From 445931907d329d6e5c2a65ae17972e2f48121904 Mon Sep 17 00:00:00 2001
From: Nathalie Triches <ntriches@bgc-jena.mpg.de>
Date: Thu, 5 Oct 2023 16:43:44 +0200
Subject: [PATCH] changes during and between field work in Abisko 2023
* changed scripts according to data that was sampled
* differences between May (all GHG on data logger), July (mess), and
Sept (all GHG on data logger)
* added micro habitat and plot number to plot
* all scripts not clean
---
20230314_simple_habitat_comparison.R | 23 +++-
preprocessing/functions/plot_ghg_conc_2023.R | 121 +++++++++++++-----
preprocessing/functions/read_raw_data_2023.R | 54 +++++++-
.../sort_ch4_conc_by_meas_period_2023.R | 4 +-
.../sort_co2_conc_by_meas_period_2023.R | 6 +-
.../functions/sort_n2o_conc_by_meas_period.R | 36 ++++--
.../sort_n2o_conc_by_meas_period_2023.R | 2 +-
preprocessing/main_script.R | 9 +-
8 files changed, 197 insertions(+), 58 deletions(-)
diff --git a/20230314_simple_habitat_comparison.R b/20230314_simple_habitat_comparison.R
index d5efa6f..3e29b85 100644
--- a/20230314_simple_habitat_comparison.R
+++ b/20230314_simple_habitat_comparison.R
@@ -72,17 +72,32 @@ abline(h=c(335,339),col="red")
library(ggplot2)
# combine data from single measurements from each plot to one boxplot
+# order boxplots in right way from palsa_lichen to pm to bog to fen
+# palsa_lichen plots: 2, 11, 18, 25, 29, 33
+# palsa_moss plots: 8, 15, 17, 27, 30, 32
+# bog plots: 7, 12, 20, 26, 28, 31
+# fen plots: 10,19,23,34,35,36
# remove plot 1
all_plots_sorted_by_habitat <- mPN2oPlotHabitat %>%
filter(plot_no != 1) %>%
- ggplot(aes(x = micro_habitat, y = n2oppb,
- group=plot_no, color = micro_habitat)) +
+ ggplot(aes(x = factor(micro_habitat, levels = c("palsa_lichen", "palsa_moss","bog","fen")), y = n2oppb,
+ group=plot_no,
+ color = micro_habitat)) +
geom_boxplot() +
# geom_text(aes(label = plot_no)) +
- labs(x = "micro habitat", y = "N2O concentration [ppb]") +
- theme(text=element_text(size=20))
+ labs(x = "Micro habitat", y = "N2O concentration [ppb]", title = "Fig. 3: Spatial variability of N2O concentrations in spring 2023") +
+ labs(caption = " 24 plots with 6 replicates grouped in micro habitats, i. e., palsa lichen (dry), palsa moss (dry), bog (wet), fen (wetter).
+ Each single boxplot represents all N2O concentrations measured in spring 2023 in one plot (= chamber placement area)
+ during chamber closure time (between 5 and 10 min). Please note that fluxes have not been calculated yet.") +
+ theme(axis.text=element_text(size=24), axis.title = element_text(size=24),
+ plot.caption = element_text(size = 22, hjust = -0, vjust = 0.2),
+ plot.title = element_text(size = 30), panel.background = element_rect(fill = "#FFFFFF"),
+ panel.border = element_rect(colour = "black", fill = NA), panel.grid.major = element_line(colour = "light grey"),
+ legend.title = element_text(size = 22), legend.text = element_text(size = 22))
+ #theme_bw()
all_plots_sorted_by_habitat
+
# Differences within micro habitat ####
# combine data from single measurements from each plot to one boxplot
# look at palsa lichen
diff --git a/preprocessing/functions/plot_ghg_conc_2023.R b/preprocessing/functions/plot_ghg_conc_2023.R
index 8328def..6d9e2b4 100644
--- a/preprocessing/functions/plot_ghg_conc_2023.R
+++ b/preprocessing/functions/plot_ghg_conc_2023.R
@@ -4,18 +4,54 @@
############### Plots for CO2 ##################################################
