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Gwet's AC1 Interrater reliability

R friends,

with some help of a friend and the original author I turn available this
function which is helping me in some analysis. Perhaps it may be useful to
others... :-)

 1.
Gwet KL. Computing inter-rater reliability and its variance in the presence
of high agreement. Br J Math Stat Psychol. 2008 ;61(Pt 1):29–48.

# AC1 statistic for 2 raters special case
# table = k x k table which represents table(rater1,rater2), must have
equal number of rows and columns
# N = population size which will be stick in standard error correction,
N=Inf is no correction.
# conflev = Confidence Level associated with the confidence interval (0.95
is the default value)

AC1 <- function(table,conflev=0.95,N=Inf,print=TRUE){
  if(dim(table)[1] != dim(table)[2]){
  stop('The table should have the same number of rows and columns!')
  }
  n <- sum(table)
  f <- n/N
  pa <- sum(diag(table))/n # formula 18
  q <- ncol(table) # number of categories
  pkk <- diag(table)/n
  pak <- sapply(1:q,function(i)sum(table[i,]))/n
  pbk <- sapply(1:q,function(i)sum(table[,i]))/n
  pik <- (pak + pbk)/2
(Continue reading)

Lisa Solomon | 2 May 22:23
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Epidemiology/Biostat at Analytics & Data Mining Conference in San Diego, California, May 23-25

Don't miss it, it's this month!

The 2012 Salford Analytics & Data Mining Conference aims to bring together
researchers, practitioners, and data enthusiasts to exchange ideas and
experiences.

Attendees will have the chance to have one-on-one meetings with the creators of the CART and RandomForests algorithms
(Dr. Adele Cutler, Dr. Jerome Friedman and Dr. Richard Olshen).

Attendees will have the chance to learn from practical and theoretical experts including:
*             Dr. Richard Olshen (Chief, Division of Biostatistics at Stanford University School of Medicine and
co-creator of CART)
*             Dr. Adele Cutler (co-developer of RandomForests with the late Leo Breiman)
*             Dr. Marsha Wilcox, Director of Epidemiology, Johnson & Johnson
*             Ben Trzaskoma, Senior Statistical Scientist, Genentech, Inc.
*             Dr. Richard Straub, Investigator at Lieber Institute for Brain Development
*             Onchee Yu, Biostatistician at Group Health Research Institute
*             Dr. Robert Aronoff, Physician/Researcher and Assistant Professor of Medicine, Milton S. Hershey
Medical Center
*             Dr. Jason Haukoos, Director of Research and Clinical Research Fellowship, Department of Emergency Medicine,
Denver Health Medical Center; Associate Professor, University of Colorado, School of Medicine;
Associate Professor, Department of Epidemiology
at the Colorado School of Public Health.
And many more!

Presentations include:
--"Applying CART to cluster analyses in asthma databases to reduce the dimensionality of testing drug interactions"
--"Algorithms to identify second breast cancer events using administrative healthcare data"
--"Genes, Cognition, and Psychosis: Insights from TreeNet Gradient Boosting and RandomForests"
--"Predicting Hospital Readmission Using TreeNet Gradient Boosting"
(Continue reading)

Iva P | 18 Mar 11:21
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Cosinor Model (Halberg, Bingham) - Multiple components - Linear, Quadratic and Cubic trends


Hello!

I have a doubt in relation with the use of the cosinor model with R when I have not only multiple components,
but also linear, quadratic and cubic trends.

I explain the details:

In simple cosinor:

Y = M + A * cos(2
* π* t / T + φ) + error

T knowed: y = M + β* X1 + ϒ* X2 + error,
 
Where X1 = cos (2 * π* t / T) and X2 = sin(2
* π* t / T)
 
In this
case, I use lm(y ~ X1 + X2) .
 
For the
multiple components case:
 
y = M + ∑Aj * cos(2 * π * t /Tj + φj) + error
 
In this
case I use:  lm(y ~ X1tot + X2tot)
 
However, in
(Continue reading)

Muhammad Arshad | 26 Feb 23:12
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Fwd: Need help to find multifactors influence‏

Dear friends,

1-I have B.I value (Dependent variable). 
2-I have land cover types in the form of % area against each B.I (that was clipped through buffer for each B.I ). Buffer was put by considering B.I behavior that can be influence by land type.  
3- I want to see the influence of land type on B.I. 
4- Suppose B.I value varies with the change in (area) one or more types of land cover. This change may be linear up to some extent but can also increase with the combination of land types. Land types can also differ from one buffer to other buffer.
5- I want to develop a Predication Model\Regression Equation to predict B.I value with the combined influence of different land use types.
6- I am confused which Regression model (Linear, Logistic, and Poisson, Exponential etc...)  Should be adopted to develop this type of relationship where factors are varying. 
7- Total study map consists of 77 land cover types and each buffer gets some land type.

