvfz RgoogleDocs_0.2.2-src.tar.gz Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz or 2. if RGoogleDocs_0.2-2.tar.gz is already a built source file then you can just issue the last of the above lines and don't need the others. On Thu, Jun 18, 2009 at 7:52 PM, Farrel Buchinskyfjb...@gmail.com wrote: What do you mean by cd the.directory.containing.RGoogleDocs Do you mean the directory where I downloaded the RGoogleDocs_0.2-2.tar.gz to? Or do you mean that I must create a directory called RGoogleDocs under Library and then change to that directory? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Mon, Mar 2, 2009 at 22:16, Gabor Grothendieck ggrothendi...@gmail.com wrote: Finally enter into the Windows console: cd the.directory.containing.RGoogleDocs Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_1.0.0.tar.gz except replace RGoogleDocs_1.0.0.tar.gz with the filename created by the build. [[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. [[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] Reading from Google Docs
Forgive my naivte, but how do I make windows find tar. In other words from where do I issue the command and what is the command. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 10:09, Duncan Murdoch murd...@stats.uwo.ca wrote: On 08/07/2009 10:02 AM, Farrel Buchinsky wrote: I have previously read R Installation and Administration. I read it again. It does not help me The relevant paragraph is below. But I need lower level instructions. Where can I find them. Follow the link. If Windows can't find tar, your toolset is installed incorrectly. Duncan Murdoch R CMD INSTALL works in Windows to install source packages if you have the source-code package files (option ยSource Package Installation Filesย in the installer) and toolset (see The Windows toolsetfile:///C:/Program%20Files/R/R-2.9.1/doc/manual/R-admin.html#The-Windows-toolset) installed. Installation of binary packages must be done by install.packages . R CMD INSTALL --help will tell you the current options under Windows (which differ from those on a Unix-alike): in particular there is a choice of the types of documentation to be installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 2009/6/19 Uwe Ligges lig...@statistik.tu-dortmund.de See the manual R Installation and Administration for information on how to install source packages on Windows. Uwe Ligges Farrel Buchinsky wrote: After issuing tar xvfz RgoogleDocs_0.2.2-src.tar.gzI am getting an error message 'tar' is not recongnized as an internal or external command, operable program or batch file. Should I use my 7-zip to open up the archive? Where should I be doing this? For instance can I do it all in my download directory or should I do it in C:\Program Files\R\R-2.9.0\library or should I manually create C:\Program Files\R\R-2.9.0\library\RGoogleDocs and do it all there or will the Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz command do that for me. Yes, you assumed correctly. I am using Windows XP. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Thu, Jun 18, 2009 at 20:17, Gabor Grothendieck ggrothendi...@gmail.comwrote: I have haven't neen following this thread but: 1. if RGoogleDocs_0.2-2.tar.gz is a source distribution (as opposed to built source) then the first line renames it so that its not the same name as the built file about to be created. The second line detars it into the RGoogleDocs directory. The third builds the built source file, RGoogleDocs_0.2-2.tar.gz. The fourth installs the built source file into R. I've assumed Windows. If you are on Linux replace rename with mv. rename RGoogleDocs_0.2-2.tar.gz RgoogleDocs_0.2.2-src.tar.gz tar xvfz RgoogleDocs_0.2.2-src.tar.gz Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz or 2. if RGoogleDocs_0.2-2.tar.gz is already a built source file then you can just issue the last of the above lines and don't need the others. On Thu, Jun 18, 2009 at 7:52 PM, Farrel Buchinskyfjb...@gmail.com wrote: What do you mean by cd the.directory.containing.RGoogleDocs Do you mean the directory where I downloaded the RGoogleDocs_0.2-2.tar.gz to? Or do you mean that I must create a directory called RGoogleDocs under Library and then change to that directory? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Mon, Mar 2, 2009 at 22:16, Gabor Grothendieck ggrothendi...@gmail.com wrote: Finally enter into the Windows console: cd the.directory.containing.RGoogleDocs Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_1.0.0.tar.gz except replace RGoogleDocs_1.0.0.tar.gz with the filename created by the build. [[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. [[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. [[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] Reading from Google Docs
Does changing the path in Windows work in real time or does one need to restart the computer for the changes to take effect. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:04, Gabor Grothendieck ggrothendi...@gmail.comwrote: Its safer just to temporarily add it to your path. Unfortunately Rtools has a find command that conflicts with the find command in Windows so if you add the Rtools bin directory to your path permanently then you could find other programs stop working. That actually happened to me once and it took the longest time until I discovered that Rtools was the culprit. If you follow the advice I gave you normally won't have that problem. On Wed, Jul 8, 2009 at 11:21 AM, Duncan Murdochmurd...@stats.uwo.ca wrote: On 08/07/2009 10:13 AM, Farrel Buchinsky wrote: Forgive my naivte, but how do I make windows find tar. In other words from where do I issue the command and what is the command. You need to install the toolset, and let the installer set your path. Duncan Murdoch Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 10:09, Duncan Murdoch murd...@stats.uwo.ca wrote: On 08/07/2009 10:02 AM, Farrel Buchinsky wrote: I have previously read R Installation and Administration. I read it again. It does not help me The relevant paragraph is below. But I need lower level instructions. Where can I find them. Follow the link. If Windows can't find tar, your toolset is installed incorrectly. Duncan Murdoch R CMD INSTALL works in Windows to install source packages if you have the source-code package files (option ยSource Package Installation Filesย in the installer) and toolset (see The Windows toolsetfile:///C:/Program%20Files/R/R-2.9.1/doc/manual/R-admin.html#The-Windows-toolset) installed. Installation of binary packages must be done by install.packages . R CMD INSTALL --help will tell you the current options under Windows (which differ from those on a Unix-alike): in particular there is a choice of the types of documentation to be installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 2009/6/19 Uwe Ligges lig...@statistik.tu-dortmund.de See the manual R Installation and Administration for information on how to install source packages on Windows. Uwe Ligges Farrel Buchinsky wrote: After issuing tar xvfz RgoogleDocs_0.2.2-src.tar.gzI am getting an error message 'tar' is not recongnized as an internal or external command, operable program or batch file. Should I use my 7-zip to open up the archive? Where should I be doing this? For instance can I do it all in my download directory or should I do it in C:\Program Files\R\R-2.9.0\library or should I manually create C:\Program Files\R\R-2.9.0\library\RGoogleDocs and do it all there or will the Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz command do that for me. Yes, you assumed correctly. I am using Windows XP. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Thu, Jun 18, 2009 at 20:17, Gabor Grothendieck ggrothendi...@gmail.comwrote: I have haven't neen following this thread but: 1. if RGoogleDocs_0.2-2.tar.gz is a source distribution (as opposed to built source) then the first line renames it so that its not the same name as the built file about to be created. The second line detars it into the RGoogleDocs directory. The third builds the built source file, RGoogleDocs_0.2-2.tar.gz. The fourth installs the built source file into R. I've assumed Windows. If you are on Linux replace rename with mv. rename RGoogleDocs_0.2-2.tar.gz RgoogleDocs_0.2.2-src.tar.gz tar xvfz RgoogleDocs_0.2.2-src.tar.gz Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz or 2. if RGoogleDocs_0.2-2.tar.gz is already a built source file then you can just issue the last of the above lines and don't need the others. On Thu, Jun 18, 2009 at 7:52 PM, Farrel Buchinskyfjb...@gmail.com wrote: What do you mean by cd the.directory.containing.RGoogleDocs Do you mean the directory where I downloaded the RGoogleDocs_0.2-2.tar.gz to? Or do you mean that I must create a directory called RGoogleDocs under Library and then change to that directory? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Mon, Mar 2, 2009 at 22:16, Gabor Grothendieck ggrothendi...@gmail.com wrote: Finally enter into the Windows console: cd the.directory.containing.RGoogleDocs Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_1.0.0.tar.gz except replace RGoogleDocs_1.0.0.tar.gz with the filename created by the build. [[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
Re: [R] Reading from Google Docs
