An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20111115/508916f3/attachment.pl>
Convert back to lower triangular matrix
9 messages · Juliet Ndukum, Jeff Newmiller, David Winsemius +4 more
This is R-help, not the linear algebra hotline. Please stay on topic.
---------------------------------------------------------------------------
Jeff Newmiller The ..... ..... Go Live...
DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/Batteries O.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---------------------------------------------------------------------------
Sent from my phone. Please excuse my brevity.
Juliet Ndukum <jpntsang at yahoo.com> wrote:
Given a vector;> ab = seq(0.5,1, by=0.1)> ab[1] 0.5 0.6 0.7 0.8 0.9 1.0 The euclidean distance between the vector elements is given by the lower triangular matrix?> dd1 = dist(ab,"euclidean")> dd1? ? 1 ? 2 ? 3 ? 4 ? 52 0.1 ? ? ? ? ? ? ? ?3 0.2 0.1 ? ? ? ? ? ?4 0.3 0.2 0.1 ? ? ? ?5 0.4 0.3 0.2 0.1 ? ?6 0.5 0.4 0.3 0.2 0.1 Convert the lower triangular matrix to a full matrix> ddm = as.matrix(dd1)> ddm? ? 1 ? 2 ? 3 ? 4 ? 5 ? 61 0.0 0.1 0.2 0.3 0.4 0.52 0.1 0.0 0.1 0.2 0.3 0.43 0.2 0.1 0.0 0.1 0.2 0.34 0.3 0.2 0.1 0.0 0.1 0.25 0.4 0.3 0.2 0.1 0.0 0.16 0.5 0.4 0.3 0.2 0.1 0.0 I would be grateful if someone could provide me with a code to convert ddm to the lower triangular matrix as before i.e. dd1 above. Your help will be greatly appreciated.JN [[alternative HTML version deleted]]
______________________________________________ R-help at 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.
On Nov 15, 2011, at 5:38 PM, Juliet Ndukum wrote:
Given a vector;> ab = seq(0.5,1, by=0.1)
ab[1] 0.5 0.6 0.7 0.8 0.9 1.0
The euclidean distance between the vector elements is given by the lower triangular matrix
dd1 = dist(ab,"euclidean")
dd1 1 2 3 4 5
2 0.1 3 0.2 0.1 4 0.3 0.2 0.1 5 0.4 0.3 0.2 0.1 6 0.5 0.4 0.3 0.2 0.1 Convert the lower triangular matrix to a full matrix
ddm = as.matrix(dd1)
ddm 1 2 3 4 5 61 0.0 0.1 0.2 0.3 0.4 0.52 0.1 0.0 0.1
0.2 0.3 0.43 0.2 0.1 0.0 0.1 0.2 0.34 0.3 0.2 0.1 0.0 0.1 0.25 0.4 0.3 0.2 0.1 0.0 0.16 0.5 0.4 0.3 0.2 0.1 0.0 I would be grateful if someone could provide me with a code to convert ddm to the lower triangular matrix as before i.e. dd1
Surely this would be the logical inverse dd1.b <- as.dist(ddm)
David Winsemius, MD West Hartford, CT
On Tue, Nov 15, 2011 at 2:38 PM, Juliet Ndukum <jpntsang at yahoo.com> wrote:
Given a vector;> ab = seq(0.5,1, by=0.1)> ab[1] 0.5 0.6 0.7 0.8 0.9 1.0 The euclidean distance between the vector elements is given by the lower triangular matrix?> dd1 = dist(ab,"euclidean")> dd1? ? 1 ? 2 ? 3 ? 4 ? 52 0.1 ? ? ? ? ? ? ? ?3 0.2 0.1 ? ? ? ? ? ?4 0.3 0.2 0.1 ? ? ? ?5 0.4 0.3 0.2 0.1 ? ?6 0.5 0.4 0.3 0.2 0.1 Convert the lower triangular matrix to a full matrix> ddm = as.matrix(dd1)> ddm? ? 1 ? 2 ? 3 ? 4 ? 5 ? 61 0.0 0.1 0.2 0.3 0.4 0.52 0.1 0.0 0.1 0.2 0.3 0.43 0.2 0.1 0.0 0.1 0.2 0.34 0.3 0.2 0.1 0.0 0.1 0.25 0.4 0.3 0.2 0.1 0.0 0.16 0.5 0.4 0.3 0.2 0.1 0.0 I would be grateful if someone could provide me with a code to convert ddm to the lower triangular matrix as before i.e. dd1 ?above.
