Displaying 20 results from an estimated 200 matches similar to: "epitools question"
2012 May 04
0
oddsratio and some basic help on epitools
Here is a working snippet.
library(epitools)
mat <- matrix(c(10,15,60,25,98, 12,10,70,28,14, 9,11,68,10,12
,8,13,20,11,58) ,ncol=2)
colnames(mat) <- c("treatmentA","treatmentB")
row.names(mat) <- paste("Cond",rep(1:10,1))
dimnames(mat) <- list("Condition" = row.names(mat), "instrument" =
colnames(mat))
> mat
instrument
2012 May 04
0
oddsratio epitool and chi-square
Here is a working snippet.
library(epitools)
mat <- matrix(c(10,15,60,25,98, 12,10,70,28,14, 9,11,68,10,12
,8,13,20,11,58) ,ncol=2)
colnames(mat) <- c("treatmentA","treatmentB")
row.names(mat) <- paste("Cond",rep(1:10,1))
dimnames(mat) <- list("Condition" = row.names(mat), "instrument" =
colnames(mat))
> mat
instrument
2009 Jul 30
3
What is the best method to produce means by categorical factors?
I am attempting to replicate some of my experience from SAS in R and assume
there are best methods for using a combination of summary(), subset, and
which() to produce a subset of mean values by categorical or ordinal
factors.
within sas I would write
proc means mean data=dataset;
class factor1 factor2
var variable1 variable2;
RUN;
producing an output with means for each variable by factor
2009 Apr 16
0
incorrect handling of NAs by na.action with lmList (package nlme) (PR#13658)
Greetings,
I just found out a bug in the function lmList of the package nlme with R
2.8.1 running under windows XP 32-bits. I have a data table with various
columns corresponding to continuous variables as well as treatment
variables taken on several years and several sites. Here is an example :
Id year treatment A treatment B variable1
variable2 variable3
1
2005 Jan 24
4
lme and varFunc()
Dear R users,
I am currently analyzing a dataset using lme(). The model I use has the
following structure:
model<-lme(response~Covariate+TreatmentA+TreatmentB,random=~1|Block/Plot,method="ML")
When I plot the residuals against the fitted values, I see a clear
positive trend (meaning that the variance increases with the mean).
I tried to solve this issue using weights=varPower(),
2011 Sep 13
1
stupid lm() question
I feel bad even asking, but:
Rgames> data(OrchardSprays)
Rgames> model<-lm(decrease~.,data=OrchardSprays)
Rgames> model
Call:
lm(formula = decrease ~ ., data = OrchardSprays)
Coefficients:
(Intercept) rowpos colpos treatmentB treatmentC
22.705 -2.784 -1.234 3.000 20.625
treatmentD treatmentE treatmentF treatmentG treatmentH
2007 Jun 11
1
epitools and R 2.5
At work after updating to R 2.5 I get an error using epitab from package
epitools, when at home (R 2.4) I get no error. Could someone help me?
Thanks
Pietro Bulian
Servizio di Onco-Ematologia Clinico-Sperimentale
I.R.C.C.S. Centro di Riferimento Oncologico
Via Franco Gallini 2
33081 Aviano (PN) - Italy
phone: +39 0434 659 412
fax: +39 0434 659 409
e-mail: pbulian at cro.it
(at work)
2009 Oct 26
1
explalinig the output of my linear model analysis
Hi,
I am new in statistics and i manage to make the linear model analysis but i
have some difficulties in explaining the results. Can someone help me
explalinig the output of my linear model analysis ? My data are with 2
variables habitat (e,s) and treatment (a,c,p) with multiple trials within.
Thank you in advance
Call:
lm(formula = a$wild ~ a$habitat/a$treatment/a$trial)
Residuals:
Min
2006 Jun 09
0
interaction terms in regression analysis
G'day,
My problem is I'm not sure how to extract effect sizes from a nonlinear
regression model with a significant interaction term.
My data sets are multiple measurements of force response to an agonist
with two superimposed treatments each having two levels.
This is very similar to the Ludbrook example in Venables and Ripley.
The experiment is that a muscle is exposed to an agonist
2008 Jul 30
1
Mixed effects model where nested factor is not the repeated across treatments lme???
Hi,
I have searched the archives and can't quite confirm the answer to this.
I appreciate your time...
