R语言在公共卫生领域的应用:基础入门篇

R是一种应用广泛的用于统计计算和绘图的语言和环境,是一种基于S语言环境而开发的免费开源的统计工具[1],S语言是由著名的贝尔实验室的John Chambers等于1976年共同开发的一种进行数据探索、统计分析、作图的解释型语言[2]。一方面,R可以提供各种统计工具,具有良好的统计分析环境;另一方面,R保留了一定的灵活性,用户可以自行编写新的统计工具[3]。由于R是一个免费开源的软件,而且可以兼容Windows、Mac、Linux等多个主流操作系统,用户数量庞大。R具有顶尖水准的制图功能,不仅可以实现复杂数据的可视化,而且操作灵活性强,制图美观,能够满足大部分用户的绘图需求。     

R统计计算环境简介

R是GNU[1]系统下的一个自由、免费、开放源代码的软件,是一套完整的数据处理、计算和制图软件系统.它是一个用于统计计算和统计制图的优秀工具,其主要功能包括:方便的数据存储和处理系统;数组运算工具(其向量、矩阵运算方面功能尤其强大);完整连贯的统计分析工具;优秀的统计制图功能;一种相当完善、简洁和高效的程序设计语言("S"语言),包括条件语句、循环语句、用户定义的递归函数以及输入输出接口.     

大气颗粒物急性健康效应的Meta分析方法及R软件实现

目的介绍大气颗粒物急性健康效应的Meta分析和利用R软件实现的方法。方法以文献数据库"1990至2013年PM_(10)对普通中国人群呼吸系统死亡影响"为例,进行Meta分析,并用R软件实现。结果示例数据库存在一定发表偏倚,合并RR值为1.0041(95%CI 1.0028～1.0054),利用剪补法调整后RR值为1.0015(95%CI 1.0002～1.0029)。结论 R软件可以方便实现大气颗粒物急性健康效应的Meta分析。     

R语言heemod包在卫生经济学评价中的应用

R在医药卫生领域的应用越来越频繁,目前多用于Meta分析、生物信息学分析和统计建模等,heemod程序包主要开发用于卫生经济学评价,包括Markov模型的构建、运行和敏感性分析等;与Excel和TreeAge等卫生经济学评价的常用软件相比,基于R进行卫生经济学研究具有开源免费、灵活性高和图形功能强大等优势,文章以实例操作的方式展示了使用heemod包构建Markov模型进行成本–效果分析的一般过程。     

Stata软件在Meta分析中异质性检验的应用

介绍Stata软件在Meta分析异质性检验中的应用.将研究实例建立数据集,采用Stata9软件中相应命令语句实现固定效应模型森林图法附带的Q统计量和统计量Ⅰ2.检验法、H值法、Galbraith图法.采用Q检验、H统计量检验出研究间是否存在异质性,Ⅰ2统计量确定异质性程度,Galbraith图可看出哪些研究是异质性来源的异常点.结论 :Stata软件中四种方法可简单、快速地实现Meta分析中异质性检验.其中H和,Ⅰ2统计量异质性检验结果较为稳健,Galbraith图可直观地显示出研究结果异质性的异常点.     

剂量反应关系Meta分析在R软件中的实现

摘要:目的　介绍如何利用R软件中实现剂量反应关系的Meta分析。方法　拟通过实例数据的演示,在R软件中,先利用Metafor程序包进行探索性二分类Meta分析,在得出意义结果的基础上再利用dosresmeta程序包进行剂量反应的Meta分析,并绘制非线性（和）或线性剂量反应曲线 结果　R软件分析结果显示:饮酒是结直肠癌的危险因素,剂量反应关系的非线性检验P值处于临界水平（0.046）。非线性剂量反应模型显示:相对于最低饮酒量（0 g/天）,每日饮酒20 g、40 g、60 g发生结直肠癌的相对危险度为:1（0.93～1.1）、1.3（1.13～1.4）、1.5（1.26～1.9）;线性剂量反应模型显示:在最低饮酒量（0 g/天）的基础上,每增加12 g,发生结直肠癌的危险增加8%,非线性或线性剂量反应曲线图形基本相似。结论　R软件可以实现剂量反应关系的Meta分析,功能强大,实用性强。     

