pdf(paste(paste("./Final_R/Output/PP/Figures/Residuals/Contrib", paste(s,t, sep="_"), sep="/"), "pdf", sep="."))
par(mfrow=c(2,3))
plot(res, which=seq(1,6,1))
par(mfrow=c(1,1))
dev.off()
res2
pre<-predict(res, df2)
prediction = data.frame(predict = pre,
p_value=res2$coefficients[8],
Year = unique(df2$Year),
Station = s,
Taxa = t)%>%
rbind(prediction)
#################
}
}
contrib %>% write.table("./Final_R/Output/PP/Data/Contrib.txt", sep=";", dec=".")
setwd("/Users/kinlan/OneDrive - Stockholm University/PhD/TimeseRies/Final_R/Output/")
zp1<- read.delim("./ZP/Data/Peak_Excluding_Nauplii_zooplankton.txt", sep=";")
str(zp1)
library(dplyr)
library(tidyr)
zp1<- zp1%>%
select(Year, Taxa, Station, Timing)
pp1<- read.delim("./PP/Data/Magnitude_phyto.txt", sep=";")
str(pp1)
View(pp1)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))
View(pp1)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))%>%
select(Taxa, Year, Station, magnitude)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))%>%
mutate(Taxa = paste(as.character(Taxa), "Magnitude", sep="_"))%>%
select(Taxa, Year, Station, magnitude)%>%
spread(Year, magnitude)
pp1<- read.delim("./PP/Data/Magnitude_phyto.txt", sep=";")
str(pp1)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))%>%
mutate(Taxa = paste(as.character(Taxa), "Magnitude", sep="_"))%>%
select(Taxa, Year, Station, magnitude)%>%
spread(Year, magnitude)
View(pp1)
pp1<- read.delim("./PP/Data/Magnitude_phyto.txt", sep=";")
str(pp1)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))%>%
mutate(Taxa = paste(as.character(Taxa), "Magnitude", sep="_"))%>%
select(Taxa, Year, Station, magnitude)%>%
spread(Taxa, magnitude)
df_1<- merge(pp1, zp1, by = c("Year", "Station"))
View(df_1)
pp2<- read.delim("./PP/Data/Timing_phyto.txt", sep=";")
View(pp2)
pp2%>%str
pp2<- pp2%>%
select(Year, Taxa2, Station, Timing)%>%
mutate(Taxa = paste(Taxa2, "Timing", sep="_"))%>%
spread(Taxa, Timing)
pp2<- read.delim("./PP/Data/Timing_phyto.txt", sep=";")
pp2<- pp2%>%
select(Year, Taxa2, Station, Timing)%>%
mutate(Taxa2 = paste(Taxa2, "Timing", sep="_"))%>%
spread(Taxa2, Timing)
View(pp2)
df_2<- merge(df_1, pp2, by=c("Year", "Station"))
View(df_2)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))%>%
mutate(Taxa = paste(as.character(Taxa), "Magnitude", sep="_"))%>%
select(Taxa, Year, Station, magnitude)%>%
spread(Taxa, magnitude)
df_1<- merge( zp1,pp1, by = c("Year", "Station"))
pp2<- read.delim("./PP/Data/Timing_phyto.txt", sep=";")
zp1<- zp1%>%
select(Year, Taxa, Station, Timing)
pp1<- read.delim("./PP/Data/Magnitude_phyto.txt", sep=";")
str(pp1)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))%>%
mutate(Taxa = paste(as.character(Taxa), "Magnitude", sep="_"))%>%
select(Taxa, Year, Station, magnitude)%>%
spread(Taxa, magnitude)
df_1<- merge( zp1,pp1, by = c("Year", "Station"))
pp2<- read.delim("./PP/Data/Timing_phyto.txt", sep=";")
pp2<- pp2%>%
select(Year, Taxa2, Station, Timing)%>%
mutate(Taxa2 = paste(Taxa2, "Timing", sep="_"))%>%
spread(Taxa2, Timing)
df_2<- merge(df_1, pp2, by=c("Year", "Station"))
View(df_2)
zp2<- read.delim("./ZP/Data/Duration_Excluding_Nauplii_zooplankton.txt", sep=";")
View(zp2)
zp2%>%str
df_3<- zp2%>%
select(Taxa, Year, Station, D25, D75, Dur)%>%
merge(df_2, by=c("Year", "Station"))
View(df_3)
df_3<- zp2%>%
select(Taxa, Year, Station, D25, D75, Dur)%>%
merge(df_2, by=c("Year", "Station", "Taxa"))
View(df_3)
df_3%>%write.table("./Combined.txt", sep=";")
df_3%>%str
Temora <- df_3%>%filter(Taxa=="Temora")
Temora%>%str
mod <- gam(Timing ~ s(D25, by = Station) + s(Spring_bloom_Magnitude, by=Station) + s(Spring_bloom_Timing, by= Station) +
Station, data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station) + s(Spring_bloom_Timing, by= Station) +
Station, data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station) + s(Spring_bloom_Timing, by= Station) +
Station, data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by= Station, k=3) +
Station, data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by= Station, k=3) , data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,# by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#
by=Station,
k=3) + s(Spring_bloom_Timing,#
by= Station,
k=3) , data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude#                      by=Station,
) + s(Spring_bloom_Timing),# by= Station,k=3) ,
