Friday, May 31, 2013

My favorite quotes of Magic School Bus

My favorite quotes of Magic School Bus (1994-1998)

It was my happy time watching Magic School Bus with my kids around 2000. The series is informative and educative, and the last but the best is a mindset of exploring and innovation. There are several quotes I don't want to forget.
  • Ms. Frizzle, "Take chances, make mistakes, get messy."
  • Ms. Frizzle, "Never say 'never.'"
These are also on the top of list of Wikiqote

Diease or not disease, a diabetic question

Diease or not disease, a diabetic question

Last a few days, I read two diabetic related articles, which both are not my cup of tea; but I am really appreciating their thoughts and contrast.
Both of authors are creative and thoughtful. Riva Greenberg is much more on the side of novelty/grassroot side (without enough evidence, to me) and Edwin Gale is much more on the side of classic/ivy tower (with typical theory/evidence, to me). I enjoy reading both articles.

Friday, May 24, 2013

Dance with my father - Luther Vandross

Dance With My Father, In Memory of My Fathers


 
"Dance With My Father"

Back when I was a child, before life removed all the innocence
 My father would lift me high and dance with my mother and me and then
 Spin me around ‘til I fell asleep
 Then up the stairs he would carry me
 And I knew for sure I was loved
 If I could get another chance, another walk, another dance with him
 I’d play a song that would never, ever end
 How I’d love, love, love
 To dance with my father again
 When I and my mother would disagree
 To get my way, I would run from her to him
 He’d make me laugh just to comfort me
 Then finally make me do just what my mama said
 Later that night when I was asleep
 He left a dollar under my sheet
 Never dreamed that he would be gone from me
 If I could steal one final glance, one final step, one final dance with him
 I’d play a song that would never, ever end
‘Cause I’d love, love, love
 To dance with my father again
 Sometimes I’d listen outside her door
 And I’d hear how my mother cried for him
 I pray for her even more than me
 I pray for her even more than me
 I know I’m praying for much too much
 But could you send back the only man she loved
 I know you don’t do it usually
 But dear Lord she’s dying
 To dance with my father again
 Every night I fall asleep and this is all I ever dream

Friday, May 17, 2013

Impact Factor Distortions

Impact Factor Distortions by Bruce Alberts
Source: Science

"This Editorial coincides with the release of the San Francisco declaration on research Assessment (DORA), the outcome of a gathering of concerned scientists at the December 2012 meeting of the American Society for Cell Biology. To correct distortions in the evaluation of scientific research, DORA aims to stop the use of the "journal impact factor" in judging an individual scientist's work. The Declaration states that the impact factor must not be used as "a surrogate measure of the quality of individual research articles, to assess an individual scientist's contributions, or in hiring, promotion, or funding decisions." DORA also provides a list of specific actions, targeted at improving the way scientific publications are assessed, to be taken by funding agencies, institutions, publishers, researchers, and the organizations that supply metrics. These recommendations have thus far been endorsed by more than 150 leading scientists and 75 scientific organizations, including the American Association for the Advancement of Science (the publisher of Science). Here are some reasons why: "

Tuesday, May 14, 2013

How to make compost

How to make compost
  • A very helpful Youtube video from howdini.com. Scott's teaching how to make compost using cheap chicken wire.

slope index of inequality (SII) and the relative index of inequality (RII).

Slope Index of Inequality (SII) and Relative Index of Inequality (RII)

The slope index of inequality (SII) and the relative index of inequality (RII) are measures of health inequality (Mackenbach, 1997). The SII and RII can be calculated through regression analysis on an indicator of the cumulative relative position of each group with respect to a socioeconomic variable account for both the socioeconomic status (SES) of the groups and the size of the population.


The groups of SES are ordered by decreasing socioeconomic status from higher to lower. Each socioeconomic category is given a score called ridit score, which reflects the average cumulative frequency of the group, a midpoint of the range in the cumulative distribution introduced by Bross (1958). For example, if the highest educated women include 20% of the population, the range of women in this category is from 0.00 to 0.20 and assigned a ridit score of 0.10 (= 0.20/2 = [0 + 0.2]/2), and if the next level of educated women include 50% of the population from .20 to 0.70, the corresponding ridit score is 0.45 (= 0.20 + 0.5/2 = [0.20 + 0.70]/2) and so forth. 
 

