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Data for "Reviewing Seas of Data: Integrating Image-Based Bio-logging and Artificial Intelligence to Enhance Marine Conservation"
This dataset contains data and Python codes associated to the manuscript: Reviewing Seas of Data: Integrating Image-Based Bio-logging and Artificial Intelligence to Enhance Marine Conservation.
Data: Underwater images and sample video collected from Adélie penguins (Pygoscelis adeliae) at the colony on Ile des Pétrels, at the Dumont d’Urville station, in Terre Adélie, East Antarctica (66°40′ S; 140°01′ E), over the 2017-2018 breeding season. Birds were equipped with video loggers (Little Leonardo, DVL400M, 61 mm × 21 mm × 15 mm, 29g) during the chick guarding stage, in which one parent guards the chicks on the nest while the other is foraging at sea to bring food back to its offspring. Only one member of a pair was captured on or when leaving the nest, when both adults were attending the nest before/during a changeover. The data collection is part of the ongoing long-term monitoring program of Adélie penguins (IPEV program 1091 l'AMMER, See-Life). Video loggers were set to start recording approximately ten hours after deployment, to maximise the chance to record underwater behaviours. After data recording started, video data were recorded for three hours at a resolution of 30 fps (frames per second). Video data were collected to quantify behaviours of Adélie penguins during foraging. Both sample images and video provide snapshots of what video loggers record (e.g. individual prey capture events, interaction with krill swarms, interaction with co-specifics, swimming).
The dataset can be manipulated and analysed with the provided Python code. The "How_To_Image_Based_bio-logging" is in both ipynb (jupyter notebook) and pdf format.
Please, read also the Read Me file included in this dataset.
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Replication data for: Fig 6.1, Dates of capture and ages of victims for single American Badger, 03 Nov 2025
FILE DESCRIPTION
Keywords: American badger, dates of capture, age of victims, Gunnison's prairie dogs
Filename = Fig 6.1, Dates of capture and ages of victims for single American badger, 03 Nov 2025.
Number of Gunnison’s prairie dogs (and their approximate ages) captured and carried to home-den per day
by a single female American Badger (Becky) from 05 June 2018 through 07 July 2018.
A gunnison adult had first emerged from its natal nursery-burrow >11 months ago,
and a juvenile had first emerged <2 months ago. “Age unknown” was either a large juvenile or a small adult.
All data shown here are from a single study-area of Gunnison's prairie dogs at Valles Caldera National Preserve in 2018.
Data in this file were checked one time by Samantha Kagel, and one time by John Hoogland shortly after creation of file in 2019.
Filename = Fig 6.1, Dates of capture and ages of victims for single American badger, 03 Nov 2025.
These data used for Fig 6.1 in Hoogland 2026.
This file ready for longterm storage on 27 May 2025
Replication data for: Fig 9.3, Bottom, Territory sizes, GPDs, 03 Dec 2025
FILE DESCRIPTION
Keywords: gunnisons, territory size, burrows per territory
File name: Fig 9.3, Bottom, Territory sizes, GPDs, 03 Dec 2025
I created this file from SYSTAT file = Clansize, which I created on 21 Oct 1997
I assume that I checked this file TWO TIMES upon creation for Hoogland 1999
I used data from this file for Hoogland 1999 (Philopatry, dispersal, and social organization…)
Changes made to this file when I created GPDs, Clan comps+types, PEFO and VCNP, spring 2020
These data are from the GPDS at Petrified Forest National Park (PEFO) only, from 1989 through 1995.
I did NOT calculate the territory sizes for certain GPD clans at PEFO. I knew
the clan sizes for many clans but had no information about the territory size.
Clan size = cumulative number of adult males (Admales), adult females (Adfems) and
nonbreeding yearling males (Yrlmales).
If a yearling male copulated, I considered him to be an adult male for this EXCEL file
These data used for Figure 9.3, bottom, in Hoogland 2026.
This file ready for longterm storage on 04 Feb 2025.
Clan type = No-Male, Half-Male, One-Male, and Multi-male. See chapter 10 Hoogland 2026.
