photofinish = photofinish,
daylengthstart = daylengthstart,
daylengthfinish = daylengthfinish,
photodirs=photodirs,
photodirf=photodirf,
soilnode = 3)
yearout<-as.data.frame(ecto$yearout)
yearsout<-as.data.frame(ecto$yearsout)
environ<-as.data.frame(ecto$environ)
debout<-as.data.frame(ecto$debout)
metout<-as.data.frame(ecto$metout)
enbal<- as.data.frame(ecto$enbal)
masbal <- as.data.frame(ecto$masbal)
ndays<- max(masbal$DAY)
par(mfrow = c(1,1))
plot(seq(1, ndays * 24) / 24, debout$WETMASS, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'pink', lwd = 2,
ylim = c(0, max(debout$WETMASS)))
points(seq(1, ndays * 24) / 24, debout$V, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'dark green', lwd = 2)
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD, type = 'l',
lwd = 2, col = 'brown')
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD-debout$WETGUT,
type = 'l', lwd = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hb)[1]], lty = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hp)[1]], lty = 2, col = 'grey')
legend(4000, max(debout$WETMASS) * 0.3,
c('repro. buffer', 'food in gut', 'reserve', 'structure'), lty = rep(1, 4),
col = c("pink", "brown", "grey", "dark green"), bty = 'n')
text(0, max(debout$WETMASS) * 1, labels = "embryo", cex = 0.85)
text((which(debout$E_H > E.Hp)[1] - which(debout$E_H > E.Hp)[1] * .5) / 24 ,
max(debout$WETMASS) * 1, labels = "immature", cex = 0.85)
text(which(debout$E_H > E.Hp)[1] * 1.2 / 24, max(debout$WETMASS) * 1,
labels = "adult", cex = 0.85)
yearout
yearsout
max(yearsout$MaxLen)
max(yearsout$MaxWgt)
#save(micro, file='../Results/microNCEP/micro_ncep_Bilpa_sint.RData')
load('Results/microNCEP/micro_ncep_Iski_sint.RData')
ecto<-ectotherm(DEB=1,
startday = startday,
viviparous=viviparous,
clutchsize = clutchsize,
clutch_ab = clutch_ab,
minclutch = minclutch,
maxclutch = maxclutch,
batch = batch,
z.mult=z.mult,
shape=shape,
alpha_max=alpha_max,
alpha_min=alpha_min,
T_F_min=T_F_min,
T_F_max=T_F_max,
T_B_min=T_B_min,
T_RB_min=T_RB_min,
T_pref=T_pref,
CT_max=CT_max,
CT_min=CT_min,
diurn=diurn,
nocturn=nocturn,
crepus=crepus,
shade_seek=shade_seek,
burrow=burrow,
climb=climb,
mindepth=mindepth,
maxdepth=maxdepth,
pct_wet=pct_wet,
z=z*z.mult,
del_M=del.M,
p_Xm=p.Xm,
kap_X=kap.X,
v=v/24,
kap=kap,
p_M=p.M/24,
E_G=E.G,
kap_R=kap.R,
k_J=k.J/24,
E_Hb=E.Hb*z.mult^3,
E_Hj=E.Hj*z.mult^3,
E_Hp=E.Hp*z.mult^3,
E_He=E.He*z.mult^3,
h_a=h.a/(24^2),
s_G=s.G,
T_REF=T.ref,
T_A=T.A,
T_AL=T.AL,
T_AH=T.AH,
T_L=T.L,
T_H=T.H,
E_0=E.0*z.mult^4,
f=f,
d_V=d.V,
d_E=d.E,
d_Egg=d.E,
mu_X=mu.X,
mu_E=mu.E,
mu_V=mu.V,
mu_P=mu.P,
kap_X_P=kap.P,
n_X=c(n.CX,n.HX,n.OX,n.ON),
n_E=c(n.CE,n.HE,n.OE,n.OE),
n_V=c(n.CV,n.HV,n.OV,n.OV),
n_P=c(n.CP,n.HP,n.OP,n.OP),
n_M_nitro=c(n.NC,n.NH,n.NO,n.NN),
L_b=L.b,
V_init=V_init,
E_init=E_init,
E_H_init=E_H_init,
stage=stage,
photostart = photostart,
photofinish = photofinish,
daylengthstart = daylengthstart,
