R/BEOI.r

In Stan125/gamlss.dist: Distributions for Generalized Additive Models for Location Scale and Shape

# ---------------------------------------------------------------------------------------
# The one inflated beta distribution (BEOI)
# created by Raydonal Ospina 01 June of 2006
# IME-USP. University of San Paulo,
# Department of Statistics. San Paulo-Brazil
# rospina@ime.usp.br
# ---------------------------------------------------------------------------------------
BEOI = function (mu.link = "logit", sigma.link = "log", nu.link = "logit") 
{
    mstats <- checklink("mu.link", "BEOI", substitute(mu.link), 
        c("logit", "probit", "cloglog", "log", "own"))
    dstats <- checklink("sigma.link", "BEOI", substitute(sigma.link), 
        c("inverse", "log", "identity"))
    vstats <- checklink("nu.link", "BEOI", substitute(nu.link), 
        c("logit", "probit", "cloglog", "log", "own"))

    structure(list(family = c("BEOI", "One Inflated Beta"),
               parameters = list(mu = TRUE, sigma = TRUE, nu = TRUE),
                    nopar = 3,
                     type = "Mixed", 
                  mu.link = as.character(substitute(mu.link)),
               sigma.link = as.character(substitute(sigma.link)), 
                  nu.link = as.character(substitute(nu.link)),
               mu.linkfun = mstats$linkfun, 
            sigma.linkfun = dstats$linkfun,
               nu.linkfun = vstats$linkfun, 
               mu.linkinv = mstats$linkinv,
            sigma.linkinv = dstats$linkinv, 
               nu.linkinv = vstats$linkinv,
                    mu.dr = mstats$mu.eta,
                 sigma.dr = dstats$mu.eta, 
                    nu.dr = vstats$mu.eta,
        dldm = function(y, mu, sigma) #first derivate of log-density respect to mu 
        {           
                  p <- mu * sigma
                  q <- (1-mu)*sigma
            mustart <-digamma(p)-digamma(q) 
            ystart  <- log(y) - log(1 - y)  
               dldm <- ifelse((y == 1) , 0, sigma * (ystart-mustart))
               dldm
        },

        d2ldm2 = function(y,mu,sigma) {        #second derivate of log-density respect to mu 
                 p <- mu * sigma
                 q <- (1-mu)*sigma
            d2ldm2 <- ifelse((y == 1) , 0,-sigma^2 * (trigamma(p)+trigamma(q)))
            d2ldm2
        },


        dldd = function(y,mu,sigma) {      #first derivate log-density respect to sigma 
                  p <- mu * sigma
                  q <- (1-mu)*sigma
            mustart <-digamma(p)-digamma(q) 
            ystart  <- log(y) - log(1 - y)
               dldd <- ifelse((y == 1),0,mu * (ystart-mustart)+log(1-y)-digamma(q)+digamma(sigma))
               dldd
        },

        d2ldd2 = function(y,mu,sigma) {      #second derivate log-density respect to sigma 
                 p <- mu * sigma
                 q <- (1-mu)*sigma
            #mustart <-digamma(p)-digamma(q) 
            d2ldd2 <- ifelse((y == 1) , 0, -(mu^2 * trigamma(p)+ 
                     (1 - mu)^2 * trigamma(q) -trigamma(sigma)))
            d2ldd2
        },

        dldv = function(y,nu) {       #first derivate log-density respect to nu
               dldv <- ifelse(y == 1, 1/nu, -1/(1 - nu))  
               dldv
        },


        d2ldv2 = function(nu) {         #second derivate log-density respect to nu
              d2ldv2 <- -1/(nu * (1 - nu))
              d2ldv2
        },
        d2ldmdd = function(y,mu,sigma) {   #partial derivate of log-density respect to mu and sigma  
                  p <- mu * sigma
                  q <- (1-mu)*sigma
            d2ldmdd <- ifelse((y == 1), 0, -sigma*(trigamma(p)*mu)-(trigamma(q)*(1-mu)))
            d2ldmdd
        },

        d2ldmdv = function(y) {  #partial derivate of log-density respect to mu and alpha
            d2ldmdv <- rep(0, length=y)
            d2ldmdv
        },
        
