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12.12.2014 admin
You are consulting for a clinical research group planning a trial to compare survival rates for proposed and standard cancer treatments.
Use the TWOSAMPLESURVIVAL statement with the TEST=LOGRANK option to compute the required sample size for the log-rank test.
The required sample size per group to achieve a power of 0.8 is 228 if the median loss time is 20 years for the proposed treatment. This post was kindly contributed by SAS and R - go there to comment and to read the full post. As we continue with our series on survival analysis, we demonstrate how to plot estimated (smoothed) hazard functions. The treatment group has dramatically higher hazard, but this drops appreciably after 6 months. Paul Alison includes macros to display estimates from parametric and semiparametric models in Survival Analysis Using SAS (2nd edition). The proc lifetest results (not shown) indicate that group 1 is the control and group 2 is the intervention. Dear readers, proc-x is looking for sponsors who would be willing to support the site in exchange for banner ads in the right sidebar of the site. ADDIS currently expects all relevant meta-data about a clinical trial to be entered prior to the entry of any measurement data.
However, quite often one starts out with some semi-structured data (such as an entry on or a table in a report) with partially or completely missing meta-data.
Note that for most of the above there is relevant previous work in the scientific literature, which will need to be evaluated prior to implementation. The prototypical time-to-event outcome is mortality: does treatment actually extend the lifespan of patients?
Meta-analysis of time-to-event data is important to summarize the evidence from multiple studies and on multiple interventions. This assumption may not be warranted, and better models can be fitted when individual patient data is available [e.g. However, individual patient data is often hard or impossible to obtain, and recent work has shown that it can instead be reconstructed from the Kaplan-Meier curve, to considerable accuracy [Guyot et al. The reconstruction method has correctly worked out the mathematical constraints that define how the individual patient data should be reconstructed.
Exact information, such as the total number of events, or the total number of patients, is not treated as a hard constraint, while approximate information extracted from the Kaplan-Meier curve is treated as if it were exact. ADDIS aims to let users quickly build datasets to answer specific clinical or policy questions. Markov Chain Monte Carlo (MCMC) methods enable the general purpose estimation of Bayesian Hierarchical Models.
Some software packages enable problem-specific languages or data structures that are subsequently translated to Bayesian Hierarchical models. To enable these use cases, a low-level serialization of Bayesian Hierarchical Models should be developed.
It is well known that for general statistical inference the number of iterations required to obtain a representative sample from the posterior distribution can not be determined in advance. When the input is provided by several independent Markov chains, these chains may have wildly varying convergence properties. It contains a wide range of statistical tests including many handy features not found in programs such as SPSS or SAS -- for example, easy analysis from summary data (as well as from raw data), nonparametric multiple comparisons, APA standard analysis write-up suggestions and more. Have you ever found a graph of some interesting information, but the graph was difficult to understand (or even misleading). I found the following immigration graph on the flowingdata website - it's a screen-capture of an animated slideshow that (I believe) was created by Alvin Chang.
It was an interesting topic, but I found the graph a bit difficult to understand, and even a bit misleading. It is difficult to read the text on the axes, since it is graph text on a black background.

