Re: [R] use logical in cor.test
Thanks for the replies. In response to Erik: What does Both[,1] show you? Both[,1] [1] 3.36 NA NA NA NA NA NA 3.92 3.50 NA NA NA NA 3.76 3.19 3.83 NA 3.66.. What does Both[,1] 2.5 show you? Both[,1]2.5 [1] TRUENANANANANANA TRUE TRUENANA NANA TRUE TRUE I understand a logical variable is binary, but don't know how to select a subset of the data (have tried the subset function, but can't seem to get it to work) Bill, when I run what you suggested, I get: tBoth - Both is.na(tBoth[tBoth 2.5]) - TRUE Error in is.na(tBoth[tBoth 2.5]) - TRUE : NAs are not allowed in subscripted assignments R - cor(tBoth, use = complete.obs) R[1,2] [1] 0.7750889 Any idea with the error message? Thanks again, Paul -- View this message in context: http://n4.nabble.com/use-logical-in-cor-test-tp1744701p1744896.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.
Re: [R] use logical in cor.test
Many thanks Peter, This did indeed work. Regards, Paul -- View this message in context: http://n4.nabble.com/use-logical-in-cor-test-tp1744701p1746008.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] use logical in cor.test
Hi, I've got 4 variables that I want to effectively 'stack' so that I have a grand R variable and a grand L variable. This works to achieve that goal: Twin1cor-with(twin.wide,cbind(ACDepthR.1,ACDepthL.1)) Twin2cor-with(twin.wide,cbind(ACDepthR.2,ACDepthL.2)) Both-rbind(Twin1cor,Twin2cor) str(Both) num [1:1858, 1:2] 3.36 NA NA NA NA NA NA 3.92 3.5 NA ... - attr(*, dimnames)=List of 2 ..$ : NULL ..$ : chr [1:2] ACDepthR.1 ACDepthL.1 I then want to perform a pearson correlation of the two variables, but exclude any value greater than 2.5. When I do this without excluding anything, with: cor.test(Both[,1],Both[,2]) I get: Pearson's product-moment correlation data: Both[, 1] and Both[, 2] t = 35.848, df = 854, p-value 2.2e-16 alternative hypothesis: true correlation is not equal to 0 95 percent confidence interval: 0.7468716 0.8005199 sample estimates: cor 0.7750889 But when I try: cor.test(Both[,1]2.5,Both[,2]2.5) I get: Pearson's product-moment correlation data: Both[, 1] 2.5 and Both[, 2] 2.5 t = 13.3192, df = 854, p-value 2.2e-16 alternative hypothesis: true correlation is not equal to 0 95 percent confidence interval: 0.3576600 0.4687099 sample estimates: cor 0.414728 I'm not sure why. I know the correlation should improve from the plot by excluding those under 2.5, but it decreases. Have I done something wrong here? Thanks, Paul -- View this message in context: http://n4.nabble.com/use-logical-in-cor-test-tp1744701p1744701.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] Exclude data using logical
Hi,
I'm wanting to exclude data more than 2 sd's from the mean before proceeding
with further analyses. I've created new logical variables (a and b) and
written them to the existing dataframe. I want to be able to subset the TRUE
observations based on another 2 factor variable. I'm assuming this is
possible, but I don't know what I'm doing wrong, as I get results that
obviously aren't correct.
Many thanks,
Paul
twin.wide$a-twin.wide$RCCT600 twin.wide$RCCT480
twin.wide$b-twin.wide$LCCT600 twin.wide$LCCT480
selVarsCCT - with(twin.wide,c('a','b'))
MZCCT - subset(twin.wide,Zygosity=='MZ',selVarsCCT)
DZCCT - subset(twin.wide,Zygosity=='DZ',selVarsCCT)
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Re: [R] Exclude data using logical
That worked. Thanks a lot David - I appreciate it. Paul -- View this message in context: http://n4.nabble.com/Exclude-data-using-logical-tp1689992p1690090.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.
Re: [R] Re order variables in a dataframe
Thanks everyone -- View this message in context: http://www.nabble.com/Reorder-variables-in-a-dataframe-tp23647222p23660941.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] Re order variables in a dataframe
This is no doubt a very basic question for most R users, but is there an easy way to reorder the variables (columns) in a dataframe (I can't seem to find an answer anywhere). I've generally been creating a new dataframe and selecting the new order I want from the old but this is time-consuming. Thanks, Paul -- View this message in context: http://www.nabble.com/Reorder-variables-in-a-dataframe-tp23647222p23647222.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.
