add MCR class to relace MCResult in case of mcr is not available

DESCRIPTION

@@ -10,15 +10,14 @@ Description: A complement to 'mcr' package, adding methods and functions to
     analyze the quantitative or qualitative performance for diagnostic assays. 
     And outliers detection, reader precision and reference range are discussed. 
     Most of the methods and algorithms refer to CLSI recommendations and NMPA 
-    guidelines. In additional, relevant plots are constructed by ggplot2 statements.
+    guidelines. In additional, relevant plots are constructed by ggplot2.
 License: GPL (>= 3)
 URL: https://github.com/kaigu1990/mcradds, https://kaigu1990.github.io/mcradds/
 BugReports: https://github.com/kaigu1990/mcradds/issues
 Encoding: UTF-8
 LazyData: true
 Depends: 
-    R (>= 3.6),
-    mcr (>= 1.3.2)
+    R (>= 3.6)
 Imports:
     boot,
     checkmate,
@@ -34,6 +33,7 @@ Imports:
 Suggests: 
     dplyr,
     knitr,
+    mcr,
     rmarkdown,
     spelling,
     testthat (>= 3.0.0),

NAMESPACE

@@ -19,6 +19,7 @@ export(h_fmt_num)
 export(h_fmt_range)
 export(h_summarize)
 export(mcreg)
+export(mcreg2)
 export(nonparRI)
 export(pearsonTest)
 export(printSummary)
@@ -35,7 +36,6 @@ exportMethods(getAccuracy)
 exportMethods(getOutlier)
 import(checkmate)
 import(ggplot2)
-import(mcr)
 import(methods)
 importFrom(DescTools,BinomCI)
 importFrom(VCA,VCAinference)

R/autoplot.R

@@ -303,15 +303,14 @@ setMethod(
 #' @param legend.digits (`integer`)\cr the number of digits after the decimal point
 #'  in the legend.
 #'
-#' @seealso [mcr::mcreg()] to see the regression parameters.
+#' @seealso [MCR-class] or [mcr::mcreg()] to see the regression parameters.
 #'
 #' @export
 #'
 #' @examples
-#'
 #' # Using the default arguments for regression plot
-#' data(creatinine, package = "mcr")
-#' fit <- mcreg(
+#' data("platelet")
+#' fit <- mcreg2(
 #'   x = platelet$Comparative, y = platelet$Candidate,
 #'   method.reg = "Deming", method.ci = "jackknife"
 #' )
@@ -326,7 +325,7 @@ setMethod(
 #' )
 setMethod(
   f = "autoplot",
-  signature = c("MCResult"),
+  signature = c("MCR"),
   definition = function(object,
                         color = "black",
                         fill = "lightgray",
@@ -345,7 +344,7 @@ setMethod(
                         x.title = NULL,
                         y.title = NULL,
                         main.title = NULL) {
-    assert_class(object, "MCResult")
+    assert_class(object, "MCR")
     assert_character(color)
     assert_character(fill)
     assert_number(size)
@@ -365,8 +364,8 @@ setMethod(
     xrange <- range(df[["x"]])
     yrange <- range(df[["y"]])
 
-    slope <- formatC(object@glob.coef[2], format = "f", legend.digits)
-    intercept <- formatC(object@glob.coef[1], format = "f", legend.digits)
+    slope <- formatC(object@coef[2], format = "f", legend.digits)
+    intercept <- formatC(object@coef[1], format = "f", legend.digits)
     fm_text <- paste0("Y = ", slope, " * X + ", intercept)
 
     p <- ggplot(data = df, aes(x = .data$x, y = .data$y))
@@ -410,15 +409,15 @@ setMethod(
     )
     shapes <- stats::setNames(
       c(
-        ifelse(is.null(reg.params[["linetype"]]), 1 , reg.params[["linetype"]]),
-        ifelse(is.null(identity.params[["linetype"]]), 1 , identity.params[["linetype"]])
+        ifelse(is.null(reg.params[["linetype"]]), 1, reg.params[["linetype"]]),
+        ifelse(is.null(identity.params[["linetype"]]), 1, identity.params[["linetype"]])
       ),
       c(fm_text, "Identity")
     )
     cols <- stats::setNames(
       c(
         ifelse(is.null(reg.params[["col"]]), 1, reg.params[["col"]]),
-        ifelse(is.null(identity.params[["col"]]), 1 , identity.params[["col"]])
+        ifelse(is.null(identity.params[["col"]]), 1, identity.params[["col"]])
       ),
       c(fm_text, "Identity")
     )

