Displaying 20 results from an estimated 200 matches similar to: "an efficient way to calculate correlation matrix"
2007 Jun 28
2
aov and lme differ with interaction in oats example of MASS?
Dear R-Community!
The example "oats" in MASS (2nd edition, 10.3, p.309) is calculated for aov and lme without interaction term and the results are the same.
But I have problems to reproduce the example aov with interaction in MASS (10.2, p.301) with lme. Here the script:
library(MASS)
library(nlme)
options(contrasts = c("contr.treatment", "contr.poly"))
# aov: Y ~
2004 Jul 27
1
re: help with lattice plot
Dear List,
I have been using R to create an xyplot using the panel function within
lattice libraries. This plot is based on the data supplied in R named
'Oats'. The graph represents oat yield by nitro level with an overlay of
each variety of oats for each nitro level.
I have three questions regarding this graph:
1) I cannot seem to specify the type of symbol used by the plot, even
though
2009 Oct 30
1
How to properly shade the background panels of an xyplot?
Dear R users,
this is a follow up of this message
http://tolstoy.newcastle.edu.au/R/e6/help/09/05/13897.html
I'm reproducing the core of it for convenience.
> //
> / data(Oats, package = "MEMSS") /
> / tp1.oats <- xyplot(yield ~ nitro | Variety + Block, /
> / data = Oats, /
> / panel = function(x, y, subscripts, ...) { /
2004 Apr 23
1
Weirdness with choose.files on Microsoft Windows (PR#6818)
Full_Name: Kevin Wright
Version: 1.8.0
OS: Windows 95
Submission from: (NULL) (170.54.59.160)
This bug also happens to me using R 1.9.0 on Windows 2000.
Took me a long time to create a reproducible bug, but I think I have succeeded.
I suspect my test function has a bug, but I don't see anything wrong. Plus, the
bug only shows up when selecting certain filenames. Nearest I can speculate,
2009 Oct 10
1
lattice auto.key drop unused levels
The following code produces a legend ("key") that mentions the unused
levels of Block.
library(MEMSS)
xyplot(yield~nitro, subset=(Block=="I" | Block=="II"), data=Oats,
group=Block, auto.key=T)
and adding "drop.unused.levels=T" does not fix it. And in fact even
the following does not solve the problem:
xyplot(yield~nitro,
2002 Apr 02
1
Repeated aov residuals
Hello,
Are there any access functions to the various residual variables that should
result from a repeated measures ANOVA ? MyAOVObject$residuals does not exist,
and simply printing MyAOVObject gives a very long print of all fields in the
result list, many of which I can't see what they are exactly :
$error.qr$qraux, for instance.
What I would like basically is to inspect those residuals
2009 Apr 21
3
broken example: lme() + multcomp() Tukey on repeated measures design
I am trying to do Tukey HSD comparisons on a repeated measures expt.
I found the following example on r-help and quoted approvingly elsewhere.
It is broken. Can anyone please tell me how to get it to work?
I am using R 2.4.1.
> require(MASS) ## for oats data set
> require(nlme) ## for lme()
> require(multcomp) ## for multiple comparison stuff
> Aov.mod <- aov(Y ~ N + V +
2009 Oct 12
3
xyplot does not find variable in data
When we call a lattice function such as xyplot, to what extent does
the "data" designation cause the function to look inside the "data"
for variables?
In the examples below, the "subset" argument understands that
"Variety" is a variable in the data.
But the "scales" argument does not understand that "nitro" is a
variable in the data.
2010 Jan 19
1
A model-building strategy in mixed-effects modelling
Dear all,
Consider a completely randomized block design (let's use data(Oats)
irrespoctive of the split-plot design it was arranged in). Look:
library(nlme)
fit <- lme(yield ~ nitro, Oats, random = ~1|Block, method="ML")
fit2 <- lm(yield ~ nitro + Block, Oats)
anova(fit, fit2)
gives this:
Model df AIC BIC logLik Test L.Ratio p-value
fit 1 4 624.3245
2011 Nov 29
2
Help needed in reproducing a plot
Hello,
can anybody tell me how to produce a plot like the one in
http://cran.r-project.org/web/packages/lme4/vignettes/Implementation.pdf
on page 13, Figure 6?
