streda 28. júla 2010
Multiple Tables Sweave/Latex - Stack Overflow
utorok 27. júla 2010
Obesity - Which Obesity Indicators Are Better Predictors of Metabolic Risk[quest]: Healthy Twin Study
spss
medcalc for comparing pairs of AUC ROC
blog on blogging GO DOWN
https://addons.mozilla.org/en-US/firefox/addon/1730/
Regression Statistical Procedure
ROC curve comparison, software, statistics etc.
2. methods for doing this - comparing AUC ROC of two curves (predictors), Delong 1988, Hanley 1982 ...., permutation/boostrapping CI ...
CF binormal distribution assumption.
SPSS - SE AUC ROC - two methods (options)
1. nonparametric,
2. - bi-negative exponential distribution????
*xxx* cf. Park et al 2004 Korean ..Journal - very nice intro, nonmath, but insightful what has to be done...., includes explanation on PARAMETRIC vs nonPARAMETRIC ROC estimation (smooth vs empirical), cf concept of partial AUC ROC
--- give nice and simple overview on assumptions, and when PARAMETRIC vs NONparametric methods should be used. (continuous, ordinal, skewed, sparse categories etc).
*xxx* more technical-but educational - SUGI .... tutorial on SAS macro that is able to compute p-value for difference between two AUC ROC, explaining different statistical approaches
more technical: SAS help on nonparametric comparison of two ROC curves.
the journal article reference and Rcode for three different methods of calculation of SE of AUC ROC. R forum -- (ref. Hajian-Tilaki, Hanley 2002?
Rcode for the DeLong method of AUC ROC SE estimation - nonparametric
ROCKIT by prof Metz from CHICAGO, free, downloaded, but IMHO will t ake some time to get around, to prepare input file, etc.
cf things with bootstraping, jacknifing etc, nonparametric tests.
- cf childhood predictors of young onset T2DM ... Franks et al. DIABETES 2007 = methods
CF comparison of 8 software packages for performing ROC analysis. (Stephan ClinChem 2003
medcalc by SCHOONJANS - commercial sw for cox hazard, ROC
Jane, Longton, Pepe 2009: Accommodating Covariates in ROC Analysis
ROC EXPLANATION
from Park 2004. cf Lyssenko, Meigs 2008 NEJMcf values of test from 0.5 (random guess) to 1 (perfect predictor).
One of the most popular measures is the area under
the ROC curve (AUC) (1, 2). AUC is a combined measure
of sensitivity and specificity. AUC is a measure of the
overall performance of a diagnostic test and is interpreted
as the average value of sensitivity for all possible values of
specificity (1, 2). It can take on any value between 0 and 1,
since both the x and y axes have values ranging from 0 to
1. The closer AUC is to 1, the better the overall diagnostic
performance of the test, and a test with an AUC value of 1
is one that is perfectly accurate (Fig. 2). The practical lower
limit for the AUC of a diagnostic test is 0.5. The line
segment from 0, 0 to 1, 1 has an area of 0.5 (Fig. 2). If we
were to rely on pure chance to distinguish those subjects
with versus those without a particular disease, the resulting
ROC curve would fall along this diagonal line, which is
referred to as the chance diagonal (Fig. 2) (1, 2). A diagnos-
Comparison of data analysis packages: R, Matlab, SciPy, Excel, SAS, SPSS, Stata - Brendan O'Connor's Blog
Receiver Operating Characteristic (ROC) Curve: Practical Review for Radiologists
Plot ROC curve and lift chart in R « Heuristic Andrew
"[R] ROC curve from logistic regression"
ROC curve comparison
methods
parametric, nonparametric
deLong, Hanley ... references included in reference.
SPSSX-L archives -- December 1999 (#254)
ROCKIT compare ROC AUC
Differences in the binormal ROC curve parameters a and b (related to the difference in the mean and of the standard deviations of the two latest normal distributions used in the fit)
Difference in the areas (Az) under the two estimated binormal ROC curves"
ROC curves comparison - comp.soft-sys.stat.spss | Google Groups
> them is significantly different compared to the others ? I know how to
> draw a ROC curve in SPSS 15 but I do not know how to compare two
> curves to highlight significant (or insignificant) difference, by p-
> value."
pondelok 26. júla 2010
OpenClinica User Manual/FindingOIDs - Wikibooks, collection of open-content textbooks
XML EDITOR FREE - SERNA
BY SYSTEX -- CF PLONE CMS, ZOPE ???
