Displaying 20 results from an estimated 120 matches similar to: "lme, groupedData, random intercept and slope"
2011 Sep 02
2
How to keep the same class?
Hello
Please see the example below
> class(testX)
[1] "matrix"
> class(testX[1,])
[1] "numeric"
Why not matrix? What am I missing here? Is there a way to keep the same
class?
The reason for the question is that I want to implement a k-step ahead
prediction for my own routines and R wrecks does not seem to like [1,] as
shown below.
>
2004 Jul 12
6
proportions confidence intervals
Dear R users
this may be a simple question - but i would appreciate any thoughts
does anyone know how you would get one lower and one upper confidence
interval for a set of data that consists of proportions. i.e. taking a
usual confidence interval for normal data would result in the lower
confidence interval being negative - which is not possible given the data
(which is constrained between
2012 Jun 05
1
Do YOU know an equation for splines (ns)?
Hi,
I am looking at the change in N concentration in plant roots over 4 time
points and I have fit a spline to the data using ns and lme:
fit10 <- lme( N~ns(day, 3), data = rcn10G)
I may want to adjust the model a little bit, but for now, let's assume it's
good. I get output for the fixed effects:
Fixed: N ~ ns(day, 3)
(Intercept) ns(day, 3)1 ns(day, 3)2 ns(day, 3)3
2008 Oct 10
0
Problems and bugs in vgam()
Hello R-Users,
I have recently run into several problems using vgam() in the VGAM
package. I am hoping someone might have some solutions...
Briefly, I have been trying to fit GAM models for zero-altered negative
binomial models.
1. When fitting smoothed parameters (e.g. s(X, df=2)) changing the
degrees-of-freedom has no effect on the level of smoothing (e.g. number
of knots for the
2012 May 31
0
splines and ns equation
Hi,
I am looking at the change in N concentration in plant roots over 4 time
points and I have fit a spline to the data using ns and lme:
fit10 <- lme( N~ns(day, 3), data = rcn10G)
I may want to adjust the model a little bit, but for now, let's assume it's
good. I get output for the fixed effects:
Fixed: N ~ ns(day, 3)
(Intercept) ns(day, 3)1 ns(day, 3)2 ns(day, 3)3
1.15676524
2004 Feb 07
1
display functions in groupedData and lme
I'm trying to set up a mixed model to solve using lme. It will have 3
fixed effects, two random effects and two interaction terms.
I've been reading Pinheiro's and Bates's book on the nmle library, but
find the part about display functions to be unclear. When creating a
groupedData object from a data.frame, you need to enter a function of the
form: response ~primary|grouping
2007 Mar 04
1
plot groupedData in nlme
Hi,
Does anyone know how to make the color of the lines all black when
plotting groupedData with an outer factor:
For example,
library(nlme)
plot(Dialyzer, outer=~QB, key=F)
This generated colored curves in R.2.4.1. How to make all the curves black ?
(or how to alter the color (type) of lines for the nlme groupedData
plotting function in general?)
Thanks
Qiong
2002 Oct 30
1
groupedData
Dear all,
I tried to create a groupedData object, where the grouping factor
is not ordered.
Here ist the code:
library(nlme)
test<-groupedData(conc~Time|Subject,order.groups=F,data=as.data.frame(Theoph))
> getGroups(test)
Levels: 6 < 7 < 8 < 11 < 3 < 2 < 4 < 9 < 12 < 10 < 1 < 5
I still get an ordered factor. As always thanks for your help
peter
2004 Jul 23
2
lme4 groupedData is missing
help.search("groupedData") says that it's part of the lme4 package, but it
appears not to be there (details below). Is this because lme4 is new and
(perhaps) still under development?
> update.packages()
trying URL `http://cran.r-project.org/bin/windows/contrib/1.9/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 19113 bytes
opened URL
downloaded 18Kb
>
2004 Aug 26
1
Plotting groupedData objects
I am trying to create a plot similar to Figure 3.2 in Bates and Pinheiro.
I have repeated measurements on about 80 subjects from 2 treatment groups.
I would like to have the panels for the two treatment groups in separate
groups and within those groups have the panels ordered on maximum value
(as is the default).
