Tidy the code and text and modify function

  - Apply 72 in all text and code;
  - Make dashes after commented sentences go until max column;
  - Replace the switch() statment by a do.call() in the
    mc_link_function().
  - Replace = by <- in assignments.

R/mc_link_function.R

@@ -2,69 +2,76 @@
 #'
 #' @description  The \code{mc_link_function} is a customized call of the
 #' \code{\link[stats]{make.link}} function.
-#' Given the name of a link function, it returns a list with two elements.
-#' The first element is the inverse of the link function applied on the linear predictor
-#' \eqn{\mu = g^{-1}(X\beta).} The second element is the derivative of mu with respect to the regression
-#' parameters \eqn{\beta}. It will be useful when computing the quasi-score function.
+#' 
+#' Given the name of a link function, it returns a list with two
+#' elements.  The first element is the inverse of the link function
+#' applied on the linear predictor \eqn{\mu = g^{-1}(X\beta).} The
+#' second element is the derivative of mu with respect to the regression
+#' parameters \eqn{\beta}. It will be useful when computing the
+#' quasi-score function.
 #'
 #' @param beta A numeric vector of regression parameters.
-#' @param X  A design matrix, see \code{\link[stats]{model.matrix}} for details.
-#' @param offset  A numeric vector of offset values. It will be sum up on the linear predictor as a
-#' covariate with known regression parameter equals one (\eqn{\mu = g^{-1}(X\beta + offset)}).
-#' If no offset is present in the model, set offset = NULL.
-#' @param link  A string specifing the name of the link function. mcglm implements the following
-#' link functions: logit, probit, cauchit, cloglog, loglog, identity, log, sqrt, 1/mu^2 and inverse.
+#' @param X A design matrix, see \code{\link[stats]{model.matrix}} for
+#'     details.
+#' @param offset A numeric vector of offset values. It will be sum up on
+#'     the linear predictor as a covariate with known regression
+#'     parameter equals one (\eqn{\mu = g^{-1}(X\beta + offset)}).  If
+#'     no offset is present in the model, set offset = NULL.
+#' @param link A string specifing the name of the link function. mcglm
+#'     implements the following link functions: logit, probit, cauchit,
+#'     cloglog, loglog, identity, log, sqrt, 1/mu^2 and inverse.
 #' @return A list with two elements: mu and D.
-#' @seealso \code{\link[stats]{model.matrix}}, \code{\link[stats]{make.link}}.
-#' @details The link function is an important component of the multivariate covariance generalized
-#' linear model, since it link the expectation of the response variable with the covariates.
-#' Let \eqn{\beta} a \eqn{p x 1} regression parameter vector and \eqn{X} an
-#' \eqn{n x p} design matrix. The expected value of a response variable \eqn{Y} is given by
-#' \deqn{E(Y) = g^{-1}(X\beta),} where \eqn{g} is the link function and \eqn{\eta = X\beta}
-#' is the linear predictor. Let \eqn{D} be a \eqn{n \times p}
-#' matrix whose entries are given by the derivatives of \eqn{mu} with respect to \eqn{\beta}.
-#' Such matrix will be required by the fitting algorithm. The function \code{mc_link_function} returns
-#' a list where the first element is mu (n x 1) vector and the second D (n x p) matrix.
+#' @seealso \code{\link[stats]{model.matrix}},
+#'     \code{\link[stats]{make.link}}.
+#' @details The link function is an important component of the
+#'     multivariate covariance generalized linear model, since it link
+#'     the expectation of the response variable with the covariates.
+#'     Let \eqn{\beta} a \eqn{p x 1} regression parameter vector and
+#'     \eqn{X} an \eqn{n x p} design matrix. The expected value of a
+#'     response variable \eqn{Y} is given by \deqn{E(Y) =
+#'     g^{-1}(X\beta),} where \eqn{g} is the link function and \eqn{\eta
+#'     = X\beta} is the linear predictor. Let \eqn{D} be a \eqn{n \times
+#'     p} matrix whose entries are given by the derivatives of \eqn{mu}
+#'     with respect to \eqn{\beta}.  Such matrix will be required by the
+#'     fitting algorithm. The function \code{mc_link_function} returns a
+#'     list where the first element is mu (n x 1) vector and the second
+#'     D (n x p) matrix.
 #' @examples
 #' x1 <- seq(-1, 1, l = 5)
 #' X <- model.matrix(~ x1)
-#' mc_link_function(beta = c(1,0.5), X = X, offset = NULL, link = 'log')
-#' mc_link_function(beta = c(1,0.5), X = X, offset = rep(10,5), link = 'identity')
+#' mc_link_function(beta = c(1,0.5), X = X,
+#'                  offset = NULL, link = 'log')
+#' mc_link_function(beta = c(1,0.5), X = X,
+#'                  offset = rep(10,5), link = 'identity')
 #' @export
 #' @import assertthat
 