        d2ldddv = function(y) {   #partial derivate of log-density respect to sigma and alpha
            d2ldddv <- rep(0, length=y)
            d2ldddv
        },        
        G.dev.incr = function(y, mu, sigma, nu, ...){  # Global deviance
            -2 * dBEOI(y, mu, sigma, nu, log = TRUE)
        },

        rqres = expression({     # (Normalize quantile) residuals
            uval <- ifelse(y == 1, nu * runif(length(y), 0, 1), 
                (1 - nu) * pBEOI(y, mu, sigma, nu))
            rqres <- qnorm(uval) 
        }),
           mu.initial = expression(mu <- (y + mean(y))/2),
        sigma.initial = expression(sigma <- rep(1, length(y))),
           nu.initial = expression(nu <- rep(0.3, length(y))),
             mu.valid = function(mu) all(mu > 0 & mu < 1),
          sigma.valid = function(sigma) all(sigma > 0),
             nu.valid = function(nu) all(nu > 0 & nu < 1),
              y.valid = function(y) all(y > 0 & y <= 1)),
                class = c("gamlss.family", "family"))
}

#----------------------------------------------------------------------------------------
########## Densitx  function of One Inflated Beta ##########
dBEOI = function (x, mu = 0.5, sigma = 1, nu = 0.1, log = FALSE) 
{

    if (any(mu <= 0)|any(mu >= 1)) 
        stop(paste("mu must be beetwen 0 and 1 ", "\n", ""))
    if (any(sigma < 0))  #In this parametrization  sigma = phi
        stop(paste("sigma must be positive", "\n", ""))
    if (any(nu <= 0)|any(nu >= 1))  #In this parametrization  nu = alpha
        stop(paste("nu must be beetwen 0 and 1 ", "\n", ""))
    if (any(x <= 0)|any(x >1) ) 
        stop(paste("x must be beetwen (0, 1]", "\n", ""))

    a = mu * sigma
    b = (1 - mu) * sigma

    log.beta = dbeta(x, shape1 = a, shape2 = b, ncp = 0, log = TRUE)
        
    log.lik <- ifelse(x == 1, log(nu), log(1 - nu) + log.beta)
    if (log == FALSE) 
        fy <- exp(log.lik)
    else fy <- log.lik
    fy
}

#----------------------------------------------------------------------------------------
########## Acumulate  function distribution of One Inflated Beta ##########

pBEOI = function (q, mu = 0.5, sigma = 1, nu = 0.1, lower.tail = TRUE, log.p = FALSE) 
{

    if (any(mu <= 0)|any(mu >= 1)) 
        stop(paste("mu must be beetwen 0 and 1 ", "\n", ""))
    if (any(sigma < 0))  #In this parametrization  sigma = phi
        stop(paste("sigma must be positive", "\n", ""))
    if (any(nu <= 0)|any(nu >= 1))  #In this parametrization  nu = alpha
        stop(paste("nu must be beetwen 0 and 1 ", "\n", ""))
 
    a = mu * sigma
    b = (1 - mu) * sigma

    cdf <- ifelse((q > 0 & q < 1), (1-nu)*pbeta(q, shape1 = a, 
        shape2 = b, ncp = 0, lower.tail = TRUE, log.p = FALSE), 0)
 #   cdf <- ifelse((q == 0), nu, cdf)    ##Estou aqui
    cdf <- ifelse((q >= 1), 1, cdf)

    if (lower.tail == TRUE) 
        cdf <- cdf
    else cdf = 1 - cdf
    if (log.p == FALSE) 
        cdf <- cdf
    else cdf <- log(cdf)
    cdf
}




