Re: [R] Where did lost variables go
On Mon, 30 Dec 2013 20:42:53 -0500 David Parkhurst parkh...@indiana.edu wrote: I have several variables in a data frame that aren't listed by ls() after I attach that data frame. Where did they go, and how can I stop the hidden ones from masking the local ones? Thanks for any help. David You really need to offer more information, e.g. a reproducible example that includes just how how moved data into your data frame. As it is, the only reasonable suggestion is to try and find your lost singleton socks, the missing variablee may be hiding with them. Alternatively the lost variables may have taken off to Never Never Land to hang with the Lost Boys. One simple possibility is that the missing variables were actually never read in to the data frame. Have you ever seen those variables in your data frame? Did you try str(dataframe)? As regards hidden and local, you'll - again - have to be a good deal more explicit. JDougherty __ 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] Where did lost variables go, with example
Hi you are confusing yourself and maybe other audience. With ls() you list objects in your environment (usually stored in .RData file) and loaded with starting R. Let me guess. You probably have 2 data frames All8 and All8Sites. They have some variables inside and you can see structure of any object by str str(All8) you can see names of these variables by names names(All8) you can use those variables by e.g. All8Sites$X You probably managed somehow to save variables from data.frame to independent objects in your environment, which can be confusing. Maybe it is time to read R-intro which is located in doc folder of your R installation. Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of David Parkhurst Sent: Tuesday, December 31, 2013 5:39 PM To: Duncan Murdoch; r-help@r-project.org Subject: Re: [R] Where did lost variables go, with example Thank you. I've tried what you're suggesting, at an earlier suggestion from another respondent, and I don't find my variable in any of lists ls() through ls(7). I'm just going back to using R after being away from statistics for several years. I'm thinking I might uninstall R, then reinstall it, and redo my work so far (I've kept the commands elsewhere), and avoid using attach, as someone else has suggested. David On 12/31/2013 11:32 AM, Duncan Murdoch wrote: On 13-12-31 9:48 AM, David Parkhurst wrote: Two or three respondents asked for an example of my problem. Here's what's happening to me now. I can't reproduce how I got to this point, though: ls() [1] All8 All8Sites A B C i n D F X Error: object 'X' not found attach(All8Sites) ls() [1] All8 All8Sites A B C i n D F X is one of the variables in the data frame I attached in the third command above, but it's not listed by ls(). If I enter X now, its values ARE listed, but it's hiding somewhere. What is happening here? How can I get the variables in that data frame listed when I attach it? Use search() to see the search list. Your dataframe will likely be in position 2. Use ls(2) to see the variables there. Duncan Murdoch [[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] Where did lost variables go, with example
On 31 Dec 2013, at 17:32 , Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-12-31 9:48 AM, David Parkhurst wrote: Two or three respondents asked for an example of my problem. Here's what's happening to me now. I can't reproduce how I got to this point, though: ls() [1] All8 All8Sites A B C i n D F X Error: object 'X' not found attach(All8Sites) ls() [1] All8 All8Sites A B C i n D F X is one of the variables in the data frame I attached in the third command above, but it's not listed by ls(). If I enter X now, its values ARE listed, but it's hiding somewhere. What is happening here? How can I get the variables in that data frame listed when I attach it? Use search() to see the search list. Your dataframe will likely be in position 2. Use ls(2) to see the variables there. Or ls(All8Sites). Notice, by the way, that this is subtly but importantly different from ls(All8Sites). E.g., attach(airquality) ls(2) [1] Day Month Ozone Solar.R TempWind ls(airquality) [1] Day Month Ozone Solar.R TempWind search() [1] .GlobalEnvairqualitypackage:stats [4] package:graphics package:grDevices package:utils [7] package:datasets package:methods Autoloads [10] package:base ls(airquality) [1] Day Month Ozone Solar.R TempWind rm(Month, pos=2) ls(airquality) [1] Day Month Ozone Solar.R TempWind ls(airquality) [1] Day Ozone Solar.R TempWind detach() ls(airquality) Error in as.environment(pos) : no item called airquality on the search list -pd Duncan Murdoch __ 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. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] Where did lost variables go
I have several variables in a data frame that aren't listed by ls() after I attach that data frame. Where did they go, and how can I stop the hidden ones from masking the local ones? Thanks for any help. David [[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] Where did lost variables go
