diff --git a/graphes/SA_daily_gs_FULL.jpeg b/graphes/SA_daily_gs_FULL.jpeg
index 96481e3677d691f9b9dc707f2100b91134caaa7b..e604a99ba527efc4463a651a8c4b301a0bf744f7 100644
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diff --git a/graphes/SA_ecos_radiation_components.jpeg b/graphes/SA_ecos_radiation_components.jpeg
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diff --git a/graphes/figure_Ts_to_gs.jpeg b/graphes/figure_Ts_to_gs.jpeg
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diff --git a/graphes/figure_diff_VPD.jpeg b/graphes/figure_diff_VPD.jpeg
index 4a1509eb52ed248e40d0723f2a93692b64ee4aad..eea54b160ad06268a6d69815f3f439aa94428dea 100644
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diff --git a/scripts/fig_diff_VPD.R b/scripts/fig_diff_VPD.R
index 7c946aa9fd6f1ec2122ee4ad728bde26744b6fa6..b42a6d7800d27f13abf3dc74f5d19aa6dd884638 100644
--- a/scripts/fig_diff_VPD.R
+++ b/scripts/fig_diff_VPD.R
@@ -91,7 +91,8 @@ tib_diff_VPD %>%
#limits = date(ymd(c("2020-07-15","2020-09-01"))),
sec.axis = sec_axis(trans = ~.,
breaks = tick_dates),
- expand = c(0.002,0.003))+scale_y_discrete("time (hh:mm)", breaks = function(x){x[c(TRUE,rep(F,times=5))]})-> p3
+ expand = c(0.002,0.003))+
+ scale_y_discrete("Time (UT+1)", labels = str_pad(seq(0,21,by =3),side = "left",width = "2",pad = "0"),breaks = function(x){x[c(TRUE,rep(F,times=5))]})-> p3
#######################################
plot_grid(p1, p2, p3+theme(legend.position = "none"), get_legend(p3),
ncol=1, align="hv",axis = "tblr", rel_heights = c(0.4,0.4,0.4,0.1)) %>%
diff --git a/scripts/figure_SA_energy_storage.R b/scripts/figure_SA_energy_storage.R
index 818f7dcc00a9d25d7f1bde2b04577838a4e37d57..b03a1d22ad9f6af2eadd0906d7f27a9eb195e903 100644
--- a/scripts/figure_SA_energy_storage.R
+++ b/scripts/figure_SA_energy_storage.R
@@ -43,7 +43,7 @@ library(InraeThemes)
legend.key.size = unit(c(2,2),"mm"), axis.ticks.length = unit(-1,"mm"), axis.ticks = element_line(size = .2), axis.line = element_line("black",size=0),
legend.direction = "vertical", legend.spacing = unit(1,"mm"), legend.position = c(0.825,0.88), legend.background = element_blank(),
panel.background = element_rect(colour = "black"))+
- labs(fill = "radiative component"),NA,
+ labs(fill = "radiative component"), NA,
Storage_ecosystem %>%
pivot_longer(-c(TIMESTAMP, S)) %>%
@@ -53,10 +53,10 @@ library(InraeThemes)
ggplot() +
geom_col(aes(TIMESTAMP, value, fill = name), size = .2)+
geom_text(aes(x = day + dhours(to_add), label = label),y = 70, data = dates_Denis %>% mutate(label = LETTERS[6:10], to_add = rep(1,each = 5)),size = 3)+
- scale_x_datetime(date_breaks = "4 hours", date_labels = "%H", expand = c(0.05,0.01))+
+ scale_x_datetime("Time (UT+1)",date_breaks = "4 hours", date_labels = "%H", expand = c(0.05,0.01))+
scale_y_continuous(expression(W~m^-2),expand = c(0.02,0.01),breaks = c(-3:3*20) )+
scale_fill_manual("Storage terms", values = RColorBrewer::brewer.pal(5,"Set2") , guide = guide_legend(direction = "vertical",title.position = "top", title.hjust = 0))+
- theme(axis.title.x = element_blank(), plot.margin = unit(c(1,1,0,1),"mm"), text = element_text(size=6), axis.text = element_text(size = 6),legend.text.align = .5,
+ theme(axis.title.x = element_text(size = 6), plot.margin = unit(c(1,1,0,1),"mm"), text = element_text(size=6), axis.text = element_text(size = 6),legend.text.align = .5,
strip.background = element_blank(), strip.text = element_blank(),