File name: Fig 9.3, Bottom, Territory sizes, GPDs, 03 Dec 2025
Clan size = number of adults and yearlings in home coterie territory
Territory size is in hectares
No information on number of burrow entrances per clan territory
No information on territory sizes or burrow-counts for Utah prairie dogs
Notice that these data from GPDs at PEFO only--I did not calculate territory
sizes for gunnisons at the Redondo Meadow Colony (RMC) at Valles Caldera
National Preserve (VCNP) or for gunnisons at the Visitor Center Colony at VCN
Replication data for: Fig 8.1, 8.5, 8.7, and 8.8, Alarm call frequencies, Males, BTPDs, 19 Nov 2025
FILE DESCRIPTION
Keywords: alarm calls, BTPDs, age, ARS, coterie size, sex
Filename = Fig 8.1, 8.5, 8.7, 8.8, Male alarm call frequencies, BTPDs, 19 Nov 2025
OLDFile name = BTPDs, Male alarm call frequencies, 29 Jan 2025
Date = 11 March 2019
This file was created for my first book (Hoogland 1995).
All the data were checked TWO TIMES for that book
BTPD is a unique marker for each prairie dog, from 1 through 149.
Note that this file is for BTPD MALES only. I have another file for BTPD FEMALES.
I made several changes to this file in February and March 2019
Four females lost their litters shortly after weaning, and before we
started to pull badgers. I score variable = NEWCLASS = 3 for three of these
females, and NEWCLASS = for the 4th female, because she
was the only female in her coterie with a male born in a different coterie.
The females were R66-WA7 in 1978, R56-RSBB in 1978, RR7 in 1978, and 92 in 1979.
I have now checked this file several times. Note that most of the
stats for this file are IDENTICAL to the output for my book. In particular,
stats for cotsize and age and year and BTPD are IDENTICAL. I have made
changes to variables = NEWCLASS (a new variable) and CALLFREQ (which
was formerly called CALL PROB) for my first book.
Year = year when frequency of alarm calling recorded in response to moving
stuffed specimen of American badger
BTPD = Unique number for each BTPD MALE
This unique number does NOT correspond to eartag.
Newclass caller = type of kin in home territory
0 = no known kin in home territory (r <0.0313)
1 = distant kin only in home territory (first and second full or half cousins, aunts,
uncles, nephews, nieces, nonlittermate siblings)
For class = 1, 0.0625 < r < 0.2500
2 = littermate siblings in home territory
3 = mother in home territory
4 = offspring in home territory
Proportion times for alarm call = proportion of times BTPD gave alarm call in response to moving stuffed badger = callfreq
Trials = number of experimental runs with moving stuffed badger
Age = age in years of BTPD
Coterie size = number of adult BTPDs in home territory
Note for class caller: The number indicates the closest kin in the
home territory, with or without other possible kin.
Example: If a BTPD had offspring and full first cousins in the
home territory, the class caller would be 4
Note for littermate siblings: For this analysis, I make no attempt
to discriminate between full siblings (same mother, same father)
and half-siblings (same mother, different father).
WEANLINGS = number of offspring at first juvenile emergence sired by male
On 08 March, I discover the following note from the summaries of
alarm calls for BTPD males: "In 1983, this number [babynum = babies = weanlings] =
the number of babies AT THE TIME OF BADGER PULLS--in other years, this
number probably = number of babies weaned [in the home territory]".
This note explains when the number for WEANLINGS is sometimes so high,
because the number is the SUM of all the WEANLINGS in the home territory--
either at the time of badger pulls (better) or just after weaning (not
as good). Note, however, the loss of juvenile shortly after weaning
was usually low for BTPDs in most years.
On 11 March, this file is now ready for statistical analyses.
Remember: As for all other files, variable = NEWCLASS is
based on MATERNAL KINSHIPS. I do not consider
paternal kinships other than father-juvenile offspring.
So, if a father and known or possible son were in the same
breeding coterie territory, I consider NEWCLASS = 0. I have
very few cases of this latter scenario (<5, probably)
BTPD marker = designated marker for each BTPD marked with Nyanzol dye
For some BTPD males, we collected information on callfreq for >=2 years
Callfreq = Proportion of times for alarm call to moving stuffed badger
Cotsize = number of adults and yearlings in home coterie territory
Weanlings = Number of weanlings in home coterie territory
These data used for Figures 8.1 , 8.5, 8.7 and 8.8--but NOT 8.6--on Hoogland 2026.
This file ready for longterm storage on 19 Nov 2025.