Hooray! I got it to work. Here is what I think happened.My hold up was that the tar command was not working. If you recall, when I issued the command: tar xvfz RgoogleDocs_0.2.2-src.tar.gz cmd.exe told me it could not be found I reran Rtools29.exe which is the Rtools setup program which offered to change my path. However it still did not work. I went to lunch and took the opportunity to reboot my computer. When I retried after lunch the tar command worked and everything thereafter worked. I think that the file C:\Program Files\R\Rtools\bin\tar.exe could not be found earlier. I just looked back at my path and I see that C:\Program Files\R\Rtools\bin is on the path. RgoogleDocs 0.2-2 is amazing. I can now read data straight into a dataframe. The fact that I am always reading from realtime data is astounding. sheets.con = getGoogleDocsConnection(getGoogleAuth(fjb...@gmail.com, password here, service = wise)) ts2=getWorksheets(Consents Received,sheets.con)# put the name of the spreadsheet in the inverted commas names(ts2) sheetAsMatrix(ts2$Sheet1,header=TRUE, as.data.frame=TRUE, trim=TRUE) MAGIC Boy oh boy that process of getting source to binary was super painful. Now that I have the package as binary I can share the whole folder with my coworker and she is able to use RGoogleDocs. I intend to use the same process for the other two windows machines that I use. I really do not want to go through the same installation and path hassles all over again. Should I post my directory containing the binary files somewhere so that others do not have to experience pain. Does etiquette dictate that I should post the directory to help other or does etiquette dictate that it is Duncan Temple Lang's code and thus it his prerogative to distribute his work as he wishes? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:59, Farrel Buchinsky fjb...@gmail.com wrote: Does changing the path in Windows work in real time or does one need to restart the computer for the changes to take effect. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:04, Gabor Grothendieck ggrothendi...@gmail.comwrote: Its safer just to temporarily add it to your path. Unfortunately Rtools has a find command that conflicts with the find command in Windows so if you add the Rtools bin directory to your path permanently then you could find other programs stop working. That actually happened to me once and it took the longest time until I discovered that Rtools was the culprit. If you follow the advice I gave you normally won't have that problem. On Wed, Jul 8, 2009 at 11:21 AM, Duncan Murdochmurd...@stats.uwo.ca wrote: On 08/07/2009 10:13 AM, Farrel Buchinsky wrote: Forgive my naivte, but how do I make windows find tar. In other words from where do I issue the command and what is the command. You need to install the toolset, and let the installer set your path. Duncan Murdoch Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 10:09, Duncan Murdoch murd...@stats.uwo.ca wrote: On 08/07/2009 10:02 AM, Farrel Buchinsky wrote: I have previously read R Installation and Administration. I read it again. It does not help me The relevant paragraph is below. But I need lower level instructions. Where can I find them. Follow the link. If Windows can't find tar, your toolset is installed incorrectly. Duncan Murdoch R CMD INSTALL works in Windows to install source packages if you have the source-code package files (option ยSource Package Installation Filesย in the installer) and toolset (see The Windows toolsetfile:///C:/Program%20Files/R/R-2.9.1/doc/manual/R-admin.html#The-Windows-toolset) installed. Installation of binary packages must be done by install.packages . R CMD INSTALL --help will tell you the current options under Windows (which differ from those on a Unix-alike): in particular there is a choice of the types of documentation to be installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 2009/6/19 Uwe Ligges lig...@statistik.tu-dortmund.de See the manual R Installation and Administration for information on how to install source packages on Windows. Uwe Ligges Farrel Buchinsky wrote: After issuing tar xvfz RgoogleDocs_0.2.2-src.tar.gzI am getting an error message 'tar' is not recongnized as an internal or external command, operable program or batch file. Should I use my 7-zip to open up the archive? Where should I be doing this? For instance can I do it all in my download directory or should I do it in C:\Program Files\R\R-2.9.0\library or should I manually create C:\Program Files\R\R-2.9.0\library\RGoogleDocs and do it all there or will the Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz command do that for me. Yes, you assumed correctly. I am using Windows XP. Farrel Buchinsky Google Voice
[R] Getting value rather than formula in RGoogleDocs
Is there an easy way to read the value of the cells rather than the formula?So for instance in a cell whose value was created by simply using the value from the cell immediately to the left in the Google spreadsheet I would prefer to get the value rather than =RC[-1] When one exports with Google Spreadsheets as a csv then that does not happen. I am using the following line of code in R y2009-sheetAsMatrix(ts2$y2009,header=TRUE, as.data.frame=TRUE, trim=TRUE) Farrel Buchinsky Google Voice Tel: (412) 567-7870 [[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] Reading from Google Docs
Dear Duncan On my home computer I was able to use install.packages(RGoogleDocs, repos = http://www.omegahat.org/R;) But, alas it would not read the data in the spreadsheet. It went back to its nasty ways Error in !includeEmpty : invalid argument type That is what I was getting with version 0.2-1.You then sent me link to 0.2-2 (in source code) which is what worked. Is it possible that that the windows binary version you put in omegahat was 0.2-1 and not 0.2-2? I did not know how to tell what version had been installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 22:53, Duncan Temple Lang dun...@wald.ucdavis.eduwrote: Farrel Buchinsky wrote: Boy oh boy that process of getting source to binary was super painful. Now that I have the package as binary I can share the whole folder with my coworker and she is able to use RGoogleDocs. I intend to use the same process for the other two windows machines that I use. I really do not want to go through the same installation and path hassles all over again. Should I post my directory containing the binary files somewhere so that others do not have to experience pain. Does etiquette dictate that I should post the directory to help other or does etiquette dictate that it is Duncan Temple Lang's code and thus it his prerogative to distribute his work as he wishes? Etiquette is one thing and the license another. Both encourage you to help others and make the binary available to others. And indeed, I hope that Windows users do build binaries for others and remove the additional work from those who provide the software in the first place. Having seen this thread today, I did put a binary version of RGoogleDocs on the Omegahat repository so install.packages(RGoogleDocs, repos = http://www.omegahat.org/R;) should install it and, if I had had time earlier, saved you the hardship of building the binary. Sorry to do it so soon after. D. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:59, Farrel Buchinsky fjb...@gmail.com wrote: Does changing the path in Windows work in real time or does one need to restart the computer for the changes to take effect. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 12:04, Gabor Grothendieck ggrothendi...@gmail.comwrote: Its safer just to temporarily add it to your path. Unfortunately Rtools has a find command that conflicts with the find command in Windows so if you add the Rtools bin directory to your path permanently then you could find other programs stop working. That actually happened to me once and it took the longest time until I discovered that Rtools was the culprit. If you follow the advice I gave you normally won't have that problem. On Wed, Jul 8, 2009 at 11:21 AM, Duncan Murdochmurd...@stats.uwo.ca wrote: On 08/07/2009 10:13 AM, Farrel Buchinsky wrote: Forgive my naivte, but how do I make windows find tar. In other words from where do I issue the command and what is the command. You need to install the toolset, and let the installer set your path. Duncan Murdoch Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, Jul 8, 2009 at 10:09, Duncan Murdoch murd...@stats.uwo.ca wrote: On 08/07/2009 10:02 AM, Farrel Buchinsky wrote: I have previously read R Installation and Administration. I read it again. It does not help me The relevant paragraph is below. But I need lower level instructions. Where can I find them. Follow the link. If Windows can't find tar, your toolset is installed incorrectly. Duncan Murdoch R CMD INSTALL works in Windows to install source packages if you have the source-code package files (option ยSource Package Installation Filesย in the installer) and toolset (see The Windows toolsetfile:///C:/Program%20Files/R/R-2.9.1/doc/manual/R-admin.html#The-Windows-toolset) installed. Installation of binary packages must be done by install.packages . R CMD INSTALL --help will tell you the current options under Windows (which differ from those on a Unix-alike): in particular there is a choice of the types of documentation to be installed. Farrel Buchinsky Google Voice Tel: (412) 567-7870 2009/6/19 Uwe Ligges lig...@statistik.tu-dortmund.de See the manual R Installation and Administration for information on how to install source packages on Windows. Uwe Ligges Farrel Buchinsky wrote: After issuing tar xvfz RgoogleDocs_0.2.2-src.tar.gzI am getting an error message 'tar' is not recongnized as an internal or external command, operable program or batch file. Should I use my 7-zip to open up the archive? Where should I be doing this? For instance can I do it all in my download directory or should I do it in C:\Program Files\R\R-2.9.0\library or should I manually create C:\Program Files\R\R-2.9.0\library\RGoogleDocs and do it all
Re: [R] Reading from Google Docs
After issuing tar xvfz RgoogleDocs_0.2.2-src.tar.gzI am getting an error message 'tar' is not recongnized as an internal or external command, operable program or batch file. Should I use my 7-zip to open up the archive? Where should I be doing this? For instance can I do it all in my download directory or should I do it in C:\Program Files\R\R-2.9.0\library or should I manually create C:\Program Files\R\R-2.9.0\library\RGoogleDocs and do it all there or will the Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz command do that for me. Yes, you assumed correctly. I am using Windows XP. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Thu, Jun 18, 2009 at 20:17, Gabor Grothendieck ggrothendi...@gmail.comwrote: I have haven't neen following this thread but: 1. if RGoogleDocs_0.2-2.tar.gz is a source distribution (as opposed to built source) then the first line renames it so that its not the same name as the built file about to be created. The second line detars it into the RGoogleDocs directory. The third builds the built source file, RGoogleDocs_0.2-2.tar.gz. The fourth installs the built source file into R. I've assumed Windows. If you are on Linux replace rename with mv. rename RGoogleDocs_0.2-2.tar.gz RgoogleDocs_0.2.2-src.tar.gz tar xvfz RgoogleDocs_0.2.2-src.tar.gz Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_0.2-2.tar.gz or 2. if RGoogleDocs_0.2-2.tar.gz is already a built source file then you can just issue the last of the above lines and don't need the others. On Thu, Jun 18, 2009 at 7:52 PM, Farrel Buchinskyfjb...@gmail.com wrote: What do you mean by cd the.directory.containing.RGoogleDocs Do you mean the directory where I downloaded the RGoogleDocs_0.2-2.tar.gz to? Or do you mean that I must create a directory called RGoogleDocs under Library and then change to that directory? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Mon, Mar 2, 2009 at 22:16, Gabor Grothendieck ggrothendi...@gmail.com wrote: Finally enter into the Windows console: cd the.directory.containing.RGoogleDocs Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_1.0.0.tar.gz except replace RGoogleDocs_1.0.0.tar.gz with the filename created by the build. [[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] Reading from Google Docs
