From e1e61afb4e39638a5ca4753837a70da63c6cd169 Mon Sep 17 00:00:00 2001 From: AJ Rossini Date: Thu, 4 Oct 2012 15:07:06 +0200 Subject: [PATCH] update org format (srcname -> name) update some of the todo docs. clean up content. Signed-off-by: AJ Rossini --- TODO.org | 79 +++++++++++++++++++++++++++++++++------------------------------- 1 file changed, 41 insertions(+), 38 deletions(-) diff --git a/TODO.org b/TODO.org index 5ae13fd..3956657 100644 --- a/TODO.org +++ b/TODO.org @@ -1,5 +1,5 @@ -Time-stamp: <2012-10-04 02:40:24 tony> +Time-stamp: <2012-10-04 04:10:12 tony> Creation: <2008-09-08 08:06:30 tony> * Intro and Metadata @@ -93,11 +93,11 @@ current (possibly incomplete) set of lisp dependencies <2012-10-04 Thu> ?? cl-plplot : cffi -* Tasks to Do [4/19] +* Tasks to Do [4/21] Usually, we need to load it before going on. -#+srcname: loadit +#+name: loadit #+begin_src lisp (ql:quickload :cls) #+end_src @@ -118,7 +118,7 @@ current (possibly incomplete) set of lisp dependencies <2012-10-04 Thu> - State "TODO" from "" [2010-10-12 Tue 13:47] This is an example of a custom setup, not really interesting at this point except to remind Tony how to program. -#+srcname: loader +#+name: loader #+begin_src lisp (in-package :cl-user) (progn @@ -174,7 +174,7 @@ current (possibly incomplete) set of lisp dependencies <2012-10-04 Thu> the other systems that provide testing, when people add them to the mix of libraries that we need, along with examples of how to use. -#+srcname: ex-cls-unittest +#+name: ex-cls-unittest #+begin_src lisp (in-package :lisp-stat-unittests) (run-tests :suite 'lisp-stat-ut) @@ -190,7 +190,7 @@ current (possibly incomplete) set of lisp dependencies <2012-10-04 Thu> The following needs to be solved in order to have a decent installation qualification (IQ) and performance qualification (PQ) -#+srcname: cls-unittest +#+name: cls-unittest #+begin_src lisp (in-package :lisp-stat-unittests) (asdf:oos 'asdf:test-op 'cls) @@ -200,7 +200,7 @@ installation qualification (IQ) and performance qualification (PQ) and check documentation to see if it is useful. -#+srcname: +#+name: unittest-ex #+begin_src lisp (in-package :lisp-stat-unittests) @@ -305,7 +305,7 @@ installation qualification (IQ) and performance qualification (PQ) The following needs to work, and a related syntax for resampling and similar synthetic data approaches (bootstrapping, imputation) ought to use similar syntax as well. -#+srcname: DataSetNameScoping +#+name: DataSetNameScoping #+begin_src lisp (in-package :ls-user) (progn @@ -356,7 +356,7 @@ installation qualification (IQ) and performance qualification (PQ) Seems to generally work, need to ensure that we use this for appropriate typing. -#+srcname: DFvarTyping +#+name: DFvarTyping #+begin_src lisp (in-package :ls-user) (defparameter *df-test* @@ -434,45 +434,29 @@ installation qualification (IQ) and performance qualification (PQ) CL-VARIATES is a system developed by Gary W King. It uses streams with seeds, and is hence reproducible. (Random comment: why do CL programmers as a class ignore computational reproducibility?) -**** DONE [#B] load and verify - - State "DONE" from "CURR" [2010-11-04 Thu 18:59] \\ - load, init, and verify performance. - - State "CURR" from "TODO" [2010-11-04 Thu 18:58] - - State "TODO" from "" [2010-11-04 Thu 18:58] - <2010-11-30 Tue> : just modified cls.asd to ensure that we load - as appropriate the correct random variate package. + The main problem with this system is licensing. It has a weird + licensing schema which prevents -#+srcname: Loading-CL-VARIATES +#+name: Loading-CL-VARIATES #+begin_src lisp (in-package :cl-user) - (asdf:oos 'asdf:load-op 'cl-variates) - (asdf:oos 'asdf:load-op 'cl-variates-test) + (ql:quickload :cl-variates) + ;;(ql:quickload :cl-variates-test) #+end_src -#+results: -: # -: NIL - - -#+srcname: CL-VARIATES-UNITTESTS +#+name: CL-VARIATES-UNITTESTS #+begin_src lisp - (in-package :cl-variates-test) ;; check tests (run-tests :suite 'cl-variates-test) (describe (run-tests :suite 'cl-variates-test)) - #+end_src -**** DONE [#B] Examples of use - - State "DONE" from "CURR" [2010-11-05 Fri 15:39] \\ - basic example of reproducible draws from the uniform and normal random - number streams. - - State "CURR" from "TODO" [2010-11-05 Fri 15:39] - - State "TODO" from "" [2010-11-04 Thu 19:01] + basic example of reproducible draws from the uniform and normal + random number streams. -#+srcname: CL-VARIATES-REPRO +#+name: CL-VARIATES-REPRO #+begin_src lisp (in-package :cl-variates-user) @@ -542,22 +526,35 @@ installation qualification (IQ) and performance qualification (PQ) *** TODO [#B] LLA evaluation - State "TODO" from "" [2010-10-12 Tue 14:13] -;;; experiments with LLA + +LLA is an SBCL targetted linear algebra library from Tamas Papp + +#+NAME LLA-experiments +#+BEGIN_SRC lisp (in-package :cl-user) (asdf:oos 'asdf:load-op 'lla) (in-package :lla-user) +;;; experiment here +#+END_SRC *** CURR [#B] Lisp-Matrix system evaluation - State "CURR" from "TODO" [2010-10-12 Tue 14:13] - State "TODO" from "" [2010-10-12 Tue 14:13] + in progress + *** TODO [#B] LispLab system evaluation - State "TODO" from "" [2010-10-12 Tue 14:13] +LL is an SBCL targetted linear algebra library from --- + ** TODO [#B] Statistical Procedures to implement - State "TODO" from "" [2010-10-14 Thu 00:12] -*** PFIM +*** TODO [#C] PFIM + +#+BEGIN_SRC lisp + (in-package :cls-user) ;;;; PFIM notes @@ -679,15 +676,16 @@ where (dolist (parameterJ parameters) (setf (aref IM I J) (differentiate (differentiate loglikelihood parameterI) parameterJ)))))) +#+END_SRC *** difference between empirical, fisherian, and ...? information. -*** Example of Integration with CL-GENOMIC +*** TODO [#C] Example of Integration with CL-GENOMIC - State "TODO" from "" [2010-10-12 Tue 14:03] CL-GENOMIC is a very interesting data-structure strategy for manipulating sequence data. -#+srcname: +#+name: CL-GENOMIC #+begin_src lisp (in-package :cl-user) (asdf:oos 'asdf:compile-op :ironclad) @@ -699,6 +697,7 @@ where (make-aa "agc9zz") ;; error expected #+end_src + ** TODO [#B] Documentation and Examples [0/3] - State "TODO" from "" [2010-10-14 Thu 00:12] @@ -715,7 +714,11 @@ where Place proposals for features, work, etc here... ** <2011-12-29 Thu> new stuff First new proposal is to track proposals. + * Rejoinder + This project is dedicated to all the lisp hackers out there who provided the basic infrastructure to get so far so fast with minimal effort on my part. + + And to all the people trying to help to get this off the ground. -- 2.11.4.GIT