I considered data from the same BTPD male in different years to be independent.
Filename = Fig 8.1, 8.5, 8.7, 8.8, Male alarm call frequencies, BTPDs, 19 Nov 202
Replication data for: Fig 10.2, Upper right, GPDs, clan type vs clan size vs copfems, 10 Dec 2025
FILE DESCRIPTION
Keywords: Gunnison's prairie dog, clan size, clan type, copulating females
File name = Fig 10.2, Upper right, GPDs, clan type vs clan size vs copfems, 10 Dec 2025
OLDFile name = GPDs, Clantype vs clansize, 11 Feb 2025
These data are the means and standard errors only.
I cannot find the RAW DATA for these numbers. I could find and re-calculate, if necessary.
I did, however, check the means and standard errors
TWO TIMES when I created Figure 10.2 (on 11 Feb 2025?).
These data are from ALL THREE GPD colonies: Petrified
Forest National Park PEFO), Redondo Meadow Colony RMC) at Valles
Caldera National Preserve (VCNP) and Visitor Center Colony (VCC) at VCNP
These data used for Figure 10.2 in Hoogland 2026.
This file ready for longterm storage on 11 Feb 2025.
Clansize = clan size = number of adult and yearling GPDs living in same clan territory
Clantype = Clan type. See below for definitions.
Females that copulated = number of females in coterie that copulated
Female GPDs first copulated as yearlings, and almost ALL GPD females copulated
No-male clan had no resident sexually mature male in May
Half-male clan shared a single sexually mature male in May with another clan
One-male clan had a single resident sexually mature male in May
Multi-male clan had >=2 sexually mature males in May
For more information about clan types, see Chapter 10 of Hoogland 2025
File name = Fig 10.2, Upper right, GPDs, clan type vs clan size vs copfems, 10 Dec 2025
All clan sizes and clan types are from MAY
Replication data for: Fig 9.5, 9.6, 0.7. 10.5, UPDs, clansize, clantype, clancomposition, 04 Dec 2025
FILE DESCRIPTION
Keywords: UPDs, clansize, clantype, clancomposition
File name: Fig 9.5, 9.6, 0.7. 10.5, UPDs, clansize, clantype, clancomposition, 04 Dec 2025
This file has now been checked TWO TIMES by JLH alone
OLD File name = UPDs, clan sizes, comps, 06 April 2020
Note well: For this file, I counted each male in a half-male coterie as 1 rather than 0.5.
I used this same logic for half-male coteries of BTPDs and GPDs.
Clan type = 0 = No male clan = no resident sexually mature male
Clan type = 0.5 = half-male clan
Clan type = 1 = one-male clan
Clan type = 2 = two-male clan
See Chapter 10 of Hoogland 2006 for descriptions of UPD clan types
SM males = sexually mature males, regardless of age
Adfems = adult female, all of whom copulated
Yrl males = sexually immature yearling males
If a yrlmale was sexually mature, I considered him to be a SM MALE
These clan sizes are for MAY.
If one SI male was in a clan and another SI male lived in that clan and
shared another clan, I consider the number of SI males to be TWO.
If two SM males shared the same two clans, then I consider each clan
to have TWO SM males
Some changes on 04 April 2020:
All data in this file checked TWO TIMES by JLH alone on 06 April 2020
Clan composition = composition within clan regarding sex and adult vs yearling
These data used for Figures 9.5, 9.6, 9.7, and 10.5 in Hoogland 2026.
This file ready for longterm storage on 05 Feb 2025.
Clansize = number of adults and yearlings in same clan territory
SM = sexually mature SIM = sexually immature males= sexually inactive male
File name: Fig 9.5, 9.6, 0.7. 10.5, UPDs, clansize, clantype, clancomposition, 04 Dec 202
Replication data for: Filename: Fig 5.13, Lower left, Date of estrus by clan for each female, UPDs, 20 May 2025
FILE DESCRIPTION
Keywords: Utah prairie dog, estrus date by coterie
Filename: Fig 5.13, Lower left, Date of estrus by clan for each female, UPDs, 20 May 2025
OLD file name = UPD within-clan synchrony, 1997. 11 Nov 2016--which I cannot find!
These data are from 1997 only, for the UPDs at the Horse Corral Colony of Bryce Canyon National Park
So, on 20 May 2025 I re-create this file from HARDCOPY from 11 Nov 2016.
