History of AFNI updates  

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December 30, 2019 10:58AM
The linear mixed-effects modeling program 3dLME has been around for many years. However, one bottleneck of 3dLME has become suffocating: the limited adaptivity of random-effects specifications. A new program 3dLMEr has been just created to expand the adaptivity of 3dLME.

3dLMEr is a revised and advanced version of its elder brother 3dLME in the sense that the former is much more flexible in specifying the random-effects components than the latter. In addition, 3dLMEr uses the R package 'lmerTest' while 3dLME was written with the R package 'nlme', and the statistic values for main effects and interactions are approximated with the Satterthwaite's approach. The greater flexibility of 3dLMEr lies in its adoption of random-effects notations by the R package 'lme4', as nicely summarized in the following table (change the variable 'group' in the table to 'subject' in the neuroimaging context) :

[afni.nimh.nih.gov]
(adopted from [bbolker.github.io])

Similar to 3dLME, all the main effects and interactions are automatically available in the output while simple effects that tease apart those main effects and interactions would have to be requested through the option -gltCode -glfCode. Also, the 3dLMEr interface is largely similar to 3dLME except

1) the random-effects components are incorporated as part of the model specification, and thus the user is fully responsible in properly formulating the model structure through '-model ...' (option -ranEeff in 3dLME is no longer necessary for 3dLMEr);

2) the specifications for simple and composite effects through -gltCode and -glfCode are slightly simplified (the lable for each effect is part of -gltCode and -glfCode, and no more -gltLabel is needed); and

3) all the statistic values for simple effects (specified through -gltCode) are stored in the output as Z-statisc while main effects, interactions and the composite effects (specified through -gltCode) are represented in the output as chi-square with 2 degrees of freedom. The fixed number of DFs (i.e., 2) for the chi-square statistic, regardless of the specific situation, is not related to the real number of factor levels and is adopted simply for convenience because of the varying DFs due to the Satterthwaite approximation.

Gang



Edited 7 time(s). Last edit at 01/02/2020 10:44AM by Gang.
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New program 3dLMEr for linear mixed-effects modeling

Gang December 30, 2019 10:58AM

Re: New program 3dLMEr for linear mixed-effects modeling

Yue January 08, 2020 05:22PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang January 09, 2020 12:01PM

Re: New program 3dLMEr for linear mixed-effects modeling

Yue January 14, 2020 11:15AM

Re: New program 3dLMEr for linear mixed-effects modeling

Andrew Davis April 24, 2020 01:11PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang April 24, 2020 02:39PM

Re: New program 3dLMEr for linear mixed-effects modeling

Andrew Davis April 25, 2020 11:46AM

Re: New program 3dLMEr for linear mixed-effects modeling

Andrew Davis April 30, 2020 04:02PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang April 30, 2020 05:53PM

Re: New program 3dLMEr for linear mixed-effects modeling

Andrew Davis April 30, 2020 09:07PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang May 01, 2020 02:42PM

Re: New program 3dLMEr for linear mixed-effects modeling

Andrew Davis May 02, 2020 12:12PM

Re: New program 3dLMEr for linear mixed-effects modeling

ben88 August 03, 2020 07:53PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang August 04, 2020 07:53AM

Re: New program 3dLMEr for linear mixed-effects modeling

ben88 August 04, 2020 08:14AM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang August 04, 2020 08:59AM

Re: New program 3dLMEr for linear mixed-effects modeling

ben88 August 12, 2020 04:33PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang August 13, 2020 02:36PM

Re: New program 3dLMEr for linear mixed-effects modeling

aojha17 September 14, 2020 10:56AM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang September 14, 2020 02:13PM

Re: New program 3dLMEr for linear mixed-effects modeling

aojha17 September 18, 2020 07:32PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang September 21, 2020 08:31PM

Re: New program 3dLMEr for linear mixed-effects modeling

aojha17 September 22, 2020 03:41PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang September 22, 2020 04:00PM

Re: New program 3dLMEr for linear mixed-effects modeling

aojha17 September 22, 2020 09:01PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang September 23, 2020 10:09AM

Re: New program 3dLMEr for linear mixed-effects modeling

aojha17 September 23, 2020 11:21AM

Re: New program 3dLMEr for linear mixed-effects modeling

henrybrice October 20, 2020 09:06AM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang October 20, 2020 12:31PM

Re: New program 3dLMEr for linear mixed-effects modeling

henrybrice October 20, 2020 03:22PM

Re: New program 3dLMEr for linear mixed-effects modeling

Gang October 20, 2020 09:05PM

Re: New program 3dLMEr for linear mixed-effects modeling

henrybrice October 21, 2020 05:43AM



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