R Journal最新文献_第8页

rpsftm: An R Package for Rank Preserving Structural Failure Time Models rpsftm:保秩结构失效时间模型的R包

IF 2.1 4区计算机科学

R Journal Pub Date : 2017-12-04 DOI: 10.32614/RJ-2017-068

Annabel Allison, I. White, S. Bond

引用次数: 8

rpsftm: An R Package for Rank Preserving Structural Failure Time Models. rpsftm:一个保秩结构失效时间模型的R包。

IF 2.1 4区计算机科学

R Journal Pub Date : 2017-12-04

Annabel Allison, Ian R White, Simon Bond

{"title":"rpsftm: An R Package for Rank Preserving Structural Failure Time Models.","authors":"Annabel Allison, Ian R White, Simon Bond","doi":"","DOIUrl":"","url":null,"abstract":"Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect, ψ, is estimated by balancing counter-factual event times (that would be observed if no treatment were received) between treatment groups. G-estimation is used to find the value of ψ such that a test statistic Z(ψ) = 0. This is usually the test statistic used in the intention-to-treat analysis, for example, the log rank test statistic. We present an R package that implements the method of rpsftm.","PeriodicalId":51285,"journal":{"name":"R Journal","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2017-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5858764/pdf/emss-76528.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35937148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MDplot: Visualise Molecular Dynamics MDplot:可视化分子动力学

IF 2.1 4区计算机科学

R Journal Pub Date : 2017-05-10 DOI: 10.32614/RJ-2017-007

Christian Margreitter, C. Oostenbrink

{"title":"MDplot: Visualise Molecular Dynamics","authors":"Christian Margreitter, C. Oostenbrink","doi":"10.32614/RJ-2017-007","DOIUrl":"https://doi.org/10.32614/RJ-2017-007","url":null,"abstract":"The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step.\u0000\u0000\u0000AVAILABILITY\u0000The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.","PeriodicalId":51285,"journal":{"name":"R Journal","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2017-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44420577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

MDplot: Visualise Molecular Dynamics. MDplot:可视化分子动力学。

IF 2.1 4区计算机科学

R Journal Pub Date : 2017-05-10

Christian Margreitter, Chris Oostenbrink

{"title":"MDplot: Visualise Molecular Dynamics.","authors":"Christian Margreitter, Chris Oostenbrink","doi":"","DOIUrl":"","url":null,"abstract":"The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step.Availability: The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.","PeriodicalId":51285,"journal":{"name":"R Journal","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2017-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570379/pdf/emss-73867.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35450358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

autoimage: Multiple Heat Maps for Projected Coordinates. autoimage:投影坐标的多个热图。

IF 2.1 4区计算机科学

R Journal Pub Date : 2017-01-01 Epub Date: 2017-05-10

Joshua P French

引用次数: 0

Working with Daily Climate Model Output Data in R and the futureheatwaves Package. 使用R中的每日气候模型输出数据和未来热浪包进行工作。

IF 2.1 4区计算机科学

R Journal Pub Date : 2017-01-01 Epub Date: 2017-06-08 DOI: 10.32614/rj-2017-032

G Brooke Anderson, Colin Eason, Elizabeth A Barnes

引用次数: 2

Hosting Data Packages via drat: A Case Study with Hurricane Exposure Data. 通过草案托管数据包:飓风暴露数据的案例研究。