daylengthfinish = daylengthfinish,
photodirs=photodirs,
photodirf=photodirf,
soilnode = 3)
yearout<-as.data.frame(ecto$yearout)
yearsout<-as.data.frame(ecto$yearsout)
environ<-as.data.frame(ecto$environ)
debout<-as.data.frame(ecto$debout)
metout<-as.data.frame(ecto$metout)
enbal<- as.data.frame(ecto$enbal)
masbal <- as.data.frame(ecto$masbal)
ndays<- max(masbal$DAY)
par(mfrow = c(1,1))
plot(seq(1, ndays * 24) / 24, debout$WETMASS, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'pink', lwd = 2,
ylim = c(0, max(debout$WETMASS)))
points(seq(1, ndays * 24) / 24, debout$V, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'dark green', lwd = 2)
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD, type = 'l',
lwd = 2, col = 'brown')
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD-debout$WETGUT,
type = 'l', lwd = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hb)[1]], lty = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hp)[1]], lty = 2, col = 'grey')
legend(4000, max(debout$WETMASS) * 0.3,
c('repro. buffer', 'food in gut', 'reserve', 'structure'), lty = rep(1, 4),
col = c("pink", "brown", "grey", "dark green"), bty = 'n')
text(0, max(debout$WETMASS) * 1, labels = "embryo", cex = 0.85)
text((which(debout$E_H > E.Hp)[1] - which(debout$E_H > E.Hp)[1] * .5) / 24 ,
max(debout$WETMASS) * 1, labels = "immature", cex = 0.85)
text(which(debout$E_H > E.Hp)[1] * 1.2 / 24, max(debout$WETMASS) * 1,
labels = "adult", cex = 0.85)
yearout
yearsout
max(yearsout$MaxLen)
max(yearsout$MaxWgt)
ecto<-ectotherm(DEB=1,
startday = startday,
viviparous=viviparous,
#clutchsize = clutchsize,
clutch_ab = clutch_ab,
minclutch = minclutch,
maxclutch = maxclutch,
batch = batch,
z.mult=z.mult,
shape=shape,
alpha_max=alpha_max,
alpha_min=alpha_min,
T_F_min=T_F_min,
T_F_max=T_F_max,
T_B_min=T_B_min,
T_RB_min=T_RB_min,
T_pref=T_pref,
CT_max=CT_max,
CT_min=CT_min,
diurn=diurn,
nocturn=nocturn,
crepus=crepus,
shade_seek=shade_seek,
burrow=burrow,
climb=climb,
mindepth=mindepth,
maxdepth=maxdepth,
pct_wet=pct_wet,
z=z*z.mult,
del_M=del.M,
p_Xm=p.Xm,
kap_X=kap.X,
v=v/24,
kap=kap,
p_M=p.M/24,
E_G=E.G,
kap_R=kap.R,
k_J=k.J/24,
E_Hb=E.Hb*z.mult^3,
E_Hj=E.Hj*z.mult^3,
E_Hp=E.Hp*z.mult^3,
E_He=E.He*z.mult^3,
h_a=h.a/(24^2),
s_G=s.G,
T_REF=T.ref,
T_A=T.A,
T_AL=T.AL,
T_AH=T.AH,
T_L=T.L,
T_H=T.H,
E_0=E.0*z.mult^4,
f=f,
d_V=d.V,
d_E=d.E,
d_Egg=d.E,
mu_X=mu.X,
mu_E=mu.E,
mu_V=mu.V,
mu_P=mu.P,
kap_X_P=kap.P,
n_X=c(n.CX,n.HX,n.OX,n.ON),
n_E=c(n.CE,n.HE,n.OE,n.OE),
n_V=c(n.CV,n.HV,n.OV,n.OV),
n_P=c(n.CP,n.HP,n.OP,n.OP),
n_M_nitro=c(n.NC,n.NH,n.NO,n.NN),
L_b=L.b,
V_init=V_init,
E_init=E_init,
E_H_init=E_H_init,
stage=stage,
photostart = photostart,
photofinish = photofinish,
daylengthstart = daylengthstart,
daylengthfinish = daylengthfinish,
photodirs=photodirs,
photodirf=photodirf,
soilnode = 3)
yearout<-as.data.frame(ecto$yearout)
yearsout<-as.data.frame(ecto$yearsout)