data=Temora, method="REML")
plot(mod, pages=1)
Temora <- df_3%>%filter(Taxa=="Temora", Station=="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude#                      by=Station,
) + s(Spring_bloom_Timing),# by= Station,k=3) ,
data=Temora, method="REML")
Temora <- df_3%>%filter(Taxa=="Temora", Station =="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1)
plot(mod, pages=1, residuals = T)
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=5) + s(Spring_bloom_Timing,# by= Station,
k=5) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=10) + s(Spring_bloom_Timing,# by= Station,
k=10) , data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=5) + s(Spring_bloom_Timing,# by= Station,
k=5) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Temora", Station =="BY5")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=5) + s(Spring_bloom_Timing,# by= Station,
k=5) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
Temora <- df_3%>%filter(Taxa=="Temora", Station =="BY5")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=5) + s(Spring_bloom_Timing,# by= Station,
k=5) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
View(df_3)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=5) + s(Spring_bloom_Timing,# by= Station,
k=5) + s(D25, k=5) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=5) + s(Spring_bloom_Timing,# by= Station,
k=5) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Acartia", Station =="BY5")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=5) + s(Spring_bloom_Timing,# by= Station,
k=5) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Acartia", Station =="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
unique(df_3$Taxa)
Temora <- df_3%>%filter(Taxa=="Synchaeta", Station =="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Synchaeta", Station =="BY5")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Centropages", Station =="BY5")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Centropages", Station =="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
pp1<- read.delim("./PP/Data/Magnitude_phyto.txt", sep=";")
str(pp1)
pp1 <- pp1%>%mutate(Taxa = ifelse(Taxa == "Total" & Season == "Summer bloom", "Summer_bloom", ifelse(Taxa == "Total" & Season == "Spring bloom", "Spring_bloom", as.character(Taxa))))%>%
mutate(Taxa = paste(as.character(Taxa), "Magnitude", sep="_"),
magnitude = log(magnitude))%>%
select(Taxa, Year, Station, magnitude)%>%
spread(Taxa, magnitude)
df_1<- merge( zp1,pp1, by = c("Year", "Station"))
pp2<- read.delim("./PP/Data/Timing_phyto.txt", sep=";")
pp2<- pp2%>%
select(Year, Taxa2, Station, Timing)%>%
mutate(Taxa2 = paste(Taxa2, "Timing", sep="_"))%>%
spread(Taxa2, Timing)
df_2<- merge(df_1, pp2, by=c("Year", "Station"))
zp2<- read.delim("./ZP/Data/Duration_Excluding_Nauplii_zooplankton.txt", sep=";")
zp2%>%str
df_3<- zp2%>%
select(Taxa, Year, Station, D25, D75, Dur)%>%
merge(df_2, by=c("Year", "Station", "Taxa"))
df_3%>%write.table("./Combined.txt", sep=";")
df3<-df_3
unique(df_3$Taxa)
Temora <- df_3%>%filter(Taxa=="Centropages", Station =="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Centropages", Station =="BY5")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Temora", Station =="BY5")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
Temora <- df_3%>%filter(Taxa=="Temora", Station =="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,#                      by=Station,
k=3) + s(Spring_bloom_Timing,# by= Station,
k=3) , data=Temora, method="REML")
plot(mod, pages=1, residuals = T, pch=1)
summary(mod)
abiotic <- read.delim("./Physical/Data/Abiotic.txt", sep=";")
View(abiotic)
str(abiotic)
abiotic<-abiotic%>%
mutate(Parameter=paste(Parameter, Group, sep="_"))%>%filter(Group == "Mar-May")%>%
select(Year2, Parameter, Station, Value)
abiotic%>%str
names(abiotic)<- c("Year", "Parameter", "Station", "Value")
abiotic<- abiotic %>%spread(Parameter, Value)
df_4 <- merge(df_3, abiotic, by=c("Station", "Year"))
View(df_4)
df_4%>%write.table("./Combined.txt", sep=";")
zp2<- read.delim("./ZP/Data/Duration_Excluding_Nauplii_zooplankton.txt", sep=";")
zp2%>%str
df_4%>%str
Temora <- df_3%>%filter(Taxa=="Temora", Station =="BY31")
Temora%>%str
Temora <- df_4%>%filter(Taxa=="Temora", Station =="BY31")
Temora%>%str
abiotic<-abiotic%>%filter(Group == "Mar-May")%>%
select(Year2, Parameter, Station, Value)
