version 1.2-8

cran · Mar 3, 2020 · dcf1bd0 · dcf1bd0
1 parent 74dc263
commit dcf1bd0
Show file tree

Hide file tree

Showing 19 changed files with 758 additions and 776 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,21 +1,22 @@
 Package: mmcm
 Type: Package
 Title: Modified Maximum Contrast Method
-Version: 1.2-7
+Version: 1.2-8
 Authors@R: c(
   person("Kengo", "Nagashima", email = "nshi1201@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4529-9045")),
   person("Yasunori", "Sato", role = c("aut")))
-Imports: mvtnorm, OpenMPController
+Imports: mvtnorm
 Description: An implementation of modified maximum contrast methods (Sato et al. (2009) <doi:10.1038/tpj.2008.17>;
   Nagashima et al. (2011) <doi:10.2202/1544-6115.1560>) and the maximum contrast method (Yoshimura et al. (1997)
   <doi:10.1177/009286159703100213>): Functions mmcm.mvt() and mcm.mvt() give P-value by using randomized quasi-Monte
   Carlo method with pmvt() function of package 'mvtnorm', and mmcm.resamp() gives P-value by using a permutation method.
 License: GPL-3
-RoxygenNote: 6.0.1
+Encoding: UTF-8
+RoxygenNote: 7.0.2
 NeedsCompilation: yes
-Packaged: 2018-02-26 05:46:05 UTC; NAGASHIMA
+Packaged: 2020-03-03 19:06:21 UTC; nshi1
 Author: Kengo Nagashima [aut, cre] (<https://orcid.org/0000-0003-4529-9045>),
   Yasunori Sato [aut]
 Maintainer: Kengo Nagashima <nshi1201@gmail.com>
 Repository: CRAN
-Date/Publication: 2018-02-26 11:42:42 UTC
+Date/Publication: 2020-03-04 00:10:02 UTC
diff --git a/MD5 b/MD5
@@ -1,21 +1,21 @@
-21fb0f401548f3ac21a6ee734fb8cb8c *DESCRIPTION
-f8d2f86a8eb3d7906b8e9ecac9cd7e8f *NAMESPACE
-2fb1d055c70ad789d09fcd93dd66f156 *NEWS.md
-c7d39ce0f19faa3349f6ecfefc09771b *R/mcm.mvt.R
-23d727ad84fd4cc9170db471bd10f19a *R/mmcm.mvt.R
-580c405f762b55bb0983dd5f945cea6e *R/mmcm.resamp.R
+62b0b61ec8c6745a7183ba0149d69bf3 *DESCRIPTION
+a3259bae424c2ffc886a6d9a5197752e *NAMESPACE
+8779f72aea6ab89d000e62dd0b0a8d8a *NEWS.md
+e4df20d4ef83aaa7644855907d0191d6 *R/mcm.mvt.R
+16d894115487303edd84caf32bea3d8e *R/mmcm.mvt.R
+e5089c8169d24b7bfb60bdb441999114 *R/mmcm.resamp.R
 2a2adf851a5c6ccc1973da435abe41cb *R/package.R
 82c42fb0da3176c8683cda87e565191d *R/print.mmcm.R
 e4ae4adfbeb49e7ee862151ed3f1ec6d *R/utils.R
-2ebf449e7836eba51567a8c830319c76 *README.md
-cf99cf87d37f5eea81cfca2a23c41d6b *inst/CITATION
-003fdd71b8afc0bd4ec14d48011fe926 *man/mcm.mvt.Rd
-9fd5a873ee2a4d0d75f5239b4590d4de *man/mmcm-package.Rd
-62729137511444cb663be7caa2e6da51 *man/mmcm.mvt.Rd
-396de21cf4945a742a574df5c67ec941 *man/mmcm.resamp.Rd
-0beec9d851d36e349df90e322ae783ff *man/print.mmcm.Rd
-5109f0b38d17f2e69a1418a1cc804039 *man/reexports.Rd
-3aa4d79c226dafc525ce3c26da376e0e *src/Makevars
-94cf30c8a4fb9675720721d73ce1aeb2 *src/mmcm.resamp.c
-5626fa6c1969752e528c730b66efabf7 *src/mmcm.resamp.h
-d37f1462bebf0baaa1c7b7be04db9b44 *src/packagename_init.c
+932d7eeafe97aed6d49d3be9b80b9de8 *README.md
+5a33c74816d6f6dbe1807e434d094733 *inst/CITATION
+1ee7393564bb24a87d403f8158041962 *man/mcm.mvt.Rd
+a9675194d81498e34fddae5dc78e33de *man/mmcm-package.Rd
+e947d7d5f34409dc70c863b3ca7943cc *man/mmcm.mvt.Rd
+d1935214625ee2d9d39e1f40bd29893f *man/mmcm.resamp.Rd
+1ff90180b2ad073a207c800940048ec4 *man/print.mmcm.Rd
+cc95d7f6a3584d78a46ab1d0fc6a8c78 *man/reexports.Rd
+a50a482491952af759aa86ba625fc238 *src/Makevars
+144b4e2a569c6bcc60a11876efa7b533 *src/mmcm.resamp.c
+9ac2e6edeb6c2dc9f6cac617c2b80083 *src/mmcm.resamp.h
+bf34d68701daf9291691616fda7b5e55 *src/packagename_init.c
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,11 +1,10 @@
-# Generated by roxygen2: do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(print,mmcm)
 export(GenzBretz)
 export(mcm.mvt)
 export(mmcm.mvt)
 export(mmcm.resamp)
-importFrom(OpenMPController,omp_set_num_threads)
 importFrom(mvtnorm,GenzBretz)
 importFrom(mvtnorm,pmvt)
 importFrom(stats,var)

