Abstract：
:Correlated survival outcomes occur quite frequently in the biomedical research. Available software is limited, particularly if we wish to obtain smoothed estimate of the baseline hazard function in the context of random effects model for correlated data. The main objective of this paper is to describe an R package called frailtypack that can be used for estimating the parameters in a shared gamma frailty model with possibly right-censored, left-truncated stratified survival data using penalized likelihood estimation. Time-dependent structure for the explanatory variables and/or extension of the Cox regression model to recurrent events are also allowed. This program can also be used simply to obtain directly a smooth estimate of the baseline hazard function. To illustrate the program we used two data sets, one with clustered survival times, the other one with recurrent events, i.e., the rehospitalizations of patients diagnosed with colorectal cancer. We show how to fit the model with recurrent events and time-dependent covariates using Andersen-Gill approach.
journal_name
Comput Methods Programs Biomedjournal_title
Computer methods and programs in biomedicineauthors
Rondeau V,Gonzalez JRdoi
10.1016/j.cmpb.2005.06.010subject
Has Abstractpub_date
2005-11-01 00:00:00pages
154-64issue
2eissn
0169-2607issn
1872-7565pii
S0169-2607(05)00144-6journal_volume
80pub_type
杂志文章abstract：:In this study, the virtual reality (VR) proprioception rehabilitation system was developed for stroke patients to use proprioception feedback in upper limb rehabilitation by blocking visual feedback. To evaluate its therapeutic effect, 10 stroke patients (onset>3 month) trained proprioception feedback rehabilitation f...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2013.09.006
更新日期：2014-01-01 00:00:00
abstract：:This paper describes a distributed collaborative effort between industry and academia to systematize data management in an academic biomedical laboratory. Heterogeneous and voluminous nature of research data created in biomedical laboratories make information management difficult and research unproductive. One such co...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2015.11.001
更新日期：2016-04-01 00:00:00
abstract：:A PC-based real-time quality control (QC) system for multitest analyzers has been developed as a prototype. The system is built with use of a relational database management system (DBMS). Control values from the various analytical channels are stored and administrated with use of the DBMS. The control values collected...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/0169-2607(91)90042-r
更新日期：1991-02-01 00:00:00
abstract：:Blood vessels in ophthalmoscope images play an important role in diagnosis of some serious pathologies on retinal images. Hence, accurate extraction of vessels is becoming a main topic of this research area. Matched filter (MF) implementation for blood vessel detection is one of the methods giving more accurate result...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2009.04.005
更新日期：2009-11-01 00:00:00
abstract：:The aim of DILEMMA is to provide tools for the development of decision support systems for use in general medical practice, hospital-based cancer care, and shared care of cancer and cardiology patients. In primary care, the project intends to provide aids to clinical performance in prescribing, referral and the use of...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/0169-2607(94)90011-6
更新日期：1994-10-01 00:00:00
abstract：:When underlying distributions are unknown and sample sizes are small, permutation tests may have superior features to parametric tests, such as smaller type I error and more accurate probability values when testing the null hypothesis. However, permutation tests are not widely used in clinical trials because of their ...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2005.03.010
更新日期：2005-08-01 00:00:00
abstract：BACKGROUND AND OBJECTIVE:The presence of circulating tumor cells in the patient's blood is a clinical factor that indicates the initiation of metastasis. METHODS:In this paper, a microfluidic device is designed to separate, enumerate, and to diagnose cancer cells from the patient's blood sample. Here, we present a new...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2019.105147
更新日期：2020-03-01 00:00:00
abstract：BACKGROUND AND OBJECTIVE:In the last decade, Ultrasound-Guided Regional Anesthesia (UGRA) gained importance in surgical procedures and pain management, due to its ability to perform target delivery of local anesthetics under direct sonographic visualization. However, practicing UGRA can be challenging, since it require...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2018.03.013
更新日期：2018-07-01 00:00:00
abstract：:Label fusion multi-atlas approaches for image segmentation can give better segmentation results than single atlas methods. We present a multi-atlas label fusion strategy based on probabilistic weighting of distance maps. Relationships between image similarities and segmentation similarities are estimated in a learning...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2012.12.006
更新日期：2013-06-01 00:00:00
abstract：:In the case of an unexpected high frequency of serious adverse events (SAE), statistical methods are needed to help in the decision making process as to continuation of accrual to the trial. This paper describes an R package, named SAE that implements a method recently developed by defining stopping rules after each o...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2011.05.005
更新日期：2011-11-01 00:00:00
abstract：:A method to determine the shapes of a thermally fluctuating phospholipid vesicle is described. The vesicle that was attached at one point to a glass plate was submitted to a flow. It was observed by an inverted optical microscope using phase contrast technique. A large number of consecutive video images were digitised...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/S0169-2607(03)00065-8
更新日期：2004-03-01 00:00:00
abstract：BACKGROUND AND OBJECTIVE:Cartilage cracks and fissures may occur due to certain daily life activities such as sports practice, blunt trauma, and matrix fibrillation during early osteoarthritis. These cracks could further grow at the macroscopic level, alter the load distribution pattern in the matrix, limit the joint r...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2020.105648