################################################################################
+# CO2 scatter and boxplot with plot number and meas_ID
+meas_ID <- measPeriodCo2$meas_ID
+
+for (i in unique(meas_ID)){
+ fileID <- i
+ measID_loc <- i
+ rows_measID_loc <- which(measPeriodCo2$meas_ID == measID_loc)
+ first_row_measID_loc <- rows_measID_loc[1]
+
+ d <- subset(measPeriodCo2, meas_ID == i)
+ # summer 2023
+ # png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/07_summer/202307_co2mp_", fileID, ".png"),
+ # height=8, width=12, pointsize=8, bg="white", units="in", res=200)
+ # autumn 2023
+ png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/09_autumn/202309_co2mp_", fileID, ".png"),
+ height=4, width=8, pointsize=8, bg="white", units="in", res=200)
+ par(mfrow = c(2,2))
+ plot(d$datetime_datalogger, d$co2ppm_licor)
+ title(main = paste("measurement period", i, "plot", measPeriodCo2$plot[first_row_measID_loc]
+ ))
+ # hist(d$n2oppm_aeris, breaks = 15)
+ boxplot(d$co2ppm_licor)
+ plot(d$par)
+ plot(d$h2oppm_licor)
+ par(mfrow = c(1,1))
+ dev.off()
+}
+
# original data without any modifications (5 min), CO2 data from Licor
+# WITHOUT TITLES
meas_ID <- measPeriodCo2$meas_ID
for (i in unique(meas_ID)){
fileID <- i
d <- subset(measPeriodCo2, meas_ID == i)
- png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/co2-licor-mp_", fileID, ".png"),
+ # summer 2023
+ png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/07_summer/202307_co2-licor-mp_", fileID, ".png"),
height=4, width=8, pointsize=8, bg="white", units="in", res=200)
+ # autumn 2023
+ # png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/09_autumn/co2-licor-mp_", fileID, ".png"),
+ # height=4, width=8, pointsize=8, bg="white", units="in", res=200)
par(mfrow = c(1,2))
plot(d$datetime_datalogger, d$co2ppm_licor)
# abline(reg)
title(main = i)
+ title(main = paste("measurement period", i, "plot", measPeriodCo2$plot,
+ mPN2oPlotHabitat$plot_no[first_row_measID_loc],
+ mPN2oPlotHabitat$micro_habitat[first_row_measID_loc]))
#hist(d$co2ppm_licor, breaks = 15)
boxplot(d$co2ppm_licor)
#plot(d$airTdegC)
@@ -66,18 +102,27 @@ for (i in unique(meas_ID)){
#################### CH4 plots #################################################
################################################################################
-meas_ID <- measPeriodCh4$meas_ID
+# CH4 plots and boxplots with plot and meas_ID
-# str(measPeriodCh4)
+meas_ID <- measPeriodCh4$meas_ID
for (i in unique(meas_ID)){
fileID <- i
+ measID_loc <- i
+ rows_measID_loc <- which(measPeriodCh4$meas_ID == measID_loc)
+ first_row_measID_loc <- rows_measID_loc[1]
+
d <- subset(measPeriodCh4, meas_ID == i)
- png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/ch4mp_", fileID, ".png"),
+ # summer 2023
+ # png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/07_summer/202307_ch4mp_", fileID, ".png"),
+ # height=4, width=8, pointsize=8, bg="white", units="in", res=200)
+ # autumn 2023
+ png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/09_autumn/202309_ch4mp_", fileID, ".png"),
height=4, width=8, pointsize=8, bg="white", units="in", res=200)
par(mfrow = c(1,2))
plot(d$datetime_datalogger, d$ch4ppb)
- title(main = i)
+ title(main = paste("measurement period", i, "plot", measPeriodCh4$plot[first_row_measID_loc]
+ ))
#hist(d$ch4ppm, breaks = 15)
boxplot(d$ch4ppb)
#plot(d$airTdegC)
