# Introduction to RprobitB In RprobitB: Bayes Estimation of Latent Class Mixed Multinomial Probit Models

knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )  library(RprobitB)  RprobitB is an R package that can be used to fit latent class mixed multinomial probit (LCMMNP) models to simulated or empirical data. RprobitB is licensed under the GNU General Public License v3.0. Do you found a bug or request a feature? Please tell us! The package name RprobitB is a portmanteau, combining R (the programming language), probit (the model name) and B (for Bayes, the estimation method). RprobitB is able to • estimate probit models on discrete choice panel data, • approximate any underlying mixing distributions through a mixture of normal distributions, • update the number of latent classes within the algorithm on a weight-based strategy, • perform estimation in a Bayesian framework via Gibbs sampling, thereby avoiding numerical maximization or approximation of the model's likelihood. At this point, you may ask yourself: ## Installing RprobitB To install the latest version of RprobitB, run install.packages("RprobitB") in your R console. ## Using RprobitB To use RprobitB, follow these steps: 1. Specify the model, see below for details. 2. Run RprobitB::rpb(<list of model specifications>). 3. You get on-screen information and model results in an output folder. ## LCMMNP model Assume that we observe the choices of$N$decision makers which decide between$J$alternatives at each of$T$choice occasions.[^1] Specific to each decision maker, alternative and choice occasion, we furthermore observe$P_f+P_r$choice attributes that we use to explain the choices. The first$P_f$attributes are connected to fixed coefficients, the other$P_r$attributes to random coefficients following a joint distribution mixed across decision makers. Person$n$'s utility$\tilde{U}{ntj}$for alternative$j$at choice occasion$t$is modelled as \tilde{U}{ntj} = \tilde{W}{ntj}'\alpha + \tilde{X}{ntj}'\beta_n + \tilde{\epsilon}_{ntj} for$n=1,\dots,N$,$t=1,\dots,T$and$j=1,\dots,J$, where •$\tilde{W}_{ntj}$is a vector of$P_f$characteristics of$j$as faced by$n$at$t$corresponding to the fixed coefficient vector$\alpha \in {\mathbb R}^{P_f}$, •$\tilde{X}{ntj}$is a vector of$P_r$characteristics of$j$as faced by$n$at$t$corresponding to the random, decision maker-specific coefficient vector$\beta_n \in {\mathbb R}^{P_r}$, where$\beta_n$is distributed according to some$P_r$-variate distribution$g{P_r}$, • and$(\tilde{\epsilon}{nt:}) = (\tilde{\epsilon}{nt1},\dots,\tilde{\epsilon}{ntJ})' \sim \text{MVN}{J} (0,\tilde{\Sigma})$is the models' error term vector for$n$at$t$, which in the probit model is assumed to be multivariate normally distributed with zero mean and covariance matrix$\tilde{\Sigma}$. As is well known, any utility model needs to be normalized with respect to level and scale in order to be identified. Therefore, we consider the transformed model $$U_{ntj} = W_{ntj}'\alpha + X_{ntj}'\beta_n + \epsilon_{ntj},$$$n=1,\dots,N$,$t=1,\dots,T$and$j=1,\dots,J-1$, where (choosing$J$as the reference alternative)$U_{ntj}=\tilde{U}{ntj} - \tilde{U}{ntJ}$,$W_{ntj}=\tilde{W}{ntj}-\tilde{W}{ntJ}$,$X_{ntj}=\tilde{X}{ntj}-\tilde{X}{ntJ}$and$\epsilon_{ntj}=\tilde{\epsilon}{ntj}-\tilde{\epsilon}{ntJ}$, where$(\epsilon_{nt:}) = (\epsilon_{nt1},...,\epsilon_{nt(J-1)})' \sim \text{MVN}_{J-1} (0,\Sigma)$and$\Sigma$denotes a covariance matrix with the top-left element restricted to one. While taking utility differences in order to normalize the model with respect to level is a standard procedure, alternatives to fixing an error term variance in order to normalize with respect to scale exist, for example fixing an element of$\alpha$. Let$y_{nt}=j$denote the event that decision maker$n$chooses alternative$j$at choice occasion$t$. Assuming utility maximizing behaviour of the decision makers, the decisions are linked to the utilities via $$y_{nt} = \sum_{j=1}^{J-1} j\cdot 1 \left (U_{ntj}=\max_i U_{nti}>0 \right) + J \cdot 1\left (U_{ntj}<0 ~\text{for all}~j\right),$$ where$1(A)$equals$1$if condition$A$is true and$0$else. We approximate the mixing distribution$g_{P_r}$for the random coefficients\footnote{Here and below we use the abbreviation$(\beta_n)n$as a shortcut to$(\beta_n){n =1,...,N}$the collection of vectors$\beta_n,n=1,...,N$.