#----- reset your R session. ------------------------------------------
rm(list=ls())
graphics.off()
#----- load required packages -----------------------------------------
library(tidyverse)
library(ggplot2)
library(ggthemes)
library(gridExtra)
#----- source required functions --------------------------------------
source("R/circular_linear_plots.R")
#----------------------------------------------------------------------
#----------------------------------------------------------------------
#-------- Phenology data --------------------------------------------
#----------------------------------------------------------------------
data <- readRDS("data/jungle_rhythms_data_manuscript_leaf_repro.rds")
#----------------------------------------------------------------------
#----------------------------------------------------------------------
#--- get selected species DECIDUOUS label
#----------------------------------------------------------------------
overview <- read.csv("data/summ_species_pheno_characteristics.csv",
header = TRUE,
sep = ",",
stringsAsFactors = FALSE)
overview_dec <- overview %>%
filter(grepl("deciduous",deciduousness)) %>%
filter(site_years_with_phenophase > 0) %>%
arrange_at("species_full")
sp_dec <- unique(overview_dec$species_full)
# groups of 5 species (5 species per page in the supplementary info)
sp_dec1 <- paste(sp_dec[1:5],collapse = "|")
sp_dec2 <- paste(sp_dec[6:10],collapse = "|")
sp_dec3 <- paste(sp_dec[11:15],collapse = "|")
sp_dec4 <- paste(sp_dec[16:20],collapse = "|")
sp_dec5 <- paste(sp_dec[21:25],collapse = "|")
sp_dec6 <- paste(sp_dec[26:30],collapse = "|")
sp_dec7 <- paste(sp_dec[31:34],collapse = "|")
#------
# plots
#------
# sequence 1
plot_dec1 <- circular_linear_plot(data = data,
species_name = sp_dec1,
leg_gradient = c(0,0.3,1),
title_name = "(b) Deciduous")
pdf("~/Desktop/deciduous1.pdf",8.85,12.1)
plot(plot_dec1)
dev.off()
# sequence 2
plot_dec2 <- circular_linear_plot(data = data,
species_name = sp_dec2,
leg_gradient = c(0,0.3,1),
title_name = "(b) Deciduous - continued")
pdf("~/Desktop/deciduous2.pdf",8.85,12.1)
plot(plot_dec2)
dev.off()
# sequence 3
plot_dec3 <- circular_linear_plot(data = data,
species_name = sp_dec3,
leg_gradient = c(0,0.3,1),
title_name = "(b) Deciduous - continued")
pdf("~/Desktop/deciduous3.pdf",8.85,12.1)
plot(plot_dec3)
dev.off()
# sequence 4
plot_dec4 <- circular_linear_plot(data = data,
species_name = sp_dec4,
leg_gradient = c(0,0.3,1),
title_name = "(b) Deciduous - continued")
pdf("~/Desktop/deciduous4.pdf",8.85,12.1)
plot(plot_dec4)
dev.off()
# sequence 5
plot_dec5 <- circular_linear_plot(data = data,
species_name = sp_dec5,
leg_gradient = c(0,0.3,1),
title_name = "(b) Deciduous - continued")
pdf("~/Desktop/deciduous5.pdf",8.85,12.1)
plot(plot_dec5)
dev.off()
# sequence 6
plot_dec6 <- circular_linear_plot(data = data,
species_name = sp_dec6,
leg_gradient = c(0,0.3,1),
title_name = "(b) Deciduous - continued")
pdf("~/Desktop/deciduous6.pdf",8.85,12.1)
plot(plot_dec6)
dev.off()
# sequence 7
# changed legend position
plot_dec7 <- circular_linear_plot(data = data,
species_name = sp_dec7,
leg_pos = c(1,0.12),
leg_gradient = c(0,0.3,1),
title_name = "(b) Deciduous - continued")
pdf("~/Desktop/deciduous7.pdf",8.85, 9.8)
plot(plot_dec7)
dev.off()
#-------------------------------------------------------------------
#--- get selected species EVERGREEN
#-------------------------------------------------------------------
overview_ever <- overview %>%
