examples/13 -dendroAnalystExample_Bidaux.R
In nasserdr/dendroSense: Analyzing dendrometers data the easy way.
library(readr)
library(lubridate)
library(dendRoAnalyst)
library(dplyr)
library(ggplot2)
library(xts)
library(chron)
# install.packages("forecast")
# install.packages("curl")
# install.packages("dendrometeR")
# All files in one dataframe
#### Daily stats all dendros________________________________________________________________________________________________________________________
#### ________________________________________________________________________________________________________________________
#### ________________________________________________________________________________________________________________________
#### ________________________________________________________________________________________________________________________
idir = "~/mnt/Data-Work-RE/26_Agricultural_Engineering-RE/263_DP/03_Persoenliche_Unterlagen/Wata/08-R_dendro_files/Bidaux/2020/dendro_nogaps15min_nojumps"
odir = "~/mnt/Data-Work-RE/26_Agricultural_Engineering-RE/263_DP/03_Persoenliche_Unterlagen/Wata/08-R_dendro_files/Bidaux/2020"
files <- list.files(idir, pattern = '*.csv')
all_dendros <- NULL
for(file in files){
dendro_df <- read.csv(file.path(idir, file), header = TRUE, sep = ",", stringsAsFactors = FALSE)
#s <- substr(file, 1,4)
s <- strsplit(file, '_')
s <- s[[1]][3]
dendro_df[,1] <- as_datetime(dendro_df[,1], tz = "UTC", format = NULL)
#dendro_df[,1] <- as.POSIXct(dendro_df[,1])
#dendro_df[,1] <- as.POSIXct(dendro_df[,1], format= "%Y-%m-%d %H:%M:%OS", usetz= FALSE)
#Daily_status
daily_stats_dendro <- daily.data(dendro_df, TreeNum = 1)
# Adding maximum daily shrinkage
daily_stats_dendro <- daily_stats_dendro %>%
mutate(MDS = max - min, dendro = s)
# Adding a temporary col to compute the DR
daily_stats_dendro$temp <- c(daily_stats_dendro$max[2:nrow(daily_stats_dendro)], NA)
# Computing the DR and selecting the needed cols
# DR = MaxSD(Day + 1) - MinSD(Day)
# Daily Growth (MXSD(Day + 1) - MXSD (Day))
daily_stats_dendro <- daily_stats_dendro %>%
mutate(DR = temp - min, DG = temp - max) %>%
select(dendro, DOY, min, max, MDS, DG, DR)
# Cumulative growth (simple cumulative function for the SGC)
daily_stats_dendro <- daily_stats_dendro %>%
mutate(CumGrowth = cumsum(DR))
all_dendros <- rbind(all_dendros, daily_stats_dendro)
}
# DOY in date
d_all <- all_dendros
d_all <- na.omit(d_all)
str(d_all)
all_dendros$date <- as.Date(all_dendros$DOY, origin="2020-01-01")
write.table(all_dendros, file.path(odir, 'all_dendros_stats.csv'), row.names = FALSE, sep = ';')
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
somePDFPath = "C:\\temp\\some.pdf"
pdf(file=somePDFPath)
for (i in seq(5,10))
{
par(mfrow = c(2,1))
VAR1=rnorm(i)
VAR2=rnorm(i)
plot(VAR1,VAR2)
}
dev.off()
#####Plot_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
day_s <- yday("2021-07-06")
day_e <- yday("2021-08-06")
sc_stats <- phase.sc(all_dendros,
TreeNum = 1,
smoothing = 1,
outputplot = TRUE,
days = c(day_s, day_e))
all_dendros$phase <- sc_stats$SC_phase$Phases
all_dendros$phase <- as.factor(all_dendros$phase)
all_dendros$phase <- recode(all_dendros$phase, "1" = "Shrinkage", "2" = "Expansion", "3" = "Increment")
na.omit(all_dendros)
my_dend_filterd <- all_dendros %>%
filter(yday(datetime) <= day_e) %>%
filter(yday(datetime) >= day_s)
