R/qc_md_general_checks.R

Defines functions qc_env_vars_presence qc_factor_values qc_md_cols qc_env_dics qc_plant_dics qc_species_dics qc_stand_dics qc_site_dics create_dic

Documented in create_dic qc_env_dics qc_env_vars_presence qc_factor_values qc_md_cols qc_plant_dics qc_site_dics qc_species_dics qc_stand_dics

################################################################################
#' Variable dictionaries for metadata
#'
#' \code{create_dic} creates a dictionary containing metadata variable names
#' and expected class. It is intended as an internal function.
#'
#' After loading metadata sheets, introduced variables and their classes must be
#' checked in order to ensure data correctness. For that, we need dictionaries
#' containing all the expected variables and their corresponding classes to
#' compare. This function works inside of \code{\link{qc_col_class}}, so there
#' is no need to call it directly
#'
#' @family Quality Checks Functions
#'
#' @param dic_name Name of the metadata sheet of which dictionary is needed.
#'   It must be one of \code{site_md}, \code{stand_md}, \code{species_md},
#'   \code{plant_md} or \code{environmental_md}.
#'
#' @return A named list, variable names being the index and class the value

# START
# Function declaration
create_dic <- function(dic_name, parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({
    # STEP 0
    # Argument checking
    # check if dictionary name is one of the five kinds of metadata allowed
    accepted_sheets <- c('site_md', 'stand_md', 'species_md',
                         'plant_md', 'environmental_md')

    if (!is.character(dic_name) || !(dic_name %in% accepted_sheets)) {
      stop('Provided dicitonary name is not a character or is not a valid name.',
           ' Please see function help for information about valid dictionary names')
    }

    # STEP 1
    # Get the kind of metadata and populate the dictionary

    # 1.1 site metadata
    if (dic_name == 'site_md') {
      dic <- list(si_name = 'character', si_country = 'character',
                  si_contact_firstname = 'character', si_contact_lastname = 'character',
                  si_contact_email = 'character', si_contact_institution = 'character',
                  si_addcontr_firstname = 'character', si_addcontr_lastname = 'character',
                  si_addcontr_email = 'character', si_addcontr_institution = 'character',
                  si_lat = c('numeric', 'integer'), si_long = c('numeric', 'integer'),
                  si_elev = c('numeric', 'integer'), si_igbp = 'character',
                  si_paper = 'character', si_dist_mgmt = 'character',
                  si_flux_network = 'logical', si_dendro_network = 'logical',
                  si_remarks = 'character', si_code = 'character')

      # 1.1.1 return dic
      return(dic)
    }

    # 1.2 stand metadata
    if (dic_name == 'stand_md'){
      dic <- list(st_name = 'character', st_growth_condition = 'character',
                  st_treatment = 'character', st_age = c('numeric', 'integer'),
                  st_height = c('numeric', 'integer'), st_density = c('numeric', 'integer'),
                  st_basal_area = c('numeric', 'integer'), st_lai = c('numeric', 'integer'),
                  st_aspect = 'character', st_terrain = 'character',
                  st_soil_depth = c('numeric', 'integer'), st_soil_texture = 'character',
                  st_sand_perc = c('numeric', 'integer'), st_silt_perc = c('numeric', 'integer'),
                  st_clay_perc = c('numeric', 'integer'), st_remarks = 'character',
                  si_code = 'character')

      # 1.2.1 return dic
      return(dic)
    }

    # 1.3 Species metadata
    if (dic_name == 'species_md') {
      dic <- list(sp_name = 'character', sp_ntrees = c('numeric', 'integer'),
                  sp_leaf_habit = 'character', sp_basal_area_perc = c('numeric', 'integer'),
                  si_code = 'character')

      # 1.3.1 return dic
      return(dic)
    }

    # 1.4 Plant metadata
    if (dic_name == 'plant_md') {
      dic <- list(pl_name = c('character', 'numeric', 'integer'), pl_species = 'character',
                  pl_treatment = 'character', pl_dbh = c('numeric', 'integer'),
                  pl_height = c('numeric', 'integer'), pl_age = c('numeric', 'integer'),
                  pl_social = 'character', pl_sapw_area = c('numeric', 'integer'),
                  pl_sapw_depth = c('numeric', 'integer'), pl_bark_thick = c('numeric', 'integer'),
                  pl_leaf_area = c('numeric', 'integer'), pl_sens_meth = 'character',
                  pl_sens_man = 'character', pl_sens_cor_grad = 'character',
                  pl_sens_cor_zero = 'character', pl_sap_units = 'character',
                  pl_sens_length = c('numeric', 'integer'), pl_sens_hgt = c('numeric', 'integer'),
                  pl_sens_timestep = c('numeric', 'integer'), pl_radial_int = 'character',
                  pl_azimut_int = 'character', pl_remarks = 'character',
                  pl_code = 'character', si_code = 'character',
                  pl_sens_calib = 'logical')

