diff --git a/R/data_book.R b/R/data_book.R index 4ec489a..9687d16 100644 --- a/R/data_book.R +++ b/R/data_book.R @@ -26,6 +26,193 @@ #' \item{\code{get_red_flag_column_names(data_name)}}{Gets the names of red flag columns in the specified data table.} #' \item{\code{get_CRI_column_names(data_name)}}{Gets the names of CRI columns in the specified data table.} #' \item{\code{get_corruption_column_name(data_name, type)}}{Gets the name of the corruption column in the specified data table.} +#' \item{\code{import_data(data_tables = list(), data_tables_variables_metadata = rep(list(data.frame()),length(data_tables)), data_tables_metadata = rep(list(list()),length(data_tables)), data_tables_filters = rep(list(list()),length(data_tables)), data_tables_column_selections = rep(list(list()),length(data_tables)), imported_from = as.list(rep("",length(data_tables))), data_names = NULL, messages=TRUE, convert=TRUE, create=TRUE, prefix=TRUE, add_to_graph_book = TRUE)}}{Imports data into the DataBook from a list of data tables and their metadata.} +#' \item{\code{replace_instat_object(new_instat_object)}}{Replaces the current instat object with a new one.} +#' \item{\code{set_data_objects(new_data_objects)}}{Sets the data objects for the DataBook.} +#' \item{\code{copy_data_object(data_name, new_name, filter_name = "", column_selection_name = "", reset_row_names = TRUE)}}{Copies a data object with optional filtering and column selection.} +#' \item{\code{import_RDS(data_RDS, keep_existing = TRUE, overwrite_existing = FALSE, include_objects = TRUE, include_metadata = TRUE, include_logs = TRUE, include_filters = TRUE, include_column_selections = TRUE, include_calculations = TRUE, include_comments = TRUE)}}{Imports data from an RDS file into the DataBook.} +#' \item{\code{clone_data_object(curr_data_object, include_objects = TRUE, include_metadata = TRUE, include_logs = TRUE, include_filters = TRUE, include_column_selections = TRUE, include_calculations = TRUE, include_comments = TRUE, ...)}}{Clones a data object with options to include various components.} +#' \item{\code{clone_instat_calculation(curr_instat_calculation, ...)}}{Clones an instat calculation.} +#' \item{\code{import_from_ODK(username, form_name, platform)}}{Imports data from ODK (Open Data Kit).} +#' \item{\code{set_meta(new_meta)}}{Sets the metadata for the DataBook.} +#' \item{\code{set_objects(new_objects)}}{Sets the objects for the DataBook.} +#' \item{\code{append_data_object(name, obj, add_to_graph_book = TRUE)}}{Appends a data object to the DataBook.} +#' \item{\code{get_data_objects(data_name, as_list = FALSE, ...)}}{Gets data objects from the DataBook.} +#' \item{\code{get_data_frame(data_name, convert_to_character = FALSE, stack_data = FALSE, include_hidden_columns = TRUE, use_current_filter = TRUE, filter_name = "", use_column_selection = TRUE, column_selection_name = "", remove_attr = FALSE, retain_attr = FALSE, max_cols, max_rows, drop_unused_filter_levels = FALSE, start_row, start_col, ...)}}{Gets a data frame from the DataBook with various options.} +#' \item{\code{get_variables_metadata(data_name, data_type = "all", convert_to_character = FALSE, property, column, error_if_no_property = TRUE, direct_from_attributes = FALSE, use_column_selection = TRUE)}}{Gets the variables metadata for the specified data table.} +#' \item{\code{get_column_data_types(data_name, columns)}}{Gets the data types of the specified columns in the data table.} +#' \item{\code{get_column_labels(data_name, columns)}}{Gets the labels of the specified columns in the data table.} +#' \item{\code{get_data_frame_label(data_name, use_current_filter = FALSE)}}{Gets the label of the data frame.} +#' \item{\code{get_data_frame_metadata(data_name, label, include_calculated = TRUE, excluded_not_for_display = TRUE)}}{Gets the metadata of the data frame.} +#' \item{\code{get_combined_metadata(convert_to_character = FALSE)}}{Gets combined metadata from all data tables.} +#' \item{\code{get_metadata(name, ...)}}{Gets metadata for the specified name.} +#' \item{\code{get_data_names(as_list = FALSE, include, exclude, excluded_items, include_hidden = TRUE, ...)}}{Gets the names of the data tables in the DataBook.} +#' \item{\code{get_data_changed(data_name)}}{Checks if the data has changed.} +#' \item{\code{get_variables_metadata_changed(data_name)}}{Checks if the variables metadata has changed.} +#' \item{\code{get_metadata_changed(data_name)}}{Checks if the metadata has changed.} +#' \item{\code{get_calculations(data_name)}}{Gets the calculations for the specified data table.} +#' \item{\code{get_calculation_names(data_name, as_list = FALSE, excluded_items = c())}}{Gets the names of the calculations for the specified data table.} +#' \item{\code{dataframe_count()}}{Gets the count of data frames in the DataBook.} +#' \item{\code{set_data_frames_changed(data_name = "", new_val)}}{Sets the changed status for data frames.} +#' \item{\code{set_variables_metadata_changed(data_name = "", new_val)}}{Sets the changed status for variables metadata.} +#' \item{\code{set_metadata_changed(data_name = "", new_val)}}{Sets the changed status for metadata.} +#' \item{\code{add_columns_to_data(data_name, col_name = "", col_data, use_col_name_as_prefix = FALSE, hidden = FALSE, before, adjacent_column = "", num_cols, require_correct_length = TRUE, keep_existing_position = TRUE)}}{Adds columns to the specified data table.} +#' \item{\code{get_columns_from_data(data_name, col_names, from_stacked_data = FALSE, force_as_data_frame = FALSE, use_current_filter = TRUE, remove_labels = FALSE, drop_unused_filter_levels = FALSE)}}{Gets columns from the specified data table.} +#' \item{\code{create_graph_data_book()}}{Creates a graph data book.} +#' \item{\code{add_object(data_name = NULL, object_name = NULL, object_type_label, object_format, object)}}{Adds an object to the DataBook.} +#' \item{\code{get_object_names(data_name = NULL, object_type_label = NULL, as_list = FALSE, ...)}}{Gets the names of the objects in the DataBook.} +#' \item{\code{get_objects(data_name = NULL, object_type_label = NULL)}}{Gets the objects from the DataBook.} +#' \item{\code{get_object(data_name = NULL, object_name)}}{Gets a specific object from the DataBook.} +#' \item{\code{get_object_data(data_name = NULL, object_name, as_file = FALSE)}}{Gets the data of a specific object from the DataBook.} +#' \item{\code{get_objects_data(data_name = NULL, object_names = NULL, as_files = FALSE)}}{Gets the data of multiple objects from the DataBook.} +#' \item{\code{get_last_object_data(object_type_label, as_file = TRUE)}}{Gets the data of the last object of a specified type from the DataBook.} +#' \item{\code{rename_object(data_name, object_name, new_name, object_type = "object")}}{Renames an object in the DataBook.} +#' \item{\code{delete_objects(data_name, object_names, object_type = "object")}}{Deletes objects from the DataBook.} +#' \item{\code{reorder_objects(data_name, new_order)}}{Reorders the objects in the DataBook.} +#' \item{\code{get_from_object(data_name, object_name, value1, value2, value3)}}{Gets values from a specified object in the DataBook.} +#' \item{\code{add_filter(data_name, filter, filter_name = "", replace = TRUE, set_as_current_filter = FALSE, na.rm = TRUE, is_no_filter = FALSE, and_or = "&", inner_not = FALSE, outer_not = FALSE)}}{Adds a filter to the specified data table.} +#' \item{\code{add_filter_as_levels(data_name, filter_levels, column)}}{Adds filter levels to the specified column.} +#' \item{\code{current_filter(data_name)}}{Gets the current filter for the specified data table.} +#' \item{\code{set_current_filter(data_name, filter_name = "")}}{Sets the current filter for the specified data table.