分散分析についてANOVA（Analysis of Variance）
分散分析
数学いらずの医科統計学で、統計の概念的な理解を深めているのですが、 分散分析の理解については、以下の書籍や、リンクなどを参考に数式含めて再学習しました。
この東京大学出版会シリーズ、赤の統計学入門、緑の人文・社会科学の統計学と並んで、よく纏まっています。
あくまで、数式は使わずに言葉で纏めておきます。
一元配置分散分析
１つの要因への従属変数への影響を分析する（3グループ以上でも可能）。
http://elsur.jpn.org/resource/anova.pdf
- 平方和を分解
- 平均平方を算出
- 検討したい要因についてF（変動部分と誤差部分の二つの分散比）を求め、帰無仮説の棄却の有無を判断
これらのばらつきが有意に差があるなら、「平均値には差がある」という判断ができる。
例えば、A組、B組、C組の生徒に身長差があるかどうかを検証する。
多元配置分散分析
複数の 要因 (2 つ以上) による従属変数への影響を分析する。
この場合に、要因間の交互作用（interaction）を考慮する必要がある。
http://www.u.tsukuba.ac.jp/~hirai.akiyo.ft/forstudents/eigokyouikugaku7.files/2013_5_28.pdf
Clinical Pictureを投稿する
前回、レターを投稿するで好評いただいたので、clinical pictureに関しても纏めておきます。 ＊2019年10月19日Radiology追記しました。
投稿先あれこれ
NEJM
Please include a title for your submission. The title should contain no more than eight words. No more than two authors may be listed. Please provide the name, highest academic degree, address, e-mail address, telephone number, and fax number of each author. The legend should contain no more than 150 words.
http://www.nejm.org/page/author-center/images-in-clinical-medicine
JAMA
"What Would You Do Next?" with 4 single-phrase plausible treatment options describing possible courses of action with 1 being preferred Case presentation: 250 words Discussion: 500-600 words ≤10 references ≤3 authors 1-2 small figures Patient permission may be needed
Gastroenterology
Clinical Challenges and Images in GI (See full information about article types here) This article type is presented as an unknown with the diagnosis hinging on the correct interpretation and integration of the image and clinical data. Submissions must adhere to the following guidelines: Manuscript: only Microsoft Word documents will be accepted. Title Page: title (cannot reveal diagnosis); authors' names (limit of three); authors' institutions; corresponding author contact information; conflict of interest statement (for all authors). Word Count: Q&A format (one page each). Abstract: not required. Tables/Figures: no limit. Please submit figures as separate attachments in JPEG, TIFF, EPS, or PDF formats (300 PPI resolution). Each figure should be labeled with letters only (i.e., no subpanels). All necessary information pertaining to figures must be included in the text (i.e., no figure legends). The inclusion of three or more images will qualify the submission for online-only publication. References: limited to three.
Clinical Gastroenterology and Hepatology
Image of the Month Image of the Month presents a striking clinical image(s) that is meant to challenge and inform the reader. Although priority will be given to exceptionally unique submissions, and those that are not similar to recently published cases; authors should be encouraged to present quality images of more commonly encountered diseases and conditions. All submissions should contain no more than four (4) color or black and white images of 300 dpi resolution. Images should be accompanied by a Word document containing a brief description of no more than 200 words. The text should succinctly present relevant clinical information, including a short description of the patient's history, relevant findings, clinical course, response to treatment, and condition at last follow-up. No more than three authors are allowed on each submission. Contributors must provide their names, addresses, phone, and e-mail addresses.
http://www.cghjournal.org/content/authorinfo
Canadian Medical Association Journal
Clinical images Images are chosen because they are particularly intriguing, classic or dramatic. Preference is given to common presentations of important rare conditions and important unusual presentations of common problems. Structure: 300 word limit; up to two authors; up to three references formatted in the Vancouver style figure and case pertaining to a real patient; clear, appropriately labelled, high-resolution images must be accompanied by a figure caption A brief case description is followed by a concise explanation of the educational significance of the images that typically includes epidemiology, differential diagnosis, investigations, management and prognosis For examples, see Clinical images
Cleveland Clinic Journal of Medicine
http://www.mdedge.com/ccjm/page/clinical-picture
Netherland Journal of Medicine
Photo quiz A photo quiz should not exceed 500 words and include no more than two figures and four references conform the Vancouver style. Abbreviations of measurements should be quoted in SI units.
QJM（Quarterly Journal of Medicine）
Clinical pictures should be no more than 500 words. Ideally, we suggest 200-300 words. Only one figure file is allowed for the image. The selected figure file may contain two images (labelled figure 1a and 1b). Clinical pictures should have six references or fewer. The patient's consent is required for photographs of the patient. Consent should be in the form of a letter (written by author or patient) and must be signed by the patient.
