fit_mpt: Multiverse Analysis for MPT Models

Description Usage Arguments Details Value References Examples

View source: R/fit_mpt.R

Description

Performs a multiverse analysis for multinomial processing tree (MPT) models across maximum-likelihood/frequentist and Bayesian estimation approaches. For the frequentist approaches, no pooling (with and without parametric or nonparametric bootstrap) and complete pooling are implemented using MPTinR. For the Bayesian approaches, no pooling, complete pooling, and three different variants of partial pooling are implemented using TreeBUGS. Requires data on a by-participant level with each row corresponding to data from one participant (i.e., different response categories correspond to different columns) and the data can contain a single between-subjects condition. Model equations need to be passed as a .eqn model file and category labels (first column in .eqn file) need to match the column names in data. Results are returned in one tibble with one row per estimation method.

Usage

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fit_mpt(model, dataset, data, id = NULL, condition = NULL,
  core = NULL, method)

Arguments

model

A model definition, typically the path to an .eqn model file containing the model equations. Category names need to match column names in data.

dataset

scalar character vector. Name of the data set that will be copied to the results tibble.

data

A data.frame containing the data. Column names need to match category names in model (i.e., different from MPTinR behavior, order of categories is not important, matching is done via name).

id

scalar character vector. Name of the column that contains the subject identifier. If not specified, it is assumed that each row represents observations from one participant.

condition

scalar character vector. Name of the column specifying a between-subjects factor. If not specified, no between-subjects comparisons are performed.

core

character vector defining the core parameters of interest, e.g., core = c("Dn", "Do"). All other parameters are treated as auxiliary parameters.

method

character vector specifying which analysis approaches should be performed (see Description below). Defaults to all available methods.

Details

This functions is a fancy wrapper for packages MPTinR and TreeBUGS applying various frequentist and Bayesian estimation methods to the same data set using a single MPT model and collecting the results in one tibble where each row corresponds to one estimation method. Note that parameter restrictions (e.g., equating different parameters or fixing them to a constant) need to be part of the model (i.e., the .eqn file) and cannot be passed as an argument.

The settings for the various methods are specified via function mpt_options. The default settings use all available cores for calculating the boostrap distribution as well as independent MCMC chains and should be appropriate for most situations.

The data can have a single between-subjects condition (specified via condition). This condition can have more than two levels. If specified, the pairwise differences between each level, the standard error of the differences, and confidence-intervals of the differences are calculated for each parameter. Please note that condition is silently converted to character in the output. Thus, a specific ordering of the factor levels in the output cannot be guaranteed.

Parameter differences or other support for within-subject conditions is not provided. The best course of action for within-subjects conditions is to simply include separate trees and separate sets of parameters for each within-subjects condition. This allows to at least compare the estimates for each within-subjects condition across estimation method.

Implemented Methods

Maximum-likelihood estimation with MPTinR via fit.mpt:

Maximum-likelihood estimation with HMMTreeR

Bayesian estimation with TreeBUGS

Frequentist/Maximum-Likelihood Methods

For the complete pooling asymptotic approach, the group-level parameter estimates and goodness-of-fit statistics are the maximum-likelihood and G-squared values returned by MPTinR. The parameter differences are based on these values, the standard errors of the difference is simply the pooled standard error of the individual parameters. The overall fit (column gof) is based on an additional fit to the completely aggregated data.

For the no pooling asymptotic approach, the individual-level maximum-likelihood estimates are reported in column est_indiv and gof_indiv and provide the basis for the other results. Whether or not an individual-level parameter estimate is judged as identifiable (column identifiable) is based on separate fits with different random starting values. If, in these separate, fits the same objective criterion is reached several times (i.e., Log.Likelihood within .01 of best fit), but the parameter estimate differs (i.e., different estimates within .01 of each other), then an estimate is flagged as non-identifiable. If they are the same (i.e., within .01 of each other) they are marked as identifiable. The group-level parameters are simply the means of the identifiable individual-level parameters, the SE is the SE of the mean for these parameter (i.e., SD/sqrt(N), where N excludes non-identifiable parameters and thise estimated as NA), and the CI is based on mean and SE. The group-level and overall fit is the sum of the individual G-squares, sum of individual-level df, and corresponding chi-square df. The difference between the conditions and corresponding statistics are based on a t-test comparing the individual-level estimates (again, after excluding non-identifiable estimates). The CIs of the difference are based on the SEs (which are derived from a linear model equivalent to the t-test).