      # 1.4.1 return dic
      return(dic)
    }

    # 1.5 Environmental metadata
    if (dic_name == 'environmental_md') {
      dic <- list(env_time_zone = 'character', env_time_daylight = 'logical',
                  env_timestep = c('numeric', 'integer'), env_ta = 'character',
                  env_rh = 'character', env_vpd = 'character',
                  env_sw_in = 'character', env_ppfd_in = 'character',
                  env_netrad = 'character', env_ws = 'character',
                  env_precip = 'character', env_swc_shallow_depth = c('numeric', 'integer'),
                  env_swc_deep_depth = c('numeric', 'integer'), env_plant_watpot = 'character',
                  env_leafarea_seasonal = 'character', env_remarks = 'character',
                  si_code = 'character')

      # 1.5.1 return dic
      return(dic)
    }

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'create_dic', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'create_dic', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'create_dic', sep = '.'))})


}

################################################################################
#' Dictionary creation for site_md variables
#'
#' \code{qc_site_dics} function creates a dictionary for the selected variable
#' containing the accepted values for that variable
#'
#' In order to check if factor variables have a valid value or have been bad
#' formatted/introduced in the data template, first it is needed to have a list
#' of accepted values for each variable. This function creates that list to
#' use in the checks.
#'
#' @section Accepted variables:
#' The factor variables in site_md are \code{si_country}, \code{si_dist_mgmt}
#' and \code{si_igbp}.
#'
#' @family Dictionaries
#'
#' @param variable Variable name in which the dictionary is needed as character
#'   vector (e.g. \code{'si_igbp'}).
#'
#' @return A character vector containing the valid values for the provided
#'   variable

# START
# Function declaration
qc_site_dics <- function(variable, parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({

    # STEP 0
    # Argument checks
    # valid variables for site_md
    accepted_vars <- c('si_country', 'si_dist_mgmt', 'si_igbp')
    if (!(variable %in% accepted_vars)) {
      stop('Variable provided (', variable,') is not adequate for creating a dictionary.',
           ' Please see "Accepted variables" section of the function help.')
    }

    # STEP 1
    # Get the variable and populate the dictionary
    # 1.1 si_country
    if (variable == 'si_country') {
      res <- c('AFG', 'ALA', 'ALB', 'DZA', 'ASM', 'AND', 'AGO', 'AIA', 'ATA',
               'ATG', 'ARG', 'ARM', 'ABW', 'AUS', 'AUT', 'AZE', 'BHS', 'BHR',
               'BGD', 'BRB', 'BLR', 'BEL', 'BLZ', 'BEN', 'BMU', 'BTN', 'BOL',
               'BES', 'BIH', 'BWA', 'BVT', 'BRA', 'IOT', 'BRN', 'BGR', 'BFA',
               'BDI', 'CPV', 'KHM', 'CMR', 'CAN', 'CYM', 'CAF', 'TCD', 'CHL',
               'CHN', 'CXR', 'CCK', 'COL', 'COM', 'COG', 'COD', 'COK', 'CRI',
               'CIV', 'HRV', 'CUB', 'CUW', 'CYP', 'CZE', 'DNK', 'DJI', 'DMA',
               'DOM', 'ECU', 'EGY', 'SLV', 'GNQ', 'ERI', 'EST', 'ETH', 'FLK',
               'FRO', 'FJI', 'FIN', 'FRA', 'GUF', 'PYF', 'ATF', 'GAB', 'GMB',
               'GEO', 'DEU', 'GHA', 'GIB', 'GRC', 'GRL', 'GRD', 'GLP', 'GUM',
               'GTM', 'GGY', 'GIN', 'GNB', 'GUY', 'HTI', 'HMD', 'VAT', 'HND',
               'HKG', 'HUN', 'ISL', 'IND', 'IDN', 'IRN', 'IRQ', 'IRL', 'IMN',
               'ISR', 'ITA', 'JAM', 'JPN', 'JEY', 'JOR', 'KAZ', 'KEN', 'KIR',
               'PRK', 'KOR', 'KWT', 'KGZ', 'LAO', 'LVA', 'LBN', 'LSO', 'LBR',
               'LBY', 'LIE', 'LTU', 'LUX', 'MAC', 'MKD', 'MDG', 'MWI', 'MYS',
               'MDV', 'MLI', 'MLT', 'MHL', 'MTQ', 'MRT', 'MUS', 'MYT', 'MEX',
               'FSM', 'MDA', 'MCO', 'MNG', 'MNE', 'MSR', 'MAR', 'MOZ', 'MMR',
               'NAM', 'NRU', 'NPL', 'NLD', 'NCL', 'NZL', 'NIC', 'NER', 'NGA',
               'NIU', 'NFK', 'MNP', 'NOR', 'OMN', 'PAK', 'PLW', 'PSE', 'PAN',
               'PNG', 'PRY', 'PER', 'PHL', 'PCN', 'POL', 'PRT', 'PRI', 'QAT',
               'REU', 'ROU', 'RUS', 'RWA', 'BLM', 'SHN', 'KNA', 'LCA', 'MAF',
               'SPM', 'VCT', 'WSM', 'SMR', 'STP', 'SAU', 'SEN', 'SRB', 'SYC',
               'SLE', 'SGP', 'SXM', 'SVK', 'SVN', 'SLB', 'SOM', 'ZAF', 'SGS',
               'SSD', 'ESP', 'LKA', 'SDN', 'SUR', 'SJM', 'SWZ', 'SWE', 'CHE',
               'SYR', 'TWN', 'TJK', 'TZA', 'THA', 'TLS', 'TGO', 'TKL', 'TON',
               'TTO', 'TUN', 'TUR', 'TKM', 'TCA', 'TUV', 'UGA', 'UKR', 'ARE',
               'GBR', 'USA', 'UMI', 'URY', 'UZB', 'VUT', 'VEN', 'VNM', 'VGB',
               'VIR', 'WLF', 'ESH', 'YEM', 'ZMB', 'ZWE')

