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iso_ta200.R
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iso_ta200.R
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library(ggplot2)
library(lubridate)
library(reshape)
library(gridExtra)
library(RColorBrewer)
col <- rev(brewer.pal(8, "Spectral"))
col.2 <- rev(brewer.pal(8, "YlGnBu"))
# set working directory
wd <- setwd("C:/Users/IOtte/Documents/Desktop/training/")
### load data
iso <- read.csv2("iso_calc.csv", header = T)
ta200 <- read.csv("C:/Users/IOtte/Documents/Desktop/plot_air_temperatur/iso_ta200_monthly.csv", header = TRUE)
#wd.sv <- read.csv2("C:/Users/IOtte/Desktop/unpack/wd/sav0_week.csv", header = TRUE)
wd.sv <- read.csv("C:/Users/IOtte/Desktop/sav0_wd.csv", header = TRUE)
# format wd data
#wd.sv.d <- wd.sv.d[, -2]
#wd.sv.d$datetime <- substr(wd.sv.d$datetime, 1, 10)
#wd.sv.d$datetime <- as.Date(wd.sv.d$datetime)
wd.sv$datetime <- substr(wd.sv$datetime, 1, 10)
wd.sv$datetime <- as.Date(wd.sv$datetime)
## Sort temperature data
ta200 <- melt(ta200)
colnames(ta200) <- c("plotID", "date", "ta200")
ta200$year <- substr(ta200$date, 26,29)
ta200$mon <- substr(ta200$date, 31,32)
ta200 <- ta200[, -2]
ta200$date <- paste(ta200$year, ta200$mon, sep = "-")
ta200 <- ta200[, -3]
ta200 <- ta200[, -3]
## Aggregate iso plot data to monthly mean values
# build monthly mean values of d18-16, dD_H & dexcess
iso.mns <- aggregate(cbind(iso$d18_16, iso$dD_H, iso$d.excess),
by = list(substr(iso$date_sample, 1, 7),
iso[, 4], iso[, 5], iso[, 6]),
FUN = "mean", na.rm = TRUE)
colnames(iso.mns) <- c("date", "plotID", "type", "elevation","d18_16", "dD_H", "dexcess")
# build monthly sums of amount_mm
amnt.smm <- aggregate(iso$amount_mm,
by = list(substr(iso$date_sample, 1, 7),
iso[, 4], iso[, 5], iso[, 6]),
FUN = "sum", na.rm = TRUE)
colnames(amnt.smm) <- c("date", "plotID", "type", "elevation", "amount")
# merge monthly mean of d18-16 & dD_H and monthly sums of amount_mm
iso.mnth <- merge(iso.mns, amnt.smm)
## Merge iso.mns and ta200 to iso.ta200
iso.ta200 <- merge(iso.mnth, ta200)
## subsetting for better facility of instruction
rain <- subset(iso.ta200, iso.ta200$type == "rain")
tf <- subset(iso, iso$type == "tf")
fog <- subset(iso, iso$type == "fog")
sav5 <- subset(rain, rain$plotID == "sav5")
hom4 <- subset(rain, rain$plotID == "hom4")
nkw1 <- subset(rain, rain$plotID == "nkw1")
flm1 <- subset(rain, rain$plotID == "flm1")
foc6 <- subset(rain, rain$plotID == "foc6")
foc0 <- subset(rain, rain$plotID == "foc0")
fpo0 <- subset(rain, rain$plotID == "fpo0")
fpd0 <- subset(rain, rain$plotID == "fpd0")
fer0 <- subset(rain, rain$plotID == "fer0")
nkw1.cor <- cor(nkw1$d18_16, nkw1$amount_mm, method = "pearson", use = "complete.obs")
fer0.cor <- cor(fer0$d18_16, fer0$dexcess, method = "spearman", use = "complete.obs")
fpd0.cor <- cor(fpd0$d18_16, fpd0$dexcess, method = "spearman", use = "complete.obs")
fpo0.cor <- cor(fpo0$d18_16, fpo0$dexcess, method = "spearman", use = "complete.obs")
foc0.cor <- cor(foc0$d18_16, foc0$dexcess, method = "spearman", use = "complete.obs")
foc6.cor <- cor(foc6$d18_16, foc6$dexcess, method = "spearman", use = "complete.obs")
flm1.cor <- cor(flm1$d18_16, flm1$dexcess, method = "spearman", use = "complete.obs")
hom4.cor <- cor(hom4$d18_16, hom4$dexcess, method = "spearman", use = "complete.obs")
sav5.cor <- cor(sav5$d18_16, sav5$dexcess, method = "spearman", use = "complete.obs")
fer0.cor <- cor(fer0$d18_16, fer0$amount, method = "spearman", use = "complete.obs")
fpd0.cor <- cor(fpd0$d18_16, fpd0$amount, method = "spearman", use = "complete.obs")
fpo0.cor <- cor(fpo0$d18_16, fpo0$amount, method = "spearman", use = "complete.obs")
foc0.cor <- cor(foc0$d18_16, foc0$amount, method = "spearman", use = "complete.obs")
foc6.cor <- cor(foc6$d18_16, foc6$amount, method = "spearman", use = "complete.obs")
flm1.cor <- cor(flm1$d18_16, flm1$amount, method = "spearman", use = "complete.obs")
hom4.cor <- cor(hom4$d18_16, hom4$amount, method = "spearman", use = "complete.obs")
sav5.cor <- cor(sav5$d18_16, sav5$amount, method = "spearman", use = "complete.obs")
fer0.cor <- cor(fer0$d18_16, fer0$ta200, method = "spearman", use = "complete.obs")
fpd0.cor <- cor(fpd0$d18_16, fpd0$ta200, method = "spearman", use = "complete.obs")
