R/import_param.R

In kkhamis/opticalWQ: opticalWQ (a Package for processing high-freq data from optical sensors)

time_setup<-function(df, parse="ymd HMS",round="30 minutes"){
        df$TS<-lubridate::parse_date_time(paste(df$date_time), parse)
        df<-dplyr::mutate(df, h=lubridate::hour(TS))
        df<-dplyr::mutate(df, min=lubridate::minute(TS))
        df<-dplyr::mutate(df, doy=lubridate::yday(TS))
        df<-dplyr::mutate(df, TS_round=lubridate::round_date(TS, round))
        df<-dplyr::mutate(df, h_min=paste(h,":",min))
}

import_param <-
        function(path,
                 date_format = "ymd HMS",
                 single_sensor = T,
                 sensor) {
                ###----initial data extraction------------------------
                if (single_sensor == T) {
                        files <- dir(
                                path = path,
                                recursive = T,
                                pattern = "003R",
                                full.names = T
                        )

                        df <- files %>% purrr::map( ~ readr::read_delim(.x,
                                                          delim = ";", na = "#NV")) %>%
                                purrr::reduce(rbind) %>% janitor::clean_names() %>%
                                dplyr::filter(!stringr::str_detect(name, "(scaled)")) %>%
                                time_setup() %>%
                                dplyr::select(-dplyr::starts_with("comment"))

                        df_scaled <- files %>% purrr::map( ~ readr::read_delim(.x,
                                                                 delim = ";", na = "#NV")) %>%
                                purrr::reduce(rbind) %>% janitor::clean_names() %>%
                                dplyr::filter(stringr::str_detect(name, "(scaled)")) %>%
                                time_setup() %>%
                                dplyr::select(-dplyr::starts_with("comment"))

                        list(df = df, df_scaled = df_scaled)

                } else if (single_sensor == F) {
                        ls <- list()
                        for (i in 1:length(sensor)) {
                                files <- dir(
                                        path = path,
                                        recursive = T,
                                        pattern = sensor[i],
                                        full.names = T
                                )
                                df <- files %>% purrr::map( ~ readr::read_delim(.x,
                                                                  delim = ";", na = "#NV")) %>%
                                        purrr::reduce(rbind) %>% janitor::clean_names() %>%
                                        dplyr::filter(!stringr::str_detect(name, "(scaled)")) %>%
                                        time_setup() %>%
                                        dplyr::select(-dplyr::starts_with("comment"))

                                df_scaled <- files %>% purrr::map( ~ readr::read_delim(.x,
                                                                         delim = ";", na = "#NV")) %>%
                                        purrr::reduce(rbind) %>% janitor::clean_names() %>%
                                        dplyr::filter(stringr::str_detect(name, "(scaled)")) %>%
                                        time_setup() %>%
                                        dplyr::select(-dplyr::starts_with("comment"))
                                ls[[i]] <- list(df = df, df_scaled = df_scaled)
                                names(ls)[[i]]  <- sensor[i]

                        }
                        list(sensor_list = ls)
                }
        }


test1<-import_param(path = "D:/Uni work/Postdoc 2019-2020/Field work/India field_Patna-2019/Trios/All_Nov_trios data/DATA/OPUS",single_sensor = T)

#test2<-import_param(path = "D:/Uni work/Postdoc 2019-2020/Field work/India field_Patna-2019/Trios/opus cal 2019",single_sensor = F,sensor=c("R7213","R7214","R7215"))