legend.key.size = unit(c(2,2),"mm"), axis.ticks.length = unit(-1,"mm"), axis.ticks = element_line(size = .2), axis.line = element_line("black",size=0),
legend.spacing = unit(1,"mm"), legend.position = c(0.825,0.165), legend.background = element_blank(),
diff --git a/scripts/figure_Ts_to_gs.R b/scripts/figure_Ts_to_gs.R
index 28fcb48370ff740e8bbb12c8b22a61b33a95b46b..16aeddf4f2accb51b0a01454fc24dfdbb436a892 100644
--- a/scripts/figure_Ts_to_gs.R
+++ b/scripts/figure_Ts_to_gs.R
@@ -123,7 +123,6 @@ rbind(tib_env_var$donnee[[1]] %>%
data = fig_segments %>% filter(variable == var)) +
geom_text(aes(x=xtext,y=ytext, label = LETTER), inherit.aes = F, data = panel, size = textsize/1.5) +
geom_line() + geom_point() +
- scale_x_datetime(date_breaks = "2 hours", date_labels = "%H", expand = c(0.01,0.01))+
themeP+
theme(text = element_text(size = axis_textsize*1.8),
legend.title = element_blank(),
@@ -150,6 +149,16 @@ rbind(tib_env_var$donnee[[1]] %>%
}else{
scale_y_continuous(name = ytitle, labels =function(x) format(x, scientific = TRUE) )}
} +
+ {if(var !="gc"){
+ scale_x_datetime(date_breaks = "2 hours", date_labels = "%H", expand = c(0.01,0.01))
+ }else{
+ scale_x_datetime("Time (UT+1)",date_breaks = "2 hours", date_labels = "%H", expand = c(0.01,0.01))}
+ } +
+ {if(var !="gc"){
+ theme()
+ }else{
+ theme(axis.title.x = element_text(size = axis_textsize*1.5))}
+ } +
# colours
{if(var !="gc"){
scale_colour_manual(var,values = c("crown" = palette_gs[1], "canopy" = palette_gs[2]), label = labels)
diff --git a/scripts/figure_daily_gs.R b/scripts/figure_daily_gs.R
index e90991c288a04fe701b3ab4cfa477b81bdf9e6cb..9e40dca017bc4fe399a95693fec7733d37ccdb40 100644
--- a/scripts/figure_daily_gs.R
+++ b/scripts/figure_daily_gs.R
@@ -10,17 +10,21 @@ if (sys.nframe() == 0) {# must be run manually if this is the file on which we a
source(file.path("scripts","general_variables.R"))
################################################################################
#### daily gs (sapflux methods only) under different env conditions ####
- {gc_compa %>%
- mutate(day=date(TIMESTAMP)) %>%
- filter(day %in% ymd(dates_kept$day)) %>%
- left_join(dates_kept, by ="day") %>%
- filter(day !=ymd("2020-08-19")) %>%
- filter(between(hour(TIMESTAMP),6,23)) %>%
- mutate(gc = ifelse(gc <0,0,gc)) %>%
- filter(TIMESTAMP != ymd_hm("2020-07-07 23:00") | method != "PMT") %>%
- filter(method !="PMEC") %>%
- group_by(method,day) %>%
- mutate(gc_mean = mean(gc, na.rm =T)) %>%
+gc_prep <- gc_compa %>%
+ mutate(day=date(TIMESTAMP)) %>%
+ filter(day %in% ymd(dates_kept$day)) %>%
+ left_join(dates_kept %>%
+ mutate(REW_f2=fct_recode(REW_f,"2~\u2265~REW" = "low", "10~\u2265~REW~\u2265~2" = "medium", "REW~\u2265~10" = "high")) %>%
+ mutate(VPD_f2=fct_recode(VPD_f,"D \u2264 2" = "low", "2 \u2264 D <3" = "medium", "D \u2264 3.5" = "high")), by ="day") %>%
+ filter(day !=ymd("2020-08-19")) %>%
+ filter(between(hour(TIMESTAMP),6,23)) %>%
+ mutate(gc = ifelse(gc <0, 0, gc)) %>%
+ filter(TIMESTAMP != ymd_hm("2020-07-07 23:00") | method != "PMT") %>%
+ group_by(method,day) %>%
+ mutate(gc_mean = mean(gc, na.rm =T))
+
+{ gc_prep %>%
+ filter(method !="PMEC") %>%
filter(gc < 3*gc_mean) %>%
group_by(VPD_f) %>%
mutate(gc_max = max(gc, na.rm = T)) %>%
@@ -31,13 +35,14 @@ if (sys.nframe() == 0) {# must be run manually if this is the file on which we a
REW_f = fct_relabel(REW_f,~paste(.,"~REW",sep=""))) %>%
mutate(condition = sprintf("atop(%s,%s)",VPD_f,REW_f)) %>%
mutate(xtext = ymd_hm(ifelse(day == ymd("2020-07-05"),"2020-01-01 19:00","2020-01-01 23:30"))) %>%
- ggplot(aes(TIMESTAMP2, gc,linetype = method, colour = method))+