A reproducible example would do well here David Best Simon On 31 Dec 2013, at 02:42, David Parkhurst parkh...@indiana.edu wrote: I have several variables in a data frame that aren't listed by ls() after I attach that data frame. Where did they go, and how can I stop the hidden ones from masking the local ones? Thanks for any help. David [[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] Where did lost variables go
G'day David, On Mon, 30 Dec 2013 20:42:53 -0500 David Parkhurst parkh...@indiana.edu wrote: Some wild guesses in the absence of a reproducible example. I have several variables in a data frame that aren't listed by ls() after I attach that data frame. ls() list the objects in the global environment. If you attach a data frame it is attached to the search path, typically after the global environment. Type 'search()' to see your search path. ls() list the global environment, the first entry in the list and called .GlobalEnv. Your data frame should be listed as an object in that environment. Assuming the name of your data frame is 'foo', then there should be the name 'foo' somewhere in the list of names returned by 'search()'. Assuming 'foo' is listed in the second position, then 'ls(2)' should list all the objects found at that location of the search path, i.e. all the variables in your data frame. Where did they go, See above. and how can I stop the hidden ones from masking the local ones? Do you mean with local ones those in the global environment and by hidden ones those that you couldn't find? I.e. is there an object bar listed by 'ls()' but also an object bar listed by 'ls(2)' (i.e. your data frame 'foo' contained a variable with name 'bar')? Then it is the other way round, the local ones are hiding the hidden ones. For that reason attaching data frames has its dangers. It allows to easily access the variables in the data frame, but any changes to a variable creates a local copy. Thus, any change *will* not propagate back to the data frame! Hopefully the commands below will clarify further. Cheers, Berwin R foo - data.frame(bar=rnorm(2), fubar=runif(2)) R ls() [1] foo R attach(foo) R search() [1] .GlobalEnvfoo package:stats [4] package:graphics package:grDevices package:utils [7] package:datasets package:methods Autoloads [10] package:base R ls(2) [1] bar fubar R bar [1] -0.07741633 1.05804653 R fubar [1] 0.08516929 0.82718383 R bar - what now R ls() [1] bar foo R bar [1] what now R ls(2) [1] bar fubar R get(bar, pos=2) [1] -0.07741633 1.05804653 R foo bar fubar 1 -0.07741633 0.08516929 2 1.05804653 0.82718383 R detach(2) R bar [1] what now R fubar Error: object 'fubar' not found R foo bar fubar 1 -0.07741633 0.08516929 2 1.05804653 0.82718383 R attach(foo) The following object is masked _by_ .GlobalEnv: bar R bar [1] what now R fubar [1] 0.08516929 0.82718383 R detach(2) R bar [1] what now R fubar Error: object 'fubar' not found R foo bar fubar 1 -0.07741633 0.08516929 2 1.05804653 0.82718383 __ 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] Where did lost variables go
Gents: I would add that: 1) attach() should probably no longer be used in R, for all the reasons (and more) cited, 2) The preferred alternative these days is to use lists, including data frames, as containers and make liberal use of the ?with and ?within functions. Environments can also be useful, but are more complicated as their semantics differ. S4 classes and objects are probably also relevant. Comments, criticisms, links, additions, and subtractions welcome, as this issue comes up regularly here and it would be nice to have consensus wisdom to refer to. Cheers, Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. H. Gilbert Welch On Tue, Dec 31, 2013 at 2:14 AM, Berwin A Turlach berwin.turl...@gmail.com wrote: G'day David, On Mon, 30 Dec 2013 20:42:53 -0500 David Parkhurst parkh...@indiana.edu wrote: Some wild guesses in the absence of a reproducible example. I have several variables in a data frame that aren't listed by ls() after I attach that data frame. ls() list the objects in the global environment. If you attach a data frame it is attached to the search path, typically after the global environment. Type 'search()' to see your search path. ls() list the global environment, the first entry in the list and called .GlobalEnv. Your data frame should be listed as an object in that environment. Assuming the name of your data frame is 'foo', then there should be the name 'foo' somewhere in the list of names returned by 'search()'. Assuming 'foo' is listed in the second position, then 'ls(2)' should list all the objects found at that location of the search path, i.e. all the variables in your data frame. Where did they go, See above. and how can I stop the hidden ones from masking the local ones? Do you mean with local ones those in the global environment and by hidden ones those that you couldn't find? I.e. is there an object bar listed by 'ls()' but also an object bar listed by 'ls(2)' (i.e. your data frame 'foo' contained a variable with name 'bar')? Then it is the other way round, the local ones are hiding the hidden ones. For that reason attaching data frames has its dangers. It allows to easily access the variables in the data frame, but any changes to a variable creates a local copy. Thus, any change *will* not propagate back to the data frame! Hopefully the commands below will clarify further. Cheers, Berwin R foo - data.frame(bar=rnorm(2), fubar=runif(2)) R ls() [1] foo R attach(foo) R search() [1] .GlobalEnvfoo package:stats [4] package:graphics package:grDevices package:utils [7] package:datasets package:methods Autoloads [10] package:base R ls(2) [1] bar fubar R bar [1] -0.07741633 1.05804653 R fubar [1] 0.08516929 0.82718383 R bar - what now R ls() [1] bar foo R bar [1] what now R ls(2) [1] bar fubar R get(bar, pos=2) [1] -0.07741633 1.05804653 R foo bar fubar 1 -0.07741633 0.08516929 2 1.05804653 0.82718383 R detach(2) R bar [1] what now R fubar Error: object 'fubar' not found R foo bar fubar 1 -0.07741633 0.08516929 2 1.05804653 0.82718383 R attach(foo) The following object is masked _by_ .GlobalEnv: bar R bar [1] what now R fubar [1] 0.08516929 0.82718383 R detach(2) R bar [1] what now R fubar Error: object 'fubar' not found R foo bar fubar 1 -0.07741633 0.08516929 2 1.05804653 0.82718383 __ 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] Where did lost variables go, with example
Two or three respondents asked for an example of my problem. Here's what's happening to me now. I can't reproduce how I got to this point, though: ls() [1] All8 All8Sites A B C i n D F X Error: object 'X' not found attach(All8Sites) ls() [1] All8 All8Sites A B C i n D F X is one of the variables in the data frame I attached in the third command above, but it's not listed by ls(). If I enter X now, its values ARE listed, but it's hiding somewhere. What is happening here? How can I get the variables in that data frame listed when I attach it? Thanks to all. David [[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] Where did lost variables go, with example
On 13-12-31 9:48 AM, David Parkhurst wrote: Two or three respondents asked for an example of my problem. Here's what's happening to me now. I can't reproduce how I got to this point, though: ls() [1] All8 All8Sites A B C i n D F X Error: object 'X' not found attach(All8Sites) ls() [1] All8 All8Sites A B C i n D F X is one of the variables in the data frame I attached in the third command above, but it's not listed by ls(). If I enter X now, its values ARE listed, but it's hiding somewhere. What is happening here? How can I get the variables in that data frame listed when I attach it? Use search() to see the search list. Your dataframe will likely be in position 2. Use ls(2) to see the variables there. Duncan Murdoch __ 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] Where did lost variables go, with example
On 13-12-31 11:38 AM, David Parkhurst wrote: Thank you. I've tried what you're suggesting, at an earlier suggestion from another respondent, and I don't find my variable in any of lists ls() through ls(7). Are you sure that X is really the name of a column in the dataframe? names(All8Sites) will tell you all the names that are there. I'm just going back to using R after being away from statistics for several years. I'm thinking I might uninstall R, then reinstall it, and redo my work so far (I've kept the commands elsewhere), and avoid using attach, as someone else has suggested. It's not likely to be necessary to reinstall R, but it shouldn't hurt. Duncan Murdoch David On 12/31/2013 11:32 AM, Duncan Murdoch wrote: On 13-12-31 9:48 AM, David Parkhurst wrote: Two or three respondents asked for an example of my problem. Here's what's happening to me now. I can't reproduce how I got to this point, though: ls() [1] All8 All8Sites A B C i n D F X Error: object 'X' not found attach(All8Sites) ls() [1] All8 All8Sites A B C i n D F X is one of the variables in the data frame I attached in the third command above, but it's not listed by ls(). If I enter X now, its values ARE listed, but it's hiding somewhere. What is happening here? How can I get the variables in that data frame listed when I attach it? Use search() to see the search list. Your dataframe will likely be in position 2. Use ls(2) to see the variables there. Duncan Murdoch __ 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] Where did lost variables go, with example
Thank you. I've tried what you're suggesting, at an earlier suggestion from another respondent, and I don't find my variable in any of lists ls() through ls(7). I'm just going back to using R after being away from statistics for several years. I'm thinking I might uninstall R, then reinstall it, and redo my work so far (I've kept the commands elsewhere), and avoid using attach, as someone else has suggested. David On 12/31/2013 11:32 AM, Duncan Murdoch wrote: On 13-12-31 9:48 AM, David Parkhurst wrote: Two or three respondents asked for an example of my problem. Here's what's happening to me now. I can't reproduce how I got to this point, though: ls() [1] All8 All8Sites A B C i n D F X Error: object 'X' not found attach(All8Sites) ls() [1] All8 All8Sites A B C i n D F X is one of the variables in the data frame I attached in the third command above, but it's not listed by ls(). If I enter X now, its values ARE listed, but it's hiding somewhere. What is happening here? How can I get the variables in that data frame listed when I attach it? Use search() to see the search list. Your dataframe will likely be in position 2. Use ls(2) to see the variables there. Duncan Murdoch [[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.
