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目的：医療系(臨床／疫学他）のパッケージを蓄積します。（追加歓迎） #contents ---- *CRAN Task View [#n618b43f] **Medical Image Analysis 医用画像分析[#yfebbb51] http://cran.md.tsukuba.ac.jp/web/views/MedicalImaging.html~ **Survival Analysis 生存分析 [#e5ab7f10] http://cran.md.tsukuba.ac.jp/web/views/Survival.html~ **Analysis of Pharmacokinetic Data 薬物動態データの分析[#ndf90700] http://cran.md.tsukuba.ac.jp/web/views/Pharmacokinetics.html~ **Statistical Genetics 統計遺伝学[#mdff4a85] http://cran.md.tsukuba.ac.jp/web/views/Genetics.html *bioconductor [#ia9bef6a] http://www.bioconductor.org/ *医用画像分析 [#r7d83c98] **oro.dicom: Rigorous - DICOM Input / Output [#e0f1f310] Data input/output functions for data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard, part of the Rigorous Analytics bundle.~ http://cran.md.tsukuba.ac.jp/web/packages/oro.dicom/ DICOM形式のファイルはHeaderデータとImageデータで構成されています。 oro.dicomを使ってDICOM形式からANALIZE形式およびNIfTI形式に変換は可能ですが、AFNI形式には変換できません。AFNI形式のデータの読み書きには、fmriパッケージを使うことができます。 oro.dicom中のオブジェクト一覧 |項目|説明| |create3D |DICOM Headers/Imagesから配列を作成| |dec2base |10進数を任意の基数で表した文字列に変換| |dicom.dic |DICOM Header情報のルックアップテーブル| |dicom2analyze |DICOM HeaderをAnalyze形式に変換| |dicom2nifti |DICOM HeaderをNIfTI形式に変換| |dicomInfo |単一のDICOMファイルを読み込み| |dicomSeparate |ディレクトリ内の全てのDICOMファイルを読み込む| |dicomTable |DICOM Headerからデータフレームを作成| |extractHeader |DICOM Headerから単一のフィールドを抽出| |floating.header |DICOM Headerを扱うための内部関数| |getOrientation |方向余弦(Direction Cosine)を解剖学上の方向に変換| |header2matrix |DICOM Headerフィールドを行列に変換| |is.axial |軸状断（体軸に直交する平面）であるかどうかを判別| |matchHeader |与えた文字列がDICOM Headerフィールドにマッチするかどうかを判別| |nextHeader |与えた文字列とDICOM Headerフィールドがマッチするかを判別し、エラー処理またはループから脱出する| |str2time |DICOM Time/Date Entryを変換する| |swapDimension |DICOM Headerフィールドを使ってResliceを行う| |writeHeader |DICOMテーブルをASCIIファイルに書き出す| **tractor.base: Basic functions for the TractoR (tractography with R) bundle [#nb682dd5] The tractor.base package consists of functions for working with magnetic resonance images. It can read and write image files stored in Analyze, NIfTI and DICOM formats (DICOM support is read only), generate images for use as regions of interest, and manipulate and visualise images.~ http://cran.md.tsukuba.ac.jp/web/packages/tractor.base/ **dti: DTI/DWI Analysis [#xd3e13cb] Diffusion Weighted Imaging is a Magnetic Resonance Imaging modality, that measures diffusion of water in tissues like the human brain. The package contains R-functions to process diffusion-weighted data in the context of the diffusion tensor model (DTI). This includes the calculation of anisotropy measures and, most important, the implementation of our structural adaptive smoothing algorithm as described in K. Tabelow, J. Polzehl, V. Spokoiny, and H.U. Voss, Diffusion Tensor Imaging: Structural Adaptive Smoothing, Neuroimage 39(4), 1763-1773 (2008).~ http://cran.md.tsukuba.ac.jp/web/packages/dti/ **dcemri: A Package for Medical Image Analysis [#fd53ff56] A collection of routines and documentation that allows one to perform a quantitative analysis of dynamic contrast-enhanced or diffusion-weighted MRI data. Medical imaging data should be organized using either the Analyze or NIfTI data formats.~ http://cran.md.tsukuba.ac.jp/web/packages/dcemri/ **fmri: Analysis of fMRI experiments [#t83097fe] The library contains R-functions to perform an fmri analysis as described in Tabelow, K., Polzehl, J., Voss, H.U., and Spokoiny, V. Analysing fMRI experiments with structure adaptive smoothing procedures, NeuroImage, 33:55-62 (2006).~ http://cran.md.tsukuba.ac.jp/web/packages/fmri/ |項目|説明| |cutroi |I/O function| |extract.data |Extract data or residuals from a fmridata object| |fmri.design |Linear Model for FMRI Data| |fmri.detrend |Detrend fMRI time series| |fmri.gui |Graphical user interface| |fmri.lm |Linear Model For FMRI Data| |fmri.pvalue |P-values| |fmri.smooth |Smoothing Statistical Parametric Maps| |fmri.stimulus |Linear Model for FMRI Data| |fmriica |Independent Component Analysis| |ngca |Non-Gaussian Component Analysis| |plot.fmridata |I/O functions| |print.fmridata |I/O functions| |read.AFNI |I/O function| |read.ANALYZE |I/O Functions| |read.DICOM |I/O function| |read.NIFTI |I/O Functions| |summary.fmridata |I/O functions| |write.AFNI |I/O functions| |write.ANALYZE |I/O Functions| |write.NIFTI |I/O Functions| http://cran.md.tsukuba.ac.jp/web/packages/fmri/ **AnalyzeFMRI: Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format [#r71c5a5d] Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.