      # 1.1.1 return the dic
      return(res)
    }

    # 1.2 si_dist_mgmt
    if (variable == 'si_dist_mgmt') {
      res <- c('Agriculture', 'Drought', 'Fire', 'Forestry', 'Grazing',
               'Hydrologic event', 'Land cover change', 'Pests and disease',
               'NULL')

      # 1.2.1 return the dic
      return(res)
    }

    # 1.3 si_igbp
    if (variable == 'si_igbp') {
      res <- c('BSV', 'CRO', 'CSH', 'CVM', 'DBF', 'DNF', 'EBF',
               'ENF', 'MF', 'OSH', 'SAV', 'URB', 'WET', 'WSA')

      # 1.3.1 return the dic
      return(res)
    }

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_site_dics', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_site_dics', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_site_dics', sep = '.'))})

}

################################################################################
#' Dictionary creation for stand_md variables
#'
#' \code{qc_stand_dics} function creates a dictionary for the selected variable
#' containing the accepted values for that variable
#'
#' In order to check if factor variables have a valid value or have been bad
#' formatted/introduced in the data template, first it is needed to have a list
#' of accepted values for each variable. This function creates that list to
#' use in the checks.
#'
#' @section Accepted variables:
#' The factor variables in stand_md are \code{st_growth_condition},
#' \code{st_aspect}, \code{st_terrain} and \code{st_soil_texture}.
#'
#' @family Dictionaries
#'
#' @param variable Variable name in which the dictionary is needed as character
#'   vector (e.g. \code{'st_aspect'}).
#'
#' @return A character vector containing the valid values for the provided
#'   variable

# START
# Function declaration
qc_stand_dics <- function(variable, parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({

    # STEP 0
    # Argument checks
    # valid variables for site_md
    accepted_vars <- c('st_growth_condition', 'st_aspect',
                       'st_terrain', 'st_soil_texture')
    if (!(variable %in% accepted_vars)) {
      stop('Variable provided (', variable,
           ') is not adequate for creating a dictionary.',
           ' Please see "Accepted variables" section of the function help.')
    }

    # STEP 1
    # Get the variable and populate the dictionary
    # 1.1 st_growth_condition
    if (variable == 'st_growth_condition') {
      res <- c('Naturally regenerated, unmanaged', 'Naturally regenerated, managed',
               'Plantation, managed', 'Plantation, unmanaged', 'Orchard',
               'Urban')

      # 1.1.1 return the dic
      return(res)
    }

    # 1.2 st_aspect
    if (variable == 'st_aspect') {
      res <- c('Flat', 'N', 'E', 'S', 'W')

      # 1.2.1 return the dic
      return(res)
    }

    # 1.3 st_terrain
    if (variable == 'st_terrain') {
      res <- c('Flat', 'Undulated/Variable', 'Valley', 'Gentle slope (<2 %)',
               'Medium Slope (>2 %, <5%)', 'Significant Slope (>5%, <10%)',
               'Strong Slope (>10%)', 'Hilltop')

