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

  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:

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:

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.

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Ramón Díaz-Uriarte

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