#' @import XML

#' @import data.table

#' @import yaml

#' @importFrom Rcpp evalCpp

NULL

#' The S4 class which holds all the CCHIC patient record - served as a database.

#'

#' @description  ccRecord is a class to hold the raw episode data parsed directly 

#' from XML or CSV files.

#' @field nepisodes is an integer number indicates the total number of episode

#'       the record is holding.

#' @field dmgtb a data.table containing all the demographic information of each

#'       episode, including site_id, NHS number, PAS number, admission date/time,

#'       and discharge date/time. This field is usually left empty.

#' @field infotb a data.table holding the parsing information of each episode such as the

#'       parsing time and from which file it parsed from.

#' @field episdoes a list of ccEpisode objects. 

#' @exportClass ccRecord

#' @export ccRecord

#' @examples

#' heart_rate <- data.frame(seq(10), rep(70, 10)) # NIHR_HIC_ICU_0108

#' site_id <- "Q70" #  NIHR_HIC_ICU_0002

#' episode_id <- "0000001" # NIHR_HIC_ICU_0005

#'

#' # Create a new episode 

#' ep <- new.episode(list(NIHR_HIC_ICU_0108=heart_rate, 

#'                          NIHR_HIC_ICU_0002=site_id, 

#'                          NIHR_HIC_ICU_0005=episode_id)) 

#' 

#' # modifying records 

#' rec <- ccRecord() # a new record 

#' rec <- rec + ep # adding a new episode to the record

#' rec <- rec + NULL # adding nothing to the record

#' rec <- rec + rec # adding a record to a record

#' # Adding a list of episodes 

#' rec <- ccRecord()

#' ep1 <- new.episode()

#' ep2 <- new.episode()

#' eps.list <- list(ep1, ep2)

#' new.rec <- rec + eps.list

ccRecord <- setClass("ccRecord", 

                      slots=c(nepisodes="integer", dmgtb="data.table", 

                              infotb="data.table", episodes="list"),

                      prototype=prototype(nepisodes=as.integer(0), 

                                          infotb=data.table(), 

                                          dmgtb=data.table()))

#' The S4 class which holds data of a single episode. 

#' 

#' @field site_id character string. Site ID, if presented, otherwise "NA".

#' @field episode_id character string. Episode ID, if presented, otherwise "NA".

#' @field nhs_number character string. NHS number, if presented, otherwise "NA".

#' @field pas_number character string. PAS number, if presented, otherwise "NA".

#' @field parse_file character string. The source XML file. If the source is not a file then "NA".

#' @field t_admission POSIXct. Time of Admission to the ICU, if presented, otherwise NA.

#' @field t_discharge POSIXct. Time of discharge of the ICU, if presented, otherwise NA.

#' @field parse_time POSIXct. Parse time. 

#' @field data A list which holds all the data of this episode which is indexed by NIHIC code. 

#' @exportClass ccEpisode 

ccEpisode <- setClass("ccEpisode", 

                       slots=c(site_id="character", 

                               episode_id="character",

                               nhs_number="character",

                               pas_number="character",

                               t_admission="POSIXct", 

                               t_discharge="POSIXct",

                               parse_file="character",

                               parse_time="POSIXct", 

                               data="list"), 

                       prototype=prototype(site_id="NA", 

                                           episode_id="NA", 

                                           nhs_number="NA",

                                           pas_number="NA", 

                                           t_admission=as.POSIXct(NA), 

                                           t_discharge=as.POSIXct(NA), 

                                           parse_file="NA",

                                           parse_time=as.POSIXct(NA),

                                           data=list()))

index.record <- function(rec) {

    }

    # id will be filled in the following sequence, NHS number, PAS number,

    # site-episode combination and unknown tags. 

    }

}

#' Adding a list of ccEpisode to ccRecord

#' 

#' @description Adding a list of one or multiple ccEpisode objects to a

#' ccRecord object, the information table (infotb) will be updated automatically.