I am ok with getting plots similar to Figs 3.1 and 3.2, but can't see how
to
2006 Jan 13
0
update 'groupedData' and 'lme' objects
Dear R users, I have the following code:
----------------------------------------
require(nlme)
myfunc <- function(data, n, m, maxIter = 3){
working <- groupedData(formula = y~x|id, data=data)
val <- NULL
r <- 0
while(r < maxIter){
new.data <- data.frame(x=rnorm(n),y=rnorm(n),id=rep(1:n,each=m))
working <- update(working, data = new.data)
# val <- some
2006 Mar 09
1
Suppress legend in plotting groupedData
Dear All,
I would be grateful if you can tell how can I suppress the legend (automatically created) when I plot a groupedData.
suppose that I have data farme df_0 which contains the following columns: ID represents the clusters, t represents time of observation, Y: the variable of interest and X a binary covariate. Then:
df_1 <- groupedData(Y ~ t | ID)
plot(df_1,
2006 Nov 10
0
Can plot(augPred()) be used with objects that are not groupedData?
Dear Friends,
Is there a workaround to this problem or must the object plotted by
plot(augPred(object, ...)) be a grouped object?
score <- c(108, 103, 96, 84, 118, 110, 129, 90, 84, 96,
105, 113, 96, 117, 107, 85, 125, 107, 128, 84, 104,
100, 114, 117, 110, 127, 106, 92, 125, 96, 123, 101,
100, 103, 105, 132, 122, 133, 107, 99, 116, 91, 128,
113, 88, 105, 112, 130)
mcc
2006 Nov 22
1
plotting a groupedData object
Hello all,
I am plotting a groupedData object and the key at the top of the graph runs
off the page. I don't want to set key=F because it is useful (or would be if
I could see it).
Is it possible to explicitly cause the key to wrap? I have used this
function before with no trouble but now I have just 5 groups with rather
long descriptions (which I can't meaningfully shorten).
2008 Jul 11
0
GroupedData for three way randomized block. LME
I am trying to fit a formula to my data, but I just can't find the right way
to do it.
My experiment consists of manipulating FRUITS and VEGETATION to two levels
each(intact or removed) on 12 experimental plots.
This leaves me with 4 treatment combinations
Fruit intact Vegetation removed
Fruit int. Veget int.
Fruit rem. Veget rem.
Fruit rem. Veget. intac
those treatements are distributed
2009 Oct 11
0
Plotting groupedData objects by levels of a factor
Hi,
I'm trying to plot a grouped data object for modelling maximum branch
size by distance from stem apex:
>MAXBRD.group <- groupedData(MAXBRD ~ Dtop | Type/Site/Tree,
inner=~Status, data=MAXBRD.data).
The following code produces a plot of MAXBRD ~ Dtop for each site type:
>plot(MAXBRD.group, collapse=1, display=1, aspect=1.2, pch=20, inner=~1,
main="MAXBRD with
2007 Feb 07
0
Plotting groupedData objects
Hi all.
I have what I'm guessing is a fairly easy question.
I want to plot groupedData objects, but there are a large number of subjects in my data. When I use the simple command
plot(MyData)
where MyData is a groupedData object, there are simply too many individual plots to see anything. I would like, say, 15 per page and for the plots to cover multiple pages. All of the individuals have a
2009 Jul 14
1
Problem with GroupedData
Hi,
I have an original data frame with 8 columns of variables, which are stored in 'data1' frame.
data1 <- read.csv("E:\\PHD GLASGOW UNIVERSITY\\Data\\R\\Colin\\Cailness21.csv")
attach(data1)
names(data1)
[1] "Date" "d" "m" "y" "Time"
[6] "Depth" "Temp"
2008 Jul 19
1
wroung groupedData despite reading Bates and Pinheiro 3 times
Hi everyone. I am trying to add a formula to my data using the groupedData
function.
My experiment consists of randomized block design using fruits, vegetation
and time as factors. The idea is to see if fruits, vegetation and time
explain the abundance of mice. I am using tree density as a covariate.
So I tried to fit the following structure to my data.
>
2000 Jul 24
1
How to use groupedData() within a function?
Dear Group:
I have been trying to write an R function within which the function
groupedData() would be used.
The following is a sample program:
#######################
sid<-rep(1:6,times=2)
time<-c(1:12)
trt<-rep(letters[1:3],times=4)
tem<-data.frame(sid,time,trt)
test1.fun<- function(dat=dat)
{
groupedData(time ~ trt|sid, data=dat)
}
test1.fun(dat=tem)