@@ -107,6 +152,7 @@ for (i in unique(meas_ID)){
################# Plots for N2O ################################################
################################################################################
+# RUN THIS FIRST
# enable plot comparison (copy-paste from 20230414_simple_habitat_comparison)
# code needs to be cleaned!
@@ -155,34 +201,8 @@ for (iLine in 1:nrow(measPeriodMetaDataDF)){
}
}
-# non-modified measurement periods (5 min)
-# check what fucks the Aeris up
-meas_ID <-mPN2oPlotHabitat$meas_ID
-for (i in unique(meas_ID)){
- fileID <- i
- measID_loc <- i
- rows_measID_loc <- which(mPN2oPlotHabitat$meas_ID == measID_loc)
- first_row_measID_loc <- rows_measID_loc[1]
-
- d <- subset(mPN2oPlotHabitat, meas_ID == i)
- png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/n2omp_aeris-check2_", fileID, ".png"),
- height=8, width=12, pointsize=8, bg="white", units="in", res=200)
- par(mfrow = c(2,2))
- plot(d$datetime_datalogger, d$n2oppb)
- title(main = paste("measurement period", i, "plot", mPN2oPlotHabitat$plot_no[first_row_measID_loc],
- mPN2oPlotHabitat$micro_habitat[first_row_measID_loc]))
- plot(d$datetime_datalogger, d$h2oppm_aeris)
- plot(d$datetime_datalogger, d$airpreshPa)
- plot(d$datetime_datalogger, d$chamberRH)
- #boxplot(d$n2oppb)
- #plot(d$airTdegC)
- par(mfrow = c(1,1))
- dev.off()
-}
-
-
-####### TRIAL with habitat and collar number! ############
+####### plots with habitat and collar number! ############
meas_ID <-mPN2oPlotHabitat$meas_ID
for (i in unique(meas_ID)){
@@ -192,7 +212,11 @@ for (i in unique(meas_ID)){
first_row_measID_loc <- rows_measID_loc[1]
d <- subset(mPN2oPlotHabitat, meas_ID == i)
- png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/n2omp_", fileID, ".png"),
+ # summer 2023
+ # png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/07_summer/202307_n2omp_", fileID, ".png"),
+ # height=4, width=8, pointsize=8, bg="white", units="in", res=200)
+ # autumn 2023
+ png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/09_autumn/202309_n2omp_", fileID, ".png"),
height=4, width=8, pointsize=8, bg="white", units="in", res=200)
par(mfrow = c(1,2))
plot(d$datetime_datalogger, d$n2oppb)
@@ -219,6 +243,35 @@ for (i in unique(meas_ID)){
# same with
### mPN2oPlotHabitat$micro_habitat[first_row_measID_loc]
+# non-modified measurement periods (5 min)
+# check what fucks the Aeris up
+meas_ID <-mPN2oPlotHabitat$meas_ID
+
+for (i in unique(meas_ID)){
+ fileID <- i
+ measID_loc <- i
+ rows_measID_loc <- which(mPN2oPlotHabitat$meas_ID == measID_loc)
+ first_row_measID_loc <- rows_measID_loc[1]
+
+ d <- subset(mPN2oPlotHabitat, meas_ID == i)
+ png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/n2omp_aeris-check2_", fileID, ".png"),
+ height=8, width=12, pointsize=8, bg="white", units="in", res=200)
+ par(mfrow = c(2,2))
+ plot(d$datetime_datalogger, d$n2oppb)
+ title(main = paste("measurement period", i, "plot", mPN2oPlotHabitat$plot_no[first_row_measID_loc],
+ mPN2oPlotHabitat$micro_habitat[first_row_measID_loc]))
+ plot(d$datetime_datalogger, d$h2oppm_aeris)
+ plot(d$datetime_datalogger, d$airpreshPa)
+ plot(d$datetime_datalogger, d$chamberRH)
+ #boxplot(d$n2oppb)
+ #plot(d$airTdegC)
+ par(mfrow = c(1,1))
+ dev.off()
+}
+
+
+
+
@@ -230,7 +283,7 @@ meas_ID <- measPeriodN2o$meas_ID
for (i in unique(meas_ID)){
fileID <- i
d <- subset(measPeriodN2o, meas_ID == i)
- png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/n2omp_", fileID, ".png"),
+ png(filename=paste0("/home/ntriches/Nextcloud/aniwa/01_qarctic/data_analysis/figures_processing/2023/09_autumn/n2omp_", fileID, ".png"),
height=4, width=8, pointsize=8, bg="white", units="in", res=200)
par(mfrow = c(1,2))
plot(d$datetime_datalogger, d$n2oppm_aeris)