environ<-as.data.frame(ecto$environ)
debout<-as.data.frame(ecto$debout)
metout<-as.data.frame(ecto$metout)
enbal<- as.data.frame(ecto$enbal)
masbal <- as.data.frame(ecto$masbal)
ndays<- max(masbal$DAY)
par(mfrow = c(1,1))
plot(seq(1, ndays * 24) / 24, debout$WETMASS, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'pink', lwd = 2,
ylim = c(0, max(debout$WETMASS)))
points(seq(1, ndays * 24) / 24, debout$V, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'dark green', lwd = 2)
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD, type = 'l',
lwd = 2, col = 'brown')
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD-debout$WETGUT,
type = 'l', lwd = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hb)[1]], lty = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hp)[1]], lty = 2, col = 'grey')
legend(4000, max(debout$WETMASS) * 0.3,
c('repro. buffer', 'food in gut', 'reserve', 'structure'), lty = rep(1, 4),
col = c("pink", "brown", "grey", "dark green"), bty = 'n')
text(0, max(debout$WETMASS) * 1, labels = "embryo", cex = 0.85)
text((which(debout$E_H > E.Hp)[1] - which(debout$E_H > E.Hp)[1] * .5) / 24 ,
max(debout$WETMASS) * 1, labels = "immature", cex = 0.85)
text(which(debout$E_H > E.Hp)[1] * 1.2 / 24, max(debout$WETMASS) * 1,
labels = "adult", cex = 0.85)
yearout
yearsout
#save(micro, file='../Results/microNCEP/micro_ncep_Bilpa_sint.RData')
load('Results/microNCEP/micro_ncep_Bilpa_sint.RData')
ecto<-ectotherm(DEB=1,
startday = startday,
viviparous=viviparous,
#clutchsize = clutchsize,
clutch_ab = clutch_ab,
minclutch = minclutch,
maxclutch = maxclutch,
batch = batch,
z.mult=z.mult,
shape=shape,
alpha_max=alpha_max,
alpha_min=alpha_min,
T_F_min=T_F_min,
T_F_max=T_F_max,
T_B_min=T_B_min,
T_RB_min=T_RB_min,
T_pref=T_pref,
CT_max=CT_max,
CT_min=CT_min,
diurn=diurn,
nocturn=nocturn,
crepus=crepus,
shade_seek=shade_seek,
burrow=burrow,
climb=climb,
mindepth=mindepth,
maxdepth=maxdepth,
pct_wet=pct_wet,
z=z*z.mult,
del_M=del.M,
p_Xm=p.Xm,
kap_X=kap.X,
v=v/24,
kap=kap,
p_M=p.M/24,
E_G=E.G,
kap_R=kap.R,
k_J=k.J/24,
E_Hb=E.Hb*z.mult^3,
E_Hj=E.Hj*z.mult^3,
E_Hp=E.Hp*z.mult^3,
E_He=E.He*z.mult^3,
h_a=h.a/(24^2),
s_G=s.G,
T_REF=T.ref,
T_A=T.A,
T_AL=T.AL,
T_AH=T.AH,
T_L=T.L,
T_H=T.H,
E_0=E.0*z.mult^4,
f=f,
d_V=d.V,
d_E=d.E,
d_Egg=d.E,
mu_X=mu.X,
mu_E=mu.E,
mu_V=mu.V,
mu_P=mu.P,
kap_X_P=kap.P,
n_X=c(n.CX,n.HX,n.OX,n.ON),
n_E=c(n.CE,n.HE,n.OE,n.OE),
n_V=c(n.CV,n.HV,n.OV,n.OV),
n_P=c(n.CP,n.HP,n.OP,n.OP),
n_M_nitro=c(n.NC,n.NH,n.NO,n.NN),
L_b=L.b,
V_init=V_init,
E_init=E_init,
E_H_init=E_H_init,
stage=stage,
photostart = photostart,
photofinish = photofinish,
daylengthstart = daylengthstart,
daylengthfinish = daylengthfinish,
photodirs=photodirs,
photodirf=photodirf,
soilnode = 3)
yearout<-as.data.frame(ecto$yearout)
yearsout<-as.data.frame(ecto$yearsout)
environ<-as.data.frame(ecto$environ)
debout<-as.data.frame(ecto$debout)