~ http://cran.md.tsukuba.ac.jp/web/packages/AnalyzeFMRI/ **RImageJ: R bindings for ImageJ [#ya865ac4] Bindings between R and the ImageJ java based image processing and Analysis platform~ http://cran.md.tsukuba.ac.jp/web/packages/RImageJ/~ ImageJはその思想的祖先であるNIHimageと同様にアメリカ国立衛生研究所 (NIH) で開発されたオープンソースのパブリックドメインの画像処理ソフトウェア。Java1.1以降のVM上で動作し、Mac OS X、Mac OS、Windows、Linux、ザウルス用のソフトウェアが開発サイトから入手できる。~ **PET: Simulation and Reconstruction of PET Images [#jd65e324] This package implements different analytic/direct and iterative reconstruction methods of Peter Toft. It also offer the possibility to simulate PET data.~ http://cran.md.tsukuba.ac.jp/web/packages/PET/ **diffractometry: Baseline identification and peak decomposition for x-ray diffractograms [#yd7d4911] Residual-based baseline identification and peak decomposition for x-ray diffractograms as introduced in Davies/Gather/Mergel/Meise/Mildenberger (2008).~ http://cran.md.tsukuba.ac.jp/web/packages/diffractometry/ *疫学 [#sa31b9e1] **epiR: Functions for analysing epidemiological data [#ic717133] A package for analysing epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.~ http://cran.md.tsukuba.ac.jp/web/packages/epiR/ **epibasix: Elementary Epidemiological Functions for a Graduate Epidemiology\Biostatistics Course [#zb8ab01d] This package contains elementary tools for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement (kappa, sensitivity/specificity). Appropriate print and summary statements are also written to facilitate interpretation wherever possible. This package is a work in progress, so any comments or suggestions would be appreciated. Source code is commented throughout to facilitate modification. The target audience includes graduate students in various epi/biostatistics courses.~ http://cran.md.tsukuba.ac.jp/web/packages/epibasix/ **epicalc: Epidemiological calculator [#m89890e4] Functions making R easy for epidemiological calculation.~ http://cran.md.tsukuba.ac.jp/web/packages/epicalc/ **epitools: Epidemiology Tools [#a467d7ea] EpiTools: R Package for Epidemiologic Data and Graphics~ http://cran.md.tsukuba.ac.jp/web/packages/epitools/ **amei: Adaptive Management of Epidemiological Interventions [#idf21472] This package provides a flexible statistical framework for generating optimal epidemiological interventions that are designed to minimize the total expected cost of an emerging epidemic while simultaneously propagating uncertainty regarding underlying disease parameters through to the decision process via Bayesian posterior inference. The strategies produced through this framework are adaptive: vaccination schedules are iteratively adjusted to reflect the anticipated trajectory of the epidemic given the current population state and updated parameter estimates.~ http://cran.md.tsukuba.ac.jp/web/packages/amei/ **surveillance: Outbreak detection algorithms for surveillance data [#k8c5ee5e] A package implementing statistical methods for the surveillance of infectious diseases. This boils down to modelling and outbreak detection of univariate and multivariate time series of counts resulting from routinely collected public health surveillance data. Currently the package contains an implementation of the typically outbreak detection procedures such as Stroup et. al (1989), Farrington et. al (1996), Rossi et al (1999), Rogerson and Yamada (2001), a Bayesian approach and a detector based on generalized likelihood ratios (GLR). Furthermore, inference methods for the infectious disease model in Held et al (2005) are provided. The package contains several real-world datasets and the ability to simulate outbreak data.~ http://cran.md.tsukuba.ac.jp/web/packages/surveillance/ **diseasemapping: Calculate SMR's from population and case data [#g6ea13c2] works with regular data set file and shape file.~ http://cran.md.tsukuba.ac.jp/web/packages/diseasemapping/ //**Lifetable Calculations [#l0106493] //Allows the calculation of lifetables using demographic methods, and particularly the estimation of life expectancy in people at increased relative risk and excess risk of death. Status - Working, but only limited features. Email for now if you want it.~ //https://r-forge.r-project.org/projects/lifetables/ **rmodest [#h0631820] Rmodest is a package that will allow you to easily fit mortality functions to your survival data, and to test hypotheses about your data.~ https://r-forge.r-project.org/projects/rmodest/ **DCluster 空間疫学 : Functions for the detection of spatial clusters of diseases [#nab49487] A set of functions for the detection of spatial clusters of disease using count data. Bootstrap is used to estimate sampling distributions of statistics.