ggplot(my_dend_filterd, aes(datetime, T3B2)) +
geom_point(aes(colour = factor(phase)), shape = 16, size= 3)+
scale_color_manual(values = c("Shrinkage" = "red", "Expansion" = "#fcb854", "Increment" = "darkgreen")) +
theme(
plot.title = element_text(hjust = 0.5),
axis.text.x = element_text(color="#000000"),
axis.text.y = element_text(color="#000000"),
text=element_text(family = 'Arial', size = 14),
panel.background = element_rect(fill = "white"),
axis.line = element_line(size = 0.5),
legend.key = element_rect(fill = "white"),
legend.position = "top",
strip.placement = 'inside',
strip.background = element_blank()
) +
ylab(paste0("Stem diameter (","\U00B5", "m)")) +
xlab("Day") +
guides(
colour=guide_legend(title="Phase"),
)
zg_stats <- phase.zg(all_dendros,
TreeNum = 1,
outputplot = TRUE,
days = c(day_s, day_e),
ylab1 = "Stem size variation [µm]",
ylab2 = "TWD [µm]")
cols <- c("1" = "red", "2" = "darkgreen", "3" = "orange")
plot(zg_stats$ZG_phase$TWD)
# Remove Median
daily_stats_dendro <- all_dendros %>% select()
dendro_df$doy <- yday(all_dendros$date)
dendro_df$phase_sc <- sc_stats$SC_phase$Phases
#plot
ggplot(data = all_dendros, aes(x = date, y = T1A1)) + geom_line()
# DOY = days
# Add Daily Net Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY). First day being an NA
# Add Recovery: Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY)
# Create the "date" equivalent to "yday"
daily_stats_dendro$Date <- as.Date(daily_stats_dendro$DOY)
# Tree Water Deficit (average and max) - To be taken from the ZG_phase
daily_stats_dendro$Max.twd <- zg_stats$ZG_cycle$Max.twd
daily_stats_dendro$Avg.twd <- zg_stats$ZG_cycle$Avg.twd
#
# # Add phases and duration_h (to be taken from ZG_Phase)
daily_stats_dendro$phases <- zg_stats$ZG_cycle$Phases
daily_stats_dendro$duration_h <- zg_stats$ZG_cycle$Duration_h
#' This code takes excel input files, each of which is a dendrometer signal (
#' one dendro per file only - the base and dendro name can be recognized from
#' the file name) and does the following:
#' - Gather all the dataframe of all dendro together
#
write.table(all_dendros, file.path(odir, 'all_dendros_stats.csv'), row.names = FALSE, sep = ';')
#
# idir <- "~/mnt/agroscope/Data-Work/26_Agricultural_Engineering-RE/263_DP/03_Persoenliche_Unterlagen/Wata/08-R_dendro_files/Hassan/5-Jumps_fixed_partitioned"
# files <- list.files(idir, pattern = '*.csv')
#
# file <- files[1]
# dendro_df <- read.csv(file.path(idir, file), header = TRUE, sep = ";", stringsAsFactors = FALSE)
# colnames(dendro_df) <- c('Time', 'T2')
# dendro_df$Date <- date(dendro_df$Time)
#
# day_s = yday(dendro_df$Date[1])
# day_s
# day_e =yday(last(dendro_df$Date))
# day_e
#
# zg_stats <- phase.zg(dendro_df,
# TreeNum = 1,
# outputplot = TRUE,
# days = c(day_s, day_e))
# #
# dendro_xts <- as.xts(
# x = dendro_df$T2,
# order.by = dendro_df$Time
# )
# plot.xts(dendro_xts)
#
#
#
#
# dates <- unique(date(dendro_df$Time))
# dendro_df <- dendro_df[as.Date(dendro_df$Time) != last(dates),]
#
# # Problem with the sample numbers and missing data. There should be a gap filling thingy
# daily_stats_dendro <- daily.data(dendro_day, TreeNum = 1)
# sc.phase<-phase.sc(df=gf_nepa17, TreeNum=1, smoothing=12, outputplot=TRUE, days=c(150,160))
#
# dendro_day <- dendro_df[64:254,]
# rownames(dendro_day) <- NULL
# before <- dendro_day[1:65,]
# bet <- data.frame(
# Time = '2017-01-02 16:00:15',
# T2 = 2000
# )
# after <- dendro_day[66:nrow(dendro_day),]
# f <- rbind(before, bet, after)
# sc_stats <- phase.sc(df = f, TreeNum = 1, smoothing = 12, outputplot=TRUE, days = c(date("2017-01-03"), date("2017-01-04")))
#
# dendro_df$date <- as.Date(dendro_df$Time)
# s <- dendro_df %>% group_by(date) %>% tally()
# zg_stats <- phase.zg(dendro_df,
# TreeNum = 1,
# outputplot = TRUE,
# days = c(1,2))
#
#
# plot(zg_stats$ZG_phase$TWD)
#
# # Remove Median
# daily_stats_dendro <- daily_stats_dendro %>% select(-median)
#
# dendro_df$doy <- yday(dendro_df$date)
# dendro_df$phase_sc <- sc_stats$SC_phase$Phases
# #plot
# ggplot(data = dendro_df, aes(x = date, y = T1A1)) + geom_line()
#
# # DOY = days
# # Add Daily Net Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY). First day being an NA
# # Add Recovery: Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY)
#
# # Create the "date" equivalent to "yday"
# daily_stats_dendro$Date <- as.Date(daily_stats_dendro$DOY)
#
# # Tree Water Deficit (average and max) - To be taken from the ZG_phase
# daily_stats_dendro$Max.twd <- zg_stats$ZG_cycle$Max.twd
# daily_stats_dendro$Avg.twd <- zg_stats$ZG_cycle$Avg.twd
# #
# # # Add phases and duration_h (to be taken from ZG_Phase)
# daily_stats_dendro$phases <- zg_stats$ZG_cycle$Phases
# daily_stats_dendro$duration_h <- zg_stats$ZG_cycle$Duration_h
#
# }
#
#
# file <- files[1]
# stat_dendro(file)
#
#
# library(dendRoAnalyst)
# data(gf_nepa17)
# sc.phase<-phase.sc(df=gf_nepa17, TreeNum=1, smoothing=12, outputplot=TRUE, days=c(150,160))
nasserdr/dendroSense documentation built on Dec. 21, 2021, 11:11 p.m.
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library(readr)
library(lubridate)
library(dendRoAnalyst)
library(dplyr)
library(ggplot2)
library(xts)
library(chron)
# install.packages("forecast")
# install.packages("curl")
# install.packages("dendrometeR")
# All files in one dataframe
#### Daily stats all dendros________________________________________________________________________________________________________________________
#### ________________________________________________________________________________________________________________________
#### ________________________________________________________________________________________________________________________
#### ________________________________________________________________________________________________________________________
idir = "~/mnt/Data-Work-RE/26_Agricultural_Engineering-RE/263_DP/03_Persoenliche_Unterlagen/Wata/08-R_dendro_files/Bidaux/2020/dendro_nogaps15min_nojumps"
odir = "~/mnt/Data-Work-RE/26_Agricultural_Engineering-RE/263_DP/03_Persoenliche_Unterlagen/Wata/08-R_dendro_files/Bidaux/2020"
files <- list.files(idir, pattern = '*.csv')
all_dendros <- NULL
for(file in files){
dendro_df <- read.csv(file.path(idir, file), header = TRUE, sep = ",", stringsAsFactors = FALSE)
#s <- substr(file, 1,4)
s <- strsplit(file, '_')
s <- s[[1]][3]
dendro_df[,1] <- as_datetime(dendro_df[,1], tz = "UTC", format = NULL)
#dendro_df[,1] <- as.POSIXct(dendro_df[,1])
#dendro_df[,1] <- as.POSIXct(dendro_df[,1], format= "%Y-%m-%d %H:%M:%OS", usetz= FALSE)
#Daily_status
daily_stats_dendro <- daily.data(dendro_df, TreeNum = 1)
# Adding maximum daily shrinkage
daily_stats_dendro <- daily_stats_dendro %>%
mutate(MDS = max - min, dendro = s)
# Adding a temporary col to compute the DR
daily_stats_dendro$temp <- c(daily_stats_dendro$max[2:nrow(daily_stats_dendro)], NA)
