---
title: Package development for PMDA Oncology inquiries
tags:  #r with pharma lab meetup 1  
author: [森岡裕[SASユーザー総会世話人]](https://convert.docswell.com/user/6484025)
site: [Docswell](https://www.docswell.com/)
thumbnail: https://bcdn.docswell.com/page/KE4WVK6PJ1.jpg?width=480
description: Package development for PMDA Oncology inquiries by 森岡裕[SASユーザー総会世話人]
published: April 05, 26
canonical: https://convert.docswell.com/s/6484025/KVJ1PX-2026-04-05-102130
---
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Package development
for PMDA Oncology
inquiries
PHUSE OST
Shunsuke Goto
Hiro Kosako
Tomoyuki Namai
Hiroki Yamanobe
Yuichi Nakajima


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本日の発表のゴール
PHUSE OSTの活動の一環である{anaume} packageについて知っていただく
{anaume}を例に、一般的なPackageの構成要素について理解を深める
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Introduction of {anaume}
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Challenges regarding to AE analysis of PMDA queries
in oncology
Age group
•
A large number of similar-format reports
are required within a short period.
ALL AE
•
No standardized format like those
defined by the FDA.
AE with
Grade >=3
-> This leads to challenges in preparation
and streamlining.
Serious AE
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Package to solve this challenge: {anaume}
•
Analysis Utility for AE Mapping & Embedding
•
Package to accelerate table generation for query from PMDA
•
Using ARD to generate table
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Analysis Results Data (ARD) is structured dataset that
represents the outputs of statistical analyses.
CDISC-AnalysisResultsLogicalModel-Presentation-FINAL.pdf
Analysis Results Datasets – Analysis Results Datasets Using Open-Source Tools from the {pharmaverse}
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Strong points of using ARD
Standardization
Efficiency
Reproductivity
/Automation
• Uniformity of summary table aggregation units,
column names, and results between analyses
• Quick tabulation and re-formatting
• Enable QC easier
• The same analysis logic can be easily applied to other
study or subgroup.
• ARD can be used in a variety of ways, such as in
tables, R Shiny, figures, etc.
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Working flow from data to reports using ARD
ADaM
ARD
Reports
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make_ae_type()
To create event
flag
jpn_query_overview()
To create ARD for summary information
Inquiry # 1
AE1
Analysis Results
(summary)
For AE1
ARD Summary
For AE1
ｊpn_query_summary_pt
To create ARD for PT summary
ADAE
make_ae_type()
To create event
flag
Analysis Results
(PT summary)
For AE1
ARD PT
summary
For AE1
jpn_query_overview()
To create ARD for summary information
Inquiry # 1
AE2
ARD Summary
For AE2
Analysis Results
(summary)
For AE1
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Step1: Define the event
make_ae_type()
To create event
flag
jpn_query_overview()
To create ARD for summary information
Step3: Generate outputs from ARD
Inquiry # 1
AE1
Analysis Results
(summary)
For AE1
ARD Summary
For AE1
ｊpn_query_summary_pt
To create ARD for PT summary
ADAE
make_ae_type()
To create event
flag
Step2: Create Inquiry
ARD # 1
AE2
Analysis Results
(PT summary)
For AE1
ARD PT
summary
For AE1
jpn_query_overview()
To create ARD for summary information
ARD Summary
For AE2
Analysis Results
(summary)
For AE1
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Step1: Define the event
make_ae_type
•
Define conditions for target AEs and display labels for tables
•
Create an object of class ae_type (essentially a list)
•
Pass this object as an argument to subsequent functions for flexible analysis
> make_ae_type("aeg3", "AE >= Grade 3",expr(AEGRD == "Y"))
ae_type
id: aeg3
Label to be displayed
Condition for this ae type
label: AE >= Grade 3
condition: AEGRD == "Y"
> ae_types <- list(
+
make_ae_type("any_ae",
+
make_ae_type("aeg3",
+
make_ae_type("sae",
+
make_ae_type("fatal",
+
make_ae_type("disc",
+
make_ae_type("itrr",
+
make_ae_type("redu",
+ )
"Any AE",
"AE >= Grade 3",
"Any SAE",
"Fatal SAEs",
"AE leads drug withdraw",
"AE leads drug interrupt",
"AE leads to dose reduction",
expr(TRUE)),
expr(AEGRD == "Y")),
expr(AESER == "Y")),
expr(AESER == "Y" & AEFAT == "Y")),
expr(AEDISCON == "Y")),
expr(AEITRR == "Y")),
expr(AEREDUCE == "Y"))
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Step2: Create ARD
jpn_query_overview/ｊpn_query_summary_pt
•
jpn_query_overview()
– Function to Generate ARD for AE Overview
•
ｊpn_query_summary_pt()
– Function to Generate ARD for AE by PT
Both functions internally use {cards}.