}$\beta=(\beta_n){n}$by a mixture of$P_r$-variate normal densities$\phi{P_r}$with mean vectors$b=(b_c){c}$and covariance matrices$\Omega=(\Omega_c){c}$using$C$components, i.e. $$\beta_n\mid b,\Omega \sim \sum_{c=1}^{C} s_c \phi_{P_r} (\cdot \mid b_c,\Omega_c),$$ where$(s_c){c}$are weights satisfying$0 < s_c\leq 1$for$c=1,\dots,C$and$\sum_c s_c=1$. One interpretation of the latent class model is obtained by introducing variables$z=(z_n)_n$allocating each decision maker$n$to class$c$with probability$s_c$, i.e. \text{Prob}(z_n=c)=s_c \quad \text{and} \quad \beta_n \mid z,b,\Omega \sim \phi{P_r}(\cdot \mid b_{z_n},\Omega_{z_n}). We call this model the latent class mixed multinomial probit (LCMMNP) model.[^2] [^1]: For notational simplicity, the number of choice occasions$T$is assumend to be the same for each decision maker here. However, RprobitB allows for a different number of choice occasions for each decision maker. [^2]: We note that the model collapses to the (normally) mixed multinomial probit model if$P_r>0$and$C=1$and to the basic multinomial probit model if$P_r=0$. ## Latent class updating scheme Updating the number$C$of latent classes is done within the algorithm by executing the following weight-based updating scheme. • Class$c$is removed, if$s_c<\epsilon_{\text{min}}$, i.e. if the class weight$s_c$drops below some threshold$\epsilon_{\text{min}}$. This case indicates that class$c$has a negligible impact on the mixing distribution. • Class$c$is splitted into two classes$c_1$and$c_2$, if$s_c>\epsilon_\text{max}$. This case indicates that class$c$has a high influence on the mixing distribution whose approximation can potentially be improved by increasing the resolution in directions of high variance. Therefore, the class means$b_{c_1}$and$b_{c_2}$of the new classes$c_1$and$c_2$are shifted in opposite directions from the class mean$b_c$of the old class$c$in the direction of the highest variance. • Two classes$c_1$and$c_2$are joined to one class$c$, if$\lVert b_{c_1} - b_{c_2} \rVert<\epsilon_{\text{distmin}}$, i.e. if the euclidean distance between the class means$b_{c_1}$and$b_{c_2}$drops below some threshold$\epsilon_{\text{distmin}}$. This case indicates location redundancy which should be repealed. The parameters of$c$are assigned by adding the values of$s$from$c_1$and$c_2$and averaging the values for$b$and$\Omega$. ## Specifying a LCMMNP model in RprobitB RprobitB specifications are grouped in the named lists • model (model information), • data (data information), • parm (true parameter values), • lcus (latent class updating scheme parameters), • init (initial values for the Gibbs sampler), • prior (prior parameters), • mcmc (Markov chain Monte Carlo parameters), • norm (normalization information), • out (output settings). You can either specify none, all, or selected parameters. Unspecified parameters are set to default values. ### model • N, the number (greater or equal one) of decision makers • T, the number (greater or equal one) or vector (of length N) of choice occasions for each decision maker • J, the number (greater or equal two) of choice alternatives (fixed across decision makers and choice occasions) • P_f, the number of attributes that are connected to fixed coefficients (can be zero) • P_r, the number of attributes that are connected to random, decision maker specific coefficients (can be zero) • C, the number of latent classes (ignored if P_r = 0) ### data If data = NULL, data is simulated from the model defined by model and parm. To model empirical data, specify • data_raw, the data frame of choice data in wide format[^3], must contain columns named "id" (unique identifier for each decision maker) and "choice" (the chosen alternatives) • cov_col, a numeric vector specifying the columns of data_raw with covariates • cov_ord, a character vector specifying the order of the