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@SaraVarela
SaraVarela committed Jul 16, 2019
1 parent 84d66fc commit c65f735
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Showing 2 changed files with 53 additions and 32 deletions.
29 changes: 19 additions & 10 deletions leer_climas_paleoclim.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ setwd("C:\\Users\\sara.varela\\Documents\\CIENCIAS\\mariana_araucaria")
costa<- readShapePoly ("ne_10m_land.shp")

# load paleoclim layers
setwd ("C:\\Users\\sara.varela\\Documents\\CIENCIAS\\mariana_araucaria\\paleoclim_org")
carpetas<- list.files ()
i<- 8
for (i in 1:8){
Expand Down Expand Up @@ -56,7 +57,7 @@ datos<- datos [complete.cases(datos), ]
summary (datos)

# set percentile to drop out
x1<- 0.07
x1<- 0.01

min_t<- quantile (datos$bio_1, x1)
max_t<- quantile (datos$bio_1, 1-x1)
Expand Down Expand Up @@ -102,48 +103,56 @@ eval(parse(text=foo))

# build raw figure

tiff ("lala.tif", width = 500, height = 1000, units = "px")
tiff ("PaleoClim_envelope.tif", width = 500, height = 1000, units = "px")
par (mfrow=c(2,4))
plot (map_1, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="present", xlim=c(-55, -30), ylim=c(-45, 0))
main="present", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
plot (araucaria, add=T)
points (coord2)

plot (map_2, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="0.3-4.2 kybp", xlim=c(-55, -30), ylim=c(-45, 0))
main="0.3-4.2 kybp", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
points (polen [polen$X0.3_4.2 ==1,2:3 ])

plot (map_3, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="4.2-8.3 kybp", xlim=c(-55, -30), ylim=c(-45, 0))
main="4.2-8.3 kybp", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
points (polen [polen$X4.2_8.3 ==1, 2:3 ])

plot (map_4, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="8.3-11.7 kybp", xlim=c(-55, -30), ylim=c(-45, 0))
main="8.3-11.7 kybp", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
points (polen [polen$X8.3_11.7 ==1,2:3 ])

plot (map_5, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="11.7-12.9 kybp", xlim=c(-55, -30), ylim=c(-45, 0))
main="11.7-12.9 kybp", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
points (polen [polen$X11.7_12.9 ==1, 2:3 ])

plot (map_6, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="12.9-14.7 kybp", xlim=c(-55, -30), ylim=c(-45, 0))
main="12.9-14.7 kybp", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
points (polen [polen$X12.9_14.7 ==1, 2:3 ])

plot (map_7, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="14.7-17 kybp", xlim=c(-55, -30), ylim=c(-45, 0))
main="14.7-17 kybp", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
points (polen [polen$X14.7_17 ==1, 2:3 ])

plot (map_8, col=c("#00000000","#00006090"), legend=F, axes=F, box=F,
main="LGM", xlim=c(-55, -30), ylim=c(-45, 0))
main="LGM", xlim=c(-55, -30), ylim=c(-45, -20))
plot (wrld_simpl, add=T)
points (polen [polen$lgm ==1, 2:3 ])

dev.off()

stabi<- (map_1 + map_2 + map_3 + map_4 + map_5 + map_6 + map_7 + map_8)

pdf ("stability_paleoclim.pdf")
plot (stabi)
plot (araucaria, add=T)
points (coord2)
plot (wrld_simpl, add=T)
dev.off()
56 changes: 34 additions & 22 deletions leer_ecoclimate_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ map_holocene<- CCSMpres[[1]]$bio.1*0
map_lgmaximum<- CCSMpres[[1]]$bio.1*0
sta<- 0
areas_res<- NULL

res_maps<- list ()
x<- 1
for (i in 1:7){
nicho_pres<- as.data.frame (extract (lala[[x]], coord))
Expand All @@ -103,7 +103,7 @@ for (i in 1:7){

datos<- datos [complete.cases(datos), ]
# set percentile to be drop out
x1<- 0.02
x1<- 0.01

min_t<- quantile (datos$bio.1, x1)
max_t<- quantile (datos$bio.1, 1-x1)
Expand Down Expand Up @@ -135,11 +135,9 @@ for (i in 1:7){
map_pres_precipmin<- reclassify (lala[[x]]$bio.16, c(-Inf, min_pmin, 0, min_pmin, max_pmin, 1, max_pmin, +Inf, 0))
map_ts<- reclassify (lala[[x]]$bio.4, c(-Inf, min_ts, 0, min_ts, max_ts, 1, max_ts, +Inf, 0))

map1<- map_pres * map_pres_tmin * map_pres_tmax * map_ts *
map_pres_precip * map_pres_precipmax * map_pres_precipmin
map1<- map_pres * map_pres_tmin * map_pres_tmax * map_ts * map_pres_precip * map_pres_precipmax * map_pres_precipmin
map1<- mask (map1, costa)


