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downsample_gaze not found #27
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Hi! that function does not take |
Hello! thanks for the quick response. What if I change the variable name, will the results be correct or by beeing scaled before (with the pupilz method) it will create bad results ? |
Sorry but now by checking the functions in the code section I am a little bit confused. If I made the pupilz convertion in the re-scaling section, what parameter should I be putting in the pup_missing, pup_outliers and mad_removal ?? sorry if it is clearer but I can't figure it out , this is that section of the code :
Tanks a lot for any help possible ! |
Change |
Just to be clear here type="pupilz" is not correct as the type is either pupil or gaze. It is not asking for a column name |
So, the pupilz created should not be used as a replacement of pupil in the next steps ? That is the part I am confused about. |
You can use pupilz but in the downsample function type is suppose to be either pupil or gaze
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Subject: [External] Re: [dmirman/gazer] downsample_gaze not found (Issue #27)
So, the pupilz created should not be used as a replacement of pupil in the next steps ? That is the part I am confused about.
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Ok, I think I understand, thank you. Last question, in case I used the timbinz to create the pupilz variable, should I run the baseline_correction_pupil_msg function with pupil_colname= 'pupilz' instead of pupil_colname= 'pup_interp' ? Or does the pupilz became just a replacement for the pupil variable? , so in the code when you use pupil I should be using pupilz instead but when you are using pup_interp and baselinecorrectedp continue using those? |
In those functions, your pupilz would be changed to pup_interp in the function
for instance here whatever you specified as pupil_colname in the baseline_correction function will be changed to pupil_avg and then to pupil_interp in the function. (the pupil_interp variable created is interpolated with your z score var). You should be able to carry on without changing the defaults. |
My suggestion would be to take your pupilz column and change it to pupil and run the pipeline on that |
Thank you very much for your help and the gazeR package ! |
Hi @jgeller112 , I'm working with @vicentemunozlh. I think there are two questions in this Issue. First, regarding the use of Second, provided the application of Our question is rooted in the fact the data frame timebinz<- baseline_pupil %>%
group_by(subject,trial) %>%
mutate(pupilz = scale(baselinecorrectedp)) is correct or not. We have a similar question regarding the application of Artifact rejection through MAD since you use mad_removal<- pup_outliers %>%
group_by(subject,trial) %>%
mutate(speed = speed_pupil(baselinecorrectedp, time)) %>%
mutate(MAD=calc_mad(speed, n=16)) %>%
filter(speed < MAD) Note that we use |
First, regarding the use of type=pupilz in downsample_gaze function. We got that available types are either gaze or pupilonly. As I said, this is an argument function and not where you put your pupil variable name. This function assumes your pupil variable is called The paper assumes you have used gazeR consistent names
Call pupilz (baselinecorrectedp) so it is consistent with gazeR names and carry one with preprocessing . Note that we use time instead of time_zero in the call to speed_pupil since we believe it is a typo. Yep! Here is most up-to-date paper with corrections: https://psyarxiv.com/4qwr8/ mad_removal<- pup_outliers %>% I performed this correction on non-baseline corrected data (pup_interp). I guess it could be done on the baseline corrected pupil column as well. In the MAD pupil paper (https://d-nb.info/1167304861/34) it was done on non-baselined data. |
Hello, thanks for the great algorithm!
every other function is working great for me exept for the downsample_gaze one. The error showed in the console is the following:
Is there a reason why or am I just applying it wrong??
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