Input

Temporal series of environmental conditions

During simulations, three temporal series of environmental features influenced the life of the individuals: the river temperature, the river flow and the marine growth conditions (a variable synthesizing marine environment effects on growth, see section).

1. These series can be observed data. To do so, use the R functions called from the demoIbasam file:

• Load your data:

mm <- data.frame(temperatures=your_temp_data, logrelflow=your_flow_data)

with mm being a data frame containing daily water temperatures (in Celsius) and water flow (log of m^3/s) over the period to be simulated (years*365).

• Comment the line corresponding to the river_climate_model function (which generates environmental values):

demoIbasam <-
function (nYears, CC_Temp, CC_Amp, plotting = TRUE, window = FALSE, returning = FALSE, 
    success = TRUE, empty = TRUE) 
{
    empty()
    def <- defaultParameters()
    #mm <- river_climate_model(nYears + 1, CC_Temp, CC_Amp)
    Reset_environment()
    Prepare_environment_vectors(mm$temperatures, mm$logrelflow)
    setup_environment_parameters(def$envParam)
...

• Load the modified demoIbasam function:

source(demoIbasam.R)

2. Use observed data for the parameterization of the model (see section).

TO DO

• link to files
• script to analyse data and get parameters estimates

Then, simulations utilize a set of the 3 series generated from stochastic climate models (see river climate and ocean climate sections).