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, rdiaz@ligarto.org.
      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

The HP 48 programs (exp6, beh6, anq6, cl6) are used, with the HP 48, to collect data.
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.
The preprocessed output is fed to antipa.
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.
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):

all1, all2, etc, are no longer used. All2 is "expanded in line"; all2 (actually called all1 now) is defined as a local variable at the beginning of the program.
I have rechecked the program, and there have been some minor changes.
I have tried to add more protection against other possible mistakes, but the program is not full-proof, of course. Here are some comments:
- If you press "Lizard lost" (Z) twice, it is only the last one that counts, in terms of alarms. This is what is of most help when using the program. If you make a mistake and press Z, you can "correct" it, and then, at the end, when you press the last "Z", this is the one which counts. This is DIFFERENT from what happens with "No access"; here, is the first one which counts; again, this is likely to be the most helpful implementation. In contrast to what happens with Z, it is unlikely that you will press SPC unless the animal is really SPC.
- One nasty mistake: suppose you have the sequence: 0...SPC.T.0....Z; here, you made a mistake, and pressed SPC, but it was not right. The calculator will tell there was only 1 run; and this is the only thing that makes sense, because it MUST interpret the T as a T done after either a SPC or a lost, and those T no longer increase the counter. This is the only way to handle appropriately the normal, correct, sequence of data entrance. If that happens, a solution is to key: 0...SPC.0.T.0...Z; here, you'll get the right number of moves, if SPC was a mistake.
- Flag 10 allows to distinguish between the antipredator and the approach 1 runs. In approach 1, if the lizard moves, its first movement, sets the alarm, and further movements wont. It is the same for lizard lost: if you press lizard lost, only the first sets the alarm. If you press move and then lost, only move works, and if you press lost and then move, the alarm was set by lost. The idea is that: a) you can press move after the lizard has reemerged, so it is not reasonable to give any move the ability to set alarms; b) with lizard-lost the problem is that, if you allow it to set alarms after movement, animals that tend to get lost a while after moving will have their alarms set later than animals that just move; this could introduce perverse biases, etc. So here, in opposition to the safeguard in the antipredator part, you better not make mistakes when pressing lizard lost (if that is the first thing after I move).

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:

Flags

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:

2:Controls the while loop in bheav. Never touch it.
4:Controls alarms in antipredator part.
5:Controls no access in antipredator.
6:Controls alarms for the duration of focal session, in the "focal" part.

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

New flags are:

Flags 20,21, and 22: control whether we are in:

Flag 20 Flag 21 Flag 22

Focal clear clear clear

Approach 1 clear clear set

Antipredator set clear clear

Anq4 doesn't matter set doesn't matter

These flags modify program flow both in exp12 and in beh4.
Flag 30: if set, the treatment is control, otherwise it is an intruder (this flag will control, in beh4, the working of some alarms).
Flag 31: if clear, it means there is still no attack, bite, or poke; if clear, at least one of either of those behaviors already happened. This is to know when the alarm for those should be set (in the first one). If the flag is set, the alarm for those behaviors will not be set again; it is only set when the first one takes place.
Flag 32: if set, animal is lost.
System flags 43 and 44 are used to control what the calculator does with alarms and alarm indexes. They allow for nicer output, etc.

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:

We could set a constant time after something like "lizard pays attention"; but this is a very subjective assessment, and I will tend to make this shorter in the control than in the intruder case: for the intruder, I will judge the lizard to have payed attention when it looks at the intruder and does some high intensity displays. I do not expect the intruder to do displays to the control, so as soon as it looks at the control, I will tend to consider it has "payed attention". Also, with this method I will tend to make some time intervals (till antipred) longer than they need to be.
We could set a constant time after I leave the control or intruder. But animals that hide will have shorter times between attack to intruder and antipredator than animals that don't hide. So, animals that are more shy have, systematically, sorter times till antipredator. This is a very dangerous systematic bias.
We could set a constant time after attack; this seems the best. But there are some details: a) What about controls? Controls will not be attacked, so the best I can do is leave the stimulus there for some time, more or less similar to the time the stimulus is left there when the intruder is alive. (so focal is exposed to control, when focal is NOT hiding, for similar time as if it were an intruder, when NOT hiding) b) What if attack is not over? I cannot wait forever, so I set a maximum time for the antipredator, after the attack is initiated; this I have set to 10 minutes; c) What if no attack: I wait a maximum of 8 minutes and 30 seconds for an attack to take place. But, if everything goes well, the main alarm will be the one that is set for 5' after the attack stops; I consider an attack to be over when the focal is no longer running after the intruder for at least 15".

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.

If an animal is lost, I set up alarm ALR for time equal to treap, and set flag 32.
If an animal reappears (i.e, does likely stuff after reappearing, such as move, bobs, Gbobs, or keying found), then, as flag 32 should be set, I delete all alarms, set the alarm for the 15" scans, and set the corresponding alarm either for control (with TCONTR) or for maximum time till attack (ALAT, with tatck, and set flag 31). Alarm 32 is cleared.
An animal could reemerge doing an attack, bite or poke as the first thing; in such case, I set alarms for scans and AL1 for taas --maximum time an attack can last before giving an antipred-- (flag 31 is cleared).
When an attack, bite or poke takes place (not first thing after being lost), the "2 delalarm" is used to get rid of the "maximum time till attack" alarm (ALAT); also, flag 31 is cleared, so this will not be done again in successive bites, attacks, or pokes. And AL1 for taas is set. So this case and the above are very similar.
When an attack ends, AL1 is set for 5'. BUT: note that if the attack started at minute 1, and ended at minute 7, the alrm will be set for minute 12. But before this alarm works, the alarms for taas (10 minutes) will be activated; this is to prevent a very long sequence due to a very long attack, that ends and then is followed by the 5'; this way, the maximum time between an attack and the antipr is 10', regardless of whether the attack ends or not.
The work of TCONTR is simple: a first time (TIP2: time I place 2) is recorded when I am back, or when the focal reappears if it hide; and this is subtracted from the time AL1 is activated [there is a subtraction of 1.2 seconds, because of a lag (due to the beeps, etc).]
The alarms for the scans only present when the animal is not hiding.
If there is an attack in control (well,maybe the can is very aggression-provoking, or the animal went crazy, or a real intruder shows up), things will work as if there was an intruder.

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

The programs are exp15, cl5, beh5, anq5. They are very similar to the ones with # 4.
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.
Now I fix the duration of the attack: 3 minutes; then I take the intruder back, wait another 3', and give the antipredator test.
I wait a maximum of 15' till an animal attacks.
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.
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.
Flag 30: if set, it is a control, if clear it is an intruder;
Flag 31: if clear still no attack or bite or poke; set: some.
taat: duration of attack; now datck; taas: time after attack ends: now taae; treap: eliminated.
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.

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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.

5. COMBINING DOCUMENTS

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."

6. COLLECTIONS OF DOCUMENTS

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.

7. AGGREGATION WITH INDEPENDENT WORKS

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.

8. TRANSLATION

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.

9. TERMINATION

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.

10. FUTURE REVISIONS OF THIS LICENSE

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 http://www.gnu.org/copyleft/.

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

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