The individual-level estimates of the bootstrap based no-pooling approaches are identical to the asymptotic ones. However, the SE is the SD of the bootstrapped distribution of parameter estimates, the CIs are the corresponding quantiles of the bootstrapped distribution, and the p-value is obtained from the bootstrapped G-square distribution. Identifiability of individual-level parameter estimates is also based on the bootstrap distribution of estimates. Specifically, we calculate the range of the CI (i.e., maximum minus minimum CI value) and flag those parameters as non-identifiable for which the range is larger than mpt_options()$max_ci_indiv, which defaults to 0.99. Thus, in the default settings we say a parameter is non-identifiable if the bootstrap based CI extends from 0 to 1. The group-level estimates are the mean of the identifiable individual-level estimates. And difference between conditions is calculated in the same manner as for the asymptotic case using the identifiable individual-level parameter esatimates.

Latent-class approach

The latent-class approach is fitted by interfacing HMMTree, a software package that is only available on Microsoft Windows Machines. To install this software and the necessary R interface, use devtools::install_github("methexp/HMMTreeR"). It is currently not possible to estimate models that contain parameters that are fixed to numerical values. Multiple latent-class models with differing number of latent classes are estimated. The model that obtains the lowest AIC while still being identified is selected for extracting parameter estimates The returned group-level parameter estimates are calculated as the weighted mean of parameter estimates of latent classes. Corresponding SEs are given by the square root of the weighted mean of class-wise squared SEs. Goodness-of-fit statistics are M1, M2, S1, and S2 as described by Klauer(2006).

Bayesian Methods

The simple approaches fit fixed-effects MPT models. "simple" uses no pooling and thus assumes independent uniform priors for the individual-level parameters. Group-level means are obtained as generated quantities by averaging the posterior samples across participants. "simple_pooling" aggregates observed frequencies across participants and assumes a uniform prior for the group-level parameters.

The latent-trait approaches transform the individual-level parameters to a latent probit scale using the inverse cumulative standard normal distribution. For these probit values, a multivariate normal distribution is assumed at the group level. Whereas "trait" estimates the corresponding correlation matrix of the parameters (reported in the column est_rho), "trait_uncorrelated" assumes that the parameters are uncorrelated.

For all Bayesian methods, the posterior distribution of the parameters is summarized by the posterior mean (in the column est), posterior standard deviation (se), and credbility intervals (ci_*). For parameter differences (test_between) and correlations (est_rho), Bayesian p-values are computed (column p) by counting the relative proportion of posterior samples that are smaller than zero. Goodness of fit is tested with the T1 statistic (observed vs. posterior-predicted average frequencies, focus = "mean") and the T2 statistic (observed vs. posterior-predicted covariance of frequencies, focus = "cov").

Value

A tibble with one row per estimation method and the following columns:

  1. model: Name of model file (copied from model argument), character

  2. dataset: Name of data set (copied from dataset argument), character

  3. pooling: character specifying the level of pooling with three potential values: c("complete", "no", "partial")

  4. package: character specifying the package used for estimation with two potential values: c("MPTinR", "TreeBUGS")

  5. method: character specifying the method used with the following potential values: c("asymptotic", "PB/MLE", "NPB/MLE", "simple", "trait", "trait_uncorrelated", "beta", "betacpp")

  6. est_group: Group-level parameter estimates per condition/group.

  7. est_indiv: Individual-level parameter estimates (if provided by method).

  8. est_rho: Estimated correlation of individual-level parameters on the probit scale (only in method="trait").

  9. test_between: Parameter differences between the levels of the between-subjects condition (if specified).

  10. gof: Overall goodness of fit across all individuals.

  11. gof_group: Group-level goodness of fit.

  12. gof_indiv: Individual-level goodness of fit.

  13. fungibility: Posterior correlation of the group-level means pnorm(mu) (only in method="trait").

  14. test_homogeneity: Chi-square based test of participant homogeneity proposed by Smith and Batchelder (2008). This test is the same for each estimation method.

  15. convergence: Convergence information provided by the respective estimation method. For the asymptotic frequentist methods this is a tibble with rank of the Fisher matrix, the number of parameters (which should match the rank of the Fisgher matrix), and the convergence code provided by the optimization algorithm (which is nlminb). The boostrap methods contain an additional column, parameter, that contains the information which (if any) parameters are empirically non-identifiable based on the bootstrapped distribution of parameter estimates (see above for exact description). For the Bayesian methods this is a tibble containing information of the posterior dsitribution (i.e., mean, quantiles, SD, SE, n.eff, and R-hat) for each parameter.