} +#' \item{\code{get_filter(data_name, filter_name)}}{Gets a filter by name from the specified data table.} +#' \item{\code{get_filter_as_logical(data_name, filter_name)}}{Gets a filter as a logical vector from the specified data table.} +#' \item{\code{get_current_filter(data_name)}}{Gets the current filter for the specified data table.} +#' \item{\code{get_filter_row_names(data_name, filter_name)}}{Gets the row names that match a specified filter in the data table.} +#' \item{\code{get_current_filter_name(data_name)}}{Gets the name of the current filter for the specified data table.} +#' \item{\code{get_filter_names(data_name, as_list = FALSE, include = list(), exclude = list(), excluded_items = c())}}{Gets the names of the filters in the specified data table.} +#' \item{\code{remove_current_filter(data_name)}}{Removes the current filter from the specified data table.} +#' \item{\code{filter_applied(data_name)}}{Checks if a filter is applied to the specified data table.} +#' \item{\code{filter_string(data_name, filter_name)}}{Gets the filter string for a specified filter in the data table.} +#' \item{\code{get_filter_as_instat_calculation(data_name, filter_name)}}{Gets a filter as an instat calculation from the specified data table.} +#' \item{\code{add_column_selection(data_name, column_selection, name = "", replace = TRUE, set_as_current = FALSE, is_everything = FALSE, and_or = "|")}}{Adds a column selection to the specified data table.} +#' \item{\code{current_column_selection(data_name)}}{Gets the current column selection for the specified data table.} +#' \item{\code{set_current_column_selection(data_name, name = "")}}{Sets the current column selection for the specified data table.} +#' \item{\code{get_column_selection(data_name, name)}}{Gets a column selection by name from the specified data table.} +#' \item{\code{get_column_selection_column_names(data_name, filter_name)}}{Gets the column names for a specified filter in the data table.} +#' \item{\code{get_column_selected_column_names(data_name, column_selection_name = "")}}{Gets the names of the selected columns in the specified data table.} +#' \item{\code{get_current_column_selection(data_name)}}{Gets the current column selection for the specified data table.} +#' \item{\code{get_current_column_selection_name(data_name)}}{Gets the name of the current column selection for the specified data table.} +#' \item{\code{get_column_selection_names(data_name, as_list = FALSE, include = list(), exclude = list(), excluded_items = c())}}{Gets the names of the column selections in the specified data table.} +#' \item{\code{remove_current_column_selection(data_name)}}{Removes the current column selection from the specified data table.} +#' \item{\code{column_selection_applied(data_name)}}{Checks if a column selection is applied to the specified data table.} +#' \item{\code{replace_value_in_data(data_name, col_names, rows, old_value, old_is_missing = FALSE, start_value = NA, end_value = NA, new_value, new_is_missing = FALSE, closed_start_value = TRUE, closed_end_value = TRUE, locf = FALSE, from_last = FALSE)}}{Replaces values in the specified columns and rows of the data table.} +#' \item{\code{paste_from_clipboard(data_name, col_names, start_row_pos = 1, first_clip_row_is_header = TRUE, clip_board_text)}}{Pastes data from the clipboard into the specified columns of the data table.} +#' \item{\code{rename_column_in_data(data_name, column_name = NULL, new_val = NULL, label = "", type = "single", .fn, .cols = everything(), new_column_names_df, new_labels_df, ...)}}{Renames a column in the specified data table.} +#' \item{\code{frequency_tables(data_name, x_col_names, y_col_name, n_column_factors = 1, store_results = TRUE, drop = TRUE, na.rm = FALSE, summary_name = NA, include_margins = FALSE, return_output = TRUE, treat_columns_as_factor = FALSE, page_by = "default", as_html = TRUE, signif_fig = 2, na_display = "", na_level_display = "NA", weights = NULL, caption = NULL, result_names = NULL, percentage_type = "none", perc_total_columns = NULL, perc_total_factors = c(), perc_total_filter = NULL, perc_decimal = FALSE, margin_name = "(All)", additional_filter, ...)}}{Creates frequency tables for the specified data table.} +#' \item{\code{anova_tables(data_name, x_col_names, y_col_name, signif.stars = FALSE, sign_level = FALSE, means = FALSE)}}{Creates ANOVA tables for the specified data table.} +#' \item{\code{cor(data_name, x_col_names, y_col_name, use = "everything", method = c("pearson", "kendall", "spearman"))}}{Calculates correlations for the specified columns in the data table.} +#' \item{\code{remove_columns_in_data(data_name, cols, allow_delete_all = FALSE)}}{Removes columns from the specified data table.} +#' \item{\code{remove_rows_in_data(data_name, row_names)}}{Removes rows from the specified data table.} +#' \item{\code{get_next_default_column_name(data_name, prefix)}}{Gets the next default column name for the specified data table.} +#' \item{\code{get_column_names(data_name, as_list = FALSE, include = list(), exclude = list(), excluded_items = c(), max_no, use_current_column_selection = TRUE)}}{Gets the column names in the specified data table.} +#' \item{\code{reorder_columns_in_data(data_name, col_order)}}{Reorders the columns in the specified data table.} +#' \item{\code{insert_row_in_data(data_name, start_row, row_data = c(), number_rows = 1, before = FALSE)}}{Inserts rows into the specified data table.} +#' \item{\code{get_data_frame_length(data_name, use_current_filter = FALSE)}}{Gets the length of the data frame in the specified data table.} +#' \item{\code{get_next_default_dataframe_name(prefix, include_index = TRUE, start_index = 1)}}{Gets the next default name for a data frame in the DataBook.} +#' \item{\code{delete_dataframes(data_names, delete_graph_book = TRUE)}}{Deletes data frames from the DataBook.} +#' \item{\code{remove_link(link_name)}}{Removes a link from the DataBook.} +#' \item{\code{get_column_factor_levels(data_name, col_name = "")}}{Gets the factor levels of a column in the specified data table.} +#' \item{\code{get_factor_data_frame(data_name, col_name = "", include_levels = TRUE, include_NA_level = FALSE)}}{Gets a factor data frame for the specified column in the data table.} +#' \item{\code{sort_dataframe(data_name, col_names = c(), decreasing = FALSE, na.last = TRUE, by_row_names = FALSE, row_names_as_numeric = TRUE)}}{Sorts the specified data table.} +#' \item{\code{rename_dataframe(data_name, new_value = "", label = "")}}{Renames the specified data table.} +#' \item{\code{convert_column_to_type(data_name, col_names = c(), to_type, factor_values = NULL, set_digits, set_decimals = FALSE, keep_attr = TRUE, ignore_labels = FALSE, keep.labels = TRUE)}}{Converts the specified columns to a different type in the data table.} + +# got from here +#' \item{\code{append_to_variables_metadata(data_name, col_names, property, new_val = "")}}{Appends a new value to the specified property in the variables metadata for the given columns in the specified data table.} +#' \item{\code{append_to_dataframe_metadata(data_name, property, new_val = "")}}{Appends a new value to the specified property in the dataframe metadata for the specified data table.} +#' \item{\code{append_to_metadata(property, new_val = "", allow_override_special = FALSE)}}{Appends a new value to the specified property in the overall metadata, with an option to override special properties.} +#' \item{\code{add_metadata_field(data_name, property, new_val = "")}}{Adds a new metadata field to the specified data table or to the overall metadata.} +#' \item{\code{reorder_dataframes(data_frames_order)}}{Reorders the data frames in the object based on the provided order.