R/l3_water_sample_gen.R
In raphidoc/lighthouse: Database management and processing workflow for ocean optics science
Defines functions
l3_water_sample_gen
Documented in
l3_water_sample_gen
#' @name l3_water_sample_gen
#' @title l3_water_sample_gen
#' @author Raphael Mabit
#'
#' @description Generate a data base (one file by parameter) from L1 water sample files.
#' Different methods are aplicated depending on the type of parameter.
#' For Ag and Ap parameter, it takes the output of RspectroAbs package.
#' For SPM (Chl-a to be implemented) it read a .csv such as "link to example table"
#'
#' @param project The top level folder of the project
#'
#' @param mission Optional, name for data base file.
#' If none is providen, it is taken from the project name.
#'
#' @param params Character vector used to select for which parameters data bases should be created
#'
#' @import dplyr
#' @import stringr
#' @export
#'
l3_water_sample_gen <- function(project,mission="",params=c("SPM","Ag","Ap")) {
# Setup -------------------------------------------------------------------
if (!exists("mission") || mission == "" ) {
mission <- str_split(project,"/")[[1]]
mission <- mission[length(mission)]
message("mission name empty, taking name of the project: ",mission)
}
L1 <- file.path(project,"L1")
L3 <- file.path(project,"L3","WaterSample")
CheckList <- lighthouse::check_project(project, L1)
if (CheckList["Proot"][[1]] == F) {stop(project,"is not a project root folder")}
SyntheFile = list.files(path = project, pattern = "data_synthesis|Data_Synthesis", full.names = T)
Synthesis <- data.table::fread(SyntheFile, colClasses = "character", data.table = F)
LogFile <- list.files(file.path(L1,"WaterSample"),pattern = "water_sample_log", full.names = T)
if (length(LogFile) == 0) {
stop("No water_sample_log found in: ",file.path(L1,"WaterSample"))
} else if (length(LogFile) > 1) {
stop("Multiple water_sample_log found in: ",file.path(L1,"WaterSample"),
"\n",str_c(LogFile, collapse = "\n"))
}
LabLog <- data.table::fread(LogFile, colClasses = "character", data.table = F) %>% mutate(Zsample=as.numeric(Zsample))
handyParams <- list.dirs(file.path(L1,"WaterSample"), recursive = F ,full.names = F)
# SPM ---------------------------------------------------------------------
if (any(str_detect(params, "SPM")) && any(str_detect(handyParams, "^SPM$"))) {
SPMfile <- list.files(file.path(L1,"WaterSample","SPM"), pattern = ".*SPM.*\\.csv$", full.names = T)
if (length(SPMfile) > 1) {
stop("Multiple SPM files foud: \n", SPMfile)
} else if (length(SPMfile) == 0) {
stop("No SPM file found, name must contain 'SPM' and end with '.csv'")
} else {
SPM_data <- data.table::fread(SPMfile, colClasses = "character", data.table = F)
}
# units detector to be extended
handyUnit <- paste0("(?<=_)(mg|ml)$")
SPMunits <- unique(na.omit(str_extract(names(SPM_data), handyUnit)))
if (length(SPMunits) < 2) {
weightUnit <- readline("missing units to calculate SPM, enter a unit for weight :")
volUnit <- readline("missing units to calculate SPM, enter a unit for volume :")
} else if (length(SPMunits) > 2) {
stop("Too many units detected: ",SPMunits)
} else {
weightUnit <- na.omit(str_extract(SPMunits, "mg"))
volUnit <- na.omit(str_extract(SPMunits, "ml"))
names(SPM_data) <- str_remove(names(SPM_data), "_(mg|ml)")
}
if (all(weightUnit != c("mg"))) {
stop(weightUnit,", not implemented")
}
if (all(volUnit != c("ml"))) {
stop(volUnit,", not implemented")
}
# Calculate SPM, PIM and POM for replicates, in [mg.L-1]
SPM_tbl <- SPM_data %>% select(SID, Replicate, V, Wbase, Wdry, Wburn) %>%
mutate(V = as.numeric(V), Wbase = as.numeric(Wbase), Wdry = as.numeric(Wdry), Wburn= as.numeric(Wburn) ) %>%