The first time I did it I had no idea how I did it. Yesterday I struggled and tried every combination to get it to work and eventually it worked. Once again I do not know what I did to get it to work. Now today I am trying to install a version that I downloaded today. And once again I am banging my head against the wall When I run Rcmd build RGoogleDocs from the cmd prompt I get Error: cannot change to directory 'RGoogleDocs' What error have I perpetrated? I have changed my starting directory to almost every imaginable directory and I have put a copy of RGoogleDocs_0.2-2.tar.gz almost everywhere. I also once got * checking for file 'RGoogleDocs/DESCRIPTION' ... No and there it stopped Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Mon, Mar 2, 2009 at 22:16, Gabor Grothendieck ggrothendi...@gmail.comwrote: Download and install each of R, Rtools and MiKTeX. Each of these have automated installers so its just a matter of pressing Enter repeatedly. You don't have to change your path if you place Rcmd.bat from http://batchfiles.googlecode.com anywhere on your path (so it can be found). To see your path try this from the Windows console: path Finally enter into the Windows console: cd the.directory.containing.RGoogleDocs Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_1.0.0.tar.gz except replace RGoogleDocs_1.0.0.tar.gz with the filename created by the build. It should now be installed. On Mon, Mar 2, 2009 at 8:59 PM, Farrel Buchinsky fjb...@gmail.com wrote: I was able to extract RGoogleDocs with 7-zip. That was when I began to appreciate the gravity of what Prof Ripley was saying. I am on a windows xp machine and the RGoogleDocs download does not have a windows binary version. Instead it has only a source package. I started using the R-admin manual to step through the process and got nowhere in about 45 minutes. Then I tried using the automated package building servicehttp://win-builder.r-project.org/you could try. and got nowhere because I did not know what R CMD build is. Can I find someone to do it for me or can I find someone who will give me a couple of basic steps at a time? I am desperate to say goodbye to individual static Microsoft Access or Microsoft Excel spreadsheets being the repository for my data. Farrel Buchinsky Sent from: Pittsburgh Pennsylvania United States. Yes, you can install source packages on Windows: the R-admin manual gives you a detailed guide to the tools that you will need to do so. It even tells you about an automated package building service you could try. RGoogleDocs depends on RCurl and XML, both of which I provide Windows binaries for (and are much trickier to install because of their external software requirements). Farrel Buchinsky GrandCentral Tel: (412) 567-7870 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[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. [[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] Reading from Google Docs
What do you mean by cd the.directory.containing.RGoogleDocs Do you mean the directory where I downloaded the RGoogleDocs_0.2-2.tar.gz to? Or do you mean that I must create a directory called RGoogleDocs under Library and then change to that directory? Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Mon, Mar 2, 2009 at 22:16, Gabor Grothendieck ggrothendi...@gmail.comwrote: Finally enter into the Windows console: cd the.directory.containing.RGoogleDocs Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_1.0.0.tar.gz except replace RGoogleDocs_1.0.0.tar.gz with the filename created by the build. [[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] RGoogleDocs: can now see documents but cannot get content.
Where do I get 0.2-2 from?If I go to http://www.omegahat.org/RGoogleDocs/ I can only find Last Release: 0.2-1http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.2-1.tar.gz (08 May 2009) Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Wed, May 20, 2009 at 12:28, Duncan Temple Lang dun...@wald.ucdavis.eduwrote: Hi Farrel This particular problem is a trivial issue of an argument out of place due to a change in the function definition during the development. There is a new version of the package (0.2-2) and it also uses a slightly different approach (and function) to pull the values into the form of an R data frame. Please try that and hopefully it will work. The code in the run.pdf (or run.html) file on the Web page and in the package works and is the best and shortest example of sheetAsMatrix(). Let me know if there are still problems. D. Farrel Buchinsky wrote: The author of the package, Duncan Temple Lang posted an update. I have installed it and now can list my spreadsheets but alas I cannot read the data within any of them. Has anybody been able to get it to work. I would love to see a real live example of sheetAsMatrix I am not sure how to specify sheet and con = sh...@connection. I have tried many ways but just get: Error in !includeEmpty : invalid argument type Windows Vista (with UAC disabled) R 2.9.0 Farrel Buchinsky [[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. [[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] RGoogleDocs: can now see documents but cannot get content.
I already downloaded 0.2-2 -If my memory serves me correctly. If we just go by date, have you updated the files on the server since May 18? Farrel Buchinsky Google Voice Tel: (412) 567-7870 Sent from Pittsburgh, Pennsylvania, United States On Wed, May 20, 2009 at 12:28, Duncan Temple Lang dun...@wald.ucdavis.eduwrote: Hi Farrel This particular problem is a trivial issue of an argument out of place due to a change in the function definition during the development. There is a new version of the package (0.2-2) and it also uses a slightly different approach (and function) to pull the values into the form of an R data frame. Please try that and hopefully it will work. The code in the run.pdf (or run.html) file on the Web page and in the package works and is the best and shortest example of sheetAsMatrix(). Let me know if there are still problems. D. Farrel Buchinsky wrote: The author of the package, Duncan Temple Lang posted an update. I have installed it and now can list my spreadsheets but alas I cannot read the data within any of them. Has anybody been able to get it to work. I would love to see a real live example of sheetAsMatrix I am not sure how to specify sheet and con = sh...@connection. I have tried many ways but just get: Error in !includeEmpty : invalid argument type Windows Vista (with UAC disabled) R 2.9.0 Farrel Buchinsky [[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. [[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.
[R] Converting a list to a data frame or columns at the least
I have a column in which dates and times are specified thus m/d/ HH:MM:SS Alas, some entries do not include the time and therefore are only m/d/ so I used read.csv and specified that the relevant column should be read as is and it remained as a character variable. I then split the value on the space split.dt.time -strsplit(teacher$Date.and.Time.of.Lesson, ) that gives me a list where each item on the list has two elements if the time was specified and only 1 element if the time was not specified. How do I take that list and make all the 1st elements go into one column and all the second elements go into a second column; where there is no time I would like the value to be missing (NA) I tried playing around with do.call(rbind... so I tried the following unsuccessfully do.call(rbind,lapply(teacher$Date.and.Time.of.Lesson, function(i) strsplit(i, )) ) rbind(strsplit (teacher$Date.and.Time.of.Lesson, )) do.call(rbind(data.frame(strsplit (teacher$Date.and.Time.of.Lesson, Farrel Buchinsky [[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.
[R] RGoogleDocs: can now see documents but cannot get content.
The author of the package, Duncan Temple Lang posted an update. I have installed it and now can list my spreadsheets but alas I cannot read the data within any of them. Has anybody been able to get it to work. I would love to see a real live example of sheetAsMatrix I am not sure how to specify sheet and con = sh...@connection. I have tried many ways but just get: Error in !includeEmpty : invalid argument type Windows Vista (with UAC disabled) R 2.9.0 Farrel Buchinsky [[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.
[R] Printing data as a narrative or form letter rather than as a table
How would one print the information in a table without having to view it as a table? I have a dataframe with about 30 columns and 50 rows. About 7 rows contain human subjects where something is just not right and I need to manually work out what is going on with them and maybe even call them to ensure we have the data correct. It is really inconvenient to view the 7 patients in a table. Instead, I would want to print the information so that it looks like this. I guess what I am asking is how does one use print() or cat() to create a form letter. data frame column names are dob, date.of.dx, registration.nr, first.name, last.name, human.contact, comment... Human subject 1 dob=5/5/2003, date.of.dx=5/8/2003, registration.nr=568956TJGH, first.name=Farrel, last.name=Buchinsky, human.contact=yes, comment=Spoke with human subject on Tuesday December 27, 2008. They asked questions about the study and wanted to enroll. I told them I would get back to them within a week, date.enrolled=01/05/2009, wt=20 ... Human Subject 2 dob=5/8/2006, date.of.dx=7/72007, registration.nr=579293TGGG, first.name=Marmeduk, last.name=Marmite, human.contact=yes, comment=parent bumped into me at meeting and had lots of questions, we spoke for 2 hours, they lived in Norway until 2 years ago, date.enrolled=01/23/2009, wt=10 ... (by the way...all fictitious) Farrel Buchinsky Sent from Pittsburgh, Pennsylvania, United States [[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.
