Document contents

The set of programs Structure and use of the bundle What the HP 48 programs do The C++ programs How the programs work: details Some details of how alarms and counter work in the antipredator part Duration of focal session New stuff for the exp programs Standardizing times General comments on flow of program Comments on a program version for the experiment in Fazenda Santo Antonio Enclosures version (the one available) GNU Free Documentation License How to use this License for your documents

Documentation for BehHP48: a set of HP 48 Calculator Programs for Recording Behavior

      Copyright (c)  1996, 2004 Ramón Díaz-Uriarte,
      Permission is granted to copy, distribute and/or modify this document
      under the terms of the GNU Free Documentation License, Version 1.2
      or any later version published by the Free Software Foundation;
      with no Invariant Sections, no Front-Cover Texts, and no Back-Cover
      Texts.  A copy of the license is included in the section entitled
      "GNU Free Documentation License".

The set of programs

The BehHP48 program bundle consists of three main subroutines: beh6, anq6, and exp6 (CL is a utility program that tells you the time,date, and memory available, and deletes unnecessary junk --that is created if you exit the program abnormally). In addition, two C++ programs (antipa and antipb) produce human-editable output for checking and fixing (antipa) and return the behavioral data, such as time to hide, time hiding, etc (antipb).

Structure and use of the bundle

  1. The HP 48 programs (exp6, beh6, anq6, cl6) are used, with the HP 48, to collect data.
  2. After data from one or more lizards is collected, it is preprocessed to get rid of certain symbols, etc. I used an infamous word processor that I will not name to do that task. A macro is included at the bottom of antipa.cpp. Today, I would no doubt conduct that task with a Python program.
  3. The preprocessed output is fed to antipa.
  4. Now, the output from antipa is fixed it, during the behavioral recording sequence, you typed the wrong key, or whatever. Essentially, what antipa does is put the hard-to-edit output of the HP programs in an easy to edit format, that allows correction of mistakes, etc.
  5. The corrected output is fed to antipb. This produces the basic stuff that will then be analyzed (e.g., time hiding, time to full exposure, etc, etc).

What the HP 48 programs do

Basically: at the start of the run (which is controlled by beh6) you are asked a few initial questions (lizard ID, enclosure number, etc). There is code that will allow to enter focal data, but that is commented now. Then, the whole set of actions starts, and the program produces beeps and messages at prespecified times, to let you know what to do (e.g., introduce intruder, etc). Then, at the right time and sequence of events, the beh6 program is started, and run from within exp6. beh6 contains the set of key combinations (and noises) for the behaviors. Finally, at a prespecified time the anq6 program is launched, which is used to collect some extra information at the end of the run.

The C++ programs

These were written using the Borland IDE. They use some deprecated style, for example, for inclusion of header files, etc. But they at least compile without errors (only the warning about the header) under GNU/Linux, using g++ (version 3.3, as of this writing). [Today, I'd probably write this part with Python instead of C++; at that time, however, I new nothing about Python, and I wanted to learn C++, so this looked like a good training opportunity.]

The programs that were used for the experiments cited are antipa.cpp and antipb.cpp (and their corresponding header files). However, I also include antip20.h, because it defines several classes and methods that would be used to process the focal data, and obtain frequency of displays and other behaviors.

The C++ programs will not be commented any further in these notes.

How the programs work: details

[For information on the workings of alarms see below].

exp6 is the master program. It first initializes flags, clears junk, etc. Then, it asks several questions. And, right before calling the beh6 program for the focal part, it initializes Ts and Te, which are used to keep track of the duration of the focal session (see below: Duration of focal session). When you start the program (and if flags are in the proper state) you always enter this module.

beh6 has been called; it is operating as the focal program. When the predetermined duration of the focal is due, an alarm sounds. Then, you press the 65.3 (left arrow and division) to signal the end of the focal session. This sets flag 3. Flag 3, plus flag 7 (which was set when you started exp1) make the beh6 program behav appropriately for this second part: when you press 0 you will see "My move", you will not mess with the counter of antipred moves, and, when the animal moves or is lost, the appropriate alarm is set. As you see, the approach part is really another set of cycles over the while loop in beh6, without exiting it; we did this by not changing the value of flag 2; as flag 2 is still set, in between the focal and the approach part, the while loop is still working. But, after the animal moves or is lost in the approach phase, if you press the 65.3 you will exit the loop. After exiting the loop, beh6 calls exp1 again, but now with a different value for flag 8.