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,11 @@
 # The 'mmcm' package
 
 
+## Changes in version 1.2-8 (2020-03-04)
+
+* Updated for R 4.0.0 
+
+
 ## Changes in version 1.2-7 (2018-02-26)
 
 * Updated according to the CRAN policies 

diff --git a/R/mcm.mvt.R b/R/mcm.mvt.R
@@ -123,9 +123,10 @@
 #' 
 #' ## Example 2 ##
 #' #  for dataframe
-#' #  true response pattern: pos = 1 dominant  model c=( 1,  1, -2)
-#' #                               2 additive  model c=(-1,  0,  1)
-#' #                               3 recessive model c=( 2, -1, -1)
+#' #  true response pattern:
+#' #    pos = 1 dominant  model c=( 1,  1, -2)
+#' #          2 additive  model c=(-1,  0,  1)
+#' #          3 recessive model c=( 2, -1, -1)
 #' set.seed(3872435)
 #' x <- c(
 #'   rnorm(130, mean =  1 / 6, sd = 1),
@@ -147,21 +148,11 @@
 #' contrast <- rbind(
 #'   c(-1, 0, 1), c(-2, 1, 1), c(-1, -1, 2)
 #' )
-#' mmcmtapply <- function(r) {
-#'   mcm.mvt(
-#'     xx$x[xx$pos==r[1]], xx$g[xx$pos==r[1]],
-#'     contrast
-#'   )
-#' }
-#' y <- tapply(xx$pos, xx$pos, mmcmtapply)
-#' yy <- data.frame(
-#'   Pos       = as.vector(names(y)),
-#'   Pval      = as.vector(sapply(y, "[[", 3)),
-#'   Pattern   = as.vector(sapply(y, "[[", 7)),
-#'   QMC_Error = as.vector(sapply(y, "[[", 9))
-#' )
+#' y <- by(xx, xx$pos, function(x) mmcm.mvt(x$x, x$g,
+#'   contrast))
+#' y <- do.call(rbind, y)[,c(3,7,9)]
 #' # miss-detection!
-#' yy
+#' y
 #' @keywords htest
 #' @importFrom stats var
 #' @importFrom mvtnorm pmvt

diff --git a/R/mmcm.mvt.R b/R/mmcm.mvt.R
@@ -128,9 +128,10 @@
 #' 
 #' ## Example 2 ##
 #' #  for dataframe
-#' #  true response pattern: pos = 1 dominant  model c=( 1,  1, -2)
-#' #                               2 additive  model c=(-1,  0,  1)
-#' #                               3 recessive model c=( 2, -1, -1)
+#' #  true response pattern:
+#' #    pos = 1 dominant  model c=( 1,  1, -2)
+#' #          2 additive  model c=(-1,  0,  1)
+#' #          3 recessive model c=( 2, -1, -1)
 #' set.seed(3872435)
 #' x <- c(
 #'   rnorm(130, mean =  1 / 6, sd = 1),
@@ -152,20 +153,10 @@
 #' contrast <- rbind(
 #'   c(-1, 0, 1), c(-2, 1, 1), c(-1, -1, 2)
 #' )
-#' mmcmtapply <- function(r) {
-#'   mmcm.mvt(
-#'     xx$x[xx$pos==r[1]], xx$g[xx$pos==r[1]],
-#'     contrast
-#'   )
-#' }
-#' y <- tapply(xx$pos, xx$pos, mmcmtapply)
-#' yy <- data.frame(
-#'   Pos       = as.vector(names(y)),
-#'   Pval      = as.vector(sapply(y, "[[", 3)),
-#'   Pattern   = as.vector(sapply(y, "[[", 7)),
-#'   QMC_Error = as.vector(sapply(y, "[[", 9))
-#' )
-#' yy
+#' y <- by(xx, xx$pos, function(x) mmcm.mvt(x$x, x$g,
+#'   contrast))
+#' y <- do.call(rbind, y)[,c(3,7,9)]
+#' y
 #' @keywords htest
 #' @importFrom stats var
 #' @importFrom mvtnorm pmvt