Dates of estrus shown here are Julian dates.
Julian date of copulation = 71 = 12 March, for example.
Julian date of parturition = 84 = March 25, for example.
These Julian data are for NON-LEAP years.
Julian dates for leap years after 28 February differ by 1 day.
This file contains data from only UPD clans in which >=2 females came into estrus
Note: This file includes ONLY THOSE UPD CLANS FOR
WHICH WE HAVE >= 2 COPDATES
This EXCEL file checked TWO TIMES on 20 May 2025.
These data used for Fig 5.13, Lower left, in Hoogland 2026.
This file ready for longterm storage on 19 May 2025.
Filename: Fig 5.13, Lower left, Date of estrus by clan for each female, UPDs, 24 Oct 2025
UPD clan designation = unique numerical designation for each UPD clan in 1994
BTPD = black-tailed prairie dog GPD = Gunnison's prairie dog
WTPD = white-tailed prairie dog UPD = Utah prairie do
Haploceratoidea fam., gen. and sp. indet. (Ammonoida, Ammonitida)
This dataset includes the slices of the specimens MNHN.F.A99982, MNHN.F.A99984 and MNHN.F.A99986 assigned to Haploceratoidea fam., gen. and sp. indet. (Ammonoida, Ammonitida), which were micro-CT scanned at the AST-RX (“Accès Scientifique à la Tomographie à Rayons X”) at the UMS 2700, MNHN (Paris, France), with the following parameters: voltage, 150 kV; current, 200 µA
Replication data for: Fig 10.8, Top right, GPDs, clan size and clan type vs male ARS, 17 Dec 2025
FILE DESCRIPTION
Keywords: GPDs, clan size, clan type, male ARS
File name = Fig 10.8, Top right, GPDs, clan size and clan type vs male ARS, 17 Dec 2025
OLDFile name = GPDs, Clan TYPE vs Male ARS, 23 Sept 2021
Today I have created this file by starting with File name = GPDs, Male ARS vs clan size, 05 Sept 2021
Today I add variable = clan type
In this file, clantype = 0.5 = Half-male clan, for which >=1 are controlled by single male
Clantype = 1 = One male clan
Clantype = 2 = Multi-male clan
Clantype = 0 = Male that lived alone, with no other females in his territory, who did not DISAPPEAR shortly after mating season
If a GPD male mated and then disappeared in early April, I did not assign a clantype
This file has been checked TWO TIMES for clan type on 23 Sept 2021.
Notice that I have only ONE case of Clantype = 0. Almost no solitary GPD males.
Other data were checked TWO TIME earlier. See below.
Note that multi-male clans were VERY RARE at RMC and VCC, but were
much more common at PEFO. All in this file from RMC and VCC.
Microsats = microsatellites
This file includes ONLY THOSE GPD MALES THAT COPULATED WITH >=1 FEMALE--
OR MALES KNOWN TO SIRE OFFSPRING FROM MICROSATS--i.e., I have EXCLUDED GPD males
for which I have no evidence of copulation from either observations or microsats
Note: All GPD data are from RMC and VCC, with NO DATA from PEFO--because I do not have
any information via microsats about siring of GPD offspring at PEFO
OLDFile name = GPDs, Male ARS vs clan size, 05 Sept 2021
I started this file from File name = GPDs, Male RS for cops,babies,yrls, 01 April 2021
Details below for GPDs, Male RS for cops,babies,yrls, 01 April 2021 and related files
My plan is to use only data from VCNP's RMC and VCC, because I hope to have
microsat data on paternities from those colonies. In this plan, I will NOT include info
from PEFO, from which I have no information on paternities from microsats
I will keep info from PEFO on Sexpartners for now
If a GPD male had >=2 half clans, I used the LARGER of the two half-clans
for clan size for the WTPD male.
In 2013, for example, GPD male-8 had one half-clan of size 12 (8A) and
two half clans of size 4 (8B and 8C). For GPD-male-8 for this file, I used clan size = 12
If TWO GPD males shared the same multi-male clan, I used the same clan
size for both males. In 2013, for example, I used the same clan size of 20
for both male-0 and male-41. Multi-male clans were rare for GPDs.
