Displaying 20 results from an estimated 900 matches similar to: "S's plclust and R's hclust"
2003 Jun 26
2
Change default parameters of panel.smooth
Hello,
can anyome tell me how to access the full script of the panel.smooth function so that I can change the thickness of the smoothing line or its colour ?
All I could access is :
> panel.smooth
function (x, y, col = par("col"), bg = NA, pch = par("pch"),
cex = 1, col.smooth = "red", span = 2/3, iter = 3, ...)
{
points(x, y, pch = pch, col = col, bg =
2003 Jun 18
2
install pls.pcr package
How do you install a package from CRAN ? I want to install pls.pcr, so I have downloaded pls.pcr_0.1.1.tar.gz but when I try to install it using the install package(s) from local zip file(s) option it says :
> install.packages(choose.files('',filters=Filters[c('zip','All'),]), .libPaths()[1], CRAN = NULL)
Error in file(file, "r") : unable to open connection
2003 Jun 25
2
Pairs with different colours
Does anybody know how to make pairs graphics with dots of different colours depending on the value of a categorical variable ?
Thanks,
Arnaud
*************************
Arnaud DOWKIW
Department of Primary Industries
J. Bjelke-Petersen Research Station
KINGAROY, QLD 4610
Australia
T : + 61 7 41 600 700
T : + 61 7 41 600 728 (direct)
F : + 61 7 41 600 760
**************************
2003 May 09
1
Principal coordinates analysis
Dear all,
Does anyone know how to run Principal Coordinates Analysis (PCoA) from a
squared euclidean dissimilarity matrix with R ?
Thanks,
*************************
Arnaud DOWKIW
Department of Primary Industries
J. Bjelke-Petersen Research Station
KINGAROY, QLD 4610
Australia
T : + 61 7 41 600 700
T : + 61 7 41 600 728 (direct)
F : + 61 7 41 600 760
**************************
2003 Jul 24
1
pls regression - optimal number of LVs
Dear R-helpers,
I have performed a PLS regression with the mvr function from the pls.pcr package an I have 2 questions :
1- do you know if mvr automatically centers the data ? It seems to me that it does so...
2- why in the situation below does the output say that the optimal number of latent variables is 4 ? In my humble opinion, it is 2 because the RMS increases and the R2 decreases when 3 LVs
2003 Jul 23
0
pls.pcr compared to Unscrambler
Dear R-helpers,
Has anybody ever tried to compare pls regression outputs from the pls.pcr R-package developped by Wehrens with outputs from the Unscrambler software developped by CAMO company ?
I find very different outputs and wonder if this comes from differences between methods/algorithms SIMPLS (pls.pcr) and PLS1 (Unscrambler).
Arnaud
*************************
Arnaud DOWKIW
Department of
2011 Sep 12
1
hclust and cutree: identifying branches as classes
Good afternoon,
After cuting a hierarchical tree using cutree(), how to check correspondances between classes and branches?
This is what we do:
srndpchc <- hclust(dist(srndpc$x[1:1000,1:3]),method="ward") #creation of hierarchical tree
plclust(srndpchc,hmin=20000) #visualisation
srndpchc20000 = cutree(srndpchc,h=20000) #returns 4 classes
table(srndpchc20000 )
srndclass20000 =
2004 Jul 02
2
hclust
im using plclust and want the labels to be different colors.
i took a look at getS3method("plot","hclust")
and saw a call to .Internal. i looked at the help on .Internal and dont
know where to go next. any help appreciated!
thanks,
rafael
2005 Mar 24
2
font sizes for row.names of dendograms
Dear R
I recently performed a cluster analysis. It produced the dendogram no
problem but unfortunately the font size of the row.names were all cluttered
due to their large size
So I tried to change the font size using
plclust(cluster.results, labels=iris$specie, cex=0.8)
and R came back to me saying
Error in plclust(cluster.results, labels = iris$specie, cex = 0.8) :
unused argument(s)
2000 Aug 31
2
Multiv / hierclust / plclust
I use hierclust (hierarchical clustering) in multiv package. In the
documentation it is said that plclust (plotting a dendrogram) is
available in S-plus. Can I find it anywhere (I have searched through
http://lib.stat.cmu.edu/S and found only quotations of plclust in
multiv) or is it only part of the S package (which I don't have)?