diff --git a/R/mmcm.resamp.R b/R/mmcm.resamp.R
@@ -93,6 +93,8 @@
 #' @param abseps specifies the absolute error tolerance (default: 0.001)
 #' @param seed a single value, interpreted as an integer;
 #' see \code{\link[base:Random]{set.seed()}} function. (default: NULL)
+#' @param nthread sthe number of threads used in parallel computing, or FALSE 
+#' that means single threading (default: 2)
 #' @return
 #' \item{statistic}{the value of the test statistic with a name describing it.}
 #' \item{p.value}{the p-value for the test.}
@@ -119,8 +121,6 @@
 #' @seealso
 #' \code{\link{mmcm.mvt}}
 #' @examples
-#' OpenMPController::omp_set_num_threads(2)
-#' 
 #' ## Example 1 ##
 #' #  true response pattern: dominant model c=(1, 1, -2)
 #' set.seed(136885)
@@ -142,14 +142,16 @@
 #' contrast <- rbind(
 #'   c(-1, 0, 1), c(-2, 1, 1), c(-1, -1, 2)
 #' )
-#' y <- mmcm.resamp(x, g, contrast, nsample = 20000, abseps = 0.01, seed = 5784324)
+#' y <- mmcm.resamp(x, g, contrast, nsample = 20000,
+#'                  abseps = 0.01, seed = 5784324)
 #' y
 #' 
 #' ## Example 2 ##
 #' #  for dataframe
-#' #  true response pattern: pos = 1 dominant  model c=( 1,  1, -2)
-#' #                               2 additive  model c=(-1,  0,  1)
-#' #                               3 recessive model c=( 2, -1, -1)
+#' #  true response pattern:
+#' #    pos = 1 dominant  model c=( 1,  1, -2)
+#' #          2 additive  model c=(-1,  0,  1)
+#' #          3 recessive model c=( 2, -1, -1)
 #' set.seed(3872435)
 #' x <- c(
 #'   rnorm(130, mean =  1 / 6, sd = 1),
@@ -163,7 +165,7 @@
 #'   rnorm( 10, mean = -1 / 6, sd = 1)
 #' )
 #' g   <- rep(rep(1:3, c(130, 90, 10)), 3)
-#' pos <- rep(c("rsXXXX", "rsYYYY", "rsZZZZ"), each=230)
+#' pos <- rep(c("rsXXXX", "rsYYYY", "rsZZZZ"), each = 230)
 #' xx  <- data.frame(pos = pos, x = x, g = g)
 #' 
 #' # coefficient matrix
@@ -172,26 +174,15 @@
 #'   c(-1, 0, 1), c(-2, 1, 1), c(-1, -1, 2)
 #' )
 #' 
-#' mmcmtapply <- function(r) {
-#'   mmcm.resamp(
-#'     xx$x[xx$pos==r[1]], xx$g[xx$pos==r[1]],
-#'     contrast, nsample = 10000, abseps = 0.01, seed = 5784324+as.numeric(r[1])
-#'   )
-#' }
-#' y <- tapply(xx$pos, xx$pos, mmcmtapply)
-#' yy <- data.frame(
-#'   Pos      = as.vector(names(y)),
-#'   Pval     = as.vector(sapply(y, "[[", 3)),
-#'   Pattern  = as.vector(sapply(y, "[[", 7)),
-#'   MC_Error = as.vector(sapply(y, "[[", 9))
-#' )
-#' yy
+#' y <- by(xx, xx$pos, function(x) mmcm.resamp(x$x, x$g,
+#'   contrast, abseps = 0.02, nsample = 10000))
+#' y <- do.call(rbind, y)[,c(3,7,9)]
+#' y
 #' @keywords htest
 #' @importFrom stats var
-#' @importFrom OpenMPController omp_set_num_threads
 #' @export
 mmcm.resamp <- function(x, g, contrast, alternative = c("two.sided", "less", "greater"),
-  nsample = 20000, abseps = 0.001, seed = NULL) {
+  nsample = 20000, abseps = 0.001, seed = NULL, nthread = 2) {
 