mutate(SPM = ((Wdry - Wbase) / V)*1000,
PIM = SPM-(Wdry-Wburn),
POM = SPM-PIM) %>%
# Should do a mutate_if to avoid warning caused by NA?
mutate(SPM= as.numeric(sprintf(SPM, fmt = '%#.2f')),
PIM= as.numeric(sprintf(PIM, fmt = '%#.2f')),
POM= as.numeric(sprintf(POM, fmt = '%#.2f')))
# QC request if no QC file are found in ProLog/SPM
QCfile <- list.files(file.path(project,"ProLog", "SPM"), pattern="QC[[:graph:]]+csv", full.names = T)
if (length(QCfile) == 1) {
QCSPM <- data.table::fread(QCfile, colClasses = "character", data.table = F) %>% mutate(QC=as.numeric(QC))
SPM_tbl <- SPM_tbl %>% left_join(QCSPM %>% select(SID,Replicate,QC,Comment), by=c("SID","Replicate"))
message()
QCrequest <- askYesNo("SPM QC file found, update QC report ?")
if (!is.na(QCrequest) && QCrequest) {
# will update QC report with QC info and overwrite L3 SPM
qc_spm(project, mission, LabLog, Synthesis, SPM_tbl, QCSPM)
}
SPM_tbl <- SPM_tbl %>% filter(QC>0)
} else if (length(QCfile) > 1) {
stop("more than one QC csv file found for SPM")
} else if (purrr::is_empty(QCfile)) {
message("\nNo QC files found, producing now ")
qc_spm(project, mission, LabLog, Synthesis, SPM_tbl)
# QCrequest <- readline(prompt = "")
# if (QCrequest == "y") {
# qc_spm(project, mission, LabLog, SPM_tbl)
# } else {
# message("No QC filter will be applied and all data will be used")
# }
}
SPM_nest <- SPM_tbl %>% select(SID, SPM, PIM, POM) %>% group_by(SID) %>% tidyr::nest()
SPMs <- SPM_nest %>% mutate(SPM= purrr::map_dbl(.x = data, ~ mean(.x$SPM, na.rm = T)),
PIM= purrr::map_dbl(.x = data, ~ mean(.x$PIM, na.rm = T)),
POM= purrr::map_dbl(.x = data, ~ mean(.x$POM, na.rm = T)))
SPMs <- SPMs %>% mutate(SPM= as.numeric(sprintf(SPM, fmt = '%#.2f')),
PIM= as.numeric(sprintf(PIM, fmt = '%#.2f')),
POM= as.numeric(sprintf(POM, fmt = '%#.2f'))) %>%
select(!data)