[R] Reading from Google Spreadsheets with RGoogleDocs
I cannot read google spreadsheets. I get the following error: assignment of an object of class NULL is not valid for slot access in an object of class GoogleSpreadsheet; is(value, character) is not TRUE RGoogleDocs is on the cusp of brilliance. How can I troubleshoot this apparently last remaining problem? Farrel J. Buchinsky, MD Director, Respiratory Papillomatosis Program Allegheny-Singer Research Institute 320 E. North Avenue Pittsburgh, PA 15212-4772 __ 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] Reading from Google Docs
It worked. Thank you Gabor Grothendieck. I have very little idea of what I did but I did it and it works. It is working well when I limit getDocs to documents only. However if I include everything in my request or just limit it to spreadsheets I get the following error. getDocs(con, what = http://docs.google.com/feeds/documents/private/full/-/spreadsheet;) assignment of an object of class NULL is not valid for slot access in an object of class GoogleSpreadsheet; is(value, character) is not TRUE Tried google searching and got nowhere. Farrel Buchinsky Google Voice Tel: (412) 567-7870 On Mon, Mar 2, 2009 at 22:16, Gabor Grothendieck ggrothendi...@gmail.com wrote: Download and install each of R, Rtools and MiKTeX. Each of these have automated installers so its just a matter of pressing Enter repeatedly. You don't have to change your path if you place Rcmd.bat from http://batchfiles.googlecode.com anywhere on your path (so it can be found). ย To see your path try this from the Windows console: path Finally enter into the Windows console: cd the.directory.containing.RGoogleDocs Rcmd build RGoogleDocs Rcmd INSTALL RGoogleDocs_1.0.0.tar.gz except replace RGoogleDocs_1.0.0.tar.gz with the filename created by the build. It should now be installed. On Mon, Mar 2, 2009 at 8:59 PM, Farrel Buchinsky fjb...@gmail.com wrote: I was able to extract RGoogleDocs with 7-zip. That was when I began to appreciate the gravity of what Prof Ripley was saying. I am on a windows xp machine and the RGoogleDocs download does not have a windows binary version. Instead it has only a source package. I started using the R-admin manual to step through the process and got nowhere in about 45 minutes. Then I tried using the automated package building servicehttp://win-builder.r-project.org/you could try. and got nowhere because I did not know what R CMD build is. Can I find someone to do it for me or can I find someone who will give me a couple of basic steps at a time? I am desperate to say goodbye to individual static Microsoft Access or Microsoft Excel spreadsheets being the repository for my data. Farrel Buchinsky Sent from: Pittsburgh Pennsylvania United States. Yes, you can install source packages on Windows: the R-admin manual gives you a detailed guide to the tools that you will need to do so. ย It even tells you about an automated package building service you could try. RGoogleDocs depends on RCurl and XML, both of which I provide Windows binaries for (and are much trickier to install because of their external software requirements). ย Farrel Buchinsky GrandCentral Tel: (412) 567-7870 -- Brian D. Ripley, ย ย ย ย ย ย ย ย ย rip...@stats.ox.ac.uk Professor of Applied Statistics, ย http://www.stats.ox.ac.uk/~ripley/ University of Oxford, ย ย ย ย ย ย Tel: ย +44 1865 272861 (self) 1 South Parks Road, ย ย ย ย ย ย ย ย ย ย +44 1865 272866 (PA) Oxford OX1 3TG, UK ย ย ย ย ย ย ย ย Fax: ย +44 1865 272595 ย ย ย ย [[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. __ 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] two different date formats in the same variable
How does one convert to a date format when survey respondents have used two different date formats whilst entering their data. There were clearly told to use mm/dd/ but humans being humans some entered mm/dd/yy. There was even validity checks on the forms but I allowed them to be overridden since the data is more holy than the format. The data was downloaded as a csv and read.csv was used to read in. There are several date variables (for example date of birth, date of diagnosis). Some became character vectors and others become factor vectors. Nevertheless I have accomplished most of what I want using lines such as strptime(init.consent$consent.rec,%m/%d/%Y) strptime(x,%m/%d/%Y) as.Date(x, %m/%d/%Y) But what happens when a few of the entries get messed up because they are actually formatted %m/%d/%y. Is there a robust date formatter? Alternatively how would one code (presumably using regular expressions) a transforamtion or substitution only on the errant entries and thereby turn 06/25/04 into 06/25/2004 and 03/03/59 into 03/03/1959? sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 Farrel Buchinsky __ 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] readline() is reading the entire line and not just the user input
Indeed. I can also get it to work if I type directly in Rterm. But not when running from Tinn-R. If this is a Tinn-R problem (relating to however command lines get from Tinn-R to the Rterm) then perhaps I should post it in the Tinn-R problem. Farrel Buchinsky Sent from: Pittsburgh Pennsylvania United States. On Mon, Mar 16, 2009 at 13:08, jim holtman jholt...@gmail.com wrote: Seems to work fine with RTERM under my Windows: ANSWER - readline(prompt=Are you a satisfied R user? ) Are you a satisfied R user? yes ANSWER [1] yes sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 On Mon, Mar 16, 2009 at 12:44 PM, Farrel Buchinsky fjb...@gmail.com wrote: I just discovered readline to provide user input. It is working as one would expect in Rgui but not in Rterm. In Rterm it reads the entire line of code not just the user input. How do I fix and what is the issue that I should read about? Here is my two line script: ANSWER - readline(prompt=Are you a satisfied R user? ) ANSWER So under RGUI one gets the following ANSWER - readline(prompt=Are you a satisfied R user? ) Are you a satisfied R user? yes ANSWER [1] yes Under RTERM one gets ANSWER - readline(prompt=Are you a satisfied R user? )yes Are you a satisfied R user? ANSWER [1] ANSWER - readline(prompt=\Are you a satisfied R user? \)yes So I tried to hit enter after I saw the line in the terminal and this is what I got: ANSWER - readline(prompt=Are you a satisfied R user? ) Are you a satisfied R user? ANSWER [1] ANSWER - readline(prompt=\Are you a satisfied R user? \) My R environment: Windows XP with service pack 3; R 2.8.1, tinn-R 2.2.0.2 Farrel Buchinsky __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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.
[R] readline() is reading the entire line and not just the user input
I just discovered readline to provide user input. It is working as one would expect in Rgui but not in Rterm. In Rterm it reads the entire line of code not just the user input. How do I fix and what is the issue that I should read about? Here is my two line script: ANSWER - readline(prompt=Are you a satisfied R user? ) ANSWER So under RGUI one gets the following ANSWER - readline(prompt=Are you a satisfied R user? ) Are you a satisfied R user? yes ANSWER [1] yes Under RTERM one gets ANSWER - readline(prompt=Are you a satisfied R user? )yes Are you a satisfied R user? ANSWER [1] ANSWER - readline(prompt=\Are you a satisfied R user? \)yes So I tried to hit enter after I saw the line in the terminal and this is what I got: ANSWER - readline(prompt=Are you a satisfied R user? ) Are you a satisfied R user? ANSWER [1] ANSWER - readline(prompt=\Are you a satisfied R user? \) My R environment: Windows XP with service pack 3; R 2.8.1, tinn-R 2.2.0.2 Farrel Buchinsky __ 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] Reading from Google Docs
I was able to extract RGoogleDocs with 7-zip. That was when I began to appreciate the gravity of what Prof Ripley was saying. I am on a windows xp machine and the RGoogleDocs download does not have a windows binary version. Instead it has only a source package. I started using the R-admin manual to step through the process and got nowhere in about 45 minutes. Then I tried using the automated package building servicehttp://win-builder.r-project.org/you could try. and got nowhere because I did not know what R CMD build is. Can I find someone to do it for me or can I find someone who will give me a couple of basic steps at a time? I am desperate to say goodbye to individual static Microsoft Access or Microsoft Excel spreadsheets being the repository for my data. Farrel Buchinsky Sent from: Pittsburgh Pennsylvania United States. Yes, you can install source packages on Windows: the R-admin manual gives you a detailed guide to the tools that you will need to do so. It even tells you about an automated package building service you could try. RGoogleDocs depends on RCurl and XML, both of which I provide Windows binaries for (and are much trickier to install because of their external software requirements). Farrel Buchinsky GrandCentral Tel: (412) 567-7870 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[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.
[R] forward slash vs double backslash R and Tinn-R
I installed the newest version of R and once again ran into problem
with Tinn-R failing when trying to use the R explorer. I had this
problem once before and solved it when I added the following
.trPaths = c(
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/search.txt',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/objects.txt',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/file.r',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/selection.r',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/block.r',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/lines.r')
The posted configuration file tries to accomplish this situation with
.trPaths - paste(paste(Sys.getenv('APPDATA'), '\\Tinn-R\\tmp\\',
sep=''), c('', 'search.txt', 'objects.txt', 'file.r', 'selection.r',
'block.r', 'lines.r'), sep='')
BUT IT FAILS.
Farrel Buchinsky
__
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] forward slash vs double backslash R and Tinn-R
The only apparent reason for the failure is that the elegant line
using Sys.getenv denerates filenames with double backslashes instead
of forward slashes. I am working in Windows XP and I thought that R
could use double backslashes or a single forward slash.
So what am I not understanding about the whole slash thing?
Farrel Buchinsky
On Fri, Jan 23, 2009 at 11:10, Farrel Buchinsky fjb...@gmail.com wrote:
I installed the newest version of R and once again ran into problem
with Tinn-R failing when trying to use the R explorer. I had this
problem once before and solved it when I added the following
.trPaths = c(
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/search.txt',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/objects.txt',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/file.r',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/selection.r',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/block.r',
'C:/Documents and Settings/fbuchins/Application Data/Tinn-R/tmp/lines.r')
The posted configuration file tries to accomplish this situation with
.trPaths - paste(paste(Sys.getenv('APPDATA'), '\\Tinn-R\\tmp\\',
sep=''), c('', 'search.txt', 'objects.txt', 'file.r', 'selection.r',
'block.r', 'lines.r'), sep='')
BUT IT FAILS.
