Package index • ANDESMollusque

All functions

access_db_connect(): Establish a connection to an MS Access database
add_hard_coded_value(): Add a hard-coded column with a specific value to the dataframe
andes_db_connect(): Establish a connection to the andes database
andes_str_to_oracle_date(): Convert andes datetime string form DB to Oracle date format
andes_str_to_oracle_datetime(): Convert andes datetime string form DB to Oracle datetime format
check_cols_contains_na(): Checks if all dataframe cols named in the col_names contain NA This is useful to validate if a dataframe can be written to a DB table (where some columns values cannot be null)
check_columns_present(): Make sure the columns listed in col_names are present in the dataframe
check_numeric_columns(): Make sure the columns listed in col_names have numeric (or NA) values
check_other_columns(): Make sure no other columns than the ones listed in col_names are present in the dataframe
cleanup_text(): Cleanup text form ANDES to play nice in Oracle
cols_to_numeric(): Convert all dataframe cols named in the col_names to a numeric value
create_new_access_db(): Creates a new MS Access database file
format_cod_descrip_capt(): Format COD_DESCRIP_CAPT
format_cod_esp_gen(): format the cod_esp_gen column
format_cod_secteur_releve(): Format COD_SECTEUR_RELEVE
format_cod_source_info(): Format COD_SOURCE_INFO
format_cod_strate(): Format COD_STRAT
format_cod_tech_mesure_long(): Format COD_TECH_MESURE_LONG
format_cod_typ_etat(): Format COD_TYP_ETAT
format_cod_typ_heure(): Format COD_TYP_HEURE
format_cod_typ_long(): Format COD_TYP_LONG
format_cod_typ_mesure(): format COD_TYP_MESURE
format_cod_typ_panier(): Add the formated COD_TYP_PANIER column to the dataframe This is currently hard-coded to Panier doublé TODO: implement different types depending on chosen gear code, for exmaple:
format_coordinates(): Format coordinates for TRAIT_MOLLUSQUE
format_date_deb_projet(): Format DATE_DE_PROJET
format_date_fin_projet(): Format DATE_FIN_PROJET
format_date_hre_trait(): Format dates for TRAIT_MOLLUSQUE
format_date_trait(): Format dates for TRAIT_MOLLUSQUE
format_epibiont(): Formated COD_COUVERTURE_EPIBIONT column to the dataframe
format_no_mollusque(): Format NO_MOLLUSQUE
format_no_station(): Format NO_STATION
format_seq_pecheur(): Format SEQ_PECHEUR
format_zone(): Format ZONE
generate_sql_insert_statement(): Generate a SQL statement
get_access_table_properties(): get database table properties
get_biometrie_petoncle(): Gets get_biometrie_petoncle (formatted results)
get_biometrie_petoncle_db(): Gets capture_mollusc_db (raw database results)
get_capture_mollusque(): Gets capture_mollusque (formatted results)
get_capture_mollusque_db(): Gets capture_mollusc_db (raw database results)
get_engin_mollusque(): Gets engin_mollusc (formatted results)
get_engin_mollusque_db(): Gets engin_mollusc_db (raw database results)
get_epibiont(): This fetches the specimen-level coverage data and coverts it to an average set-level metric in accordance to the legacy Oracle database.
get_freq_long_mollusque(): Gets freq_long_mollusque (formatted results)
get_freq_long_mollusque_db(): Gets freq_long_mollusque_db (raw database results)
get_legal_collection_names(): Get a list of legal collection names as a filter for get_biometrie_petoncle()
get_projet_mollusque(): Gets fishing projet_mollusque (formatted results)
get_projet_mollusque_db(): Gets fishing projet_mollusque (raw database results)
get_ref_choices(): Builds a list of legal choices (descriptions) for get ref key
get_ref_key(): Get the reference key corresponding to a value (usually from the Oracle / MSAccess reference database)
get_strate(): Get the strate from reference
get_trait_mollusque(): Gets trait_mollusque (formatted results)
get_trait_mollusque_db(): Gets trait_mollusque_db (raw database results)
init_cod_serie_hist(): Add the cod_serie_hist to the whole dataframe This value is not present in ANDES so it will have to be specified here. Run this without desc_serie_hist_f to get a list of choices.
is_andes_time_str_dst(): Verify is the ANDES dattime string is in daylight savings time
left_join(): a merge that preserves row and column order
lookup_cod_serie_hist(): Lookup entry in Oracle
lookup_cod_source_info(): Lookup COD_SOURCE_INFO
parse_andes_datetime(): Convert ANDES UTC time string and converts it to a POSIXct object
sanitize_sql_value(): Sanitize value to SQL statement
strip_alphabetic(): This function removes alphabetic characters from a string
to_oracle_coord(): Convert coordinate to Oracle format
validate_capture_mollusque(): Perform database validation checks on the dataframe
validate_engin_mollusque(): Perform database validation checks on the dataframe
validate_freq_long_mollusque(): Perform database validation checks on the dataframe
validate_projet_mollusque(): Perform database validation checks on the dataframe
validate_set_result(): Validate set result consistency
validate_trait_mollusque(): Perform database validation checks on the dataframe
write_capture_mollusque(): Write to Access file
write_engin_mollusque(): Write to Access file
write_freq_long_mollusque(): Write dataframe to Access file
write_projet_mollusque(): Write to Access file
write_trait_mollusque(): Write dataframe to Access file