covariates, where fixed-coefficient covariates come first (required for specifying random coefficients and interpretation of the model results) • cov_zst, a boolean determining whether covariates get z-standardized [^3]: The wide data format presents each different covariate in a separate column. See the vignette of the mlogit package for an example. ### parm • alpha, the fixed coefficient vector (of length model[["P_f"]]) • s, the vector of class weights (of length model[["C"]]) • b, the matrix of class means as columns (of dimension model[["P_r"]] x model[["C"]]) • Omega, the matrix of class covariance matrices as columns (of dimension model[["P_r"]]*model[["P_r"]] x model[["C"]]) • Sigma, the error term covariance matrix (of dimension model[["J"]]-1 x model[["J"]]-1) ### lcus • do_lcus, a boolean determining whether to update the number of latent classes • C0, the initial number of latent classes • Cmax, the maximal number of latent classes (greater or equal lcus[["C0"]]) • buffer, the buffer for the updating (number of iterations to wait before the next update) • epsmin, the threshold weight for removing latent classes (between 0 and 1) • epsmax, the threshold weight for splitting latent classes (between 0 and 1) • distmin, the threshold for joining latent classes (greater 0) ### init • at_true, a boolean determining whether to initialize at the true parameter values (only for simulated data) • alpha0, the initial fixed coefficient vector (of length model[["P_f"]]) • b0, the initial matrix of the class means as columns (of dimension model[["P_r"]] x model[["C"]]) • Omega0, the inital matrix of the class covariance matrices as columns (of dimension model[["P_r"]]*model[["P_r"]] x model[["C"]]) • Sigma0, the initial error term covariance matrix (of dimension model[["J"]]-1 x model[["J"]]-1) • U0, the initial matrix of utilities (of dimension model[["J"]]-1 x model[["N"]]*max(model[["T"]])) • beta0, the initial matrix of random coefficients (of dimension model[["P_r"]] x model[["N"]]) • m0, the initial vector of class sizes (of length model[["C"]]) ### prior A priori, parm[["alpha"]] ~ Normal(eta,Psi) with • eta, the expectation vector (of length model[["P_f"]]) • Psi, the covariance matrix (of dimension model[["P_f"]] x model[["P_f"]]) A priori, parm[["s"]] ~ Dirichlet(delta) with • delta, the concentration parameter (of length 1) A priori, parm[["b"]][,c] ~ Normal(xi,D) with • xi, the expectation vector (of length model[["P_r"]]) • D, the covariance matrix (of dimension model[["P_r"]] x model[["P_r"]]) A priori, matrix(parm[["Omega"]][,c],nrow=model[["P_r"]],ncol=model[["P_r"]]) ~ Inverse_Wishart(nu,Theta) with • nu, the degrees of freedom (greater than model[["P_r"]]) • Theta, the scale matrix (of dimension model[["P_r"]] x model[["P_r"]]) A priori, parm[["Sigma"]] ~ Inverse_Wishart(kappa,E) with • kappa, the degrees of freedom (greater than model[["J"]]-1) • E, the scale matrix (of dimension model[["J"]]-1 x model[["J"]]-1) ### mcmc • R: the number of iterations • B: the length of the burn-in period • Q: the thinning parameter • nprint: the step number for printing the sampling progress ### norm RprobitB automatically normalizes with respect to level by computing utility differences, where model[["J"]] is the base alternative. The normalization with respect to scale can be specified: • parameter: the normalized parameter (either "a" for a fixed non-random linear coefficient or "s" for an error-term variance) • index: the index of the parameter (between 1 and model[["P_f"]] or 1 and model[["J"]]-1, respectively) • value: the value for the fixed parameter (greater 0 if parameter = "s") ### out • id: a character, identifying the model • rdir: a character, defining the (relative) path of the folder with the model results • pp: a boolean, determining whether progress plots should be created (in any case only if model$P_r=2)
• results: a boolean, determining whether estimated parameters should be returned by the function rpb.
• waic: a boolean, determining whether to compute the widely applicable information criterion (WAIC)