益生菌对超重肥胖孕妇妊娠期糖尿病预防效果的Meta分析

目的 探讨益生菌对超重肥胖孕妇妊娠期糖尿病(GDM)的预防效果.方法 采用Meta分析的方法,通过国内外数据平台检索并筛选相关文献,对其进行方法学质量评价并使用RevMan5.4统计软件对结果进行分析.结果 最终纳入5篇文献.Meta分析结果显示,益生菌可有效控制妊娠期空腹血糖(P＜0.05),降低GDM的发病率(P＜...     

牙周病与冠心病相关性的文献系统评价

目的 评价牙周病与冠心病的关联程度,为制定预防措施提供依据.方法 检索符合本研究分析条件的牙周病与冠心病相关性文献,采用Meta分析法,进行定量综合分析.运用Rev Man 4.2分析软件和SPSS 13.0统计软件计算相关危险因素OR或RR值及95%CI,并绘制森林图.结果 共筛选出相关文献13篇,其中10篇为病例-对照研究,合并OR值为2.21,95%CI为1.91～2.56,3篇为队列研究,合并RR值=1.40,95%CI为1.28～1.54.对所有研究进行异质性检验,各研究差别无统计学意义(X2=9.08,P=0.70),采用固定效应模型进行Meta分析,表明有无牙周病对患冠心病的危险性差别有统计学意义(RR=1.43,95%CI为1.35～1.52).结论 牙周病与冠心病呈显著相关性,且可能互为致病和加重病情的危险因素.     

健康素养调查问卷数据整理的R软件实现

目的以全国居民健康素养监测调查问卷(2016年版)为例,用免费开源的R软件,对问卷数据进行不同题型判分、各分量指标得分计算及素养判断、基本情况编码转换等数据整理,并提供完整的R代码。实践证明,使用R软件实现问卷数据整理过程的程序化及其可复制性,对于各级监测样本的数据复核与汇总合并有特别意义,对监测点的数据分析人员也具有参考价值。     

联合SAS和R分析医学数据举例

SAS系统在医药卫生领域被广泛地应用。近年来,R软件〔1〕异军突起,越来越受到数据分析人员的喜爱。R作为S语言的"方言",是面向向量、数组、列表等对象进行运算的软件包,它非常擅统计计算和统计作图。在1996年,奥克兰大学统计系的Gentleman和     

多巴胺D4基因48bp可变重复序列多态性与注意缺陷多动障碍相关性的Meta分析

目的 进一步探讨多巴胺D4受体(DRD4)基因第三外显子48 bp可变重复序列(VNTR)多态性与注意缺陷多动障碍(ADHD)儿童青少年的相关情况。方法 通过中国知网(CNKI)、万方、维普、中国生物医学文献数据库(CBM)、PubMed、Cochrane Library、EBSCO、Ovid、Springer数据库,检索国内外关于DRD4基因第3外显子48 bp VNTR多态性与儿童ADHD关联性的病例对照研究,采用Meta分析综合定量分析纳入文献。结果 20篇文献共纳入3 658例ADHD患者和6 272例对照,Meta分析结果提示在总人群中4R、7R和长片段ADHD组与对照组相比差异均有统计学意义,其他片断ADHD组与对照组相比差异均无统计学意义。亚洲人群中各种重复片段的ADHD组与对照组相比差异均无统计学意义。非亚洲人群中4R、7R、短片断和长片段(＞4R)ADHD组与对照组相比差异均有统计学意义,其余重复片段差异均无统计学意义。结论 Meta分析显示总人群DRD4 48 bp 4R、7R、长片段(＞4R)与ADHD间有相关性;非亚洲人群DRD4 48 bp4R、7R、短片段、长片段(＞4R)与ADHD间有相关性;亚洲人群48 bp VNTR多态性与ADHD间均未显示有相关性。     