   ####################
   # executable check
@@ -215,6 +206,11 @@ mmcm.resamp <- function(x, g, contrast, alternative = c("two.sided", "less", "gr
   if (!is.matrix(contrast)) {
     stop(paste(DNAMEC, "must be a matrix"))
   }
+  if (!is.numeric(nthread)) {
+    nthread <- 1
+  } else if (nthread < 1) {
+    nthread <- 1
+  }
 
   x <- x[is.finite(x)]
   g <- g[is.finite(g)]
@@ -289,6 +285,7 @@ mmcm.resamp <- function(x, g, contrast, alternative = c("two.sided", "less", "gr
     as.integer(length(x)),
     as.double(abseps),
     as.integer(nalternative),
+    as.integer(nthread),
     pval=double(1),
     error=double(1)
   )

diff --git a/README.md b/README.md
@@ -10,6 +10,10 @@ give P-value by using randomized quasi-Monte Carlo method with
 'pmvt' function of package 'mvtnorm', and 'mmcm.resamp' gives
 P-value by using a permutation method.
 
+- Sato Y, Laird NM, Nagashima K, et al. A new statistical screening approach for finding pharmacokinetics-related genes in genome-wide studies. *The Pharmacogenomics Journal* 2009; **9**(2): 137--146. [doi:10.1038/tpj.2008.17](https://doi.org/10.1038/tpj.2008.17).
+- Nagashima K, Sato Y, Hamada C. A modified maximum contrast method for unequal sample sizes in pharmacogenomic studies. *Statistical Applications in Genetics and Molecular Biology* 2011; **10**(1): Article 41. [doi:10.2202/1544-6115.1560](https://doi.org/10.2202/1544-6115.1560).
+- Yoshimura I, Wakana A, Hamada C. A performance comparison of maximum contrast methods to detect dose dependency. *Drug Informatoion Journal* 1997; **31**(2): 423--432. [doi:10.1177/009286159703100213](https://doi.org/10.1177/009286159703100213).
+
 
 ## Installation
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,23 +1,23 @@
-citHeader("To cite", sQuote("mmcm"), "in publications, please use:")
-
-citEntry(
-  entry        = "Article",
-  title        = "A modified maximum contrast method for unequal sample sizes in pharmacogenomic studies",
-  author       = personList(
-                   as.person("Kengo NAGASHIMA"),
-		               as.person("Yasunori SATO"),
-		               as.person("Chikuma HAMADA")
-                 ),
-  journal      = "Statistical Applications in Genetics and Molecular Biology",
-  year         = "2011",
-  volume       = "10",
-  number       = "1",  
-  pages        = "Article 41",
-	url          = "http://dx.doi.org/10.2202/1544-6115.1560",
-  textVersion  = paste(
-    "Nagashima, K., Sato, Y., Hamada, C. (2011).", 
-	  "A modified maximum contrast method for unequal sample sizes in pharmacogenomic studies",
-	  "Stat Appl Genet Mol Biol. 10(1): Article 41.",
-    "URL: http://dx.doi.org/10.2202/1544-6115.1560"
-  )
-)
+citHeader("To cite", sQuote("mmcm"), "in publications, please use:")
+
+citEntry(
+  entry        = "Article",
+  title        = "A modified maximum contrast method for unequal sample sizes in pharmacogenomic studies",
+  author       = personList(
+                   as.person("Kengo NAGASHIMA"),
+		               as.person("Yasunori SATO"),
+		               as.person("Chikuma HAMADA")
+                 ),
+  journal      = "Statistical Applications in Genetics and Molecular Biology",
+  year         = "2011",
+  volume       = "10",
+  number       = "1",  
+  pages        = "Article 41",
+	url          = "http://dx.doi.org/10.2202/1544-6115.1560",
+  textVersion  = paste(
+    "Nagashima, K., Sato, Y., Hamada, C. (2011).", 
+	  "A modified maximum contrast method for unequal sample sizes in pharmacogenomic studies",
+	  "Stat Appl Genet Mol Biol. 10(1): Article 41.",
+    "URL: http://dx.doi.org/10.2202/1544-6115.1560"
+  )
+)