R/vblogistic.R

In spatstat/spatstat.core: Core Functionality of the 'spatstat' Family

#' Variational Bayesian Logistic regression
#' 
#' author: Tuomas Rajala < tuomas.rajala a iki.fi >
#'
#' Copyright (C) Tuomas Rajala 2014
#' GNU Public License GPL 2.0 | 3.0
#' 
#' Special version for 'spatstat'
#'
#'    $Revision: 1.6 $ $Date: 2019/04/12 03:34:48 $
#' 
####################################################
#' Used inside ppm
vblogit.fmla <- function(formula, offset, data, subset, weights,
                            verbose=FALSE, epsilon=0.01, ...) {
  mf <- match.call(expand.dots = FALSE)
  m <- match(c("formula", "data", "subset", "offset"), names(mf), 0L)
  mf <- mf[c(1L, m)]
  mf$drop.unused.levels <- TRUE
  mf[[1L]] <- quote(stats::model.frame)
  mf <- eval(mf, parent.frame())
  mt <- attr(mf, "terms")
  offset <- model.offset(mf)
  y <- model.response(mf, "any")
  X <- model.matrix(mt, mf) 
  colnames(X)[1] <- "(Intercept)"
  Vnames <- colnames(X)
  #' then we fit:
  fit <- vblogit(y=y, X=X, offset=offset, verb=verbose, eps=epsilon, ...)
  #'
  names(fit$coefficients) <- names(fit$coef) <- Vnames
  #' add some variables to conform to summary.ppm
  fit$se <- sqrt(diag(as.matrix(fit$S)))
  fit$call <- match.call(expand.dots=FALSE)
  fit$formula <- formula
  fit$method <- "vblogit"
  fit$model <- mf
  fit$terms <- mt
  fit$offset <- offset
  fit$data <- data
  fit$xlevels <- .getXlevels(mt, mf)
  fit
}
###################################################
# the fitting function:
vblogit <- local({

  ## helper functions needed:
  lambda <- function(x) { -tanh(x/2)/(4*x) }
  mygamma <- function(x) { x/2 - log(1+exp(x)) + x*tanh(x/2)/4 }
  
  vblogit <- function(y, X, offset, eps=1e-2, m0, S0, S0i, xi0,
                      verb=FALSE, maxiter=1000, ...) {
    ## Logistic regression using JJ96 idea. Ormeron00 notation.
    ## p(y, w, t) = p(y | w) p(w | t) p(t) 
    ##
    ## Y ~ Bern(logit(Xw + offset))
    ## w  ~ N(m0, S0) iid
    ##
    ## "*0" are fixed priors.
    ##
    cat2 <- if(verb) cat else function(...) NULL
    varnames <- colnames(data.frame(as.matrix(X[1:2,])))
  
    ## Write 
    N <- length(y)
    K <- ncol(X)
    #'
    #'
    #' offset
    if(missing('offset')) offset <- 0
    if(length(offset)<N) offset <- rep(offset, N)[1:N]
    #'
    #'
    #' Priors and initial estimates.
    if(missing(m0))  m0  <- rep(0, K)
    if(missing(S0))  S0  <- diag(1e5, K, K)
    #' Overwrite with priors from ppm if given.
    if(!is.null(prior.mean <- list(...)$prior.mean))
        m0 <- prior.mean
    if(!is.null(prior.var <- list(...)$prior.var))
        S0 <- prior.var
    check.nvector(m0, K, things="parameters", vname="m0")
    stopifnot(is.matrix(S0))
    if(missing(S0i)) S0i <- solve(S0)
    #' Constants:
    oo2 <- offset^2
    LE_CONST <- as.numeric( -0.5*t(m0)%*%S0i%*%m0
                           - 0.5*determinant(S0)$mod
                           + sum((y-0.5)*offset) ) 
    Sm0 <- S0i%*%m0
    #' start values for xi:
    if(missing(xi0))   xi0 <- rep(4, N) # something positive
    if(length(xi0)!=N) xi0 <- rep(xi0, N)[1:N]
  