fpo0.cor <- cor(fpo0$d18_16, fpo0$ta200, method = "spearman", use = "complete.obs")
foc0.cor <- cor(foc0$d18_16, foc0$ta200, method = "spearman", use = "complete.obs")
foc6.cor <- cor(foc6$d18_16, foc6$ta200, method = "spearman", use = "complete.obs")
flm1.cor <- cor(flm1$d18_16, flm1$ta200, method = "spearman", use = "complete.obs")
hom4.cor <- cor(hom4$d18_16, hom4$ta200, method = "spearman", use = "complete.obs")
sav5.cor <- cor(sav5$d18_16, sav5$ta200, method = "spearman", use = "complete.obs")
iso.all.lmwl.gmwl <- qplot(d18_16, dexcess, data = sav5) +
scale_x_reverse()
iso.sm <- summary(lm(rev(dexcess ~ d18_16), data = sav5))
#type <- lapply(types, function(i){
# sub <- subset(iso, iso$type == i)
#})
### build plot for presentation
### each plot seperately
col.id.rn <- c("#3288bd", "#66c2a5", "#abdda4", "#e6f598", "#fee08b", "#fdae61",
"#f46d43", "#d53e4f")
leg.rn <- c("fer0", "fpd0", "fpo0", "foc0", "foc6", "flm1", "hom4", "sav5")
col.id.fg <- c("#3288bd", "#66c2a5", "#abdda4", "#e6f598", "#fee08b", "#fdae61",
"#f46d43")
leg.fg <- c("fer0", "fpd0", "fpo0", "foc0", "foc6", "flm1", "nkw1")
## d18O
iso.d18 <- ggplot(subset(iso.ta200, iso.ta200[, 3] == "fog"),
aes(x = date, y = d18_16, group = plotID,
colour = plotID)) +
geom_line() +
scale_color_manual(values = col, limits = leg.fg, name = "Plot ID SP1") +
ylab( expression(fog ~ delta^{18}*O ~ "\u2030")) +
xlab("") +
scale_x_discrete(labels = c("11", "12", "01", "02", "03", "04", "05", "06",
"07", "08", "09", "10", "11", "12", "01", "02",
"03", "04", "05", "06", "07", "08", "09", "10",
"11")) +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(color = "gray", fill = NA),
legend.position = "none")
## dexcess
iso.dexcess <- ggplot(subset(iso.ta200, iso.ta200[, 3] == "fog"),
aes(x = date, y = dexcess, group = plotID,
colour = plotID)) +
geom_line() +
scale_color_manual(values = col, limits = leg.fg, name = "Plot ID SP1") +
ylab( expression(fog ~ dexcess ~ "\u2030")) +
xlab("") +
scale_y_reverse() +
scale_x_discrete(labels = c("11", "12", "01", "02", "03", "04", "05", "06",
"07", "08", "09", "10", "11", "12", "01", "02",
"03", "04", "05", "06", "07", "08", "09", "10",
"11")) +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(color = "gray", fill = NA),
legend.position = "none")
## temperature
iso.ta.200 <- ggplot(subset(iso.ta200, iso.ta200[, 3] == "rain"),
aes(x = date, y = ta200, group = plotID,
colour = plotID)) +
geom_line() +
scale_color_manual(values = col, limits = leg.rn, name = "Plot ID SP1") +
ylab("ta200 [??C]") +
xlab("") +
scale_x_discrete(labels = c("11", "12", "01", "02", "03", "04", "05", "06",
"07", "08", "09", "10", "11", "12", "01", "02",
"03", "04", "05", "06", "07", "08", "09", "10",
"11")) +
theme(
panel.grid.major = element_line(color = "lightgray", size = 0.01),
panel.background = element_rect(fill = NA),
panel.border = element_rect(color = "gray", fill = NA),
legend.position = "none")
## amount
amount.pl <- ggplot(subset(iso.ta200, iso.ta200[, 3] == "fog"),
aes(x = date, y = amount, group = plotID,
colour = plotID)) +
geom_line() +
scale_color_manual(values = col, limits = leg.fg, name = "Plot ID SP1") +
ylab("fog [mm]") +
xlab("") +
scale_x_discrete(labels = c("11", "12", "01", "02", "03", "04", "05", "06",
"07", "08", "09", "10", "11", "12", "01", "02",
"03", "04", "05", "06", "07", "08", "09", "10",
"11")) +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(color = "gray", fill = NA),
legend.position = "bottom")
## wind direction
wd.pl <- ggplot(wd.sv.d, aes(x = datetime, y = WD)) +
# , group = plotID,
# colour = plotID)) +
geom_point() +
scale_color_manual(values = col) + #, limits = leg.fg, name = "Plot ID SP1") +
ylab("wind direction [degree]") +
xlab("") +
scale_y_discrete(breaks = seq(0, 360, 90)) +
theme(
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(color = "gray", fill = NA))
# legend.position = "bottom")
## afterwards merging
d18.dex.amn.wd.fg <- arrangeGrob(iso.d18, iso.dexcess, amount.pl, wd.pl,
heights = c(2/9, 2/9, 3/9, 2/9),
ncol = 1)
# print "iso.mns.mnth.amnt.18O"
png("out/iso_d18_dex_amn_wd_fg.png", width = 30, height = 22, units = "cm",
res = 300, pointsize = 15)
print(d18.dex.amn.wd.fg)
dev.off()