Displaying 20 results from an estimated 800 matches similar to: "How to build phylogenetic tree by R program from distance any distance matrix"
2003 Apr 24
1
write.table problem
Dear R helpers,
I have been using the loadings function from the multiv library and I
get the typical output (see below). When I try to export these results
to a file using a write.table() I get the following error message
"Error in as.data.frame.default(x[[i]], optional = TRUE) : can't coerce
loadings into a data.frame" Any idea why write.table is doing that and
any
2012 Aug 03
1
Multiple Comparisons-Kruskal-Wallis-Test: kruskal{agricolae} and kruskalmc{pgirmess} don't yield the same results although they should do (?)
Hi there,
I am doing multiple comparisons for data that is not normally distributed.
For this purpose I tried both functions kruskal{agricolae} and
kruskalmc{pgirmess}. It confuses me that these functions do not yield the
same results although they are doing the same thing, don't they? Can anyone
tell my why this happens and which function I can trust?
kruskalmc() tells me that there are no
2009 Jun 15
0
books on Time serie
A time series text with a title that seems designed to hide its
wide scope is:
Forecasting with Exponential Smoothing
The State Space Approach
Hyndman, R.J., Koehler, A.B., Ord, J.K., Snyder, R.D.
Springer 2009.
This book is actually an excellent overview of time series theory,
ARIMA as well as state space. It is of course, in part, a manual
for the forecast and other packages in what has been
2013 Mar 28
0
using cvlm to do cross-validation
Hello,
I did a cross-validation using cvlm from DAAG package but wasn't sure how to assess the result. Does this result means my model is a good model?
I understand that the overall ms is the mean of sum of squares. But is 0.0987 a good number? The response (i.e. gailRel5yr) has min,1st Quantile, median, mean and 3rd Quantile, and max as follows: (0.462, 0.628, 0.806, 0.896, 1.000, 2.400) ?
2018 May 16
0
Systemfit
Sadly you failed to set your email program to send plain text and the data is corrupted at my end.
I also think you need to reduce the size of the data set... the intent here is to increase your understanding, not debug your particular analysis.
I will say that I am having a very challenging time understanding what you are trying to accomplish though. What are the equations that you think need
2013 Jan 27
2
rpart
Hi,
When I look at the summary of an rpart object run on my data, I get 7 nodes but when I plot the rpart object, I get only 3 nodes. Should the number of nodes not match in the results of the 2 functions (summary and plot) or it is not always the same?
Look forward to your reply,
Carol
--------------------------------------------
?summary(rpart.res)
Call:
rpart(formula = mydata$class ~ ., data
2018 May 15
2
Systemfit
OK, Let's try this again! Here is the reproducible script; it is long because I had to copy the panel dataset here. My question is related to systemfit; I don't know how to get the result for the entire panel.
#Reproducible script
Empdata<- read.csv("/Users/ngwinuiazenui/Documents/UPLOADemp.csv")
View(Empdata)
install.packages("systemfit")
2008 Feb 19
4
[LLVMdev] 2008-01-25-ByValReadNone.c Failure
Hi all,
I'm seeing this failure on my PPC G4 box running TOT with llvm-gcc
4.2. Is anyone else seeing this? I'm sure it's related to the byval
stuff that's recently gone into LLVM. I'm attaching the output of
this command:
$ llvm-gcc -emit-llvm -O3 -S -o - -emit-llvm /Users/wendling/llvm/
llvm.src/test/CFrontend/2008-01-25-ByValReadNone.c
As you can see in it, there
2008 Mar 25
1
Subset of matrix
Dear R users
I have a big matrix like
6021 1188 790 290 1174 1015 1990 6613 6288
100714
6021 1 0.658 0.688 0.474 0.262 0.163 0.137 0.32
0.252 0.206
1188 0.658 1 0.917 0.245 0.331 0.122 0.148 0.194
0.168 0.171
790 0.688 0.917 1 0.243 0.31 0.122 0.15 0.19
0.171 0.174
290 0.474
2010 Jun 26
1
predict newdata question
Hi:
I am using a subset of the below dataset to predict PRED_SUIT for
the whole dataset but I am having trouble with 'newdata'. The model
was created with 153 records and want to predict for 208 records.
wolf2 <- structure(list(gridcell = c(367L, 444L, 533L, 587L, 598L, 609L,
620L, 629L, 641L, 651L, 662L, 674L, 684L, 695L, 738L, 748L, 804L,
805L, 872L, 919L, 929L, 938L, 950L, 958L,
2018 May 15
0
Systemfit
... and the mailing list is picky about attachments... whatever you attached did not conform to the stringent requirements mentioned in the Posting Guide. Pasting the code right into the email is usually safest, though you DO have to post using plain text (as the Posting Guide indicates) or your code may get mangled by the automatic html format removal.