Instructions to Authors | QJM: An International Journal of Medicine | Oxford Academic
Journal of General Internal Medicine
Clinical images report on visual findings in clinical medicine that have educational value. They can include radiology results, high quality clinical images, or electrocardiograms. Images should have a text description that does not exceed 200 words. No more than three authors may be listed. In the initial submission (for clinical images ONLY), each image should be sent as a separate file with the submitted text.
https://jgimed.org/authors/JGIM%20Instructions%20for%20Authors.pdf
European Journal of Internal Medicine
Internal Medicine Flashcards Please see Introducing the "Internal Medicine Flashcards": Call for papers Volume 24, Issue 6, published online only. Authors: maximum 3 Image: one, single or multi-paneled. Only original, high-quality images will be considered for publication, provided they do not contain material that has been submitted or published elsewhere. If a photo of an identifiable patient is used, a specific release form must be completed and signed by the patient and enclosed to the submission. All the printed information that might identify the patient or the authors' institution (including but not limited to the hospital or patient name, date or place) should be removed from the images Main section (case description): maximum 175 words Discussion section: maximum 225 words + maximum 3 references
Guide for authors - European Journal of Internal Medicine - ISSN 0953-6205
http://www.ejinme.com/article/S0953-6205(13)00206-9/fulltext
Internal Medicine
Pictures in Clinical Medicine Images depicting an instructive case, a novel finding and/or element of current interest for clinical medicine. The manuscript text should not exceed 150 words with up to 2 references. The picture legend should not be contained. The title should be concise and contain up to 8 words and there should be no more than 4 pictures. Only 4 authors may be listed.
Instructions to Authors｜Internal Medicine
Radiology
仙台厚生病院 齋藤宏章 先生に教えていただきました。ありがとうございました。
Radiologyに掲載された、齋藤先生の論文はこちらです。
Images in Radiology
Images in Radiology are state-of-the-art images covering a range of both common and uncommon radiologic conditions. The imaging findings are compelling, visually appealing, and demonstrative. Images in Radiology captures the excitement of state-of-the-art imaging and discovery in our discipline. Images are of interest to a broad range of the readership. Images in Radiology are not intended to be case reports.
Original, high-quality images are considered for publication provided they do not contain material that has been submitted or published elsewhere. To submit an image for publication in Radiology, please follow the submission instructions below. At the discretion of the Editor, images may appear in the print version of the Journal, the electronic version, or both.
Submission
Title: no more than 8 words
Authors: no more than 2 authors
Figure Limit: 1-2 maximum
Legend word count: no more than 150 words
Figures and legend text should be in one double-spaced Word document
Figures must also be submitted in separate TIF, EPS, AI, or PSD files with 600 dpi
Include a Full Title Page
R markdownのknitr::opts_chunk設定をどうしているか。
忘備録的に。 私は、基本はこのスタイルで、
- figureの縦横比が一致するようにしている。
- tidyverseが静かに発動するようにしている。
knitr::opts_chunk$set(echo = TRUE, out.width = 480, out.height = 480, fig.width = 7,fig.height = 7) library(tidyverse, quietly = T)
他にも、何か良いsetupあれば教えてください！
レターを投稿する
レターとは
いわゆるレターとは、簡単に言うと、読者の投稿欄へのお手紙です。論文を読んで浮かんだ疑問点について著者へ問い合わせ、議論します。 critical appraisal (批判的吟味)の力を養うことが出来ます。
たかがレター、とも言われますが、されどレターです。
論文を読んで、もし疑問点が生まれたら、投稿してみるのも良いでしょう。
主な医学誌のレターの投稿について、以下に纏めてみます。
医学4大誌
NEJM, JAMA, Lancet, BMJが4大誌とされていますが、それぞれ、レターの投稿を受け付けています。 投稿規定は以下のようになっています。
NEJM
Letter to the editorの投稿について(英語)
Letters in reference to a Journal article must not exceed 175 words (excluding references), and must be received within three weeks after publication of the article. Articles are available for selection on the submission site on the print publication date each Thursday and remain for three weeks. If you are responding to an Online First article that does not have a print publication date, the article will be listed under "Online Articles." Letters not related to a Journal article must not exceed 400 words (excluding references). A letter can have no more than five references and one figure or table. A letter can be signed by no more than three authors.
JAMA
Letter to the editorの投稿について(英語)
Letter to the Editor Letters discussing a recent article in this journal should be submitted within 4 weeks of the article's publication in print.3 Letters received after 4 weeks will rarely be considered. Letters should not exceed 400 words of text and 5 references, 1 of which should be to the recent article. Letters may have no more than 3 authors. The text should include the full name, academic degrees, and a single institutional affiliation for each author and the email address for the corresponding author. Letters must not duplicate other material published or submitted for publication and should not include unpublished data. Letters not meeting these specifications are generally not considered. Letters being considered for publication ordinarily will be sent to the authors of the original article, who will be given the opportunity to reply. Letters will be published at the discretion of the editors and are subject to abridgement and editing for style and content.
