A log book or diary to track all the steps taken for a project

A log book or diary to track all the steps taken for a project,

I became a member of Research Gate (http://www.researchgate.net/home.Home.html).
In the next posts I give some of the questions and answers formulated by me.

The first one is posted by Julia Law:

Diary of research steps as preface to writing up methodology
I would appreciate advice on methods used to write up a log book or diary to track all the steps I am taking for a few projects I am working on. I would like to develop a template to use for future projects also, so any suggestions as to what works and what doesn't would be appreciated. Thanks!

Your question is an interesting one. I have done some work on this problem.

But the way you formulate your question is a bit to general to answer in a satisfactory way. In particular, it is unclear in what field of research your projects are. Different disciplines have different methods to plan and specify research. For instance, in Medicine it is usual to formulate a protocol that is first thoroughly discussed by a local research committy before it is submitted to a medical ethical committy for assessment. There is also a diagramming method developed to specify a clinical trial (CONSORT statement), although I am doubtful about its usefulnes. However, most medical journals require such a statement for articles that describe intended research.

I have stressed the importance of properly documenting the steps taken in data analysis in our book (See Section 15.1 in Adèr, Mellenbergh and Hand, 2008). I also proposed a special diagramming method to represent methodological knowledge (See Appendix B of the same book). But in practice projects are quite varied and it is difficult to think up a general method to formally specify research procedures, let alone to develop a template that could be generally used. But maybe your own projects are quite similar and then the above may be useful.

Finally, for my own projects I always use a program called `Advanced Diary'. It is commercially available for a few dollars and makes it possibly to log each of your projects separately.

I hope this helps.

Herman Adèr

Adèr, H. J., Mellenbergh, G. J. and Hand, D. J. (2008). Advising on research methods: A consultant's companion. Johannes van Kessel: Huizen, The Netherlands.

The book has its own website: www.jvank.nl/ARMHome that links to Google Books so that you can inspect it online.

Advising on research methods. Selected topics 2011

A charming booklet containing papers on various methodological topics will be published next February, 15. It was written by participants of the yearly course `Methodological Advice' at the University of Amsterdam, this Fall. The idea was for the students to get acquainted with the whole process of drafting, submitting, reviewing, adapting and correcting for which so often support is asked during methodological consultancy.
The booklet has its own website:
Please take a look.
Herman

 

Addition to Sampling with and without replacement

The difference between sampling with replacement and sampling without replacement is twofold:

1. In the former case a temporal order is essentially assumed during the sampling process. Elements {a_1, a_2, .....,a_n} are drawn one after another, and at any time during the process, the same set of elements to draw from (S, say) is available.
2. Sampling without replacement can also be described as `grabbing', taking all the elements {a_1, a_2, ...,a_n} of the sample at the same time. If done sequentially, that set has to be adapted since the element that has been drawn should be removed. If  the initial set of elements to draw from is indicated by S_0, at each draw the set  from has to be adapted in the following way: S_i = S_(i-1) \ a_i.   

Funnily enough, sampling without replacement as occurs in real life research is essentially sequential and the above formulation in 2 seems counterintuitive since there is no distinct background set S apart from the sampling frame (Hand, 2008) and the population P (Think of a clinical trial in which patients are included one after another).  

In short, the two sampling mechanisms are very different and are applied in different situations.
Sampling without replacement is the sampling procedure that is commonly used in all emperical research.
Sampling with replacement is used in resampling strategies like bootstrapping. In such cases the notion of population from which the sample is drawn, is remote.

However, sampling with replacement also occurs in real life sampling, for instance in Capture-Recapture sampling aimed at determining population size of animals in a habitat, see section 12.3.6 of Agresti's book.

References
Alan Agresti (2002). Categorical data analysis. Second edition. Hoboken, NJ: Wiley.
David J. Hand (2008). Sampling. In H. J. Adèr, G. J. Mellenbergh, & D. J. Hand, Advising on research methods: A consultant's companion, Chapter 5. Huizen, The Netherlands: Van Kessel.

Sampling with and without replacement

In the bootstrapping literature (Efron & Tibshirani, 1993), the idea of ‘sampling with replacement’ is essential. It indicates that different bootstrap samples of size n are drawn from the same data set of size n, without producing the original data set over and over again. For instance, bootstrap samples from the data set of the numbers {1,9,11,12} may be: {1,1,11,12}; {1,9,11,9}; {1,9,11,12} and so on.
However, the procedure underlying sampling with replacement differs completely from sampling without replacement, in which the same unit can never appear twice.
In fact, sampling with replacement supposes that units are drawn one after another, and that a copy of the unit that was drawn is put back into the data (the actual replacement). In contrast, sampling without replacement allows to ‘grab’ n units at the same time.
The same effect as the sequential drawing described above for sampling with replacement would be obtained if n units were grabbed from a data set consisting of n copies of the original data. The data set would then be of size n².

References

Efron, B., & Tibshirani, R. J. (1993). An introduction to the bootstrap. New York: Chapman & Hall.

Multiple imputed missings in a dependent variable: How to analyze them?

During the analysis of the International PIRLS project, a comparative study on reading comprehension of students of Grade 4 and 5, the following problem was encountered during the analysis phase:
Some of the dependent variables (the plausible scores) are obtained by doing multiple impution on several scores (5 times). Usually, properly analyzing the data sets resulting from multiple imputation makes it necessary to do the analysis of each data set separately and then afterwards, combining the results in some way (as far as I know, the only standard statistical package that does this for you automatically, is Mplus).
However, in case the dependent variable is imputed, one can use a repeated measurement design. In the case described above, an extra level was added to a multilevel analysis with the 5 plausible scores as a repeated measurement.
Drawback of this approach in multilevel analysis (MLwiN) is that the data sets which are already enormous in this case, are quintupled.

Herman

Distribution outside Belgium and the Netherlands

It turned out to be very difficult to get distribution of the ARM book (Advising on research methods: A consultant's companion by Adèr, Mellenbergh and Hand) via Barnes and Noble in the US up and running.
Until these problems are solved, readers outside Belgium and the Netherlands can order directly from the publisher, Johannes van Kessel Publishing at: Publishing@jvank.nl. They charge only local mailing costs (euro 6.20). Please contact them by email. To order via bol.com, van Stockum or Selexyz see: www.jvank.nl/ARMHome
The proceedings of the 2007 KNAW symposium `Advising on research methods' can also be ordered by contacting the publisher.

Herman

Proceedings of the KNAW colloquium on Advising now accessible via Google Books

We submitted the text of the Proceedings of the 2007 Colloquium `Advising on research methods' to Google Books. The book is now accessible. In Google Books, search for `Advising on research methods' or for the ISBN number 9789079418039.
Herman