On May 15, 2018 7:04:31 AM PDT, Bert Gunter
2018 May 15
1
Systemfit
Unless there is good reason not to, always cc the list -- there are lots of
smarter folks than I on it who can help.
I may or may not have time to look at this. Hopefully someone else will.
-- Bert
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip
2013 Feb 23
2
assign index to colnames(matrix)
Hello, I’m trying to follow the syntax of a script from a journal website. In order to create a regression formula used later in the script, the regression matrix must have column names “X1”, “X2”, etc. I have tried to assign these column names to my matrix ScoutRSM.mat using a for loop, but I don’t know how to interpret the error message. Suggestions? Thanks, Paul
2005 Jan 25
3
multi-class classification using rpart
Hi,
I am trying to make a multi-class classification tree by using rpart.
I used MASS package'd data: fgl to test and it works well.
However, when I used my small-sampled data as below, the program seems
to take forever. I am not sure if it is due to slowness or there is
something wrong with my codes or data manipulation.
Please be advised !
The data is described as the output from str()
2006 Oct 15
4
Hide line ends behind unfilled circles?
Dear r-helpers,
xx <- c(0.000, 0.210, 0.714, 0.514, 1.000, 0.190, 0.590, 0.152)
yy <- c(0.000, 0.265, 0.256, 0.521, 0.538, 0.761, 0.821, 1.000)
aa <- c(19, 19, 19, 21, 19, 21, 21, 21)
x0 <- xx[c(1, 1, 2, 2, 2, 3, 3, 4, 4, 4, 5, 6, 6, 7)]
y0 <- yy[c(1, 1, 2, 2, 2, 3, 3, 4, 4, 4, 5, 6, 6, 7)]
x1 <- xx[c(2, 3, 3, 4, 6, 4, 5, 5, 6, 7, 7, 7, 8, 8)]
y1 <- yy[c(2, 3, 3, 4, 6, 4, 5,
2011 Apr 14
1
Overlaying images at nodes of phylogenetic tree
Can you recommend an R library that will help me create a diagram of a
phylogenetic tree on which specific images are placed at appropriate nodes of
the tree?
For example, I have specific image files associated with each member of the
phylogenetic tree, and I would like to automate the display of the image next to
the correct node of the tree. I can provide an image file with an example.
2010 Nov 11
1
metafor: including phylogenetic non-independence among species?
Hello, Is it possible to include information about phylogenetic relatedness
among species (when species are replicates for each study within a
meta-analysis) in a meta-anlaysis in the metafor package?
Alternatively, I wonder if the method f Lajeunesse 2009 American Naturalist
has been adopted in R in any fashion?
Thanks, Scott Chamberlain
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2012 Jun 18
0
Obtaining r-squared values from phylogenetic autoregression in ape
Hello,
I am trying to carry out a phylogenetic autoregression to test whether my
data show a phylogenetic signal, but I keep calculating bizzare R-squared
values.
My script is:
> library(ape)
> x <-
2007 Jan 26
1
Package for phylogenetic tree analyses
Hi
I am looking for a package that
1. reads in a phylogenetic tree in NEXUS format
2. given two members/nodes on the tree, can return the
distance between the two using the tree.
I came across the following packages on CRAN
ouch, ape, apTreeShape, phylgr all of which seem to
provide extensive range of functions for reading in a
Nexus-format tree and performing phylogenetic
analyses, tree
2013 Jun 04
0
Mixed effects model with a phylogenetic tree/ distance, matrix as a random effect
Take a look at lmekin() in the coxme package. The motivating data set for my development
of coxme was the Minnesota Family Breast Cancer project: 24050 subjects in 462 families.
The random effect is an intercept per subject with sigma^2 K as its variance where K is
the kinship matrix (1 for self-self, .5 for parent-child or sib-sib, .25 for uncle-neice,
etc). lmekin is a linear models front