After reproduce, spawners either died (semelparous) or survived reproduction (primo-spawners).
#Survival pre-reproduction
It concerns only spawners during reproduction, and this phase has been shown highly dependent on water (Walburg and Nichols, 1967).
For the American shad (Alosa sapidissima), spawning occurs between 8°C to 26°C, with most of individuals reproduced between 14-21°C (Limburg et al, 2003).
Leggett and Whitney (1972) found a median temperature for spawning of 16-20°C for York, St Johns and Connecticut Rivers.
## Thermal range using GAMs
To adjust the temperature thresholds and enhance model predictive capacity at the northern edge of species distribution, parameter values for spawners survival before and after spawning were obtained using generalized additive models (GAM) (Hastie and Tibshirani 1990). Observations of presence/absence across the 1900-1950 period (pristine distribution) are predicted regarding the average temperature times series observed across the 98 watersheds composing the environment of GR3D-U.S.
Either summer or spring temperature are used as environmental variables depending the season at which each process occurs.
In GR3D, spawning occurs in river at the beginning of spring, so the spawner survival during reproduction was linked to spring temperature time-series in river.
```{r build a df for presence/absence over the 1900-1950 period }
rectTemperature = function(Tmin, Topt, Tmax, pct = 0.8, col ='red'){
optRange = thermalRange(pct, Tmin , Topt, Tmax)
rect = data.frame(xmin = c(-Inf, Tmin, optRange["upper"], Tmax),
xmax = c(Tmin, optRange["lower"], Tmax, Inf),
ymin = -Inf,
ymax = Inf,
alpha = c(.3,.6,.6,.3),
col = c(col, 'grey', 'grey', col))
return(rect)
}
```
```{r Observations of presence/absence according to temperature, include = TRUE, fig.cap= 'Temperature experienced by spawners during their river stage in spring'' }
#plot of temperature ranges
obs_spg <- nea_presence_temp %>%
ggplot() +
geom_point(aes(spring_river_temperature,obs_1900_1950), col = "orange", alpha = 0.3) +
labs(y = "Observed presences", x = "Spring river temperature (°C)") +
theme_bw()
#temperature range experienced by fish in river in spring in which presence or absence are recorded