#' It is the more efficient way to add multiple ccEpisode objects.

#' @param e1 ccRecord

#' @param e2 a list of ccEpisode objects

#' @return ccRecord

#' @exportMethod +

setMethod('+', c("ccRecord", "list"), 

          function(e1, e2) {

          })

#' Adding one ccEpisode object to a ccRecord 

#' 

#' @param e1 ccRecord-class

#' @param e2 ccEpisode-class

#' @return ccRecord-class 

setMethod('+', c("ccRecord", "ccEpisode"), 

          function(e1, e2) {

          })

#' Combine two ccRecord objects 

#' 

#' @param e1 ccRecord-class

#' @param e2 ccRecord-class

#' @return ccRecord-class

setMethod('+', c("ccRecord", "ccRecord"), 

          function(e1, e2) {

          })

#' Adding nothing to a ccRecord object and return the original ccRecord

#' 

#' @param e1 ccRecord-class 

#' @param e2 NULL 

setMethod('+', c("ccRecord", "NULL"), 

#' Create a new episode

#' 

#' create a new ccEpisode object by given the episode data as a

#' list. The list should be organised in data items and indexed with NIHC code,

#' e.g. NIHR_HIC_ICU_0108. 

#'

#' @param lt is a list

#' @param parse_file the file location from which the episode comes from.

#' @param parse_time the parse date and time of the episode.

#' @return ccEpisode object

#' @examples 

#' eps <- list()

#' eps[["NIHR_HIC_ICU_0018"]] <- data.frame(time=seq(10), rep(70, 10))

#' new.episode(eps)

#' 

#' @export 

new.episode <- function(lt=list(), 

                        parse_file="NA", 

                        parse_time=as.POSIXct(NA)) { 

    # character values 

    } # Time data 

}

#' loop over all episodes of a ccRecord object 

#' 

#' @param record ccRecord 

#' @param fun function 

#' @export 

for_each_episode <- function(record, fun) {

}

#' Subsetting a ccRecord object and return a list of ccEpisode objects.

#' 

#' @param x ccRecord-class

#' @param i integer vector

#' @exportMethod [[

setMethod("[[", "ccRecord",

          function(x, i) {

              }

          }

)

#' Create a subset of ccRecord object from the original one via specifying the row number of episodes.

#'

#' @param x ccRecord-class

#' @param i integer vector

#' @exportMethod [

setMethod("[", "ccRecord",

          function(x, i){ 

              }

          })

#' Create a ccRecord subsetting via selected sites.

#'

#' @param x ccRecord-class

#' @param i character vector which contains site_ids, e.g. c("Q70", "Q70W")

#' @exportMethod [

setMethod("[", signature(x="ccRecord", i="character"), 

          definition=function(x, i) {

              }

              }

          })

episode_graph <- function(ep, items=NULL) {

            else

        }

    }

    #"#1E506C""#D1746F"

}

#' Individual episode chart

#' 

#' Create an individual episode chart for its diagnosis, drugs and physiological

#' variables. Diagnosis and drugs are always included, while the user can

#' select other longitudinal data. 

#' @param r ccEpisode-class

#' @param v short name of longitudinal data. While v is not given, the chart 

#' will only display h_rate, spo2, bilirubin, platelets, pao2_fio2, gcs_total. 

#' @return a table of selected vars of an episode

#' @exportMethod plot_episode

#' @examples

#' \dontrun{

#' plot_episode(ccd@episodes[[1]]) # plot first episode with default variables. 

#' plot_episode(ccd@episodes[[1]], "h_rate") # plot first episode heart rate

#' }

setGeneric("plot_episode", function(r, v) {

})

#' Episode chart

#' 

#' @param r ccEpisode-class

#' @param v character 

setMethod("plot_episode", signature(r="ccEpisode", v="character"), 

function(r, v){

})

#' Episode chart default fields

#' 

#' @param r ccEpisode-class

setMethod("plot_episode", signature(r="ccEpisode", v="missing"), 

function(r) {

})