} +#' \item{\code{copy_columns(data_name, col_names = "", copy_to_clipboard = FALSE)}}{Copies the specified columns from the given data table, with an option to copy to the clipboard.} +#' \item{\code{drop_unused_factor_levels(data_name, col_name)}}{Drops unused factor levels from the specified column in the given data table.} +#' \item{\code{set_factor_levels(data_name, col_name, new_labels, new_levels, set_new_labels = TRUE)}}{Sets new factor levels and labels for the specified column in the given data table.} +#' \item{\code{edit_factor_level(data_name, col_name, old_level, new_level)}}{Edits an existing factor level in the specified column of the given data table.} +#' \item{\code{set_factor_reference_level(data_name, col_name, new_ref_level)}}{Sets a new reference level for the specified factor column in the given data table.} +#' \item{\code{get_column_count(data_name, use_column_selection = FALSE)}}{Returns the count of columns in the specified data table, with an option to use the current column selection.} +#' \item{\code{reorder_factor_levels(data_name, col_name, new_level_names)}}{Reorders the factor levels in the specified column of the given data table.} +#' \item{\code{get_data_type(data_name, col_name)}}{Returns the data type of the specified column in the given data table.} +#' \item{\code{copy_data_frame(data_name, new_name, label = "", copy_to_clipboard = FALSE)}}{Copies the specified data table to a new data table with an optional new name, label, and option to copy to the clipboard.} +#' \item{\code{copy_col_metadata_to_clipboard(data_name, property_names)}}{Copies the specified column metadata properties from the given data table to the clipboard.} +#' \item{\code{copy_data_frame_metadata_to_clipboard(data_name, property_names)}}{Copies the specified data frame metadata properties from the given data table to the clipboard.} +#' \item{\code{copy_to_clipboard(content)}}{Copies the given content to the clipboard.} +#' \item{\code{set_hidden_columns(data_name, col_names = c())}}{Sets the specified columns in the given data table to be hidden.} +#' \item{\code{unhide_all_columns(data_name)}}{Unhides all columns in the specified data table.} +#' \item{\code{set_hidden_data_frames(data_names = c())}}{Sets the specified data frames to be hidden.} +#' \item{\code{get_hidden_data_frames()}}{Returns the names of all hidden data frames.} +#' \item{\code{set_row_names(data_name, row_names)}}{Sets new row names for the specified data table.} +#' \item{\code{get_row_names(data_name)}}{Returns the row names of the specified data table.} +#' \item{\code{set_protected_columns(data_name, col_names)}}{Sets the specified columns in the given data table to be protected.} +#' \item{\code{get_metadata_fields(data_name, include_overall, as_list = FALSE, include, exclude, excluded_items = c())}}{Returns the metadata fields for the specified data table and overall metadata, with options to include or exclude specific fields.} +#' \item{\code{freeze_columns(data_name, column)}}{Freezes the specified columns in the given data table.} +#' \item{\code{unfreeze_columns(data_name)}}{Unfreezes all columns in the specified data table.} +#' \item{\code{is_variables_metadata(data_name, property, column, return_vector = FALSE)}}{Checks if the specified property is part of the variables metadata for the given column in the specified data table.} +#' \item{\code{data_frame_exists(data_name)}}{Checks if the specified data table exists in the object.} +#' \item{\code{add_key(data_name, col_names, key_name)}}{Adds a key to the specified data table using the given columns and key name.} +#' \item{\code{is_key(data_name, col_names)}}{Checks if the specified columns form a key in the given data table.} +#' \item{\code{has_key(data_name)}}{Checks if the specified data table has a key.} +#' \item{\code{get_keys(data_name, key_name)}}{Returns the keys for the specified data table and key name.} +#' \item{\code{add_new_comment(data_name, row = "", column = "", comment)}}{Adds a new comment to the specified data table, optionally specifying the row and column.} +#' \item{\code{get_comments(data_name, comment_id)}}{Returns the comments for the specified data table and comment ID.} +#' \item{\code{get_links(link_name, ...)}}{Returns the links for the specified link name or all links if no name is provided.} +#' \item{\code{set_structure_columns(data_name, struc_type_1 = c(), struc_type_2 = c(), struc_type_3 = c())}}{Sets the structure columns for the specified data table.} +#' \item{\code{add_dependent_columns(data_name, columns, dependent_cols)}}{Adds dependent columns to the specified columns in the given data table.} +#' \item{\code{set_column_colours(data_name, columns, colours)}}{Sets the colors for the specified columns in the given data table.} +#' \item{\code{has_colours(data_name, columns)}}{Checks if the specified columns in the given data table have colors.} +#' \item{\code{remove_column_colours(data_name)}}{Removes colors from all columns in the specified data table.} +#' \item{\code{set_column_colours_by_metadata(data_name, columns, property)}}{Sets the colors for the specified columns in the given data table based on the specified metadata property.} +#' \item{\code{graph_one_variable(data_name, columns, numeric = "geom_boxplot", categorical = "geom_bar", character = "geom_bar", output = "facets", free_scale_axis = FALSE, ncol = NULL, coord_flip = FALSE, ... = ...)}}{Creates a graph for one variable in the specified data table with options for the type of graph, axis scaling, and other parameters.} +#' \item{\code{make_date_yearmonthday(data_name, year, month, day, f_year, f_month, f_day, year_format = "%Y", month_format = "%m")}}{Creates a date column from the specified year, month, and day columns in the given data table, with options for formatting.} +#' \item{\code{make_date_yeardoy(data_name, year, doy, base, doy_typical_length = "366")}}{Creates a date column from the specified year and day of year columns in the given data table.} +#' \item{\code{set_contrasts_of_factor(data_name, col_name, new_contrasts, defined_contr_matrix)}}{Sets the contrasts for the specified factor column in the given data table.} +#' \item{\code{create_factor_data_frame(data_name, factor, factor_data_frame_name, include_contrasts = FALSE, replace = FALSE, summary_count = TRUE)}}{Creates a new data frame for the specified factor column in the given data table, with options to include contrasts and summary counts.} +#' \item{\code{split_date(data_name, col_name = "", year_val = FALSE, year_name = FALSE, leap_year = FALSE, month_val = FALSE, month_abbr = FALSE, month_name = FALSE, week_val = FALSE, week_abbr = FALSE, week_name = FALSE, weekday_val = FALSE, weekday_abbr = FALSE, weekday_name = FALSE, day = FALSE, day_in_month = FALSE, day_in_year = FALSE, day_in_year_366 = FALSE, pentad_val = FALSE, pentad_abbr = FALSE, dekad_val = FALSE, dekad_abbr = FALSE, quarter_val = FALSE, quarter_abbr = FALSE, with_year = FALSE, s_start_month = 1, s_start_day_in_month = 1, days_in_month = FALSE)}}{Splits the specified date column into multiple components such as year, month, day, etc. in the given data table.} +#' \item{\code{import_SST(dataset, data_from = 5, data_names = c())}}{Imports SST data from the specified dataset and data source, creating data tables with the specified names.