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On Mon, Jan 27, 2020 at 1:07 PM maria <frau.mar...@gmail.com> wrote:
Hi Chris,--I would like to ensure, that I'm using the correct contrast matrix to test my hypotheses in mtpc.I would like to compare graph theory measurements of patients and controls, while controlling for non-interest covariates.My design matrix looks like this (showing head and tail of brainGraph_GLM_design() with coding='effects') :Following your examples in the manual I constructed the following contrast matrix, testing the group difference (using t statistics and alternative='greater'):I'm wondering whether this is correct, even if I have no "reference group" as such? Or should it rather be -1 and 1? Does the choice of the alternative affect the results or this this merely for my own records?Furthermore, how would I have to construct the contrast to test the specific differences between more than 2 groups such as in the factor variable 'subgroups' (4 levels: 0,1,2,3)?Design matrix with effects coding:I assume this would require a post test? Is this kind of analysis possible at all in mptc?Thank you, Maria
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Do you have any idea, what could cause this? What else could I try?
Apologies, for this long post!
Thank you, Maria
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This looks to be the same problem another user posted about 2 months ago. In that case, the order of the covariates data.table (specifically, the Study.ID and/or Group columns) differed from the order in the graph list objects. Please make sure that the orders match. The function should already check for these issues, but it seems it is a bug that I did not catch previously.Let me know if it works.Chris
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Ok. Please send me a ".rda"/".RData" file with all of the data/variables I need
to perform these analyses and debug. Please also provide a ".R" script with the
code that you have been running. And finally (you can paste the text output in
email) please provide the R, igraph, and brainGraph versions you are using. It
might be helpful if you also provide operating system info, too. If you have
"devtools" you can do
devtools::session_info(c('igraph', 'brainGraph'))
Or you can use "sessionInfo" with the same arguments.
Chris
On Mon, Feb 03, 2020 at 09:02 AM, maria <frau.mar...@gmail.com> wrote:
> from: maria <frau.mar...@gmail.com>
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Yes, please send me a .R file with the code you have run.
Chris
On Mon, Feb 03, 2020 at 04:00 PM, maria <frau.mar...@gmail.com> wrote:
> from: maria <frau.mar...@gmail.com>
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On Wed, Feb 05, 2020 at 07:34 AM, maria <frau.mar...@gmail.com> wrote:
> from: maria <frau.mar...@gmail.com>
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1. Yes, the ordering in "X" should be by Study ID only. In v3, I will ensure
this is the case for any tables/matrices including Study IDs. Things became too
complicated when trying to account for sorting by both Group name and ID.
2. In "data.table", most operations are performed "by reference". This is
different from all (or, the vast majority) of other functions/operations in R.
Usually, when you pass a data object/variable to a function, a *copy* of that
object is passed to the function environment. The "original" object in the
Global Environment (i.e., the workspace, the environment the user is working in)
does not get affected; if the object is changed within the function, it is
really the copy of the object. With data.table, the operations are done on the
*original* object. So, from within "mtpc", it loops across all
thresholds/densities and calls "brainGraph_GLM". For the first
threshold/density, it is operating on the original "covars" table. But through
that, it makes some changes, so that the "covars" in the "mtpc" environment gets
changed instead of being left unaffected. So for the 2nd through final
thresholds, in the calls to "brainGraph_GLM", the ordering of "covars" is
different from that of the graphs, and the model (design matrix "X") becomes
incorrect.
I hope this explanation makes sense. When I finally release v3.0.0 this should
not be an issue.
Chris
On Fri, Feb 07, 2020 at 09:44 AM, maria <frau.mar...@gmail.com> wrote:
> from: maria <frau.mar...@gmail.com>
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