- geom_line(na.rm = T) + geom_point(size = 0.3, na.rm = T) +
- geom_text(aes(label = letter, y = gc_max*.95 ), x = ymd_hm("2020-01-01 06:15"),
- size = textsize/2.5, inherit.aes = F, hjust = 0) +
- geom_text(aes(label = condition, y = gc_max*.90, x = xtext),
- size = textsize/3, inherit.aes = F, hjust = 1, parse = T) +
- facet_grid(VPD_f~REW_f, scales="free_y", switch = "y")+
+ ggplot(aes(TIMESTAMP2, gc,shape = method, colour = method, size = method))+
+ # geom_line(na.rm = T) +
+ geom_point(na.rm = T) +
+ # geom_text(aes(label = letter, y = gc_max*.95 ), x = ymd_hm("2020-01-01 06:15"),
+ # size = textsize/2.5, inherit.aes = F, hjust = 0) +
+ # geom_text(aes(label = condition, y = gc_max*.90, x = xtext),
+ # size = textsize/3, inherit.aes = F, hjust = 1, parse = T) +
+ facet_grid(VPD_f2~REW_f2, scales="free_y", drop = T)+
theme(axis.line = element_line("black",size=0),
legend.position=c(0.10,0.17),
legend.text = element_text(size = textsize*1.5, hjust = 0),
@@ -63,92 +68,94 @@ if (sys.nframe() == 0) {# must be run manually if this is the file on which we a
#axis.title.y = element_blank(),
axis.title.y.right = element_blank(),
strip.placement = "outside",
- #strip.text = element_text(size = textsize), # back to before
- strip.text = element_blank(),
+ strip.text = element_text(size = textsize*1.1), # back to before
+ #strip.text = element_blank(),
strip.background = element_rect(colour =NA,fill=NA)) +
#labs(colour = parse(text="g[s]~method"), linetype = parse(text="g[s]~method") )+
- scale_colour_manual(name = expression(g[s]~ method),
- values = c("GT" = palette_gs[2],"GT'" = palette_gs[1],"PMT"= palette_gs[3]),
+ scale_colour_manual(name = expression(g[s]~ method),
+ values = c("GT" = palette_gs[2],"GT'" = palette_gs[1],"PMT"= palette_gs[3]),
+ labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")])))+
+ scale_linetype_manual(name = expression(g[s]~ method),
+ limits = c("GT","GT'","PMT"),values = c("solid","dashed","dotdash"),
labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")])))+
- scale_linetype_manual(name = expression(g[s]~ method),
- limits = c("GT","GT'","PMT"),values = c("solid","dashed","dotdash"),
- labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")])))+
- scale_x_datetime("Time (UT+1)", date_breaks = "3 hours", date_labels = "%HH", date_minor_breaks = "1 hour")+
- scale_y_continuous(parse(text="canopy~conductance~(m.s^-1)"),labels = fmt_dcimals(2),
- sec.axis = dup_axis()) } %>%
-
- ggsave2("graphes/figure_daily_gs.jpeg",.,
- width = 190, height = 120, units = "mm", bg = "white", dpi = 1000)
- ################################################################################
- {gc_compa %>%
- mutate(day=date(TIMESTAMP)) %>%
- filter(day %in% ymd(dates_kept$day)) %>%
- left_join(dates_kept, by ="day") %>%
- filter(day !=ymd("2020-08-19")) %>%
- filter(between(hour(TIMESTAMP),6,23)) %>%
- mutate(gc = ifelse(gc <0,0,gc)) %>%
- filter(TIMESTAMP != ymd_hm("2020-07-07 23:00") | method != "PMT") %>%
- group_by(method,day) %>%
- mutate(gc_mean = mean(gc, na.rm =T)) %>%
- filter(gc < 5*gc_mean) %>%
- group_by(VPD_f) %>%
- mutate(gc_max = max(gc, na.rm = T)) %>%
- select(-gc_mean) %>%
- filter(letter != "G") %>% # remove this one cause it's after August
- mutate(TIMESTAMP2 = ymd("2020-01-01")+dminutes(minute(TIMESTAMP))+dhours(hour(TIMESTAMP))) %>%
- mutate(VPD_f = fct_relabel(VPD_f,~paste(.,"~D[8]",sep="")),
- REW_f = fct_relabel(REW_f,~paste(.,"~REW",sep=""))) %>%
- mutate(condition = sprintf("atop(%s,%s)",VPD_f,REW_f)) %>%
