CAFCA - Manual


I. INSTALLATION and START-UP

Contents


A short history of CAFCA Top

CAFCA is an acronym for Collection of APL Functions for Cladistic Analysis. As indicated in the acronym all algorithms implemented in CAFCA are written in APL. APL is developed by K.E. Iverson, originally as a notational tool for mathematics, but soon implemented on IBM mainframes as an interpreted computer language. Because APL code is interpreted, programs (or functions in APL jargon) written in APL can in terms of speed hardly compete with programs written in languages as C or Pascal that are, in general, implemented as compilers. This is especially the case for algorithms that contain loops. On the other hand, APL contains very powerful operators enabling the programmer to achieve in one line of code the equivalent of dozens of lines of C or Pascal.

CAFCA was originally developed for use on mainframe computers. These versions were never distributed. When APL interpreters for personal computers became available CAFCA was ported to PC in 1985. In 1986 a menu driven user-interface was programmed and CAFCA could be distributed, eventually, as an integrated APL workspace. The main obstacle in its distribution was the need for users to separately acquire the APL interpreter as well, in order to make CAFCA run. Only after an APL interpreter with a free runtime license became available for Atari and Macintosh computers, the contraints on CAFCA's distribution could be lifted and CAFCA was ported to the Atari (1988) and to the Macintosh (1989). Soon further development was focused on the Macintosh only, including a native version for the PowerPC chip (1994). Although a Windows version is planned work has not even started yet; the development of a new user-interface being the main hick-up, the conversion of some APL code to embedded compiled C (to gain some speed) being another.


License agreement Top

Copyright © 1988-2003 M. Zandee.

Permission to use and distribute this software and its documentation for educational and research purposes is hereby granted without fee, provided the above copyright notice, author statement and this permission notice appear in all copies of this software and related documentation.

THE SOFTWARE IS PROVIDED "AS-IS" AND WITHOUT WARRANTY OF ANY KIND, EXPRESS, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.

IN NO EVENT SHALL THE AUTHOR, THE INSTITUTE OF BIOLOGY LEIDEN, OR LEIDEN UNIVERSITY BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

The Macintosh version of CAFCA was developed using APL.68000, a proprietary product of MicroAPL Ltd., which has given permission for a runtime version of APL.68000 to be distributed with the software, or to be packaged into the software as one executable. Copyright and all intellectual property rights in APL.68000 remain vested in MicroAPL Ltd.

APL.68000 is a trademark of MicroAPL Ltd. Apple and Macintosh are trademarks of Apple Computer, Inc.


Distribution Top

If there is a Read me first file present in your extracted archive, please read this file first for notification of last minute changes and possible modifications of the installation procedure. Your distribution copy contains 2 (-3) items.

Examples Top

In the Xmpls folder, several sub-folders with TEXT files are present. They are identical with the example data used in the manual. They give you an idea of how CAFCA input should look like, and you can use them to run the examples.

