pkgname <- "LogReg"
source(file.path(R.home("share"), "R", "examples-header.R"))
options(warn = 1)
options(pager = "console")
library('LogReg')

assign(".oldSearch", search(), pos = 'CheckExEnv')
cleanEx()
nameEx("est.bes")
### * est.bes

flush(stderr()); flush(stdout())

### Name: est.bes
### Title: A function to estimate betas in a logistic regression
### Aliases: est.bes
### Keywords: ~kwd1 ~kwd2

### ** Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (Y, X, intercept = TRUE, start.vals = rep(0, ncol(X) + 
    as.numeric(intercept))) 
{
    x <- start.vals
    opt <- optim(x, fn = lr.loglike, gr = NULL, Y = Y, X = X, 
        intercept = intercept, method = "BFGS", control = list(fnscale = -1), 
        hessian = T)
    beta.hat <- opt$par
    beta.cov <- solve(opt$hessian)/length(Y)
    if (intercept) {
        Xm <- cbind(rep(1, length(Y)), X)
    }
    else {
        Xm <- X
    }
    fitted.lp <- Xm %*% beta.hat
    fitted.Y <- expit(fitted.lp)
    conv <- TRUE
    if (opt$convergence != 0) {
        conv <- FALSE
        print("Optim did not converge")
    }
    return(list(ests = beta.hat, varcov = beta.cov, fitted.lp = fitted.lp, 
        fitted.Y = fitted.Y, conv = conv))
  }



cleanEx()
nameEx("expit")
### * expit

flush(stderr()); flush(stdout())

### Name: expit
### Title: The Expit Function
### Aliases: expit
### Keywords: ~kwd1 ~kwd2

### ** Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (x) 
{
    1/(1 + exp(-x))
  }



cleanEx()
nameEx("gbd")
### * gbd

flush(stderr()); flush(stdout())

### Name: gbd
### Title: A function to generate some binary regression data
### Aliases: gbd
### Keywords: ~kwd1 ~kwd2

### ** Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (n = 1000, p = 1, intercept = TRUE, betas = rep(0, p + 
    intercept), mu = rep(0, p), Sigma = diag(1, p), seed = 1) 
{
    require(MASS)
    set.seed(seed)
    X <- mvrnorm(n, mu, Sigma)
    Xm <- X
    if (intercept) {
        Xm <- cbind(rep(1, n), X)
    }
    lp <- Xm %*% betas
    pv <- expit(lp)
    Y <- rbinom(n, 1, pv)
    return(list(Y = Y, X = X))
  }



cleanEx()
nameEx("logit")
### * logit

flush(stderr()); flush(stdout())

### Name: logit
### Title: The logit function
### Aliases: logit
### Keywords: ~kwd1 ~kwd2

### ** Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (x) 
{
    return(log(x/(1 - x)))
  }



cleanEx()
nameEx("lr.loglike")
### * lr.loglike

flush(stderr()); flush(stdout())

### Name: lr.loglike
### Title: Evaluate the logistic regression log-likelihood
### Aliases: lr.loglike
### Keywords: ~kwd1 ~kwd2

### ** Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (betas, Y, X, intercept = TRUE) 
{
    if (!intercept) {
        lp <- X %*% betas
    }
    else {
        lp <- cbind(rep(1, length(Y)), X) %*% betas
    }
    pv <- expit(lp)
    return(sum(dbinom(Y, 1, pv, log = T)))
  }



cleanEx()
nameEx("plot.lrsurf")
### * plot.lrsurf

flush(stderr()); flush(stdout())

### Name: plot.lrsurf
### Title: Plot the log-likelihood surface for a single predictor
### Aliases: plot.lrsurf
### Keywords: ~kwd1 ~kwd2

### ** Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (Y, X, b0 = seq(-2, 2, by = 0.01), b1 = seq(-2, 2, by = 0.01), 
    ncl = 20) 
{
    lrs <- outer(b0, b1, "+") * 0
    for (i in 1:length(Y)) {
        lpv <- outer(b0, b1 * X[i], "+")
        lrs <- lrs + lpv * Y[i] - log(1 + exp(lpv))
    }
    image(b0, b1, lrs, xlab = expression(beta[0]), ylab = expression(beta[1]))
    contour(b0, b1, lrs, add = T, nlevels = ncl)
  }



cleanEx()
nameEx("test.data")
### * test.data

flush(stderr()); flush(stdout())

### Name: test.data
### Title: A test binary data set with two predictors
### Aliases: test.data
### Keywords: datasets

### ** Examples

data(test.data)
## maybe str(test.data) ; plot(test.data) ...



### * <FOOTER>
###
cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')