Cleaned up devtools::check() problems and bumped version

Version to 0.2.0
Updated DESCRIPTION Imports and Suggests
Tweaked documentation
Updated @ImportFrom
Added @ImportMethodsFrom bbmle summary
Roxygenised
Refreshed reference manual PDF

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: Rwtdttt
 Title: Parametric Waiting Time Distribution estimation
-Version: 0.1.0
+Version: 0.2.0
 Author: Sabrina Giometto, Malcolm Gillies, Olga Paoletti, Henrik Støvring
 Maintainer: Henrik Støvring <[email protected]>
 Description: Estimation of prescription durations and treatment
@@ -15,17 +15,14 @@ License: GPL (>= 3)
 Roxygen: list(markdown = TRUE)
 Imports: 
     bbmle,
-    class,
     data.table (>= 1.15.0),
-    dplyr,
-    haven,
     methods,
     graphics,
     rlang,
-    stats,
-    numDeriv
+    stats
 Suggests: 
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    haven
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true

NAMESPACE

@@ -22,14 +22,14 @@ importFrom(graphics,curve)
 importFrom(graphics,hist)
 importFrom(methods,as)
 importFrom(methods,is)
-importFrom(numDeriv,grad)
 importFrom(rlang,enquo)
 importFrom(rlang,eval_tidy)
 importFrom(stats,as.formula)
 importFrom(stats,formula)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)
 importFrom(stats,na.pass)
+importFrom(stats,numericDeriv)
 importFrom(stats,pexp)
 importFrom(stats,pnorm)
 importFrom(stats,pweibull)
@@ -38,3 +38,4 @@ importFrom(stats,qnorm)
 importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(stats,terms)
+importMethodsFrom(bbmle,summary)

R/dfunctions.R

@@ -7,13 +7,9 @@
 #' @param delta width of interval with positive support (x in (0; delta))
 #' @param log logical; if TRUE, density values are returned on log-scale.
 #'
-#' @return
+#' @return Density. The length of the result is the maximum of the lengths of the numerical arguments.
 #' @export
 #' @importFrom stats pnorm
-#'
-#' @examples
-#'
-#'
 
 dlnorm <- function(x, logitp, mu, lnsigma, delta = 1, log = FALSE) {
 
@@ -44,10 +40,8 @@ dlnorm <- function(x, logitp, mu, lnsigma, delta = 1, log = FALSE) {
 #' @param delta width of interval with positive support (x in (0; delta))
 #' @param log logical; if TRUE, probabilities p are given as log(p)
 #'
-#' @return
+#' @return Density. The length of the result is the maximum of the lengths of the numerical arguments.
 #' @export
-#'
-#' @examples
 dweib <- function(x, logitp, lnalpha, lnbeta, delta = 1, log = FALSE) {
 
   prob <- exp(logitp) / (1 + exp(logitp))
@@ -73,10 +67,8 @@ dweib <- function(x, logitp, lnalpha, lnbeta, delta = 1, log = FALSE) {
 #' @param delta width of interval with positive support (x in (0; delta))
 #' @param log logical; if TRUE, probabilities p are given as log(p)
 #'
-#' @return
+#' @return Density. The length of the result is the maximum of the lengths of the numerical arguments.
 #' @export
-#'
-#' @examples
 dexp <- function(x, logitp, lnbeta, delta = 1, log = FALSE) {
 
   prob <- exp(logitp) / (1 + exp(logitp))

R/sandwich.R

@@ -5,10 +5,7 @@
 #' @param fit an object of class "wtd" returned by `ranwtdttt()`
 #'
 #' @return sand_vcov returns a matrix
-#' @importFrom stats model.matrix
-#' @importFrom numDeriv grad
-#'
-#' @examples
+#' @importFrom stats model.matrix numericDeriv
 sand_vcov <- function(fit) {
   # parse model formula components
   parm_form <- unlist(strsplit(gsub(" ", "", unlist(strsplit(fit@formula, ":", fixed=T))[2]), ",", fixed=T))

R/wtd-class.R

@@ -17,6 +17,7 @@
 #'
 #' @exportClass wtd
 #' @importClassesFrom bbmle mle2
+#' @importMethodsFrom bbmle summary
 #'
 setClass("wtd", contains="mle2", slots=c(delta="numeric", dist="character",
                                          depvar="character", idvar="character",