June 02, 2005

Reference to Analysis of Data with extra zeros

Excess zeros means
inflated zeros and use is made of the Zero-inflated Poisson(ZIP)
regression. The following reference might be of help:

Lambert,D.(1992). Zero-inflated Poisson Regression with application to
defects in Manufacturing. Technometrics, vol.34, pp 1–14.

Changing the S–Plus working directory

I could not find anywhere on the internet on how to change the S-Plus working directory (version 6.2) without extensive programming knowledge.

However, when doing my usual messing about I found that if you rename the S-plus directory that has the .Data and .Prefs folders in it and start the program it will not find it and give you an opportunity to replace the location. It will then create new folders and you can copy across the original folder contents to these (copy over if you like).

Presto! New working directory. Essential if IT services keep copying over your program partition with "a new image" and destroy all your data!!

May 09, 2005


Writing about web page http://stats.math.uni-augsburg.de/JGR/

The annual Chambers Prize for Statistical Software has been won this
year by Markus Helbig of the Department of Computer-Oriented Statistics
and Data Analysis at Augsburg University in Germany for his JGR
(Jaguar) Software, a GUI for R

This is the third time since the Prize was first awarded in the year
2000 that a student from Augsburg has won.

Note – R is the free-ware version of Splus.

April 05, 2005

Some Excel add–ins

Writing about web page http://www.cse.csiro.au/poptools

Just found these (again). I have never used them, but the PopTools looks as though it might be very useful.



March 11, 2005

Missing your p–values in your stats package?

For calculating p-values from t- values in Excel:

=TDIST (abs(x), df, tails)

where x is the cell where your t values is, df= degrees of freedom and tails is 1 or 2 (abs gives absolute number and so formula can deal with –ve values)

For F- values is very similar:

=FDIST (abs(x), df1, df2)

In S-Plus to get p-values from:
t-values: pt(x, df) where x = your t-value
F-values: pf(x, df1, df2) where x = your F-value

February 24, 2005

Calculation of Exact Confidence Intervals for Proportions

This appeared on allstat (statistics email list). For all those who want their
0 < CI < 1.

1. Using Wilson's score method was a popular suggestion, and the following websites were suggested for on-line and software-based implementations:

2. Similar "Exact" intervals by Clopper-Pearson (later refined by Blaker), for which (along with other proportion interval estimations) I was able to find R implementations at:

3. A Bayesian approach with Uniform priors and sampling from the posterior distribution for interval estimation

4. Transformation using logits and likelihood estimation (with reference to Yudi Pawitan's "In all likelihood…")

February 23, 2005

Further info on Selvin's book

Follow-up to Modern Applied Biostatistical Methods (Steve Selvin) – Using S–Plus from Ecology and Epidemiology Statistics Web Forum

Yes, Selvin's Modern Applied Biostatistical methods use code throughout, not menus.
The other book from Steve Selvin I mention is Statistical Analysis of Epidemiologic Data, 2nd Edition,Oxford University Press

January 19, 2005

statistics seminar series – Cambridge

Writing about web page http://www.mrc-bsu.cam.ac.uk/Bsusite/Education/seminars.shtml


25th January
SSRI anti-depressants and Suicide

Professor Deborah Ashby, Queen Mary, University of London

8th February
Partitioning of Variance in Multilevel Models

Dr William Browne, Mathematical Sciences, University of Nottingham

8th March
The UK 2001 Foot-and-mouth Disease Epidemic (A Case Study in Individual
Level Spatial Epidemiology)

Dr Rob Deardon, Statistical Laboratory, Centre for mathematical Sciences,
University of Cambridge

The seminars start at 2:30pm in the Large Seminar, Room, 1st Floor
Institute of Public Health, University Forvie Site, Robinson
Way,Cambridge. Tea and coffee are served afterwards. All are welcome to
See website for abstracts etc

January 13, 2005

Meta Analysis (Useful publications for…)

I haven't looked at these yet, but they have been recommended to me (thanks Lucy Snow -C.o. Seyi)

Arnqvist, G. & Wooster, D. (1995) Metaanalysis – synthesizing research
findings in ecology and evolution. Trends in Ecology and Evolution 10,

Gates, S. (2002) Review of methodology of quantitative reviews using
meta-analysis in ecology. Journal of Animal Ecology 71, 547–557.