Again in exp6. If things go well, after the appropriate time for the "approach phase", the lizard will be out again. Therefore, when you are asked whether to run the antipredator or not, just press anything and enter (anything except NO!). Then, you will start the antipredator program, which works just as usual. When the beh6 was to be run for the antipredator part flag 9 was changed; now, when you exit the beh6 program, you will again call the exp1 program, and with the new value for flag 9, you call the anq6 program, which contains the antipredator questions. If you never entered the beh6 for the antipredator part, you called the anq6 program. anq6 asks you only the questions of the approach part if you never run the post-treatment antipredator test; it asks you all the questions if you run it.

(Note: beh6 is exited sometimes in the middle, sometimes in the end; this is because the alarms interrupt the program, and everything is left on the stack; that is why alarms, when due, not only produce a lovely music, but also call some program to start execution.)

Flag 8: it is not really necessary to clear flag 8 after animal lost or no access in antipred part. Because, as flag 9 is set right before the antipred part starts, the program , in next run, will run the anq6 part. It IS necessary that flag 8 is set in the approach 1 part (so that we start the antipred part, in the exp1). I leave the clearing of flag8: it is a reminiscence of the old caico programs, and could be used in the new ones.

Some details of how alarms and counter work in the antipredator part

(Some of these are slightly obsolete) In the antipredator trial, I use alarms (as usual with my antipredator programs). These alarms interrupt the flow of the program, leaving everything in the stack. I copy from the documentation of Behav4.sub:

@Most of the following comments that refer to alarms are just for the antipredator part; none of these alarms should be set with the focal program (because you should not press "my move", or "no access" , or the special "lizard lost" --different from "lost"; "lost" just means the lizard hides; "lizard lost" is ONLY when carrying out the antipredator test; is the first time the lizard is lost, as a consequence of my approach@

@Alarms: one alarm beeps so that I make my next move (15") after stopping (remember that I stop right after the first movement of the lizard after my starting to move); the second alarm beeps to end the session (7' after lizard hides). These are control alarms, and they are regulated by ALL2 and AL2. ALL2 sets the timing of the alarm (15" or 7', depending on the state of flag 4); the alarm executes AL2, which contains a set of beeps, and a call to BEHAV4.SUB. (i.e., to this very subroutine). With control alarms the flow of the program is interrupted when the alarm is due, and you are returned to the stack. Therefore, it is necessary to call BEHAV4.SUB again. The program clears system flag -44, so that the acknowledged alarms are not saved in the system alarm list. @

@The flow and flag setting can seem confusing, but they allow to correct a nasty mistake: if you get obfuscated and press Z --lost-- when the lizard is not really hiding, nothing irreparable happens; you just have to press 0 when it is time to move again, move, and continue as usual. This way, the right number of movements will be recorded@

@ Counter and alarm will be set only if the lizard moves after I have approached; if I am already stopped, but the lizard makes further movements, this should not increase the counter (or sets the alarm). When I move, I set flag 4; this flag is on until the lizard first moves --then, it clears flag 4--; if the lizard moves or suddenly hides, and flag 4 is set, then the counter counts; the alarm is set if there is movement. The alarm is cleared when the lizard hides or I get to "no access"; in these cases, the 7' alarm is set. If the lizard starts moving and then disappears, the counter only increases once, as it should be: with movement, flag 4 is cleared, and in "lost lizard" the counter is not increased@

New changes (that do affect beh6, etc):

Duration of focal session

The calculator keeps track of the net time of observation of the animal (i.e, it discounts the time the animals is lost). An alarm will sound when the net time is the same as the duration you want for the focal session. Here is how it works:

When it starts the value of TS (time starts) and TE (time elapsed) are initialized as 0 (the format is HP binary integer because these are later added to the TICKS from the HP: therefore the # 0d). When beh6 stars, the value of TS is taken from TICKS, and the alarm is set for 15' (see below for alarms). If the animal is lost, the alarms are deleted, and time elapsed is calculated as time elapsed + (hour when it is lost --obtained from TICKS-- minus starting hour --TS--). If the animal is found, the alarm is set for a time equal to 15' minus the time elapsed, and the current TICKS becomes TS.

