Merge pull request #16 from kaigu1990/mcr_removed

Remove mcr related codes as a temporary solution #15

DESCRIPTION

@@ -33,7 +33,6 @@ Imports:
 Suggests: 
     dplyr,
     knitr,
-    mcr,
     rmarkdown,
     spelling,
     testthat (>= 3.0.0),

NAMESPACE

@@ -6,23 +6,18 @@ export(VCAinference)
 export(anovaVCA)
 export(aucTest)
 export(blandAltman)
-export(calcBias)
 export(cat_with_newline)
 export(diagTab)
 export(dixon_outlier)
 export(esd.critical)
-export(getCoefficients)
 export(h_difference)
 export(h_factor)
 export(h_fmt_est)
 export(h_fmt_num)
 export(h_fmt_range)
 export(h_summarize)
-export(mcreg)
-export(mcreg2)
 export(nonparRI)
 export(pearsonTest)
-export(printSummary)
 export(refInterval)
 export(robustRI)
 export(size_ci_corr)

R/autoplot.R

@@ -11,8 +11,8 @@
 #'  default is FALSE.
 #' @param loa.line (`logical`)\cr whether to plot limit of agreement line, default is TRUE.
 #' @param ref.line.params,ci.line.params,loa.line.params (`list`)\cr parameters
-#'  (color, linetype, size) for the argument 'ref.line', 'ci.line' and 'loa.line';
-#'  eg. ref.line.params = list(col = "blue", linetype = "solid", size = 1).
+#'  (color, linetype, linewidth) for the argument 'ref.line', 'ci.line' and 'loa.line';
+#'  eg. ref.line.params = list(col = "blue", linetype = "solid", linewidth = 1).
 #' @param label (`logical`)\cr whether to add specific value label for each line
 #'  (ref.line, ci.line and loa.line). Only be shown when the line is defined as TRUE.
 #' @param label.digits (`integer`)\cr the number of digits after the decimal point
@@ -29,16 +29,10 @@
 #' @export
 #'
 #' @examples
-#' # Using creatinine dataset from `mcr` package
-#' data(creatinine, package = "mcr")
-#' object <- blandAltman(x = creatinine$serum.crea, y = creatinine$plasma.crea)
-#' autoplot(object)
-#' autoplot(object, type = "relative")
-#'
 #' # Specify the type for difference plot
 #' data("platelet")
 #' object <- blandAltman(x = platelet$Comparative, y = platelet$Candidate)
-#' autoplot(object, type = "absolute")
+#' autoplot(object)
 #' autoplot(object, type = "relative")
 #'
 #' # Set the addition parameters for `geom_point`
@@ -182,7 +176,7 @@ setMethod(
           yintercept = statmat["mean"],
           col = if (is.null(ref.line.params[["col"]])) 1 else ref.line.params[["col"]],
           linetype = if (is.null(ref.line.params[["linetype"]])) 1 else ref.line.params[["linetype"]],
-          size = if (is.null(ref.line.params[["size"]])) 0.9 else ref.line.params[["size"]]
+          linewidth = if (is.null(ref.line.params[["linewidth"]])) 0.9 else ref.line.params[["linewidth"]]
         )
 
       if (label) {
@@ -203,13 +197,13 @@ setMethod(
           yintercept = statmat["ci_lr"],
           col = if (is.null(ci.line.params[["col"]])) 1 else ci.line.params[["col"]],
           linetype = if (is.null(ci.line.params[["linetype"]])) 1 else ci.line.params[["linetype"]],
-          size = if (is.null(ci.line.params[["size"]])) 0.8 else ci.line.params[["size"]]
+          linewidth = if (is.null(ci.line.params[["linewidth"]])) 0.8 else ci.line.params[["size"]]
         ) +
         geom_hline(
           yintercept = statmat["ci_ur"],
           col = if (is.null(ci.line.params[["col"]])) 1 else ci.line.params[["col"]],
           linetype = if (is.null(ci.line.params[["linetype"]])) 1 else ci.line.params[["linetype"]],
-          size = if (is.null(ci.line.params[["size"]])) 0.8 else ci.line.params[["size"]]
+          linewidth = if (is.null(ci.line.params[["linewidth"]])) 0.8 else ci.line.params[["linewidth"]]
         )
 
       if (label) {
@@ -237,13 +231,13 @@ setMethod(
           yintercept = statmat["limit_lr"],
           col = if (is.null(loa.line.params[["col"]])) 1 else loa.line.params[["col"]],
           linetype = if (is.null(loa.line.params[["linetype"]])) 1 else loa.line.params[["linetype"]],
-          size = if (is.null(loa.line.params[["size"]])) 0.8 else loa.line.params[["size"]]
+          linewidth = if (is.null(loa.line.params[["linewidth"]])) 0.8 else loa.line.params[["linewidth"]]
         ) +
         geom_hline(
           yintercept = statmat["limit_ur"],
           col = if (is.null(loa.line.params[["col"]])) 1 else loa.line.params[["col"]],
           linetype = if (is.null(loa.line.params[["linetype"]])) 1 else loa.line.params[["linetype"]],
-          size = if (is.null(loa.line.params[["size"]])) 0.8 else loa.line.params[["size"]]
+          linewidth = if (is.null(loa.line.params[["linewidth"]])) 0.8 else loa.line.params[["linewidth"]]
         )
 
       if (label) {
@@ -308,6 +302,7 @@ setMethod(
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' # Using the default arguments for regression plot
 #' data("platelet")
 #' fit <- mcreg2(
@@ -323,6 +318,7 @@ setMethod(
 #'   legend.title = FALSE,
 #'   legend.digits = 4
 #' )
+#' }
 setMethod(
   f = "autoplot",
   signature = c("MCR"),