Please see the attached data having values extracted for each land type (a1~a77 are land type names against each BI).

I already tried to solve it with different methods. Even I made groups in term of B.I & also in term of land cover types. But still failed to find correlation with reasonable factors.

I will happy for your informative response to solve my this problem. Please let me know if my question is not clear.

Warm Regards,
Malik\Arshad


Attachment (MALIK'S DATA.xlsx): application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, 48 KiB
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Re: R-sig-Epi Digest, Vol 54, Issue 1

Taking a look at task views on survival analysis here:

http://finzi.psych.upenn.edu/views/Survival.html

it seems the package timereg may do what you want.

Abraço forte e que a força esteja com você,

Dr. Pedro Emmanuel A. A. do Brasil
Instituto de Pesquisa Clínica Evandro Chagas
Fundação Oswaldo Cruz
Rio de Janeiro - Brasil
Av. Brasil 4365,
CEP 21040-360,
Tel 55 21 3865-9648
email: pedro.brasil@...
email: emmanuel.brasil@...

---Apoio aos softwares livres
www.zotero.org - gerenciamento de referências bibliográficas.
www.broffice.org ou www.libreoffice.org - textos, planilhas ou
apresentações.
www.epidata.dk - entrada de dados.
www.r-project.org - análise de dados.
www.ubuntu.com - sistema operacional

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Grellier, James | 11 Jan 14:08

Linear excess relative risk modelling in R

Dear List,

I am attempting to carry out linear excess relative risk modelling for the
purposes of a nested case-control study of nuclear industry workers.

The majority of similar analyses in the literature have been carried out
using EPICURE, SAS or STATA, or have been implemented directly in FORTRAN.
For a number of reasons, it would be preferable for me to carry out the
analysis in R, but I am having difficulty finding an appropriate R
package.

Many thanks in advance for any advice on this matter,

James Grellier

James Grellier PhD

CREAL-Centre for Research in Environmental Epidemiology
Parc de Recerca Biomèdica de Barcelona (despatx 183.01.A)
Doctor Aiguader, 88 | 08003 Barcelona

Tel. +34 932 147 345
jgrellier@...

 <http://www.creal.cat/> www.creal.cat

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Course: Age-Period-Cohort models, Lisbon, September 2011

Course on Age-Period-Cohort models.
===================================
   Place: Lisbon
    Time: Monday 19th - Wednesday 21st September 2011. 
Deadline: 1 September 2011
     Fee: 380 EUR.
 Teacher: Bendix Carstensen, Steno Diabetes Center, Copenhagen
     URL: http://www.ceaul.fc.ul.pt/seeevent.html?id=206
          http://staff.pubhealth.ku.dk/~bxc/APC/Lisboa-2011
          ( The latter contains links to various material on the topic )
Audience: Epidemiologists and Statisticians.

Age-Period-Cohort models for mortality and morbidity rates is a useful tool for description of age- and
time-trends. But the use and in particular the reporting is not straightforward.

The course will cover both the basics of tabulation of data, modeling and choice of parametrization as well
as the more advanced aspects of Age-Period-Cohort models, including a substantial practical
component, based on computer exercises in R. Specifically the apc-tools in the Epi package for R will be
covered in some depth.

Formally no prerequisites are required, but familiarity with regression models in epidemiology and some
exposure to R will prove advantageous. 

Participants are expected to bring their own laptop, and can expect to go home with a couple of thorough
analyses of example datasets. Instructions on what to install (and how) will be given shortly after the
application deadline.
_________________________________________

Bendix Carstensen 
Senior Statistician
Steno Diabetes Center A/S
Niels Steensens Vej 2-4
DK-2820 Gentofte
Denmark
+45 44 43 87 38 (direct)
+45 30 75 87 38 (mobile)
bxc@...    
www.biostat.ku.dk/~bxc
www.steno.dk
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Running R on a Computer Cluster in the Cloud - cloudnumbers.com

Dear epidemiological data analysis and R experts,

cloudnumbers.com provides researchers and companies with the resources
to perform high performance calculations in the cloud. As
cloudnumbers.com's community manager I may invite you to register and
test R on a computer cluster in the cloud for free:
http://my.cloudnumbers.com/register

Our aim is to change the way of research collaboration is done today by
bringing together scientists and businesses from all over the world on a
single platform. cloudnumbers.com is a Berlin (Germany) based
international high-tech startup striving for enabling everyone to
benefit from the High Performance Computing related advantages of the
cloud. We provide easy access to applications running on any kind of
computer hardware: from single core high memory machines up to 1000
cores computer clusters.