# Computing the DR and selecting the needed cols
# DR = MaxSD(Day + 1) - MinSD(Day)
# Daily Growth (MXSD(Day + 1) - MXSD (Day))
daily_stats_dendro <- daily_stats_dendro %>%
mutate(DR = temp - min, DG = temp - max) %>%
select(dendro, DOY, min, max, MDS, DG, DR)
# Cumulative growth (simple cumulative function for the SGC)
daily_stats_dendro <- daily_stats_dendro %>%
mutate(CumGrowth = cumsum(DR))
all_dendros <- rbind(all_dendros, daily_stats_dendro)
}
# DOY in date
d_all <- all_dendros
d_all <- na.omit(d_all)
str(d_all)
all_dendros$date <- as.Date(all_dendros$DOY, origin="2020-01-01")
write.table(all_dendros, file.path(odir, 'all_dendros_stats.csv'), row.names = FALSE, sep = ';')
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
#____________________________________________________________________________________________________________________________________________________________
somePDFPath = "C:\\temp\\some.pdf"
pdf(file=somePDFPath)
for (i in seq(5,10))
{
par(mfrow = c(2,1))
VAR1=rnorm(i)
VAR2=rnorm(i)
plot(VAR1,VAR2)
}
dev.off()
#####Plot_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
#####_____________________________________________________________________________________________________________________________
day_s <- yday("2021-07-06")
day_e <- yday("2021-08-06")
sc_stats <- phase.sc(all_dendros,
TreeNum = 1,
smoothing = 1,
outputplot = TRUE,
days = c(day_s, day_e))
all_dendros$phase <- sc_stats$SC_phase$Phases
all_dendros$phase <- as.factor(all_dendros$phase)
all_dendros$phase <- recode(all_dendros$phase, "1" = "Shrinkage", "2" = "Expansion", "3" = "Increment")
na.omit(all_dendros)
my_dend_filterd <- all_dendros %>%
filter(yday(datetime) <= day_e) %>%
filter(yday(datetime) >= day_s)
ggplot(my_dend_filterd, aes(datetime, T3B2)) +
geom_point(aes(colour = factor(phase)), shape = 16, size= 3)+
scale_color_manual(values = c("Shrinkage" = "red", "Expansion" = "#fcb854", "Increment" = "darkgreen")) +
theme(
plot.title = element_text(hjust = 0.5),
axis.text.x = element_text(color="#000000"),
axis.text.y = element_text(color="#000000"),
text=element_text(family = 'Arial', size = 14),
panel.background = element_rect(fill = "white"),
axis.line = element_line(size = 0.5),
legend.key = element_rect(fill = "white"),
legend.position = "top",
strip.placement = 'inside',
strip.background = element_blank()
) +
ylab(paste0("Stem diameter (","\U00B5", "m)")) +
xlab("Day") +
guides(
colour=guide_legend(title="Phase"),
)
zg_stats <- phase.zg(all_dendros,
TreeNum = 1,
outputplot = TRUE,
days = c(day_s, day_e),
ylab1 = "Stem size variation [µm]",
ylab2 = "TWD [µm]")
cols <- c("1" = "red", "2" = "darkgreen", "3" = "orange")
plot(zg_stats$ZG_phase$TWD)
# Remove Median
daily_stats_dendro <- all_dendros %>% select()
dendro_df$doy <- yday(all_dendros$date)
dendro_df$phase_sc <- sc_stats$SC_phase$Phases
#plot
ggplot(data = all_dendros, aes(x = date, y = T1A1)) + geom_line()
# DOY = days
# Add Daily Net Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY). First day being an NA
# Add Recovery: Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY)
# Create the "date" equivalent to "yday"
daily_stats_dendro$Date <- as.Date(daily_stats_dendro$DOY)
# Tree Water Deficit (average and max) - To be taken from the ZG_phase
daily_stats_dendro$Max.twd <- zg_stats$ZG_cycle$Max.twd
