The package allows for only limited models as, e.g., neither random slopes, nor interaction effects are allowed. Imposing this restriction was a design decision, as it would require duplicating functionality of general purposes packages. Instead, the package itself provides some basic fitting that should be sufficient for most simple cases. However, below you will find example of how to incorporate cumulative history into a model written in Stan. This way, you can achieve maximal flexibility but still save time by reusing the code.
This is a complete Stan code for a model with log-normal distribution
for multiple runs from a single experimental session of a single
participant. The history time-constant tau is fitted,
whereas constants are used for other cumulative history parameters.
data{
// --- Complete time-series ---
int<lower=1> rowsN; // Number of rows in the COMPLETE multi-timeseries table including mixed phase.
real duration[rowsN]; // Duration of a dominance/transition phase
int istate[rowsN]; // Index of a dominance istate, 1 and 2 code for two competing clear states, 3 - transition/mixed.
int is_used[rowsN]; // Whether history value must used to predict duration or ignored
// (mixed phases, warm-up period, last, etc.)
int run_start[rowsN]; // 1 marks a beginning of the new time-series (run/block/etc.)
real session_tmean[rowsN]; // Mean dominance phase duration for both CLEAR percepts. Used to scale time-constant.
// --- A shorter clear-states only time-series ---
int clearN; // Number of rows in the clear-states only time-series
real clear_duration[clearN]; // Duration for clear percepts only.
// --- Cumulative history parameters
real<lower=0, upper=1> history_starting_values[2]; // Starting values for cumulative history at the beginning of the run
real<lower=0, upper=1> mixed_state; // Mixed state signal strength
}
parameters {
real<lower=0> tau; // history time-constant
// linear model for mu
real a;
real bH;
// variance
real<lower=0> sigma;
}
transformed parameters{
vector[clearN] mu; // vector of computed mu for each clear percept
{
// temporary variables
real current_history[2]; // current computed history
real tau_H; // tau in the units of time
real dH; // computed history difference
int iC = 1; // Index of clear percepts used for fitting
// matrix with signal levels
matrix[2, 3] level = [[1, 0, mixed_state],
[0, 1, mixed_state]];
for(iT in 1:rowsN){
// new time-series, recompute absolute tau and reset history state
if (run_start[iT]){
// reset history
current_history = history_starting_values;
// Recompute tau in units of time.
// This is relevant only for multiple sessions / participants.
// However, we left this code for generality.
tau_H = session_tmean[iT] * tau;
}
// for valid percepts, we use history to compute mu
if (is_used[iT] == 1){
// history difference
dH = current_history[3-istate[iT]] - current_history[istate[iT]];
// linear model for mu
mu[iC] = a + bH * dH;
iC += 1;
}
// computing history for the NEXT episode
// see vignette on cumulative history
for(iState in 1:2){
current_history[iState] = level[iState, istate[iT]] +
(current_history[iState] - level[iState, istate[iT]]) * exp(-duration[iT] / tau_H);
}
}
}
}
model{
// sampling individual parameters
tau ~ lognormal(log(1), 0.75);
a ~ normal(log(3), 5);
bH ~ normal(0, 1);
sigma ~ exponential(1);
// sampling data using computed mu and sampled sigma
clear_duration ~ lognormal(exp(mu), sigma);
}The data section defines model inputs. Hopefully, the
comments make understanding it fairly straightforward. However, it has
several features that although are not needed for the limited single
session / single session make it easier to generalized the code for more
complicated cases.
For example, not all dominance phases are used for fitting.
Specifically, all mixed perception phases, first dominance phase for
each percept (not enough time to form reliably history) and last
dominance phase (curtailed by the end of the block) are excluded. Valid
dominance phases are marked in is_used vector. Their total
number is stored in clearN variable and the actual
dominance durations in clear_duration. The latter is not
strictly necessary but allows us to avoid a loop and vectorize the
sampling statement
clear_duration ~ lognormal(exp(mu), sigma);.
In addition, session_tmean is a vector rather than a
scalar. This is not necessary for a single session example here but we
opted to use as it will better generalize for more complicated
cases.
bistability package provides a service function
preprocess_data() that simplifies the process of preparing
the data. However, you need to perform the last step, forming a list of
inputs for Stan sampling, yourself.
# function that checks data for internal consistency and returns a preprocessed table
df <- bistablehistory::preprocess_data(br_single_subject,
state="State",
duration="Duration",
run="Block")
# data for Stan model
stan_data <- list(
# complete time-series
rowsN = nrow(df),
duration = df$duration,
istate = df$istate,
is_used = df$is_used,
run_start = df$run_start,
session_tmean = df$session_tmean,
# only valid clear percepts
clearN = sum(df$is_used),
clear_duration = df$duration[df$is_used == 1],
# history parameters, all fixed to default values
history_starting_values = c(0, 0),
mixed_state = 0.5
)You can use this model either with rstan or
cmdstanr packages. Below is in an example using
cmdstanr, assuming that model file is called
example.stan.