Displaying 20 results from an estimated 2000 matches similar to: "GroupedData for three way randomized block. LME"
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.
>
2010 Mar 12
1
simple plot in ggplot2, wrong error bars
I was wondering if anyone could help me with this, simple problem.
I am essentially following the example on Hadley's webpage
(http://had.co.nz/ggplot2/geom_errorbar.html), but it still doesn't make any
sense to me.
df <- data.frame(trt = factor(c("intact", "intact", "removed", "removed")),
coon = c(0.093, 0.06, 0.057, 0.09), group =
2008 Jul 06
1
What is my replication unit? Lmer for binary longitudinal data with blocks and two treaments.
First I would like to say thank you for taking the time to read it.Here is my
problem.
I am running a lmer analysis for binary longitudinal (repeated measures)
data.
Basically, I manipulated fruits and vegetation to two levels each(present
and absent) and I am trying to access how these factors affect mice foraging
behavior. The design consist of 12 plots, divided in 3 blocks. So each
block
2009 Aug 20
1
ANCOVA with defined error terms
I am trying to run an ANCOVA with defined error terms. Thus I have to use
AOV and not lm.
my response variable is proportion of mice paw prints on track plates. These
plates were placed on plots that had vegetation and fruit manipulated to two
levels each (present or absent), and were sampled monthly for 14 months
(repeated measures). The fully crossed factor design was also blocked. My
sample
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
>
2018 Mar 22
0
How do I include a factor in a groupedData object? Meaning and use of inner and outer parameters
Dear John
You are only allowed to have the primary covariate on the left hand side
of the vertical bar. Other covariates go in inner or outer.
Michael
On 22/03/2018 12:59, Sorkin, John wrote:
> Windows 10 64-bit, R-Studio, R version 3.4.3
>
>
> Several questions relating to groupedData:
>
> (1) I am trying to create a groupedData object that can be used to run an analysis
2008 Jun 04
2
Constructing groupedData objects in nlme - a little problem
Dear R-help,
I am trying to create groupedData objects using the nlme library. I'm
missing something basic, I know:
Here is the first example in ch.1 of Pinheiro & Bates (2000):
library(nlme)
x2=Rail$travel;x1=Rail$Rail;eg1=data.frame(x1,x2);eg1gd=Rail
print(eg1gd)
x11();print(plot(eg1gd))
femodel=lm(x2~x1-1,data=eg1gd)
print(femodel$coefficients)
Result:
x12 x15 x11
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"
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)
2006 Dec 07
2
groupedData Error Using outer=TRUE
I'm using groupedData from nlme. I set up a groupedData data.frame with
outer=~group1. When I try to plot with outer=TRUE, I get "subscript out
of bounds." This happens most of the time. When it works, I get
spaghetti-type plots for comparing groups. But I don't understand why it
doesn't usually work.
> longa.mod.1.gd <- groupedData(mod1.logit~time|
2007 Dec 27
2
groupedData function not found
Hello,
I'm trying to use the groupedData function and R is giving me the message: Error: can not find function "groupedData"
The code is coming from a textbook so I think it should be correct:
pigs<-data.frame(cbind(pig.time,pig.id,pig.wt))
pig.growth<-groupedData(pig.wt~pig.time|pig.id,data=pigs)
I have added the package "nlme" and to confirm that it was installed
2001 Nov 19
1
scope of data in groupedData
I'm trying to write a function that has a dataframe as
an argument. Within the function, I call groupedData
to create a grouped-data object from the dataframe
argument. However, the groupedData function doesn't
seem to see the data. I'm guessing it's getting the
argument name rather than its value, but I'm not
positive.
My system: R 1.3.1 on WinNT 4.0 (Pentium II), nlme
2018 Mar 22
3
How do I include a factor in a groupedData object? Meaning and use of inner and outer parameters
Windows 10 64-bit, R-Studio, R version 3.4.3
Several questions relating to groupedData:
(1) I am trying to create a groupedData object that can be used to run an analysis that I have been able to urn using lmer. When I include the interaction terms in the groupedData opbject I get an error message stating that + is not meaningful for factors. How do I include factors in my model? See code and
2005 Mar 17
2
Repeated Measures, groupedData and lme
Hello
I am trying to fit a REML to some soil mineral data which has been
collected over the time period 1999 - 2004. I want to know if the 19
different treatments imposed, differ in terms of their soil mineral
content. A tree model of the data has shown differences between the
treatments can be attributed to the Magnesium, Potassium and organic
matter content of the soil, with Magnesium being the
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
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
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 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,
2010 Sep 10
1
lme, groupedData, random intercept and slope
Windows Vista
R 2.10.1
Does the following use of groupedData and lme produce an analysis with both random intercept and slope, or only random slope?
zz<-groupedData(y~time | Subject,data=data.frame(data),
labels = list( x = "Time",
y = "y" ),
units = list( x = "(yr)", y = "(mm)")
)
plot(zz)
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