Merge pull request #3 from xfz329/develop

0.1.3

CHANGELOG.md

@@ -1,4 +1,7 @@
 # Change logs
+## 0.1.3
+Minor update.
+* Docs update.
 ## 0.1.2
 Major update.
 * The first R-implementation version of pk4adi.

DESCRIPTION

@@ -1,13 +1,24 @@
 Package: pk4adi
 Type: Package
 Title: PK for Anesthetic Depth Indicators
-Version: 0.1.2
-Author: Jiang Feng
-Maintainer: xfz329 <[email protected]>
-Description: Calculate and compare the Anesthetic Depth Indicators PK values in R
-    The package's name pk4adi is short for "PK for Anesthetic Depth Indicators". 
-    The prediction probability (PK) was first proposed by Dr. Warren D. Smith in the paper Measuring the Performance of Anesthetic Depth Indicators. 
+Version: 0.1.3
+Authors@R: c(
+    person("Feng","Jiang",          role=c("aut","cre"), email="[email protected]"),
+    person("Hua","Li",              role="ctb"),
+    person("Mengge","Zhang",        role="ctb"),
+    person("Wanlin","Chen",         role="ctb"),
+    person("Warren D","Smith",      role="ctb"),
+    person("Robert C","Dutton",     role="ctb"),
+    person("Ty N","Smith",          role="ctb"))
+Maintainer: Feng Jiang <[email protected]>
+Description: Calculate and compare the Anesthetic Depth Indicators PK values in R language
+    The prediction probability (PK) is a widely used tool for the anesthetic depth indicators,
+    which was first proposed by Dr. Warren D. Smith in the paper 
+    Warren D. Smith; Robert C. Dutton; Ty N. Smith (1996) <doi:10.1097/00000542-199601000-00005> and
+    Warren D. Smith; Robert C. Dutton; Ty N. Smith (1996) <doi:10.1002/(SICI)1097-0258(19960615)15:11<1199::AID-SIM218>3.0.CO;2-Y>.
+    They provide the Micro xls files to calculate and compare the PK values.
     This package provide the easy-to-use API to calculate and compare the PK values using the R language. 
+    The package's name, pk4adi, is short for "PK for Anesthetic Depth Indicators". 
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2023 xfz329
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2023
+COPYRIGHT HOLDER: Zhejiang University

R/calculate_pk.R

@@ -1,15 +1,19 @@
-#' @title Compute the pk value to Measure the Performance of Anesthetic Depth Indicators.
+#' @title Compute the PK value to Measure the Performance of Anesthetic Depth Indicators.
 #'
 #' @param x_in a vector, the indicator.
 #' @param y_in a vector, the state.
 #'
 #' @return a list containing all the matrices and variables during the calculation.
-#'     The value list$type is "PK", which indicated the list is return-value of the function calculate_pk().
+#'     The value list$type is "PK", which indicated the list is the return-value of the function calculate_pk().
 #'     The type of list$basic is also a list, which contains the most important results of the function.
 #'     The type of list$matrices is also a list, which contains all the matrices during the calculation.
 #'     The type of list$details is also a list, which contains all the intermediate variables during the calculation.
 #'
-#' @references Warren D. Smith, Robert C. Dutton, Ty N. Smith; Measuring the Performance of Anesthetic Depth Indicators. Anesthesiology 1996; 84:38–51 doi: https://doi.org/10.1097/00000542-199601000-00005.
+#' @references Warren D. Smith, Robert C. Dutton, Ty N. Smith; Measuring the Performance of Anesthetic Depth Indicators. 
+#'     Anesthesiology 1996; 84:38–51 doi: https://doi.org/10.1097/00000542-199601000-00005.
+#' @references Warren D. Smith, Robert C. Dutton, Ty N. Smith; A measure of association for assessing prediction accuracy 
+#'     that is a generalization of nonparametric ROC area. Statistics in Medicine 1996; 15: 1119-1215 
+#'     doi: https://doi.org/10.1002/(SICI)1097-0258(19960615)15:11<1199::AID-SIM218>3.0.CO;2-Y.
 #'
 #' @import data.table
 #'
@@ -18,17 +22,17 @@
 #' @examples
 #' x1 <- c(0, 0, 0, 0, 0, 0)
 #' y1 <- c(1, 1, 1, 1, 1, 2)
-#' ans <- calculate_pk(x1, y1)
+#' ans1 <- calculate_pk(x1, y1)
 #'
 #' ## show the most important results.
-#' print(ans$basic)
+#' print(ans1$basic)
 #'
 #' x2 <- c(1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 6)
 #' y2 <- c(1, 1, 1, 1, 1, 2, 1, 1, 3, 3, 2, 2, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 3)
 #' ans2 <- calculate_pk(x2, y2)
 #'
 #' ## show the full results.
-#' print(ans)
+#' print(ans2)
 calculate_pk <- function(x_in, y_in) {
     x <- x_in
     y <- y_in

R/compare_pks.R

@@ -1,4 +1,4 @@
-#' @title Compare two answers of the pk values.
+#' @title Compare two answers of the PK values.
 #'
 #' @description Both of the two input have to be the output of the function calculate_pk().
 #'
@@ -7,12 +7,16 @@
 #' @param pk2 a list, the output of the function calculate_pk().
 #'
 #' @return a list containing all the variables during the calculation.
-#'     The value list$type is "PKC", which indicated the list is return-value of the function compare_pk().
+#'     The value list$type is "PKC", which indicated the list is the return-value of the function compare_pk().
 #'     The type of list$group is also a list, which contains the normal distribution test results for the group variables.
 #'     The type of list$pair is also a list, which contains the t distribution test results for the pair variables.
 #'     The type of list$details is also a list, which contains all the intermediate variables during the calculation.
 #'
-#' @references Warren D. Smith, Robert C. Dutton, Ty N. Smith; Measuring the Performance of Anesthetic Depth Indicators. Anesthesiology 1996; 84:38–51 doi: https://doi.org/10.1097/00000542-199601000-00005.
+#' @references Warren D. Smith, Robert C. Dutton, Ty N. Smith; Measuring the Performance of Anesthetic Depth Indicators. 
+#'     Anesthesiology 1996; 84:38–51 doi: https://doi.org/10.1097/00000542-199601000-00005.
+#' @references Warren D. Smith, Robert C. Dutton, Ty N. Smith; A measure of association for assessing prediction accuracy 
+#'     that is a generalization of nonparametric ROC area. Statistics in Medicine 1996; 15: 1119-1215 
+#'     doi: https://doi.org/10.1002/(SICI)1097-0258(19960615)15:11<1199::AID-SIM218>3.0.CO;2-Y.
 #'
 #' @importFrom stats pnorm
 #' @importFrom stats pt

README.md

@@ -77,17 +77,17 @@ The best way to use this package is to use R scripts.
 ```r
 x1 <- c(0, 0, 0, 0, 0, 0)
 y1 <- c(1, 1, 1, 1, 1, 2)
-ans <- calculate_pk(x1, y1)
+ans1 <- calculate_pk(x1, y1)
 
 ## show the most important results.
-print(ans$basic)
+print(ans1$basic)
 
 x2 <- c(1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 6)
 y2 <- c(1, 1, 1, 1, 1, 2, 1, 1, 3, 3, 2, 2, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 3)
 ans2 <- calculate_pk(x2, y2)
 
 ## show the full results.
-print(ans)
+print(ans2$basic)
 ```
 You will get the following output.
 ```r