SII (rate difference) is the slope of the regression line (b) estimated by the weighted least squares method and represents the change in measured outcome/event when the position of the SES changes by one unit.

RII (rate ratios) can be which can be estimated in two ways: one way is to divide the SII by the mean level of population health or by the frequency of the health problem in the population; the other way is to divide the predicted value of the regression at the highest point (range=1) by the predicted value of the regression at the lowest point (range=0). The second method for the RII is calculated by log-linear—or logistic—regression after the logarithmic—or logit—transformation of the dependent variable. One way to facilitate the interpretation of this measure of the second method may be to express the RII as a percentage by subtracting 1 from it and multiplying the result by 100 (see Table 1 below) (Regidor, 2004).

Other References:

Calculation of SII and RII using aggregated data (modified from the paper of Regidor, 2004)



SII of the year 1990 = 104.4, the beta coefficient (b) of a linear regression of Ridit90 and Mort90.
RII of the year 1990 can be calculated as SII/(average mortality rate) = 104/134 = 0.7761 (Measures of Health Disparity - NCI (pdf))

Calculation of SII and RII using individual data - Stata 12 (modified from the paper of Ernstsen, 2012)


ID
Men
Survey
Smoking
Ridit
Age
1
1
1
0
0.34
53
2
0
1
1
0.55
48
3
0
2
0
0.34
55
4
1
3
1
0.34
40

Estimating Relative Index of Inequality (RII) for smoking in men at the first survey:

.glm i.smoking ridit age if survey==1 & men==1, fam(bin) link(log) nolog eform

Estimating Slope Index of Inequality (SII) for smoking in men at the first survey:

.glm i.smoking ridit age if survey==1 & men==1, fam(bin) link(identity)

Estimating trend in RII and SII over time for men:

.glm i.smoking c.ridit##survey age if men==1, fam(bin) link(log) nolog eform
.glm i.smoking c.ridit##survey age if men==1, fam(bin) link(identity)

Estimating gender differences in RII and SII at each survey:

.glm i.smoking c.ridit##men age if survey==1, fam(bin) link(log) nolog
.glm i.smoking c.ridit##men age if survey==1, fam(bin) link(identity)

Estimating if RII and SII changed differently over time in men and women:

.glm i.smoking c.ridit##men##survey age, fam(bin) link (log) nolog
.glm i.smoking c.ridit##men##survey age, fam(bin) link (identity) nolog

New features mentioned in SAS Tech Report, May 2013

New features mentioned in SAS Tech Report, May 2013

I haven't use SAS for my projects for a while. Today I read the SAS Tech Report in my emailbox. The Graphics focus area has been updated and is a great place to learn some new features/PROC SGPLOT. SAS is working hard on making better graphics.

Chris Daman has posted a few blogs about multilevel analysis:

Saturday, May 11, 2013

Does 3 minutes of exercise and two fasts a week (5:2) work?

Does 3 minutes of exercise and two fasts a week (5:2) and others
 
A few weeks ago, I watched a presention on PBS channel by Dr. Michael Mosley about he dealed with his high blood glucose (diabetes). He amazingly found 3 minutes of exercise and two fasts a week works for him.
Grant (2017). Running on empty (TheScientist)


Francesco (2018): A time to fast, Ludwig (2018): Dietary fat: From foe to friend?

The ancient civilization also practiced this similar activity (fasting) for good health and longevity long times ago: some are simple, some are much more complicated, called 'Inedia' and Chinese called this '辟谷' (Pi Gu). Dr. Michael Mosley did a great job on promoting this activity, and he makes this more practiable.

Friday, May 10, 2013

Integrated Health Interview Series

Integrated Health Interview Series (IHIS)

If you're working on trend projects using US National Health Interview Survey. IHIS, a database of NHIS data that facilitates trend analyses, can be a big helper. This well-organized online documents included NHIS annual data from the 1960s to the present. You can easily linked to additional variables in NHIS public use data and comprehensive on-line documentation.

Thursday, May 09, 2013

Medicare Provider Charge Data

Medicare Provider Charge Data
 
"As part of the Obama administration's work to make our health care system more affordable and accountable, data are being released that show significant variation across the country and within communities in what hospitals charge for common inpatient services.
 