# SPMs_table <- data.table::data.table(SPM_tbl)
# SPMs_stats <- data.table::setDT(SPMs_table)[,list(SPM_Mean=mean(SPM),
# SPM_Max=max(SPM),
# SPM_Min=min(SPM),
# SPM_Median=as.numeric(median(SPM)),
# SPM_Std=sd(SPM),
# PIM_Mean=mean(PIM),
# PIM_Max=max(PIM),
# PIM_Min=min(PIM),
# PIM_Median=as.numeric(median(PIM)),
# PIM_Std=sd(PIM),
# POM_Mean=mean(POM),
# POM_Max=max(POM),
# POM_Min=min(POM),
# POM_Median=as.numeric(median(POM)),
# POM_Std=sd(POM)), by=SID]
# Significant digit formating this way could be great !
# SPMs_Stats %>% group_by(SID) %>% tidyr::nest() %>%
# purrr::map_dbl(. = data , ~ as.numeric(sprintf(., fmt = '%#.2f')))
lighthouse::check_l3(project, L3, set="SPM")
write.csv(SPMs,
file = file.path(L3,"SPM",
paste0("SPMs_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
# readr::write_csv(SPMs_stats,
# path = file.path(L3,"SPM",
# paste0("SPMs_stats_DB_",Sys.Date(),"_",mission,".csv")))
write.csv(SPM_tbl,
file = file.path(L3,"SPM",
paste0("SPMs_table_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
} else if (any(str_detect(params, "SPM")) && !any(str_detect(handyParams, "^SPM$"))) {
warning("SPM data base requested but no 'SPM' folder found under WaterSample, skiping.\n",immediate. = T)
}
# Ag ----------------------------------------------------------------------
if (any(str_detect(params, "Ag")) && any(str_detect(handyParams, "^Ag$"))) {
DataFolder <- file.path(L1,"WaterSample","Ag","RData")
if (!dir.exists(DataFolder)) {stop("folder ", DataFolder," does not exist")}
DataFiles <- list.files(DataFolder, pattern = ".RData$", full.names = T)
Ag_table <- data.frame()
for (i in seq_along(DataFiles)){
load(DataFiles[i])
ID <- str_extract(Ag$ID, "[:digit:]+")
wl <- Ag$Lambda
# which Ag to use .offset or .fitted
#Agdata <- Ag$Ag.fitted
Agdata <- Ag$Ag.offset
temp <- data.frame(ID,t(Agdata))
names(temp) <- c("SID",paste0("Ag_",wl))
if(check_wl_consistency(Ag_table, temp, DataFiles, i)) {
tryCatch(Ag_table <- bind_rows(Ag_table, temp))
} else {
Ag_table <- bind_rows(Ag_table, temp)
}
}
lighthouse::check_l3(project, L3, set="Ag")
write.csv(Ag_table,
file = file.path(L3,"Ag",
paste0("Ag_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
} else if (any(str_detect(params, "Ag")) && !any(str_detect(handyParams, "^Ag$"))) {
warning("Ag data base requested but no 'Ag' folder found under WaterSample, skiping.\n", immediate. = T)
}
# Ap ----------------------------------------------------------------------
if (any(str_detect(params, "Ap")) && any(str_detect(handyParams, "^Ap$"))) {
DataFolder <- file.path(L1,"WaterSample","Ap","RData")
if (!dir.exists(DataFolder)) {stop("folder ", DataFolder," does not exist")}
DataFiles <- list.files(DataFolder, pattern = "[[:digit:]]{3}.RData$", full.names = T)
# declare empty df to be filed by rowbind
Ap_table <- data.frame()
Anap_table <- data.frame()
Aph_table <- data.frame()
for (i in seq_along(DataFiles)){
load(DataFiles[i])
# Ap
Ap_data <- A$Ap$Ap.Stramski.mean
if (is.null(Ap_data)) {
warning("No Ap data in: ", DataFiles[i],"\n")
} else {
ID <- A$Ap$ID
wl <- A$Ap$Lambda
temp <- data.frame(ID,t(Ap_data))
names(temp) <- c("SID",paste0("Ap_",wl))
if(check_wl_consistency(Ap_table, temp, DataFiles, i)) {
tryCatch(Ap_table <- bind_rows(Ap_table, temp))
} else {
Ap_table <- bind_rows(Ap_table, temp)
}
}
# Anap
Anap_data <- A$Anap$Ap.Stramski.mean
if (is.null(Anap_data)) {
warning("No Anap data in: ", DataFiles[i],"\n")
} else {
ID <- A$Anap$ID
wl <- A$Anap$Lambda
temp <- data.frame(ID,t(Anap_data))
names(temp) <- c("SID",paste0("Anap_",wl))
if(check_wl_consistency(Anap_table, temp, DataFiles, i)) {
tryCatch(Anap_table <- bind_rows(Anap_table, temp))
} else {
Anap_table <- bind_rows(Anap_table, temp)
}
}
# Aph no ID and Lambda, take the last available (i.e, Ap or Anap)
# ID <- A$Aph.Stramski$ID
# wl <- A$Aph.Stramski$Lambda
Aph_data <- A$Aph.Stramski$Aph
if (is.null(Aph_data)) {
warning("No Aph data in: ", DataFiles[i],"\n")
} else {
temp <- data.frame(ID,t(Aph_data))
names(temp) <- c("SID",paste0("Aph_",wl))
if(check_wl_consistency(Aph_data, temp, DataFiles, i)) {
tryCatch(Aph_table <- bind_rows(Aph_table, temp))
} else {
Aph_table <- bind_rows(Aph_table, temp)
}
}
}
lighthouse::check_l3(project, L3, set="Ap")
write.csv(Ap_table,
file = file.path(L3,"Ap",
paste0("Ap_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
write.csv(Anap_table,
file = file.path(L3,"Ap",
paste0("Anap_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
write.csv(Aph_table,
file = file.path(L3,"Ap",
paste0("Aph_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
} else if (any(str_detect(params, "Ap")) && !any(str_detect(handyParams, "^Ap$"))) {
warning("Ap data base requested but no 'Ap' folder found under WaterSample, skiping.\n",immediate. = T)
}
}
#boot_median <- function(d,i) {median(d[i])}
#
# test <- SPMstats %>% mutate(booted = purrr::map(.x= data,
# ~ boot::boot(data = .x$SPM,
# statistic = boot_median,
# R = 1000,
# stype = "i")))
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Defines functions l3_water_sample_gen
Documented in l3_water_sample_gen
#' @name l3_water_sample_gen
#' @title l3_water_sample_gen
#' @author Raphael Mabit
#'
#' @description Generate a data base (one file by parameter) from L1 water sample files.