Farrel Buchinsky
__
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] R Threatens SAS According to The NYT
The article was dugg on Digg. http://digg.com/software/Data_Analysts_Captivated_by_R_s_Power_3 If you Digg, why not digg this. Farrel Buchinsky __ 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] Reading from Google Docs
I saw a thread from September 24 in which Duncan Temple Lang told us: - The package currently has no Rd files, but there is a brief user's guide. The package is available from http://www.omegahat.org/RGoogleDocs I could not find it by using Tinn-R or RGui's package install tool. Then when I went to the website I saw that package is only available as http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.1-0.tar.gz To my knowledge tar.gz is only for Linux. Does this mean that I cannot run it on a windows machine. Please tell me that there is a way to run it on a Windows machine. Farrel Buchinsky GrandCentral Tel: (412) 567-7870 __ 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] Reading from Google Docs
Great. I have previously installed 7zip. It worked well. I installed the files. See below (way below). When I entered library(RGoogleDocs) it did not run. So I just ran auth.R Then I was able to run auth -getGoogleAuth(fjb...@gmail.com,mypassword) con = getConnection(auth) con$getDocs() all worked until this point when I got Error in con$getDocs : $ operator not defined for this S4 class str(con) Formal class 'GoogleDocsConnection' [package ] with 0 slots list() I have just seen Prof Brian Ripley's correspondence. I had installed RCurl and XML from the Tinn-R R controlling:packages button. It appears to me that I need to check out R-admin manual. Is there a simple generic r script that I could run to determine if my RCurl and XML are running properly? C:\Program Files\R\R-2.7.2\library\RGoogleDocs\ inst DIR 12/15/2008 17:27:57 R DIR 12/15/2008 17:27:57 DESCRIPTION 777 9/24/2008 12:47:59 1 file(s), 2 folder(s) 777 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\ doc DIR 12/15/2008 17:27:57 sampleDocsDIR 12/15/2008 17:44:07 0 file(s), 2 folder(s)0 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\doc\ basics.html 5,867 9/24/2008 11:27:38 basics.pdf8,873 9/24/2008 11:30:51 basics.xml3,504 9/24/2008 11:27:34 GNUmakefile 39 9/24/2008 11:24:44 run.html 14,150 9/24/2008 12:46:41 run.pdf 13,643 9/24/2008 12:44:39 run.xml 9,257 9/24/2008 12:44:23 7 file(s), 0 folder(s) 55,333 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\sampleDocs\ SampleDoc.doc22,016 9/24/2008 12:44:23 SampleSpreadsheet.xls17,408 9/24/2008 12:44:23 2 file(s), 0 folder(s) 39,424 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\R\ auth.R8,183 9/24/2008 12:44:23 1 file(s), 0 folder(s)8,183 bytes Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Mon, Dec 15, 2008 at 17:12, Gustavo Carvalho gustavo.bi...@gmail.com wrote: Hello, You can probably extract a .tar.gz using 7zip on Windows. Regards, Gustavo. On Mon, Dec 15, 2008 at 8:07 PM, Farrel Buchinsky fjb...@gmail.com wrote: I saw a thread from September 24 in which Duncan Temple Lang told us: - The package currently has no Rd files, but there is a brief user's guide. The package is available from http://www.omegahat.org/RGoogleDocs I could not find it by using Tinn-R or RGui's package install tool. Then when I went to the website I saw that package is only available as http://www.omegahat.org/RGoogleDocs/RGoogleDocs_0.1-0.tar.gz To my knowledge tar.gz is only for Linux. Does this mean that I cannot run it on a windows machine
Re: [R] Reading from Google Docs
When I rungetDocs(con) I get this error: Error in getDocs(con) : could not find function xmlParse Where should xmlParse be coming from? You had asked where I got the idea to enter con$getDocs(). I got it from run.html. But now that you bring the words In the future, we might to my attention I can see that I should not have tried it. Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Mon, Dec 15, 2008 at 19:28, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Farrel Buchinsky wrote: Great. I have previously installed 7zip. It worked well. I installed the files. See below (way below). When I entered library(RGoogleDocs) it did not run. So I just ran auth.R Then I was able to run auth -getGoogleAuth(fjb...@gmail.com,mypassword) con = getConnection(auth) con$getDocs() all worked until this point when I got Error in con$getDocs : $ operator not defined for this S4 class str(con) Formal class 'GoogleDocsConnection' [package ] with 0 slots list() If you use getDocs(con) it should work, assuming auth and con are appropriate. Where did you see that con$getDocs() should work? In the documentation file run.xml, there is the line In the future, we might provide an interface that avoids this such as con$getDocs() ... So, as it says, it is in the future. D. I have just seen Prof Brian Ripley's correspondence. I had installed RCurl and XML from the Tinn-R R controlling:packages button. It appears to me that I need to check out R-admin manual. Is there a simple generic r script that I could run to determine if my RCurl and XML are running properly? C:\Program Files\R\R-2.7.2\library\RGoogleDocs\ inst DIR 12/15/2008 17:27:57 R DIR 12/15/2008 17:27:57 DESCRIPTION 777 9/24/2008 12:47:59 1 file(s), 2 folder(s) 777 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\ doc DIR 12/15/2008 17:27:57 sampleDocsDIR 12/15/2008 17:44:07 0 file(s), 2 folder(s)0 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\doc\ basics.html 5,867 9/24/2008 11:27:38 basics.pdf8,873 9/24/2008 11:30:51 basics.xml3,504 9/24/2008 11:27:34 GNUmakefile 39 9/24/2008 11:24:44 run.html 14,150 9/24/2008 12:46:41 run.pdf 13,643 9/24/2008 12:44:39 run.xml 9,257 9/24/2008 12:44:23 7 file(s), 0 folder(s) 55,333 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\sampleDocs\ SampleDoc.doc22,016 9/24/2008 12:44:23 SampleSpreadsheet.xls17,408 9/24/2008 12:44:23 2 file(s), 0 folder(s) 39,424 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\R\ auth.R8,183 9/24/2008 12:44:23 1 file(s), 0 folder(s
Re: [R] Reading from Google Docs
I have loaded the XML package. Should the function not be xmlTreeParse? Look at this library(XML) help(xmlParse) No documentation for 'xmlParse' in specified packages and libraries: you could try 'help.search(xmlParse)' help.search(xmlParse) Help files with alias or concept or title matching 'xmlParse' using fuzzy matching: supportsExpat(XML) Determines which native XML parsers are being used. xmlEventHandler(XML)Default handlers for the SAX-style event XML parser xmlParent(XML) Get parent node of XMLInternalNode or ancestor nodes xmlStopParser(XML) Terminate an XML parser xmlTreeParse(XML) XML Parser Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Mon, Dec 15, 2008 at 19:56, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Farrel Buchinsky wrote: When I rungetDocs(con) I get this error: Error in getDocs(con) : could not find function xmlParse Where should xmlParse be coming from? From the XML package. You had asked where I got the idea to enter con$getDocs(). I got it from run.html. But now that you bring the words In the future, we might to my attention I can see that I should not have tried it. Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Mon, Dec 15, 2008 at 19:28, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Farrel Buchinsky wrote: Great. I have previously installed 7zip. It worked well. I installed the files. See below (way below). When I entered library(RGoogleDocs) it did not run. So I just ran auth.R Then I was able to run auth -getGoogleAuth(fjb...@gmail.com,mypassword) con = getConnection(auth) con$getDocs() all worked until this point when I got Error in con$getDocs : $ operator not defined for this S4 class str(con) Formal class 'GoogleDocsConnection' [package ] with 0 slots list() If you use getDocs(con) it should work, assuming auth and con are appropriate. Where did you see that con$getDocs() should work? In the documentation file run.xml, there is the line In the future, we might provide an interface that avoids this such as con$getDocs() ... So, as it says, it is in the future. D. I have just seen Prof Brian Ripley's correspondence. I had installed RCurl and XML from the Tinn-R R controlling:packages button. It appears to me that I need to check out R-admin manual. Is there a simple generic r script that I could run to determine if my RCurl and XML are running properly? C:\Program Files\R\R-2.7.2\library\RGoogleDocs\ inst DIR 12/15/2008 17:27:57 R DIR 12/15/2008 17:27:57 DESCRIPTION 777 9/24/2008 12:47:59 1 file(s), 2 folder(s) 777 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\ doc DIR 12/15/2008 17:27:57 sampleDocsDIR 12/15/2008 17:44:07 0 file(s), 2 folder(s)0 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\doc\ basics.html 5,867 9/24/2008 11:27:38 basics.pdf8,873 9/24/2008 11:30:51 basics.xml3,504 9/24/2008 11:27:34 GNUmakefile 39 9/24/2008 11:24:44 run.html 14,150 9/24/2008 12:46:41 run.pdf 13,643 9/24/2008 12:44:39 run.xml 9,257 9/24/2008 12:44:23 7 file(s), 0 folder(s) 55,333 bytes C:\Program Files\R\R-2.7.2\library
