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INTRODUCTION
Welcome
to the Proyecto Primates Protocol Site! In the following pages you will find
detailed information on the different protocols that are being used for data
collection, as well as protocols that are necessary for the management of the
project and for collecting samples both in
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BEHAVIOR |
PROJECT MANAGEMENT |
SAMPLES |
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WHAT IS A PROTOCOL?
CHARACTERISTICS
OF OUR PROTOCOL
TYPES OF
DATA TO BE COLLECTED
DESCRIPTIONS OF FORMS, SUBFORMS AND TABS IN DATABASE
WHAT
IS A PROTOCOL?
A protocol
consists of a detailed description of the methods used to collect data. The
reality is that, no matter what anyone might say, no one can read a published
scientific paper and precisely replicate the described methods, because the
methods published in articles are not sufficiently detailed to allow that. But,
everyone should be able to replicate the methods of a study by following the
“protocol” used for the study. The use of protocols is common in laboratory
settings, where it is important to have explicit instructions. For example, a
protocol would indicate if you should centrifuge a reaction for 10 or 12
seconds. Although protocols do not appear to be used that often by field
biologists, we are convinced that they are extraordinarily useful.
The secret
to checking if a protocol is complete and ready to be followed is to
“visualize” the entire data collection process: close your eyes, think about
what you are going to do step by step, and make sure the protocol details that
process precisely. For example, you are watching an animal and the alarm on
your watch beeps: What do you see? What data you write down? In
formulating a protocol, you need to be very explicit and leave little in doubt
or ambiguous about what data an observer should be recording. Never think,
“It’s obvious”! Instead, try to leave a minimum of things open to the
interpretation of the observer.
In this
project, you will be part of one of the first studies (we think THE first
study!) where researchers are trying to collect truly comparable data on four
different species of primates in two different countries with a set of unified
protocols. The emphasis of our protocol is on the QUALITY of the data we aim to
collect, not the quantity.
CHARACTERISTICS OF OUR PROTOCOL
Our sampling
procedure is designed so that all data can be collected by a single person.
There is a lot of different kinds of data to collect, and we expect it to be
collected, recorded, and entered into the computer in a very specific way, so
you must reread the protocol pertinent to your work once a month during the
first week of the month to make sure you remember everything you need to be
doing.
Our
protocols have been designed to ensure that the collection of CERTAIN kinds of
data is done in an exactly comparable manner for all primate species being
studied both in
To
accomplish this goal, is of paramount importance that: 1- the protocols take
precedence over what other students, assistants or even researchers may
say. You are responsible for reading the protocols and following
them. You must not assume that what you are being told is correct, 2- all
observers need to practice inter-observer reliability or go through procedures
together. Once per month, at the beginning of the month, all observers
should go to collect FOCAL SAMPLES together on the same animals,
simultaneously. Data for practicing inter-reliability should be collected in
data books or on the Palm, but you should note in the Comments section
for that FOCAL SAMPLE that the sample was one where inter-observer reliability
was being evaluated. When that data is entered or passed into the Proyecto
Primates Master Database, mark the checkbox for Inter-Observer Reliability
and note which observer collected the “real” focal data in the Comments
section. That way the various data from the various observers collecting data
simultaneously can be looked independently of other data being analyzed.
TYPES OF DATA TO BE COLLECTED
There are a
number of different types of data that you will be recording in the field
and/or laboratory. The data we are collecting is organized in a hierarchical or
nested fashion. All “inner level” data pertain to corresponding higher levels,
but not all “higher level” data have associated “inner level” data. Below
you will find a table with all the different protocols that you may need to
become familiar depending on the specifics of your work. Regardless of
the kind of data you will be collecting, there are three numbers that are
extremely important and need to be entered consistently everywhere: OBSERVER SAMPLE NUMBER, AVISTAJE
NUMBER AND FOCAL SAMPLE NUMBER.
WRITE THE OS, AV, AND FS NUMBERS IN ALL PERTINENT PLACES IN DATA BOOK (i.e.,
observer data should have OS number; avistaje data should have OS and AV
number; focal samples should have OS, AV, and OS numbers). Detailed
instructions for each of those follow.
OBSERVER
SAMPLES serve to organize almost all of the data being collected by each
individual person on this project and also gives us an idea of how observers are
spending their time and of what parts of our protocol are difficult and may
need modification. This constitutes the highest level of organization of the
database, and EVERY person affiliated with Proyecto Primates in
This is simple and MANDATORY – these data MUST be collected each day, and there
is no excuse for not doing it. The database has been reorganized so that this
information must be added. Almost everything else in the database is pegged to
a particular OBSERVER SAMPLE.
