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At least 1,315 records · Page 73Linked to original sources

PubMed1991

The assessment of bioequivalence in a two-period cross-over design: development of a simple BASIC program.

The complete algorithms needed in the calculation of confidence intervals on the basis of observations from a two-way cross-over bioequivalence trial are described. They do not contain assumptions as to the expected sampling distribution or possible period effects. The algorithms were used in a BASIC program, which was developed subsequently. Its validity is demonstrated here with a set of literature data. The program is available from the authors upon request.

Algorithms↗

PubMed1991

Object-oriented design and programming in medical decision support.

The concept of object-oriented design and programming has recently received a great deal of attention from the software engineering community. This paper highlights the realisable benefits of using the object-oriented approach in the design and development of clinical decision support systems. These systems seek to build a computational model of some problem domain and therefore tend to be exploratory in nature. Conventional procedural design techniques do not support either the process of model building or rapid prototyping. The central concepts of the object-oriented paradigm are introduced, namely encapsulation, inheritance and polymorphism, and their use illustrated in a case study, taken from the domain of breast histopathology. In particular, the dual roles of inheritance in object-oriented programming are examined, i.e., inheritance as a conceptual modelling tool and inheritance as a code reuse mechanism. It is argued that the use of the former is not entirely intuitive and may be difficult to incorporate into the design process. However, inheritance as a means of optimising code reuse offers substantial technical benefits.

Adult↗

PubMed1991

Randomization tests: statistics for experimenters.

Randomization (permutation) tests free the experimenter from the constraints of random sampling, a known error distribution and equal variances, to give a direct answer to the question "how likely is such a large (or small) result if the applied treatments had no effect?" The "result" may be the difference in mean responses, a correlation coefficient or any other value of interest. A randomization test is not a different statistical test but a different, and always valid, method of determining statistical significance. The familiar t-test and F-test can be carried out by data permutation without any parametric assumptions being fulfilled. A particular advantage of this method is that unbalanced designs and missing values are easily accommodated. Even with only a small number of subjects the number of permutations will be large and a computer is necessary if the randomization test is to be of practical value. To make this method of determining statistical significance generally available an interactive microcomputer program, forming a comprehensive package for the design and analysis of experiments, has been prepared.

Mathematical Computing↗

PubMed1992

GOFCOX: a computer program for the goodness-of-fit analysis of the Cox proportional hazards model.

GOFCOX is a user-friendly FORTRAN program for assessing the adequacy of the Cox proportional hazards model. The underlying methodology is based on the comparison of the maximum partial likelihood estimator and a weighted parameter estimator. The latter is the root to an estimation equation that assigns varying weights to the individual contributions to the partial likelihood score function. The weighted and unweighted parameter estimators have the same expectation under the Cox model, but tend to differ when the model is inappropriate. The GOFCOX program computes a rich class of weighted parameter estimators and corresponding goodness-of-fit test statistics. The program runs on both mainframe computers and microcomputers. The running time is minimal even for large data sets. A simple example is provided to illustrate the features of the program.

Computers, Mainframe↗

PubMed1992

Cohen's weighted kappa with Turbo Pascal (FORTRAN).

A microcomputer based Turbo Pascal and FORTRAN program for Cohen's weighted kappa (kappa w) is given. Three clinical applications for kappa w are also presented. A typical data file, the Pascal and FORTRAN program listing and corresponding output are given.

Carotid Stenosis↗

PubMed1992

TWINAN90: a FORTRAN program for conducting ANOVA-based and likelihood-based analyses of twin data.

We discuss the program, TWINAN90, which can perform several different types of analysis of twin data. TWINAN90 incorporates the ANOVA-based twin analyses from the TWINAN twin analysis program, and also includes maximum likelihood estimation of parameters from three path models. Another feature of TWINAN90 is the optional output of a pedigree file which can be read by the quantitative genetics package FISHER. The diagnostic features of the program make TWINAN90 useful also for preliminary analyses prior to the use of more sophisticated modeling procedures which are available in packages such as LISREL and FISHER. An annotated printout from TWINAN90 is presented to illustrate the statistical analyses performed in the program.

Analysis of Variance↗

PubMed1992

PINTRACE: a computer program for assessment of pin positions in routine radiographs of femoral neck fractures.