as.dist(ddm) Peter
1. Please post in plain text, not HTML (as the posting guide asks!) 2. This might actually be an R question -- is ?lower.tri what you want? -- Bert On Tue, Nov 15, 2011 at 2:50 PM, Jeff Newmiller
<jdnewmil at dcn.davis.ca.us> wrote:
This is R-help, not the linear algebra hotline. Please stay on topic. --------------------------------------------------------------------------- Jeff Newmiller ? ? ? ? ? ? ? ? ? ? ? ?The ? ? ..... ? ? ? ..... ?Go Live... DCN:<jdnewmil at dcn.davis.ca.us> ? ? ? ?Basics: ##.#. ? ? ? ##.#. ?Live Go... ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?Live: ? OO#.. Dead: OO#.. ?Playing Research Engineer (Solar/Batteries ? ? ? ? ? ?O.O#. ? ? ? #.O#. ?with /Software/Embedded Controllers) ? ? ? ? ? ? ? .OO#. ? ? ? .OO#. ?rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity. Juliet Ndukum <jpntsang at yahoo.com> wrote:
Given a vector;> ab = seq(0.5,1, by=0.1)> ab[1] 0.5 0.6 0.7 0.8 0.9 1.0 The euclidean distance between the vector elements is given by the lower triangular matrix?> dd1 = dist(ab,"euclidean")> dd1? ? 1 ? 2 ? 3 ? 4 ? 52 0.1 ? ? ? ? ? ? ? ?3 0.2 0.1 ? ? ? ? ? ?4 0.3 0.2 0.1 ? ? ? ?5 0.4 0.3 0.2 0.1 ? ?6 0.5 0.4 0.3 0.2 0.1 Convert the lower triangular matrix to a full matrix> ddm = as.matrix(dd1)> ddm? ? 1 ? 2 ? 3 ? 4 ? 5 ? 61 0.0 0.1 0.2 0.3 0.4 0.52 0.1 0.0 0.1 0.2 0.3 0.43 0.2 0.1 0.0 0.1 0.2 0.34 0.3 0.2 0.1 0.0 0.1 0.25 0.4 0.3 0.2 0.1 0.0 0.16 0.5 0.4 0.3 0.2 0.1 0.0 I would be grateful if someone could provide me with a code to convert ddm to the lower triangular matrix as before i.e. dd1 above. Your help will be greatly appreciated.JN ? ? ? [[alternative HTML version deleted]]
______________________________________________ R-help at 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 at 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.
Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20111115/9cda38be/attachment.pl>
Hi, The obvious answer is don't use attach() and you'll never have that problem. And see further comments inline.
On Tue, Nov 15, 2011 at 6:05 PM, Steven Yen <syen at utk.edu> wrote:
Can someone help me with this variable/data reading issue?
I read a csv file and transform/create an additional variable (called y).
The first set of commands below produced different sample statistics
for hw11$y and y
In the second set of command I renameuse the variable name yy, and
sample statistics for $hw11$yy and yy are identical.
Using y <- yy fixed it, but I am not sure why I would need to do that.
That "y" appeared to have come from a variable called "y" from
another data frame (unrelated to the current run).
Help!
?> setwd("z:/homework")
?> sink ("z:/homework/hw11.our", append=T, split=T)
?> hw11 <- read.csv("ij10b.csv",header=T)
?> hw11$y <- hw11$e3
?> attach(hw11)
The following object(s) are masked _by_ '.GlobalEnv':
? ? y
Look there. R even *told* you that it was going to use the y in the global environment rather than the one you were trying to attach. The other solution: don't save your workspace. Your other email on this topic suggested to me that there is a .RData file in your preferred working directory that contains an object y, and that's what is interfering with what you think should happen. Deleting that file, or using a different directory, or removing y before you attach the data frame would all work. But truly, the best possible strategy is to avoid using attach() so you don't have to worry about which object named y is really being used because you specify it explicitly.
?> (n <- dim(hw11)[1])
[1] 13765
?> summary(hw11$y)
? ? Min. ?1st Qu. ? Median ? ? Mean ?3rd Qu. ? ? Max.
? 0.0000 ? 0.4500 ? 1.0000 ? 1.6726 ? 2.0000 140.0000
?> length(hw11$y)
[1] 13765
?> summary(y)
? ?Min. 1st Qu. ?Median ? ?Mean 3rd Qu. ? ?Max.
0.00000 0.00000 0.00000 0.24958 0.00000 1.00000
?> length(y)
[1] 601
?>
?> setwd("z:/homework")
?> sink ("z:/homework/hw11.our", append=T, split=T)
?> hw11 <- read.csv("ij10b.csv",header=T)
?> hw11$yy <- hw11$e3
?> attach(hw11)
?> hw11$yy <- hw11$e3
?> summary(hw11$yy)
? ? Min. ?1st Qu. ? Median ? ? Mean ?3rd Qu. ? ? Max.