Meta—analysis及其在流行病学中的应用

Ｍｅｔ－ａｎａｌｙｓｉｓ是对先前研究资料进行合并分析的一种新的研究方法，其原理简单、系统，结果全面、量化，可靠性好，为流行病学研究提供了一种强有力的统计分析手段，本文介绍了这种方法的基本原理，讨论讨论了在流行病学应用中的一些问题，试用于极低频电磁与儿童白血病关系的研究，结果表明儿童白血的发生与极低频电磁场暴露有关。     

Meta-analysis of diagnostic test data: a bivariate Bayesian modeling approach

In the last decades, the amount of published results on clinical diagnostic tests has expanded very rapidly. The counterpart to this development has been the formal evaluation and synthesis of diagnostic results. However, published results present substantial heterogeneity and they can be regarded as so far removed from the classical domain of meta-analysis, that they can provide a rather severe test of classical statistical methods. Recently, bivariate random effects meta-analytic methods, which model the pairs of sensitivities and specificities, have been presented from the classical point of view. In this work a bivariate Bayesian modeling approach is presented. This approach substantially extends the scope of classical bivariate methods by allowing the structural distribution of the random effects to depend on multiple sources of variability. Meta-analysis is summarized by the predictive posterior distributions for sensitivity and specificity. This new approach allows, also, to perform substantial model checking, model diagnostic and model selection. Statistical computations are implemented in the public domain statistical software (WinBUGS and R) and illustrated with real data examples.     

Genotypic relative risks under ordered restriction

In mapping diseases of complex aetiology, conventional linkage approaches narrow the location of the disease susceptibility locus to quite a large region so that candidate gene association studies are then necessary to further isolate these genes. However, even in the simplest scenario where the candidate locus is bi-allelic, two statistical tests with various correcting factors have been proposed: a chi-square 1 df test (counting chromosomes) which may be slightly conservative and a 2 df chi-square test (counting genotypes) which may lack power because of the extra degree of freedom. This paper introduces a better and more powerful alternative which turns out to be a compromise between the two existing statistical tests. The asymptotic distribution of this test statistic is determined and the efficacy of the 3 tests are compared under different genetic models by simulation. Genet. Epidemiol. 15:135–146,1998. © 1998 Wiley-Liss, Inc.     

Meta-analysis

Meta-analysis corresponds to all systematic methods which use statistical techniques for combining results from several independent studies. The aim is to get a consistent estimation of the global effect of a procedure on a specified outcome. The technique allows us to increase the power of statistical testing, and to get information which cannot be drawn from one individual study. Two approaches are possible, and often combined: the qualitative approach consists of weighing various studies according to their methodological quality; the quantitative approach consists of pooling the results of different studies, in order to generate results with a higher statistical power. A meta-analysis is a long and rigorous process, which follows several steps: statement of objectives; definition of articles inclusion and exclusion criteria; literature search; collection of data and evaluation of the quality of each study; tests for homogeneity; pooling; sensitivity analyses; presentation of results; and conclusions. Meta-analysis has several advantages: it estimates the size of an effect; it improves the generalizability; it compels to rigor; it lessens the part of subjectivity. When meta-analysis is cautiously and properly done, it brings new useful information, and helps physicians and health policy makers in answering to a specific question.     