For 0-41 in 2013, I do not use clan size--because smaller clans with large territory
almost certainly existed
For 44 in 2013, I use smaller clan (44a) for 44 (clansize = 4), because I new so little about clan-44B
For 28 in 2013, I no not use any information. Smaller clans within large territory seem likely.
For 49 in 2017, I use clan size = 4 (no females in his other half-clan of clan size = 5)
Clan sizes checked TWO TIMES on 05 Sept 2021
Other data were checked two times for earlier files.
I DO use GPD male-31 in 2018. We observed only 2 cops, but he sired babies from 5 litters.
Note on 23 Sept 2021: For clan size for males that disappeared, I used clan size in May for the
clan where the disappearing male would have been.
Note on 23 Sept 2021:Clan sizes are for MAY of each year
OLDFile name = GPDs, Male ARS for cops, PEFO and VCNP, 11 April 2021
I created this file by combining data from the following two EXCEL files:
File name = GPDs, Male RS for cops,babies,yrls, 01 April 2021 [and]
File name = GPDs, Male ARS and LRS for cops, 13 Jan 2021
Details from both files immediately below
OLD File name = GPDs, Male RS for cops,babies,yrls, 01 April 2021
I created this file from File name = GPDs, Male ARS-LRS summaries, 31 March 2021. See notes below.
OKtouse = 0 = we did not see many of the copulations--probably <50%
OKtouse = 1 = we documented most of the copulations--probably > 50%
I checked all the data on Age and Sexpartners on the hard-copy summary sheets ONE TIME ONLY---
I found only 1 error, so I did not check a second time
This file has been checked TWO TIMES on 02 April 2021
In particular, I checked the new data for Sexpartners, OK to use, and Age on 02 April 2021
For GPDs from VCC of VCNP, I use a suffix of "V" for every GPD marker and eartag--
to reduce possible confusion with GPDS from RMC of VCNP
All data in this file are from GPD males that copulated with >=1 female
All data from males that were not observed to copulate are EXCLUDED from this file
For several males listed in this file that copulated with >=1 female, we
have NO EVIDENCE FROM MICROSATS that those males sired >=1 emergent juvenile.
Copulating males that evidently did not sire any offspring include the following:
For 2013: 28 (123)
For 2014: 108 (C47), 25 (439), 32 (593)
For 2015: 20#2 (815), 107 (C39)
For 2016: 37#2 (C99)
For 2017: 24 (203)
For 2018: 32 (79), 6 (395). 14 (55), 47 (435), 17 (O235)
Date = 31 March 2021
This new file checked TWO TIMES for Weanlings and Yearlings on 31 March-02 April 2021
Weanlings = cumulative number of babies sired by each male per year
Yearlings = cumulative number of sired babies sired that survived for >=9 months after weaning.
OLDFile name = GPDs, Male ARS-LRS summaries, 31 March 2021
I made this file directly from file = GPDs, Male ARS-LRS for cops, babies, yrls, 30 March 2021
Details immediately below for GPDs, Male ARS-LRS for cops, babies, yrls, 30 March 2021
Name of file = GPDs, Male ARS-LRS for cops, babies, yrls, 30 March 2021
No information on survivorship of juveniles for 2016 (last year at VCNP's RMC)
or 2018 (last year at VCNP's VCC)
Number in parenthesis after number of babies or yearlings for a male = number
of babies or yearlings ESTIMATED or INFERRED. I only made estimates or
inferences that seemed reasonable. For example, if microsats showed that the single male that
copulated with the mother sired 2 of 3 babies, I inferred paternity to that male for the third baby as well.
Similarly, if microsats showed for a litter of 6 that one of two copulating males sired 2 babies and that the
other of two copulating ales sired 2 babies, then I inferred paternity for 3 babies for both males.
If a female copulated with 2 males, for example, and 1 of the copulating males sired three of four babies
and we have NO INFORMATION from microsats for the fourth babies, then I inferred that the male that sired
three of the babies (from microsats) also sired the fourth baby as well. I only
made this inference if the one male sired AT LEAST HALF of babies. So, if a female copulated
with two males and weaned five babies, for example, and if one of the copulating males sired two babies and we have
NO INFORMATION from microsats for the other three babies, I have NOT inferred paternities for any of those 3 babies.
For this file I have made no attempt to include information for body mass or age of the copulating males.
