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)


CRAN Task View

Medical Image Analysis 医用画像分析

http://cran.md.tsukuba.ac.jp/web/views/MedicalImaging.html

Survival Analysis 生存分析

http://cran.md.tsukuba.ac.jp/web/views/Survival.html

Analysis of Pharmacokinetic Data 薬物動態データの分析

http://cran.md.tsukuba.ac.jp/web/views/Pharmacokinetics.html

Statistical Genetics 統計遺伝学

http://cran.md.tsukuba.ac.jp/web/views/Genetics.html

bioconductor

http://www.bioconductor.org/

医用画像分析

oro.dicom: Rigorous - DICOM Input / Output

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
create3DDICOM Headers/Imagesから配列を作成
dec2base10進数を任意の基数で表した文字列に変換
dicom.dicDICOM Header情報のルックアップテーブル
dicom2analyzeDICOM HeaderをAnalyze形式に変換
dicom2niftiDICOM 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
dicomTableDICOM Headerからデータフレームを作成
extractHeaderDICOM Headerから単一のフィールドを抽出
floating.headerDICOM 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
header2matrixDICOM 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
str2timeDICOM Time/Date Entryを変換する
swapDimensionDICOM Headerフィールドを使ってResliceを行う
writeHeaderDICOM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

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

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

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

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
cutroiI/O function
extract.dataExtract data or residuals from a fmridata object
fmri.designLinear Model for FMRI Data
fmri.detrendDetrend fMRI time series
fmri.guiGraphical user interface
fmri.lmLinear Model For FMRI Data
fmri.pvalueP-values
fmri.smoothSmoothing Statistical Parametric Maps
fmri.stimulusLinear Model for FMRI Data
fmriicaIndependent Component Analysis
ngcaNon-Gaussian Component Analysis
plot.fmridataI/O functions
print.fmridataI/O functions
read.AFNII/O function
read.ANALYZEI/O Functions
read.DICOMI/O function
read.NIFTII/O Functions
summary.fmridataI/O functions
write.AFNII/O functions
write.ANALYZEI/O Functions
write.NIFTII/O Functions

AnalyzeFMRI: Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format

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

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

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

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

epiR: Functions for analysing epidemiological data

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

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

Functions making R easy for epidemiological calculation.
http://cran.md.tsukuba.ac.jp/web/packages/epicalc/

epitools: Epidemiology Tools

EpiTools?: R Package for Epidemiologic Data and Graphics
http://cran.md.tsukuba.ac.jp/web/packages/epitools/

amei: Adaptive Management of Epidemiological Interventions

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

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

works with regular data set file and shape file.
http://cran.md.tsukuba.ac.jp/web/packages/diseasemapping/

rmodest

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

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

DiagnosisMed?: Diagnostic test accuracy evaluation for medical professionals

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/

Optimal Two-stage Phase II Design

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

RHRV: Heart rate variability analysis of ECG data

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

MIfuns: Pharmacometric tools for data preparation, analysis, simulation, and reporting

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

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

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

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

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

Estimation of pharmacokinetic parameters using non-compartmental theory
http://cran.md.tsukuba.ac.jp/web/packages/PK/

mixlow: mixlow method for assessing drug synergism

mixlow software for assessing drug synergism/antagonism
http://cran.md.tsukuba.ac.jp/web/packages/mixlow/

tdm: A Tool for Therapeutic Drug Monitoring (TDM)

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

rhosp: Side effect risks in hospital : simulation and estimation

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/


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Last-modified: 2015-03-01 (日) 01:15:59 (1717d)