diff --git a/preprocessing/functions/read_raw_data_2023.R b/preprocessing/functions/read_raw_data_2023.R
index 4b09de8..45050de 100644
--- a/preprocessing/functions/read_raw_data_2023.R
+++ b/preprocessing/functions/read_raw_data_2023.R
@@ -13,7 +13,12 @@ get_datalogger_raw_data <- function(mainDir, dataDir, expYear){
print("start get_datalogger_raw_data")
# import data from data logger (CO2 + CH4 fluxes, soil moisture and temp data)
if (expYear == "2023"){
- inputFile <- "20230511-30_stordalen_datalogger_data.csv"
+ # spring 2023
+ # inputFile <- "20230511-30_stordalen_datalogger_data.csv"
+ # summer 2023
+ # inputFile <- "202307_stordalen_datalogger_data.csv"
+ # autumn 2023
+ inputFile <- "20230922_stordalen_datalogger_data.csv"
} else if (expYear == "2024"){
print("NOT YET available")
}
@@ -80,7 +85,11 @@ get_field_mp_meta_data_DF <- function(mainDir, dataDir, expYear){
print("start get_field_mp_meta_data_DF")
if (expYear == "2023"){
- inputFile <- "202305_field-data.csv"
+ # spring 2023
+ # summer 2023
+ inputFile <- "202309_field-data_final.csv"
+ # autumn 2023
+ # inputFile <- "20230909_field-data_final.csv"
} else if (expYear == "2024"){
print(" NOT YET available")
}
@@ -126,3 +135,44 @@ get_field_mp_meta_data_DF <- function(mainDir, dataDir, expYear){
print("end get_field_mp_meta_data_DF")
return(field_mp_meta_data_DF_polished)
}
+
+###############################################################################
+################ get data from Aeris JULY 2023 ################################
+###############################################################################
+
+# "Aeris" data = N2O/CO2 concentrations stored on Aeris analyser
+# function needs R dplyr package (load in main script)
+
+get_aeris_raw_data <- function(mainDir, dataDir, expYear){
+
+ print("start get_aeris_raw_data")
+ # import data from Aeris (N2O and CO2 fluxes)
+ if (expYear == "2023"){
+ inputFile <- "20230709-17_stordalen_aeris-n2o_data.csv"
+ } else if (expYear == "2024"){
+ print("NOT YET available")
+ }
+ inputFile <- paste0(dataDir, "/" ,expYear, "/", inputFile)
+ aeris_raw_data <- read.csv(inputFile)
+
+
+ # polish dataframe
+ aeris_data_polished <- aeris_raw_data %>%
+ # remove columns that are not needed
+ select(-2:-4, -8, -9) %>%
+ # rename columns
+ rename(datetime_aeris=1, co2ppm=2, h2oppm=3, n2oppm=4) %>%
+ # change date to POSIXct and characters to numeric
+ mutate(
+ datetime_aeris = as.POSIXct(datetime_aeris, format="%m/%d/%Y %H:%M:%OS", tz="UTC"),
+ mutate(across(where(is.character), as.numeric))
+ )
+
+ # change format to UTC
+ # aeris_data_polished$datetime_aeris <- format(aeris_data_polished$datetime_aeris,
+ # "%m/%d/%Y %H:%M:%OS %Z", tz="UTC")
+
+ setwd(mainDir)
+ print("end get_aeris_raw_data")
+ return(aeris_data_polished)
+}
diff --git a/preprocessing/functions/sort_ch4_conc_by_meas_period_2023.R b/preprocessing/functions/sort_ch4_conc_by_meas_period_2023.R
index c29d622..323bade 100644
--- a/preprocessing/functions/sort_ch4_conc_by_meas_period_2023.R
+++ b/preprocessing/functions/sort_ch4_conc_by_meas_period_2023.R
@@ -57,7 +57,7 @@ create_ch4_conc_sorted_by_mp <- function(mainDir, dataDir, expYear){
# ... look for start of the measurement period 10 seconds later (= add)
if (length(first_row) < 1){
print("search start after ..")
- for (i in 1:10){
+ for (i in 1:20){
print(paste0("adding start time by: ", i))
added_start_time <- meas_start_end$datetime_start + as.difftime(i, units="secs", tz = "UTC")
first_row <- which(fluxMetaLicor$datetime_datalogger == added_start_time)
@@ -76,7 +76,7 @@ create_ch4_conc_sorted_by_mp <- function(mainDir, dataDir, expYear){
# look for start of the measurement period 15 seconds earlier (= reduce)
if (length(last_row) < 1){
print("searching end ..")