In
In
You MUST review your Observer Samples after they are entered (especially if you are uploading them from the Palm!). Every Observer sample MUST have the following fields filled out:
Observer Sample Number
Observer
Date Dates in your book and in the database should all have the same format: DD-MMM-YY, e.g., "21-JUL-06".
Time Start AM
Time Finish AM
General
Activity AM
Time Start PM
Time Finish PM
General Activity PM
If you do the same activity all day, that should be entered TWICE, once for General Activity AM and once for General Activity PM. The Time Finish AM should then be entered as noon and the Time Start PM should also be entered as noon.
The fields "Avistaje Link", "Obs Activity Link", "Weather Link", and "Phenology Link" should ALL simply match the "Obs Sample ID" -- these fields are redundant in Access but are used by HanDBase to link tables. These fields are not seen in the forms, only in the tables.
NOTE: you do not need to enter any more detail on your observer activities other than your general activity in the Morning and Afternoon! This was an onerous thing that we were doing last year, but we have gotten rid of it. However, the old data remains in the database in the Obs Activity Data table.
Most of the data you will collect in the field are organized around AVISTAJES
(“sightings”) or encounters, either with your focal group of animals or with
other groups or species. These data are to be collected in the Avistaje section
of your data book or the Palm data logger and entered in the Avistaje SubForm
of the Database.
You must
collect AVISTAJE data EVERY TIME you encounter monkeys of any species, no
matter whether you collect any other kind of data on them that day. This
includes the animals you see while doing any field work activity. Every
separate encounter you have within a given observer-day in the field
constitutes a new AVISTAJE. For example, suppose you are with a group of
sakis in the morning and you go back to camp for lunch (which should be rare!)
or heavy rains force you to stop data collection. If you then return to the
same group and do more sampling in the afternoon, the afternoon sampling
session is considered a new AVISTAJE (since your original encounter
“ended”) and the session should get a new number when the data are entered into
the computer.
How much
data you will collect and the time spent in collecting AVISTAJE data will
depend on the situation. For example, in
If data are not available for a given cell, enter "Not
Available", but do NOT leave those cells blank.
If you are entering data only on the Palm, be SURE you review your Avistaje data immediately after you have transferred it to make sure you have entered EVERYTHING that needs to be entered (i.e., that none of the required fields are blank or contain odd pieces of information. Do not simply upload and forget about it! Do this BEFORE you delete the data from your Palm.
The fields "Range Data Link", "Focal Sample Link", "Biological Sample Link", "Feeding Bout Link", "Marked Tree Link", and "Ad Lib Data Link" should ALL have simply match the "Avistaje Sample ID" -- these fields are redundant in Access but are used by HanDBase to link tables. They are not shown in the forms, only in the tables.
DESCRIPTION
OF FORMS, SUBFORMS AND TABS IN PROYECTO PRIMATES DATABASE
The Field Data Entry Form in the Database has the following
five subforms in the following order from left to right: Avistajes, Phenology,
Biological Samples, and Mapping Data. In the following pages we provide
detailed instructions on how the data you collect MUST be entered in the
various subforms.
There are other kinds of data that are not entered in the Proyecto Primates Database: FRUIT MORPHOLOGY (see the Fruit Morphology Data Collection protocol) and CLIMATOLOGICAL DATA for the site, including temperature, humidity, and rainfall (see the Climatological Data Collection protocol).
AVISTAJES SUBFORM:
For each AVISTAJE associated with a follow of a focal group
of animals, there will be a number of additional types of data you will be
collecting, including Demography and
Census Data, Ranging Data, Marked Trees Data , Feeding
Bouts Data, Focal Samples Data, and
Ad Libitum Data.
The Avistajes subform has six Tabs that address each of the different kinds of data listed below:
Data on group size and composition and on presence/absence of known group members (Demography and Census Data).
Data on ranging patterns, habitat use, general group activity, and weather conditions (Ranging Data).
Data on the locations, identity, and collections made for feeding trees (Marked TreesData).
Data on diet and feeding bout characteristics (Feeding Bout Data).
Behavioral Data, including systematically collected data (Focal Samples)
Opportunistic observations (Ad Libitum Data).
Data on group size and composition and on
presence/absence of known group members.
Ranging Data Tab:
Throughout a follow, you will record the location of the group being observed
every 20 minutes – on the hour and at 20
and 40 min past the hour – even if those
points fall during a FOCAL SAMPLE. If you cannot take the position during the
FOCAL SAMPLE, try to remember where you were and take the position after the
end of the focal sample.
Some of the ranging data are recorded with the AVISTAJE for the group you are
following since the AVISTAJE asks for the time and position where you first
encounter monkeys and where you leave or lose them. The additional data on
group locations recorded during a follow are recorded in the Ranging Data
section of your data book or the Palm data logger.