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Step2: Create ARD
ex) jpn_query_overview
•
jpn_query_overview()
> jpn_query_overview(
+
data = adae,
+
denominator = adsl,
+
ae_types = ae_types,
+
by = TRT01A
+ )
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Step3: Create outputs from ARD
•
Provide template program to generate table from ARD
instead of functions for flexible modification in actual queries.
•
Generate Output from ARD using:
✓{gt}
✓{gtsummary}
✓{tfrmt}
•
Next Slides Will Show Examples Using {tfrmt}
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Structure of R package
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Basic components of R Package
•
DESCRIPTION
•
NAMESPACE
•
R
•
README
•
man
•
Vignettes
•
_pkgdown.yml
•
tests
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Basic components of R Package
•
DESCRIPTION
•
NAMESPACE
•
R
•
README
•
man
•
vignettes
•
_pkgdown.yml
•
tests
Packageに必須となるMetadata
Packageに含まれるR pgm
Document
PackageのValidation用のUnit test
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Basic components of R Package
•
DESCRIPTION
•
NAMESPACE
•
R
•
README
•
man
•
vignettes
•
_pkgdown.yml
•
tests
Packageに必須となるMetadata
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Metadata
DESCRIPTION
•
パッケージ名、概要、作者、ライセンス、依存関係（Depends/Imports/Suggests など）と
いった 全体情報を宣言
Package: anaume
Title: Adverse Event Analysis Utilities for Clinical Trials
Version: 0.0.0.9000
Authors@R:
person("First", "Last", , "first.last@example.com", role = c("aut", "cre"))
Description: Provides utilities for summarizing adverse events in clinical
trials following Japanese regulatory conventions. Includes helpers for
defining AE type filters, binding datasets by AE type, and generating
ARD (Analysis Results Data) objects.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
R (>= 3.5)
Imports:
cli,
dplyr,
purrr,
rlang,
cards
Suggests:
testthat (>= 3.0.0)
Config/testthat/edition: 3
URL: https://github.com/yourname/anaume
BugReports: https://github.com/yourname/anaume/issues
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Metadata
NAMESPACE
•
どの関数・クラス等をPackageから参照できるようにするかを決める
•
他パッケージの関数等を自パッケージからどう参照するかを決める（imports）
•
通常Manualでは編集しない
S3method(format,ae_type)
S3method(print,ae_type)
export(ae_condition)
export(ae_id)
export(ae_label)
export(jpn_query_aggregate)
export(jpn_query_base)
export(jpn_query_overview)
export(make_ae_type)
export(merge_ae_types)
importFrom(cards,ard_stack_hierarchical)
importFrom(dplyr,all_of)
importFrom(dplyr,filter)
importFrom(dplyr,group_vars)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(purrr,map_dfr)
importFrom(rlang,enquo)
importFrom(rlang,eval_tidy)
importFrom(rlang,quo_is_null)
importFrom(tidyselect,eval_select)
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Basic components of R Package
•
DESCRIPTION
•
NAMESPACE
•
R
•
README
•
man
•
vignettes
•
_pkgdown.yml
•
tests
Packageに含まれるR pgm
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Programs
R pgm
•
関数などの R コードを格納する。
•
.R ファイルは、パッケージ読み込み時に自動的にソースされる。
•
外部に公開されるかどうかは NAMESPACE によって制御される。
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Basic components of R Package
•
DESCRIPTION
•
NAMESPACE
•
R
•
README
•
man
•
vignettes
•
_pkgdown.yml
•
tests
Document
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Document
Readme
•
GithubやGithub pagesのTop pageに表示される内容
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Github pagesとは？？
•
GitHub のリポジトリ内容から、Webサイト（HTML/CSS/JS）を公開できる機能
•
Packageの使い方などの情報を掲載するために使用されることが多い
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Document
man
•
各関数のDocumentを格納したFolder
•
各関数のDocumentはGithub pagesやRstudioの
Help画面に表示される。
•
Manualでは編集しないことが多く、roxygenに
よって記載した内容がDocumentとなる
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roxygen
•
R コード中のコメントから、ドキュメント（man/*.Rd）やNAMESPACE を自動生成する仕組み。
•
コードとドキュメントを同じ場所で管理することで、保守性を高める。
#' Create an `ae_type` object
#'
#' @param id ID value for the object.