filter(grepl("evergreen",deciduousness)) %>%
filter(site_years_with_phenophase > 0) %>%
arrange_at("species_full")
sp_ever <- unique(overview_ever$species_full)
# groups of 5 species (5 species per page in the supplementary info)
sp_ever1 <- paste(sp_ever[1:4],collapse = "|") # up to 4 for the first page which includes figure description
sp_ever2 <- paste(sp_ever[5:9],collapse = "|")
sp_ever3 <- paste(sp_ever[10:14],collapse = "|")
sp_ever4 <- paste(sp_ever[15:19],collapse = "|")
sp_ever5 <- paste(sp_ever[20:24],collapse = "|")
sp_ever6 <- paste(sp_ever[25:29],collapse = "|")
sp_ever7 <- paste(sp_ever[30:34],collapse = "|")
sp_ever8 <- paste(sp_ever[35:39],collapse = "|")
sp_ever9 <- paste(sp_ever[40:44],collapse = "|")
sp_ever10 <- paste(sp_ever[45:49],collapse = "|")
sp_ever11 <- paste(sp_ever[50:54],collapse = "|")
sp_ever12 <- paste(sp_ever[55:59],collapse = "|")
sp_ever13 <- paste(sp_ever[60:64],collapse = "|")
#------
# plots
#------
# sequence 1
# changed legend position
plot_ever1 <- circular_linear_plot(data = data,
species_name = sp_ever1,
leg_pos = c(1,0.125),
title_name = "(a) Evergreen")
pdf("~/Desktop/evergreen1.pdf",8.85,9.8) # freq. with 3 digits
plot(plot_ever1)
dev.off()
# sequence 2
plot_ever2 <- circular_linear_plot(data = data,
species_name = sp_ever2,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen2.pdf",8.85,12.1)
plot(plot_ever2)
dev.off()
# sequence 3
plot_ever3 <- circular_linear_plot(data = data,
species_name = sp_ever3,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen3.pdf",8.85,12.1)
plot(plot_ever3)
dev.off()
# sequence 4
plot_ever4 <- circular_linear_plot(data = data,
species_name = sp_ever4,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen4.pdf",8.85,12.1)
plot(plot_ever4)
dev.off()
# sequence 5
plot_ever5 <- circular_linear_plot(data = data,
species_name = sp_ever5,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen5.pdf",8.85,12.1)
plot(plot_ever5)
dev.off()
# sequence 6
plot_ever6 <- circular_linear_plot(data = data,
species_name = sp_ever6,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen6.pdf",8.85,12.1)
plot(plot_ever6)
dev.off()
# sequence 7
plot_ever7 <- circular_linear_plot(data = data,
species_name = sp_ever7,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen7.pdf",8.85,12.1)
plot(plot_ever7)
dev.off()
# sequence 8
plot_ever8 <- circular_linear_plot(data = data,
species_name = sp_ever8,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen8.pdf",8.85,12.1)
plot(plot_ever8)
dev.off()
# sequence 9
plot_ever9 <- circular_linear_plot(data = data,
species_name = sp_ever9,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen9.pdf",8.85,12.1)
plot(plot_ever9)
dev.off()
# sequence 10
plot_ever10 <- circular_linear_plot(data = data,
species_name = sp_ever10,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen10.pdf",8.85,12.1)
plot(plot_ever10)
dev.off()
# sequence 11
plot_ever11 <- circular_linear_plot(data = data,
species_name = sp_ever11,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen11.pdf",8.85,12.1)
plot(plot_ever11)
dev.off()
# sequence 12
plot_ever12 <- circular_linear_plot(data = data,
species_name = sp_ever12,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen12.pdf",8.85,12.1)
plot(plot_ever12)
dev.off()
# sequence 13
plot_ever13 <- circular_linear_plot(data = data,
species_name = sp_ever13,
title_name = "(a) Evergreen - continued")
pdf("~/Desktop/evergreen13.pdf",8.85,12.1)
plot(plot_ever13)
dev.off()
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