(Even if you make a mistake and press found when it shouldn't nothing bad happens: all alarms are deleted at exit of the program, and all are deleted at Lost; therefore, the first alarm you will hear is the one corresponding to the first found after the animal was lost. If you press lost twice, only the first one after a found is valid --flag 6 takes care of this).

Alarms: to the time for the alarm in ticks (8192 * 60 *15) you subtract the TE (after making it a real); this is divided by 29491200 (the number of ticks in an hour), to get the time for the alarm as fractions of hour (decimal representation); this number is converted into a regular HH.MMSSsss number, and added to the current time, to set the hour of the alarm.

New stuff for the exp programs

There have been many additional changes. Main changes:


In the previous version, the use of flags was a bit confusing and there were redundancies; now, it is still confusing, but not so much. Before, flags 3,7,8,9, and 10 were partially redundant. These are no longer used. Now, flags are as follows:

These flags did the same thing in the previous version, and have not been changed.

New flags are:

Standardizing times

When the treatment is control, and if the animal is NOT hiding, we wait a specified time (TCONTR) to give the antipredator test. TCONTR is variable, and is equal to the time that was waited between leaving the intruder (or control) and giving the antipr test in the last previous test. If the animal hides when I place the intruder, then TCONR is equal to the time between the animal reemerges and the antipredator test is given. [Actually, time is calculated as time between pressing 2 (83.1) and the time the final alarm was due in the previous (successful) test; either it there was an intruder, who was attacked, or there was a control; not if the previous was a case where the focal did not reemerge. Note that this is the time we want; when the alarm sounds, we then will proceed to the antipr. test; this is what makes most similar the real time between 2 and antipr in the control and the previous trial].

It is not possible to completely standardize times. There are other options, which are probably worse:

General comments on flow of programs for HP

Here are some comments on how the program works for the approach 1 part (the others are documented above); some other things can be found on the comments in the code itself.

Comments on a program version for the experiment in Fazenda Santo Antonio

  1. The programs are exp15, cl5, beh5, anq5. They are very similar to the ones with # 4.
  2. In anq5, there are changes in the questions asked; basically, there are no questions about location (of course, because I have no maps), and many other questions have been deleted: I need to be very fast, and avoid making useless questions.
  3. Now I fix the duration of the attack: 3 minutes; then I take the intruder back, wait another 3', and give the antipredator test.
  4. I wait a maximum of 15' till an animal attacks.
  5. If control, the time between I leave the can and give the antipredator is equal to the time, in the previous intruder, between I left the can and gave the antipred. test.
  6. ALA: it is the alarm set when first attack/bite/poke; computes Tcontr; time is datck. AL1: used in appr, after I press 2; time is taae. ALR: if animal does not attack in tatck. ALC: alarm end control.
  7. Flag 30: if set, it is a control, if clear it is an intruder;
  8. Flag 31: if clear still no attack or bite or poke; set: some.
  9. taat: duration of attack; now datck; taas: time after attack ends: now taae; treap: eliminated.
  10. When I leave the animal I press 1, when I recover it I press 2; at the end of recovery, when pressing, taae is set.

Enclosures version (the one available)

Follows the stuff for Fazenda, but some differences: TCONTR is not used now, and so ALA is not used. When I start to move the intruder, I press 0; when the intruder is back, I press 1; when it starts to come out I press "."; and when it is all back, I p ress 2. After that, we wait 2 minutes. There are a few other changes in the antipredator questions; they are documented in the program itself.

GNU Free Documentation License

Version 1.2, November 2002

Copyright (C) 2000,2001,2002  Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.


The purpose of this License is to make a manual, textbook, or other functional and useful document "free" in the sense of freedom: to assure everyone the effective freedom to copy and redistribute it, with or without modifying it, either commercially or noncommercially. Secondarily, this License preserves for the author and publisher a way to get credit for their work, while not being considered responsible for modifications made by others.