Our platform provides several advantages:

* Turn fixed into variable costs and pay only for the capacity you need.
Watch our latest saving costs with cloudnumbers.com video:
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our latest cloudnumbers.com in a nutshell video:
http://www.youtube.com/watch?v=0ZNEpR_ElV0&feature=player_embedded

* Be released from ongoing technological obsolescence and continuous
maintenance costs (e.g. linking to libraries or system dependencies)

* Accelerated your R, C, C++, Fortran, Python, ... calculations through
parallel processing and great computing capacity - more than 1000 cores
are available and GPUs are coming soon.

* Share your results worldwide (coming soon).

* Get high speed access to public databases.

* We have developed a security architecture that meets high requirements
of data security and privacy. Read our security white paper:
http://d1372nki7bx5yg.cloudfront.net/wp-content/uploads/2011/06/cloudnumberscom-security.whitepaper.pdf

This is only a selection of our top features. To get more information
check out our web-page (http://www.cloudnumbers.com/) or follow our blog
about cloud computing, HPC and HPC applications (with R):
http://cloudnumbers.com/blog

Register and test for free now at cloudnumbers.com:
http://my.cloudnumbers.com/register

We are looking forward to get your feedback and consumer insights.

Best
Markus

-- 
Dr. rer. nat. Markus Schmidberger 
Senior Community Manager 

Cloudnumbers.com GmbH
Chausseestraße 6
10119 Berlin 

www.cloudnumbers.com 
E-Mail: markus.schmidberger <at> cloudnumbers.com 

************************* 
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Geschäftsführer: Erik Muttersbach, Markus Fensterer, Moritz v. 
Petersdorff-Campen 

Diese Nachricht kann vertrauliche Informationen enthalten. Sollten Sie 
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Martyn Plummer | 26 Apr 15:48
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Course: Statistical Practice in Epidemiology with R

Many of the subscribers to R-SIG-Epi will be familiar with the course
Statistical Practice in Epidemiology with R, which normally takes place
in Tartu, Estonia.  This year, the course will take place in Lyon,
France 5-9 September. 

The course is intended for epidemiologists and statisticians who wish to
use R  for statistical modelling and analysis of epidemiological data.
The aim of the course is to give participants access to a set of tools
in current use by statisticians in epidemiology. The course requires
fairly good understanding of statistical principles and some familiarity
with epidemiological concepts and study types.

The course is mainly practically oriented with more than half the 
time at the computer.

For more information see 
http://www.iarc.fr/en/education-training/R/
http://www.pubhealth.ku.dk/~BXC/SPE/

To apply for the course, download and fill in the application form. The
deadline for applications is 21 May.

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Barbour, Russell | 30 Mar 23:37
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OR in HGLM

Dear All,

I  was  wondering how I can  generate adjusted odds  ratio confidence intervals  using the hglm package? I  know
you can simply  use the exponential of the estimate to get the OR,  but I  am not sure how you  can get the 
equivalent of the " logistic.display"  in epicalc that will also  generate the  CI's.  I  know this is   very 
elementary  question.

Russell " Skip" Barbour  Ph.D.
Yale School  of Medicine
135 College St.  Suit 200
New Haven ,  CT. 06510
Tel: 203 764 4332
Fax: 203 764 4353
Email: russell.barbour@...<mailto:russell.barbour@...>

Doubt grows with knowledge.
Johann Wolfgang von Goethe<http://www.brainyquote.com/quotes/quotes/j/johannwolf380192.html>

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luca candeloro | 22 Mar 15:03
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Sourveillance package

Hi,
I'm using the function algo.farrington() in package surveillance to detect
mortality greater than expected for a given region.
As described in Farrington method, it should be possible to take into
account for population at risk but I can't find the way to do this whit the
specified R package/function.
Does anyone know how may I do?
Thanks,
Luca

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