import _ from 'lodash';
import { adjust_lenhei } from './z-score-helper';
import {
  standardize_sex_var,
  standardize_oedema_var,
  age_to_days,
  age_to_months,
  round
} from './utils';
import anthro_zscore_length_for_age from './z-score-length-for-age';
import anthro_zscore_weight_for_age from './z-score-weight-for-age';
import anthro_zscore_weight_for_lenhei from './z-score-weight-for-lenhei';
import anthro_zscore_bmi_for_age from './z-score-bmi-for-age';
import anthro_zscore_head_circumference_for_age from './z-score-head-circumference-for-age';
import anthro_zscore_arm_circumference_for_age from './z-score-arm-circumference-for-age';
import anthro_zscore_triceps_skinfold_for_age from './z-score-triceps-skinfold-for-age';
import anthro_zscore_subscapular_skinfold_for_age from './z-score-subscapular-skinfold-for-age';

// ' Calculate z-scores for the eight anthropometric indicators
// '
// ' @description
// '
// ' This function calculates z-scores for the eight anthropometric indicators,
// ' weight-for- age, length/height-for-age, weight-for-length/height,
// ' body mass index (BMI)-for-age, head circumference-for-age,
// ' arm circumference-for-age, triceps skinfold-for-age and subscapular
// ' skinfold-for-age based on the WHO Child Growth Standards.
// '
// ' @param sex A numeric or text variable containing gender information.
// '            If it is numeric, its values must be: 1 for males and 2 for
// '            females. If it is character, it must be "m" or "M" for males
// '            and "f" or "F" for females. No z-scores will be calculated
// '            if sex is missing.
// ' @param age A numeric variable containing age information; age can be
// '            in either days or months (if optional argument is_age_in_month
// '            is set to TRUE). An exact age in days is expected and should
// '            not be rounded if age is in months. Age-related z-scores will
// '            NOT be calculated if age is missing (NA).
// ' @param is_age_in_month A logical flag; if TRUE, variable age unit will be
// '            treated as months. The function converts it to days by dividing
// '            age by 30.4375 and rounding it to integer so that reference
// '            tables can be used. When unspecified, the default value FALSE
// '            is used and age unit is treated as days.
// ' @param weight A numeric variable containing body weight information, which
// '               must be in kilograms. Weight-related z-scores are not
// '               calculated if body weight is missing.
// ' @param lenhei A numeric variable containing length (recumbent length) or
// '               height (standing height) information, which must be in
// '               centimeters. Length/height-related z-scores will not be
// '               calculated if lenhei is missing. For children with age
// '               below 24 months (i.e. below 731 days) and standing height
// '               measured, the function converts it to recumbent length by
// '               adding 0.7 cm; and for children with age equal and above
// '               24 months and measured in recumbent length, the function
// '               converts it to standing height by subtracting 0.7 cm.
// '               This way all the z-scores calculated by this function are
// '               length-based for children below 24 months, and
// '               height-based otherwise. This converted length/height
// '               according to age is assigned to the variable clenhei in
// '               the resulting data.frame.
// ' @param measure A character variable indicating whether recumbent length
// '                or standing height was measured for each observation.
// '                The values of this variable must be "L" or "l" for recumbent
// '                length, and "H" or "h" for standing height.
// '                Although it is highly recommended that this variable
// '                is provided according to the measurements taken in
// '                the survey, it is possible to run the analysis without
// '                specifying this variable. If unspecified, the default
// '                vector with all missing values is used. The function
// '                imputes the missing values according to the
// '                following algorithm:
// '                \itemize{
// '                \item If age is not missing, then it is recumbent length
// '                      if age below 24 months (731 days), and standing height
// '                      if age equal and above 24 months.
// '                \item If age is missing, then it is recumbent length if
// '                      measurement < 87 cm and standing height
// '                      if measurement >= 87 cm.
// '                }
// ' @param headc A numeric variable containing head circumference information,
// '              which must be in centimeters. Head circumference-for-age
// '              z-scores are not calculated if head circumference is missing.