#' Different methods are aplicated depending on the type of parameter.
#' For Ag and Ap parameter, it takes the output of RspectroAbs package.
#' For SPM (Chl-a to be implemented) it read a .csv such as "link to example table"
#'
#' @param project The top level folder of the project
#'
#' @param mission Optional, name for data base file.
#' If none is providen, it is taken from the project name.
#'
#' @param params Character vector used to select for which parameters data bases should be created
#'
#' @import dplyr
#' @import stringr
#' @export
#'
l3_water_sample_gen <- function(project,mission="",params=c("SPM","Ag","Ap")) {
# Setup -------------------------------------------------------------------
if (!exists("mission") || mission == "" ) {
mission <- str_split(project,"/")[[1]]
mission <- mission[length(mission)]
message("mission name empty, taking name of the project: ",mission)
}
L1 <- file.path(project,"L1")
L3 <- file.path(project,"L3","WaterSample")
CheckList <- lighthouse::check_project(project, L1)
if (CheckList["Proot"][[1]] == F) {stop(project,"is not a project root folder")}
SyntheFile = list.files(path = project, pattern = "data_synthesis|Data_Synthesis", full.names = T)
Synthesis <- data.table::fread(SyntheFile, colClasses = "character", data.table = F)
LogFile <- list.files(file.path(L1,"WaterSample"),pattern = "water_sample_log", full.names = T)
if (length(LogFile) == 0) {
stop("No water_sample_log found in: ",file.path(L1,"WaterSample"))
} else if (length(LogFile) > 1) {
stop("Multiple water_sample_log found in: ",file.path(L1,"WaterSample"),
"\n",str_c(LogFile, collapse = "\n"))
}
LabLog <- data.table::fread(LogFile, colClasses = "character", data.table = F) %>% mutate(Zsample=as.numeric(Zsample))
handyParams <- list.dirs(file.path(L1,"WaterSample"), recursive = F ,full.names = F)
# SPM ---------------------------------------------------------------------
if (any(str_detect(params, "SPM")) && any(str_detect(handyParams, "^SPM$"))) {
SPMfile <- list.files(file.path(L1,"WaterSample","SPM"), pattern = ".*SPM.*\\.csv$", full.names = T)
if (length(SPMfile) > 1) {
stop("Multiple SPM files foud: \n", SPMfile)
} else if (length(SPMfile) == 0) {
stop("No SPM file found, name must contain 'SPM' and end with '.csv'")
} else {
SPM_data <- data.table::fread(SPMfile, colClasses = "character", data.table = F)
}
# units detector to be extended
handyUnit <- paste0("(?<=_)(mg|ml)$")
SPMunits <- unique(na.omit(str_extract(names(SPM_data), handyUnit)))
if (length(SPMunits) < 2) {
weightUnit <- readline("missing units to calculate SPM, enter a unit for weight :")
volUnit <- readline("missing units to calculate SPM, enter a unit for volume :")
} else if (length(SPMunits) > 2) {
stop("Too many units detected: ",SPMunits)
} else {
weightUnit <- na.omit(str_extract(SPMunits, "mg"))
volUnit <- na.omit(str_extract(SPMunits, "ml"))
names(SPM_data) <- str_remove(names(SPM_data), "_(mg|ml)")
}
if (all(weightUnit != c("mg"))) {
stop(weightUnit,", not implemented")
}
if (all(volUnit != c("ml"))) {
stop(volUnit,", not implemented")
}
# Calculate SPM, PIM and POM for replicates, in [mg.L-1]
SPM_tbl <- SPM_data %>% select(SID, Replicate, V, Wbase, Wdry, Wburn) %>%
mutate(V = as.numeric(V), Wbase = as.numeric(Wbase), Wdry = as.numeric(Wdry), Wburn= as.numeric(Wburn) ) %>%
