Wednesday, May 22, 2013

Some R Code Using SAScii

For example, I want use Adult Demographic File from NHANES III. To import it using SAScii

library(SAScii)
SAScode <- "ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/nhanes/nhanes3/1A/adult.sas"
ftpdata <-"ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/nhanes/nhanes3/1A/adult.dat"
data <- read.SAScii(ftpdata, SAScode, beginline=5)

Because the line with INPUT in the SAS code file begins at line 5, I gave the option begineline=5. Of course, it assumes that you have downloaded and installed the package ‘SAScii’. Now you can save this file in any desirable format or use it for further downstream analysis. It does take quite sometime, longer than what it would take using SAS, but it does produce desired output.

Tuesday, May 21, 2013

An Interesting R Package–SAScii

For several surveys, such as NHANES III, data for many files is available in ASCII format with SAS code. However, those of us, who want to use that data in R, it is little cumbersome to use first SAS, import data into it, then transfer data into a format that can be imported into R. I came across of this relatively new package, SAScii, that uses the ASCII format and then SAS code to directly import data into R. Quite nice.

REDUCE Trial – My Thoughts

This week, REDUCE trial was published in JAMA “Short-term vs Conventional Glucocorticoid Therapy in Acute Exacerbations of Chronic Obstructive Pulmonary Disease; The REDUCE Randomized Clinical Trial” JAMA. 2013;():1-9. doi:10.1001/jama.2013.5023.

REDUCE (Reduction in the Use of Corticosteroids in Exacerbated COPD), was a randomized, non-inferiority multicenter trial in 5 Swiss teaching hospitals that enrolled 314 patients (between March 2006 through February 2011) who had presented to the emergency department with acute COPD exacerbation and were past or present smokers (≥20 pack-years) without a history of asthma. Participants were treated with 40 mg of prednisone daily for either 5 or 14 days in a placebo-controlled, double-blind fashion. The predefined non-inferiority criterion was an absolute increase in exacerbations of at most 15% or a 6 months follow-up. The trial found that 5-day treatment with systemic glucocorticoids was non-inferior to 14-day treatment with regard to re-exacerbation within 6 months of follow-up but significantly reduced glucocorticoid exposure.

The trial results are interesting for those of us who actually practice medicine and see COPD patients on a regular basis with exacerbations. There are three settings in which the results of this trial can potentially impact practice. In office practice, there are definitely some patients who would do just fine with 5 days course of prednisone and these are patients who get prescribed Medrol dose pack. On the other hand, there are patients who need longer courses of steroids and for such patients it is important to give them longer courses of steroids (up to 14 days and sometimes even longer) to keep them out of hospital. Interestingly, based on only the severity of the patient’s symptoms and signs alone, it is impossible to predict who will need longer treatment. It is only history of the patients that tells what will work. The practice in Emergency Department is unlikely to be much different than in an office setting except that there may be patients with more severe exacerbation. There too, history is the only helpful thing. However, once patients are admitted to the hospital, it is likely that these are those subsets of patients who didn’t respond as quickly to steroids in ED and thus needed admission with persistent severe symptoms. For such patients, it remains a possibility that a larger number (if not all) of them will need longer therapy.

Thus, in my view, if a patient is new to me and presents with COPD exacerbation and I don’t have historical information on this patient, I will feel comfortable in giving this patient a 5-day course of steroids. Otherwise, if I have some additional information telling me that shorter course will not be helpful, I should go for longer course.