Re: [R] Reading from Google Docs
I took the liberty of replacing all the xmlParse in auth.R with xmlTreeParse. Alas still no joy. getDocs(con) Error in UseMethod(xpathApply) : no applicable method for xpathApply Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Mon, Dec 15, 2008 at 20:00, Farrel Buchinsky fjb...@gmail.com wrote: I have loaded the XML package. Should the function not be xmlTreeParse? Look at this library(XML) help(xmlParse) No documentation for 'xmlParse' in specified packages and libraries: you could try 'help.search(xmlParse)' help.search(xmlParse) Help files with alias or concept or title matching 'xmlParse' using fuzzy matching: supportsExpat(XML) Determines which native XML parsers are being used. xmlEventHandler(XML)Default handlers for the SAX-style event XML parser xmlParent(XML) Get parent node of XMLInternalNode or ancestor nodes xmlStopParser(XML) Terminate an XML parser xmlTreeParse(XML) XML Parser Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Mon, Dec 15, 2008 at 19:56, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Farrel Buchinsky wrote: When I rungetDocs(con) I get this error: Error in getDocs(con) : could not find function xmlParse Where should xmlParse be coming from? From the XML package. You had asked where I got the idea to enter con$getDocs(). I got it from run.html. But now that you bring the words In the future, we might to my attention I can see that I should not have tried it. Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Mon, Dec 15, 2008 at 19:28, Duncan Temple Lang dun...@wald.ucdavis.edu wrote: Farrel Buchinsky wrote: Great. I have previously installed 7zip. It worked well. I installed the files. See below (way below). When I entered library(RGoogleDocs) it did not run. So I just ran auth.R Then I was able to run auth -getGoogleAuth(fjb...@gmail.com,mypassword) con = getConnection(auth) con$getDocs() all worked until this point when I got Error in con$getDocs : $ operator not defined for this S4 class str(con) Formal class 'GoogleDocsConnection' [package ] with 0 slots list() If you use getDocs(con) it should work, assuming auth and con are appropriate. Where did you see that con$getDocs() should work? In the documentation file run.xml, there is the line In the future, we might provide an interface that avoids this such as con$getDocs() ... So, as it says, it is in the future. D. I have just seen Prof Brian Ripley's correspondence. I had installed RCurl and XML from the Tinn-R R controlling:packages button. It appears to me that I need to check out R-admin manual. Is there a simple generic r script that I could run to determine if my RCurl and XML are running properly? C:\Program Files\R\R-2.7.2\library\RGoogleDocs\ inst DIR 12/15/2008 17:27:57 R DIR 12/15/2008 17:27:57 DESCRIPTION 777 9/24/2008 12:47:59 1 file(s), 2 folder(s) 777 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\ doc DIR 12/15/2008 17:27:57 sampleDocsDIR 12/15/2008 17:44:07 0 file(s), 2 folder(s)0 bytes C:\Program Files\R\R-2.7.2\library\RGoogleDocs\inst\doc\ basics.html 5,867 9/24/2008 11:27:38 basics.pdf8,873 9/24/2008 11:30:51 basics.xml3,504 9/24/2008 11:27:34 GNUmakefile 39 9/24/2008 11:24:44 run.html 14,150 9/24/2008 12:46:41 run.pdf 13,643 9/24/2008 12:44:39 run.xml 9,257 9/24/2008 12:44:23
Re: [R] converting multiple columns from POSIX* to Date
Something strange. The lapply only processed the first row and then wrote that value to every row of the original dataframe. It is as if the lapply is indeed processing every item on the list, namely each column, but the ifelse or the as.Date is getting messed up. Not only is it only processing the first row but it is also returning the value as numbers rather than dates. I am now playing around with Hadley Wickham's plyr package. So far looking good but still need to work out a few things. Farrel Buchinsky GrandCentral Tel: (412) 567-7870 On Wed, Dec 10, 2008 at 19:08, Marc Schwartz marc_schwa...@comcast.netwrote: Use inherits() then rather than class(): DF[] - lapply(DF, function(x) ifelse(inherits(x, POSIXt), as.Date(x), x)) That should hopefully work better than my first attempt. HTH, Marc Schwartz on 12/10/2008 05:47 PM Farrel Buchinsky wrote: I will try that but I am somewhat skeptical since when I go class(date.of.birth) I get not just one word but two: POSIXt POSIXct. Will that not mess up the logical test When I tried the following: lapply(as.list(dataframename),class)==POSIXt every item was false Farrel Buchinsky GrandCentral Tel: (412) 567-7870 Dear Farrel, Determine the class of each column and apply as.Date() just to those which class is POSIX. For more details see ?class. Here is an example assuming that you're data is named mydata: apply(mydata, 2, function(x) ifelse( class(x)==POSIXt | class(x)==POSIXlt , as.Date(x) , x ) ) HTH, Jorge On Wed, Dec 10, 2008 at 6:26 PM, Farrel Buchinsky fjb...@gmail.com wrote: converting a POSIX class variable to a date class is easy. dates-as.Date(x) #where X is of class POSIX How does one do that to all columns in a data frame that are of POSIX class and leave all the other columns (integers, factors) as is. Feel free to reply with just one or two buzzwords that I could then search for to find how to do it. Farrel Buchinsky __ 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. [[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.
[R] converting multiple columns from POSIX* to Date
converting a POSIX class variable to a date class is easy. dates-as.Date(x) #where X is of class POSIX How does one do that to all columns in a data frame that are of POSIX class and leave all the other columns (integers, factors) as is. Feel free to reply with just one or two buzzwords that I could then search for to find how to do it. Farrel Buchinsky __ 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] converting multiple columns from POSIX* to Date
I will try that but I am somewhat skeptical since when I go class(date.of.birth) I get not just one word but two: POSIXt POSIXct. Will that not mess up the logical test When I tried the following: lapply(as.list(dataframename),class)==POSIXt every item was false Farrel Buchinsky GrandCentral Tel: (412) 567-7870 Dear Farrel, Determine the class of each column and apply as.Date() just to those which class is POSIX. For more details see ?class. Here is an example assuming that you're data is named mydata: apply(mydata, 2, function(x) ifelse( class(x)==POSIXt | class(x)==POSIXlt , as.Date(x) , x ) ) HTH, Jorge On Wed, Dec 10, 2008 at 6:26 PM, Farrel Buchinsky [EMAIL PROTECTED] wrote: converting a POSIX class variable to a date class is easy. dates-as.Date(x) #where X is of class POSIX How does one do that to all columns in a data frame that are of POSIX class and leave all the other columns (integers, factors) as is. Feel free to reply with just one or two buzzwords that I could then search for to find how to do it. Farrel Buchinsky __ 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] Power calculations where two samples are of unequal size
I have used the function power.t.test() (power calculations for one and two sample t tests) but have noted that it handles the samples as being the same size. How does one handle sample sizes that are different. In other words how does one handle unbalanced designs. Farrel Buchinsky __ 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] outputting (writing) output into a dataframe
I have solved this problem once before but don't recall exactly how. Is there a url that shows how? What I want to do now is quite specific but my query is actually very general There are many functions in which one specifies several parameters and an output is generated. Well what happens if one wants to specify a range of parameters and have the output written to a data frame. To demonstrate: p1 -15:25/100# so that I can vary the p1 from 0.15 to 0.25 for (i in p1) print(power.prop.test(p1=i,p2=0.5*i,power=0.8, sig.level=0.05)) That prints a whole flurry of pretty outputs but I actually want it to output into a data frame so that I can plot it? Farrel Buchinsky __ 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] Tinn-R explorer used to be my friend
I have upgraded everything lately and can no longer get the Tinn-R explorer to work. I think I have had this problem before but cannot recall how I solved it.I run Tinn-R 2.0.0.7 and Rgui version 2.7.2 When I click on the explorer button I get trObjList(envir='.GlobalEnv', pattern='', group='', path=.trPaths[3]) Error in trObjList(envir = .GlobalEnv, pattern = , group = , path = .trPaths[3]) : unused argument(s) (envir = .GlobalEnv) I have ensured that the correct profile loads by using (from within Tinn-R) RConfigurePermanent(Rprofile.site). Is this a known bug or am I just getting tripped up. Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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.
