0README

Wed Jul 27 21:41:36 MST 2005


/Simplex-1994
|-- 0README
|
`-- Lib			executables, sources, tests, man page, for simplex
    |					fitting programs;
    |					also code for an S function
    |-- 0README			placeholder = ref to ../0README
    |-- 0NOTE			notes on fit results from 1991 and 1994 sources
    |-- 1-NOTE			info mostly relevant to S version of simplex fit
    |-- 1-READMEZ		more info relevant to S version of simplex fit
    |
    |-- Makefile
    |-- ldhfit			executable, fit of ldh enzyme rate data 
    |-- ldhfit.c		C source for custom fitting function
    |
    |-- powellfit		executable, minimization of quartic function
    |-- powell.c		C source for custom fitting function
    |
    |-- simpfront.c		interface fitting function to simplex library
    |
    |			simplex library
    |-- simpdefs.h
    |-- simpdev.c		quadratic fit
    |-- simpfit.c		nelder-mead simplex fit
    |-- simplib0.c
    |-- simpmain.c		control fit - call simpdev and simpfit
    |
    |-- ldhfit.dat		input for ldhfit - data, cntrl val, param val
    |-- powell.dat		input for powellfit - cntrl val, param val
    |-- simpfit.dat.template
    |
    |-- simplex.1		man page - groff man macros -> various formats
    |-- simplex.1.ps
    |-- simplex.1.txt
    |-- simplex.1.txt-nobs	nobs = no backspaces
    |
    |-- S			directory - S scripts for S simplex function
    |   |-- Puro.S
    |   |-- ldhfn.S
    |   |-- powell.S
    |   |-- simpS.c
    |   |-- simpStest.c
    |   |-- simpStest.h
    |   |-- simpfit.S
    |   |-- simpfit.all.s
    |   `-- simpfit.d
    |
    |-- tests			directory - test ldhfit and powellfit;
    |   |				    compare output under macosx with
    |	|				    old (1994) output, under 4d30
    |   |-- ldhfit.out-1994-4d30
    |   |-- ldhfit.test-macosx
    |   |-- powell.out-1994-4d30
    |   `-- powell.test-macosx
    |
    `-- tests-14		directory - tests comparing ldhfit from 1994
        |				    sources with ldhfit, 1991 sources;
	|				    all compiles and runs under macosx;
	|				    1991 data was modified for compat.
	|				    with 1994 ldhfit (add bounds);
	|				 symbols: 
	|				    11 = 1991 ldhfit run with 1991 data
	|				    14 = 1991 ldhfit run with 1994 data
	|				    41 = 1994 ldhfit run with 1991 data
	|				    44 = 1994 ldhfit run with 1994 data
	|				 results and analysis:
	|				    in 0NOTE
        |-- 0NOTE
        |-- diff-14-11			diff file btwn results encoded
        |-- diff-14-44			similar
        |-- ldhfit.dat1991-mod		1991 data, modified addn bounds
        |-- ldhfit.dat1994		1994 data
        |-- ldhfit1991.test1991-macosx	   11 - results from run as encoded 
        |-- ldhfit1991.test1994-macosx	   14
        |-- ldhfit1994.test1991-macosx     41
        `-- ldhfit1994.test1994-macosx     44
	
There are sources for simplex fitting under the directory Simplex-1994.
However, the Simplex-1991 sources and functions are more to be
recommended to a prospective user: the screen and disk outputs are
controllable from the command line and are optionally much more
verbose.  The 1991 and 1994 programs give identical results with
the same set of data, except for differently-structured output.
The 1994 sources, derived from the 1991, were designed to provide a
C-coded function for S, that could be loaded and called from within
S and S functions.  The standalone fitting programs under
Simple-1994 are afterthoughts.

For those interested in the implementation of the Nelder-Mead
algorithm and the matrix operations of the quadratic fit, the 1994
sources are more heavily commented than the 1991.


John Rupley
 rupley@u.arizona.edu -or- jar@rupley.com
 30 Calle Belleza, Tucson AZ 85716 - (520) 325-4533; fax - (520) 325-4991
 Dept. Biochemistry & Molecular Biophysics, Univ. Arizona, Tucson AZ 85721