The practice of systematic reviews. IV. Pooling results from separate studies]

Meta-analysis comprises the analysis of the data gathered in a systematic review. Meta-analysis can be defined as the combination of pooling results of similar studies into one overall estimate of the effect on the one hand and the exploration of sources of heterogeneity between studies on the other. A general statistical model is available for pooling the estimates of various types of effect parameters. Pooling enables the estimation of the effect of an intervention or exposure as precisely as possible (with narrow confidence intervals) which allows detection of minor effects. The Mantel-Haenszel method is also an excellent method for pooling effect parameters of dichotomous outcomes. Pooling provides an efficient means of summarizing the available knowledge.     

健康指数构建的统计分析流程及实现

  目的  基于综合评价理论探索并归纳健康指数构建的统计分析流程,开发相关R包用于软件实现,为健康指数研究开发一套快捷高效的评价工具,实现一键生成高度集成的综合指数及评价结果,以期为监管部门提供科学可靠的评价信息与决策依据。  方法  使用R 4.1.3软件开发EvaModels包,结合健康指数构建的统计分析流程对EvaModels包内各项函数进行整体介绍与参数解释,分析比较各类方法的适用场景,并以公立医院持续发展指数构建为例进行演示分析。  结果  健康指数构建包括确定指数研究主题、构建评价指标体系、多指标综合评价及评价结果可视化四大流程。所开发的EvaModels包共内置九个函数,通过多种方法实现指标筛选、数据标准化、指标赋权和综合评价等功能,可满足多种评价问题的分析需求,基本覆盖健康指数构建的统计分析流程。  结论  EvaModels包通过一组函数将健康指数构建中涉及统计分析的工作流程自动化、简单化,过程与代码易于解读与调用,提高了健康指数构建的便捷性和可操作性。     

When plagiarism becomes research.

There are three possible levels of analysis in clinical research. Primary analysis deals with the original analysis of research study data. Secondary analysis is a reanalysis of the original data, either to address the original question through better techniques or to address a new question using old data. Meta-analysis is a statistical analysis of many studies done to summarize a body of literature. Meta-analysis is particularly helpful in an area in which original research studies have produced conflicting results because it enables analysis of the impact of study characteristics upon the end result. The family practitioner as a consumer of research needs to become familiar with the technique of meta-analysis because it is appearing with increasing frequency in the medical literature. Still somewhat controversial, meta-analysis requires a rigorous approach to ensure its validity: this editorial is written to assist the family practitioner in an understanding of the meta-analytic technique and point out important features that need to appear in any published meta-analysis.     

中国儿童家长EV71疫苗的接种意愿及影响因素Meta分析

目的 了解中国儿童家长对肠道病毒71型（Enterovirus 71,EV71）疫苗的接种意愿及影响因素,为手足口病（Hand, foot and mouth disease,HFMD）防控提供新策略。方法 系统检索相关中英文数据库,纳入符合条件的文献,运用R 3.5.2软件进行Meta合并分析。结果 共计39篇文献纳入研究,合计样本量36526例。合并EV71疫苗接种意愿为67.68%（95%CI:62.31%～72.62%）,亚组分析显示女性家长较男性家长的疫苗接种意愿高,差异有统计学意义（P=0.006）。不愿意接种的主要原因是顾虑疫苗的安全性55.70%(95%CI:48.49%～62.78%)和有效性28.44%(95%CI:21.73%～35.66%)。结论 我国儿童家长的EV71疫苗接种意愿还有待提高,积极有效的宣传和提高疫苗安全质量对EV71疫苗接种有着重要的意义。     

Do polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR) gene affect the risk of childhood acute lymphoblastic leukemia?

Meta-analysis has become an important statistical tool in genetic association studies, since it may provide more powerful and precise estimates. However, meta-analytic studies are prone to several potential biases not only because the preferential publication of ``positive' studies but also due to difficulties in obtaining all relevant information during the study selection process. In this letter, we point out major problems in meta-analysis that may lead to biased conclusions, illustrating an empirical example of two recent meta-analyses on the relation between MTHFR polymorphisms and risk of acute lymphoblastic leukemia that, despite the similarity in statistical methods and period of study selection, provided partially conflicting results.