} + +# dont have from here +#' \item{\code{make_inventory_plot(data_name, date_col, station_col = NULL, year_col = NULL, doy_col = NULL, element_cols = NULL, add_to_data = FALSE, year_doy_plot = FALSE, coord_flip = FALSE, facet_by = NULL, graph_title = "Inventory Plot", graph_subtitle = NULL, graph_caption = NULL, title_size = NULL, subtitle_size = NULL, caption_size = NULL, labelXAxis, labelYAxis, xSize = NULL, ySize = NULL, Xangle = NULL, Yangle = NULL, scale_xdate, fromXAxis = NULL, toXAxis = NULL, byXaxis = NULL, date_ylabels, legend_position = NULL, xlabelsize = NULL, ylabelsize = NULL, scale = NULL, dir = "", row_col_number, nrow = NULL, ncol = NULL, key_colours = c("red", "grey"), display_rain_days = FALSE, facet_xsize = 9, facet_ysize = 9, facet_xangle = 90, facet_yangle = 90, scale_ydate = FALSE, date_ybreaks, step = 1, rain_cats = list(breaks = c(0, 0.85, Inf), labels = c("Dry", "Rain"), key_colours = c("tan3", "blue")))}}{Creates an inventory plot for the specified data table with various customization options.} + +#' \item{\code{import_NetCDF(nc, path, name, only_data_vars = TRUE, keep_raw_time = TRUE, include_metadata = TRUE, boundary, lon_points = NULL, lat_points = NULL, id_points = NULL, show_requested_points = TRUE, great_circle_dist = FALSE)}}{Imports data from a NetCDF file, with options to specify the data variables, time format, metadata inclusion, and boundaries.} +#' \item{\code{infill_missing_dates(data_name, date_name, factors, start_month, start_date, end_date, resort = TRUE)}}{Infills missing dates in the specified data table using the provided date column and factors.} +#' \item{\code{get_key_names(data_name, include_overall = TRUE, include, exclude, include_empty = FALSE, as_list = FALSE, excluded_items = c())}}{Returns the key names for the specified data table, with options to include overall keys, exclude specific keys, and return as a list.} +#' \item{\code{remove_key(data_name, key_name)}}{Removes the specified key from the given data table.} +#' \item{\code{add_climdex_indices(data_name, climdex_output, freq = "annual", station, year, month)}}{Adds climdex indices to the specified data table, with options for frequency, station, year, and month.} +#' \item{\code{is_metadata(data_name, str)}}{Checks if the specified string is part of the metadata for the given data table.} +#' \item{\code{get_climatic_column_name(data_name, col_name)}}{Returns the climatic column name for the specified column in the given data table.} +#' \item{\code{merge_data(data_name, new_data, by = NULL, type = "left", match = "all")}}{Merges new data into the specified data table using the provided columns and merge type.} +#' \item{\code{get_corruption_data_names()}}{Returns the names of all data tables with corruption data.} +#' \item{\code{get_corruption_contract_data_names()}}{Returns the names of all data tables with corruption contract data.} +#' \item{\code{get_database_variable_names(query, data_name, include_overall = TRUE, include, exclude, include_empty = FALSE, as_list = FALSE, excluded_items = c())}}{Returns the database variable names for the specified query and data table, with options to include overall variables, exclude specific variables, and return as a list.} +#' \item{\code{get_nc_variable_names(file = "", as_list = FALSE, ...)}}{Returns the variable names from the specified NetCDF file, with an option to return as a list.} +#' \item{\code{has_database_connection()}}{Checks if there is a database connection.} +#' \item{\code{database_connect(dbname, user, host, port, drv = RMySQL::MySQL())}}{Connects to a database using the provided credentials and driver.} +#' \item{\code{get_database_connection()}}{Returns the current database connection.} +#' \item{\code{set_database_connection(dbi_connection)}}{Sets the database connection to the specified DBI connection object.} +#' \item{\code{database_disconnect()}}{Disconnects from the current database.} +#' \item{\code{import_from_climsoft(stationfiltercolumn = "stationId", stations = c(), elementfiltercolumn = "elementId", elements = c(), include_observation_data = FALSE, include_observation_flags = FALSE, unstack_data = FALSE, include_elements_info = FALSE, start_date = NULL, end_date = NULL)}}{Imports data from CLIMSOFT using the specified filters and options for observation data, flags, and unstacking.} +#' \item{\code{import_from_iri(download_from, data_file, data_frame_name, location_data_name, path, X1, X2 = NA, Y1, Y2 = NA, get_area_point = "area")}}{Imports data from IRI using the specified parameters for download, file path, coordinates, and area type.} +#' \item{\code{export_workspace(data_names, file, include_graphs = TRUE, include_models = TRUE, include_metadata = TRUE)}}{Exports the workspace to a file, including the specified data tables, graphs, models, and metadata.} +#' \item{\code{set_links(new_links)}}{Sets the links in the object to the specified new links.} +#' \item{\code{display_daily_graph(data_name, date_col = NULL, station_col = NULL, year_col = NULL, doy_col = NULL, climatic_element = NULL, upper_limit = 100, bar_colour = "blue", rug_colour = "red")}}{Displays a daily graph for the specified data table with options for columns, element, colors, and limits.} +#' \item{\code{create_variable_set(data_name, set_name, columns)}}{Creates a variable set with the specified name and columns in the given data table.} +#' \item{\code{update_variable_set(data_name, set_name, columns, new_set_name)}}{Updates the specified variable set with new columns and optionally a new name in the given data table.} +#' \item{\code{delete_variable_sets(data_name, set_names)}}{Deletes the specified variable sets from the given data table.} +#' \item{\code{get_variable_sets_names(data_name, include_overall = TRUE, include, exclude, include_empty = FALSE, as_list = FALSE, excluded_items = c())}}{Returns the names of variable sets for the specified data table, with options to include overall sets, exclude specific sets, and return as a list.} +#' \item{\code{get_variable_sets(data_name, set_names, force_as_list = FALSE)}}{Returns the specified variable sets from the given data table, with an option to force the result as a list.} +#' \item{\code{crops_definitions(data_name, year, station, rain, day, rain_totals, plant_days, plant_lengths, start_check = TRUE, season_data_name, start_day, end_day, definition_props = TRUE, print_table = TRUE)}}{Defines crop parameters for the specified data table using the provided columns and options for seasons, days, and properties.} +#' \item{\code{tidy_climatic_data(x, format, stack_cols, day, month, year, stack_years, station, element, element_name="value", ignore_invalid = FALSE, silent = FALSE, unstack_elements = TRUE, new_name)}}{Converts wide-format daily climatic data to long format using the specified columns and options for format, elements, and validation.} +#' \item{\code{get_geometry(data)}}{Returns the geometry column for the specified data table.} +#' \item{\code{package_check(package)}}{Checks if the specified package is installed and returns information about its version and availability.} +#' \item{\code{download_from_IRI(source, data, path = tempdir(), min_lon, max_lon, min_lat, max_lat, min_date, max_date, name, download_type = "Point", import = TRUE)}}{Downloads data from IRI using the specified source, data, coordinates, date range, and options for download type and import.} +#' \item{\code{patch_climate_element(data_name, date_col_name = "", var = "", vars = c(), max_mean_bias = NA, max_stdev_bias = NA, time_interval = "month", column_name, station_col_name = station_col_name)}}{Patches the specified climate element in the given data table using the provided columns and options for bias, time interval, and station.} +#' \item{\code{visualize_element_na(data_name, element_col_name, element_col_name_imputed, station_col_name, x_axis_labels_col_name, ncol = 2, type = "distribution", xlab = NULL, ylab = NULL, legend = TRUE, orientation = "horizontal", interval_size = interval_size, x_with_truth = NULL, measure = "percent")}}{Visualizes missing data for the specified element in the given data table using the provided columns and options for labels, legend, orientation, and measure.