      # 1.3.1 return the dic
      return(res)
    }

    # 1.4 st_soil_texture
    if (variable == 'st_soil_texture') {
      res <- c('SAND', 'LOAM', 'SILT', 'CLAY')

      # return the dic
      return(res)
    }

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_stand_dics', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_stand_dics', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_stand_dics', sep = '.'))})

}

################################################################################
#' Dictionary creation for species_md variables
#'
#' \code{qc_species_dics} function creates a dictionary for the selected variable
#' containing the accepted values for that variable
#'
#' In order to check if factor variables have a valid value or have been bad
#' formatted/introduced in the data template, first it is needed to have a list
#' of accepted values for each variable. This function creates that list to
#' use in the checks.
#'
#' @section Accepted variables:
#' The factor variables in species_md are \code{sp_leaf_habit}.
#'
#' @family Dictionaries
#'
#' @param variable Variable name in which the dictionary is needed as character
#'   vector (e.g. \code{'sp_leaf_habit'}).
#'
#' @return A character vector containing the valid values for the provided
#'   variable

# START
# Function declaration
qc_species_dics <- function(variable = 'sp_leaf_habit',
                            parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({
    # STEP 0
    # Argument checks
    # valid variables for site_md
    accepted_vars <- c('sp_leaf_habit')
    if (!(variable %in% accepted_vars)) {
      stop('Variable provided (', variable,
           ') is not adequate for creating a dictionary.',
           ' Please see "Accepted variables" section of the function help.')
    }

    # STEP 1
    # Get the variable and populate the dictionary
    # 1.1 sp_leaf_habit
    res <- c('evergreen', 'cold deciduous', 'drought deciduous', 'marcescent')

    # 1.1.1 return dic
    return(res)

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_species_dics', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_species_dics', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_species_dics', sep = '.'))})


}

################################################################################
#' Dictionary creation for plant_md variables
#'
#' \code{qc_plant_dics} function creates a dictionary for the selected variable
#' containing the accepted values for that variable
#'
#' In order to check if factor variables have a valid value or have been bad
#' formatted/introduced in the data template, first it is needed to have a list
#' of accepted values for each variable. This function creates that list to
#' use in the checks.
#'
#' @section Accepted variables:
#' The factor variables in plant_md are \code{pl_social}, \code{pl_sens_meth},
#' \code{pl_sens_man}, \code{pl_sens_cor_grad}, \code{pl_sens_cor_zero},
#' \code{pl_sap_units}, \code{pl_radial_int} and \code{pl_azimut_int}.
#'
#' @family Dictionaries
#'
#' @param variable Variable name in which the dictionary is needed as character
#'   vector (e.g. \code{'pl_sap_units'}).
#'
#' @return A character vector containing the valid values for the provided
#'   variable

# START
# Function declaration
qc_plant_dics <- function(variable, parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({

    # STEP 0
    # Argument checks
    # valid variables for site_md
    accepted_vars <- c('pl_social', 'pl_sens_meth', 'pl_sens_man',
                       'pl_sens_cor_grad', 'pl_sens_cor_zero',
                       'pl_sap_units', 'pl_radial_int', 'pl_azimut_int')
    if (!(variable %in% accepted_vars)) {
      stop('Variable provided (', variable,
           ') is not adequate for creating a dictionary.',
           ' Please see "Accepted variables" section of the function help.')
    }

    # STEP 1
    # Get the variable and populate the dictionary
    # 1.1 pl_social
    if (variable == 'pl_social') {
      res <- c('dominant', 'codominant', 'suppressed')

      # 1.1.1 return the dic
      return(res)
    }

    # 1.2 pl_sens_meth
    if (variable == 'pl_sens_meth') {
      res <- c('CAG', 'HD', 'CHP', 'CHD', 'HFD', 'HPTM',
               'HR', 'SFPLUS', 'SHB', 'TSHB', 'Other/unknown')

      # 1.2.1 return the dic
      return(res)
    }

    # 1.3 pl_sens_man
    if (variable == 'pl_sens_man') {
      res <- c('Lab made', 'Dynamax', 'UP GmbH', 'Ecomatik', 'PlantSensors',
               'ICT International', 'Ems Brno', 'East30', 'Tranzflo', 'Phytech',
               'Puech Asociados', 'Advanced Measurements and Controls',
               'HortResearch', 'Greenspan Technology', 'Other/unknown')