- mutate(stresslevel = ifelse(letter =="A","least stress:",ifelse(letter == "I","maximal stress:",NA))) %>%
- mutate(xtext = ymd_hm(ifelse(day %in% ymd("2020-07-16","2020-07-30"),"2020-01-01 19:30","2020-01-01 23:30"))) %>%
- ggplot(aes(TIMESTAMP2, gc,linetype = method, colour = method))+
- geom_line(na.rm = T) + geom_point(size = 0.3, na.rm = T) +
- geom_text(aes(label = letter, y = gc_max*.95 ), x = ymd_hm("2020-01-01 06:15"),
- size = textsize/2.5, inherit.aes = F, hjust = 0) +
- geom_text(aes(label = condition, y = gc_max*.90, x = xtext),
- size = textsize/3, inherit.aes = F, hjust = 1, parse = T) +
- geom_text(aes(label = stresslevel, y =gc_max*.90, x=xtext - dhours(5)), size = textsize/3,inherit.aes = F, hjust = 1)+
- facet_grid(VPD_f~REW_f, scales="free_y", switch = "y")+
- theme(axis.line = element_line("black",size=0),
- legend.position=c(0.10,0.17),
- legend.text = element_text(size = textsize*1.5, hjust = 0),
- legend.title = element_text(size = textsize*1.5, hjust = .5),
- legend.key.height = unit(3,"mm"),
- legend.key = element_rect(fill = NA),
- legend.background = element_rect(fill = NA),
-
- panel.border = element_rect(colour="black", fill=NA, size=1),
- panel.background = element_rect(fill = NA),
-
- axis.ticks = element_line(size = .3),
- axis.ticks.length = unit(-.15, units = "cm"),
-
- axis.title = element_text(size = textsize),
- axis.title.x.bottom = element_blank(),
- axis.text.x = element_text(size =textsize , vjust = -1),
- axis.text.x.top = element_blank(),
- axis.ticks.x.top = element_blank(),
-
- axis.text.y = element_text(size = textsize, hjust = - 0.5),
- axis.text.y.right = element_blank(),
- #axis.title.y = element_blank(),
- axis.title.y.right = element_blank(),
- strip.placement = "outside",
- #strip.text = element_text(size = textsize), # back to before
- strip.text = element_blank(),
- strip.background = element_rect(colour =NA,fill=NA)) +
- scale_colour_manual(name = expression(g[s]~ method),
- values = c("GT" = palette_gs[2],"GT'" = palette_gs[1],"PMT"= palette_gs[3], "PMEC" = "dark grey"),
+ scale_shape_manual(name = expression(g[s]~ method),
+ limits = c("GT","GT'","PMT"),values = c(1,16,2),
+ labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")])))+
+ scale_size_manual(name = expression(g[s]~ method),
+ limits = c("GT","GT'","PMT"),values = c(0.3,0.5,0.3),
+ labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")])))+
+ scale_x_datetime("Time (UT+1)", date_breaks = "3 hours", date_labels = "%H", date_minor_breaks = "1 hour")+
+ scale_y_continuous(parse(text="canopy~conductance~(m.s^-1)"),labels = fmt_dcimals(2),
+ sec.axis = dup_axis()) } %>%
+
+ ggsave2("graphes/figure_daily_gs.jpeg",.,
+ width = 190, height = 120, units = "mm", bg = "white", dpi = 1000)
+################################################################################
+{gc_prep %>%
+ filter(gc < 3*gc_mean) %>%
+ group_by(VPD_f) %>%
+ mutate(gc_max = max(gc, na.rm = T)) %>%
+ select(-gc_mean) %>%
+ filter(letter != "G") %>% # remove this one cause it's after August
+ mutate(TIMESTAMP2 = ymd("2020-01-01")+dminutes(minute(TIMESTAMP))+dhours(hour(TIMESTAMP))) %>%
+ mutate(VPD_f = fct_relabel(VPD_f,~paste(.,"~D[8]",sep="")),
+ REW_f = fct_relabel(REW_f,~paste(.,"~REW",sep=""))) %>%
+ mutate(condition = sprintf("atop(%s,%s)",VPD_f,REW_f)) %>%
+ mutate(xtext = ymd_hm(ifelse(day == ymd("2020-07-05"),"2020-01-01 19:00","2020-01-01 23:30"))) %>%
+ ggplot(aes(TIMESTAMP2, gc,shape = method, colour = method, size = method))+
