[1] "Got NaN as a result of calling pnorm with: 1.5 -0.227865514090563 -4.05e-05" Why is pnorm being called with a negative sigma?? Happens on line 51 or likelihood.R Need to find what is setting sigma to negative value.
Create simplest possible vignette, to analyze just one condition. Basically filter data and then call analyzeOneCondition
Does the namespace for annotate() , ggplot2::annotate somehow get screwed up so you have to specify ggplot2::annotate?
#knowing the grouping variable for the facets #how do I keep one x from each condition? This is basically like stat_summary #See https://stackoverflow.com/questions/15720545/use-stat-summary-to-annotate-plot-with-number-of-observations
#No, unfortunately stat_summary only gets the numbers, this is the way to do it https://stackoverflow.com/a/46791112/302378 Have to create separate dataset and geom_text call to add the annotations
Add set.seed(1) # Reproducibility to everything
Add inferential stats to analyze_experiment.Rmd vignette
Pesky fitting errors. Error in grad.default(ufn, ans$par, ...) : function returns NA at 1.4434927002511e-050.000135401581392880.000100001 distance from x. I have started a test to investigate this in test-fit_model.R
Add for the nReplicates parameter roxygen a link to the notes on how many fits are needed for stability
add a link somewhere, somehow to BackwardsLtrs (Google Drive) E2/compareMATLABtoR.html
For comparing models, for the AB case of having two episodes, Pat used Bayesian Information Criteria (BIC) for the single- and dual-episode models, based on the combined T1 and T2 distribution, to determine when there is evidence of a second attentional episode. in AB_compare_models.m
For comparing guessing only to mixture, Pat did:
% % Test for a significant difference in log likelihoods % [h,pValue,stat,cValue] = lratiotest(-minNegLogLikelihood,-uniformNegLogLikelihood,nFreeParameters,pCrit);
The mixture model has 3 degrees of freedom I think (e, u, sigma) and the guessing distrbiutino zero.
Use RStudio->Build->Test or
Damn you can't see the vignettes unless you install the proper package from tgz etc or https://stackoverflow.com/questions/33614660/knitr-rmd-vignettes-do-not-appear-with-vignette?rq=1
This can be investigated in test_analyzeOneCondition's test "can combine results of analyzeOneConditionDf into dataframe"
analyzeOneConditionDF turned warnings into a string.
warnings
can't be converted from character to list. Fixedinside calc_curves_dataframe in test-calc_curves_dataframe
in bind_rows_(x, .id) :
Column warnings
can't be converted from character to list
Still getting this error e.g. in inspectHistograms.Rmd in jackie project. Do I have the latest version? Because what is the relationship to the message given by analyze_experiment.Rmd: " Unequal factor levels: coercing to characterbinding ". I dimly remember that "binding character and factor vector, coercing into character vector"
"call" in simplewarning sometimes has two fucking parts!
For a long time the vignettes were lost no matter which RStudio build thing I ran. Until I did devtools::build_vignettes() devtools::load_all(".")
Then I build source package in case that's needed to install from GitHub, but it doesn't work. Turns out a further complication is that build_vignettes is no longer an option in install_github, instead you have to do: devtools::install_github('alexholcombe/mixRSVP', build = TRUE, build_opts = c("--no-resave-data", "--no-manual")) This does not include the option of not building the vignettes, so it results in building the vignettes.
For adding an image for a vignette, it should also be in the vignette source directory
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