piatok 16. júla 2010
stratified analysis, epidemiology
stratified analysis
by greenland sander.
googlebooks.
http://books.google.sk/books?id=Z3vjT9ALxHUC&pg=PA283&lpg=PA283&dq=interaction+versus+stratified+analysis&source=bl&ots=aOMKdIWH9T&sig=BvQKFnUsjzqtUO4hMImdFX0o4cQ&hl=sk&ei=RpUoTOGbNISWONSypasC&sa=X&oi=book_result&ct=result&resnum=7&ved=0CEIQ6AEwBg#v=onepage&q=interaction%20versus%20stratified%20analysis&f=false
Personalized medicine and genomics: challenges and... [Med Decis Making. 2010 May-Jun] - PubMed result
R Data Analysis Examples: Logit Regression
Logit Regression"
centering variables
http://books.google.sk/books?id=VtU3-y7LaLYC&pg=PA67&lpg=PA67&dq=centering+log+transformed+variables&source=bl&ots=cxvr4vpkkG&sig=A9C67EqnIkg34i_zKRiPOxdRGxI&hl=sk&ei=M4I5TKn5BMqmOI2L7YoK&sa=X&oi=book_result&ct=result&resnum=7&ved=0CD8Q6AEwBjgK#v=onepage&q=centering%20log%20transformed%20variables&f=true
Experimental design and data analysis for biologists Od autorov: Gerald Peter Quinn,Michael J. Keough
test for trend
a dummy variable in a logistic regression analysis?"
Epidemiologic Perspectives & Innovations | Full text | Trend tests for the evaluation of exposure-response relationships in epidemiological exposure studies
Comparison of GE Centricity electronic medical rec... [Popul Health Manag. 2010] - PubMed result
Information resources for epidemiologists: Textbooks
SPSS syntax to change string into numeric variable and vice versa, including a decimal or comma separator
Applications, programs and R statistical functions for epidemiology
IAS Literature e-Newsletter: June 2010
Society Literature e-Newsletter
JUNE 2010"
Association between increasing levels of hemoglobi... [Coron Artery Dis. 2010] - PubMed result
štvrtok 15. júla 2010
QMSS e-Lessons | Introduction
Čo všetko musíte voziť vo svojom aute - Pravda.sk
Tomáš Andrejčák 15. júla 2010 8:47"
nedeľa 11. júla 2010
CENTERING VARIABLES REFS Linear Mixed Models: Statnotes, from North Carolina State University, Public Administration Program
centering variables - collinearity in interaction terms, SAS, animation, demo
Linear Mixed Models: Statnotes, from North Carolina State University, Public Administration Program: "Centering. It is customary to center data prior to running LMM or HLM. Centering means subtracting the mean, so means become zero. Two main types of centering are group mean centering and grand mean centering. For instance, in a study of PerformanceScore, there might be a PerformanceIndividualScore at level 1 and a PerformanceAgencyScore at level 2, where the latter was a mean score for all employees in an agency. The researcher might center PerformanceIndividualScore for individuals by centering on their group (agency) means, where groups were agencies, on the theory that group performance influenced individual performance and differences from the group means should therefore be the variable of interest. Or one could center each PerformanceIndividualScore on the grand mean of all such scores across agencies. Grand mean centering is preferred over group mean centering unless there is theoretical justification for the latter."
Grand mean centering often improves the interpretability of coefficients because "0" now has a meaning (ex., 0 income is mean income, whereas before centering, 0 income might be out of the range of actual observations). Group mean centering, in contrast, changes the meaning of coefficients in complex ways which make coefficients hard to interpret, as different mean values are subtracted from different sets of raw scores. As a result, with group mean centering it is not possible to recalculate output back to raw score interpretations. In essence, one is dealing with a different variable after group mean centering. Grand mean centered income, for instance, will yield different slopes but the same deviance and residual errors as uncentered raw data. Group mean centered income does not. Group mean centered income is no longer simple income but rather measures income deviation from group means. The researcher must examine his or her theoretical model and decide if that is really what was wanted for the "income" variable. As noted by Kreft, de Leeuw, and Aiken (1995), the choice of centering must be made on a theoretical rather than statistical basis, and "centering around the group mean amounts to fitting a different model from that obtained by centering around the grand mean or by using raw scores" (p. 1). Most LMM/HLM software packages support various types of automatic centering. Centering considerations are further discussed in Burton (1993) and Hoffman & Gavin (1998).
