version 0.1.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: centrifugeR
 Type: Package
 Title: Non-Trivial Balance of Centrifuge Rotors
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: person("Duy Nghia", "Pham", email = "[email protected]",
     role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1349-1710"))
 Description: Find the numbers of tubes that can be loaded in centrifuge
@@ -13,10 +13,10 @@ Depends: R (>= 3.6.0)
 Imports: pracma (>= 2.2.9), grDevices, graphics, utils
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 NeedsCompilation: no
-Packaged: 2020-04-16 22:56:00 UTC; Nghia Pham
+Packaged: 2020-09-23 07:20:57 UTC; Nghia Pham
 Author: Duy Nghia Pham [aut, cre] (<https://orcid.org/0000-0003-1349-1710>)
 Maintainer: Duy Nghia Pham <[email protected]>
 Repository: CRAN
-Date/Publication: 2020-04-17 08:00:06 UTC
+Date/Publication: 2020-09-23 08:40:15 UTC

MD5

@@ -1,14 +1,16 @@
-d95115a83321f291c39f334c4745e400 *DESCRIPTION
-2feddedc1ccfe37fd6556794d484296f *NAMESPACE
-43db61f120dd6e76f18997a40171887d *R/centrifugeR-package.R
+ce853759f392760689d2046c6fb19fee *DESCRIPTION
+3af5fc3e6dfc5a06dbecb9f558084db0 *NAMESPACE
+fec74a6f6c2a159bd88f13136c33a65f *R/centrifugeR-package.R
 7b45d554c097f85b3ab182bd9557310e *R/rotorCheck.R
-65344e484e1ddbadb470d6a7d372a720 *R/rotorEqual.R
+cb42bcfdefd64e9b905c85320a9e6ed2 *R/rotorEqual.R
 c71d809258dea030959fcbeb08a7c591 *R/rotorSpeed.R
-4b6d974ac8b36bdf1798a86722f880a3 *R/rotorUnequal.R
-ac17fdef594c928cd753a572361bfa41 *R/zzz.R
+b6791096e96ffc85ae1f7b0dfdcf0f2c *R/rotorUnequal.R
+b9d5239b9c40116638086c4a78b75061 *R/rotorVerify.R
+72a264431206dd046d6f506f24e6f0c2 *R/zzz.R
 75abefbea9db81229f4d1aa8773fd523 *inst/CITATION
-c6c0ecfb0bb0f56c77c9908b83c1fb12 *man/centrifugeR-package.Rd
+e4ea5155ffa8a8932a1e9f4b86f24e2e *man/centrifugeR-package.Rd
 bb9e60d3dc45ecf2bbe9c09854ffdd96 *man/rotorCheck.Rd
-15d13414f51d8fc370379d2f3349cb38 *man/rotorEqual.Rd
+a33e22e27cef5d84c49b0f0b2ec657d8 *man/rotorEqual.Rd
 8c2bd025acf39a5c77376017773b2b69 *man/rotorSpeed.Rd
-7611e56bbdda41710997d276775ee8fc *man/rotorUnequal.Rd
+6b6bfbf5bd36611daf26344b569387a6 *man/rotorUnequal.Rd
+aa5a66e9cc172b129994243da008388e *man/rotorVerify.Rd

NAMESPACE

@@ -4,6 +4,7 @@ export(rotorCheck)
 export(rotorEqual)
 export(rotorSpeed)
 export(rotorUnequal)
+export(rotorVerify)
 importFrom(grDevices,palette)
 importFrom(grDevices,rainbow)
 importFrom(graphics,pie)

R/centrifugeR-package.R

@@ -2,7 +2,7 @@
 #'
 #' Find the numbers of tubes that can be loaded in centrifuge rotors in a single
 #' operation and show how to balance these tubes in cases of equal or unequal
-#' masses. Refer to Pham (2020) <doi:10.31224/osf.io/4xs38> for more information
+#' masses. Refer to Pham (2020) \url{https://doi.org/10.31224/osf.io/4xs38} for more information
 #' on package functionality.
 #'
 #' @author Duy Nghia Pham \email{nghiapham@@yandex.com}
@@ -17,10 +17,11 @@
 #'   balance these tubes given that they have the same mass. If their masses are
 #'   not the same, use \code{\link{rotorUnequal}} to know which tubes must be
 #'   increased in mass before they can be loaded. Also, call
+#'   \code{\link{rotorVerify}} to verify pre-existing tube configurations and
 #'   \code{\link{rotorSpeed}} if RPM/RCF conversion is needed.
 #'
 #' @section Copyright: centrifugeR: Non-Trivial Balance of Centrifuge Rotors.
-#'   Copyright (C) 2019  Duy Nghia Pham \cr \cr centrifugeR is free software:
+#'   Copyright (C) 2020  Duy Nghia Pham \cr \cr centrifugeR is free software:
 #'   you can redistribute it and/or modify it under the terms of the GNU General
 #'   Public License as published by the Free Software Foundation, either version
 #'   3 of the License, or (at your option) any later version. \cr \cr