Glass, G.V. (1976) Primary, secondary and meta-analysis of research.
Educational Researcher 5, 3–8.

Goldstein, H. & Leyland, A.H. (2001) Further topics in multilevel modelling.
Multilevel Modelling of Health Statistics (ed. by A.H.Leyland and
H.Goldstein), pp. 175–186. John Wiley and Sons, New York.

Gurevitch, J. & Hedges, L.V. (1999) Statistical issues in ecological
meta-analyses. Ecology, 80, 1142–1149.

Gurevitch, J. & Hedges, L.V. (2001) Meta-analysis. Conbining results of
independent experiments. Design and Analysis of Ecological Experiments (ed.
by S.M.Scheiner and J.Gurevitch), pp. 347–369. Oxford University Press.

Gurevitch, J., Morrow, L.L., Wallace, A. & Walsh, J.S. (1992) A
meta-analysis of competition in field experiments. American Naturalist, 140,

Hedges, L.V. & Olkin, I. (1985) Statistical Methods for Meta-Analysis.
Academic Press, London.

Hunter, J.E. & Schmidt, F.L. (2000) Fixed effects vs. random effects
meta-analysis models: Implications for cumulative research knowledge.
International Journal of Selection and Assessment 8, 275–292. 2000.

Myers, R.A. (2001) Stock and recruitment: generalisations about maximum
reproductive rate, density dependence, and variability using meta-analytic
approaches. ICES Journal of Marine Science, 58, 937–951.

Myers, R.A., Barrowman, N.J., Hutchings, J.A. & Rosenberg, A.A. (1995)
Population dynamics of exploited fish stocks at low population levels.
Science 269, 1106–1108.

Myers, R.A., MacKenzie, B.R., Bowen, K.G. & Barrowman, N.J. (2001) What is
the carrying capacity for fish in the ocean? A meta-analysis of population
dynamics of North Atlanitc cod. Canadian Journal of Fisheries and Aquatic
Sciences 58, 1464–1476.

Myers, R.A. & Mertz, G. (1998) Reducing uncertainty in the biological basis
of fisheries management by meta-analysis of data from many populations: a
synthesis. Fisheries Research 37, 51–60.

Myers, R.A., Mertz, G. & Fowlow, P.S. (1997) Maximum population growth rates
and recovery times for Atlantic cod, Gadus morhua. Fishery Bulletin 95,

Normand, S.T. (1999) Meta-analysis: formulating, evaluating, combining and
reporting. Statistics in
Medicine 18, 321–359.

Osenberg, C.W., Sarnelle, O., Cooper, S.D. & Holt, R.D. (1999) Resolving
ecological questions through meta-analysis: goals, metrics and models.
Ecology 80, 1105–1117.

Platt, R.W., Leroux, B.G. & Breslow, N. (1999) Generalised linear mixed
models for meta-analysis. Statistics in Medicine 18, 643–654.

Smith, S.J., Caudill, S.P., Steinberg, K.K. & Thacker, S.B. (1995a) On
combining dose-response data from epidemiological studies by metaanalysis.
Statistics in Medicine, 14, 531–544.

Thompson, S.G., Turner, R.M. & Arn, D.E. (2001) Multilevel models for
meta-analysis, and their application to absolute risk differences.
Statistical Methods in Medical Research 10, 375–392.

Modern Applied Biostatistical Methods (Steve Selvin) – Using S–Plus

A nice smooth introduction to S-Plus. The plus is that most of the examples used are from epidemiology, as opposed to other books on the matter I've seen. Steve Selvin has another good introductory book on Epidemiology which feature the same case studies and examples.
The downside is that there are no downloadable data sets.

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  • Thanks very much for this your solution just helped out up here in Shetland! by John Clayton on this entry
  • In R/S–plus: To find p–values for a normal distribution use pnorm(z) where z is your z value. by Matthew Walker on this entry
  • It may be easier to just move the SPLUS_Home directory to somewhere in the D drive then start S–Plus… by Sam Mason on this entry
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