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 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.
[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.
@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):
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.
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:
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 |
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:
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.
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