- for (i in 1:15){
+ for (i in 1:20){
print(paste0("reducing end time by: ", i))
reduced_end_time <- meas_start_end$datetime_end - as.difftime(i, units="secs", tz = "UTC")
last_row <- which(fluxMetaLicor$datetime_datalogger == reduced_end_time)
diff --git a/preprocessing/functions/sort_co2_conc_by_meas_period_2023.R b/preprocessing/functions/sort_co2_conc_by_meas_period_2023.R
index f2b3304..028bca4 100644
--- a/preprocessing/functions/sort_co2_conc_by_meas_period_2023.R
+++ b/preprocessing/functions/sort_co2_conc_by_meas_period_2023.R
@@ -17,7 +17,7 @@ create_co2_conc_sorted_by_mp <- function(mainDir, dataDir, expYear){
# VECTOR SOLUTION: fluxMetaLicor <- c("datetime_datalogger", "co2ppm", "champreskPa", "chamtempdegC")
fluxMetaLicor <- ch4_co2_n2o_conc_st_sm_par_data %>%
select("datetime_datalogger", "plot", "co2ppm_licor", "co2ppm_aeris",
- "par",
+ "par", "h2oppm_licor",
"soilT1degC", "soilT2degC", "soilT3degC", "soilT4degC",
"vwc12", "vwc30")
@@ -59,7 +59,7 @@ create_co2_conc_sorted_by_mp <- function(mainDir, dataDir, expYear){
# ... look for start of the measurement period 20 seconds later (= add)
if (length(first_row) < 1){
print("search start after ..")
- for (i in 1:10){
+ for (i in 1:20){
print(paste0("adding start time by: ", i))
added_start_time <- meas_start_end$datetime_start + as.difftime(i, units="secs", tz = "UTC")
first_row <- which(fluxMetaLicor$datetime_datalogger == added_start_time)
@@ -78,7 +78,7 @@ create_co2_conc_sorted_by_mp <- function(mainDir, dataDir, expYear){
# look for start of the measurement period 15 seconds earlier (= reduce)
if (length(last_row) < 1){
print("searching end ..")
- for (i in 1:15){
+ for (i in 1:20){
print(paste0("reducing end time by: ", i))
reduced_end_time <- meas_start_end$datetime_end - as.difftime(i, units="secs", tz = "UTC")
last_row <- which(fluxMetaLicor$datetime_datalogger == reduced_end_time)
diff --git a/preprocessing/functions/sort_n2o_conc_by_meas_period.R b/preprocessing/functions/sort_n2o_conc_by_meas_period.R
index ac1aa1a..3f68d53 100644
--- a/preprocessing/functions/sort_n2o_conc_by_meas_period.R
+++ b/preprocessing/functions/sort_n2o_conc_by_meas_period.R
@@ -18,11 +18,18 @@ create_n2o_data_sorted_by_measurements <- function(mainDir, dataDir, expYear){
fluxMetaAeris <- n2o_co2_conc_data %>%
select("datetime_aeris", "n2oppm")
# get air temperature, pressure, and homidity from datalogger, i.e., from ch4_co2_conc_st_sm_par_data
- fluxMetaLicor <- ch4_co2_conc_st_sm_par_data %>%
- select("datetime_datalogger", "co2ppm", "airTdegC", "airRH", "airpreshPa")
+ # 2022
+ #fluxMetaLicor <- ch4_co2_conc_st_sm_par_data %>%
+ #select("datetime_datalogger", "co2ppm", "airTdegC", "airRH", "airpreshPa")
+ # July 2023
+ fluxMetaLicor <- ch4_co2_n2o_conc_st_sm_par_data %>%
+ select("datetime_datalogger", "co2ppm_licor", "airTdegC")
## get row numbers in field meta-data DF with data from "Aeris measurement periods"
- rowNum_aeris_mp <- which(field_mp_meta_data_DF$measurement_device == "aeris")
+ # 2022
+ # rowNum_aeris_mp <- which(field_mp_meta_data_DF$measurement_device == "aeris")
+ # 2023
+ rowNum_aeris_mp <- which(field_mp_meta_data_DF$measurement_device == "aeris_7810")
print(paste0("number of measurement periods with aeris: ", length(rowNum_aeris_mp)))
print("")
@@ -44,13 +51,19 @@ create_n2o_data_sorted_by_measurements <- function(mainDir, dataDir, expYear){
# get correct according start of measurement period in case there is a time lag between the instruments
# look for start of the measurement period 15 seconds earlier (= reduce)
if (length(first_row) < 1){
- print("searching start..")