Re: [R] Re order variables in a dataframe
Thanks Simon, I should have explained myself better (although I didn't know about the order function so that's handy information). I've found a few times, I've added variables to a dataframe that I would like to 'group' with variables earlier in the datset. So I was wondering if you could somehow ask R, for example, to take that last variable and insert it at a different position in the dataframe. Thanks, Paul Simon Blomberg-4 wrote: Alphabetically, like this?: dat - data.frame(d=rnorm(3), c=rnorm(3), b=rnorm(3), a=rnorm(3)) dat d c b a 1 -0.1816733 -0.4106008 -0.2855991 -1.022951 2 -1.8326818 -0.6515208 0.3344884 -2.191836 3 1.0924867 0.1159611 -1.3409719 1.195545 dat2 - dat[,order(names(dat))] dat2 a b c d 1 -1.022951 -0.2855991 -0.4106008 -0.1816733 2 -2.191836 0.3344884 -0.6515208 -1.8326818 3 1.195545 -1.3409719 0.1159611 1.0924867 Cheers, Simon. On Wed, 2009-05-20 at 20:19 -0700, pgseye wrote: This is no doubt a very basic question for most R users, but is there an easy way to reorder the variables (columns) in a dataframe (I can't seem to find an answer anywhere). I've generally been creating a new dataframe and selecting the new order I want from the old but this is time-consuming. Thanks, Paul -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ 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/Reorder-variables-in-a-dataframe-tp23647222p23647370.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] help with plotting results of lda
Hi, I've performed an lda and obtained a classification table for some of my data: efa.dfa-lda(groups~.,efa.scores.8,CV=T) str(efa.dfa) List of 5 $ class: Factor w/ 2 levels 1,2: 1 2 1 2 1 1 2 2 1 2 ... $ posterior: num [1:160, 1:2] 0.99083 0.00852 0.93983 0.23186 0.85931 ... ..- attr(*, dimnames)=List of 2 .. ..$ : chr [1:160] 1 2 3 4 ... .. ..$ : chr [1:2] 1 2 $ terms:Classes 'terms', 'formula' length 3 groups ~ Comp.1 + Comp.2 + Comp.3 + Comp.4 + Comp.5 + Comp.6 + Comp.7 + Comp.8 + Comp.9 + Comp.10 + Comp.11 + Comp.12 + ... .. ..- attr(*, variables)= language list(groups, Comp.1, Comp.2, Comp.3, Comp.4, Comp.5, Comp.6, Comp.7, Comp.8, Comp.9, Comp.10, Comp.11, Comp.12, Comp.13, ... .. ..- attr(*, factors)= int [1:35, 1:34] 0 1 0 0 0 0 0 0 0 0 ... .. .. ..- attr(*, dimnames)=List of 2 .. .. .. ..$ : chr [1:35] groups Comp.1 Comp.2 Comp.3 ... .. .. .. ..$ : chr [1:34] Comp.1 Comp.2 Comp.3 Comp.4 ... .. ..- attr(*, term.labels)= chr [1:34] Comp.1 Comp.2 Comp.3 Comp.4 ... .. ..- attr(*, order)= int [1:34] 1 1 1 1 1 1 1 1 1 1 ... .. ..- attr(*, intercept)= int 1 .. ..- attr(*, response)= int 1 .. ..- attr(*, .Environment)=environment: R_GlobalEnv .. ..- attr(*, predvars)= language list(groups, Comp.1, Comp.2, Comp.3, Comp.4, Comp.5, Comp.6, Comp.7, Comp.8, Comp.9, Comp.10, Comp.11, Comp.12, Comp.13, ... .. ..- attr(*, dataClasses)= Named chr [1:35] numeric numeric numeric numeric ... .. .. ..- attr(*, names)= chr [1:35] groups Comp.1 Comp.2 Comp.3 ... $ call : language lda(formula = groups ~ ., data = efa.scores.8, CV = T) $ xlevels : list() table(groups, Classified=efa.dfa$class) Classified groups 1 2 1 59 21 2 10 70 but when I try to plot the results I get: plot(efa.dfa) Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf anyone have any ideas? Thanks a lot, Paul -- View this message in context: http://www.nabble.com/help-with-plotting-results-of-lda-tp23240220p23240220.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] add variable in for loop
Hi,
I'm learning to write some basic functions in R. For some data I have I'd
like to be able to add a variable to itself after each iteration in a for
loop to obtain a grandtotal for that variable so I can calculate a mean.
test-function(data){
for (i in 1:80){
meanrotation-(abs(data[i,3]-data[i,2])+abs(data[i,4]-data[i,2])+abs(data[i,5]-data[i,2])+abs(data[i,6]-data[i,2]))/4
cat(i,meanrotation,\n)
#total+=meanrotation
}
#print (total/80)
}
In perl there's an assignment operator variable+=variable2. Is there
anything like this in R to do as illustrated in the code above.