The data provided here include hospital-specific charges for the more than 3,000 U.S. hospitals that receive Medicare Inpatient Prospective Payment System (IPPS) payments for the top 100 most frequently billed discharges, paid under Medicare based on a rate per discharge using the Medicare Severity Diagnosis Related Group (MS-DRG) for Fiscal Year (FY) 2011. These DRGs represent almost 7 million discharges or 60 percent of total Medicare IPPS discharges.
 
Hospitals determine what they will charge for items and services provided to patients and these charges are the amount the hospital bills for an item or service. The Total Payment amount includes the MS-DRG amount, bill total per diem, beneficiary primary payer claim payment amount, beneficiary Part A coinsurance amount, beneficiary deductible amount, beneficiary blood deducible amount and DRG outlier amount.
 
For these DRGs, average charges and average Medicare payments are calculated at the individual hospital level. Users will be able to make comparisons between the amount charged by individual hospitals within local markets, and nationwide, for services that might be furnished in connection with a particular inpatient stay.
 
Data are being made available in Microsoft Excel (.xlsx) format and comma separated values (.csv) format."
 
 

Hospital Prices No Longer Secret As New Data Reveals Bewildering System, Staggering Cost Differences - 05/08/2013 The Huffington Post

Tuesday, May 07, 2013

Free PDF Related Utilities

Free PDF Related Utilities
  • Briss, an open-source application, is an excellent handyware for cropping/trimming PDF pages. It groups all the different page sizes in your document together and will require the user to make cropping decisions for each group of pages that is of a similar size. It provides the option to exclude certain pages or page ranges from the cropping action. It crops PDFs with simple GUI; it can crop different regions into separate pages, and multi column/pages. It's very handy.
  • ORPALIS PDF Reducer Free is a freeware version of PDF compression Software to help get existing PDF files reduced up to 80% more than concurrent products.
  • FileOptimizer is an another one for file size optimizer. It supports a lot of file types from audio/video (MP3, OGG, OGV), image (GIF, JPEG, PNG), and even office formats (DOCX, XLSX, ODT, PDF) and system files (DLL, EXE). By default, FileOptimizer will remove additional metadata, and other unneeded information, but will keep original files in your recycle bin. Notes: It might corrupt some of them especially EXE files.
  • PdfSam is a free open source tool to split and merge pdf documents (it keeps bookmarks of original pdf files).
  • PDFTK Builder and GUI for PDFTK are free graphical interfaces to the Windows version of pdftk making it much easier to use. pdftk is an electronic staple-remover, hole-punch, binder, secret-decoder-ring, and X-Ray-glasses. Pdftk is a simple tool for doing everyday things with PDF documents.
  • Foxit Reader is the high volume PDF reader providing a complete PDF creation solution, providing the power of PDF creation to every desktop. Foxit Reader Version 6 has a lot of improvement. I use PDF-XChange as an portable Apps, but I am thinking to use Foxit Reader more.
  • PDF-XChange Viewer presents users with an alternative to Adobe's Acrobat Reader. It gives users more options such as typewriter than its competition, allowing for more in-depth markups.
  • STDU Viewer is a free viewer for multiple file formats including TIFF, PDF, DjVu, XPS, JBIG2, and WWF format. Starting from 1.6.86, STDU Viewer supports MOBI/AZW and FB2 formats and from 1.6.151, It supports EPub format. You can use STDV Viewer to print the files of these formats. STDV Viewer is getting better and better.
  • SumatraPDF is a PDF, EPUB, MOBI, CHM, XPS, DjVu, CBZ and CBR reader for Windows. It's small and starts up fast.
  • PDFill PDF Tools are FREE PDF functions to merge, split, reorder, delete, encrypt, decrypt, rotate, crop and reformat PDF (change margin size) pages,  to add information, header, footer and watermark, to convert images to PDF, PDF to images or PostScript to PDF, to delete, flatten and list form fields, to scan to pdf, to create transparent image, and more.
  • K2pdfopt optimizes PDF/DJVU files for mobile e-readers (e.g. the Kindle) and smartphones. It works well on multi-column PDF/DJVU files and can re-flow text even on scanned PDF files. K2pdfopt is open source.