+ print("searching start after..")
for (i in 1:10){
- print(paste0("reducing start time by: ", i))
- reduced_start_time <- meas_start_end$datetime_start - as.difftime(15, units="secs", tz = "UTC")
- first_row_reduced <- which(fluxMetaAeris$datetime_aeris == reduced_start_time)
- if (length(last) == 1){
- print(paste0("found ", reduced_start_time))
+ print(paste0("adding start time by: ", i))
+ # 2022
+ #reduced_start_time <- meas_start_end$datetime_start - as.difftime(15, units="secs", tz = "UTC")
+ # reduced_start_time <- meas_start_end$datetime_start - as.difftime(i, units="secs", tz = "UTC")
+ # 2022
+ #first_row_reduced <- which(fluxMetaAeris$datetime_aeris == reduced_start_time)
+ # 2023
+ added_start_time <- meas_start_end$datetime_start + as.difftime(i, units="secs", tz = "UTC")
+ first_row <- which(fluxMetaAeris$datetime_aeris == added_start_time)
+ if (length(first_row) == 1){
+ print(paste0("found ", added_start_time))
break
}
}
@@ -65,7 +78,10 @@ create_n2o_data_sorted_by_measurements <- function(mainDir, dataDir, expYear){
print("searching end ..")
for (i in 1:15){
print(paste0("reducing end time by: ", i))
- reduced_end_time <- meas_start_end$datetime_end - as.difftime(30, units="secs", tz = "UTC")
+ # 2022
+ #reduced_end_time <- meas_start_end$datetime_end - as.difftime(30, units="secs", tz = "UTC")
+ # 2023
+ reduced_end_time <- meas_start_end$datetime_end - as.difftime(i, units="secs", tz = "UTC")
last_row <- which(fluxMetaAeris$datetime_aeris == reduced_end_time)
if (length(last) == 1){
print(paste0("found ", reduced_end_time))
diff --git a/preprocessing/functions/sort_n2o_conc_by_meas_period_2023.R b/preprocessing/functions/sort_n2o_conc_by_meas_period_2023.R
index fabd6e2..04ecf76 100644
--- a/preprocessing/functions/sort_n2o_conc_by_meas_period_2023.R
+++ b/preprocessing/functions/sort_n2o_conc_by_meas_period_2023.R
@@ -57,7 +57,7 @@ create_n2o_conc_sorted_by_measurements <- function(mainDir, dataDir, expYear){
# ... look for start of the measurement period 10 seconds later (= add)
if (length(first_row) < 1){
print("search start after ..")
- for (i in 1:10){
+ for (i in 1:20){
print(paste0("adding start time by: ", i))
added_start_time <- meas_start_end$datetime_start + as.difftime(i, units="secs", tz = "UTC")
first_row <- which(fluxMetaLicor$datetime_datalogger == added_start_time)
diff --git a/preprocessing/main_script.R b/preprocessing/main_script.R
index 14eb1fb..2437b9c 100644
--- a/preprocessing/main_script.R
+++ b/preprocessing/main_script.R
@@ -42,6 +42,13 @@ source("functions/read_raw_data_2023.R")
ch4_co2_n2o_conc_st_sm_par_data <- get_datalogger_raw_data(mainDir, dataDir, expYear)
field_mp_meta_data_DF <- get_field_mp_meta_data_DF(mainDir, dataDir, expYear)
+# July 2023
+# There were problems with the connection between the data logger and the Aeris
+# Only data for CH4 + CO2 25 June, 29 June, and 3 July (= no N2O data)
+# 9, 10, 13, 16, 17 July: CH4 + CO2 data on data logger, N2O in Aeris SD
+# 22 - 27 July: CH4, CO2 + N2O data on data logger
+n2o_co2_conc_data <- get_aeris_raw_data(mainDir, dataDir, expYear)
+
## 2022 #################
source("functions/read_raw_data.R")
@@ -118,8 +125,6 @@ source("functions/calc_co2_flux_licor_all_measurement_periods.R")
co2Fluxes <- calculate_co2_fluxes_licor_all_mps(measPeriodMetaDataDF, measPeriodCo2_corr)
-
-
# important!!! all is in UTC but needs to be in Sweden time in the end
--
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