mutate(SPM = ((Wdry - Wbase) / V)*1000,
PIM = SPM-(Wdry-Wburn),
POM = SPM-PIM) %>%
# Should do a mutate_if to avoid warning caused by NA?
mutate(SPM= as.numeric(sprintf(SPM, fmt = '%#.2f')),
PIM= as.numeric(sprintf(PIM, fmt = '%#.2f')),
POM= as.numeric(sprintf(POM, fmt = '%#.2f')))
# QC request if no QC file are found in ProLog/SPM
QCfile <- list.files(file.path(project,"ProLog", "SPM"), pattern="QC[[:graph:]]+csv", full.names = T)
if (length(QCfile) == 1) {
QCSPM <- data.table::fread(QCfile, colClasses = "character", data.table = F) %>% mutate(QC=as.numeric(QC))
SPM_tbl <- SPM_tbl %>% left_join(QCSPM %>% select(SID,Replicate,QC,Comment), by=c("SID","Replicate"))
message()
QCrequest <- askYesNo("SPM QC file found, update QC report ?")
if (!is.na(QCrequest) && QCrequest) {
# will update QC report with QC info and overwrite L3 SPM
qc_spm(project, mission, LabLog, Synthesis, SPM_tbl, QCSPM)
}
SPM_tbl <- SPM_tbl %>% filter(QC>0)
} else if (length(QCfile) > 1) {
stop("more than one QC csv file found for SPM")
} else if (purrr::is_empty(QCfile)) {
message("\nNo QC files found, producing now ")
qc_spm(project, mission, LabLog, Synthesis, SPM_tbl)
# QCrequest <- readline(prompt = "")
# if (QCrequest == "y") {
# qc_spm(project, mission, LabLog, SPM_tbl)
# } else {
# message("No QC filter will be applied and all data will be used")
# }
}
SPM_nest <- SPM_tbl %>% select(SID, SPM, PIM, POM) %>% group_by(SID) %>% tidyr::nest()
SPMs <- SPM_nest %>% mutate(SPM= purrr::map_dbl(.x = data, ~ mean(.x$SPM, na.rm = T)),
PIM= purrr::map_dbl(.x = data, ~ mean(.x$PIM, na.rm = T)),
POM= purrr::map_dbl(.x = data, ~ mean(.x$POM, na.rm = T)))
SPMs <- SPMs %>% mutate(SPM= as.numeric(sprintf(SPM, fmt = '%#.2f')),
PIM= as.numeric(sprintf(PIM, fmt = '%#.2f')),
POM= as.numeric(sprintf(POM, fmt = '%#.2f'))) %>%
select(!data)