#' @param label Label for the AE type.
#' @param condition Expression for
subsetting the dataset.
#'
#' @returns An `ae_type` object.
#' @export
#'
#' @examples
#' make_ae_type("all_ae", "All AEs")
#' make_ae_type("rel_ae", "Related
AEs", AEREL == "Y")
make_ae_type <- function(id, label,
condition = NULL) {
. . .
}
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Document
vignettes
•
関数横断的な内容としてDocumentを格納したFolder
•
Github pages上で、関数横断的な内容をArticlesに相当することが多い。
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Document
_pkgdown.yml
•
Github pages生成時の設定ファイル
•
サイトの見た目・構成・表示内容をYAML形式で制御する。
url: https://yuichinakaima.github.io/anaume/
template:
bootstrap: 5
lang: en
title: anaume
description: "{Package documentation for
anaume}."
repo:
url:
home: https://github.com/yuichinakaima/anaume
issue: https://github.com/yuichinakaima/anaume/issues
どの項目に何のDocumentを
配置するか等を設定
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Basic components of R Package
•
DESCRIPTION
•
NAMESPACE
•
R
•
README
•
man
•
vignettes
•
_pkgdown.yml
•
tests
PackageのValidation用のUnit test
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Test
Unit test
•
Packageでは関数やFeatureが意図通り機能しているかをDevloperがテストしている。
•
個別のTESTはtestthat folder内に保管されることが多く、testthat内の全てのtestを
testthat.Rで実行する構造を持つことが多い。
•
R CMD check 時に自動実行されるため、関数修正時に意図しない挙動の変化を防ぐ。
# This file is part of the standard setup for testthat.
# It is recommended that you do not modify it.
#
# Where should you do additional test configuration?
# Learn more about the roles of various files in:
# * https://r-pkgs.org/testing-design.html#sec-tests-filesoverview
# * https://testthat.r-lib.org/articles/special-files.html
library(testthat)
library(anaume)
test_check("anaume")
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Test
Unit testの例
test_that("make_ae_type creates ae_type object
without condition", {
obj <- make_ae_type("all_ae", "All AEs")
expect_s3_class(obj, "ae_type")
expect_equal(obj$id, "all_ae")
expect_equal(obj$label, "All AEs")
expect_true(rlang::quo_is_null(obj$condition)
)
})
意図した値が返ってくるかを確認
test_that("make_ae_type creates ae_type object
with condition", {
obj <- make_ae_type("rel_ae", "Related AEs",
AEREL == "Y")
expect_s3_class(obj, "ae_type")
expect_equal(obj$id, "rel_ae")
expect_equal(obj$label, "Related AEs")
expect_false(rlang::quo_is_null(obj$condition
))
})
条件を変えて動作確認
test_that("make_ae_type errors when id is not a
string", {
expect_error(make_ae_type(123, "label"))
expect_error(make_ae_type(c("a", "b"),
"label"))
})
意図したErrorが出ることを確認
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本日の発表のゴール（再掲）
PHUSE OSTの活動の一環である{anaume} packageについて知っていただく
{anaume}を例に、一般的なPackageの構成要素について理解を深める
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End of slides
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BU
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{cards} package
•
Part of Pharmaverse
•
R package to create ARD
ard_categorical(
data = adae,
by = c('AGEGR1','TRT01A’),
variables = AEDECOD,
denominator = adsl
)
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