install.packages("mgcv")
install.packages("readxl")
install.packages("MuMIn")
install.packages("openxlsx")
library(mgcv)
library(readxl)
library(MuMIn)
library(openxlsx)

resamp <- read_excel("C:/Users/jcarvalho/Downloads/GAM10k.xlsx")


options(na.action = "na.fail") #prevent fitting models to different datasets

RSG <- gam(Presence ~ Date * ID + s(SPL3) + s(Fish) + s(Anthropogenic) + te(Gdepth, Sal) + te(Gdepth, Temp) + s(Depth) + s(CurrentS) + s(CurrentH) + s(Distance) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSG)

RSGA <- dredge(RSG)

# Write the result to an Excel file
write.xlsx(RSGA, "RSGA.xlsx")

resamp$DateNumeric <- as.numeric(resamp$Date)
RSGT <- gam(Presence ~ te(DateNumeric, ID) + s(SPL3) + s(Fish) + s(Anthropogenic) + s(Sal) + te(Gdepth, Temp) + s(Depth) + s(CurrentS) + s(CurrentH) + s(Distance) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGT)

RSGA2 <- dredge(RSGT)

# Write the result to an Excel file
write.xlsx(RSGA2, "RSGT.xlsx")

RSGT <- gam(Presence ~ te(DateNumeric, ID) + s(SPL3) + s(Fish) + s(Anthropogenic) + s(Sal) + s(Temp) + s(Depth) + s(CurrentS) + s(CurrentH) + s(Distance) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGT)

RSGA2 <- dredge(RSGT)

# Write the result to an Excel file
write.xlsx(RSGA2, "RSGTest.xlsx")


resamp$DateNumeric <- as.numeric(resamp$Date)
RSGTNS <- gam(Presence ~ te(DateNumeric, ID) + s(Sal) + s(Temp) + s(Depth) + s(CurrentS) + s(CurrentH) + s(Distance) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGTNS)

RSGANS <- dredge(RSGTNS)

# Write the result to an Excel file
write.xlsx(RSGANS, "RSGTNStest.xlsx")




#satellite models

RSS <- gam(Presence ~ Date * ID + s(SatSal) + s(SST) + s(Depth) + s(SatSpeed) + s(SatHeading) + s(Distance) + s(Satchla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSS)

RSSA <- dredge(RSS)

# Write the result to an Excel file
write.xlsx(RSSA, "RSSA.xlsx")

resampsat$DateNumeric <- as.numeric(resampsat$Date)
RSST <- gam(Presence ~ te(DateNumeric, ID) + s(SatSal) + s(SST) + s(Depth) + s(SatSpeed) + s(SatHeading) + s(Distance) + s(Satchla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSST)

RSSA2 <- dredge(RSST)

# Write the result to an Excel file
write.xlsx(RSSA2, "RSST.xlsx")


##Top three glider
RSGT1 <- gam(Presence ~ te(DateNumeric, ID) + s(SPL3) + s(Temp) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGT1)
AICc(RSGT1)
plot(RSGT1, scale = 0)

RSGT2 <- gam(Presence ~ te(DateNumeric, ID) + s(SPL3) + s(Temp) + s(CurrentS) +s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGT2)
AICc(RSGT2)

RSGT3 <- gam(Presence ~ te(DateNumeric, ID) + s(SPL3) + s(Temp) + s(Depth) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGT3)
AICc(RSGT3)

##Top three sat
resampsat$DateNumeric <- as.numeric(resampsat$Date)
RSST1 <- gam(Presence ~ te(DateNumeric, ID) + s(SatSpeed) + s(SatHeading) + s(Satchla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSST1)
AICc(RSST1)
plot(RSST1, scheme=2, scale = 0)
plot(RSST1, scale = 0)

RSST2 <- gam(Presence ~ s(SatSal) + s(SST) + s(Depth) + s(SatSpeed) + s(SatHeading) + s(Satchla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSST2)
AICc(RSST2)

RSST3 <- gam(Presence ~ te(DateNumeric, ID) + s(SatSpeed) + s(SatHeading) + s(Satchla) + s(SST), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSST3)
AICc(RSST3)

#top three no sound
resamp$DateNumeric <- as.numeric(resamp$Date)
RSGTNS1 <- gam(Presence ~ te(DateNumeric, ID) + s(Temp) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGTNS1)
AICc(RSGTNS1)

RSGTNS2 <- gam(Presence ~ te(DateNumeric, ID) + s(Temp) + s(Depth) + s(CurrentS) + s(CurrentH) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGTNS2)
AICc(RSGTNS2)

RSGTNS3 <- gam(Presence ~ te(DateNumeric, ID) + s(Temp) + s(CurrentS) + s(Chla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGTNS3)
AICc(RSGTNS3)


RSGT1 <- gam(Presence ~ te(DateNumeric, ID) + s(Depth) + s(SST) + s(SatSpeed) + s(Satchla), family = Tweedie(p = 1.1, link = power(0)), data = resamp, method = "REML")
summary(RSGT1)
AICc(RSGT1)
plot(RSGT1, shade = T, scale = 0)