Organize research, collaborate & discover new knowledge | Mendeley
cf zotero
endnote
reference manager
piatok 9. júla 2010
logistic regression, linear trend test for OR
in LOGISTIC REGRESSION
cf to test linear trend (of OR) across quartiles we entered 4-level ordinal term representing medians of 4 quartiles of original continuous
cf Ridker Comparison of CRP and LDL - NEJM
Nieto
Shahar - 2000
find:
*** *** ***
books with worked example how to compute trends in OR logistic regression models
"logistic regression linear trend test Odds ratio how to" Jewell
Nicholas Jewell Statistics for epidemiology. p222
google books
***
statnotes
http://faculty.chass.ncsu.edu/garson/PA765/logistic.htm#contrasts
***
- Maxwell & Delaney "Designing Experiments and Analyzing Data" Lawrence Erlbaum Associates
cf old nabble- SPSS discussion forum
If you want to know more on polynomial contrasts, check specialised books,
like: Maxwell & Delaney "Designing Experiments and Analyzing Data" Lawrence
Erlbaum Associates. If you Google a bit using this search key: "Polynomial
contrasts logistic regression", you will se that it is widely used in
experimental research to test for linear and non linear trends.
*** ***
- selvin , statistical analysis for epidemiologic data, p228 - cf stata-"trend test after logistic regression"
XXX: trend test after logistic regression.
Linear versus logistic regression when the dependent variable is a dichotomy
Choosing Statistical and Epidemiologic Methods
Choosing Statistical and Epidemiologic Methods
Improving the Presentation of Results of Logistic Regression
with R"
Epidemiologic Perspectives & Innovations | Full text | Trend tests for the evaluation of exposure-response relationships in epidemiological exposure studies
Ludwig A Hothorn"
Trend Tests in Epidemiology: P-Values or Confidence Intervals?. Ludwig A. Hothorn. 1999; Biometrical Journal - Wiley InterScience
Ludwig A. Hothorn, Prof. Dr."
logistic regression, model fit, trend test, boook
Hosmer DW, Jr, Lemeshow S. Applied logistic regression 1989:25-37 John Wiley & Sons New York. .
In all analyses, we modeled Lp(a) concentrations as quartiles to avoid theClinical Chemistry. 2008;54:285-291.)
assumption of linearity and to reduce the effects of outliers. Furthermore, we
used median Lp(a) concentrations for the categories to test for linear trends
across quartiles. We categorized the data according to the 90th, 95th, and 99th
percentiles and performed threshold analyses. We also used the test of Hosmer
and Lemeshow to evaluate the goodness of fit of the data to the models (20).
štvrtok 8. júla 2010
interaction, HOW TO , REGRESSION, XXX
Sequential Moderated Multiple Regression AnalysisÓ
Continuous Moderator Variables in Multiple Regression
http://core.ecu.edu/psyc/wuenschk/MV/multReg/Moderator.doc
PGS 101-INTRODUCTION TO PSYCHOLOGY
learning and training Multilevel Modelling online course"
interaction effects centering variables
how to perform likelihood ratio test in SPSS - Hľadať v Google
how to perform likelihood ratio test in SPSS - Hľadať v Google
Formát súboru: Microsoft Word - HTML verzia
This is one use of the likelihood ratio test between two nested models (referrred to as “chi-square” in the SPSS logistic output). ...
www.upa.pdx.edu/IOA/newsom/da2/ho_logistic3.doc - Podobné"
Annotated SPSS Output: Logistic Regression
Logistic Regression"
SPSS Code Fragments: A few SPSS loops for renaming variables dynamically
SPSS Code Fragment: Graphing results in logistic regression
Graphing results in logistic regression"
streda 7. júla 2010
logistic regression, interaction CHASS - statnotes
Yes. As in OLS regression, interaction terms are constructed as crossproducts of the two interacting variables.
How are interaction effects handled in logistic regression?
The same as in OLS regression. One must add interaction terms to the model as crossproducts of the standardized independents and/or dummy independents. Some computer programs will allow the researcher to specify the pairs of interacting variables and will do all the computation automatically. In SPSS, use the categorical covariates option: highlight two variables, then click on the button that shows >a*b> to put them in the Covariates box .The significance of an interaction effect is the same as for any other variable, except in the case of a set of dummy variables representing a single ordinal variable.