Information on age and body mass vs male ARS and LRS is summarized in other chapters.
This file has been checked TWO TIMES on 29-30 March 2021.
I have excluded some cases for which paternity makes no sense.
Dognumber does not equal integer--e.g., 15.5, 33.2, 58.5--means that GPD was added after I created an
earlier, numbered file.
File name = GPDs, Male ARS and LRS for cops, 13 Jan 2021
Date = 12 Jan 2021
This file is IDENTICAL to file = GPDs, MCs vs male body mass, ARS, 06 Jan 2021
I have created this identical file so that I can keep it with other ARS files
See notes below from that file
Note on 08 Feb 2021. These data are all from PEFO from 1989 through 1995
i.e., no data from RMC or VCC of VCNP
Sexpartners = number of different females with whom a male copulated
Weanlings = number of babies sired by a male, as determined from either cops or microsatellites
Yearlings = number of sired emergent babies sired that survived for >=9 months after weaning
OLDFile name = GPDs, MCs vs male body mass, male cops, 08 Jan 2021
I derived this file from file = GPDs, MCs vs female body mass, ARS, 06 Jan 2021,
which I checked ONE TIME ONLY on 05 Jan 2021
OLDFile name = GPDs, MCs vs male body mass, male cops, 08 Jan 2021 has been checked TWO TIMES ON 08 Jan 2021
A GPD male will have the SAME EARTAGS in different years, but will have a
different Nyanzol marker in different years
For most analyses, I will consider data from the same GPD male in different
years to be statistically independent
Oktouse = 1 means that we think we observed most or all copulations
by a GPD male in a particular year
Oktouse = 0 means that we think we DID NOT OBSERVE most or all copulations
by a GPD male in a particular year
I only use AGE if I was certain--or almost certain--about a GPD male's exact age
Weanlings = all babies weaned by all females with whom a GPD male copulated.
SOME of the babies might have been sired by the copulating male, but
OTHER offspring might have been sired by other males that copulated with the GPD female
Yearlings = all yearlings reared by all females with whom a GPD male copulated.
SOME of the yrls might have been sired by the copulating male, but
OTHER yrls might have been sired by other males that copulated with the GPD female
SEXPARTNERS = minimal number of GPD females with whom GPD male copulated,
with or without MCs by the copulating male
Note GPD male with Dognum = 63.5--so that I could insert additional data for
GPD male-07 (B17, C68) in 1993.
Note also that GPD male-34 and GPD male 34#2 are DIFFERENT GPD MALES, and they
have different Dognums and different Eartags
These data used for Figure 10.8 in Hoogland 2026.
This file ready for longterm storage on 14 Feb 2025.
No-male clan had no resident sexually mature male in May
Half-male clan shared a single sexually mature male in May with another clan
One-male clan had a single resident sexually mature male in May
Multi-male clan had >=2 sexually mature males in May
For more information about clan types, see Chapter 10 of Hoogland 2025
Marchwt = male body mass in February, March, or early April--just before during, or just after mating season
Junewt = male body mass in late May or June, approximately when weanlings were first emerging from their natal burrows
yrl = yearling
No information for variable = "Dognumber" in this EXCEL file.
Notice the several notes from several earlier versions of this EXCEL file. Data for Fig 10.8 for GPDs are all accurate.
Cops = copulations
File name = Fig 10.8, Top right, GPDs, clan size and clan type vs male ARS, 17 Dec 202
Seine: Le chemin de halage de Satrouville à La Frette (1774)
Carte géoréférencée portant la date du 2 août 1774.
Elle a pour visée d'informer de l'emplacement du chemin de halage sur une partie en aval de la Seine de Chatou à La Frette.
Le chemin est lavé de rouge, ce qui signifie qu'il est construit en maçonnerie. La ligne et le sens de navigation sont figurés, ces éléments sont important dans l'action de halage qui se fait pour remonter la rivière.
En effet sur certains passages, la navigation à la voile n'est pas envisageable et les bateaux doivent être tractés, soit par des hommes soit par des animaux.
Service des Cartes et Plans des Archives Nationales. Cote AN F/14/10078/1/16.
Numérisation en 2014. Géoréférencement en 2014 par Julie DAVODET. Mise en ligne en avril 2015. Métadonnées par Julie DAVODET et Juliette AUDET.</p