thanks a lot,
Paul
Edit - I guess the other way to do this which I just realised is to assign
the output of the function to a vector and then do a summary(), but I don't
know how to do this either - help is appreciated
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[R] Help with 'boot'
Hi, I'm wanting to test for a difference in medians between 2 groups using resampling methods. I found the boot package, but don't really understand how to write the 'statistic' function required as the 2nd argument for the bootstrap test. Thanks if you can help, Paul -- View this message in context: http://www.nabble.com/Help-with-%27boot%27-tp22653487p22653487.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] JGR install problem
Hi, I thought I'd like to try out JGR, but after installing the package (and dependencies) I receive the following when I try to load it: library(JGR) Loading required package: rJava Loading required package: JavaGD Loading required package: iplots Note: On Mac OS X we strongly recommend using iplots from within JGR. Proceed at your own risk as iplots cannot resolve potential ev.loop deadlocks. 'Yes' is assumed for all dialogs as they cannot be shown without a deadlock, also ievent.wait() is disabled. Exception in thread main Error in .jnew(org/rosuda/iplots/Framework) : Failed to create object of class `org/rosuda/iplots/Framework' In addition: Warning message: In .jnew(org/rosuda/iplots/Framework) : NewObject(org/rosuda/iplots/Framework,()V,...) failed Error: package 'iplots' could not be loaded java.lang.InternalError: Can't start the AWT because Java was started on the first thread. Make sure StartOnFirstThread is not specified in your application's Info.plist or on the command line at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1822) at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1723) at java.lang.Runtime.loadLibrary0(Runtime.java:822) at java.lang.System.loadLibrary(System.java:993) at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.loadLibraries(Toolkit.java:1509) at java.awt.Toolkit.clinit(Toolkit.java:1530) at java.awt.Color.clinit(Color.java:250) at org.rosuda.ibase.Common.clinit(Common.java:47) at org.rosuda.iplots.Framework.init(Framework.java:43) iplots seems to be the problem, but I can't figure out why. I'm running 2.8.1 and OS X 10.5.6. Any ideas? Thanks a lot, Paul -- View this message in context: http://www.nabble.com/JGR-install-problem-tp22572045p22572045.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] How to do ICC
Hi,
I'm essentially wanting to calculate intra- and inter-observer variabilities
for the first principal component of an optic disc shape measure of a sample
of individuals, so from what I can work out I need to work out an intraclass
correlation coefficient(s).
For the intra-data, I have 2 measurements taken on each individual by the
same observer. For the inter-data, 2 observers have taken one measurement
each on the sample.
I've found the 'icc' function in the {psy} package, but am not sure how I'd
perform the intra- calculation as the data argument is an 'n*p matrix or
dataframe, n subjects p raters'.
Would I just substitute the replica for the rater?
Hope this makes sense - still learning about it all.
Thank you.
Paul
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Re: [R] Q about how to use Anova.mlm
Thanks a lot John - appreciate your help. Regards, Paul -- View this message in context: http://www.nabble.com/Q-about-how-to-use-Anova.mlm-tp21739443p21757533.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] Q about how to use Anova.mlm
Hi, Am newish to stats and R, so I certainly appreciate any help. Basically I have 50 inidividuals whom I have 6 photos each of their optic nerve head. I want to check that the orientation of the nerve head is consistent, ie the 6 replicates show minimal or preferably no rotation differences. I'll draw an arbitrary line between some blood vessels (same reference in each set of replicates) and determine an angle of deviation from the vertical and that angle will be my dependent variable. Subject Replicate Angle of Deviation 1 1 x 1 2 x 1 3 x 1 4 x 1 5 x 1 6 x 2 1 x 2 2 x 2 3 x 2 4 x 2 5 x 2 6 x etc I'm wanting to test for Sphericity (because I've read that you should - is this routine in a repeated measures ANOVA?) and can see that Anova.mlm in the CAR package offers this in addition to the alternative Greenhouse and Feldt tests. I just don't really know how to perform the test - can someone give me some help. Thank you. Paul Dept of Ophthalmology Uni Melbourne, Australia -- View this message in context: http://www.nabble.com/Q-about-how-to-use-Anova.mlm-tp21739443p21739443.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.
Re: [R] Q about how to use Anova.mlm
Thanks a lot for that John - really helpful. I generated some random numbers and seem to be able to get it to work, so that's great. One thing - it's come up with a 'Type III' test and given me a few warnings. What's the difference between Type II and Type III tests (if there's some basic guide you can point me to). Thank you again. Best, Paul -- View this message in context: http://www.nabble.com/Q-about-how-to-use-Anova.mlm-tp21739443p21740704.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.