      # 1.3.1 return the dic
      return(res)
    }

    # 1.4 pl_sens_cor_grad
    if (variable == 'pl_sens_cor_grad') {
      res <- c('No correction', 'NTG separately measured',
               'NTG measured in cyclic heating deisgn','NTG modelled',
               'Other/unknown')

      # 1.4.1 return the dic
      return(res)
    }

    # 1.5 pl_sens_cor_zero
    if (variable == 'pl_sens_cor_zero') {
      res <- c('Previous night zero flow', 'Long time-window zero flow',
               'Moist nights zero flow', 'Manipulative zero flow', 'Not needed',
               'Other/unknown')

      # 1.5.1 return the dic
      return(res)
    }

    # 1.6 pl_sap_units
    if (variable == 'pl_sap_units') {
      res <- c('“cm3 cm-2 h-1”', '“cm3 m-2 s-1”', '“dm3 dm-2 h-1”',
               '“dm3 dm-2 s-1”', '“mm3 mm-2 s-1”', '“g m-2 s-1”',
               '“kg m-2 h-1”', '“kg m-2 s-1”', '“cm3 s-1”',
               '“cm3 h-1”', '“dm3 h-1”', '“g h-1”', '“kg h-1”')

      # 1.6.1 return the dic
      return(res)
    }

    # 1.7 pl_radial_int
    if (variable == 'pl_radial_int') {
      res <- c('No radial correction', 'Sensor-integrated', 'Measured',
               'Corrected, measured radial variation',
               'Corrected, species coefficients', 'Corrected, other coefficients')

      # 1.7.1 return the dic
      return(res)
    }

    # 1.8 pl_azimut_int
    if (variable == 'pl_azimut_int') {
      res <- c('No azimuthal correction', 'sensor_integrated', 'measured',
               'Corrected, measured azimuthal variation')

      # 1.8.1 return the dic
      return(res)
    }

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_plant_dics', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_plant_dics', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_plant_dics', sep = '.'))})

}

################################################################################
#' Dictionary creation for environmental_md variables
#'
#' \code{qc_env_dics} function creates a dictionary for the selected variable
#' containing the accepted values for that variable
#'
#' In order to check if factor variables have a valid value or have been bad
#' formatted/introduced in the data template, first it is needed to have a list
#' of accepted values for each variable. This function creates that list to
#' use in the checks.
#'
#' @section Accepted variables:
#' The factor variables in environmental_md are \code{env_time_zone},
#' \code{env_ta}, \code{env_rh}, \code{env_vpd}, \code{env_sw_in},
#' \code{env_ppfd_in}, \code{env_netrad}, \code{env_ws}, \code{env_precip},
#' \code{env_plant_watpot} and \code{env_leafarea_seasonal}.
#'
#' @family Dictionaries
#'
#' @param variable Variable name in which the dictionary is needed as character
#'   vector (e.g. \code{'env_vpd'}).
#'
#' @return A character vector containing the valid values for the provided
#'   variable

# START
# Function declaration
qc_env_dics <- function(variable, parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({

    # STEP 0
    # Argument checks
    # valid variables for site_md
    accepted_vars <- c('env_time_zone', 'env_ta', 'env_rh', 'env_vpd',
                       'env_sw_in', 'env_ppfd_in', 'env_netrad', 'env_ws',
                       'env_precip', 'env_plant_watpot', 'env_leafarea_seasonal')
    if (!(variable %in% accepted_vars)) {
      stop('Variable provided (', variable,
           ') is not adequate for creating a dictionary.',
           ' Please see "Accepted variables" section of the function help.')
    }

    # STEP 1
    # Get the variable and populate the dictionary
    # 1.1 env_time_zone
    if (variable == 'env_time_zone') {
      res <- c('1UTC-12:00, Y', '2UTC-11:00, X', '3UTC-10:00, W', '4UTC-09:30, V†',
               '5UTC-09:00, V', '6UTC-08:00, U', '7UTC-07:00, T', '8UTC-06:00, S',
               '9UTC-05:00, R', '10UTC-04:30, Q†', '11UTC-04:00, Q',
               '12UTC-03:30, P†', '13UTC-03:00, P', '14UTC-02:00, O',
               '15UTC-01:00, N','16UTC±00:00, Z', '17UTC+01:00, A',
               '18UTC+02:00, B', '19UTC+03:00, C', '20UTC+03:30, C†',
               '21UTC+04:00, D', '22UTC+04:30, D†', '23UTC+05:00, E',
               '24UTC+05:30, E†', '25UTC+05:45, E*', '26UTC+06:00, F',
               '27UTC+06:30, F†', '28UTC+07:00, G', '29UTC+08:00, H',
               '30UTC+08:30, H†', '31UTC+08:45, H*', '32UTC+09:00, I',
               '33UTC+09:30, I†', '34UTC+10:00, K', '35UTC+10:30, K†',
               '36UTC+11:00, L', '37UTC+12:00, M', '38UTC+12:45, M*',
               '39UTC+13:00, M†', '40UTC+14:00, M†')