R/mcr.R

@@ -16,11 +16,9 @@
 #'   method.reg = "Deming", method.ci = "jackknife"
 #' )
 #' printSummary(fit)
-printSummary <- function(...) {
-  mcr::printSummary(...)
-}
-
-
+# printSummary <- function(...) {
+#   mcr::printSummary(...)
+# }
 # getCoefficients ----
 
 #' Get Regression Coefficients
@@ -39,11 +37,9 @@ printSummary <- function(...) {
 #'   method.reg = "Deming", method.ci = "jackknife"
 #' )
 #' getCoefficients(fit)
-getCoefficients <- function(...) {
-  mcr::getCoefficients(...)
-}
-
-
+# getCoefficients <- function(...) {
+#   mcr::getCoefficients(...)
+# }
 # mcreg ----
 
 #' Comparison of Two Measurement Methods Using Regression Analysis
@@ -65,9 +61,9 @@ getCoefficients <- function(...) {
 #' )
 #' printSummary(fit)
 #' getCoefficients(fit)
-mcreg <- function(...) {
-  mcr::mcreg(...)
-}
+# mcreg <- function(...) {
+#   mcr::mcreg(...)
+# }
 
 #' @rdname mcreg
 #' @aliases mcreg
@@ -80,16 +76,15 @@ mcreg <- function(...) {
 #'   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
-  )
-}
-
+# mcreg2 <- function(...) {
+#   fit <- mcr::mcreg(...)
+#   MCR(
+#     data = fit@data,
+#     coef = fit@glob.coef,
+#     mnames = fit@mnames,
+#     regmeth = fit@regmeth
+#   )
+# }
 # calcBias ----
 
 #' Systematical Bias Between Reference Method and Test Method
@@ -114,6 +109,6 @@ mcreg2 <- function(...) {
 #' calcBias(fit, x.levels = c(30, 200))
 #' calcBias(fit, x.levels = c(30, 200), type = "proportional")
 #' calcBias(fit, x.levels = c(30, 200), type = "proportional", percent = FALSE)
-calcBias <- function(...) {
-  mcr::calcBias(...)
-}
+# calcBias <- function(...) {
+#   mcr::calcBias(...)
+# }

R/pkg_methods.R

@@ -62,8 +62,8 @@ setMethod(
 #' @examples
 #'
 #' # Bland-Altman analysis
-#' data("creatinine", package = "mcr")
-#' blandAltman(x = creatinine$serum.crea, y = creatinine$plasma.crea)
+#' data("platelet")
+#' blandAltman(x = platelet$Comparative, y = platelet$Candidate)
 setMethod(
   f = "show",
   signature = "BAsummary",
@@ -257,8 +257,7 @@ setGeneric("getOutlier", function(object, ...) standardGeneric("getOutlier"))
 #' getOutlier(ba3, method = "ESD", difference = "rel")
 #'
 #' # Using "4E" as the method input
-#' data("creatinine", package = "mcr")
-#' ba4 <- blandAltman(x = creatinine$serum.crea, y = creatinine$plasma.crea)
+#' ba4 <- blandAltman(x = platelet$Comparative, y = platelet$Candidate)
 #' getOutlier(ba4, method = "4E")
 setMethod(
   f = "getOutlier",

R/referenceInterval.R

@@ -157,7 +157,7 @@ nonparRI <- function(x, ind = 1:length(x), conf.level = 0.95) {
 #' x <- calcium$Value
 #' refInterval(x, RI_method = "parametric", CI_method = "parametric")
 #' refInterval(x, RI_method = "nonparametric", CI_method = "nonparametric")
-#' refInterval(x, RI_method = "robust", CI_method = "boot")
+#' refInterval(x, RI_method = "robust", CI_method = "boot", R = 1000)
 refInterval <- function(x, out_method = c("doxin", "tukey"),
                         out_rm = FALSE,
                         RI_method = c("parametric", "nonparametric", "robust"),

_pkgdown.yml

@@ -53,10 +53,6 @@ reference:
   - size_ci_corr
   - diagTab
   - blandAltman
-  - mcreg
-  - printSummary
-  - getCoefficients
-  - calcBias
   - pearsonTest
   - spearmanTest
   - ESD_test

cran-comments.md

@@ -2,9 +2,13 @@
 
 0 errors | 0 warnings | 1 note
 
+Maintainer: 'Kai Gu <gukai1212@163.com>'
+
+   New submission
+
 * 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.
+* As `mcr` package is not available in CRAN for now, I add not running statement 
+for the examples. But users can install it from archived version.
 
 ## revdepcheck results
 

inst/WORDLIST

@@ -26,23 +26,18 @@ Jen
 LDL
 Liu
 LoA
-MCResult
 MCTab
 MMEs
 McCulloch
-NBins
 NCSS
 NMPA
 NMPA's
 NOBOUND
 NSCLC
 Newcombe
 OxLDL
-PBequi
 PDL
 PROC
-PaBa
-PaBaLarge
 QC'ed
 RandomEffects
 Reproducibility
@@ -51,7 +46,6 @@ SampleSize
 Satterthwaite
 Searle
 Statist
-Theil
 VC
 VCA
 VCoriginal
@@ -70,14 +64,14 @@ confInt
 creatinin
 dL
 eg
-equivariant
 et
 fontface
 gb
 ggplot
 immunohistochemical
 ixed
 linetype
+linewidth
 lipoprotein
 loa
 magrittr
@@ -95,15 +89,12 @@ pearson
 plr
 ppa
 ppv
-quasilinear
 quations
 refInt
 refROC
 regmeth
-regmethod
 repo
 reproducibility
-rng
 roxygen
 sas
 satterthwaite