daily_stats_dendro$Avg.twd <- zg_stats$ZG_cycle$Avg.twd
#
# # Add phases and duration_h (to be taken from ZG_Phase)
daily_stats_dendro$phases <- zg_stats$ZG_cycle$Phases
daily_stats_dendro$duration_h <- zg_stats$ZG_cycle$Duration_h
#' This code takes excel input files, each of which is a dendrometer signal (
#' one dendro per file only - the base and dendro name can be recognized from
#' the file name) and does the following:
#' - Gather all the dataframe of all dendro together
#
write.table(all_dendros, file.path(odir, 'all_dendros_stats.csv'), row.names = FALSE, sep = ';')
#
# idir <- "~/mnt/agroscope/Data-Work/26_Agricultural_Engineering-RE/263_DP/03_Persoenliche_Unterlagen/Wata/08-R_dendro_files/Hassan/5-Jumps_fixed_partitioned"
# files <- list.files(idir, pattern = '*.csv')
#
# file <- files[1]
# dendro_df <- read.csv(file.path(idir, file), header = TRUE, sep = ";", stringsAsFactors = FALSE)
# colnames(dendro_df) <- c('Time', 'T2')
# dendro_df$Date <- date(dendro_df$Time)
#
# day_s = yday(dendro_df$Date[1])
# day_s
# day_e =yday(last(dendro_df$Date))
# day_e
#
# zg_stats <- phase.zg(dendro_df,
# TreeNum = 1,
# outputplot = TRUE,
# days = c(day_s, day_e))
# #
# dendro_xts <- as.xts(
# x = dendro_df$T2,
# order.by = dendro_df$Time
# )
# plot.xts(dendro_xts)
#
#
#
#
# dates <- unique(date(dendro_df$Time))
# dendro_df <- dendro_df[as.Date(dendro_df$Time) != last(dates),]
#
# # Problem with the sample numbers and missing data. There should be a gap filling thingy
# daily_stats_dendro <- daily.data(dendro_day, TreeNum = 1)
# sc.phase<-phase.sc(df=gf_nepa17, TreeNum=1, smoothing=12, outputplot=TRUE, days=c(150,160))
#
# dendro_day <- dendro_df[64:254,]
# rownames(dendro_day) <- NULL
# before <- dendro_day[1:65,]
# bet <- data.frame(
# Time = '2017-01-02 16:00:15',
# T2 = 2000
# )
# after <- dendro_day[66:nrow(dendro_day),]
# f <- rbind(before, bet, after)
# sc_stats <- phase.sc(df = f, TreeNum = 1, smoothing = 12, outputplot=TRUE, days = c(date("2017-01-03"), date("2017-01-04")))
#
# dendro_df$date <- as.Date(dendro_df$Time)
# s <- dendro_df %>% group_by(date) %>% tally()
# zg_stats <- phase.zg(dendro_df,
# TreeNum = 1,
# outputplot = TRUE,
# days = c(1,2))
#
#
# plot(zg_stats$ZG_phase$TWD)
#
# # Remove Median
# daily_stats_dendro <- daily_stats_dendro %>% select(-median)
#
# dendro_df$doy <- yday(dendro_df$date)
# dendro_df$phase_sc <- sc_stats$SC_phase$Phases
# #plot
# ggplot(data = dendro_df, aes(x = date, y = T1A1)) + geom_line()
#
# # DOY = days
# # Add Daily Net Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY). First day being an NA
# # Add Recovery: Daily Max shrinkage (DOY+1) - Daily Max shrinkage (DOY)
#
# # Create the "date" equivalent to "yday"
# daily_stats_dendro$Date <- as.Date(daily_stats_dendro$DOY)
#
# # Tree Water Deficit (average and max) - To be taken from the ZG_phase
# daily_stats_dendro$Max.twd <- zg_stats$ZG_cycle$Max.twd
# daily_stats_dendro$Avg.twd <- zg_stats$ZG_cycle$Avg.twd
# #
# # # Add phases and duration_h (to be taken from ZG_Phase)
# daily_stats_dendro$phases <- zg_stats$ZG_cycle$Phases
# daily_stats_dendro$duration_h <- zg_stats$ZG_cycle$Duration_h
#
# }
#
#
# file <- files[1]
# stat_dendro(file)
#
#
# library(dendRoAnalyst)
# data(gf_nepa17)
# sc.phase<-phase.sc(df=gf_nepa17, TreeNum=1, smoothing=12, outputplot=TRUE, days=c(150,160))
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