} +#' \item{\code{get_data_entry_data(data_name, station, date, elements, view_variables, station_name, type, start_date, end_date)}}{Returns data entry data for the specified data table using the provided columns and options for date range, variables, and type.} +#' \item{\code{save_data_entry_data(data_name, new_data, rows_changed, comments_list = list(), add_flags = FALSE, ...)}}{Saves data entry data to the specified data table with options for adding comments, flags, and rows changed.} +#' \item{\code{import_from_cds(user, dataset, elements, start_date, end_date, lon, lat, path, import = FALSE, new_name)}}{Imports data from CDS using the specified user, dataset, elements, date range, coordinates, and options for file path and import.} +#' \item{\code{add_flag_fields(data_name, col_names, key_column_names)}}{Adds flag fields to the specified columns in the given data table, using the provided key columns.} +#' \item{\code{remove_empty(data_name, which = c("rows","cols"))}}{Removes empty rows or columns from the specified data table.} +#' \item{\code{replace_values_with_NA(data_name, row_index, column_index)}}{Replaces values with NA in the specified rows and columns of the given data table.} +#' \item{\code{has_labels(data_name, col_names)}}{Checks if the specified columns in the given data table have labels.} +#' \item{\code{wrap_or_unwrap_data(data_name, col_name, column_data, width, wrap = TRUE)}}{Wraps or unwraps the specified column data in the given data table to the specified width.} #' } #' #' @export @@ -176,7 +363,671 @@ DataBook <- R6::R6Class("DataBook", #' @return The name of the corruption column. get_corruption_column_name = function(data_name, type) { self$get_data_objects(data_name)$get_corruption_column_name(type) + }, + + + #' @title Append Property to Variables Metadata + #' @description Appends a new property and its value to the metadata of specified columns in a data table. + #' @param data_name The name of the data table. + #' @param col_names A vector of column names to which the property should be appended. + #' @param property The name of the property to append. + #' @param new_val The value of the property to append. Default is an empty string. + #' @return None + append_to_variables_metadata = function(data_name, col_names, property, new_val = "") { + self$get_data_objects(data_name)$append_to_variables_metadata(col_names, property, new_val) + }, + + #' @title Append Property to Dataframe Metadata + #' @description Appends a new property and its value to the metadata of a data table. + #' @param data_name The name of the data table. + #' @param property The name of the property to append. + #' @param new_val The value of the property to append. Default is an empty string. + #' @return None + append_to_dataframe_metadata = function(data_name, property, new_val = "") { + self$get_data_objects(data_name)$append_to_metadata(property, new_val) + }, + + #' @title Append Property to Metadata + #' @description Appends a new property and its value to the metadata of the current object. + #' @param property The name of the property to append. + #' @param new_val The value of the property to append. Default is an empty string. + #' @param allow_override_special Boolean flag to allow overriding special properties. Default is FALSE. + #' @return None + append_to_metadata = function(property, new_val = "", allow_override_special = FALSE) { + if(missing(property)) stop("property and new_val arguments must be specified.") + if(!is.character(property)) stop("property must be of type character") + if(!allow_override_special && property %in% c("class")) message("Cannot override property: ", property, ". Specify allow_override_special = TRUE to replace this property.") + else { + attr(self, property) <- new_val + self$metadata_changed <- TRUE + self$append_to_changes(list(Added_metadata, property)) + } + }, + + #' @title Add Metadata Field + #' @description Adds a new metadata field and its value to the specified data table or all data tables. + #' @param data_name The name of the data table. Use overall_label to apply to all data tables. + #' @param property The name of the property to append. + #' @param new_val The value of the property to append. Default is an empty string. + #' @return None + add_metadata_field = function(data_name, property, new_val = "") { + if(missing(property)) stop("property and new_val arguments must be specified.") + if(data_name == overall_label) { + invisible(sapply(self$get_data_objects(), function(x) x$append_to_metadata(property, new_val))) + } else { + invisible(sapply(self$get_data_objects(data_name, as_list = TRUE), function(x) x$append_to_variables_metadata(property = property, new_val = new_val))) + } + }, + + #' @title Reorder Dataframes + #' @description Reorders the dataframes in the object according to the specified order. + #' @param data_frames_order A vector specifying the new order of dataframes. + #' @return None + reorder_dataframes = function(data_frames_order) { + if(length(data_frames_order) != length(names(private$.data_sheets))) stop("number data frames to order should be equal to number of dataframes in the object") + if(!setequal(data_frames_order, names(private$.data_sheets))) stop("data_frames_order must be a permutation of the dataframe names.") + self$set_data_objects(private$.data_sheets[data_frames_order]) + self$data_objects_changed <- TRUE + }, + + #' @title Copy Columns + #' @description Copies specified columns from a data table to another location or clipboard. + #' @param data_name The name of the data table. + #' @param col_names A vector of column names to copy. + #' @param copy_to_clipboard Boolean flag to copy to clipboard. Default is FALSE. + #' @return None + copy_columns = function(data_name, col_names = "", copy_to_clipboard = FALSE) { + if(copy_to_clipboard){ + col_data_obj <- self$get_columns_from_data(data_name = data_name, col_names = col_names, force_as_data_frame = TRUE) + self$copy_to_clipboard(content = col_data_obj) + }else{ + self$get_data_objects(data_name)$copy_columns(col_names = col_names) + } + }, + + #' @title Drop Unused Factor Levels + #' @description Drops unused levels from a factor column in the specified data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the column. + #' @return None + drop_unused_factor_levels = function(data_name, col_name) { + self$get_data_objects(data_name)$drop_unused_factor_levels(col_name = col_name) + }, + + #' @title Set Factor Levels + #' @description Sets new levels for a factor column in the specified data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the column. + #' @param new_labels A vector of new labels for the factor levels. + #' @param new_levels A vector of new levels. + #' @param set_new_labels Boolean flag to set new labels. Default is TRUE. + #' @return None + set_factor_levels = function(data_name, col_name, new_labels, new_levels, set_new_labels = TRUE) { + self$get_data_objects(data_name)$set_factor_levels(col_name = col_name, new_labels = new_labels, new_levels = new_levels, set_new_labels = set_new_labels) + }, + + #' @title Edit Factor Level + #' @description Edits a level in a factor column in the specified data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the column. + #' @param old_level The old level to replace. + #' @param new_level The new level to set. + #' @return None + edit_factor_level = function(data_name, col_name, old_level, new_level) { + self$get_data_objects(data_name)$edit_factor_level(col_name = col_name, old_level = old_level, new_level = new_level) + }, + + #' @title Set Factor Reference Level + #' @description Sets the reference level for a factor column in the specified data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the column. + #' @param new_ref_level The new reference level. + #' @return None + set_factor_reference_level = function(data_name, col_name, new_ref_level) { + self$get_data_objects(data_name)$set_factor_reference_level(col_name = col_name, new_ref_level = new_ref_level) + }, + + #' @title Get Column Count + #' @description Returns the number of columns in the specified data table. + #' @param data_name The name of the data table. + #' @param use_column_selection Boolean flag to use column selection. Default is FALSE. + #' @return The number of columns. + get_column_count = function(data_name, use_column_selection = FALSE) { + return(self$get_data_objects(data_name)$get_column_count(use_column_selection)) + }, + + #' @title Reorder Factor Levels + #' @description Reorders the levels of a factor column in the specified data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the column. + #' @param new_level_names A vector specifying the new order of factor levels. + #' @return None + reorder_factor_levels = function(data_name, col_name, new_level_names) { + self$get_data_objects(data_name)$reorder_factor_levels(col_name = col_name, new_level_names = new_level_names) + }, + + #' @title Get Data Type + #' @description Returns the data type of the specified column in the given data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the column. + #' @return The data type of the column. + get_data_type = function(data_name, col_name) { + self$get_data_objects(data_name)$get_data_type(col_name = col_name) + }, + + #' @title Copy Data Frame + #' @description Copies a data frame to a new name or clipboard. + #' @param data_name The name of the data table. + #' @param new_name The new name for the copied data frame. + #' @param label A label for the new data frame. Default is an empty string. + #' @param copy_to_clipboard Boolean flag to copy to clipboard. Default is FALSE. + #' @return None + copy_data_frame = function(data_name, new_name, label = "", copy_to_clipboard = FALSE) { + if(copy_to_clipboard){ + self$copy_to_clipboard(content = self$get_data_frame(data_name)) + }else{ + if(new_name %in% names(private$.data_sheets)) stop("Cannot copy data frame since ", new_name, " is an existing data frame.") + curr_obj <- self$get_data_objects(data_name)$clone(deep = TRUE) + if(missing(new_name)) new_name <- next_default_item(data_name, self$get_data_names()) + self$append_data_object(new_name, curr_obj) + new_data_obj <- self$get_data_objects(new_name) + new_data_obj$data_changed <- TRUE + new_data_obj$set_data_changed(TRUE) + if(label != "") { + new_data_obj$append_to_metadata(property = "label" , new_val = label) + new_data_obj$set_metadata_changed(TRUE) + } + } + }, + + #' @title Copy Column Metadata to Clipboard + #' @description Copies the metadata of specified columns to the clipboard. + #' @param data_name The name of the data table. + #' @param property_names A vector of property names to copy. Default is all properties. + #' @return None + copy_col_metadata_to_clipboard = function(data_name, property_names) { + if(missing(property_names)){ + self$copy_to_clipboard(content = self$get_variables_metadata(data_name = data_name)) + }else{ + self$copy_to_clipboard(content = self$get_variables_metadata(data_name = data_name, property = property_names)) + } + }, + + #' @title Copy Data Frame Metadata to Clipboard + #' @description Copies the metadata of the specified data table to the clipboard. + #' @param data_name The name of the data table. + #' @param property_names A vector of property names to copy. Default is all properties. + #' @return None + copy_data_frame_metadata_to_clipboard = function(data_name, property_names) { + if(missing(property_names)){ + self$copy_to_clipboard(content = self$get_data_frame_metadata(data_name = data_name)) + }else{ + self$copy_to_clipboard(content = self$get_data_frame_metadata(data_name = data_name, label = property_names)) + } + }, + + #' @title Copy to Clipboard + #' @description Copies the specified content to the clipboard. + #' @param content The content to copy to the clipboard. + #' @return None + copy_to_clipboard = function(content) { + clipr::write_clip(content = content) + }, + + #' @title Set Hidden Columns + #' @description Sets the specified columns as hidden in the given data table. + #' @param data_name The name of the data table. + #' @param col_names A vector of column names to set as hidden. + #' @return None + set_hidden_columns = function(data_name, col_names = c()) { + self$get_data_objects(data_name)$set_hidden_columns(col_names = col_names) + }, + + #' @title Unhide All Columns + #' @description Unhides all columns in the specified data table or all data tables if data_name is missing. + #' @param data_name The name of the data table. If missing, applies to all data tables. + #' @return None + unhide_all_columns = function(data_name) { + if(missing(data_name)) { + invisible(sapply(self$get_data_objects(), function(obj) obj$unhide_all_columns())) + } else { + self$get_data_objects(data_name)$unhide_all_columns() + } + }, + + #' @title Set Hidden Data Frames + #' @description Sets the specified data tables as hidden. + #' @param data_names A vector of data table names to set as hidden. + #' @return None + set_hidden_data_frames = function(data_names = c()) { + invisible(sapply(data_names, function(x) self$append_to_dataframe_metadata(data_name = x, property = is_hidden_label, new_val = TRUE))) + unhide_data_names <- setdiff(self$get_data_names(), data_names) + invisible(sapply(unhide_data_names, function(x) self$append_to_dataframe_metadata(data_name = x, property = is_hidden_label, new_val = FALSE))) + }, + + #' @title Get Hidden Data Frames + #' @description Returns a list of hidden data tables. + #' @return A vector of hidden data table names. + get_hidden_data_frames = function() { + all_data_names <- names(private$.data_sheets) + visible_data_names <- all_data_names[sapply(all_data_names, function(x) !isTRUE(self$get_data_objects(x)$get_metadata(label = is_hidden_label)))] + hidden_data_names <- setdiff(all_data_names, visible_data_names) + return(hidden_data_names) + }, + + #' @title Set Row Names + #' @description Sets the row names for the specified data table. + #' @param data_name The name of the data table. + #' @param row_names A vector of row names to set. + #' @return None + set_row_names = function(data_name, row_names) { + self$get_data_objects(data_name)$set_row_names(row_names = row_names) + }, + + #' @title Get Row Names + #' @description Returns the row names of the specified data table. + #' @param data_name The name of the data table. + #' @return A vector of row names. + get_row_names = function(data_name) { + self$get_data_objects(data_name)$get_row_names() + }, + + #' @title Set Protected Columns + #' @description Sets the specified columns as protected in the given data table. + #' @param data_name The name of the data table. + #' @param col_names A vector of column names to set as protected. + #' @return None + set_protected_columns = function(data_name, col_names) { + self$get_data_objects(data_name)$set_protected_columns(col_names = col_names) + }, + + #' @title Get Metadata Fields + #' @description Returns the metadata fields of the specified data table. + #' @param data_name The name of the data table. + #' @param include_overall Boolean flag to include overall metadata fields. Default is TRUE. + #' @param as_list Boolean flag to return the result as a list. Default is FALSE. + #' @param include A vector of metadata fields to