The data is stored in:
library(nlme)
data(Oats)
Cheers
--
View this message in context: http://r.789695.n4.nabble.com/Help-needed-in-reproducing-a-plot-tp4119603p4119603.html
Sent from the R help mailing list archive at
2001 Nov 22
2
Missing panels in multipanel lme lattice/trellis
Dear R-supporters,
I have results of lme similar to those shown in Fig. 1.21, p.51 of
Pinheiro/Bates. However, In my data set, one of the panels is missing, leading
to an ugly frame shift of the following panels.
How can I replace one of the panels by an empty one to restore the raster?
Dieter Menne
---------------------------------------
Dr. Dieter Menne
Biomed Software
72074 T?bingen
Tel
2006 Sep 23
1
variance-covariance structure of random effects in lme
Dear R users,
I have a question about the patterned variance-covariance structure for the random effects in linear mixed effect model.
I am reading section 4.2.2 of "Mixed-Effects Models in S and S-Plus" by Jose Pinheiro and Douglas Bates.
There is an example of defining a compound symmetry variance-covariance structure for the random effects in a
split-plot experiment on varieties of
2008 Apr 16
1
transposition problem
Hi use Rs,
I have a csv file:
"1989-90","1990-91"
Barley,23,34
Oats,15,16
Which I want to turn into:
year, Barley, Oats
1 "1989-90", 23, 15
2 "1990-91",34,16
Transpose doesn't quite do it, is there a standard way?
Cheers,
Geoff Russell
2007 Apr 20
2
sorting data in R
hello,
I'd like know how to sort a data frame in R for example how I should do to sort by Catholic with swiss data frame like below
thanks
Fertility Agriculture Examination Education Catholic Infant.Mortality
Courtelary 80.2 17.0 15 12 9.96 22.2
Delemont 83.1 45.1 6 9 84.84 22.2
2008 May 19
6
Sample Code, quick simple openid auth
You''ll need to install the ''openid'' gem for this, and require it in
your camping app:
class Login < R ''/login''
def get
this_url = ''http:'' + URL(''/login'').to_s
unless input.finish.to_s == ''1''
# start doing the auth here
begin
2005 Dec 05
2
plot() and points() precision control
Hi all,
I have a problem in that when I plot points that have a high degree of
precision, some significant rounding seems to occur, resulting in
uneccessary overlap of my points. Is there a way to specify the
resolution or precision in plotting functions? Is there an underlying
grid I have to modify somehow?
Many Thanks,
Jon
--
Mares eat oats and does eat oats and little lambs eat ivy. A
2008 Aug 25
1
aov, lme, multcomp
I am doing an analysis and would like to use lme() and the multcomp
package to do multiple comparisons. My design is a within subjects
design with three crossed fixed factors (every participant sees every
combination of three fixed factors A,B,C). Of course, I can use aov() to
analyze this with an error term (leaving out the obvious bits):
y ~ A*B*C+Error(Subject/(A*B*C))
I'd also like
2007 Apr 23
1
extract from a data frame
hello,
I'd like know how to do to extract data from a frame for example
how can I do to extract only the data where variety=victory or variety=golden rain
thanks.
> Oats
Block Variety nitro yield
1 I Victory 0.0 111
2 I Victory 0.2 130
3 I Victory 0.4 157
4 I Victory 0.6 174
5 I Golden Rain 0.0 117
6 I Golden Rain
2006 Oct 09
1
split-plot analysis with lme()
Dear R-help,
Why can't lme cope with an incomplete whole plot when analysing a split-plot
experiment? For example:
R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.3.1 (2006-06-01)
> library(nlme)
> attach(Oats)
> nitro <- ordered(nitro)
> fit <- lme(yield ~ Variety*nitro, random=~1|Block/Variety)
> anova(fit)
numDF denDF F-value
2010 Nov 04
3
ANOVA table and lmer
The following output results from fitting models using lmer and lm to
data arising from a split-plot experiment (#320 from "Small Data Sets"
by Hand et al. 1994). The data is given at the bottom of this message.
My question is why is the sum of squares for variety (V) different in
the ANOVA table generated from the lmer model fit from that generated by
the lm model fit. The