[R] Reading OpenOffice Calc spreadsheet into R
I am in awe of the project you developed but wish to do something simpler. I have recently decided to give up on Microsoft Office and wish to use OpenOffice exclusively. In the past I have used the RODBC package to read data from excel files. Do you know how to read data directly from OpenOffice calc files into R? Farrel Buchinsky __ 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] using as.POSIXlt on multiple columns or multiple objects
If I want to convert one column to date and time format that R can understand and manipulate then I would do this initial$Started-as.POSIXlt(initial$Started) But what happens if I have many such columns and I do not want to have my code be stuffed with 10 similar lines (one for each variable aka column aka vector aka object) I thought I could be clear and use the list function and do this. list(initial$Started ,initial$Finished,full.ques$started.ful ,full.ques$finished.ful) - lapply(list(initial$Started ,initial$Finished,full.ques$started.ful ,full.ques$finished.ful),as.POSIXlt) But I got: Error in list(initial$Started, initial$Finished, full.ques$started.ful, : could not find function list- I am clearly missing some basic R issue here. What am I missing? -- Farrel Buchinsky __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Differentiate alphanumeric vs numeric strings
This is fantastic. As a future note to myself and to others who may stumble upon this: further documentation for all one's heart could desire is in the base help system at. Regular Expressions as used in R - regexp Pattern Matching and Replacement - grep Split the Elements of a Character Vector - strsplit The following worked in my situation: channel2007-odbcConnectAccess(filename for 2007 data) tables -sqlTables(channel2007)[,3] tables -grep([[:digit:]],tables,value=TRUE) all2007 -sqlFetch(channel2007, tables[1]) for (f in tables[-1]) all2007-rbind(all2007, sqlFetch(channel2007, f)) Thanks for your help On Thu, Apr 24, 2008 at 11:34 PM, jim holtman [EMAIL PROTECTED] wrote: The following will return the indices or the values of character strings that are all numeric: x - c(12345, 123AS23, A123, 398457) grep(^[[:digit:]]*$, x) # index [1] 1 4 grep(^[[:digit:]]*$, x, value=TRUE) # values [1] 12345 398457 On Thu, Apr 24, 2008 at 10:39 PM, Farrel Buchinsky [EMAIL PROTECTED] wrote: I have a bunch of tables in a Microsoft Access database. An updated database is sent to me every week containing a new table. I know that is inefficient and weird but welcome to my life. I want to read the tables whose names are something such as 040207 but not the ones that have alphanumeric names such as everyone. Using RODBC I am easily able to create a character vector of the names of the tables. Is there a function that can differentiate values consisting only of digits (numerics) as opposed to ones that contain letters (and perhaps digts as well)? I am sure there is. What is it and where should I have found it? -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 __ 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] merging more than 2 data frames
I have created a merged data frame and in turn merged that with another dataframe. I could see how it could become a pain if you had lots of dataframes. I would try running a for loop...but have never done it. joseph [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Hi merge() takes only 2 data frames. What can you do to it to make take more than two data frames? or is there another function that does that? Thanks joseph Looking for last minute shopping deals? [[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. __ 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] Tinn-R not working well with latest R
I can easily get R to open without an error. I simply removed the Tinn-R related lines from the Rprofile.site file C:\Program Files\R-2.6.2\etc\Rprofile.site but then when I try to manually load the svIDE library by entering library(svIDE) from the command line, I get a similar error. So when you say Than paste in the command, what command are you referring to? What do you change it to? Schmitt, Corinna [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Hallo, I had the same problems before. I think the best solution is that you just copy the needed codepart out of Tinn-R with Ctr+C. Then open R directly from your desktop NOT from Tinn-R. Than paste in the command. you can still make changes in the command when you have not pressed enter by using the arrow buttons of the keyboard. put the curse where you want in the command line and change it. Hope that is what you want. I cannot imitate your example. Corinna [[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. __ 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] genetics package not working
Finally I found something that provides lower level examples. I was looking around the genetics package. I came across write.pop.file(genetics) and there I found the format of 'pedigree' files is documented at http://www.sph.umich.edu/csg/abecasis/GOLD/docs/pedigree.html That reference lays out exactly the format that is being used. Farrel Buchinsky [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] From crawling around the internet it appears to me as if genetics has given way to GeneticsBase and is part of bioconductor. The basic data structure has changed to something called geneSet class. There is a pdf document that promises to help me. http://www.bioconductor.org/packages/2.1/bioc/vignettes/GeneticsBase/inst/doc/SummaryTables.pdf. Unfortunately it does not. My dataset which was created using genetics package does not seem to fit (or should I say does not seem to easily fit) the read in formats demonstrated in the document: standard pedigree format, hapmap format, Pfizer format, Perlegen format. Can anyone point me to a resource with lower level instructions and examples? My format is as follows (rs numbers are not correct but do not worry about that detail) str(ped.seq[,2:15]) 'data.frame': 608 obs. of 14 variables: $ pedigree : int 1 1 2 3 3 4 4 5 6 6 ... $ id: Factor w/ 30 levels 1,2,3,4,..: 3 2 3 3 2 3 2 3 3 2 ... $ id.father : int 1 0 1 1 0 1 0 1 1 0 ... $ id.mother : int 2 0 2 2 0 2 0 2 2 0 ... $ PtCode: Factor w/ 608 levels AJM16001FA,AJM16001MO,..: 74 73 77 117 116 80 79 83 86 85 ... $ HS.nr : int 32940 32941 32960 32963 32964 32967 32968 32970 32972 32973 ... $ affected : int 2 1 2 2 1 2 1 2 2 1 ... $ sex : int 2 2 1 1 2 1 2 2 2 2 ... $ rs11684: Factor w/ 1 level C/C: 1 1 1 1 1 1 1 1 1 1 ... ..- attr(*, allele.names)= chr C ..- attr(*, allele.map)= chr [1, 1:2] C C $ rs1144: Factor w/ 3 levels A/A,G/A,G/G: 3 3 3 3 3 2 3 3 3 3 ... ..- attr(*, allele.names)= chr G A ..- attr(*, allele.map)= chr [1:3, 1:2] A G G A ... $ rs120: Factor w/ 2 levels A/A,A/G: 1 1 1 1 1 1 1 1 1 1 ... ..- attr(*, allele.names)= chr A G ..- attr(*, allele.map)= chr [1:2, 1:2] A A A G Farrel Buchinsky [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work summary(founders[,59]) to prove that it is a genotype class class(founders[,59]) [1] genotype factor Now when I issue the command: summary(founders[,59]) I get: Error in attr(retval, which) - which : attempt to set an attribute on NULL In addition: Warning message: $ operator is deprecated for atomic vectors, returning NULL in: x$allele.names Clearly, I am missing something. What am I missing? -- Farrel Buchinsky [[alternative HTML version deleted]] __ [EMAIL PROTECTED] 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. __ [EMAIL PROTECTED] 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] Tinn-R not working well with latest R
I recently installed R 2.6.2 and am getting errors on startup that relate to
svIDE being loaded by Tinn-R.
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Warning messages:
1: '\A' is an unrecognized escape in a character string
2: unrecognized escape removed from ;for Options\AutoIndent: 0=Off,
1=follow language scoping and 2=copy from previous line\n
3: In grep(paste([{]TclEval , topic, [}], sep = ), tclvalue(.Tcl(dde
services TclEval {})), :
argument 'useBytes = TRUE' will be ignored
Loading required package: svMisc
Loading required package: R2HTML
Any idea what is going on.
I use R 2.6.2 on windows xp
I also started R without the profile that Tinn-R made.
If I manualy enter library(svIDE) then I get.
library(svIDE)
Warning messages:
1: '\A' is an unrecognized escape in a character string
2: unrecognized escape removed from ;for Options\AutoIndent: 0=Off,
1=follow language scoping and 2=copy from previous line\n
So the underlying problem may be svIDE
see: http://tolstoy.newcastle.edu.au/R/e2/help/07/04/15738.html
Apparently, because of this error, several great features in Tinn-R are not
working properly.
Any solutions or workarounds?
--
Farrel
[[alternative HTML version deleted]]
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Re: [R] Analyzing Publications from Pubmed via XML
The problem is that the RSS feed you linked to, does not contain the
year of the article in an easily accessible XML element. Rather you
have to process the HTML content of the description element - which,
is something R could do, but you'd be using the wrong tool for the job.
Yes. I have noticed that there two sorts of xml that pubmed will
provide. The kind I had hooked into was an rss feed which provides a
lot of the information simply as a formatted table for viewing in a
rss reader. There is another way to get the xml to come out with more
tags. However, I found the best way to do this is probably through the
bioconductor annotate package
x - pubmed(18046565, 17978930, 17975511)
a - xmlRoot(x)
numAbst - length(xmlChildren(a))
absts - list()
for (i in 1:numAbst) {
absts[[i]] - buildPubMedAbst(a[[i]])
}
I am now trying to work through that approach to see what I can come up with.