include. Default is all fields. + #' @param exclude A vector of metadata fields to exclude. Default is none. + #' @param excluded_items A vector of metadata fields to exclude. Default is an empty vector. + #' @return A vector or list of metadata fields. + get_metadata_fields = function(data_name, include_overall, as_list = FALSE, include, exclude, excluded_items = c()) { + if(!missing(data_name)) { + if(data_name == overall_label) { + out = names(self$get_combined_metadata()) + if(length(excluded_items) > 0){ + ex_ind = which(out %in% excluded_items) + if(length(ex_ind) != length(excluded_items)) warning("Some of the excluded_items were not found in the list of objects") + if(length(ex_ind) > 0) out = out[-ex_ind] + } + if(as_list) { + lst = list() + lst[[data_name]] <- out + return(lst) + } + else return(out) + } else { + return(self$get_data_objects(data_name)$get_variables_metadata_fields(as_list = as_list, include = include, exclude = exclude, excluded_items = excluded_items)) + } + } else { + out = list() + if(include_overall) out[[overall_label]] <- names(self$get_combined_metadata()) + for(data_obj_name in self$get_data_names()) { + out[[data_obj_name]] <- self$get_data_objects(data_obj_name)$get_variables_metadata_fields(as_list = FALSE, include = include, exclude = exclude) + } + return(out) + } + }, + + #' @title Freeze Columns + #' @description Freezes the specified columns in the given data table. + #' @param data_name The name of the data table. + #' @param column A vector of column names to freeze. + #' @return None + freeze_columns = function(data_name, column) { + self$get_data_objects(data_name)$freeze_columns(column = column) + }, + + #' @title Unfreeze Columns + #' @description Unfreezes all columns in the specified data table. + #' @param data_name The name of the data table. + #' @return None + unfreeze_columns = function(data_name) { + self$get_data_objects(data_name)$unfreeze_columns() + }, + + #' @title Is Variables Metadata + #' @description Checks if the specified property is metadata for the given columns in the data table. + #' @param data_name The name of the data table. + #' @param property The name of the property to check. + #' @param column The name of the column. + #' @param return_vector Boolean flag to return the result as a vector. Default is FALSE. + #' @return A boolean value indicating if the property is metadata for the columns. + is_variables_metadata = function(data_name, property, column, return_vector = FALSE) { + self$get_data_objects(data_name)$is_variables_metadata(property, column, return_vector) + }, + + #' @title Data Frame Exists + #' @description Checks if the specified data table exists. + #' @param data_name The name of the data table. + #' @return A boolean value indicating if the data table exists. + data_frame_exists = function(data_name) { + return(data_name %in% names(private$.data_sheets)) + }, + + #' @title Add Key + #' @description Adds a key to the specified columns in the given data table. + #' @param data_name The name of the data table. + #' @param col_names A vector of column names to add as keys. + #' @param key_name The name of the key. + #' @return None + add_key = function(data_name, col_names, key_name) { + self$get_data_objects(data_name)$add_key(col_names, key_name) + names(col_names) <- col_names + self$add_link(data_name, data_name, col_names, keyed_link_label) + invisible(sapply(self$get_data_objects(), function(x) if(!x$is_metadata(is_linkable)) x$append_to_metadata(is_linkable, FALSE))) + }, + + #' @title Is Key + #' @description Checks if the specified columns are keys in the given data table. + #' @param data_name The name of the data table. + #' @param col_names A vector of column names to check. + #' @return A boolean value indicating if the columns are keys. + is_key = function(data_name, col_names) { + self$get_data_objects(data_name)$is_key(col_names) + }, + + #' @title Has Key + #' @description Checks if the specified data table has a key. + #' @param data_name The name of the data table. + #' @return A boolean value indicating if the data table has a key. + has_key = function(data_name) { + self$get_data_objects(data_name)$has_key() + }, + + #' @title Get Keys + #' @description Returns the keys of the specified data table. + #' @param data_name The name of the data table. + #' @param key_name The name of the key. Default is all keys. + #' @return A list of keys. + get_keys = function(data_name, key_name) { + self$get_data_objects(data_name)$get_keys(key_name) + }, + + #' @title Add New Comment + #' @description Adds a new comment to the specified row and column in the given data table. + #' @param data_name The name of the data table. + #' @param row The name of the row. + #' @param column The name of the column. + #' @param comment The comment text. + #' @return None + add_new_comment = function(data_name, row = "", column = "", comment) { + if (!self$has_key(data_name)) stop("A key must be defined in the data frame to add a comment. Use the Add Key dialog to define a key.") + if (!".comment" %in% self$get_data_names()) { + comment_df <- data.frame(sheet = character(0), + row = character(0), + column = character(0), + id = numeric(0), + comment = character(0), + time_stamp = as.POSIXct(c())) + self$import_data(data_tables = list(.comment = comment_df)) + self$add_key(".comment", c("sheet", "row", "id"), "key1") + } + comment_df <- self$get_data_frame(".comment", use_current_filter = FALSE) + curr_df <- self$get_data_frame(data_name, use_current_filter = FALSE) + if(row != ""){ + curr_row <- curr_df[row.names(curr_df) == row, ] + key <- self$get_keys(data_name)[[1]] + key_cols <- as.character(key) + key_vals <- paste(sapply(curr_row[, key_cols], as.character), collapse = "__") + } else { + key_vals <- "" + } + curr_comments <- comment_df[comment_df$sheet == data_name & comment_df$row == key_vals, ] + new_id <- 1 + if (nrow(curr_comments) > 0) new_id <- max(curr_comments$id) + 1 + comment_df[nrow(comment_df) + 1, ] <- list(sheet = data_name, + row = key_vals, + column = column, + id = new_id, + comment = comment, + time_stamp = Sys.time()) + self$get_data_objects(".comment")$set_data(new_data = comment_df) + }, + + #' @title Get Comments + #' @description Returns the comments for the specified data table and comment ID. + #' @param data_name The name of the data table. + #' @param comment_id The ID of the comment. + #' @return A data frame of comments. + get_comments = function(data_name, comment_id) { + self$get_data_objects(data_name)$get_comments(comment_id) + }, + + #' @title Get Links + #' @description Returns the links for the specified link name or all links. + #' @param link_name The name of the link. Default is all links. + #' @return A list of links. + get_links = function(link_name, ...) { + if(!missing(link_name)) { + if(!link_name %in% names(private$.links)) stop(link_name, " not found.") + return(private$.links[[link_name]]) + } else { + return(private$.links) + } + }, + + #' @title Set Structure Columns + #' @description Sets the structure columns for the specified data table. + #' @param data_name The name of the data table. + #' @param struc_type_1 A vector of column names for the first structure type. + #' @param struc_type_2 A vector of column names for the second structure type. + #' @param struc_type_3 A vector of column names for the third structure type. + #' @return None + set_structure_columns = function(data_name, struc_type_1 = c(), struc_type_2 = c(), struc_type_3 = c()) { + self$get_data_objects(data_name)$set_structure_columns(struc_type_1, struc_type_2, struc_type_3) + }, + + #' @title Add Dependent Columns + #' @description Adds dependent columns to the specified columns in the