#----------------------------------------------------------------------------------------
########## Quantile function of One Inflated Beta ##########

qBEOI = function (p, mu = 0.5, sigma = 1, nu = 0.1, lower.tail = TRUE,
        log.p = FALSE)
{
    if (any(mu <= 0)|any(mu >= 1)) 
        stop(paste("mu must be beetwen 0 and 1 ", "\n", ""))
    if (any(sigma < 0))  #In this parametrization  sigma = phi
        stop(paste("sigma must be positive", "\n", ""))
    if (any(nu <= 0)|any(nu >= 1))  #In this parametrization  nu = alpha
        stop(paste("nu must be beetwen 0 and 1 ", "\n", ""))

    if (log.p == TRUE) 
        p <- exp(p)
    else p <- p
    if (lower.tail == TRUE) 
        p <- p
    else p <- 1 - p
    if (any(p < 0) | any(p > 1)) 
        stop(paste("p must be between 0 and 1", "\n", ""))

    a = mu * sigma
    b = (1 - mu) * sigma

    suppressWarnings(q <- ifelse( p <= 1-nu, qbeta(p/(1-nu), 
            shape1 = a, shape2 = b, lower.tail = TRUE, log.p = FALSE),1))
    q
}



#----------------------------------------------------------------------------------------
######## Random generation function of One Inflated Beta ########

rBEOI = function (n, mu = 0.5, sigma = 1, nu = 0.1) 
{
    if (any(mu <= 0) | any(mu >= 1)) 
        stop(paste("mu must be between 0 and 1", "\n", ""))
    if (any(sigma < 0))  #In this parametrization  sigma = phi
        stop(paste("sigma must be positive", "\n", ""))
    if (any(nu <= 0)|any(nu >= 1))  #In this parametrization  nu = alpha
        stop(paste("nu must be beetwen 0 and 1 ", "\n", ""))
    if (any(n <= 0)) 
        stop(paste("n must be a positive integer", "\n", ""))
    n <- ceiling(n)
    p <- runif(n)
    r <- qBEOI(p, mu = mu, sigma = sigma, nu = nu)
    r
}

#dat<-rBEOI(100, mu=.5, sigma=5, nu=0.1)


#----------------------------------------------------------------------------------------
########## plot the function density of One Inflated Beta ##########

plotBEOI = function (mu = .5, sigma = 1, nu = 0.1, from = 0.001, to = 1, n = 101, 
    ...) 
{
    y = seq(from = 0.001, to = to, length.out = n)
    pdf <- dBEOI(y, mu = mu, sigma = sigma, nu = nu)
    pr1 <- c(dBEOI(1, mu = mu, sigma = sigma, nu = nu))
    print(pr1)
    p1 <- c(1)
    plot(pdf ~ y, main = "One Inflated Beta", ylim = c(0, max(pdf, 
        pr1)), type = "l")
    points(p1, pr1, type = "h")
    points(p1, pr1, type = "p", col = "blue")
}

#----------------------------------------------------------------------------------------
#calculates the expected value of the response for a One Inflated Beta fitted model 
meanBEOI = function (obj) 
{
    if (obj$family[1] != "BEOI") 
        stop("the object do not have a BEOI distribution")
    meanofY <- (fitted(obj, "nu"))+((1 - fitted(obj, "nu")) * fitted(obj, "mu"))
    meanofY
}

#----------------------------------------------------------------------------------------

#----------------------------------------------------------------------------------------
#Examples

#BEOI()# gives information about the default links for the BEOI distribution
#dat<-rBEOI(1000, mu=.5, sigma=5, nu=0.1)
#hist(dat)        
#mod1<-gamlss(dat~1,sigma.formula=~1, nu.formula=~1, family=BEOI) # fits a constant for mu, sigma and nu
#
#fitted(mod1)[1]
#
#summary(mod1)
#
#fitted(mod1,"mu")[1]
#fitted(mod1,"sigma")[1]
#fitted(mod1,"nu")[1]

#plot(function(y) dBEOI(y, mu=.5 ,sigma=5, nu=0.1), 0.001, 1,type="p")
#plot(function(y) pBEOI(y, mu=.5 ,sigma=5, nu=0.1), 0.0001, 0.9999)
#plot(function(y) qBEOI(y, mu=.5 ,sigma=5, nu=0.1), 0.0001, 0.9999)
#plot(function(y) qBEOI(y, mu=.5 ,sigma=5, nu=0.1, lower.tail=FALSE), 0.0001, 0.9999)