  16. estimation: Time it took for each estimation method and group.

  17. options: Options used for estimation. Obtained by running mpt_options()

With the exception of the first five columns (i.e., after method) all columns are list columns typically holding one tibble per cell. The simplest way to analyze the results is separately per column using unnest. Examples for this are given below.

References

Smith, J. B., & Batchelder, W. H. (2008). Assessing individual differences in categorical data. Psychonomic Bulletin & Review, 15(4), 713-731. https://doi.org/10.3758/PBR.15.4.713

Klauer, K.C. (2006). Hierarchical multinomial processing tree models: A latent-class approach. Psychometrika, 71 (1), 7-31. https://doi.org/10.1007/s11336-004-1188-3

Examples

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# ------------------------------------------------------------------------------
# MPT model definition & Data

EQN_FILE <- system.file("extdata", "prospective_memory.eqn", package = "MPTmultiverse")
DATA_FILE <- system.file("extdata", "smith_et_al_2011.csv", package = "MPTmultiverse")

### if .csv format uses semicolons ";" (e.g., German format):
# data <- read.csv2(DATA_FILE, fileEncoding = "UTF-8-BOM")
### if .csv format uses commata "," (international format):
data <- read.csv(DATA_FILE, fileEncoding = "UTF-8-BOM")
data <- data[c(1:10, 113:122),]  ## select only subset of data for example
head(data)

COL_CONDITION <- "WM_EX"  # name of the variable encoding group membership

# experimental condition should be labeled meaningfully ----
unique(data[[COL_CONDITION]])

data[[COL_CONDITION]] <- factor(
  data[[COL_CONDITION]]
  , levels = 1:2
  , labels = c("low_WM", "high_WM")
)

# define core parameters:
CORE <- c("C1", "C2")

## Not run: 
op <- mpt_options() 
## to reset default options (which you would want) use:
mpt_options("default")

mpt_options() # to see the settings 
## Note: settings are also saved in the results tibble
  
## without specifying method, all are used per default
fit_all <- fit_mpt(
  dataset = DATA_FILE
  , data = data
  , model = EQN_FILE
  , condition = COL_CONDITION
  , core = CORE
)

mpt_options(op) ## reset options  

## End(Not run)

load(system.file("extdata", "prospective_memory_example.rda", package = "MPTmultiverse"))

# Although we requested all 10 methods, only 9 worked:
fit_all$method
# Jags variant of beta MPT is missing.

# the returned method has a plot method. For example, for the group-level estimates:
plot(fit_all, which = "est")

## Not run: 
### Full analysis of results requires dplyr and tidyr (or just 'tidyverse')
library("dplyr")
library("tidyr")

## first few columns identify model, data, and estimation approach/method
## remaining columns are list columns containing the results for each method
## use unnest to work with each of the results columns
glimpse(fit_all) 

## Let us inspect the group-level estimates
fit_all %>% 
  select(method, pooling, est_group) %>% 
  unnest() 

## which we can plot again
plot(fit_all, which = "est")

## Next we take a look at the GoF
fit_all %>% 
  select(method, pooling, gof_group) %>% 
  unnest() %>% 
  as.data.frame()

# Again, we can plot it as well
plot(fit_all, which = "gof2")  ## use "gof1" for overall GoF

## Finally, we take a look at the differences between conditions
fit_all %>% 
  select(method, pooling, test_between) %>% 
  unnest() 

# and then we plot it
plot(fit_all, which = "test_between")


### Also possible to only use individual methods:
only_asymptotic <- fit_mpt(
  method = "asymptotic_no"
  , dataset = DATA_FILE
  , data = data
  , model = EQN_FILE
  , condition = COL_CONDITION
  , core = CORE
)

glimpse(only_asymptotic)

bayes_complete <- fit_mpt(
  method = c("simple_pooling")
  , dataset = DATA_FILE
  , data = data
  , model = EQN_FILE
  , condition = COL_CONDITION
  , core = CORE
)
glimpse(bayes_complete)


## End(Not run)

mpt-network/hmpt documentation built on Jan. 6, 2019, 2:06 a.m.