Fix URLs in README, convert to roxygenv0.2.3

- The roxygen conversion was done using Rd2roxygen
- Also edit _pkgdown.yml to group the reference
- Use markdown bullet lists for lod and loq docs

1 files changed, 50 insertions, 0 deletions

diff --git a/R/loq.R b/R/loq.R
index 26d6a53..a4dbcfe 100644
--- a/R/loq.R
+++ b/R/loq.R
@@ -1,15 +1,65 @@
+#' Estimate a limit of quantification (LOQ)
+#' 
+#' The limit of quantification is the x value, where the relative error of the
+#' quantification given the calibration model reaches a prespecified value 1/k.
+#' Thus, it is the solution of the equation \deqn{L = k c(L)}{L = k * c(L)}
+#' where c(L) is half of the length of the confidence interval at the limit L
+#' (DIN 32645, equivalent to ISO 11843). c(L) is internally estimated by
+#' \code{\link{inverse.predict}}, and L is obtained by iteration.
+#' 
+#' @aliases loq loq.lm loq.rlm loq.default
+#' @param object A univariate model object of class \code{\link{lm}} or
+#' \code{\link[MASS:rlm]{rlm}} with model formula \code{y ~ x} or \code{y ~ x -
+#' 1}, optionally from a weighted regression. If weights are specified in the
+#' model, either \code{w.loq} or \code{var.loq} have to be specified.
+#' @param alpha The error tolerance for the prediction of x values in the
+#' calculation.
+#' @param \dots Placeholder for further arguments that might be needed by
+#' future implementations.
+#' @param k The inverse of the maximum relative error tolerated at the desired
+#' LOQ.
+#' @param n The number of replicate measurements for which the LOQ should be
+#' specified.
+#' @param w.loq The weight that should be attributed to the LOQ. Defaults to
+#' one for unweighted regression, and to the mean of the weights for weighted
+#' regression. See \code{\link{massart97ex3}} for an example how to take
+#' advantage of knowledge about the variance function.
+#' @param var.loq The approximate variance at the LOQ. The default value is
+#' calculated from the model.
+#' @param tol The default tolerance for the LOQ on the x scale is the value of
+#' the smallest non-zero standard divided by 1000. Can be set to a numeric
+#' value to override this.
+#' @return The estimated limit of quantification for a model used for
+#' calibration.
+#' @note 
+#' * IUPAC recommends to base the LOQ on the standard deviation of the
+#' signal where x = 0.
+#' * The calculation of a LOQ based on weighted regression is non-standard and
+#' therefore not tested. Feedback is welcome.
+#' @seealso Examples for \code{\link{din32645}}
+#' @examples
+#' 
+#' m <- lm(y ~ x, data = massart97ex1)
+#' loq(m)
+#' 
+#' # We can get better by using replicate measurements
+#' loq(m, n = 3)
+#' 
+#' @export
 loq <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto", 
   var.loq = "auto", tol = "default")
 {
   UseMethod("loq")
 }
 
+#' @export
 loq.default <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto",
   var.loq = "auto", tol = "default")
 {
   stop("loq is only implemented for univariate lm objects.")
 }
 
+#' @export
 loq.lm <- function(object, ..., alpha = 0.05, k = 3, n = 1, w.loq = "auto",
   var.loq = "auto", tol = "default")
 {