      # 1.1.1 return the dic
      return(res)
    }

    # 1.2 env_ta, rh, vpd, sw_in, ppfd_in, netrad, ws and precip
    if (variable %in% c('env_ta', 'env_rh', 'env_vpd',
                        'env_sw_in', 'env_ppfd_in', 'env_netrad', 'env_ws',
                        'env_precip')) {
      res <- c('Above canopy', 'Within canopy', 'Clearing',
               'Off-site', 'Not provided')

      # 1.2.1 return the dic
      return(res)
    }

    # 1.3 env_plant_watpot
    if (variable == 'env_plant_watpot') {
      res <- c('leaf: predawn', 'leaf: midday', 'xylem: predawn', 'xylem: midday',
               'leaf: predawn and midday', 'xylem: predawn and midday',
               'xylem: continuous', 'leaf: continuous')

      # 1.3.1 return the dic
      return(res)
    }

    # 1.4 env_leafarea_seasonal
    if (variable == 'env_leafarea_seasonal') {
      res <- c('stand level', 'species level', 'tree level', 'NULL')

      # 1.4.1 return the dic
      return(res)
    }

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_env_dics', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_env_dics', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_env_dics', sep = '.'))})

}

################################################################################
#' Metadata columns check
#'
#' \code{qc_md_cols} checks if the columns of the provided metadata return the
#' correct class, as well as indicates any NAs present and the absence of any
#' mandatory variable.
#'
#' After loading the metadata, columns classes and presence/absence of mandatory
#' variables must be checked in order to continue with the quality check
#' workflow. This function returns a summary of the metadata columns and their
#' state.
#'
#' @family Quality Checks Functions
#'
#' @param metadata Data frame containing the metadata in which the test will be
#'   made.
#'
#' @param dic Name of the metadata dictionary to use as character. It must be
#'   one of the following: \code{'stand_md'}, \code{'site_md'},
#'   \code{'species_md'}, \code{'plant_md'} or \code{'environmental_md'}
#'
#' @return A data frame with variable names in one column and result of the
#'   checks in teh following columns
#'
#' @export

# START
# Function declaration

qc_md_cols <- function(metadata, dic,
                       parent_logger = 'test') {

  # Using calling handlers for logging
  withCallingHandlers({

    # STEP 0
    # Argument checks
    # metadata is a data frame?
    if (!is.data.frame(metadata)) {
      stop('Metadata object is not a data frame')
    }

    # check if dictionary name is one of the five kinds of metadata allowed
    accepted_sheets <- c('site_md', 'stand_md', 'species_md',
                         'plant_md', 'environmental_md')

    if (!is.character(dic) || !(dic %in% accepted_sheets)) {
      stop('Provided dictionary name is not a character or is not a valid name.',
           ' Please see function help for information about valid dictionary names')
    }

    # STEP 1
    # Initialise result objects and dictionary
    dictionary <- create_dic(dic) # dictionary
    md_variables <- names(metadata) # variable names
    presence_res <- vector() # results of presence test
    classes_res <- vector() # results of class test
    det_class_res <- vector() # detected class
    na_res <- vector() # results of NA test

    # STEP 2
    # Checks
    for (name in names(dictionary)) {
      # 2.1 Presence test
      p_res <- name %in% md_variables
      presence_res <- c(presence_res, p_res)

      # 2.2 Class test
      d_res <- class(metadata[[name]])
      c_res <- any(dictionary[[name]] == d_res)
      # c_res <- identical(class(metadata[[name]]),
      #                    as.character(dictionary$Class[dictionary$Name == name]))
      classes_res <- c(classes_res, c_res)
      det_class_res <- c(det_class_res, d_res)

      # 2.3 NA test
      if (p_res) {
        n_res <- all(is.na(metadata[[name]]))
        na_res <- c(na_res, n_res)
      } else {
        n_res <- NA
        na_res <- c(na_res, n_res)
      }
    }

