plot-individuals-dendro.Rmd

Import libs and define global vars
```{r}
source("lib-dendro.R")

library(ggplot2)
library(dplyr)

### DEFINE GLOBAL VARS ###
PATH = '/home/akronix/workspace/dendro';
setwd(PATH)

DATA_DIR = 'processed/Penaflor-processed'

# lentiscos = c(92223485, 92232435, 92232429, 92232425, 92232432) 
# sabinas = c(92232422, 92232436, 92232430, 92232434, 92232433, 92232427, 92232428, 92232431, 92232426)

TreeList <- read.table("TreeList.txt",header=T)

Qi = TreeList %>% filter(class == "Quercus") %>% pull(series)
P_D = TreeList %>% filter(class == "D") %>% pull(series)
P_ND = TreeList %>% filter(class == "ND") %>% pull(series)
```

Define plot functions
```{r}
plot_line<- function(data, title, y = data$value) {
  ggplot(data = data,  aes(x=ts, y=y )) +
  ggtitle(title) +
  geom_line() +
  #geom_line( aes (linetype = "Quercus Ilex"), col='darkgreen', show.legend	= F) +
  labs(x=expression(''),
       y=expression(Delta*" D (um)"))+
  theme_bw() +
  geom_hline(yintercept=0,lty=2,linewidth=0.2)+
  #facet_grid(class~.,scales = "free_y")+
  scale_x_datetime(date_breaks = "1 month", date_labels="%b %Y") +
  theme(axis.text.x = element_text(angle = 30, hjust=1))
}
```
  
Read data and plot it one by one and save it to a pdf file
```{r}
list_files <- list.files(file.path(".",DATA_DIR), pattern="*.csv$", full.names=TRUE)

pdf("dendrometers_Penaflor_plots.pdf", onefile = TRUE)
for (dendro.fn in list_files) {
  dendro.db <- read.one.processed(dendro.fn)
  if (first(dendro.db$series) %in% Qi) specie = "Quercus"
  else if(first(dendro.db$series) %in% P_D) specie = "Declining Pine"
  else if(first(dendro.db$series) %in% P_ND) specie = "Non-Declining Pine"
     # ifelse(dendro.db$series %in% lentiscos, "Pistacia Lentiscus", "Juniperus Phoenicea")
   
  print(plot_line(dendro.db, paste(dendro.db$series, '-', specie)))
}
dev.off()
```