// ' @param armc A numeric variable containing arm circumference information,
// '             which must be in centimeters. Arm circumference-for-age z-scores
// '             are not calculated if arm circumference is missing.
// ' @param triskin A numeric variable containing triceps skinfold information,
// '             which must be in millimeters. Triceps skinfold-for-age z-scores
// '             are not calculated if triceps skinfold is missing.
// ' @param subskin A numeric variable containing subscapular skinfold information,
// '             which must be in millimeters. Subscapular skinfold-for-age z-scores
// '             are not calculated if subscapular skinfold is missing.
// ' @param oedema The values of this character variable must be "n", "N" or "2"
// '             for non-oedema, and "y", "Y", "1" for oedema. Although it is highly
// '             recommended that this variable is provided by the survey,
// '             it is possible to run
// '             the analysis without specifying this variable. If unspecified,
// '             the default vector of all "n" with values considered as
// '             non-oedema is used. Missing values will be
// '             treated as non-oedema. For oedema, weight related z-scores
// '             (zwei, zwfl and zbmi) are NOT calculated (set to missing),
// '             BUT they are treated as being < -3 SD in the weight-related
// '             indicator prevalence (\code{\link{anthro_prevalence}})
// '             estimation.
// '
// '
// ' @return A data.frame with three types of columns. Columns starting with a
// ' "c" are cleaned versions of the input arguments. Columns beginning with
// ' a "z" are the respective z-scores and columns prefixed by a "f" indicate
// ' if these z-scores are flagged (integers).
// ' The number of rows is given by the length
// ' of the input arguments.
// '
// ' The following columns are returned:
// ' \itemize{
// ' \item{\code{clenhei}} converted length/height for deriving z-score
// ' \item{\code{cbmi}} BMI value based on length/height given by clenhei
// '
// ' \item{\code{zlen}} Length/Height-for-age z-score
// ' \item{\code{flen}} 1, if \code{abs(zlen) > 6}
// '
// ' \item{\code{zwei}} Weight-for-age z-score
// ' \item{\code{fwei}} 1, if \code{zwei < -6} or \code{zwei > 5}
// '
// ' \item{\code{zwfl}} Weight-for-length/height z-score
// ' \item{\code{fwfl}} 1, if \code{abs(zwfl) > 5}
// '
// ' \item{\code{zbmi}} BMI-for-age z-score
// ' \item{\code{fbmi}} 1, if \code{abs(zbmi) > 5}
// '
// ' \item{\code{zhc}} Head circumference-for-age z-score
// ' \item{\code{fhc}} 1, if \code{abs(zhc) > 5}
// '
// ' \item{\code{zac}} Arm circumference-for-age z-score
// ' \item{\code{fac}} 1, if \code{abs(zac) > 5}
// '
// ' \item{\code{zts}} Triceps skinfold-for-age z-score
// ' \item{\code{fts}} 1, if \code{abs(zts) > 5}
// '
// ' \item{\code{zss}} Subscapular skinfold-for-age z-score
// ' \item{\code{fss}} 1, if \code{abs(zss) > 5}
// '
// ' }
// '
// ' If not all parameter values have equal length, parameter values will be
// ' repeated to match the maximum length of all arguments except
// ' \code{is_age_in_month} using \code{rep_len}. This happens without warnings.
// '
// ' Z-scores are only computed for children younger than 60 months (age in months < 60)
// '
// ' @references
// ' WHO Multicentre Growth Reference Study Group (2006). WHO Child Growth Standards: Length/height-for-age, weight-for-age, weight-for-length, weight-for-height and body mass index-for-age: Methods and development.
// ' Geneva: World Health Organization; pp 312. (web site: http://www.who.int/childgrowth/publications/en/ )
// '
// ' WHO Multicentre Growth Reference Study Group (2007). WHO Child Growth Standards: Head circumference-for-age, arm circumference-for-age, triceps skinfold-for-age and subscapular skinfold-for-age: Methods and development.
// ' Geneva: World Health Organization; pp 217. (web site: http://www.who.int/childgrowth/publications/en/ )
// '
// ' @examples
// ' # you can either use the function to compute zscores for specific values
// ' anthro_zscores(sex = "f", age = 10, is_age_in_month = TRUE, weight = 10)
// '
// ' # values will be recycled so not all input values need to be of the same length
// ' anthro_zscores(sex = "f", age = c(10, 20, 30), weight = 10)
// '
// ' # or use it with a compute dataset
// ' \dontrun{
// ' your_data_set <- read.csv("<your survey>.csv")
// ' with(
// '   your_data_set,
// '   anthro_zscores(
// '     sex = sex, age = age_in_days,
// '     weight = weight, lenhei = lenhei
// '   )
// ' )
// ' }
// ' @include anthro.R
// ' @include assertions.R
// ' @export
type anthro_zscores = {
  sex: string | 1 | 2,
  age?: number,
  is_age_in_month?: boolean,
  weight?: number,
  lenhei?: number,
  measure?: string,
  headc?: number,
  armc?: number,
  triskin?: number,
  subskin?: number,
  oedema?: string
};
export default function anthro_zscores({
  sex,
  age,
  is_age_in_month = false,
  weight,
  lenhei,
  measure,
  headc,
  armc,
  triskin,
  subskin,
  oedema = 'n',
}: anthro_zscores)  {

