R 包未加载 `Imports` 包

Question

我正在开发一个包，该包的功能依赖于许多其他包中的 dplyr。正如 H. Wickham 在他的 R Packages 一书中所建议的那样，我在 Description 文件中的 Imports 下包含了所有必要的包。

Imports:
  apaTables,
  data.table,
  dplyr,
  magrittr,
  plyr,
  rlang,
  sjstats,
  stats

然后在函数体中使用namespace(函数的细节这里就不用说了，我想强调的是我用的是推荐的packagename::fun() Hadley 在他的书中推荐的格式):

#'
#' @title Confidence intervals for Partial Eta Squared
#' @name partialeta_sq_ci
#' @author Indrajeet Patil
#'
#' @param lm_object stats::lm linear model object
#' @param conf.level Level of confidence for the confidence interval
#' @importFrom magrittr %>%
#' @export

partialeta_sq_ci <- function(lm_object, conf.level = 0.95) {
  # get the linear model object and turn it into a matrix and turn row names into a variable called "effect"
  # compute partial eta-squared for each effect
  # add additional columns containing data and formula that was used to create these effects

  x <-
    dplyr::left_join(
      # details from the anova results
      x = data.table::setDT(x = as.data.frame(as.matrix(
        stats::anova(object = lm_object)
      )),
      keep.rownames = "effect"),
      # other information about the results (data and formula used, etc.)
      y = data.table::setDT(x = as.data.frame(
        cbind(
          "effsize" = sjstats::eta_sq(
            model = stats::anova(object = lm_object),
            partial = TRUE
          ),
          "data" = as.character(lm_object$call[3]),
          "formula" = as.character(lm_object$call[2])
        )
      ),
      keep.rownames = "effect"),
      # merge the two preceding pieces of information by the common element of Effect
      by = "effect"
    )
  # create a new column for residual degrees of freedom
  x$df2 <- x$Df[x$effect == "Residuals"]
  # remove sum of squares columns since they will not be useful
  x <-
    x %>%
    dplyr::select(.data = .,
                  -c(base::grep(pattern = "Sq", x = names(x))))
  # remove NAs, which would remove the row containing Residuals (redundant at this point)
  x <- na.omit(x)
  # rename to something more meaningful and tidy
  x <- plyr::rename(x = x,
                    replace = c("Df" = "df1",
                                "F value" = "F.value"))
  # rearrange the columns
  x <-
    x[, c("F.value",
          "df1",
          "df2",
          "effect",
          "effsize",
          "Pr(>F)",
          "data",
          "formula")]
  # convert the effect into a factor
  x$effect <- as.factor(x$effect)
  # for each type of effect, compute partial eta-squared confidence intervals, which would return a list
  ci_df <-
    plyr::dlply(
      .data = x,
      .variables = .(effect),
      .fun = function(data)
        apaTables::get.ci.partial.eta.squared(
          F.value = data$F.value,
          df1 = data$df1,
          df2 = data$df2,
          conf.level = conf.level
        )
    )
  # get elements from the effect size confidence intervals list into a neat dataframe
  ci_df <-
    plyr::ldply(
      .data = ci_df,
      .fun = function(x)
        cbind("LL" = x[[1]],
              "UL" = x[[2]])
    )
  # merge the dataframe containing effect sizes with the dataframe containing rest of the information
  effsize_ci <- base::merge(x = x,
                            y = ci_df,
                            by = "effect")
  # returning the final dataframe
  return(effsize_ci)

}

但是当我构建包并使用该函数时，它给了我以下错误-

Error in x %>% dplyr::select(.data = ., -c(base::grep(pattern = "Sq",  : 
  could not find function "%>%"

我做错了什么？

附言如果您需要更多详细信息，GitHub 存储库:https://github.com/IndrajeetPatil/ipmisc有问题的功能:https://github.com/IndrajeetPatil/ipmisc/blob/master/R/partialeta_sq_ci.R描述文件:https://github.com/IndrajeetPatil/ipmisc/blob/master/DESCRIPTION

Answer 1

总结一下，这里有几个问题:

• 使用 packagename::fun() 是一个不错的选择，但对运算符(operator)来说效果不佳。特别是对于管道 (%>%)，使用例如相反，一个函数会破坏它的目的。

• @importFrom 标签比 @import 更可取，因为它更狭窄和明确。这两个都会在调用 roxygen2::roxygenize() 时影响 NAMESPACE 文件。但是请注意，roxygen 不会混淆用户定义的 NAMESPACE 文件，因为通常情况下人们更愿意自己手动处理它(例如，当包提供 S3 类和/或方法时), 然后需要撤消 roxygen 的覆盖。删除现有的 NAMESPACE 文件会让 roxygen 重新创建它。 Roxygen 通常会在 NAMESPACE 文件中添加一行以识别它是否应该更新它:

  # Generated by roxygen2: do not edit by hand

• DESCRIPTION 文件中的依赖项既没有被 roxygen 修改，也没有 roxygen 将它们添加到 NAMESPACE(请注意，这否则会导致完整的包导入，我们宁愿通过 @importFrom)。 DESCRIPTION 文件需要手动处理，确保 Imports: 部分涵盖通过 NAMESPACE 使用的所有包，即通过 @import 和 @ importFrom，以及通过 packagename::fun()