Analysis Recipes
The Prediction Registry describes events and specifies analytical parameters to document the details of the prediction. However, since most events are processed in the same way, the term standard analysis
(#1 below) is used. This refers to a definite set of steps that are presented in the procedures section, to avoid repetition for each item in the registry. For a small subset (about 5 to 10 % depending on the criteria for the standardization) some other analysis recipe is used. In these cases, sufficient detail is usually given in place. Most of these other
analyses are what we call device variance analyses
and the algorithmic recipe for these can also be given in a separate, general description (#3 below), to which we can refer in the event descriptions. Here, with some contextual discussion, are the major recipies.
As of this writing in late August, 2002, we are considering whether we should change from the correlated meanshift (standard) analysis to the device variance for the default procedure. There are good arguments for doing so, including that it may be more sensitive. In any case, we intend to apply both algorithms to all events where this is feasible, in order to learn more about the question. For an interim period, we will use the composite probability of the two measures as the formal output probability. This will, in effect give an average outcome.
Beginning in mid2002, Peter Bancel posed the question,
Without any a priori's, how many different
recipesare in the prediction registry and how do results look in subgroups?By
recipeI simply mean a precise procedure that will get me from the raw data to a stated formal GCP df and Chisquare for each event. I want to count how many of these recipes there are and count how many predictions go with each recipe. And eventually ask if effect size changes with group.
We begin to answer these questions here, by describing the analysis algorithms. This is work in progress.
Recipe #1: The Standard Analysis
 Specify a period(s) of time
 Get the raw trial counts for all the N regs for this time. If more than one time period is specified, concatenate for each reg.
 Convert the N reg data sets to zscores using mean = 100 and var = 50.
 Calc a Z for each second as Z = Sum[z]/Sqrt[N]. (Stouffer Z)
 Sum Z^2 over all seconds. Note: df = number of seconds.
 Calc an equivalent chi^2 on 600df (pvalues are identical).
 The resulting chi^2 and df=600 can be used to give a composite result for different predictions.
If there is a need to modify this recipe for a given prediction, then it's a new recipe and the prediction goes into a new group. A good, if very specialized example, is the formal prediction for event 38, which requires appropriate modification of Recipe #1 to replicate the stated GCP result. The prediction for event 38 was specified as two contiguous segments, predefined to show positive and negative expected deviations, respectively. Duplicating the analysis and the GCP bottom line
result obviously requires something extra to be added to recipe #1.
Recipe #1.5 (Follows Recipe #1 with an additional step:)
 Specify a period(s) of time
 Get the raw trial counts for all the N regs for this time. If more than one time period is specified, concatenate for each reg.
 Convert the N reg data sets to zscores using mean = 100 and var = 50.

For each period with a negativegoing prediction, invert the sign of the zscores.
(The added step.)  Calc a Z for each second as Z = Sum[z]/Sqrt[N]. (Stouffer Z)
 Sum Z^2 over all seconds. Note: df = number of seconds.
 Calc an equivalent chi^2 on 600df ( pvalues are identical).
 The resulting chi^2 and df=600 can be used to give a composite zscores.
The next recipe is for predictions that are listed as having 15minute
resolution. Steps 13 are the same as #1. Although they use the same basic measurable (a composite signed Zscore across eggs; Stouffer Z). The 15min resolution events may be considered a separate group because recipe's #1 and #2 give different results for the same identified event. In general, blocking in this way changes the outcome in proportion to the blocking size. Thus if someone wishes to reproduce the GCP results from the data they need to know the exact recipe and which events go with which recipe.
Recipe #2:
 Specify a period(s) of time
 Get the raw trial counts for all the N regs for this time. If more than one period, concatenate for each reg.
 Convert the N reg data sets to zscores using mean = 100 and var = 50.
 For each reg, form a zscore over 15 minutes (900 seconds) as : W=Sum[z]/Sqrt[900].
 Sum all W^2. Note: df = (number of 15 minute blocks)x(number of regs).
 Use Sum[W^2] and df in the composite result of all predictions.
Predictions for several events in the formal database were specified in a fundamentally different manner that examines the variability among the individual egg scores. One way to express this is as the concatenation across eggs of their squared zscores. The result is a Chisquare distributed quantity, that can be composed over the period of interest much as in Recipe #1. The formal analyses use a direct computation of the variance among the eggs (which is essentially the same measure).
Recipe #3: The Device Variance Analysis
 Specify a period(s) of time
 Get the raw trial counts for all the N regs for this time. If more than one time period is specified, concatenate for each reg.
 Calc the variance (Var) of the egg trial counts for each second.
 Cumulate the deviation of the variance from expectation [Cumsum (Var  50)] or [Cumsum (Var  eVar) where eVar is empirical expectation for Var calculated as Mean (Var)]
 Extract contiguous data for the full day surrounding the period in step 1.
 Compute probability of the maximum absolute deviation during the period, based on 10,000 random permutations of the contiguous data.