abiotic%>%str
names(abiotic)<- c("Year", "Parameter", "Station", "Value")
abiotic<- abiotic %>%spread(Parameter, Value)
df_4 <- merge(df_3, abiotic, by=c("Station", "Year"))
df_4%>%write.table("./Combined.txt", sep=";")
df_4%>%str
unique(df_3$Taxa)
Temora <- df_4%>%filter(Taxa=="Temora", Station =="BY31")
Temora%>%str
abiotic <- read.delim("./Physical/Data/Abiotic.txt", sep=";")
str(abiotic)
abiotic<-abiotic%>%filter(Group == "Mar-May")%>%
select(Year2, Parameter, Station, Value)
abiotic%>%str
names(abiotic)<- c("Year", "Parameter", "Station", "Value")
abiotic<- abiotic %>%spread(Parameter, Value)
df_4 <- merge(df_3, abiotic, by=c("Station", "Year"))
df_4%>%write.table("./Combined.txt", sep=";")
df_4%>%str
unique(df_3$Taxa)
Temora <- df_4%>%filter(Taxa=="Temora", Station =="BY31")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) , data=Temora, method="REML")
plot(mod, residuals = T, pch=1, cex=1)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3) , data=Temora, method="REML")
plot(mod, residuals = T, pch=1, cex=1)
plot(mod, residuals = T, pch=1, cex=1)
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1)
plot(mod, residuals = T, pch=1, cex=1, shade = T)
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
summary(mod)
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3) + s(Total.Nitrogen.Tot.N, k=3), data=Temora, method="REML")
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3) + s(Total.phosphorus.Tot.P, k=3), data=Temora, method="REML")
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3), data=Temora, method="REML")
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
summary(mod)
Temora <- df_4%>%filter(Taxa=="Temora")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,by=Station k=3) + s(Spring_bloom_Timing,by=Station k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3), data=Temora, method="REML")
Temora <- df_4%>%filter(Taxa=="Temora")
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude,by=Station, k=3) + s(Spring_bloom_Timing,by=Station, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3), data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude k=3) + s(Spring_bloom_Timing k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3)+ Station, data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
plot(mod, residuals = T, pch=1, cex=1, shade = T)
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3)+ Station, data=Temora, method="REML")
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, by=Station) + s(Temperature.CTD, k=3) + s(SST, k=3)+ Station, data=Temora, method="REML")
# https://noamross.github.io/gams-in-r-course
# Chapter 1 ------
mcycle <- MASS::mcycle
head(mcycle)
plot(mcycle)
lm_mod <- lm(accel~times, data=mcycle)
termplot(lm_mod)
plot(lm_mod, residuals=T)
library(mgcv)
gam_mod <- gam(accel ~ s(times), data = mcycle)
plot(gam_mod, residuals = TRUE, pch = 1)
gam_mod_k3 <- gam(accel ~s(times, k=3), data=mcycle)
gam_mod_k20 <- gam(accel ~s(times, k=20), data=mcycle)
par(mfrow=c(1,2))
plot(gam_mod_k3, residuals= T, pch=1)
plot(gam_mod_k20, residuals=T, pch=1)
#Extract the smoothing parameter
gam_mod <- gam(accel ~s(times), data=mcycle, method="REML")
gam_mod$sp
gam_mod_s1 <- gam(accel ~s(times), data=mcycle, sp=0.1)
gam_mod_s2 <- gam(accel ~s(times), data=mcycle, sp=0.0001)
par(mfrow=c(1,2))
plot(gam_mod_s1, residuals = T, pch=1)
plot(gam_mod_s2, residuals=T, pch=1)
gam_mod_sk <- gam(accel ~s(times, k=50), data=mcycle, sp=0.0001)
par(mfrow=c(1,1))
plot(gam_mod_sk, residuals=T, pch=1)
library(gamair)
data("mpg", package = "gamair")
head(mpg)
plot(mpg)
# fit the model
mod_city <- gam(city.mpg ~ s(weight) + s(length) + s(price), data=mpg, method="REML")
plot(mod_city, pages = 1)
# fit the model
mod_city2 <- gam(city.mpg ~ s(weight) + s(length) + s(price) +
fuel + drive + style
, data=mpg, method="REML")
plot(mod_city2, pages = 1, all.terms = T)
mod_city3 <- gam(city.mpg ~ s(weight, by = drive) + s(length, by=drive) + s(price, by= drive) +
drive, data=mpg, method="REML")
head(mpg)
plot(mpg)
str(mpg)
Temora <- df_4%>%filter(Taxa=="Temora")%>%
mutate(Station = factor(Station, levels=c("BY31", "BY5")))
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, by=Station) + s(Temperature.CTD, k=3) + s(SST, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(3,2))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
