GitHub - crowding/thesis: A "reproducible" R/stan/knitr dissertation.

To run through fitting these models and creating graphs, do:

unpack fitAll plotFits makeDiagnostics

Name		Name	Last commit message	Last commit date
comments		comments
discussion-outline.oo3		discussion-outline.oo3
energy		energy
model.graffle		model.graffle
monk @ 2e2ede4		monk @ 2e2ede4
notes		notes
numdensity-stimulus.graffle		numdensity-stimulus.graffle
odd_writing		odd_writing
presentation		presentation
staircase		staircase
static_html		static_html
stimuli-direction-content-white.graffle		stimuli-direction-content-white.graffle
stimuli-direction-content.graffle		stimuli-direction-content.graffle
stimuli-envelope-white.graffle		stimuli-envelope-white.graffle
.gitattributes		.gitattributes
.gitignore		.gitignore
.gitmodules		.gitmodules
CenterSurroundModel.sten_disabled.R		CenterSurroundModel.sten_disabled.R
CompareStanFits.R		CompareStanFits.R
DiagnoseBadCalc.R		DiagnoseBadCalc.R
Endpoints.stan.R		Endpoints.stan.R
FitPlots.R		FitPlots.R
Hemifield.stan.R		Hemifield.stan.R
Makefile		Makefile
Mather1985Stimulus.pdf		Mather1985Stimulus.pdf
Monkfile		Monkfile
MotionEnergyLinear.stan.R		MotionEnergyLinear.stan.R
MotionEnergyRepulsion.stan.R		MotionEnergyRepulsion.stan.R
MotionEnergySoftMin.stan.R		MotionEnergySoftMin.stan.R
NineModels.R		NineModels.R
OnlyMotionEnergy.stan.R		OnlyMotionEnergy.stan.R
OnlyOpponentMotion.stan.R		OnlyOpponentMotion.stan.R
ProportionalMotionEnergy.stan.R		ProportionalMotionEnergy.stan.R
README.md		README.md
README_data.md		README_data.md
SlopeModel.stan.R		SlopeModel.stan.R
SoftMinModel.stan.R		SoftMinModel.stan.R
StanModel.R		StanModel.R
SummationField.stan.R		SummationField.stan.R
VectorizedSlopeModel.stan.R		VectorizedSlopeModel.stan.R
ZankerSmall.pdf		ZankerSmall.pdf
_master.lyx		_master.lyx
_master_preamble.tex		_master_preamble.tex
_part1.tex		_part1.tex
_preamble.tex		_preamble.tex
abstract.lyx		abstract.lyx
apalike-doi.bst		apalike-doi.bst
bibliography.bib		bibliography.bib
bicontrast_series_trials.csv		bicontrast_series_trials.csv
chapter		chapter
cheatsheet.graffle		cheatsheet.graffle
check_predictions.R		check_predictions.R
cleanup		cleanup
collect_times.R		collect_times.R
colors.R		colors.R
combined.model.R		combined.model.R
compareLogProbs.R		compareLogProbs.R
compileStan.R		compileStan.R
content-bias.ograph		content-bias.ograph
content-bias.pdf		content-bias.pdf
content-narrow.ograph		content-narrow.ograph
content-narrow.pdf		content-narrow.pdf
content-sensitivity.ograph		content-sensitivity.ograph
content-sensitivity.pdf		content-sensitivity.pdf
content-wide.ograph		content-wide.ograph
content-wide.pdf		content-wide.pdf
content_series_calculations.csv		content_series_calculations.csv
content_series_trials.csv		content_series_trials.csv
contours.R		contours.R
contours.md		contours.md
custom.css		custom.css
cuts.lyx		cuts.lyx
data.RData		data.RData
dataset_wtf.md		dataset_wtf.md
demo_carenv.mov		demo_carenv.mov
demo_carenv.png		demo_carenv.png
demo_circle_16.mov		demo_circle_16.mov
demo_circle_16.png		demo_circle_16.png
demo_circle_22.mov		demo_circle_22.mov
demo_circle_22.png		demo_circle_22.png
demo_circle_6.mov		demo_circle_6.mov
demo_circle_6.png		demo_circle_6.png
demo_circles.mov		demo_circles.mov
demo_circles.png		demo_circles.png
demo_counter.mov		demo_counter.mov
demo_counter.png		demo_counter.png
demo_eyemovements.mov		demo_eyemovements.mov
demo_eyemovements.png		demo_eyemovements.png
demo_segment.mov		demo_segment.mov
demo_segment.png		demo_segment.png
demo_single.mov		demo_single.mov
demo_single.png		demo_single.png
demo_stimuli.mov		demo_stimuli.mov
demo_stimuli.png		demo_stimuli.png
demos.lyx		demos.lyx
density.calibration.R		density.calibration.R
density.lyx		density.lyx
density.modeling.R		density.modeling.R
density.rawplot.R		density.rawplot.R
density_library.R		density_library.R

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