--
Farrel Buchinsky
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Re: [R] Analyzing Publications from Pubmed via XML
On Dec 13, 2007 11:35 PM, Robert Gentleman [EMAIL PROTECTED] wrote: or just try looking in the annotate package from Bioconductor Yip. annotate seems to be the most streamlined way to do this. 1) How does one turn the list that is created into a dataframe whose column names are along the lines of date, title, journal, authors etc 2) I have already created a standing search in pubmed using MyNCBI. There are many ways I can feed those results to the pubmed() function. The most brute force way of doing it is by running the search and outputing the data as a UI List and getting that into the pubmed brackets. A way that involved more finesse would allow me to create a rss feed based on my search and then give the rss feed url to the pubmed function. Or perhaps once could just plop the query inside the pubmed functions pubmed(somefunction(Laryngeal Neoplasms[MeSH] AND Papilloma[MeSH]) OR (((recurrence[TIAB] NOT Medline[SB]) OR recurrence[MeSH Terms] OR recurrent[Text Word]) AND respiratory[All Fields] AND ((papilloma[TIAB] NOT Medline[SB]) OR papilloma[MeSH Terms] OR papillomatosis[Text Word]))) Does somefunction exist? If there are any further questions do you think I should migrate this conversation to the bioconductor mailing list? Farrel Buchinsky __ 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] Analyzing Publications from Pubmed via XML
I am afraid not! The only thing I know about Python (or Perl, Ruby etc) is that they exist and that I have been able to download some amazing freeware or open source software thanks to their existence. The XML package and specifically the xmlTreeParse function looks as if it is begging to do the task for me. Is that not true? On Dec 13, 2007 9:12 PM, Rajarshi Guha [EMAIL PROTECTED] wrote: On Dec 13, 2007, at 9:03 PM, Farrel Buchinsky wrote: I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse( http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi? rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT- ,isURL=TRUE) But getting from there to a dataframe in which one column would be the name of the journal and another column would be the year (to keep things simple) seems to be beyond my capabilities. If you're comfortable with Python (or Perl, Ruby etc), it'd be easier to just extract the required stuff from the raw feed - using ElementTree in Python makes this a trivial task Once you have the raw data you can read it into R --- Rajarshi Guha [EMAIL PROTECTED] GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- A committee is a group that keeps the minutes and loses hours. -- Milton Berle -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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.
[R] Analyzing Publications from Pubmed via XML
I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse( http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT- ,isURL=TRUE) But getting from there to a dataframe in which one column would be the name of the journal and another column would be the year (to keep things simple) seems to be beyond my capabilities. Has anyone ever done this and could you share your script? Are there any published examples where the end result is a dataframe. I guess what I am looking for is an easy and simple way to parse the feed and extract the data. Alternatively how does one turn an RSS feed into a CSV file? -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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] Calculating proportions from a data frame rather than a table
No. Not really.What you have done seems to be similar to what I could do with the reshape library. rawer-melt(coinfection,id.var=study) # please refer to my post immediately before this. I am still unable to make use of prop.table and margin.table functions. On 10/3/07, Deepayan Sarkar [EMAIL PROTECTED] wrote: On 10/3/07, Farrel Buchinsky [EMAIL PROTECTED] wrote: Your solution would work if the data frame contained the raw data. In that case the table function as you outlined would be a table crossing all the levels of column 1 with all the levels of column 2. Instead my data frame is the table. It is an aggregate table (I may be using the wrong buzzwords here). Does this help: foo - Titanic[,2,2,] foo Survived Class No Yes 1st 4 140 2nd 13 80 3rd 89 76 Crew 3 20 bar - as.data.frame.table(foo) bar Class Survived Freq 1 1st No4 2 2nd No 13 3 3rd No 89 4 Crew No3 5 1st Yes 140 6 2nd Yes 80 7 3rd Yes 76 8 Crew Yes 20 xtabs(Freq ~ Class + Survived, data = bar) # compare with foo Survived Class No Yes 1st4 140 2nd 13 80 3rd 89 76 Crew 3 20 -Deepayan -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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] Calculating proportions from a data frame rather than a table
Thank you. It comes close but not exactly what I wanted. I had to scrap my column that contained character values. That column noted the name of the study. Let me try show you here Best if viewed in courier font coinfection study HPV6 HPV11 CoInfect other 1 Wiatrak 2004 31234 0 2 Draganov 20066143 0 3 Gabbott 1997 19241 0 4 Gerein 2005 17140 7 5 Michael 20058 50 1 6Rabah 2001 29320 0 7 Maloney 20064 47 0 str(coinfection) 'data.frame': 7 obs. of 5 variables: $ study : chr Wiatrak 2004 Draganov 2006 Gabbott 1997 Gerein 2005 ... $ HPV6: num 31 6 19 17 8 29 4 $ HPV11 : num 23 14 24 14 5 32 4 $ CoInfect: num 4 3 1 0 0 0 7 $ other : num 0 0 0 7 1 0 0 I had tried the following and was getting nowhere as.table(coinfection) Error in as.table.default(coinfection) : cannot coerce into a table as.table(coinfection[,-1]) Error in as.table.default(coinfection[, -1]) : cannot coerce into a table Thanks to you was able to make some progress. as.table(as.matrix(coinfection)) study HPV6 HPV11 CoInfect other 1 Wiatrak 2004 31 2340 2 Draganov 2006 6 1430 3 Gabbott 1997 19 2410 4 Gerein 2005 17 1407 5 Michael 2005 8501 6 Rabah 200129 3200 7 Maloney 2006 4470 SO FAR THIS LOOKS GOOD BUT THEN LOOK prop.table(as.table(as.matrix(coinfection)),1)#the main reason for doing this Error in sum(..., na.rm = na.rm) : invalid 'type' (character) of argument prop.table(as.table(as.matrix(coinfection[,-1])),1)#this is to get rid of the variable called study HPV6 HPV11 CoInfect other 1 0.53448276 0.39655172 0.06896552 0. 2 0.26086957 0.60869565 0.13043478 0. 3 0.43181818 0.54545455 0.02272727 0. 4 0.44736842 0.36842105 0. 0.18421053 5 0.57142857 0.35714286 0. 0.07142857 6 0.47540984 0.52459016 0. 0. 7 0.2667 0.2667 0.4667 0. WORKS PERFECTLY, EXACTLY WHAT I WANTED EXCEPT I HAVE LOST THE NAME OF THE STUDY AND HAVE TO GO BACK TO LOOK AT WHICH DATA BELONGS TO WHICH STUDY. THIS WOULD NOT HAVE HAPPENED IF I HAD THE DATA IN ITS RAWEST FORM: A TWO COLUMN DATA FRAME WHERE COLUMN ONE WAS THE STUDY AND COLUMN 2 WAS A FACTOR (LEVELS BEING hpv 6, hpv 11, coinfection, other). SUCH A DATA FRAME WOULD HAVE HAD 253 rows. Then I could have used table(column1,column2) and I could have got all this data as a table and the study name would be preserved. It is not that big a deal that I have to look elsewhere to find the study name but it seems silly that I cannot analyze data that is not in the raw state. I am sure there is a way. I just do not know it. On 10/3/07, Rolf Turner [EMAIL PROTECTED] wrote: I think that what you need to do is as.table(as.matrix(dff)) E.g. melvin - data.frame(x=c(3,1,3,2),y=c(3,3,4,5)) clyde - as.table(as.matrix(melvin)) prop.table(clyde,1) x y A 0.500 0.500 B 0.250 0.750 C 0.4285714 0.5714286 D 0.2857143 0.7142857 HTH. cheers, Rolf Turner ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.com ## -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 __ 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] Calculating proportions from a data frame rather than a table
Incidentally, the feature becomes really powerful when one uses functions such as addmargins together with prop.table as in coinf.table -as.matrix(coinfection) prop.table(coinf.table,1) # to see proportions from each HPV type per study addmargins(coinf.table)# to see totals within study and accross all studies prop.table(addmargins(coinf.table,1),1)# to see proportions for all studies added together On 10/3/07, Farrel Buchinsky [EMAIL PROTECTED] wrote: Genius! Thank you very much. Yes indeed I should have thought of that. For some reason I have a mental blank about the use of row.names and instead I repeatedly put that kind of data as a column in the data frame. Thank you for the rescue. -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 __ 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] Calculating proportions from a data frame rather than a table
When one has raw data it is easy to create a table of one variable against another and then calculate proportions For example a.nice.table-table(a,b) prop.table(a.nice.table,1) However, I looked at several papers and created a data frame of the aggregate data. That means I acually created a table except it is a data frame. The first column lists the name of the first author and the year. I cannot find how to convert the data frame to a table so I can use great functions such as prop.table and margin.table. Alas I tried, rowSums but it provides lousy output without listing the names of th papers. I have thought of going through the reshape package but I suspect that there is an easier way to convert a data frame to a table. Is there? -- Farrel Buchinsky [[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] Calculating proportions from a data frame rather than a table
How do you create a table from a data frame? I tried as.table( name.of.data.frame) but it bombed out. I will include the exact error message in my next posting. If I recall correctly, it said that the data.frame could not be coerced to a table. On 10/2/07, John Kane [EMAIL PROTECTED] wrote: What am I missing here? Cannot you just create the table from the data.frame and apply prop.table()to it? --- Farrel Buchinsky [EMAIL PROTECTED] wrote: When one has raw data it is easy to create a table of one variable against another and then calculate proportions For example a.nice.table-table(a,b) prop.table(a.nice.table,1) However, I looked at several papers and created a data frame of the aggregate data. That means I acually created a table except it is a data frame. The first column lists the name of the first author and the year. I cannot find how to convert the data frame to a table so I can use great functions such as prop.table and margin.table. Alas I tried, rowSums but it provides lousy output without listing the names of th papers. I have thought of going through the reshape package but I suspect that there is an easier way to convert a data frame to a table. Is there? -- Farrel Buchinsky Be smarter than spam. See how smart SpamGuard is at giving junk email the boot with the All-new Yahoo! Mail at http://mrd.mail.yahoo.com/try_beta?.intl=ca -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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.