par(mfrow=c(3,3))
plot(mod, residuals = T, pch=1, cex=1, shade = T)
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
par(mfrow=c(3,3))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, k=3) + s(Spring_bloom_Timing, k=3) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, k=3) + s(SST, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(3,3))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by=Station, k=3) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(3,3))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=5) + s(Spring_bloom_Timing, by=Station, k=5) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by=Station, k=3) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = T, all.terms = T)
summary(mod)
plot(mod, residuals = T, pch=1, cex=1, shade = T)
summary(mod)
plot(mod, residuals = T, pch=1, cex=1, shade = F)
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = F)
Temora <- df_4%>%filter(Taxa=="Acartia")%>%
mutate(Station = factor(Station, levels=c("BY31", "BY5")))
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by=Station, k=3) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = F)
summary(mod)
Temora <- df_4%>%filter(Taxa=="Centropages")%>%
mutate(Station = factor(Station, levels=c("BY31", "BY5")))
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by=Station, k=3) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = F)
summary(mod)
Temora <- df_4%>%filter(Taxa=="Pseudocalanus")%>%
mutate(Station = factor(Station, levels=c("BY31", "BY5")))
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by=Station, k=3) + s(Salinity.CTD, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = F)
summary(mod)
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by=Station, k=3) + s(Salinity.CTD, by=Station, k=3)+ s(Salinity_60m, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = F)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Summer_bloom_Timing, by=Station, k=3) + s(Salinity.CTD, by=Station, k=3)+ s(Salinity_60m, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = F)
summary(mod)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Summer_bloom_Timing, by=Station, k=3) #+ s(Salinity.CTD, by=Station, k=3)+ s(Salinity_60m, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)
+ Station, data=Temora, method="REML")
par(mfrow=c(5,3))
plot(mod, residuals = T, pch=1, cex=1, shade = F)
par(mfrow=c(3,3))
plot(mod, residuals = T,all.terms = T, pch=1, cex=1, shade = F)
summary(mod)
Temora <- df_4%>%filter(Taxa=="Temora")%>%
mutate(Station = factor(Station, levels=c("BY31", "BY5")))
Temora%>%str
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Summer_bloom_Timing, by=Station, k=3) #+ s(Salinity.CTD, by=Station, k=3)+ s(Salinity_60m, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)
+ Station, data=Temora, method="REML")
par(mfrow=c(3,3))
plot(mod, residuals = T,all.terms = T, pch=1, cex=1, shade = F)
mod <- gam(Timing ~ s(Spring_bloom_Magnitude, by=Station, k=3) + s(Spring_bloom_Timing, by=Station, k=3)+
s(Summer_bloom_Magnitude, by=Station, k=3) + s(Summer_bloom_Timing, by=Station, k=3)#+ s(Salinity.CTD, by=Station, k=3)+ s(Salinity_60m, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)
+ Station, data=Temora, method="REML")
par(mfrow=c(3,3))
plot(mod, residuals = T,all.terms = T, pch=1, cex=1, shade = F)
summary(mod)
mod <- gam(Timing ~ #s(Spring_bloom_Magnitude, by=Station, k=3) +
s(Spring_bloom_Timing, by=Station, k=3)+
#  s(Summer_bloom_Magnitude, by=Station, k=3)
+ s(Summer_bloom_Timing, by=Station, k=3)#+ s(Salinity.CTD, by=Station, k=3)+ s(Salinity_60m, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)
+ Station, data=Temora, method="REML")
par(mfrow=c(3,3))
plot(mod, residuals = T,all.terms = T, pch=1, cex=1, shade = F)
summary(mod)
Temora <- df_4%>%filter(Taxa=="Acartia")%>%
mutate(Station = factor(Station, levels=c("BY31", "BY5")))
Temora%>%str
mod <- gam(Timing ~ #s(Spring_bloom_Magnitude, by=Station, k=3) +
s(Spring_bloom_Timing, by=Station, k=3)+
#  s(Summer_bloom_Magnitude, by=Station, k=3)
+ s(Summer_bloom_Timing, by=Station, k=3)#+ s(Salinity.CTD, by=Station, k=3)+ s(Salinity_60m, by=Station, k=3) + s(Temperature.CTD, by=Station, k=3) + s(SST, by=Station, k=3)
+ Station, data=Temora, method="REML")
par(mfrow=c(3,3))
plot(mod, residuals = T,all.terms = T, pch=1, cex=1, shade = F)
summary(mod)