更新日期：2020-10-01 00:00:00
abstract：:This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on ...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2008.04.007
更新日期：2008-08-01 00:00:00
abstract：BACKGROUND AND OBJECTIVE:Gene regulatory networks (GRNs) are essential for understanding most molecular processes. In this context, the so-called model-free approaches have an advantage modeling the complex topologies behind these dynamic molecular networks, since most GRNs are difficult to map correctly by any other m...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2019.05.030
更新日期：2019-08-01 00:00:00
abstract：:A first software (JHS) for the elaboration of job histories oriented toward risks was designed and results published In an article "A software for the elaboration of Job Histories". This article presents a second software (JES), based on the use of a job-exposure matrix designed for one company. The matrix is essentia...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/0169-2607(92)90056-d
更新日期：1992-09-01 00:00:00
abstract：:Accurate and fast approaches for automatic ECG data classification are vital for clinical diagnosis of heart disease. To this end, we propose a novel multistage algorithm that combines various procedures for dimensionality reduction, consensus clustering of randomized samples and fast supervised classification algorit...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2013.08.002
更新日期：2013-12-01 00:00:00
abstract：:Articular cartilage (AC) is a biological tissue that allows the distribution of mechanical loads and movement of joints. The presence of these mechanical loads influences the behavior and physiological condition of AC. The loads may cause damaged by fatigue through injuries due to repeated accumulated stresses. The ai...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2011.02.003
更新日期：2011-12-01 00:00:00
abstract：:Steady state flux balance analysis (FBA) for cellular metabolism is used, e.g., to seek information on the activity of the different pathways under equilibrium conditions, or as a basis for kinetic models. In metabolic models, the stoichiometry of the system, commonly completed with bounds on some of the variables, is...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2009.07.007
更新日期：2010-02-01 00:00:00
abstract：:Optimal sampling schedule (OSS) is of great interest in biomedical experiment design, as it can improve the physiological parameter estimation precision and significantly reduce the samples required. A number of well designed algorithms and software packages have been developed, which deal with the instantaneous measu...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/s0169-2607(00)00114-0
更新日期：2001-04-01 00:00:00
abstract：:Tokyo Hitachi Hospital, Hitachi Ltd., has used a hospital-wide PACS for over 1 year. The system runs a 100 Mb/s optical fiber network over the whole hospital including wards and outpatient clinic rooms, with 11 image workstations. The network links digital imaging modalities such as X-CT, MRI, computed radiography (CR...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/0169-2607(94)90190-2
更新日期：1994-05-01 00:00:00
abstract：BACKGROUND AND OBJECTIVE:Accurate segmentation of prostate and its zones constitute an essential preprocessing step for computer-aided diagnosis and detection system for prostate cancer (PCa) using diffusion-weighted imaging (DWI). However, low signal-to-noise ratio and high variability of prostate anatomic structures ...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2020.105572
更新日期：2020-11-01 00:00:00
abstract：:The standard software for non-linear mixed-effect analysis of pharmacokinetic/pharmacodynamic (PK/PD) data is NONMEM while the non-linear mixed-effects package NLME is an alternative as long as the models are fairly simple. We present the nlmeODE package which combines the ordinary differential equation (ODE) solver p...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2004.01.001
更新日期：2004-10-01 00:00:00
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/s0169-2607(01)00153-5
更新日期：2002-04-01 00:00:00
abstract：:Statistical tests are often performed to discover which experimental variables are reacting to specific treatments. Time-series statistical models usually require the researcher to make assumptions with respect to the distribution of measured responses which may not hold. Randomization tests can be applied to data in ...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2010.04.010
更新日期：2011-01-01 00:00:00
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2004.12.007
更新日期：2005-05-01 00:00:00
abstract：:Carefully collected, high-quality data are crucial in biomedical visualization, and it is important that the user community has ready access to both this data and the high-performance computing resources needed by the complex, computational algorithms that will process it. Biological researchers generally require data...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2010.08.009
更新日期：2012-06-01 00:00:00
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/0169-2607(91)90093-9
更新日期：1991-12-01 00:00:00
abstract：:Lung cancer is one of the most common forms of cancer resulting in over a million deaths per year worldwide. In this paper, the usage of support vector machine (SVM) classification for lung cancer is investigated, presenting a systematic quantitative evaluation against Boosting, Decision trees, k-nearest neighbor, LAS...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2013.04.016
更新日期：2013-08-01 00:00:00
abstract：:NONMEM is an extremely powerful tool for nonlinear mixed-effect modelling and simulation of pharmacokinetic and pharmacodynamic data. However, it is a console-based application whose output does not lend itself to rapid interpretation or efficient management. NONMEMory has been created to be a comprehensive project ma...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/j.cmpb.2005.02.003
更新日期：2005-06-01 00:00:00
abstract：:This paper discusses the theory and implementation of a modular data analysis system for the calculation and imaging of regional cerebral blood flow. The program may be generalized to any system requiring instantaneous and controllable visual data display, and we have set it up for compartmental analysis as described ...
journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
doi：10.1016/0169-2607(89)90091-6
更新日期：1989-05-01 00:00:00