ANIMAL.DST A binary matrix representing the distribution of taxa (rows) from ANIMAL over areas (columns). To be used in a biogeographic analysis to derive an area data matrix, jointly with ANIMAL.TRE as representing the cladogram.
ANIMAL.ars A binary matrix representing the distribution of areas (rows) from ANIMAL over taxa (columns). To be used in a biogeographic analysis to derive an area data matrix, jointly with ANIMAL.TRE as representing the cladogram. The areas (rows) are provided with names. It eliminates the use of ANMLAREA.NMS
ANIMAL.TRE A binary matrix representing a cladogram for 5 taxa (taxa in rows, nodes of cladogram in columns). Can be used in a biogeographic analysis, jointly with ANIMAL.DST, to derive an area data matrix.
ANIMAREA.ASC A text file with the multstate expression of an area data matrix for ANIMAL. It is equivalent to the use of the binary expression in conjunction with the partitioning vector ANIMAREA.CPV
ANIMAREA.BIN Binary area-data matrix for ANIMAL. Can be used to run a biogeographic analysis. When used in conjunction with ANIMAREA.CPV a multi-state expression will result (Also available separately as ANIMAREA.ASC).
ANIMAREA.CPV Partitioning vector for the binary area-data matrix ANIMAREA..BIN
ANMLAREA.NMS A text file with the names of the areas (rows) in ANIMAL.DST
PLANT.ASC Multi-state data matrix, with taxa represented by the rows and characters by the columns. To be used in a primary character analysis.
PLANT.NMS Namelist for taxa in PLANT.ASC or PLANTB.INP
PLANTB.INP Binary data matrix, with taxa represented by the rows, and character states by the columns. To be used for primary character analysis. The equivalent of PLANT.ASC except for an unresolved polytypism in character 9.
PLANTB.CPV Column partitioning vector for PLANTB.INP. Without it CAFCA cannot know which columns in PLANTB.INP represent the character states within each character.
PLANT.ars A binary matrix representing the distribution of areas (rows) from PLANTB.INP over taxa (columns). To be used in a biogeographic analysis to derive an area-data matrix, jointly with PLANT.TRE as representing the cladogram. The areas (rows) are provided with names. It eliminates the use of PLNTAREA.NMS
PLANT.DST A binary matrix representing the distribution of taxa (rows) from PLANTB.INP over areas (columns). To be used in a biogeographic analysis to derive an area-data matrix, jointly with PLANT.TRE as representing the cladogram.
PLANT.TRE A binary matrix representing a cladogram for 5 taxa (taxa in rows, nodes of cladogram in columns). Can be used in a user-tree evaluation, or in a biogeographic analysis.
PLNTAREA.ASC A text file with the multi-state expression of an area-data matrix for PLANT. It is equivalent to the use of the binary expression in conjunction with the partitioning vector PLNTAREA.CPV
PLNTAREA.BIN Binary area-data matrix for PLANT. Can be used to run a biogeographic analysis. When used in conjunction with PLNTAREA.CPV a multi-state expression will result (Also available separately as PLNTAREA.ASC).
PLNTAREA.CPV Partitioning vector for the binary area-data matrix PLNTAREA..BIN
PLNTAREA.NMS A text file with the names of the areas (rows) in PLANT.DST
SECOND.BIN A binary data matrix, with many taxa relative to the number of characters. Its primary analysis will result in unresolved cladograms. Therefore it can be used in a secondary analysis (directly after its primary analysis, or, much better, after saving the results of the primary analysis to an OutputFile). All its columns are equivalent (characters with only one state) and it therefore needs no column partitioning vector.
SECOND.pau.trees Cladograms for SECOND.BIN matrix as generated by PAUP.
Alcidae Data matrix for the Alcidae (Aves) from Strauch (1984). Used in the comparison of CAFCA with character compatibility analysis.
Alcidae.nex Idem, in NEXUS format. Ready to be used in PAUP
Meacham81 Data matrix from Meacham (1981; his table 1). Used in the comparison of CAFCA with character compatibility analysis.
Meach81.nex Idem, in NEXUS format. Ready to be used in PAUP.
B&McLt716.dst Distribution of 5 major groups of ostariophysans from table 7.16 in Brooks & McLennan (1991).
B&McLt716.tre Their cladogram; fig 7.30 in idem.
B&McLt717a.dst Distribution of tapeworm genus Acanthobothrium from table 7.17 in Brooks & McLennan (1991).
B&McLt717a.tre Their cladogram; fig 7.32a in idem.
B&McLt717b.dst Distribution of tapeworm genus Potamotrygonocestus from table 7.17 in Brooks & McLennan (1991).
B&McLt717b.tre Their cladogram; fig 7.32b in idem.
B&McLt717c.dst Distribution of tapeworm genus Rhinebothroides from table 7.17 in Brooks & McLennan (1991).
B&McLt717c.tre Their cladogram; fig 7.32c in idem.
B&McLt727.dst Distribution of amphilinid flatworms from table 7.27 in Brooks & McLennan (1991).
B&McLt727.tre Their cladogram; fig 7.54 in idem.