R/mcr.R

@@ -69,6 +69,26 @@ mcreg <- function(...) {
   mcr::mcreg(...)
 }
 
+#' @rdname mcreg
+#' @aliases mcreg
+#'
+#' @export
+#' @examples
+#'
+#' # use `MCR` class instead of `MCResult` class in `mcr` package
+#' mcreg2(
+#'   x = platelet$Comparative, y = platelet$Candidate,
+#'   method.reg = "Deming", method.ci = "jackknife"
+#' )
+mcreg2 <- function(...) {
+  fit <- mcr::mcreg(...)
+  MCR(
+    data = fit@data,
+    coef = fit@glob.coef,
+    mnames = fit@mnames,
+    regmeth = fit@regmeth
+  )
+}
 
 # calcBias ----
 

R/package.R

@@ -4,7 +4,6 @@
 #'
 "_PACKAGE"
 
-#' @import mcr
 #' @import checkmate
 #' @import ggplot2
 #' @import methods

R/pkg_class.R

@@ -272,3 +272,48 @@ tpROC <- function(testROC, refROC, method, H0, stat) {
     testROC = testROC, refROC = refROC, method = method, H0 = H0, stat = stat
   )
 }
+
+# MCR-class ----
+
+#' Method Comparison Regression Class
+#'
+#' @description `r lifecycle::badge("experimental")`
+#'
+#' The `MCR` class serves as a simplified version of `MCResult` from `mcr` package.
+#' As the `mcr` package are not available in CRAN, this class is took as the temporary
+#' replacement of it, which only contains the some necessaries for `autoplot`.
+#'
+#' @slot data data
+#' @slot coef coef
+#' @slot mnames mnames
+#' @slot regmeth regmeth
+#'
+#' @rdname MCR-class
+#' @aliases MCR
+setClass(
+  "MCR",
+  slots = c(
+    data = "data.frame",
+    coef = "numeric",
+    mnames = "character",
+    regmeth = "character"
+  )
+)
+
+# MCR-constructors ----
+
+#' @rdname MCR-class
+#'
+#' @param data (`data.frame`)\cr original data.
+#' @param coef (`numeric`)\cr a numeric vector contains slope and intercept.
+#' @param mnames (`character`)\cr name of X and Y assays, default are 'Method1'
+#'  and 'Method2' if you have not defined them in `mcreg` function.
+#' @param regmeth (`character`)\cr name of regression.
+#'
+#' @return An object of class `MCR`.
+#'
+MCR <- function(data, coef, mnames, regmeth) {
+  new("MCR",
+    data = data, coef = coef, mnames = mnames, regmeth = regmeth
+  )
+}

_pkgdown.yml

@@ -15,6 +15,7 @@ reference:
   - BAsummary
   - RefInt
   - tpROC
+  - MCR
 - title: Internal Helper Functions
   contents:
   - cat_with_newline

cran-comments.md

@@ -3,6 +3,8 @@
 0 errors | 0 warnings | 1 note
 
 * This is a new release.
+* Suggests or Enhances not in mainstream repositories: `mcr`. Because `mcr` package 
+is not available in CRAN. But users can install it from archived version.
 
 ## revdepcheck results
 

inst/WORDLIST

@@ -65,6 +65,7 @@ ananlysis
 apa
 ci
 clopper
+coef
 confInt
 creatinin
 dL
@@ -81,6 +82,7 @@ lipoprotein
 loa
 magrittr
 mcr
+mnames
 nlr
 npa
 npv
@@ -97,6 +99,7 @@ quasilinear
 quations
 refInt
 refROC
+regmeth
 regmethod
 repo
 reproducibility

revdep/.gitignore

@@ -0,0 +1,7 @@
+checks
+library
+checks.noindex
+library.noindex
+cloud.noindex
+data.sqlite
+*.html

tests/testthat/test-autoplot.R

@@ -33,7 +33,7 @@ test_that("autoplot works as expected for BAsummary class with multiple argument
 
 test_that("autoplot works as expected for MCResult class with default arguments", {
   data(creatinine, package = "mcr")
-  object <- mcreg(
+  object <- mcreg2(
     x = platelet$Comparative, y = platelet$Candidate,
     method.reg = "Deming", method.ci = "jackknife"
   )
@@ -44,7 +44,7 @@ test_that("autoplot works as expected for MCResult class with default arguments"
 
 test_that("autoplot works as expected for MCResult class with multiple arguments", {
   data(creatinine, package = "mcr")
-  object <- mcreg(
+  object <- mcreg2(
     x = platelet$Comparative, y = platelet$Candidate,
     method.reg = "PaBa", method.ci = "bootstrap"
   )