This License is a kind of "copyleft", which means that derivative works of the document must themselves be free in the same sense. It complements the GNU General Public License, which is a copyleft license designed for free software.

We have designed this License in order to use it for manuals for free software, because free software needs free documentation: a free program should come with manuals providing the same freedoms that the software does. But this License is not limited to software manuals; it can be used for any textual work, regardless of subject matter or whether it is published as a printed book. We recommend this License principally for works whose purpose is instruction or reference.


This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License. Such a notice grants a world-wide, royalty-free license, unlimited in duration, to use that work under the conditions stated herein. The "Document", below, refers to any such manual or work. Any member of the public is a licensee, and is addressed as "you". You accept the license if you copy, modify or distribute the work in a way requiring permission under copyright law.

A "Modified Version" of the Document means any work containing the Document or a portion of it, either copied verbatim, or with modifications and/or translated into another language.

A "Secondary Section" is a named appendix or a front-matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document's overall subject (or to related matters) and contains nothing that could fall directly within that overall subject. (Thus, if the Document is in part a textbook of mathematics, a Secondary Section may not explain any mathematics.) The relationship could be a matter of historical connection with the subject or with related matters, or of legal, commercial, philosophical, ethical or political position regarding them.

The "Invariant Sections" are certain Secondary Sections whose titles are designated, as being those of Invariant Sections, in the notice that says that the Document is released under this License. If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant. The Document may contain zero Invariant Sections. If the Document does not identify any Invariant Sections then there are none.

The "Cover Texts" are certain short passages of text that are listed, as Front-Cover Texts or Back-Cover Texts, in the notice that says that the Document is released under this License. A Front-Cover Text may be at most 5 words, and a Back-Cover Text may be at most 25 words.

A "Transparent" copy of the Document means a machine-readable copy, represented in a format whose specification is available to the general public, that is suitable for revising the document straightforwardly with generic text editors or (for images composed of pixels) generic paint programs or (for drawings) some widely available drawing editor, and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters. A copy made in an otherwise Transparent file format whose markup, or absence of markup, has been arranged to thwart or discourage subsequent modification by readers is not Transparent. An image format is not Transparent if used for any substantial amount of text. A copy that is not "Transparent" is called "Opaque".

Examples of suitable formats for Transparent copies include plain ASCII without markup, Texinfo input format, LaTeX input format, SGML or XML using a publicly available DTD, and standard-conforming simple HTML, PostScript or PDF designed for human modification. Examples of transparent image formats include PNG, XCF and JPG. Opaque formats include proprietary formats that can be read and edited only by proprietary word processors, SGML or XML for which the DTD and/or processing tools are not generally available, and the machine-generated HTML, PostScript or PDF produced by some word processors for output purposes only.

The "Title Page" means, for a printed book, the title page itself, plus such following pages as are needed to hold, legibly, the material this License requires to appear in the title page. For works in formats which do not have any title page as such, "Title Page" means the text near the most prominent appearance of the work's title, preceding the beginning of the body of the text.

A section "Entitled XYZ" means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language. (Here XYZ stands for a specific section name mentioned below, such as "Acknowledgements", "Dedications", "Endorsements", or "History".) To "Preserve the Title" of such a section when you modify the Document means that it remains a section "Entitled XYZ" according to this definition.

The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document. These Warranty Disclaimers are considered to be included by reference in this License, but only as regards disclaiming warranties: any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License.


You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License, the copyright notices, and the license notice saying this License applies to the Document are reproduced in all copies, and that you add no other conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute. However, you may accept compensation in exchange for copies. If you distribute a large enough number of copies you must also follow the conditions in section 3.

You may also lend copies, under the same conditions stated above, and you may publicly display copies.


If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than 100, and the Document's license notice requires Cover Texts, you must enclose the copies in covers that carry, clearly and legibly, all these Cover Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on the back cover. Both covers must also clearly and legibly identify you as the publisher of these copies. The front cover must present the full title with all words of the title equally prominent and visible. You may add other material on the covers in addition. Copying with changes limited to the covers, as long as they preserve the title of the Document and satisfy these conditions, can be treated as verbatim copying in other respects.

