Displaying 20 results from an estimated 5000 matches similar to: "correlation structure"
2007 Jun 12
0
nlme model
I am having trouble figuring out the right form for the nlme arguments. I do have examples in Modern and Applied Statistics with S and from other sources, but I still can't figure it out.
I am trying to estimate species richness (sr) in streams across minnesota. My predictor variables are depth (d), habitat diversity (habdiv), drainage area (da) and an indicator variable representing the
2007 Apr 11
0
Error with corCompSymm and lme fit for repeated measures
Dear R Friends,
I need help with an error associated with corCompSymm in an lme fit.
I am using a mixed effects model to analyze a split-plot with
repeated measures and would like to fit with the compound symmetry
correlation structure. This problem doesn't occur when using
corAR1 or any of the other structures. I would greatly appreciate
help on how to solve this issue.
Here's my
2005 Jan 21
0
gamm with correlation structure question
Dear group,
I am trying to use gamm() in mgcv. Here's the
scenario. The data frame has approx. 110K
observations with information on paediatric
readmission binary outcome (Y/N) and total volume of
their most responsible physician as the covariate.
Since any physician can have multiple patients, the
data contains clustering structure which I am trying
to account for. My original formula is
2006 Oct 16
1
linear mixed effects models with breakpoints
Hi folks
I have some data to which I've been fitting linear mixed effects
models. I am currently using a lme model in the nlme package, with terms
for random effects due to repeated measures on individuals and the
corCAR1 serial correlation structure. However, there is some suggestion
in the data (and from theory) that a breakpoint (change point) model may
be more appropriate. Scott, Norman
2005 Nov 07
1
repeated values, nlme, correlation structures
Dear listers,
As an exercise, I am trying to fit a logistic model with nlme. Blue tit
pulli (youngs) were weighted occasionnally (for field reasons) along
time in 17 nestboxes. Individuals where not idenfied but their age was
known. This means that for a given age several measurements were done
but individuals could not be identified from a time to the other. This
makes repeated values for
2011 Jul 21
0
gls yields much smaller std. errors with different base for contrasts
Dear List,
After running a compound symmetric model using gls, I realized that
the default contrasts were not the ones that made the most sense given
the biological relationships among the factor levels. When I either
changed the factor levels to re-arrange the order they occur in the
gls model (not shown below) OR specifically change the contrasts I get
the exact same estimates for the
2006 Nov 20
1
My own correlation structure with nlme
Dear all,
I am trying to define my own corStruct which is different from the
classical one available in nlme. The structure of this correlation is
given below.
I am wondering to know how to continue with this structure by using
specific functions (corMatrix, getCovariate, Initialize,...) in order to
get a structure like corAR1, corSymm which will be working for my data.
Thanks in advance.
2005 May 17
0
problem with gls : combining weights and correlation structure
Dear R-users,
I hope you will have time to read me and I will try to be brief. I am also
sorry for my poor english.
I used gls function from the package nlme to correct two types of bias in my
database. At first, because my replicates are spatially aggregated, I would
like to fit a corStruct function like corLin, corSpher, corRatio, corExp or
corGaus in my gls model, and simultaneously,
2007 Oct 23
1
distributing the values of data frame to a vector based on......
I am trying to distribute the entries of a data frame (dat) to a vector (water) based on the values of two other vectors (region and year). region is also the columns and year the rows of the data frame (dat). I can write a bunch of ifelse statements or I created the for statement below - but there must be a simpler way?? The for statement probably won't work if I am distributing a non
2018 Feb 26
0
How to model repeated measures negative binomial data with GEE or GLMM
Goal: use GEE or GLMM to analyze repeated measures data in R
GEE problem: can?t find a way to do GEE with negative binomial family in R
GLMM problem: not sure if I?m specifying random effect correctly
Study question: Does the interaction of director and recipient group affect
rates of a behavior?
Data:
Animals (n = 38) in one of 3 groups (life stages): B or C.