    est <- list(m=m0, S=S0, Si=S0i, xi=xi0)
    #'
    #'
    #'
    ## loop
    le <- -Inf
    le_hist <- le
    loop <- TRUE
    iter <- 0
    #' initials:
    la <- lambda(xi0)
    Si <- S0i - 2 * t(X*la)%*%X
    S <- solve(Si)
    m <- S%*%( t(X)%*%( (y-0.5) + 2*la*offset ) + Sm0  )
    #'
    #' Main loop:
    while(loop){
      old <- le
      #' update variational parameters
      M <- S+m%*%t(m)
      #' Make sure M is symmetric in case of numerical errors:
      M <- (M+t(M))/2
      L <- t(chol(M))
      V <- X%*%L
      dR <- rowSums(V^2)
      dO <- 2*offset*c(X%*%m)
      xi2 <- dR + dO + oo2
      xi <- sqrt(xi2)
      la <- lambda(xi)
      #' update post covariance
      Si <- S0i - 2 * t(X*la)%*%X
      S <- solve(Si)
      #' update post mean
      m <- S%*%( t(X)%*%( (y-0.5) + 2*la*offset ) + Sm0  )
      #' compute the log evidence
      le <-  as.numeric( 0.5*determinant(S)$mod
                        + sum( mygamma(xi) )
                        + sum(oo2*la)
                        + 0.5*t(m)%*%Si%*%m
                        + LE_CONST)
      #' check convergence 
      devi <- le - old
      if(devi < 0)
        warning("Log-evidence decreasing; try different starting values for xi.")
      loop <- abs(devi) > eps & (iter<-iter+1) <= maxiter
      le_hist <- c(le_hist, le)
      cat2("diff:", devi, "             \r")
    }
    if(iter == maxiter) warning("Maximum iteration limit reached.")
    cat2("\n")
    ## done. Compile:
    est <- list(m=m, S=S, Si=Si, xi=xi, lambda_xi=la)
    #' Marginal evidence
    est$logLik <- le
    #' Compute max logLik with the Bernoulli model;
    #' this should be what glm gives:
    est$logLik_ML <- as.numeric( t(y)%*%(X%*%m+offset)
                                - sum( log( 1 + exp(X%*%m+offset)) ) )
    #' Max loglik with the approximation
    est$logLik_ML2 <- as.numeric(  t(y)%*%(X%*%m + offset)
                                 + t(m)%*%t(X*la)%*%X%*%m
                                 - 0.5*sum(X%*%m)
                                 + sum(mygamma(xi))
                                 + 2*t(offset*la)%*%X%*%m
                                 + t(offset*la)%*%offset
                                 - 0.5 * sum(offset)  )
    #' some additional parts, like in glm output
    est$coefficients <- est$m[,1]
    names(est$coefficients) <- varnames
    est$call <- sys.call()
    est$converged <- !(maxiter==iter)
    #' more additional stuff
    est$logp_hist <- le_hist
    est$parameters <- list(eps=eps, maxiter=maxiter)
    est$priors <- list(m=m0, S=S0)
    est$iterations <- iter
    class(est) <- "vblogit"
    ## return
    est
  }

  vblogit
})


###################################################
#' Predict method
predict.vblogit <- local({

  sigmoid <- function(e) 1/(1+exp(-e))

  predict.vblogit <- function(object, newdata = NULL,
                              type = c("link", "response", "terms"),
                              se.fit = FALSE,
                              dispersion = NULL,
                              terms = NULL,
                              na.action = na.pass, 
                              ...) {
    type <- match.arg(type)
    if(type != "response") stop("type not supported.")
    if(missing(newdata)) {
      stop("not implemented.")
    }
    else{  # newdata
      #' build the new covariate matrix, inspired by predict.lm
      tt <- terms(object)
      Terms <- delete.response(tt)
      m <- model.frame(Terms, newdata, na.action = na.action, 
                       xlev = object$xlevels)
      X <- model.matrix(Terms, m, contrasts.arg = object$contrasts)
      offset <- rep(0, nrow(X))
      if (!is.null(off.num <- attr(tt, "offset"))) 
        for (i in off.num)
          offset <- offset + eval(attr(tt, "variables")[[i + 1]], newdata)
      if (!is.null(object$call$offset)) 
        offset <- offset + eval(object$call$offset, newdata)
      #' predict using probit approximation to logit-function
      mu <- object$m
      S <- object$S
      mua <- as.numeric(X%*%mu)+offset
      #' was:        s2a <- diag(X%*%S%*%t(X) )
      s2a <- quadform(X, S)
      predictor <- sigmoid( as.numeric( mua/sqrt(1+pi*s2a/8) ) ) 
      names(predictor) <- rownames(X)
    }
    predictor
  }

  predict.vblogit
})



# ###################################################
# print method
print.vblogit <- function(x, ...) {
  splat("Variational Bayes logistic regression fit")
  cat("\nCall: ")
  print(x$call)
  cat("\nCoefficients:\n")
  print(x$coefficients)
  cat("\n")
  splat("Log-likelihood:", x$logLik)
  splat("Converged:", x$converged)
  splat("Convergence threshold:", x$parameters$eps)
  splat("Iterations / max:", x$iterations, "/", x$parameters$maxiter)
  splat("* Caution: the estimates are conditional on convergence.")
  invisible(NULL)
}
####################################################
# vblogit family method
family.vblogit <- function(object, ...) binomial()

####################################################
#' vblogit fit summary method
summary.vblogit <- function(object, ...) {
  splat("Variational Bayes logistic regression fit")
  cat("\nCall: ")
  print(object$call)
  splat("\nCoefficients and posterior 95% central regions:")
  vna <- names(object$coefficients)
  s <- sqrt(diag(object$S))
  q0 <- qnorm(c(0.025, 0.975))
  m <- as.numeric(object$m)
  df <- data.frame(estimate=m,
                   "low 0.05"=m+s*q0[1],
                   "high 97.5"=m+s*q0[2],
                   "prior mean"=object$priors$m,
                   "prior var"=diag(object$priors$S))
  rownames(df) <- vna
  print(df)
  cat("\n")
  splat("Lower bound for log-likelihood:", object$logLik)
  invisible(NULL)
}

####################################################
# Coef
coef.vblogit <- function(object, ...) object$coefficients

####################################################
# Log-evidence
logLik.vblogit <- function(object, ...) {
  object$logLik
}