Positions should be noted as distances and angles from reference points on the
trails and transects or trees that have already been mapped. Whenever you can,
it is better to take a position using a trail point rather than a tree as a
reference point, but a nearby tree is better than a much further trail point.
All location data should be recorded in your data book in the form of
“Distance, Compass Angle, Reference Point”. Do NOT record location data in any
other way! Use the codes “m” for meters and “d” for degrees without inserting
spaces after the commas. Example: “09:20 20m,250d,AV-05-021”. You should
practice estimating distances as you walk on the trails, which are marked at
regular intervals. Count your paces for 25 meters and then use that to guide
your distance estimates. You will get pretty good at estimating distances of up
to 40 or 50 meters using your paces! From time to time, bring out the laser
range finder and check yourself!
IMPORTANT NOTE: When you note an angle, the angle should be AS IF YOU WERE
STANDING AT THE MAPPED REFERENCE POINT. This means that if you take an angle
from where the monkeys are back to a mapped point, you will have to invert the
angle (e.g., an angle of 180 degrees read from where the monkeys are back to a
reference point corresponds to an angle of 360 degrees from the reference
point).
When you enter the data in the database you can enter ranging data comments.
You should classify each ranging data point as one of the following:
We cannot stress enough how absolutely critical the accurate
and systematic collection of the ranging data is for this project. You should
not be missing more than a few ranging points in any given full day follow. Be
especially conscientious of writing down the CORRECT tree number if you use a
tree as a mapping point. It is very easy to accidentally invert two digits or
to assume you know the tree number without looking at the metal tag, but this
causes a lot of problems if you are wrong, because such errors are VERY HARD to
correct post-hoc. If you are far away from a reference point or simply cannot
stop to take the ranging data, and especially you are in a seldom used part of
the group’s range or far away from trails, the ranging data are especially important.
In this case, you may need to put up a temporary flag with the date and time
and find your way back to that spot on a different day to map it. When you do
this, be sure to go back and write in the data in the APPROPRIATE PLACE IN YOUR
DATA BOOK or Palm. Please do this sparingly, however, and REMOVE the temporary
flagging once you go back to map the point.
In addition to collecting ranging data every 20 minutes, you should
also note
the predominant activity of the group at that point as either
“Resting”,
“Foraging”, “Moving”, ,
“Socializing”, “Vocalizing”,
“Other”, “Active Fuera de
Vista”, “Inactive Fuera de Vista”,
“Unknown” and “Not Recorded”.
You will also use these points to keep an informal
running
record of weather conditions, which we can use to examine the
relationship
between weather variables and particular behaviors such as army ant
foraging by
saki monkeys. There are two different weather variables to record at
the 20
minute point: Light/Rain conditions and Wind conditions. Light/Rain
should be
classified on a scale representing the degree of cloud cover and rain:
“Rain”,
“Drizzle”, “Cloudy”, “Partly
Cloudy”, “Slightly Cloudy”, “Full Sun”
and “Mostly
Cloudy” for daytime observations, “Clear Night”,
“Moon Visible”, “Moon
Partially Visible”, “Moon Not Visible” and
“Dark” for nighttime observations.
Wind condition is classified on a 3-point scale: “No
Wind”, “Slight
Breeze”, and “Windy”.
Note that taking weather data this way during
AVISTAJES supercedes our old way of collecting weather data all of the time
during OBSERVER SAMPLES and should be easier to do consistently.
How to enter the data:
REMEMBER, the goal is to automate the assignment of actual X,Y coordinates to your ranging points... we cannot look up the X,Y value for a reference point that does not exist in the database (or that cannot be found), thus the above conventions are ESSENTIAL to successfully search the database for reference point location.
To continue gathering data on the diets and
ecological strategies of the taxa we are studying, we mark and map the
locations of feeding trees and we estimate the time spent in feeding patches of
various species. Thus, each time you find your target taxon feeding in a food
patch, you will mark the tree and record a number of pieces of data concerning
the feeding source. You only need to mark only patches fed in by a group or
individual monkey for more than five “group-feeding” minutes (i.e., “major”
food sources: those fed in by a single animal for 5 minutes, or by several
animals for a total of 5 “monkey minutes” over the course of the day). You
should train your ears to listen for the sound of falling fruits and you should
get in the habit of looking at your watch when you first hear fruits dropping
in order to accurately assess whether or not to mark a patch.