Lancet
Correspondence
• We welcome correspondence on content published in The Lancet or on other topics of interest to our readers
• Letters for publication in the print journal must reach us within 2 weeks of publication of the original item and should be no longer than 250 words
• Letters of general interest, unlinked to items published in the journal, can be up to 400 words long
• Correspondence letters are not usually peer reviewed (we rarely publish original research or Case Reports in this section), but the journal might invite replies from the authors of the original publication, or pass on letters to these authors
• Only one table or figure is permitted, and there should be no more than five references and five authors
• All accepted letters are edited, and proofs will be sent out to authors before publication
• Some letters might be chosen for online-only publication
BMJ
Responding to articles (rapid responses, letters)(英語)
We won’t publish responses that we consider inappropriate. We won’t publish responses that are likely to end us up in legal difficulties or that are obscene, libellous (or would require us spending time or money to establish that they aren't), or in some other way illegal—for example, inciting racial hatred, contempt of court, breach of intellectual property rights. We won’t publish responses that are over 1000 words long (excluding references), incomprehensible, insubstantial, written in capital letters, not written in English, almost entirely a quote from somewhere else, gratuitously rude, or blatant advertising. We also won’t publish responses that give information on patients without their written consent, are sent by someone who does not provide adequate and accurate personal details, including a functioning email address, or are from people we suspect have used an alias or who do not respond to email. However, it is for us to decide whether we believe it appropriate to post a given response.
こうした一流誌の採択率は10%とも言われています。
JAMA Oncology
Letters discussing a recent article in this journal should be submitted within 4 weeks of the article's publication online.3 Letters received after 4 weeks will rarely be considered. Letters should not exceed 400 words of text and 5 references, 1 of which should be to the recent article. Letters may have no more than 3 authors. The text should include the full name, academic degrees, and a single institutional affiliation for each author and the email address for the corresponding author. Letters must not duplicate other material published or submitted for publication and should not include unpublished data. Letters not meeting these specifications are generally not considered. Letters being considered for publication ordinarily will be sent to the authors of the original article, who will be given the opportunity to reply. Letters will be published at the discretion of the editors and are subject to abridgement and editing for style and content.
レターの例
どのようなものが発表されているか見ることは勉強になります。
どの雑誌にも、advanced searchがあり、キーワード+発表形態(+雑誌名)で絞ることが出来ます。
NEJM
colorectal cancer chemotherapy, 過去十年, other (発表形態)での検索例
JAMA
ここはadvanced searchではなく、検索したものに、左のチェックボックスにチェックする形であった。
colorectal cancer chemotherapy, JAMA, Letterでの検索例
Lancet
colorectal cancer chemotherapy, The Lancet, correspondenceでの検索例
BMJ
colorectal cancer chemotherapy(title またはabstract), letterでの検索例
参考文献
http://jamanetwork.com/journals/jama/article-abstract/182156
参考書籍
批判的吟味をするためには、以下の本がおすすめです。
Users' Guides to the Medical Literature: A Manual for Evidence-Based Clinical Practice
kindle版 Users' Guides to the Medical Literature: A Manual for Evidence-Based Clinical Practice
tableone パッケージでtable1をつくる
臨床研究のtable1は
臨床系の研究で、図表を見ると、まず高確率で遭遇するtable1
八割がたこういう患者背景だ。
（リンク先が「図」表記になっているッ・・・！）
これをいとも簡単に作成できるR packageがある。その名も・・・
tableone
table1 = 表１だ。 早速つかってみる。UCIのopen data "fertility"を用いる。
library(tableone)
res<-read.csv("http://archive.ics.uci.edu/ml/machine-learning-databases/00244/fertility_Diagnosis.txt", na.strings = "NA", as.is=T, header = F)
colnames(res) <- c("season", "age", "childish_diseases", "trauma", "surgery", "fever", "alcohol", "smoking", "sitting", "diagnosis")
#Create a variable list which we want in Table 1
listVars <- colnames(res)[-c(1)]
#Define categorical variables
catVars <- listVars[-which(listVars %in% c("age"))]
#Total Population
table1 <- CreateTableOne(vars = listVars, data = res, factorVars = catVars, strata = "diagnosis")
table1
summary(table1)
Table 1 (diagnosisでグループ分けしたもの)
continuous variablesのサマリー
categorical variablesのサマリー
p値
csvで保存する
tabMat <- print(table1) write.csv(tabMat, file = "myTable.csv")