A new method for determination of pin positions in internally fixated femoral neck fractures is described. In AP and lateral radiographs of the hip, measurements are made of the cervicofemoral angles, the diameter of the femoral head and neck, and the distances from the central femoral neck axis to each pin. From these values the positions of the fixation pins in defined straight AP and lateral projections are determined by geometric calculations. A computer program in BASIC was developed to perform the calculations and to produce graphic displays of cross-sections of the femoral head and neck with the corrected pin positions indicated. For routine radiographic examinations with unknown inclination angles of the X-ray beams, the error of the method is less than 5% of the femoral head diameter. With conventional methods of determining pin positions the error can exceed 25% of the femoral head diameter.

Algorithms↗

PubMed1992

A combined one- and two-way analysis of variance microcomputer program.

A simple microcomputer program in BASIC is designed to compute both the one-way and two-way analysis of variance. The program is an interactive one and can be easily and promptly used for statistical analysis of biomedical data. The applicability of the program is illustrated by data obtained from the percutaneous absorption of dihydroergotamine into the excised skin of rabbits.

Analysis of Variance↗

PubMed1993

NONMEM version III implementation on a VAX 9000: a DCL procedure for single-step execution and the unrealized advantage of a vectorizing FORTRAN compiler.

There is great interest within the FDA, academia, and the pharmaceutical industry to provide more detailed information about the time course of drug concentration and effect in subjects receiving a drug as part of their overall therapy. Advocates of this effort expect the eventual goal of these endeavors to provide labeling which reflects the experience of drug administration to the entire population of potential recipients. The set of techniques which have been thus far applied to this task has been defined as population approach methodologies. While a consensus view on the usefulness of these techniques is not likely to be formed in the near future, most pharmaceutical companies or individuals who provide kinetic/dynamic support for drug development programs are investigating population approach methods. A major setback in this investigation has been the shortage of computational tools to analyze population data. One such algorithm, NONMEM, supplied by the NONMEM Project Group of the University of California, San Francisco has been widely used and remains the most accessible computational tool to date. The program is distributed to users as FORTRAN 77 source code with instructions for platform customization. Given the memory and compiler requirements of this algorithm and the intensive matrix manipulation required for run convergence and parameter estimation, this program's performance is largely determined by the platform and the FORTRAN compiler used to create the NONMEM executable. Benchmark testing on a VAX 9000 with Digital's FORTRAN (v. 1.2) compiler suggests that this is an acceptable platform. Due to excessive branching within the loops of the NONMEM source code, the vector processing capabilities of the KV900-AA vector processor actually decrease performance. A DCL procedure is given to provide single step execution of this algorithm.

Algorithms↗

PubMed1995

Cochran Q test with Turbo BASIC.

A microcomputer program written in Turbo BASIC for the sequential application of the Cochran Q test is given. A clinical application where the test is used in order to explore the structure of the agreement between observers is also presented. A program listing is available on request.

Mathematical Computing↗

PubMed1995

Construction of molecular evolutionary phylogenetic trees from DNA sequences based on minimum complexity principle.

Ever since the discovery of a molecular clock, many methods have been developed to reconstruct the molecular evolutionary phylogenetic trees. In this paper, we deal with the problem from the viewpoint of an inductive inference and apply Rissanen's minimum description length principle to extract the minimum complexity phylogenetic tree. Our method describes the complexity of the molecular phylogenetic tree by three terms which are related to the tree topology, the sum of the branch lengths and the difference between the model and the data measured by logarithmic likelihood. Five mitochondrial DNA sequences, from the human, the common chimpanzee, the pygmy chimpanzee, the gorilla and the orangutan, are used for investigating the validity of this method. It is suggested that this method might be superior to the traditional method in that it still shows good accuracy even near the root of phylogenetic trees.

Algorithms↗

PubMed1995

SEQPWR and SEQOPR: computer programs for design of maximum information trials based on group sequential logrank tests.

The maximum information trial paradigm for clinical trials with failure time data was recognized and has been investigated. With the maximum information trial paradigm, a study is concluded when a prespecified maximum number of events of interest, thus maximum information, has been accrued if there was no early stopping due to treatment difference or lack thereof. We present two interactive FORTRAN programs for use in designing maximum information trials based on group sequential logrank tests. The program SEQPWR computes the attainable power of group sequential logrank tests given the combinations of the accrual and follow-up durations. The program SEQOPR allows the users to investigate the operating characteristics of the maximum information trial given the information fractions of interim analyses. A clinical trial from the Eastern Cooperative Oncology Group is provided to illustrate the usage and features of the programs.