Re: [R] Save object summary to file
Thanks Yihui and to others who replied privately. Very helpful information. Regards, Paul pgseye wrote: Hi, Am wanting to save the summary of a PCA to file. Have tried: write.table(summary(PCA), file=PCAvar.txt, sep=\t) but receive: Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class summary.princomp into a data.frame What am I doing wrong? Thanks -- View this message in context: http://www.nabble.com/Save-object-summary-to-file-tp19447000p19450595.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] Save object summary to file
Hi, Am wanting to save the summary of a PCA to file. Have tried: write.table(summary(PCA), file=PCAvar.txt, sep=\t) but receive: Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class summary.princomp into a data.frame What am I doing wrong? Thanks -- View this message in context: http://www.nabble.com/Save-object-summary-to-file-tp19447000p19447000.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.
Re: [R] PCA and % variance explained
Thanks everyone, Paul -- View this message in context: http://www.nabble.com/PCA-and---variance-explained-tp19388970p19410675.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] PCA and % variance explained
After doing a PCA using princomp, how do you view how much each component contributes to variance in the dataset. I'm still quite new to the theory of PCA - I have a little idea about eigenvectors and eigenvalues (these determine the variance explained?). Are the eigenvalues related to loadings in R? Thanks, Paul -- View this message in context: http://www.nabble.com/PCA-and---variance-explained-tp19388970p19388970.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] Label 2 groups in PCA different colours
Hi, I'm wanting to do a PCA on some data which is comprised of two different groups (to see how well the groups are discriminated). Is there a way to change the colour of the datapoints in a biplot so that I can easily see which group is which (eg objects 1-100, red, 101-200, black). Might be simple, but I'm new to R and can't seem to find how to do this. Thanks. Paul -- View this message in context: http://www.nabble.com/Label-2-groups-in-PCA-different-colours-tp19354077p19354077.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.
Re: [R] Write lower half of distance matrix only
Great, thanks for that Jim, It does what I need it do do. Regards, Paul jholtman wrote: Does this do what you want: x - matrix(1:25,5) x [,1] [,2] [,3] [,4] [,5] [1,]16 11 16 21 [2,]27 12 17 22 [3,]38 13 18 23 [4,]49 14 19 24 [5,]5 10 15 20 25 x[upper.tri(x)] - NA write.table(x, na=, row.names=FALSE, col.names=FALSE) 1 2 7 3 8 13 4 9 14 19 5 10 15 20 25 On Fri, Jul 25, 2008 at 8:30 AM, pgseye [EMAIL PROTECTED] wrote: Thanks Jim, The morphometry software I mentioned outputs distance matrices in the format: 0. 7.1598 0. 8.7241 8.3506 0. 9.5217 7.2457 2.5642 0. I would have liked to write to a file the same type of matrix in R, to ensure the same data format. Mantel for Windows is optimally setup to take this type of matrix. Thanks jholtman wrote: How do you want the lower half written out? can you give us an example of the input matrix and then what you would expect to see on the output. Is it still a matrix with the upper half set to zero/NA? Do you want it as a vector? What is the other program expecting as input? You need to provide more information so that we can provide suggestions. On Fri, Jul 25, 2008 at 7:03 AM, pgseye [EMAIL PROTECTED] wrote: Hi, I'm very new to R. I want to know if there is any way to write only the lower half of a distance matrix created in R to a csv file for example. I get the 'cannot coerce class dist into a data.frame' message when I try. I have used as.matrix and can write to a file this way, but as a full matrix. The reason I only want the lower half is that I've been doing some Mantel correlations with distance matrices (of Procrustes distances) generated by other (geometric morphometric) software that are in this format. However, I'm needing to use an alternative such as R to calculate distance matrices of Fourier coefficients which the other software can't do. So far, the Mantel correlations calculated from these two matrices (with R and also another software (Mantel for Windows)) are slightly different (when they should be exactly the same) and I'm wondering whether it's because the input format is different (ie one full, one half). Thanks, Paul -- View this message in context: http://www.nabble.com/Write-lower-half-of-distance-matrix-only-tp18649556p18649556.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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ 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/Write-lower-half-of-distance-matrix-only-tp18649556p18650794.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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ 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/Write-lower-half-of-distance-matrix-only-tp18649556p18662636.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] Write lower half of distance matrix only
Hi, I'm very new to R. I want to know if there is any way to write only the lower half of a distance matrix created in R to a csv file for example. I get the 'cannot coerce class dist into a data.frame' message when I try. I have used as.matrix and can write to a file this way, but as a full matrix. The reason I only want the lower half is that I've been doing some Mantel correlations with distance matrices (of Procrustes distances) generated by other (geometric morphometric) software that are in this format. However, I'm needing to use an alternative such as R to calculate distance matrices of Fourier coefficients which the other software can't do. So far, the Mantel correlations calculated from these two matrices (with R and also another software (Mantel for Windows)) are slightly different (when they should be exactly the same) and I'm wondering whether it's because the input format is different (ie one full, one half). Thanks, Paul -- View this message in context: http://www.nabble.com/Write-lower-half-of-distance-matrix-only-tp18649556p18649556.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.