Thanks
---------------
Charles RAUX,
Laboratoire
2005 Nov 09
1
Replace missing values in spatial design using moving average
Dera R helpers,
I have a (x,y,z) data file where x and y are spatial coordinates and z a
variable. I have some missing values in the z column and I would like to
replace them with an optimized estimation from the neighbour cells. I could
not find any function in R to do that. Is anybody aware of such function ?
Maybe someone knows how to implement the Papadakis method in R...
Thanks for your
2003 Dec 01
0
Changing distance scale in plclust()
I want to plot the cluster trees from the results of hclust() on different
datasets, but all with the same distance scale corresponding to the dataset
with the largest distance range. However, plclust() does not accept ylim
values. Does anyone know of a way around this problem?
Mike White
2005 Nov 29
0
Error in plclust
Hi all,
I need to plot a dendrogram, but I built a hclust object. Follow the code
lines:
>dendObject<-list(merge=merge,height=height,order=order,labels=labels,call="hclust(d=d)",method="complete",
dist.method="euclidean")
>class(dendObject)<-"hclust"
>plclust(dendObject,axes=FALSE)
Error in cl[[2]] : subscript out of bounds
Anybody can help
2004 Sep 10
1
swiss.x
Is the swiss data set in R the same as S dataset swiss.x .
I was trying out some clustering by doing the following that I got from
Venables and Ripley's book.
h<-hclus(dist(swiss.x), method= "connected")
plclust(h)
cutree(h,3)
plclust(clorder(h,cutree(h,3)))
I tried swiss instead of swiss.x, it doesnot seem happy.
Thanks ../Murli
2005 Jul 13
1
Boxcox transformation / homogeneity of variances
Dear r-helpers,
Prior to analysis of variance, I ran the Boxcox function (MASS library) to
find the best power transformation of my data. However, reading the Boxcox
help file, I cannot figure out if this function (through its associated
log-likelihood function) corrects for * normality only * or if it also
induces * homogeneity of variances *. I found in Biometry (Sokal and Rohlf,
p. 419)
2004 May 10
3
Colouring hclust() trees
I have a data set with 6 variables and 251 cases.
The people who supplied me with this data set believe that it falls
naturally into three groups, and have given me a rule for determining
group number from these 6 variables.
If I do
scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...))
stuff.dist <- dist(scaled.stuff)
stuff.hc <- hclust(stuff.dist)
2003 Sep 02
5
Strange problem.
Hi, everyone,
I am a new user of R. Recently, I tried the following commands, but couldn't make them work. If any one of you has some ideas about it, please help me. The commands are
>std<-1000
>mean<-8000
>prior<-function(n){1/(sqrt(2*pi)*std)*exp(-1.0*(n-mean)^2/(2*std^2))}
>plot(prior,1,15000)
>post<-function(n){
+ if(n < 9543)
+ 0
+ else
+ prior(n)/n
+
2016 Jul 27
3
Lost trusted domain in samba-4.4.4
Here is my smb.conf:
[/usr/local/samba/var] # cat /etc/config/smb.conf
[global]
client schannel = false
server schannel = false
client ipc signing = false
client signing = false
server signing = false
winbind sealed pipes = false
require strong key = false
passdb backend = smbpasswd
workgroup = HC1
security = ADS
server string =
encrypt passwords = Yes
username level = 0
map to guest = Bad User
2007 Sep 17
1
side bars on dendrograms with latticeExtra
Dear all,
I am using the heatmap representations of latticeExtra package and I
would be interested to draw color side bars representing the groups of a
factor of interest. From my understanding of :
> help(dendrogramGrob)
...
The 'add' argument can be used for additional annotation at the
base of the dendrogram. It should be a list with one component
for each row,
2005 May 31
1
Loading matrices and other things
Hi all,
I'm new to R, so needless to say I have a couple questions (which I hope
I haven't missed through the documentation).
I have several files in lower triangular matrix form. For each of these
matrices, I want to perform some form of hierarchical clustering on each
matrix and capture the output of the clustering.
The first problem I run into is actually loading the matrix file