+ # geom_line(na.rm = T) +
+ geom_point(na.rm = T) +
+ # geom_text(aes(label = letter, y = gc_max*.95 ), x = ymd_hm("2020-01-01 06:15"),
+ # size = textsize/2.5, inherit.aes = F, hjust = 0) +
+ # geom_text(aes(label = condition, y = gc_max*.90, x = xtext),
+ # size = textsize/3, inherit.aes = F, hjust = 1, parse = T) +
+ facet_grid(VPD_f2~REW_f2, scales="free_y", drop = T)+
+ theme(axis.line = element_line("black",size=0),
+ legend.position=c(0.10,0.17),
+ legend.text = element_text(size = textsize*1.5, hjust = 0),
+ legend.title = element_text(size = textsize*1.5, hjust = .5),
+ legend.key.height = unit(3,"mm"),
+ legend.key = element_rect(fill = NA),
+ legend.background = element_rect(fill = NA),
+
+ panel.border = element_rect(colour="black", fill=NA, size=1),
+ panel.background = element_rect(fill = NA),
+
+ axis.ticks = element_line(size = .3),
+ axis.ticks.length = unit(-.15, units = "cm"),
+
+ axis.title = element_text(size = textsize*1.1),
+ axis.title.x.bottom = element_text(size = textsize*1.1, vjust = 0),
+ axis.text.x = element_text(size =textsize , vjust = -1),
+ axis.text.x.top = element_blank(),
+ axis.ticks.x.top = element_blank(),
+
+ axis.text.y = element_text(size = textsize, hjust = - 0.5),
+ axis.text.y.right = element_blank(),
+ #axis.title.y = element_blank(),
+ axis.title.y.right = element_blank(),
+ strip.placement = "outside",
+ strip.text = element_text(size = textsize*1.1), # back to before
+ #strip.text = element_blank(),
+ strip.background = element_rect(colour =NA,fill=NA)) +
+ scale_colour_manual(name = expression(g[s]~ method),
+ values = c("GT" = palette_gs[2],"GT'" = palette_gs[1],"PMT"= palette_gs[3], "PMEC" = "dark grey"),
+ labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")]),expression(g[paste("s",",PMEC")])))+
+ scale_linetype_manual(name = expression(g[s]~ method),
+ limits = c("GT","GT'","PMT","PMEC"),values = c("solid","dashed","dotdash","twodash"),
labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")]),expression(g[paste("s",",PMEC")])))+
- scale_linetype_manual(name = expression(g[s]~ method),
- limits = c("GT","GT'","PMT","PMEC"),values = c("solid","dashed","dotdash","twodash"),
- labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")]),expression(g[paste("s",",PMEC")])))+
- scale_x_datetime( date_breaks = "3 hours", date_labels = "%HH", date_minor_breaks = "1 hour")+
- scale_y_continuous(parse(text="canopy~conductance~(m.s^-1)"),labels = fmt_dcimals(2),
- sec.axis = dup_axis())} %>%
-
- ggsave2("graphes/SA_daily_gs_FULL.jpeg",.,
- width = 190, height = 120, units = "mm", bg = "white", dpi = 1000)
+ scale_shape_manual(name = expression(g[s]~ method),
+ limits = c("GT","GT'","PMT","PMEC"),values = c(1,16,2,2),
+ labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")]),expression(g[paste("s",",PMEC")])))+
+ scale_size_manual(name = expression(g[s]~ method),
+ limits = c("GT","GT'","PMT","PMEC"),values = c(0.3,0.5,0.3,0.3),
+ labels = c(expression(g[paste("s",",GT")]),expression(g[paste("s",",GT'")]),expression(g[paste("s",",PMT")]),expression(g[paste("s",",PMEC")])))+
+ scale_x_datetime("Time (UT+1)", date_breaks = "3 hours", date_labels = "%H", date_minor_breaks = "1 hour")+
+ scale_y_continuous(parse(text="canopy~conductance~(m.s^-1)"),labels = fmt_dcimals(2),
+ sec.axis = dup_axis())} %>%
+
+ ggsave2("graphes/SA_daily_gs_FULL.jpeg",.,
+ width = 190, height = 120, units = "mm", bg = "white", dpi = 1000)
################################################################################
}