B&McLt727.utr The cladogram of their hosts; fig 7.56 in idem.
B&McLt728.dst Distribution of the tapeworm genus Alcataenia from table 7.28 in Brooks & McLennan (1991).
B&McLt728.tre Their cladogram; fig 7.57 in idem.
B&McLt728.host.tre Independent cladogram for hosts (seabirds). To be used as user tree
B&McLt728.bin Binary data matrix resulting from the combination of the tapeworm cladogram and the distribution of tapeworms over seabirds.
B&McLt728.cpv Its partitioning vector for columns
B&McLt728.asc Multi state expression of B&McLt728.bin
Brooks90f5.dst Distribution of 8 species of amphilinid flatworms from figure 5 (table 4) in Brooks (1990).
Brooks90f5.tre Their cladogram; fig 5 in idem.
Brooks90f7.dst Distribution of 8 species of amphilinid flatworms from figure 7 (table 5) in Brooks (1990). (Indo-Malaysia represented twice).
Brooks90f7.tre Their cladogram; fig 5 in idem.
Brooks90f13.dst Distribution of 4 hypothetical species from figure 13 (table 8) in Brooks (1990).
Brooks90f13.tre Their cladogram; fig 5 in idem.
Brooks90f18a.dst Distribution of 5 hypothetical species from figure 18a (table 11) in Brooks (1990).
Brooks90f18a.tre Their cladogram; fig 18a in idem.
Brooks90f18b.dst Distribution of 4 hypothetical species from figure 18b (table 11) in Brooks (1990).
Brooks90f18b.tre Their cladogram; fig 18b in idem.
Brooks90t11.bin Binary area-data matrix based on the distributional data and cladograms of two taxa in fig 18a and 18b.
Brooks90t11.nex Idem in NEXUS format
Brooks90t11.og.nex Idem, but including a full-zero out-area
Brooks90t11.cpv Partitioning vector for columns in the binary area-data matrix, Brooks90t11.bin.
Brooks90f21a.dst Distribution over 6 hypothetical areas of 6 hypothetical species from figure 21a (table 13) in Brooks (1990).
Brooks90f21a.tre Their cladogram; fig 21a in idem.
Brooks90f21b.dst Distribution over 6 hypothetical areas of 7 hypothetical species from figure 21b (table 11) in Brooks (1990).
Brooks90f21b.tre Their cladogram; fig 21b in idem.
Brooks90f24a.dst Neotropical distribution of 7 species from the genus Selenidera from figure 24a (table 15) in Brooks (1990).
Brooks90f24a.tre Their cladogram; fig 21a in idem.
Brooks90f24b.dst Neotropical distribution of 7 species from the genus Pionopsitta from figure 24b (table 15) in Brooks (1990).
Brooks90f24b.tre Their cladogram; fig 21b in idem.
Brooks90f24c.dst Neotropical distribution of 3 species from the Pteroglossus viridis group from figure 24c (table 15) in Brooks (1990).
Brooks90f24c.tre Their cladogram; fig 21c in idem.
Brooks90f24d.dst Neotropical distribution of 6 species from the genus Pteroglossus bitorquatus group from figure 24d (table 15) in Brooks (1990).
Brooks90f24d.tre Their cladogram; fig 21d in idem.
Crusea.asc Data matrix for Crusea from Estabrook & Anderson (1978).
Crusea.nex Idem, in NEXUS format.
Gopher.tre Cladogram for gophers as used in Page 1993, fig 11
Lice.dst Distribution of chewing lice over species of gopher; Page 1993, fig 11.
Lice.tre Cladogram for chewing lice; Page 1993, fig 11.
Page90.fig3.dst Distribution of three hypothetical species over 4 hypothetical areas; from Page 1990, fig 3.
Page90.fig3.tre The species cladogram; fig 3 in idem.
Page93.fig10.dst Distribution of five hypothetical species over four hypothetical areas; from Page 1993, fig 10.
Page93.fig10.tre The species cladogram; fig 10a in idem.
Page93.fig10.bin The binary area-data matrix derived from the cladogram and distribution matrix in Page93.fig10.tre and Page93.fig10.dst
Page93.fig10.nex Idem, in NEXUS format.


Installation Top

If you received your copy of CAFCA on a floppy disk, make a copy of your distribution disk. Store the original and use the copy.

  1. If there's a Read me first file present on the distribution disk, double click or select and open it for reading.
    If that file describes an installation routine, follow that recipe and skip the points 2 & 3 below.
  2. Make a new folder on your hard disk and name it CAFCA.
  3. Double click the self-extracting archived file you received or downloaded. When prompted by the unpacking program, indicate the CAFCA folder you just made in step 2 to copy the extracted files onto.


Start-Up Top

Start your Mac with your own System™ and Finder™. To start CAFCA, double click the file name, or select the name and Open the file from the File menu. Once CAFCA is up you will see this opening screen, except that the About CAFCA window will contain your registration, unless you downloaded CAFCA from //biology.leidenuniv.nl/~zandee/index.html.

Click anywhere on the screen to make the start-up window disappear. Now you are ready to run. If you want to Quit for now, select Quit from the OutputFile menu, or type Command-Q and confirm (Yes) in the next dialog.


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© M. Zandee 1996.