-# Generic link function ---------------------------
+## Generic link function -----------------------------------------------
 mc_link_function <- function(beta, X, offset, link) {
     assert_that(noNA(beta))
     assert_that(noNA(X))
     if (!is.null(offset)) 
         assert_that(noNA(offset))
-    switch(link, logit = {
-        output <- mc_logit(beta = beta, X = X, offset = offset)
-    }, probit = {
-        output <- mc_probit(beta = beta, X = X, offset = offset)
-    }, cauchit = {
-        output <- mc_cauchit(beta = beta, X = X, offset = offset)
-    }, cloglog = {
-        output <- mc_cloglog(beta = beta, X = X, offset = offset)
-    }, loglog = {
-        output <- mc_loglog(beta = beta, X = X, offset = offset)
-    }, identity = {
-        output <- mc_identity(beta = beta, X = X, offset = offset)
-    }, log = {
-        output <- mc_log(beta = beta, X = X, offset = offset)
-    }, sqrt = {
-        output <- mc_sqrt(beta = beta, X = X, offset = offset)
-    }, `1/mu^2` = {
-        output <- mc_invmu2(beta = beta, X = X, offset = offset)
-    }, inverse = {
-        output <- mc_inverse(beta = beta, X = X, offset = offset)
-    }, stop(gettextf("%s link not recognised", sQuote(link)), domain = NA))
+    link_name <- c("logit", "probit", "cauchit", "cloglog", "loglog",
+                   "identity", "log", "1/mu^2", "inverse")
+    link_func <- c("mc_logit", "mc_probit", "mc_cauchit", "mc_cloglog",
+                   "mc_loglog", "mc_identity", "mc_log", "mc_invmu2",
+                   "mc_inverse")
+    names(link_func) <- link_name
+    if (!link %in% link_name) {
+        stop(gettextf(paste0("%s link not recognised. ",
+                             "Available links are: ",
+                             paste(link_name, collapse = ", "),
+                             "."),
+                      sQuote(link)), domain = NA)
+    }
+    output <- do.call(link_func[link],
+                      args = list(beta = beta, X = X, offset = offset))
     return(output)
 }
 
 #' @rdname mc_link_function
-# Logit link function ---------------------------
+## Logit link function -------------------------------------------------
 mc_logit <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
@@ -75,7 +82,7 @@ mc_logit <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-# Probit link function ---------------------------
+## Probit link function ------------------------------------------------
 mc_probit <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
@@ -87,7 +94,7 @@ mc_probit <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-# Cauchit link function ---------------------------
+## Cauchit link function -----------------------------------------------
 mc_cauchit <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
@@ -99,7 +106,7 @@ mc_cauchit <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-# Complement log-log link function ---------------------------
+## Complement log-log link function ------------------------------------
 mc_cloglog <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
@@ -111,7 +118,7 @@ mc_cloglog <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-## Log-log link function ---------------------------
+## Log-log link function -----------------------------------------------
 mc_loglog <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
@@ -123,7 +130,7 @@ mc_loglog <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-## Identity link function ---------------------------
+## Identity link function ----------------------------------------------
 mc_identity <- function(beta, X, offset) {
     eta <- X %*% beta
     if (!is.null(offset)) {
@@ -133,7 +140,7 @@ mc_identity <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-## Log link function ---------------------------
+## Log link function ---------------------------------------------------
 mc_log <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
@@ -144,7 +151,7 @@ mc_log <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-## Square-root link function ---------------------------
+## Square-root link function -------------------------------------------
 mc_sqrt <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
@@ -155,25 +162,25 @@ mc_sqrt <- function(beta, X, offset) {
 }
 
 #' @rdname mc_link_function
-## Inverse mu square link function ---------------------------
+## Inverse mu square link function -------------------------------------
 mc_invmu2 <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
         eta <- eta + offset
     }
-    mu = make.link("1/mu^2")$linkinv(eta = eta)
-    Deri = make.link("1/mu^2")$mu.eta(eta = eta)
+    mu <- make.link("1/mu^2")$linkinv(eta = eta)
+    Deri <- make.link("1/mu^2")$mu.eta(eta = eta)
     return(list(mu = mu, D = X * Deri))
 } 
 
 #' @rdname mc_link_function
-## Inverse link function ---------------------------
+## Inverse link function -----------------------------------------------
 mc_inverse <- function(beta, X, offset) {
     eta <- as.numeric(X %*% beta)
     if (!is.null(offset)) {
         eta <- eta + offset
     }
-    mu = make.link("inverse")$linkinv(eta = eta)
-    Deri = make.link("inverse")$mu.eta(eta = eta)
+    mu <- make.link("inverse")$linkinv(eta = eta)
+    Deri <- make.link("inverse")$mu.eta(eta = eta)
     return(list(mu = mu, D = X * Deri))
 }