在RStudio中记录R包中的R6类和方法

Question

我正在努力学习R6类及其方法的文档。我的目标是在RStudio中获取方法的自动完成。目前，我只获取方法的名称，但没有通常使用roxygen2记录带参数等功能的帮助信息。

目前，这是我的班级：

#' @importFrom R6 R6Class
MQParameters <- R6::R6Class(
  'MQParameters',
  public=list(
    initialize=function(file_path=NA) {
      private$location <- file_path
      mq_parameters <- read.delim(file_path, stringsAsFactors=FALSE)
      mq_parameters <-
        setNames(mq_parameters$Value, mq_parameters$Parameter)
      private$mq_version <- unname(mq_parameters['Version'])
      private$fasta_file <-
        gsub('\\\\', '/', strsplit(mq_parameters['Fasta file'], ';')[[1]])
    },
    # this method returns the version
    getVersion=function() {
      private$mq_version
    },
    # this methods returns the fastafile.
    # @param new_param it is possible to rewrite the basedir.
    getFastaFile=function(new_basedir=NA) {
      if(is.na(new_basedir)) {
        private$fasta_file
      } else {
        file.path(new_basedir, basename(private$fasta_file))
      }
    }
  ),
  private=list(
    location=NULL,
    mq_version=NULL,
    fasta_file=NULL
  )
)

如果您有兴趣测试这个课程，这里有一个可重复的例子：

df <- data.frame(Parameter=c('Version', 'Fasta file'),
                 Value=c('1.5.2.8','c:\\a\\b.fasta'))
write.table(df, 'jnk.txt', sep='\t', row.names=F)

p <- MQParameters$new('jnk.txt')
p$getVersion()
# [1] "1.5.2.8"
p$getFastaFile()
# [1] "c:/a/b.fasta"
p$getFastaFile(new_basedir='.')
# [1] "./b.fasta"

我不知道如何记录参数，因为参数实际上属于创建者但不属于类。函数内其他方法的参数怎么样？
使用它的方法记录课程的首选方法是什么？

我很想得到＃34;正常＆＃34;来自RStudio的功能，例如点击F1直接进入帮助页面。

通过搜索互联网，我在Github上看到了一些关于这个话题的报告，但是他们已经有一年多了。

更新

感谢mikeck的答案，我现在有了一个很好的文档和它的方法。但我仍然缺乏的是获得函数/方法及其参数的提示的可能性，如此屏幕截图中的常见函数：

我想知道我是否可以以某种方式手动注册我的函数，但由于它没有特定的名称（它总是与您用于对象OBJECTNAME$methodeCall()的变量对象名一起））我不＃ 39;不知道该怎么做。

Answer 1

我的理解是，使用与您的班级相同的NULL来记录@name对象是最简单的，因为这提供了最大的灵活性。我在我的一个包中使用了R6类;你可以查看roxygen here。我在下面列了一个小样本：

#' Python Environment
#' 
#' The Python Environment Class. Provides an interface to a Python process.
#' 
#' 
#' @section Usage:
#' \preformatted{py = PythonEnv$new(port, path)
#'
#' py$start()
#' 
#' py$running
#' 
#' py$exec(..., file = NULL)
#' py$stop(force = FALSE)
#' 
#' }
#'
#' @section Arguments:
#' \code{port} The port to use for communication with Python.
#' 
#' \code{path} The path to the Python executable.
#' 
#' \code{...} Commands to run or named variables to set in the Python process.
#'
#' \code{file} File containing Python code to execute.
#' 
#' \code{force} If \code{TRUE}, force the Python process to terminate
#'   using a sytem call.
#' 
#' @section Methods:
#' \code{$new()} Initialize a Python interface. The Python process is not 
#'   started automatically.
#'   
#' \code{$start()} Start the Python process. The Python process runs 
#'   asynchronously.
#'
#' \code{$running} Check if the Python process is running.
#'   
#' \code{$exec()} Execute the specified Python 
#'   commands and invisibly return printed Python output (if any).
#'   Alternatively, the \code{file} argument can be used to specify
#'   a file containing Python code. Note that there will be no return 
#'   value unless an explicit Python \code{print} statement is executed.
#' 
#' \code{$stop()} Stop the Python process by sending a request to the 
#'   Python process. If \code{force = TRUE}, the process will be 
#'   terminated using a system call instead.
#'
#' @name PythonEnv
#' @examples
#' pypath = Sys.which('python')
#' if(nchar(pypath) > 0) { 
#'   py = PythonEnv$new(path = pypath, port = 6011)
#'   py$start()
#'   py$running
#'   py$stop(force = TRUE)
#' } else 
#' message("No Python distribution found!")
NULL

#' @export
PythonEnv = R6::R6Class("PythonEnv", cloneable = FALSE,
  # actual class definition...