  //  clean sex
  const csex = standardize_sex_var(sex);

  //  clean oedema, we set all oedema not being "y" to "n"
  const oedema_clean = standardize_oedema_var(oedema);

  if(!csex) { 
    console.error('Sex is required in order to calculate z-scores')
  }

  if(!age && csex) { // This will need to be adjusted if the "name" fields of the underlying anthro functions are changed
    console.info('Age not provided, returning only weight for length z-score without height adjustment')
    const output = {
      cbmi: undefined,
      clenhei: lenhei,
      cmeasure: undefined,
      csex,
      fac: undefined,
      fbmi: undefined,
      fhc: undefined,
      flen: undefined,
      fss: undefined,
      fts: undefined,
      fwei: undefined,
      zac: undefined,
      zbmi: undefined,
      zhc: undefined,
      zlen: undefined,
      zss: undefined,
      zts: undefined,
      zwei: undefined,
      ...anthro_zscore_weight_for_lenhei({
        weight,
        lenhei: lenhei,
        lenhei_unit: undefined,
        sex: csex,
        oedema: oedema_clean,
      }),
    }
    return output
  }
    
  //  clean measure
  let cmeasure: string | undefined = _.toLower(_.trim(measure));
  cmeasure = ['l', 'h'].includes(cmeasure) ? cmeasure : undefined;

  const age_in_days = age ? age_to_days(age, is_age_in_month) : undefined;
  const age_in_months = age ? age_to_months(age, is_age_in_month) : undefined;

  //  we consider a height measure for children younger than 9 months as
  //  implausible
  cmeasure = (!_.isEmpty(cmeasure)
    && age_in_months
    && cmeasure === 'h'
    && age_in_months < 9) ? undefined : cmeasure;

  const clenhei = lenhei && age_in_days ? adjust_lenhei(age_in_days, cmeasure, lenhei) : undefined;

  const cbmi = weight && clenhei ? round(weight / ((clenhei / 100) ** 2)): undefined;

  if (age_in_days && age_in_months && csex) {
  const output = {
    clenhei,
    cbmi,
    cmeasure,
    csex,
    ...anthro_zscore_length_for_age({
      lenhei: clenhei,
      age_in_days,
      age_in_months,
      sex: csex,
    }),
    ...anthro_zscore_weight_for_age({
      weight,
      age_in_days,
      age_in_months,
      sex: csex,
      oedema: oedema_clean,
    }),
    ...anthro_zscore_weight_for_lenhei({
      weight,
      lenhei: clenhei,
      lenhei_unit: cmeasure,
      age_in_days,
      age_in_months,
      sex: csex,
      oedema: oedema_clean,
    }),
    ...anthro_zscore_bmi_for_age({
      bmi: cbmi,
      age_in_days,
      age_in_months,
      sex: csex,
      oedema: oedema_clean,
    }),
    ...anthro_zscore_head_circumference_for_age({
      headc,
      age_in_days,
      age_in_months,
      sex: csex,
    }),
    ...anthro_zscore_arm_circumference_for_age({
      armc,
      age_in_days,
      age_in_months,
      sex: csex,
    }),
    ...anthro_zscore_triceps_skinfold_for_age({
      triskin,
      age_in_days,
      age_in_months,
      sex: csex,
    }),
    ...anthro_zscore_subscapular_skinfold_for_age({
      subskin,
      age_in_days,
      age_in_months,
      sex: csex,
    }),
  };
  return output
  }
}