If the required texts for either cover are too voluminous to fit legibly, you should put the first ones listed (as many as fit reasonably) on the actual cover, and continue the rest onto adjacent pages.

If you publish or distribute Opaque copies of the Document numbering more than 100, you must either include a machine-readable Transparent copy along with each Opaque copy, or state in or with each Opaque copy a computer-network location from which the general network-using public has access to download using public-standard network protocols a complete Transparent copy of the Document, free of added material. If you use the latter option, you must take reasonably prudent steps, when you begin distribution of Opaque copies in quantity, to ensure that this Transparent copy will remain thus accessible at the stated location until at least one year after the last time you distribute an Opaque copy (directly or through your agents or retailers) of that edition to the public.

It is requested, but not required, that you contact the authors of the Document well before redistributing any large number of copies, to give them a chance to provide you with an updated version of the Document.


You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above, provided that you release the Modified Version under precisely this License, with the Modified Version filling the role of the Document, thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it. In addition, you must do these things in the Modified Version:

If the Modified Version includes new front-matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document, you may at your option designate some or all of these sections as invariant. To do this, add their titles to the list of Invariant Sections in the Modified Version's license notice. These titles must be distinct from any other section titles.

You may add a section Entitled "Endorsements", provided it contains nothing but endorsements of your Modified Version by various parties--for example, statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard.

You may add a passage of up to five words as a Front-Cover Text, and a passage of up to 25 words as a Back-Cover Text, to the end of the list of Cover Texts in the Modified Version. Only one passage of Front-Cover Text and one of Back-Cover Text may be added by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover, previously added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but you may replace the old one, on explicit permission from the previous publisher that added the old one.

The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version.


You may combine the Document with other documents released under this License, under the terms defined in section 4 above for modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents, unmodified, and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their Warranty Disclaimers.

The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work.

In the combination, you must combine any sections Entitled "History" in the various original documents, forming one section Entitled "History"; likewise combine any sections Entitled "Acknowledgements", and any sections Entitled "Dedications". You must delete all sections Entitled "Endorsements."


You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects.

You may extract a single document from such a collection, and distribute it individually under this License, provided you insert a copy of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document.


A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or distribution medium, is called an "aggregate" if the copyright resulting from the compilation is not used to limit the legal rights of the compilation's users beyond what the individual works permit. When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document.

If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half of the entire aggregate, the Document's Cover Texts may be placed on covers that bracket the Document within the aggregate, or the electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that bracket the whole aggregate.


Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will prevail.

If a section in the Document is Entitled "Acknowledgements", "Dedications", or "History", the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title.


You may not copy, modify, sublicense, or distribute the Document except as expressly provided for under this License. Any other attempt to copy, modify, sublicense or distribute the Document is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.


The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. See

Each version of the License is given a distinguishing version number. If the Document specifies that a particular numbered version of this License "or any later version" applies to it, you have the option of following the terms and conditions either of that specified version or of any later version that has been published (not as a draft) by the Free Software Foundation. If the Document does not specify a version number of this License, you may choose any version ever published (not as a draft) by the Free Software Foundation.

How to use this License for your documents

To use this License in a document you have written, include a copy of the License in the document and put the following copyright and license notices just after the title page:
      Copyright (c)  YEAR  YOUR NAME.
      Permission is granted to copy, distribute and/or modify this document
      under the terms of the GNU Free Documentation License, Version 1.2
      or any later version published by the Free Software Foundation;
      with no Invariant Sections, no Front-Cover Texts, and no Back-Cover
	 Texts.  A copy of the license is included in the section entitled "GNU
      Free Documentation License".

If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts, replace the "with...Texts." line with this:

    with the Invariant Sections being LIST THEIR TITLES, with the
    Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.

If you have Invariant Sections without Cover Texts, or some other combination of the three, merge those two alternatives to suit the situation.

If your document contains nontrivial examples of program code, we recommend releasing these examples in parallel under your choice of free software license, such as the GNU General Public License, to permit their use in free software.

Ramón Díaz-Uriarte

Valid XHTML 1.0! Viewable With Any