R/rotorEqual.R

@@ -5,6 +5,9 @@
 #'
 #' @param n an integer, the number of rotor buckets.
 #' @param k an integer, the number of tubes.
+#' @param seed an integer, the seed for random number generation. Setting a seed
+#'   ensures the reproducibility of the result. See \code{\link{set.seed}} for
+#'   more details.
 #'
 #' @details The number of rotor buckets \code{n} ranges from \code{4} to
 #'   \code{48}. The number of tubes \code{k} must be greater than \code{0} and
@@ -29,7 +32,8 @@
 #' rotorEqual(30, 19)
 #'
 #' @export
-rotorEqual <- function (n, k) {
+rotorEqual <- function (n, k, seed = 2019) {
+    set.seed(seed)
     if (n < 4 | n > 48) {
         stop("The rotor must have at least 4 buckets and no more than 48 buckets. \n")
     }

R/rotorUnequal.R

@@ -6,6 +6,9 @@
 #' @param n an integer, the number of rotor buckets.
 #' @param mass a numeric vector with optional \code{names} attribute, the masses
 #'   (and optional names) of tubes.
+#' @param seed an integer, the seed for random number generation. Setting a seed
+#'   ensures the reproducibility of the result. See \code{\link{set.seed}} for
+#'   more details.
 #'
 #' @details The number of rotor buckets \code{n} ranges from \code{4} to
 #'   \code{48}. The number of tubes (i.e. \code{length(mass)}) should not be
@@ -48,7 +51,8 @@
 #' rotorUnequal(30, small.samples)
 #'
 #' @export
-rotorUnequal <- function (n, mass = NULL) {
+rotorUnequal <- function (n, mass = NULL, seed = 2019) {
+    set.seed(seed)
     if (n < 4 | n > 48) {
         stop("The rotor must have at least 4 buckets and no more than 48 buckets. \n")
     }
@@ -57,9 +61,6 @@ rotorUnequal <- function (n, mass = NULL) {
         input <- scan("", list(character(), numeric()))
         mass <- "names<-"(input[[2]], input[[1]])
     }
-    if (sum(mass <= 0) > 0) {
-        warning("Mass values should be positive. \n")
-    }
     if (is.null(names(mass))) {
         nm <- vector()
         for (i in seq(length(mass))) {
@@ -69,7 +70,10 @@ rotorUnequal <- function (n, mass = NULL) {
     }
     k <- length(mass)
     if (k == 0 | k > n) {
-        stop("The number of tubes must not be 0 or greater than the number of rotor buckets. \n")
+        stop("The number of tubes must neither be 0 nor greater than the number of rotor buckets. \n")
+    }
+    if (sum(mass <= 0) > 0) {
+        stop("Mass values must be positive. \n")
     }
     prime <- unique(factors(n))
     coeff <- mapply(seq, 0, n / prime, SIMPLIFY = FALSE)

R/rotorVerify.R

@@ -0,0 +1,55 @@
+#' Verify Centrifuge Balance
+#'
+#' \code{rotorVerify} checks whether the rotor is balanced given the positions
+#' of tubes of equal mass.
+#'
+#' @param n an integer, the number of rotor buckets.
+#' @param pos an integer vector, the positions of tubes.
+#'
+#' @details The number of rotor buckets \code{n} ranges from \code{4} to
+#'   \code{48}. The positions of tubes \code{pos} ranges from 1 to \code{n}.
+#'
+#' @return \code{rotorVerify} returns \code{1} if the rotor is balanced and
+#'   \code{0} if the rotor is unbalanced.
+#'
+#' @references Johnsson M. Balancing a centrifuge. R-bloggers. 2016. Available
+#'   from: \url{https://www.r-bloggers.com/2016/06/balancing-a-centrifuge/}.
+#'
+#' @seealso \code{\link{rotorCheck}} for checking centrifuge rotors.
+#'
+#' @examples
+#' rotorVerify(30, c(10, 20, 30))
+#' rotorVerify(30, c(1, 11, 21, 4, 28))
+#'
+#' @export
+rotorVerify <- function (n, pos) {
+    if (n < 4 | n > 48) {
+        stop("The rotor must have at least 4 buckets and no more than 48 buckets. \n")
+    }
+    k <- length(pos)
+    if (k == 0 | k > n) {
+        stop("The number of tubes must neither be 0 nor greater than the number of rotor buckets. \n")
+    }
+    if (sum(pos < 1 | pos > n | pos != floor(pos) | duplicated(pos)) > 0) {
+        stop("The positions of tubes must be different integers ranging from 1 to n. \n")
+    }
+    prime <- unique(factors(n))
+    coeff <- mapply(seq, 0, n / prime, SIMPLIFY = FALSE)
+    coeff.com <- do.call(expand.grid, coeff)
+    linear <- apply(coeff.com, 1, function(x) dot(x, prime))
+    if (!k %in% linear | !(n - k) %in% linear) {
+        stop(paste("CANNOT load", k, "tubes in a rotor with", n, "buckets. \n"))
+    }
+    p2c <- function(x){
+        theta <- (x - 1) * 2 * pi / n
+        c(cos(theta), sin(theta))
+    }
+    if (sum(abs(rowSums(sapply(pos, p2c))) < 10^-10) == 2) {
+        message("The rotor is balanced")
+        result <- 1
+    } else {
+        message("The rotor is unbalanced")
+        result <- 0
+    }
+    result
+}

R/zzz.R

@@ -1,4 +1,4 @@
 .onAttach <- function(libname, pkgname) {
-    packageStartupMessage("centrifugeR Copyright (C) 2019 Duy Nghia Pham")
+    packageStartupMessage("centrifugeR Copyright (C) 2020 Duy Nghia Pham")
     packageStartupMessage("centrifugeR is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions.")
 }