Algorithms↗

PubMed1994

Making heterogeneous medical databases interoperable.

The increasing use of computer systems for storing patient information in different hospitals, in different departments within the same hospital, in clinics and even in doctors' surgeries, is creating a problem in terms of the fragmentation of the patient record. The lack of any coordination or standardization in the way in which data are represented and stored in these different systems makes the task of finding and retrieving data that much more difficult. This paper considers two aspects of this problem and describes an architecture which can be used to overcome them.

Communication↗

PubMed1994

Development of Design-a-Trial, a knowledge-based critiquing system for authors of clinical trial protocols.

Many published clinical trials are poorly designed, suggesting that the protocol was incomplete, disorganised or contained errors. This fact, doctors' limited statistical skills and the shortage of medical statisticians, prompted us to develop a knowledge-based aid, Design-a-Trial, for authors of clinical trial protocols. This interviews a physician, prompts them with suitable design options, comments on the statistical rigour and feasibility of their proposed design and generates a 6-page draft protocol document. This paper outlines the process used to develop Design-a-Trial, presents preliminary evaluation results, and discusses lessons we learned which may apply to the developed of other medical decision-aids.

Clinical Trials as Topic↗

PubMed1994

Application of minimal spanning trees in glioma grading--a CLIPPER program for the calculation and construction of minimal spanning trees.

We present a CLIPPER program for the calculation and graphical representation of minimal spanning trees (MST) which is available on request on diskette from the authors. The MST are a useful parameter for structural cluster detection. They can be applied to grading problems in tumour biology. We present and discuss the applicability of MST by an example from the field of astrocytoma grading.

Algorithms↗

PubMed1994

A computer program for non-parametric analysis of incomplete repeated measures from two samples.

RMNP2 is an easy-to-use FORTRAN program for the analysis of repeated measures using the non-parametric two-sample tests of Wei and Lachin (J. Am. Stat. Assoc. 79 (1984) 653-661) and Wei and Johnson (Biometrika 72 (1985) 359-364). The program compares two groups of subjects or experimental units when measurements are obtained at multiple time points, or under multiple conditions, from each subject. A strength of the methodology is that subjects with missing responses at one or more time points can be included in the analysis, under the assumption that the missing value mechanism is independent of the response. In contrast to other methods that require parametric assumptions concerning the distribution of the outcome variable, RMNP2 is applicable when the response variable is continuous but not normally distributed. The program is also useful in the analysis of ordered categorical outcomes when the number of possible responses is too large to permit application of general categorical data methodology. The program can be run on microcomputers, workstations and mainframe computers. Two examples illustrating the use and features of RMNP2 are provided.

Analgesia, Obstetrical↗

PubMed1994

Computer program for the proportional hazards measurement error model.

The Cox-regression analysis based on the partial likelihood assumes that the covariates, or independent variables, are exactly measured without error. If the covariates are subject to measurement error and the error-prone observed values are used in the analysis by simply ignoring the measurement error, the results are generally biased and misleading; the bias does not diminish as the sample size is increased. The objective of the paper is to briefly describe a method searching for asymptotically unbiased estimates of the parameters correcting for the measurement error in the Cox-regression model and to present a FORTRAN program to perform the correction method; asymptotic standard errors of the corrected estimates are also obtained. The measurement error distribution, that is the conditional distribution of the observed values given the true value, must be specified. An advantage of the method described is that it does not require any assumption on the distribution of the true values; in other words, <--> values are treated as unknown fixed constants. It can accommodate tied failure times unless ties are very frequent, and any censorship or loss to follow-up are allowed as long as they are 'independent of survival'.

Likelihood Functions↗

PubMed1995

Artificial intelligence programming with LabVIEW: genetic algorithms for instrumentation control and optimization.

A genetic algorithm for instrumentation control and optimization was developed using the LabVIEW graphical programming environment. The usefulness of this methodology for the optimization of a closed loop control instrument is demonstrated with minimal complexity and the programming is presented in detail to facilitate its adaptation to other LabVIEW applications. Closed loop control instruments have variety of applications in the biomedical sciences including the regulation of physiological processes such as blood pressure. The program presented here should provide a useful starting point for those wishing to incorporate genetic algorithm approaches to LabVIEW mediated optimization of closed loop control instruments.

Algorithms↗