I have 4 treatments (fixed) and I would like to know if there is a
significant difference in metal volume (metal) between the treatments.
The experiment has 5 blocks (random) in each treatment and no block is
repeated across treatments. Within each plot there are varying numbers
of
2011 Apr 21
1
Accounting for overdispersion in a mixed-effect model with a proportion response variable and categorical explanatory variables.
Dear R-help-list,
I have a problem in which the explanatory variables are categorical,
the response variable is a proportion, and experiment contains
technical replicates (pseudoreplicates) as well as biological
replicated. I am new to both generalized linear models and mixed-
effects models and would greatly appreciate the advice of experienced
analysts in this matter.
I analyzed the
2012 Mar 04
2
Can't find all levels of categorical predictors in output of zeroinfl()
Hello,
I?m using zero-inflated Poisson regression via the zeroinfl() function to
analyze data on seed-set of plants, but for some reason, I don?t seem to be
getting the output for all three levels of my two categorical predictors.
More about my data and model:
My response variable is the number of viable seeds (AVInt), and my two
categorical predictors are elevation (Elev) and Treatment
2011 Jan 25
1
coxme and random factors
Hi
I would really appreciate some help with my code for coxme...
My data set
I'm interested in survival of animals after an experiment with 4
treatments, which was performed on males and females. I also have two
random factors:
Response variable: survival (death)
Factor 1: treatment (4 levels)
Factor 2: sex (male / female)
Random effects 1: person nested within day (2 people did
2008 Jan 24
2
testing coeficients of glm
Dear list,
i'm trying to test if a linear combination of coefficients of glm is equal
to 0. For example :
class 'cl' has 3 levels (1,2,3) and 'y' is a response variable. We want to
test H0: mu1 + mu2 - mu3 =0 where mu1,mu2, and mu3 are the means for each
level.
for me, the question is how to get the covariance matrix of the estimated
parameters from glm. but perhaps there
2011 Jun 28
2
gam confidence interval (package mgcv)
Dear R-helpers,
I am trying to construct a confidence interval on a prediction of a
gam fit. I have the Wood (2006) book, and section 5.2.7 seems relevant
but I am not able to apply that to this, different, problem.
Any help is appreciated!
Basically I have a function Y = f(X) for two different treatments A
and B. I am interested in the treatment ratios : Y(treatment = B) /
Y(treatment = A) as
2006 Nov 10
3
Confidence interval for relative risk
The concrete problem is that I am refereeing
a paper where a confidence interval is
presented for the risk ratio and I do not find
it credible. I show below my attempts to
do this in R. The example is slightly changed
from the authors'.
I can obtain a confidence interval for
the odds ratio from fisher.test of
course
=== fisher.test example ===
> outcome <- matrix(c(500, 0, 500, 8),
2010 Jan 27
1
Possible bug in fisher.test() (PR#14196)
# is there a bug in the calculation of the odds ratio in fisher.test?
# Nicholas Horton, nhorton at smith.edu Fri Jan 22 08:29:07 EST 2010
x1 = c(rep(0, 244), rep(1, 209))
x2 = c(rep(0, 177), rep(1, 67), rep(0, 169), rep(1, 40))
or1 = sum(x1==1&x2==1)*sum(x1==0&x2==0)/
(sum(x1==1&x2==0)*sum(x1==0&x2==1))
library(epitools)
or2 = oddsratio.wald(x1, x2)$measure[2,1]
or3 =
2008 Feb 19
2
Confidence Interval for SMR
Hello,
I am looking for a function which allows to calculate the confidence
interval for a standard mortality ratio. I do have vectors with the
number of observed and expected death. Has anybody a hint where to
look?
Best,
Stefan
2008 Dec 02
1
Asymmetric CIs
Hi, I was wondering if there was some sort of package or function that calculated asymmetric confidence intervals for small proportions. I thought of both the epicalc and epitools package, but I am hoping to find something where you can just plug in a standard error and point estimate and it will output the upper and lower CI bounds.
Thanks!
Sarah
2012 Jun 27
1
trend in incidence rate
I would like to compare the incidence rates of three groups. They are
supposed to have different risks so I would like to test whether there is a
increasing trend in the incidence rates. Does R or any packages provide a
trend test for incidence rates? I checked epiR and epitools. It seems they
do not have this function.
Thank you for the help.
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