~ http://cran.md.tsukuba.ac.jp/web/packages/DCluster/ *臨床診断 [#l4c25603] **DiagnosisMed: Diagnostic test accuracy evaluation for medical professionals [#of9bee32] DiagnosisMed is a package to analyze data from diagnostic test accuracy evaluating health conditions. It is being built to be used by health professionals. This package is - or soon will be - able to estimate sample size for common situations in diagnostic test accuracy, estimate sensitivity and specificity from categorical and continuous test results including some evaluations of indeterminate results, or compare different analysis strategies into measures commonly used by health professionals.~ http://cran.md.tsukuba.ac.jp/web/packages/DiagnosisMed/ //** diagnosis [#j4753db1] //An R package for evaluation of the accuracy of diagnostic tests or biomarkers for classification (screening or diagnosis) and prediction (risk or prognosis). ~ //https://r-forge.r-project.org/projects/diagnosis/ **Optimal Two-stage Phase II Design [#n7268c7f] This R package OptimPhase2 creates the optimal two-stage phase II designs with long-term endpoint. Optimality is defined to minimze either the expected sample size, expected duration of accrual and expected total study length.~ https://r-forge.r-project.org/projects/optimphase2/ *臨床検査 [#x08c39d1] **RHRV: Heart rate variability analysis of ECG data [#ac9073ea] This is a package for developing heart rate variability studies of ECG records~ http://cran.md.tsukuba.ac.jp/web/packages/RHRV/ *薬理・服薬 [#q666e2c7] **MIfuns: Pharmacometric tools for data preparation, analysis, simulation, and reporting [#aaf0855c] Pharmacometric tools for common data preparation tasks, stratified bootstrap resampling of data sets, NONMEM control stream creation/editing, NONMEM model execution, creation of standard and user-defined diagnostic plots, execution and summary of bootstrap and predictive check results, implementation of simulations from posterior parameter distributions, reporting of output tables and creation of a detailed analysis log. All functions are considered stable unless marked as beta.~ http://cran.md.tsukuba.ac.jp/web/packages/MIfuns/ **stab: data analysis of drug stability [#o1117d54] A menu-driven package for data analysis of drug stability based on ICH guideline(such as estimation of shelf-life from a 3-batch profile.)~ http://cran.md.tsukuba.ac.jp/web/packages/stab/ **PKfit: A Data Analysis Tool for Pharmacokinetics [#yfe535aa] PKfit is a nonlinear regression (including a genetic algorithm) program which was designed to perform model/curve fitting and model simulations for pharmacokinetics.~ http://cran.md.tsukuba.ac.jp/web/packages/PKfit/ **medAdherence: Medication Adherence: Commonly Used Definitions [#o83c5bd9] Medication Adherence: Commonly Used Definitions~ http://cran.md.tsukuba.ac.jp/web/packages/medAdherence/ **PhViD: Pharmacovigilance signal detection methods extended to the multiple comparison setting [#te03a04e] PhViD proposes the main pharmacovigilance signal detection methods extended to the multiple comparison setting. Those functions can be used as standard R functions or through an user friendly interface (PhViD.gui)~ http://cran.md.tsukuba.ac.jp/web/packages/PhViD/ **PK: Basic Non-Compartmental Pharmacokinetics [#e542a1c9] Estimation of pharmacokinetic parameters using non-compartmental theory~ http://cran.md.tsukuba.ac.jp/web/packages/PK/ **mixlow: mixlow method for assessing drug synergism [#s84199bf] mixlow software for assessing drug synergism/antagonism~ http://cran.md.tsukuba.ac.jp/web/packages/mixlow/ **tdm: A Tool for Therapeutic Drug Monitoring (TDM) [#jb1e14b1] TDM can be used to estimate individual pharmacokinetic parameters with one or more drug serum/plasma concentrations obtained from a single subject or multiple subjects using OpenBUGS (Bayesian inference Using Gibbs Sampling) interfaced through BRugs. Besides, it also can calculate a suggested dose with the target drug concentration (C ->D) or calculate a predicted drug concentration with a given dose (D -> C).~ http://cran.md.tsukuba.ac.jp/web/packages/tdm/ *病院・経営 [#x47d2464] **rhosp: Side effect risks in hospital : simulation and estimation [#xad4807d] Evaluating risk (that a patient arises a side effect) during hospitalization is the main purpose of this package. Several methods (Parametric, non parametric and De Vielder estimation) to estimate the risk constant (R) are implemented in this package. There are also functions to simulate the different models of this issue in order to quantify the previous estimators. It is necessary to read at least the first six pages of the report to understand the problematic.~ http://cran.md.tsukuba.ac.jp/web/packages/rhosp/