map_pres<- reclassify (lala[[x+1]]$bio.1, c(-Inf, min_t, 0, min_t, max_t, 1, max_t, +Inf, 0))
map_pres_tmin<- reclassify (lala[[x+1]]$bio.11, c(-Inf, min_tmin, 0, min_tmin, max_tmin, 1, max_tmin, +Inf, 0))
map_pres_tmax<- reclassify (lala[[x+1]]$bio.10, c(-Inf, min_tmax, 0, min_tmax, max_tmax, 1, max_tmax, +Inf, 0))
Expand All @@ -148,13 +146,11 @@ for (i in 1:7){
map_pres_precipmin<- reclassify (lala[[x+1]]$bio.16, c(-Inf, min_pmin, 0, min_pmin, max_pmin, 1, max_pmin, +Inf, 0))
map_ts<- reclassify (lala[[x]]$bio.4, c(-Inf, min_ts, 0, min_ts, max_ts, 1, max_ts, +Inf, 0))


map2<- map_pres * map_pres_tmin * map_pres_tmax * map_ts *
map_pres_precip * map_pres_precipmax * map_pres_precipmin

map2<- mask (map2, costa)


map_pres<- reclassify (lala[[x+2]]$bio.1, c(-Inf, min_t, 0, min_t, max_t, 1, max_t, +Inf, 0))
map_pres_tmin<- reclassify (lala[[x+2]]$bio.11, c(-Inf, min_tmin, 0, min_tmin, max_tmin, 1, max_tmin, +Inf, 0))
map_pres_tmax<- reclassify (lala[[x+2]]$bio.10, c(-Inf, min_tmax, 0, min_tmax, max_tmax, 1, max_tmax, +Inf, 0))
Expand All @@ -168,7 +164,8 @@ for (i in 1:7){
map3<- mask (map3, costa)

stab<- map1*map2*map3

stab2<- map1+map2+map3
res_maps [[i]]<- stab2
todo_1_0<- extract (stab, coord)
matri_1_0<- extract (stab, coord2)
big_area_1_0<- extract (stab, araucaria) [[1]]
Expand Down Expand Up @@ -245,8 +242,17 @@ for (i in 1:7){
}




## the other figures
pdf ("stab_ecoclimate.pdf")
par (mfrow =c(2,4))
for (i in 1:7){
plot (res_maps [[1]], ylim=c(-45, -10), axes=F, box=F,
legend=F, main=modelos [i])
plot (araucaria, add=T)
points (coord2)
plot (wrld_simpl, add=T)
}
dev.off()

alt2<- resample (alt, map1, method="bilinear")
alt_pres<- data.frame (alt= extract (alt2, coord), time= 0)
Expand All @@ -262,9 +268,6 @@ boxplot (alt_datos$alt ~alt_datos$time,
axis (1, labels=c("present", "Mid-Holocene", "LGM"), at=c(1,2,3))
axis(2)

summary (alt_pres)
summary (alt_glm)

pdf("alt_tiempo.pdf")
par (mfrow=c(1,3))
plot (alt2, zlim=c(0, 1500), xlim=c(-65, 30),
Expand All @@ -288,43 +291,52 @@ axis(2)

dev.off()


setwd ("C:\\Users\\sara.varela\\Documents\\CIENCIAS\\mariana_araucaria")
# ensemble
pdf("alt_tiempo.pdf")

pdf("ensemble.pdf")
par (mfrow=c(1,3), mar=c(0,0,5,0))
plot (map_lgmaximum, xlim=c(-65, 30),
ylim=c(-40, 5), axes=F, box=F,
main="LGM distribution", legend=F, zlim=c(4,7))
main="LGM distribution", legend=F, zlim=c(2,7))
points (coord_glm, col="#00006090", pch=16)
plot (wrld_simpl, add=T)
plot (map_holocene, xlim=c(-65, 30),
ylim=c(-40, 5), axes=F, box=F,
main="Holocene distribution", legend=F, zlim=c(4,7))
main="Holocene distribution", legend=F, zlim=c(2,7))
points (coord_hol, col="#00006090", pch=16)
plot (wrld_simpl, add=T)
plot (map_presente, xlim=c(-65, 30),
ylim=c(-40, 5), axes=F, box=F,
main="present distribution", zlim=c(4,7))
main="present distribution", zlim=c(2,7))
plot (araucaria, add=T)
points (coord2)
plot (wrld_simpl, add=T)
dev.off()


pdf("stability.pdf")
palette (colorRampPalette(c("red", "blue"))(7))
plot (wrld_simpl, xlim=c(-60, -30),
ylim=c(-40, -20), main="stable populations (blue)")
points (coord, col=sta, pch=16)
dev.off()

nombres<- rep (modelos, 3)

library (ggplot2)
a<- data.frame (area=as.vector (t(areas_res)), time=c(23,6,0))
variable<- nombres [order (rep (modelos, 3))]
length (variable)
dim (a)
a<- data.frame (area=as.vector (t(areas_res)), time=c(23,6,0), variable)


areas_plot<- ggplot(a, aes(x=time,y=area)) + geom_smooth(color="#00006090") + geom_point (color="#00006090")
pdf("area.pdf")
plot (areas_plot)
dev.off()
sta<- sta + coord3$stable
areas_res<- rbind (areas, areas_res)


pdf("area_modelos.pdf")
ggplot(a, aes(x=time,y=area)) + geom_line(aes(colour=variable))
dev.off()

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