When an ordinal variable has been entered as a set of dummy variables, the interaction of another variable with the ordinal variable will involve multiple interaction terms. In this case the significance of the interaction of the two variables is the significance of the change of R-square of the equation with the interaction terms and the equation without the set of terms associated with the ordinal variable. (See the StatNotes section on "Regression" for computing the significance of the difference of two R-squares).
ASSUMPTIONS:
Centered variables. As in OLS regression, centering may be necessary either to reduce multicollinearity or to make interpretation of coefficients meaningful. Centering is almost alway recommended for independent variables which are components of interaction terms in a logistic model. See the full discussion in the section on OLS regression, here.
COLLINEARITY
Is multicollinearity a problem for logistic regression the way it is for multiple linear regression?
Absolutely. The discussion in "Statnotes" under the "Regression" topic is relevant to logistic regression.
What is the logistic equivalent to the VIF test for multicollinearity in OLS regression? Can odds ratios be used?
Multicollinearity is a problem when high in either logistic or OLS regression because in either case standard errors of the b coefficients will be high and interpretations of the relative importance of the independent variables will be unreliable. In an OLS regression context, recall that VIF is the reciprocal of tolerance, which is 1 - R-squared. When there is high multicollinearity, R-squared will be high also, so tolerance will be low, and thus VIF will be high. When VIF is high, the b and beta weights are unreliable and subject to misinterpretation. For typical social science research, multicollinearity is considered not a problem if VIF <= 4, a level which corresponds to doubling the standard error of the b coefficient. As there is no direct counterpart to R-squared in logistic regression, VIF cannot be computed -- though obviously one could apply the same logic to various psuedo-R-squared measures. Unfortunately, I am not aware of a VIF-type test for logistic regression, and I would think that the same obstacles would exist as for creating a true equivalent to OLS R-squared. A high odds ratio would not be evidence of multicollinearity in itself. To the extent that one independent is linearly or nonlinearly related to another independent, multicollinearity could be a problem in logistic regression since, unlike OLS regression, logistic regression does not assume linearity of relationship among independents. Some authors use the VIF test in OLS regression to screen for multicollinearity in logistic regression if nonlinearity is ruled out. In an OLS regression context, nonlinearity exists when eta-square is significantly higher than R-square. In a logistic regression context, the Box-Tidwell transformation and orthogonal polynomial contrasts are ways of testing linearity among the independents.
tabachnick fidell - eBook Downloads
Tabachnick, B. G., & Fidell, L. S. (1996). Using multivariate statistics (3rd ed.). New York: Harper Collins. Tabachnick, B. G., & Fidell, L. S. (2001).
bit.csc.lsu.edu/~jianhua/emrah.pdf - View"
Regression Models for Count Data: Illustrations using Longitudinal Predictors of Childhood Injury -- Karazsia and van Dulmen 33 (10): 1076 -- Journal of Pediatric Psychology
logistic regression interaction testing how to - Hľadať v Google
Formát súboru: Microsoft Powerpoint - HTML verzia
Testing interactions in logistic regression is similar to OLS regression methods, in that one includes an interaction term in the model predicting a binary ..."
King: xxxx
http://faculty.washington.edu/kingkm/Logistic%20Regression/mediation%20in%20logistic.ppt
pondelok 5. júla 2010
nonparametric logistic regression - Hľadať v Google
FAQ: A comparison of different tests for trend
cf cochrane-armittage test for linear trend in genotypes (genetic association testing)
nice explanation - as how some statistical tests are something we now, but have new names. ...... at the same time a bit confusing.
FAQ: A comparison of different tests for trend: "Does Stata provide a test for trend?"
sobota 3. júla 2010
logistic regression resources
1. binary logistic regression - Rodriguez. Available at: http://data.princeton.edu/wws509/notes/c3.pdf [Cit Júl 3, 2010].
general statistical text, but on authors webpage u can find examples how to perform analysis in R statistical software. !!!!!
2. Categorical Data: Part 6: Logistic Regression. Available at: http://www.math.yorku.ca/SCS/Courses/grcat/grc6.html [Cit Júl 3, 2010]. / for SAS , but general concepts very intuitive //
3. log linear model - zrozumiteľné - Rodriguez. Available at: http://data.princeton.edu/wws509/notes/c5.pdf [Cit Júl 3, 2010].
1. linear models - rodriguez - zrozumiteľne! Available at: http://data.princeton.edu/wws509/notes/c2.pdf [Cit Júl 3, 2010].