Some individuals (~5)
2012 Mar 28
1
discrepancy between paired t test and glht on lme models
Hi folks,
I am working with repeated measures data and I ran into issues where the
paired t-test results did not match those obtained by employing glht()
contrasts on a lme model. While the lme model itself appears to be fine,
there seems to be some discrepancy with using glht() on the lme model
(unless I am missing something here). I was wondering if someone could
help identify the issue. On
2006 May 11
1
bug report - cor (PR#8852)
Full_Name: daniel t. O'Shea
Version: 2.2.1
OS: xp
Submission from: (NULL) (156.98.28.4)
using the cor command in the base package.
cor(x,y)
x is a matrix (15 rows and 1000 columns). I did not specify a column and R
crashed - shut down.
error signature
AppName:rgui.exe AppVer 2.21.51220.0
ModName: r.dll
ModVer: 2.21.51220.0
2007 Aug 21
2
summing columns of data frame by group
I have a data frame and one separate vector that is a grouping variable for the data frame. I would like to take all rows of the data frame belonging to each group and then sum the columns with out using a for statement.
Something like: take all rows of group 1 then apply(group1.data,1,sum), but do this without having to do it separately for each group. Any ideas? thank you.
Dan
2013 Jan 22
0
ordering in 'gnls' with 'corCompSymm' corStruct
Dear R-devel members,
While writing a new correlation structure similar to 'corCompSymm' and
intended to be used with 'gnls', I got puzzled with the 'Initialize' method.
Using 'Initialize' before 'gnls' may be regarded as a mean to set an
initial value for the corStruct parameter. However 'gnls' does not work
properly with a
2007 Dec 30
2
refering to variable names in lm where the variable name is in another variable
I am trying to refer to a variable name in a lm regression where the variable name is in another variable, but it does seem to work. Here is an example:
y<-rnorm(10)
dat<-data.frame(x1=rnorm(10),x2=rnorm(10),x3=rnorm(10))
nam<-c('x1','x2','x3')
library(gtools)
com<-combinations(3,2,1:3)
mod<-lm(y~nam[com[1,1]],data=dat)
#error in model frame....:variable
2011 Oct 05
2
gamm: problems with corCAR1()
Dear all,
I?m analyzing this dataset containing biodiversity indices, measured over
time (Week), and at various contaminant concentrations (Treatment). We have
two replicates (Replicate) per treatment.
I?m looking for the effects of time (Week) and contaminant concentration
(Treatment) on diversity indices (e.g. richness).
Initial analysis with GAM models showed temporal autocorrelation of
2011 Jun 02
0
allowing individual level correlations to differ by cluster in lme in R
Dear R-listers,
I am fitting bivariate mixed models for cost-effectiveness data of cluster randomized trials using lme in R. So I have individuals nested within clusters. My response variable is a vector with bivariate response (individual level costs and effects) stacked into a single column. The covariates in my models are a constant and a treatment term. They are response-specific, e.g. a
2010 Sep 10
0
covariance matrix structure for random effect in glmmPQL
Dear all,
I'm using R function "glmmPQL" in "MASS" package for generalized linear mixed model considering the temporal correlations in random effect. There are 1825 observations in my data, in which the random effect is called "Date", and there are five levels in "Date", each repeats 365 times.
When I tried
2005 Feb 23
0
corCompSymm in nlme package
We are trying to use the corCompSymm function in nlme
The example from the help pages for the corAR1 function gives the following
> corAR1(0.2, form = ~ 1 | Mare)
Correlation structure of class corAR1 representing
Phi
0.2
We are expecting a somewhat similar correlation specification with the help page
example for corCompSymm, but just get an error instead
> corCompSymm(0.5, form = ~ 1 |
2005 May 25
1
question: corCAR1 in lme
Hello all,
I am trying to use lme to examine how a response variable (Chla) changes
over time in different treatments (2 Temp & 2 Light levels). Within each
treatment combination, there are two replicate tanks (each with unique
TankID) with coral fragments in them. All tanks are subject to the same
environment until Time=0, when treatments are imposed, and Chla is measured
for each