## Default specifications of RprobitB

### model

• N = 100
• T = 10
• J = 2
• P_f = 1
• P_r = 0
• C = NA

### data

NULL

### parm

Per default, parameters are randomly drawn.

### lcus

• do_lcus = FALSE
• C0 = 5
• Cmax = 10
• buffer = 100
• epsmin = 0.01
• epsmax = 0.99
• distmin = 0.1

### init

• at_true = FALSE
• alpha0: zero vector
• b0: zero matrices for each latent class
• Omega0: unity matrices for each latent class
• Sigma0: unity matrix
• U0: zero matrix
• beta0: zero matrix
• m0: each latent class has twice the membership than the previous one

### prior

• eta = numeric(model[["P_f"]])
• Psi = matrix(1,model[["P_f"]],model[["P_f"]]); diag(Psi) = 5
• delta = 1
• xi = numeric(model[["P_r"]])
• D = matrix(1,model[["P_r"]],model[["P_r"]]); diag(D) = 5
• nu = model[["P_r"]]+2
• Theta = matrix(1,model[["P_r"]],model[["P_r"]]); diag(Theta) = 5
• kappa = model[["J"]]+1
• E = matrix(1,model[["J"]]-1,model[["J"]]-1); diag(E) = 5

### mcmc

• R = 10000
• B = R/2
• Q = 100
• nprint = floor(R/10)

### norm

• parameter = "s"
• index = "1"
• value = "1"

### out

• id = test
• rdir = tempdir()
• pp = FALSE
• return = FALSE
• waic = FALSE

## Example: Simulated data

The code below fits a mixed multinomial probit model with

• P_f = 1 fixed
• and P_r = 2 random coefficients

to simulated data with

• N = 100 decision makers,
• variable choice occasions between T = 10 and T = 20,
• J = 3 choice alternatives,
• and C = 2 true latent classes.

The number of latent classes is updated, because do_lcus = TRUE is set. The Gibbs sampler draws R = 20000 samples. By default, the model is named id = "test" and results are saved in rdir = "tempdir()" (the path of the per-session temporary directory).

set.seed(1)

### model specification
model = list("N" = 100, "T" = sample(10:20,100,replace=TRUE), "J" = 3, "P_f" = 1, "P_r" = 2, "C" = 2)
lcus  = list("do_lcus" = TRUE)
mcmc  = list("R" = 20000)

### start estimation (about 3 minutes computation time)
RprobitB::rpb("model" = model, "lcus" = lcus, "mcmc" = mcmc)


## Example: Empirical data

The code below fits a mixed multinomial probit model with P_f = 2 fixed and P_r = 2 random coefficients to the "Train" dataset of the mlogit package with

• covariates in the columns "cov_col" = 4:11,
• "price" and "comfort" linked to fixed and "time" and "change" linked to random coefficients via "cov_ord" = c("price","comfort","time","change") (remember that fixed coefficients come first),
• and z-standardized covariates ("cov_zst" = TRUE).

For normalization, the price coefficient ("parameter" = "a", "index" = 1) is fixed to "value" = -1.

### load Train data
data("Train", package = "mlogit")

### model specification
model = list("P_f" = 2, "P_r" = 2)
data  = list("data_raw" = Train, "cov_col" = 4:11, "cov_ord" = c("price","comfort","time","change"), "cov_zst" = TRUE)
lcus  = list("do_lcus" = TRUE)
mcmc  = list("R" = 1e5)
norm  = list("parameter" = "a", "index" = 1, "value" = -1)
out   = list("id" = "train", "pp" = TRUE)

### start estimation (about 20 minutes computation time)
RprobitB::rpb("model" = model, "data" = data, "lcus" = lcus, "mcmc" = mcmc, "norm" = norm, "out" = out)


## On-screen information

During estimation, you get the following on-screen information:

• a summary of the model, normalization, and Gibbs sampler settings, and (if lcus[["do_lcus"]]=TRUE) the latent class updating scheme parameters
• the sampling progress with expected time for completion (ETA)
• a summary of the posterior distribution (where x. denotes latent class number x in case of lcus[["do_lcus"]]=TRUE) with
• the true parameter values (only for simulated data)
• the posterior mean
• the posterior standard deviation
• the 5% and 95% quantile of the posterior
• the Gelman-Rubin statistic (R^)
• the model's WAIC value (if out[["waic"]]=TRUE)
• the path to the model results

## Model results

In the output folder out[["rdir"]]/out[["id"]], you can find the files

• protocol.txt, a copy of the on-screen information,
• several .rds-files of inputs and outputs,
• and different model visualizations:
• acf.pdf, the autocorrelation of the Gibbs samples with the effective sample size,
• marginal.pdf, estimated marginal distributions,
• trace.pdf, plots of the traces of the Gibbs samples,
• and, if model[["P_r"]] > 0, contour.pdf, contour plot and progress contour plots (only if out[["pp"]] = TRUE) of the Gibbs samples.

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RprobitB documentation built on May 25, 2021, 9:07 a.m.