# SPMs_table <- data.table::data.table(SPM_tbl)
# SPMs_stats <- data.table::setDT(SPMs_table)[,list(SPM_Mean=mean(SPM),
# SPM_Max=max(SPM),
# SPM_Min=min(SPM),
# SPM_Median=as.numeric(median(SPM)),
# SPM_Std=sd(SPM),
# PIM_Mean=mean(PIM),
# PIM_Max=max(PIM),
# PIM_Min=min(PIM),
# PIM_Median=as.numeric(median(PIM)),
# PIM_Std=sd(PIM),
# POM_Mean=mean(POM),
# POM_Max=max(POM),
# POM_Min=min(POM),
# POM_Median=as.numeric(median(POM)),
# POM_Std=sd(POM)), by=SID]
# Significant digit formating this way could be great !
# SPMs_Stats %>% group_by(SID) %>% tidyr::nest() %>%
# purrr::map_dbl(. = data , ~ as.numeric(sprintf(., fmt = '%#.2f')))
lighthouse::check_l3(project, L3, set="SPM")
write.csv(SPMs,
file = file.path(L3,"SPM",
paste0("SPMs_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
# readr::write_csv(SPMs_stats,
# path = file.path(L3,"SPM",
# paste0("SPMs_stats_DB_",Sys.Date(),"_",mission,".csv")))
write.csv(SPM_tbl,
file = file.path(L3,"SPM",
paste0("SPMs_table_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
} else if (any(str_detect(params, "SPM")) && !any(str_detect(handyParams, "^SPM$"))) {
warning("SPM data base requested but no 'SPM' folder found under WaterSample, skiping.\n",immediate. = T)
}
# Ag ----------------------------------------------------------------------
if (any(str_detect(params, "Ag")) && any(str_detect(handyParams, "^Ag$"))) {
DataFolder <- file.path(L1,"WaterSample","Ag","RData")
if (!dir.exists(DataFolder)) {stop("folder ", DataFolder," does not exist")}
DataFiles <- list.files(DataFolder, pattern = ".RData$", full.names = T)
Ag_table <- data.frame()
for (i in seq_along(DataFiles)){
load(DataFiles[i])
ID <- str_extract(Ag$ID, "[:digit:]+")
wl <- Ag$Lambda
# which Ag to use .offset or .fitted
#Agdata <- Ag$Ag.fitted
Agdata <- Ag$Ag.offset
temp <- data.frame(ID,t(Agdata))
names(temp) <- c("SID",paste0("Ag_",wl))
if(check_wl_consistency(Ag_table, temp, DataFiles, i)) {
tryCatch(Ag_table <- bind_rows(Ag_table, temp))
} else {
Ag_table <- bind_rows(Ag_table, temp)
}
}
lighthouse::check_l3(project, L3, set="Ag")
write.csv(Ag_table,
file = file.path(L3,"Ag",
paste0("Ag_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
} else if (any(str_detect(params, "Ag")) && !any(str_detect(handyParams, "^Ag$"))) {
warning("Ag data base requested but no 'Ag' folder found under WaterSample, skiping.\n", immediate. = T)
}
# Ap ----------------------------------------------------------------------
if (any(str_detect(params, "Ap")) && any(str_detect(handyParams, "^Ap$"))) {
DataFolder <- file.path(L1,"WaterSample","Ap","RData")
if (!dir.exists(DataFolder)) {stop("folder ", DataFolder," does not exist")}
DataFiles <- list.files(DataFolder, pattern = "[[:digit:]]{3}.RData$", full.names = T)
# declare empty df to be filed by rowbind
Ap_table <- data.frame()
Anap_table <- data.frame()
Aph_table <- data.frame()
for (i in seq_along(DataFiles)){
load(DataFiles[i])
# Ap
Ap_data <- A$Ap$Ap.Stramski.mean
if (is.null(Ap_data)) {
warning("No Ap data in: ", DataFiles[i],"\n")
} else {
ID <- A$Ap$ID
wl <- A$Ap$Lambda
temp <- data.frame(ID,t(Ap_data))
names(temp) <- c("SID",paste0("Ap_",wl))
if(check_wl_consistency(Ap_table, temp, DataFiles, i)) {
tryCatch(Ap_table <- bind_rows(Ap_table, temp))
} else {
Ap_table <- bind_rows(Ap_table, temp)
}
}
# Anap
Anap_data <- A$Anap$Ap.Stramski.mean
if (is.null(Anap_data)) {
warning("No Anap data in: ", DataFiles[i],"\n")
} else {
ID <- A$Anap$ID
wl <- A$Anap$Lambda
temp <- data.frame(ID,t(Anap_data))
names(temp) <- c("SID",paste0("Anap_",wl))
if(check_wl_consistency(Anap_table, temp, DataFiles, i)) {
tryCatch(Anap_table <- bind_rows(Anap_table, temp))
} else {
Anap_table <- bind_rows(Anap_table, temp)
}
}
# Aph no ID and Lambda, take the last available (i.e, Ap or Anap)
# ID <- A$Aph.Stramski$ID
# wl <- A$Aph.Stramski$Lambda
Aph_data <- A$Aph.Stramski$Aph
if (is.null(Aph_data)) {
warning("No Aph data in: ", DataFiles[i],"\n")
} else {
temp <- data.frame(ID,t(Aph_data))
names(temp) <- c("SID",paste0("Aph_",wl))
if(check_wl_consistency(Aph_data, temp, DataFiles, i)) {
tryCatch(Aph_table <- bind_rows(Aph_table, temp))
} else {
Aph_table <- bind_rows(Aph_table, temp)
}
}
}
lighthouse::check_l3(project, L3, set="Ap")
write.csv(Ap_table,
file = file.path(L3,"Ap",
paste0("Ap_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
write.csv(Anap_table,
file = file.path(L3,"Ap",
paste0("Anap_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
write.csv(Aph_table,
file = file.path(L3,"Ap",
paste0("Aph_DB_",Sys.Date(),"_",mission,".csv")), row.names = F)
} else if (any(str_detect(params, "Ap")) && !any(str_detect(handyParams, "^Ap$"))) {
warning("Ap data base requested but no 'Ap' folder found under WaterSample, skiping.\n",immediate. = T)
}
}
#boot_median <- function(d,i) {median(d[i])}
#
# test <- SPMstats %>% mutate(booted = purrr::map(.x= data,
# ~ boot::boot(data = .x$SPM,
# statistic = boot_median,
# R = 1000,
# stype = "i")))
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