metout<-as.data.frame(ecto$metout)
enbal<- as.data.frame(ecto$enbal)
masbal <- as.data.frame(ecto$masbal)
ndays<- max(masbal$DAY)
par(mfrow = c(1,1))
plot(seq(1, ndays * 24) / 24, debout$WETMASS, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'pink', lwd = 2,
ylim = c(0, max(debout$WETMASS)))
points(seq(1, ndays * 24) / 24, debout$V, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'dark green', lwd = 2)
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD, type = 'l',
lwd = 2, col = 'brown')
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD-debout$WETGUT,
type = 'l', lwd = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hb)[1]], lty = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hp)[1]], lty = 2, col = 'grey')
legend(4000, max(debout$WETMASS) * 0.3,
c('repro. buffer', 'food in gut', 'reserve', 'structure'), lty = rep(1, 4),
col = c("pink", "brown", "grey", "dark green"), bty = 'n')
text(0, max(debout$WETMASS) * 1, labels = "embryo", cex = 0.85)
text((which(debout$E_H > E.Hp)[1] - which(debout$E_H > E.Hp)[1] * .5) / 24 ,
max(debout$WETMASS) * 1, labels = "immature", cex = 0.85)
text(which(debout$E_H > E.Hp)[1] * 1.2 / 24, max(debout$WETMASS) * 1,
labels = "adult", cex = 0.85)
yearout
yearsout
max(yearsout$MaxLen)
max(yearsout$MaxWgt)
dates <- micro$dates
environ <- cbind(dates, environ)
environ_year <- environ[environ$YEAR==4,]
environ_year
# seasonal activity plot (dark blue = night, light blue = basking, orange = foraging)
forage <- subset(environ_year, ACT == 2)
bask <- subset(environ_year, ACT == 1)
night <- subset(metout, ZEN == 90)
day <- subset(metout, ZEN != 90)
with(night, plot(TIME / 60 ~ DOY, ylab = "Hour of Day", xlab = "Day of Year", pch = 15, cex = 2, col = 'dark blue'))
# nighttime hours
with(bask, points(TIME ~ DOY, pch = 15, cex = 2, col = 'light blue')) # basking Tbs
with(forage, points(TIME ~ DOY, pch = 15, cex = 2, col = 'orange')) # foraging Tbs
max(environ$TSUB)
min(environ$TSUB)
metout_micro <- as.data.frame(micro$metout)
plot(metout_micro$TALOC, type="l")
plot(environ$TA ~ environ$dates, type="l")
plot(environ$TC ~  environ$dates, type="l")
plot(environ_year$DAYLENGTH ~ environ_year$dates, type="l")
#save(micro, file='../Results/microNCEP/micro_ncep_Bilpa_sint.RData')
load('Results/microNCEP/micro_ncep_Unska_sint.RData')
ecto<-ectotherm(DEB=1,
startday = startday,
viviparous=viviparous,
#clutchsize = clutchsize,
clutch_ab = clutch_ab,
minclutch = minclutch,
maxclutch = maxclutch,
batch = batch,
z.mult=z.mult,
shape=shape,
alpha_max=alpha_max,
alpha_min=alpha_min,
T_F_min=T_F_min,
T_F_max=T_F_max,
T_B_min=T_B_min,
T_RB_min=T_RB_min,
T_pref=T_pref,
CT_max=CT_max,
CT_min=CT_min,
diurn=diurn,
nocturn=nocturn,
crepus=crepus,
shade_seek=shade_seek,
burrow=burrow,
climb=climb,
mindepth=mindepth,
maxdepth=maxdepth,
pct_wet=pct_wet,
z=z*z.mult,
del_M=del.M,
p_Xm=p.Xm,
kap_X=kap.X,
v=v/24,
kap=kap,