    # STEP 3
    # Create and return the result object
    result <- data.frame(Variable = names(dictionary),
                         PresenceOK = presence_res,
                         DetectedClass = det_class_res,
                         ClassOK = classes_res,
                         IsNA = na_res,
                         stringsAsFactors = FALSE)

    return(result)

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_md_cols', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_md_cols', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_md_cols', sep = '.'))})

}

################################################################################
#' Metadata factor variables check
#'
#' \code{qc_factor_values} function checks in the provided metadata if the
#' factor variables value is a valid value.
#'
#' Values for factor variables in the metadata must be checked in order to
#' ensure that they are valid (i.e. they are one of the established factor
#' value).
#'
#' @family Quality Checks Functions
#'
#' @param site,stand,species,plant,environmental Data frames with the metadata
#'   to check.
#'
#' @return A data frame with variable names, check result and NA presence as
#'   columns, as well as a column (Metadata) indicating the kind of metadata
#'   variables checked.
#'
#' @export

# START
# Function declaration
qc_factor_values <- function(site = NULL, stand = NULL, species = NULL,
                             plant = NULL, environmental = NULL,
                             parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({

    # STEP 0
    # Argument checks
    #

    # STEP 1
    # Initialize result objects
    var_name <- vector()
    res_check <- vector()
    na_presence <- vector()
    metadata <- vector()

    # STEP 2
    # Walk through metadata files and check variables
    # 2.1 site
    if (!is.null(site)) {
      si_names <- c('si_country', 'si_dist_mgmt', 'si_igbp')
      si_checks <- sapply(si_names, function(x) { site[[x]] %in% qc_site_dics(x) })
      si_nas <- sapply(si_names, function(x) { any(is.na(site[[x]])) })
      si_metadata <- rep('site', length(si_names))
      var_name <- c(var_name, si_names)
      res_check <- c(res_check, si_checks)
      na_presence <- c(na_presence, si_nas)
      metadata <- c(metadata, si_metadata)
    }

    # 2.2 stand
    if(!is.null(stand)) {
      st_names <- c('st_growth_condition', 'st_aspect',
                    'st_terrain', 'st_soil_texture')
      st_checks <- sapply(st_names, function(x) { stand[[x]] %in% qc_stand_dics(x) })
      st_nas <- sapply(st_names, function(x) { any(is.na(stand[[x]])) })
      st_metadata <- rep('stand', length(st_names))
      var_name <- c(var_name, st_names)
      res_check <- c(res_check, st_checks)
      na_presence <- c(na_presence, st_nas)
      metadata <- c(metadata, st_metadata)
    }

    # 2.3 species
    if(!is.null(species)) {
      sp_names <- c('sp_leaf_habit')
      sp_checks <- sapply(sp_names, function(x) {
        all(species[[x]] %in% qc_species_dics(x))
      })
      sp_nas <- sapply(sp_names, function(x) { any(is.na(species[[x]])) })
      sp_metadata <- rep('species', length(sp_names))
      var_name <- c(var_name, sp_names)
      res_check <- c(res_check, sp_checks)
      na_presence <- c(na_presence, sp_nas)
      metadata <- c(metadata, sp_metadata)
    }

    # 2.4 plant
    if(!is.null(plant)) {
      pl_names <- c('pl_social', 'pl_sens_meth', 'pl_sens_man',
                    'pl_sens_cor_grad', 'pl_sens_cor_zero',
                    'pl_sap_units', 'pl_radial_int', 'pl_azimut_int')
      pl_checks <- sapply(pl_names, function(x) {
        all(plant[[x]] %in% qc_plant_dics(x))
      })
      pl_nas <- sapply(pl_names, function(x) { any(is.na(plant[[x]])) })
      pl_metadata <- rep('plant', length(pl_names))
      var_name <- c(var_name, pl_names)
      res_check <- c(res_check, pl_checks)
      na_presence <- c(na_presence, pl_nas)
      metadata <- c(metadata, pl_metadata)
    }

    # 2.5 environmental
    if(!is.null(environmental)) {
      env_names <- c('env_time_zone', 'env_ta', 'env_rh', 'env_vpd',
                     'env_sw_in', 'env_ppfd_in', 'env_netrad', 'env_ws',
                     'env_precip', 'env_plant_watpot', 'env_leafarea_seasonal')
      env_checks <- sapply(env_names, function(x) { environmental[[x]] %in% qc_env_dics(x) })
      env_nas <- sapply(env_names, function(x) { any(is.na(environmental[[x]])) })
      env_metadata <- rep('environmental', length(env_names))
      var_name <- c(var_name, env_names)
      res_check <- c(res_check, env_checks)
      na_presence <- c(na_presence, env_nas)
      metadata <- c(metadata, env_metadata)
    }