还有其他替代（但类似）的实现; this example使用可能更适合您的@docType class：

#' Class providing object with methods for communication with lightning-viz server
#'
#' @docType class
#' @importFrom R6 R6Class
#' @importFrom RCurl postForm
#' @importFrom RJSONIO fromJSON toJSON
#' @importFrom httr POST
#' @export
#' @keywords data
#' @return Object of \code{\link{R6Class}} with methods for communication with lightning-viz server.
#' @format \code{\link{R6Class}} object.
#' @examples
#' Lightning$new("http://localhost:3000/")
#' Lightning$new("http://your-lightning.herokuapp.com/")
#' @field serveraddress Stores address of your lightning server.
#' @field sessionid Stores id of your current session on the server.
#' @field url Stores url of the last visualization created by this object.
#' @field autoopen Checks if the server is automatically opening the visualizations.
#' @field notebook Checks if the server is in the jupyter notebook mode.
#' #' @section Methods:
#' \describe{
#'   \item{Documentation}{For full documentation of each method go to https://github.com/lightning-viz/lightining-r/}
#'   \item{\code{new(serveraddress)}}{This method is used to create object of this class with \code{serveraddress} as address of the server object is connecting to.}
#'
#'   \item{\code{sethost(serveraddress)}}{This method changes server that you are contacting with to \code{serveraddress}.}
#'   \item{\code{createsession(sessionname = "")}}{This method creates new session on the server with optionally given name in \code{sessionname}.}
#'   \item{\code{usesession(sessionid)}}{This method changes currently used session on the server to the one with id given in \code{sessionid} parameter.}
#'   \item{\code{openviz(vizid = NA)}}{This method by default opens most recently created by this object visualization. If \code{vizid} parameter is given, it opens a visualization with given id instead.}
#'   \item{\code{enableautoopening()}}{This method enables auto opening of every visualisation that you create since that moment. Disabled by default.}
#'   \item{\code{disableautoopening()}}{This method disables auto opening of every visualisation that you create since that moment. Disabled by default.}
#'   \item{\code{line(series, index = NA, color = NA, label = NA, size = NA, xaxis = NA, yaxis = NA, logScaleX = "false", logScaleY = "false")}}{This method creates a line visualization for vector/matrix with each row representing a line, given in \code{series}.}
#'   \item{\code{scatter(x, y, color = NA, label = NA, size = NA, alpha = NA, xaxis = NA, yaxis = NA)}}{This method creates a scatterplot for points with coordinates given in vectors \code{x, y}.}
#'   \item{\code{linestacked(series, color = NA, label = NA, size = NA)}}{This method creates a plot of multiple lines given in matrix \code{series}, with an ability to hide and show every one of them.}
#'   \item{\code{force(matrix, color = NA, label = NA, size = NA)}}{This method creates a force plot for matrix given in \code{matrix}.}
#'   \item{\code{graph(x, y, matrix, color = NA, label = NA, size = NA)}}{This method creates a graph of points with coordinates given in \code{x, y} vectors, with connection given in \code{matrix} connectivity matrix.}
#'   \item{\code{map(regions, weights, colormap)}}{This method creates a world (or USA) map, marking regions given as a vector of abbreviations (3-char for countries, 2-char for states) in \code{regions} with weights given in \code{weights} vector and with \code{colormap} color (string from colorbrewer).}
#'   \item{\code{graphbundled(x, y, matrix, color = NA, label = NA, size = NA)}}{This method creates a bundled graph of points with coordinates given in \code{x, y} vectors, with connection given in \code{matrix} connectivity matrix. Lines on this graph are stacked a bit more than in the \code{graph} function.}
#'   \item{\code{matrix(matrix, colormap)}}{This method creates a visualization of matrix given in \code{matrix} parameter, with its contents used as weights for the colormap given in \code{colormap} (string from colorbrewer).}
#'   \item{\code{adjacency(matrix, label = NA)}}{This method creates a visualization for adjacency matrix given in \code{matrix} parameter.}
#'   \item{\code{scatterline(x, y, t, color = NA, label = NA, size = NA)}}{This method creates a scatterplot for coordinates in vectors \code{x, y} and assignes a line plot to every point on that plot. Each line is given as a row in \code{t} matrix.}
#'   \item{\code{scatter3(x, y, z, color = NA, label = NA, size = NA, alpha = NA)}}{This method creates a 3D scatterplot for coordinates given in vectors \code{x, y, z}.}
#'   \item{\code{image(imgpath)}}{This method uploads image from file \code{imgpath} to the server and creates a visualisation of it.}
#'   \item{\code{gallery(imgpathvector)}}{This method uploads images from vector of file paths \code{imgpathvector} to the server and creates a gallery of these images.}}


Lightning <- R6Class("Lightning",
...
)

修改

如果您正在寻找一种方法来在尝试使用类方法时显示RStudio工具提示...很遗憾，我认为您不会找到一种不需要以某种方式编写类的解决方案这消除了R6类的便利性和功能。

@ f-privé提供了一个能够做你想做的答案 - 只需将这个逻辑扩展到所有方法。例如，myclass$my_method由

访问

my_method = function(r6obj) {
  r6obj$my_method()
}
obj$my_method()
my_method(obj)      # equivalent

换句话说，您需要为每个方法创建一个包装器。这显然比使用obj$my_method()更不方便编程，并且可能首先杀死了使用R6类的有用性。

这里的问题实际上是RStudio。 IDE没有通过分析代码识别R6类的好方法，也无法区分已定义类的方法和列表或环境的元素。此外，RStudio无法提供任意功能的帮助，例如：

na.omit()         # tooltip shows up when cursor is within the parentheses
foo = na.omit
foo()             # no tooltip

这与调用特定R6对象的方法非常类似。

Answer 2

我认为R人不想使用$new(...)来获取新类的实例。他们更喜欢使用具有相同名称的函数来构造它的实例。

那么，你可以做的是重命名你的R6ClassGenerator MQParameters_R6Class并创建另一个函数

MQParameters <- function(file_path = NA) {
  MQParameters_R6Class$new(file_path)
}

然后，将此函数记录为任何其他函数，您将从RStudio获得“显示函数调用及其参数的小黄色窗口”。和快乐的R用户。