The bar heights only go to about 10 million, but the vertical axis goes to 24 million (I assume this is to make room for the map in the background?).
There is a world map in the background, but it doesn't add to the data analysis - it's just a decoration and a distraction.
I think this data is interesting and important, and it deserves a better graph - therefore I set about creating one.
I'm not a big fan of showing the world map in the background, but I decided to add that in order to show how it could be done in a way that might actually help visualize the data. I like how you've improved the bar chart and incorporated geography as a type of legend rather than as a background image. The blog content appearing on this site does not necessarily represent the opinions of SAS. The planned data analysis is a log-rank test to nonparametrically compare the overall survival curves for the two treatments.
The "Standard" curve has only one point, specifying an exponential form with a survival probability of 0.5 at year 5. Only six more patients are required in each group if the median loss time is as short as five years.
Primarily, this consists of the variables that have been measured, the times at which they have been measured, and the (sub-) populations for which they have been measured.
Thus, we would like to extend ADDIS so that such data can be imported and annotated in a flexible way. Re-design of the import process to allow more flexible handling of missing meta-data and user-driven disambiguation of the data (e.g. Making use of the more declarative and generalizable CSP formulation, extend the method to simultaneously analyze multiple survival curves. For example, a clinician might want to identify an effective drug that lacks a certain side effect (e.g. Based on the number of trials available and their heterogeneity (differences in study design, interventions, outcome measures, populations), the user may choose to make the query more specific. Their implementation in widely available software has revolutionized the practice of statistics, and popularized the Bayesian approach to statistics. Several software packages offer a higher-level model specification language that allows a single specification to be applied to different data sets.
Examples include the R packages MCMCpack, which offers a collection of models, and GeMTC, which enables the estimation of network meta-analysis models.
The specification format should closely correspond to the Directed Acyclic Graph (DAG) representation of Bayesian Hierarchical models that is used internally by many software packages. Therefore, in Markov chain Monte Carlo (MCMC) methods, convergence is usually assessed based on the actual sample obtained. One chain may have a low per-iteration cost but also slow convergence, while another may have a high per-iteration cost but also quick convergence. For example, I first thought the reddish color predominant in the bars before 1920 matched 'Oceania' in the legend (and I thought that very strange). I did notice my eye was going between the text-based legend and the map and was wondering if you placed the text partially over the continents, the map could be used as the legend with an on-the-side purple box for Not Specified.
Goes to show how data visualizations can be easily misinterpreted or maybe that was the intention to display a decline in the last decade? I did not get though why the regions in the legend are shown in reverse alphabetical order. I like having the legend and the bar segments stacked in the same order - I think this makes it easier to relate the legend to the bars. This project should focus on useful ways of presenting larger sets of trials, including tables, graphs, and charts that provide insight on the aforementioned characteristics. Based on an analysis of the current system and initial usability testing, you will develop several proposals for user interfaces that assist the user in reducing the result set. This approach is taken by the BUGS family of MCMC software (WinBUGS, OpenBUGS, JAGS) as well as STAN.

Such tools are often tightly coupled to the underlying MCMC implementation, since the existing implementations do not interoperate at all. The aim is not to construct a human-writeable format, but rather to construct a data structure that is straightforward to translate to API calls for various MCMC libraries. Theoretical results on SMAA are based on the assumption that independent samples can be drawn from the input probability distributions. This thesis project will address the convergence of SMAA when some or all of the inputs are Markov chains. In this case, it would be a waste of computational resources to draw an equal number of samples from both. Hundreds of hours of working with consultants and researchers went in to creating the interface as well as creating understandable examples and program output. I wrote some SAS code to import the Excel Spreadsheet, transpose it, and create a more standard bar chart that is easy to read, and avoids things that could cause the user to misinterpret the data. I created the map separately with Proc Gmap, and then annotated it into the Proc Gchart bar chart. Also, could the legend instead of being a separate color pallet be overlaid on the map itself? The SAS Learning Post is where you'll find tutorials, tips and practical information to help you become a better SAS user. The survival curve for patients on the standard treatment is well known to be approximately exponential with a median survival time of five years. The GROUPSURVIVAL= option assigns the survival curves to the two groups, and the ACCRUALTIME= and FOLLOWUPTIME= options specify the accrual and follow-up times.
You will discuss these proposals with the team and with potential users to identify the most promising ones. All of them have specific strengths and weaknesses, with some being much more efficient at estimating certain models than others.
Other MCMC packages offer a library for a specific programming language, and as such model specification consists of calling this library directly. It would be beneficial if alternative MCMC implementations and ABC tools could be explored for the same model. Moreover, it should be straightforward to compile higher-level specification languages, such as BUGS, to this low-level format. However, this is often not the case, as modern statistical tools often rely on methods that generate a Markov chain, i.e. The measurement consists of specific statistical summaries, such as (count, sample size) or (mean, standard deviation, sample size). You will implement prototypes for the top proposals in ADDIS 2 and evaluate them in usability studies. Moreover, in some cases Approximate Bayesian Computation (ABC) offers a powerful and more computationally efficient alternative to MCMC methods. In addition, some MCMC packages implement a variety of sampling algorithms and often include a knowledge system to select the most appropriate algorithm given the structure of the model to be estimated.
Finally, well-specified and convenient JSON and R representations of the format should be specified. Patients will be accrued uniformly over two years and then followed for an additional three years past the accrual period.
Other packages implement only a single algorithm or expect the user to select the most appropriate one. Some loss to follow-up is expected, with roughly exponential rates that would result in about 50% loss with the standard treatment within 10 years. The loss to follow-up with the proposed treatment is more difficult to predict, but 50% loss would be expected to occur sometime between years 5 and 20.

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