    # 3. Generate the results data frame and return it
    res_data <- data.frame(Variable = var_name,
                           Check_result = res_check,
                           NA_presence = na_presence,
                           Metadata = metadata,
                           stringsAsFactors = FALSE)

    return(res_data)

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_factor_values', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_factor_values', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_factor_values', sep = '.'))})

}

################################################################################
#' Check for environmental variables presence
#'
#' \code{qc_env_vars_presence} function checks if environmental variables stated
#' in metadata (environmental_md sheet) are really present in the environmental
#' data.
#'
#' The function get all the names of the possible environmental variables and
#' check the presence in metadata and data. If there is any inconsistency
#' between them.
#'
#' @family Quality Checks Functions
#'
#' @param data Data frame containing the environmental data
#'
#' @param metadata Data frame containing the environmental metadata
#'
#' @return A data frame with four columns: Variable name, Presence in metadata,
#'   Presence in data and Concordance.
#'
#' @export

# START
# Function declaration
qc_env_vars_presence <- function(data, metadata,
                                 parent_logger = 'test') {

  # Using calling handlers to logging
  withCallingHandlers({

    # STEP 0
    # Argument checking
    # Check if objects are data frames
    if (!is.data.frame(data) | !is.data.frame(metadata)) {
      stop('Data and/or metadata objects are not data frames')
    }

    # STEP 1
    # Create accepted variables names and results vectors
    accepted_vars <- c('env_ta', 'env_rh', 'env_vpd', 'env_sw_in', 'env_ppfd_in',
                       'env_netrad', 'env_ws', 'env_precip', 'env_swc_shallow_depth',
                       'env_swc_deep_depth')
    md_res <- vector()
    hd_res <- vector()
    # concordance <- vector()

    # STEP 2
    # Check which variables are in metadata
    for (var in accepted_vars) {
      if (any(is.null(metadata[[var]]),
              # supressing warnings of is.na applied to null in case of variable
              # not present
              suppressWarnings(is.na(metadata[[var]])),
              metadata[[var]] == 'Not provided')) {
        md <- FALSE
        md_res <- c(md_res, md)
      } else {
        md <- TRUE
        md_res <- c(md_res, md)
      }
      # STEP 3
      # Check which variables are in data
      # Warning: in data, variables have the "env_" part stripped, so we need to
      # strip that part in var. Also in swc_* variables, the _depth part must
      # be removed
      # if(stringr::str_replace_all(var, "(env_)|(_depth)", '') %in% names(data) &
      #    !all(is.na(data[[stringr::str_replace_all(var, "(env_)|(_depth)", '')]]))) {
      #   hd <- TRUE
      #   hd_res <- c(hd_res, hd)
      # } else {
      #   hd <- FALSE
      #   hd_res <- c(hd_res, hd)
      # }

      if (stringr::str_replace_all(var, "(env_)|(_depth)", '') %in% names(data)) {
        if (!all(is.na(data[[stringr::str_replace_all(var, "(env_)|(_depth)", '')]]))) {
          hd <- TRUE
          hd_res <- c(hd_res, hd)
        } else {
          hd <- FALSE
          hd_res <- c(hd_res, hd)
        }
      } else {
        hd <- FALSE
        hd_res <- c(hd_res, hd)
      }
    }

    # STEP 4
    # Check for concordance between metadata and data
    # for (i in 1:length(md_res)) {
    #   c_res <- md_res[i] == hd_res[i]
    #   concordance <- c(concordance, c_res)
    # }
    concordance <- sapply(1:length(md_res), function(x){
      md_res[x] == hd_res[x]
    })

    # STEP 5
    # Build results data frame and return it
    df_res <- data.frame(Name = accepted_vars,
                         Md_presence = md_res,
                         Data_presence = hd_res,
                         Concordance = concordance,
                         stringsAsFactors = FALSE)

    return(df_res)

    # END FUNCTION
  },

  # handlers
  warning = function(w){logging::logwarn(w$message,
                                         logger = paste(parent_logger,
                                                        'qc_env_vars_presence', sep = '.'))},
  error = function(e){logging::logerror(e$message,
                                        logger = paste(parent_logger,
                                                       'qc_env_vars_presence', sep = '.'))},
  message = function(m){logging::loginfo(m$message,
                                         logger = paste(parent_logger,
                                                        'qc_env_vars_presence', sep = '.'))})

}
sapfluxnet/sapfluxnetQC1 documentation built on March 1, 2019, 1 p.m.