Output

Simulated data are analysed at the end of each time step (using observe() function; inserted in demoIbasam) to follow the population evolution at different life stages (smolt at the end of winter, parr and anadromous adult after summer,...). The time spent in river and at sea, the weight and size, the sexual maturity status, the smoltification status, the location, the genetic and phenotypic values of maturation thresholds are recorded for each individual at these observation times.

Results can be stocked in a data frame:

res <- demoIbasam(10)

The res object contains a list of variables corresponding to individuals characteristics over their life time.

Variable	Description	Values	Comments
Lf	Fork length (mm)	94.1, 150.5, 96.5, 125.1, 143.9, 130.3
W	Weight (gr)	10.1, 32.7, 10.8, 19.1, 28.8, 21.4
Fat	Fat content	1.2, 1.7, 1.2, 1.3, 1.8, 1.3
AgeRiver	Age in river	1, 1, 1, 1, 1, 1
AgeSea	Age at sea	0, 0, 0, 0, 0, 0
Female	Sexe (Female = 1, Male = 0)	0, 1, 1, 0, 1, 0
Parr	Juvenile	1, 0, 1, 0, 0, 0
Mature	Maturation status /decision	0, 0, 0, 0, 0, 0
Atsea	If individual still at sea, equal 1	0, 0, 0, 0, 0, 0
Smolt	Smolt status / run toward ocean	0, 1, 0, 1, 1, 1
ID	Identification number. The last 2 numbers of the ID corresponds to the population ID (e.g. 01)	67201, 74901, 80701, 81201, 92001, 96401
DW	Weight loss	0.4, 8.9, 0.5, 5.1, 7.2, 5.4
Returns	Return to river / mature at sea	0, 0, 0, 0, 0, 0
Psurvival	Survival probability	0.5, 0.5, 0.5, 0.6, 0.6, 0.6
date	Number of days	90, 90, 90, 90, 90, 90
year	Year number	1, 1, 1, 1, 1, 1
CollecID	Population ID	1, 1, 1, 1, 1, 1
Wini	Initial weight	0.2, 0.2, 0.2, 0.2, 0.2, 0.2
SpecificGR	Individual growth rate	103.6, 108, 106.8, 111.3, 103.4, 108.7
motherID	Individual ID from mother	0, 0, 0, 0, 0, 0
fatherID	Individual ID from father	0, 0, 0, 0, 0, 0
gG	Genetic value for growth in river	0, 0, 0, 0.1, 0.1, 0
gG_sea	Genetic value for growth at sea	0, -0.1, 0, 0, 0.1, 0
gPercF	Portion of W growth allocated to Fat reserves	0.1, 0.1, 0.1, 0.1, 0.1, 0.1
pG	Phenotypic value for growth (in river)	-0.1, 0.2, -0.1, 0, 0, -0.1
pG_sea	Phenotypic value for growth at sea	0.1, 0, 0.1, -0.1, 0.1, 0
pPercF	Portion of W growth allocated to Fat reserves	0.1, 0.1, 0.1, 0.1, 0.1, 0.1
gSLmid	Genetic value for reaction norm for smoltification (slope)	89, 89, 89, 89, 89, 89	same as phenotypic value
galphaS	Genetic value for reaction norm for smoltification (intercept)	0.2, 0.2, 0.2, 0.2, 0.2, 0.2	same as phenotypic value
pSLmid	Phenotypic value for reaction norm for smoltification (slope)	89, 89, 89, 89, 89, 89	assumed this norm was identical for older parrs and constant through time
palphaS	Phenotypic value for reaction norm for smoltification (intercept)	0.2, 0.2, 0.2, 0.2, 0.2, 0.2	assumed this norm was identical for older parrs and constant through time
gFmid1	Genetic value for maturation threshold (precocious male parr)	1.4, 0.7, 1.6, 0.7, 1.4, 1
pFmid1	Phenotypic value for maturation threshold (precocious male parr)	1.2, 1.2, 1.1, 1, 1.3, 0.8
gFmid2	Genetic value for maturation threshold (precocious female parr)	40, 43, 36, 39, 48, 39
pFmid2	Phenotypic value for maturation threshold (precocious male parr)	40.8, 47.8, 42.1, 43.1, 47.5, 39.9
gFmid3	Genetic value for maturation threshold (anadromous male)	40, 72, 40, 32, 40, -24
pFmid3	Phenotypic value for maturation threshold (anadromous male)	-7.6, 105.6, 93.3, 24, 23.4, -22.2
gFmid4	Genetic value for maturation threshold (anadromous female)	70, 85, 130, 115, 145, 115
pFmid4	Phenotypic value for maturation threshold (anadromous female)	65.2, 159.9, 155.8, 32.4, 190.7, 30.8
gNeutral	Neutral gene	0.5, 0.6, 0.6, 0.4, 0.4, 0.6
motherStrat	Life history strategy of mother (age in river . age at sea)	0, 0, 0, 0, 0, 0
fatherStrat	Life history strategy of father (age in river . age at sea)	0, 0, 0, 0, 0, 0
NreproYear	Number of reproductive events	0, 0, 0, 0, 0, 0
Nrepro	Total number of reproductive events	0, 0, 0, 0, 0, 0

TO DO

• link to R script to analyse data