You will
mark with plastic tape all those trees used for foraging as described above
plus trees that you know the animals sleep in (sakis, titis, and owl monkeys
all reuse at least several sleeping trees). Mark sleeping and feeding trees (or
the trunk supporting the feeding source in the case of epiphytes,
hemiepiphytes, lianas, vines, or bromeliads) in the following way:
Flagging – EVERYONE IN PROYECTO PRIMATES IN ECUADOR SHOULD FOLLOW THESE
CONVENTIONS:
In
To mark the
tree, write the tree number on PINK FLAGGING TAPE (please ONLY use pink!) and
tie the tape around the tree, preferably UNDER (rather than around) any lianas
hanging down or attached to the trunk. You should also write the date (in “mmm
yy” format) and the initials “PP” for “Proyecto Primates” on the tape, and you
should write on the tape “Sleep” if the tree is a sleeping tree or the Life
Form of the feeding source if the tree is a feeding tree. Finally, you should
write the tree number on a metal “write-on” or engravable tag that you then put
on the tree with an aluminum nail. Go over the engraving with a black sharpie
marker to make the number stand out at a distance. Do not hammer the nail all the
way in; you should leave about an inch or so of shaft exposed on the nail to
allow the tree to grow without swallowing the tag.
Note that if
you are marking a liana or other epiphytic plant that spans several trees, you
need only tag the trunk that supports the bulk of the liana. In
The following data will be noted in the Marked Trees section of your
data book or on the Palm data logger:
AGAIN, IMPORTANT NOTE: Remember that when you note an angle, the angle should be AS IF YOU WERE STANDING AT THE MAPPED REFERENCE POINT. This means that if you take an angle from a tree back to a mapped point, you will have to invert the angle (e.g., an angle of 180 degrees read from where the monkeys are back to a reference point corresponds to an angle of 360 degrees from the reference point). Be very careful to not map a tree 180 degrees off from its true location!
Some Additional Useful
Definitions for Tree Measurements, even if not prompted to enter them in the
Database
Additionally, for each marked tree, you
will record feeding bout data in the Feeding Bouts section of your data
book or the Palm data logger for all bouts greater than 5 “monkey minutes”. You
need not worry about recording bout data for bouts lasting less than 5 minutes.
For each feeding bout, note the time (to the nearest minute) at which the first
feeder(s) entered the tree and began feeding (e.g., “10:45 BE AV-05-001” for
“Begin Eat AV-05-001 at 10:45”) and when the last feeder(s) finished feeding
(e.g., “11:15 EE AV-05-001” for “End Eat AV-05-001 at 11:15”). If you are
following some animals and arrive at a food patch where animals are already
feeding, score your arrival time as “BE Late” (“begin eat late”, check the box
“Late?”). If you need to leave a tree before the last feeders have left (e.g.,
if your focal animal leaves the feeding patch while others are still eating),
record the ending time as “EE Early” (“end eat early”, check the box “Early?”).
If you miss a BE or EE time, score it as “Not Recorded”, but please be aware
that this is a code of last resort, introduced to deal with when observers
forgot to collect data that they were supposed to collect. With the BE and EE
times, we can calculate a minimum number of minutes that the group spent
feeding in a particular patch. If the animals stop feeding in a patch for more
than five minutes, and they return to the same tree, record another set of BE
and EE times. If the animals are feeding but you do not know from which tree
you may record it as PA-05-XXX, meaning the monkeys are having a feeding bout
but you cannot be sure on which tree, therefore you cannot mark it. Also,
record the maximum number of individuals that you see feeding in the patch
simultaneously (Max # Feeders).
If the food
item is one that you do not recognize or that you have not collected
previously, MAKE A COLLECTION of both the leaves and the fruit of the plant
(note in the Marked Trees section of your data book and in the database
what collections you have made; you will enter specific information on the
collection in the Plant Collections section of the database later). It is
important to do these collections to allow us to identify the plants being
eaten. To make collections, look carefully at the tree through binoculars to
get a good idea of the appearance of the leaves and fruits and then look for
these on the ground under the tree. Carry plastic bags with you at all times to
shove these collections into until you get back to the lab. In
Enter in this tab data pertaining to observations that may have happened outside focals or that were not amenable to the systematic data collection that is done during a focal.
PHENOLOGY SUBFORM:
It is used to enter data on PHENOLOGICAL PATTERNS in
the forest (see the Phenological Data
Collection protocol).
BIOLOGICAL SAMPLES SUBFORM:
It is used to enter Data on any BIOLOGICAL SAMPLES you
collect (see the protocols for Plant
Voucher Specimens, Plant Nutrient Samples, Fecal Samples for DNA
Extraction, Fecal
Samples for Hormone Extraction, and Urine Samples for
Hormonal Analysis).
MAPPING DATA SUBFORM:
It is used to enter MAPPING DATA for trails and transects around the site (see the Flagging, Trail Maintenance and Mapping protocol).