? 0.0000 ? 0.4500 ? 1.0000 ? 1.6726 ? 2.0000 140.0000
?> length(hw11$yy)
[1] 13765
?> summary(yy)
? ? Min. ?1st Qu. ? Median ? ? Mean ?3rd Qu. ? ? Max.
? 0.0000 ? 0.4500 ? 1.0000 ? 1.6726 ? 2.0000 140.0000
?> length(yy)
[1] 13765
?>
Sarah Goslee http://www.functionaldiversity.org
1 day later
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20111117/cf8c86c4/attachment.pl>
Well, if your problem is that a workspace is being loaded automatically and you don't want that workspace, you have several options: 1. Use a different directory for each project so that the file loaded by default is the correct one. 2. Don't save your workspace, but regenerate it each time. 3. Use R --vanilla or your OS's equivalent to start R without loading anything automatically, and use load() and save() to manually manage RData files. Yes, it's convenient, but if you want to use a non-standard way of working you need to understand what you're doing. Sarah
On Thu, Nov 17, 2011 at 3:10 AM, Steven Yen <syen at utk.edu> wrote:
Thanks Sarah. I have read about the problems with attach(), and I will try
to avoid it.
I have now found the line that's causing the problem is:
setwd("z:/homework")
With that line in place, either in a program or in Rprofile.site (?), then
the moment I run R and simply enter (before reading any data)
summary(mydata)
I get sample statistics for a dozen variables!
Do not save the workspace? I thought the option to save/use a binary file is
meant to be convenient.
I like working in the same working directory, and I like .rdata files. Does
this sound hopeless? Thanks.
At 09:26 PM 11/15/2011, Sarah Goslee wrote:
Hi,
The obvious answer is don't use attach() and you'll never have
that problem. And see further comments inline.
On Tue, Nov 15, 2011 at 6:05 PM, Steven Yen <syen at utk.edu> wrote:
Can someone help me with this variable/data reading issue?
I read a csv file and transform/create an additional variable (called y).
The first set of commands below produced different sample statistics
for hw11$y and y
In the second set of command I renameuse the variable name yy, and
sample statistics for $hw11$yy and yy are identical.
Using y <- yy fixed it, but I am not sure why I would need to do that.
That "y" appeared to have come from a variable called "y" from
another data frame (unrelated to the current run).
Help!
? > setwd("z:/homework")
? > sink ("z:/homework/hw11.our", append=T, split=T)
? > hw11 <- read.csv("ij10b.csv",header=T)
? > hw11$y <- hw11$e3
? > attach(hw11)
The following object(s) are masked _by_ '.GlobalEnv':
???? y
Look there. R even *told* you that it was going to use the y in the global environment rather than the one you were trying to attach. The other solution: don't save your workspace. Your other email on this topic suggested to me that there is a .RData file in your preferred working directory that contains an object y, and that's what is interfering with what you think should happen. Deleting that file, or using a different directory, or removing y before you attach the data frame would all work. But truly, the best possible strategy is to avoid using attach() so you don't have to worry about which object named y is really being used because you specify it explicitly.
? > (n <- dim(hw11)[1])
[1] 13765
? > summary(hw11$y)
???? Min.? 1st Qu.?? Median???? Mean? 3rd Qu.???? Max.
?? 0.0000?? 0.4500?? 1.0000?? 1.6726?? 2.0000 140.0000
? > length(hw11$y)
[1] 13765
? > summary(y)
??? Min. 1st Qu.? Median??? Mean 3rd Qu.??? Max.
0.00000 0.00000 0.00000 0.24958 0.00000 1.00000
? > length(y)
[1] 601
? >
? > setwd("z:/homework")
? > sink ("z:/homework/hw11.our", append=T, split=T)
? > hw11 <- read.csv("ij10b.csv",header=T)
? > hw11$yy <- hw11$e3
? > attach(hw11)
? > hw11$yy <- hw11$e3
? > summary(hw11$yy)
???? Min.? 1st Qu.?? Median???? Mean? 3rd Qu.???? Max.
?? 0.0000?? 0.4500?? 1.0000?? 1.6726?? 2.0000 140.0000
? > length(hw11$yy)
[1] 13765
? > summary(yy)
???? Min.? 1st Qu.?? Median???? Mean? 3rd Qu.???? Max.
?? 0.0000?? 0.4500?? 1.0000?? 1.6726?? 2.0000 140.0000
? > length(yy)
[1] 13765
? >