p_M=p.M/24,
E_G=E.G,
kap_R=kap.R,
k_J=k.J/24,
E_Hb=E.Hb*z.mult^3,
E_Hj=E.Hj*z.mult^3,
E_Hp=E.Hp*z.mult^3,
E_He=E.He*z.mult^3,
h_a=h.a/(24^2),
s_G=s.G,
T_REF=T.ref,
T_A=T.A,
T_AL=T.AL,
T_AH=T.AH,
T_L=T.L,
T_H=T.H,
E_0=E.0*z.mult^4,
f=f,
d_V=d.V,
d_E=d.E,
d_Egg=d.E,
mu_X=mu.X,
mu_E=mu.E,
mu_V=mu.V,
mu_P=mu.P,
kap_X_P=kap.P,
n_X=c(n.CX,n.HX,n.OX,n.ON),
n_E=c(n.CE,n.HE,n.OE,n.OE),
n_V=c(n.CV,n.HV,n.OV,n.OV),
n_P=c(n.CP,n.HP,n.OP,n.OP),
n_M_nitro=c(n.NC,n.NH,n.NO,n.NN),
L_b=L.b,
V_init=V_init,
E_init=E_init,
E_H_init=E_H_init,
stage=stage,
photostart = photostart,
photofinish = photofinish,
daylengthstart = daylengthstart,
daylengthfinish = daylengthfinish,
photodirs=photodirs,
photodirf=photodirf,
soilnode = 3)
yearout<-as.data.frame(ecto$yearout)
yearsout<-as.data.frame(ecto$yearsout)
environ<-as.data.frame(ecto$environ)
debout<-as.data.frame(ecto$debout)
metout<-as.data.frame(ecto$metout)
enbal<- as.data.frame(ecto$enbal)
masbal <- as.data.frame(ecto$masbal)
ndays<- max(masbal$DAY)
par(mfrow = c(1,1))
plot(seq(1, ndays * 24) / 24, debout$WETMASS, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'pink', lwd = 2,
ylim = c(0, max(debout$WETMASS)))
points(seq(1, ndays * 24) / 24, debout$V, type = 'l', xlab = 'date',
ylab = paste0('wet mass (g)'), col = 'dark green', lwd = 2)
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD, type = 'l',
lwd = 2, col = 'brown')
points(seq(1, ndays * 24) / 24, debout$WETMASS-debout$WETGONAD-debout$WETGUT,
type = 'l', lwd = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hb)[1]], lty = 2, col = 'grey')
abline(v = (seq(1, ndays * 24) / 24)[which(debout$E_H>E.Hp)[1]], lty = 2, col = 'grey')
legend(4000, max(debout$WETMASS) * 0.3,
c('repro. buffer', 'food in gut', 'reserve', 'structure'), lty = rep(1, 4),
col = c("pink", "brown", "grey", "dark green"), bty = 'n')
text(0, max(debout$WETMASS) * 1, labels = "embryo", cex = 0.85)
text((which(debout$E_H > E.Hp)[1] - which(debout$E_H > E.Hp)[1] * .5) / 24 ,
max(debout$WETMASS) * 1, labels = "immature", cex = 0.85)
text(which(debout$E_H > E.Hp)[1] * 1.2 / 24, max(debout$WETMASS) * 1,
labels = "adult", cex = 0.85)
yearout
yearsout
max(yearsout$MaxLen)
max(yearsout$MaxWgt)
dates <- micro$dates
environ <- cbind(dates, environ)
environ_year <- environ[environ$YEAR==4,]
environ_year
# seasonal activity plot (dark blue = night, light blue = basking, orange = foraging)
forage <- subset(environ_year, ACT == 2)
bask <- subset(environ_year, ACT == 1)
night <- subset(metout, ZEN == 90)
day <- subset(metout, ZEN != 90)
with(night, plot(TIME / 60 ~ DOY, ylab = "Hour of Day", xlab = "Day of Year", pch = 15, cex = 2, col = 'dark blue'))
# nighttime hours
with(bask, points(TIME ~ DOY, pch = 15, cex = 2, col = 'light blue')) # basking Tbs
with(forage, points(TIME ~ DOY, pch = 15, cex = 2, col = 'orange')) # foraging Tbs
plot(environ_year$DAYLENGTH ~ environ_year$dates, type="l")