given data table. + #' @param data_name The name of the data table. + #' @param columns A vector of column names to add dependents to. + #' @param dependent_cols A vector of dependent column names. + #' @return None + add_dependent_columns = function(data_name, columns, dependent_cols) { + self$get_data_objects(data_name)$add_dependent_columns(columns, dependent_cols) + }, + + #' @title Set Column Colours + #' @description Sets the colours for the specified columns in the given data table. + #' @param data_name The name of the data table. + #' @param columns A vector of column names to set colours for. + #' @param colours A vector of colours. + #' @return None + set_column_colours = function(data_name, columns, colours) { + self$get_data_objects(data_name)$set_column_colours(columns, colours) + }, + + #' @title Has Colours + #' @description Checks if the specified columns have colours in the given data table. + #' @param data_name The name of the data table. + #' @param columns A vector of column names to check. + #' @return A boolean value indicating if the columns have colours. + has_colours = function(data_name, columns) { + self$get_data_objects(data_name)$has_colours(columns) + }, + + #' @title Remove Column Colours + #' @description Removes the colours from all columns in the specified data table. + #' @param data_name The name of the data table. + #' @return None + remove_column_colours = function(data_name) { + self$get_data_objects(data_name)$remove_column_colours() + }, + + #' @title Set Column Colours by Metadata + #' @description Sets the colours for the specified columns based on metadata in the given data table. + #' @param data_name The name of the data table. + #' @param columns A vector of column names to set colours for. + #' @param property The metadata property to use for setting colours. + #' @return None + set_column_colours_by_metadata = function(data_name, columns, property) { + self$get_data_objects(data_name)$set_column_colours_by_metadata(data_name, columns, property) + }, + + #' @title Graph One Variable + #' @description Creates a graph for a single variable in the specified data table. + #' @param data_name The name of the data table. + #' @param columns A vector of column names to graph. + #' @param numeric The type of graph for numeric columns. Default is "geom_boxplot". + #' @param categorical The type of graph for categorical columns. Default is "geom_bar". + #' @param character The type of graph for character columns. Default is "geom_bar". + #' @param output The output type for the graph. Default is "facets". + #' @param free_scale_axis Boolean flag to allow free scaling of axes. Default is FALSE. + #' @param ncol The number of columns in the output. Default is NULL. + #' @param coord_flip Boolean flag to flip coordinates. Default is FALSE. + #' @param ... Additional arguments passed to the graph function. + #' @return None + graph_one_variable = function(data_name, columns, numeric = "geom_boxplot", categorical = "geom_bar", character = "geom_bar", output = "facets", free_scale_axis = FALSE, ncol = NULL, coord_flip = FALSE, ...) { + self$get_data_objects(data_name)$graph_one_variable(columns = columns, numeric = numeric, categorical = categorical, output = output, free_scale_axis = free_scale_axis, ncol = ncol, coord_flip = coord_flip, ... = ...) + }, + + #' @title Make Date YearMonthDay + #' @description Creates a date column from year, month, and day columns in the specified data table. + #' @param data_name The name of the data table. + #' @param year The name of the year column. + #' @param month The name of the month column. + #' @param day The name of the day column. + #' @param f_year The format for the year column. + #' @param f_month The format for the month column. + #' @param f_day The format for the day column. + #' @param year_format The format for the year. Default is "%Y". + #' @param month_format The format for the month. Default is "%m". + #' @return None + make_date_yearmonthday = function(data_name, year, month, day, f_year, f_month, f_day, year_format = "%Y", month_format = "%m") { + self$get_data_objects(data_name)$make_date_yearmonthday(year = year, month = month, day = day, f_year = f_year, f_month = f_month, f_day = f_day, year_format = year_format, month_format = month_format) + }, + + #' @title Make Date YearDoY + #' @description Creates a date column from year and day of year columns in the specified data table. + #' @param data_name The name of the data table. + #' @param year The name of the year column. + #' @param doy The name of the day of year column. + #' @param base The base date for the day of year. + #' @param doy_typical_length The typical length of the day of year. Default is "366". + #' @return None + make_date_yeardoy = function(data_name, year, doy, base, doy_typical_length = "366") { + self$get_data_objects(data_name)$make_date_yeardoy(year = year, doy = doy, base = base, doy_typical_length = doy_typical_length) + }, + + #' @title Set Contrasts of Factor + #' @description Sets the contrasts for a factor column in the specified data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the column. + #' @param new_contrasts A vector of new contrasts. + #' @param defined_contr_matrix A defined contrast matrix. + #' @return None + set_contrasts_of_factor = function(data_name, col_name, new_contrasts, defined_contr_matrix) { + self$get_data_objects(data_name)$set_contrasts_of_factor(col_name = col_name, new_contrasts = new_contrasts, defined_contr_matrix = defined_contr_matrix) + }, + + #' @title Create Factor Data Frame + #' @description Creates a new data frame for a factor column in the specified data table. + #' @param data_name The name of the data table. + #' @param factor The name of the factor column. + #' @param factor_data_frame_name The name of the new data frame. + #' @param include_contrasts Boolean flag to include contrasts. Default is FALSE. + #' @param replace Boolean flag to replace the existing factor data frame. Default is FALSE. + #' @param summary_count Boolean flag to include summary count. Default is TRUE. + #' @return None + create_factor_data_frame = function(data_name, factor, factor_data_frame_name, include_contrasts = FALSE, replace = FALSE, summary_count = TRUE) { + curr_data_obj <- self$get_data_objects(data_name) + if(!factor %in% names(curr_data_obj$get_data_frame())) stop(factor, " not found in the data") + if(!is.factor(curr_data_obj$get_columns_from_data(factor))) stop(factor, " is not a factor column.") + if(self$link_exists_from(data_name, factor)) { + message("Factor data frame already exists.") + if(replace) { + message("Current factor data frame will be replaced.") + factor_named <- factor + names(factor_named) <- factor + curr_factor_df_name <- self$get_linked_to_data_name(data_name, factor_named) + if(length(curr_factor_df_name) > 0) self$delete_dataframes(curr_factor_df_name[1]) + } else { + warning("replace = FALSE so no action will be taken.") + } + } + data_frame_list <- list() + if(missing(factor_data_frame_name)) factor_data_frame_name <- paste0(data_name, "_", factor) + factor_data_frame_name <- make.names(factor_data_frame_name) + factor_data_frame_name <- next_default_item(factor_data_frame_name, self$get_data_names(), include_index = FALSE) + factor_column <- curr_data_obj$get_columns_from_data(factor) + factor_data_frame <- data.frame(levels(factor_column)) + names(factor_data_frame) <- factor + if(include_contrasts) factor_data_frame <- cbind(factor_data_frame, contrasts(factor_column)) + if(summary_count) factor_data_frame <- cbind(factor_data_frame, summary(factor_column)) + row.names(factor_data_frame) <- 1:nrow(factor_data_frame) + names(factor_data_frame)[2:ncol(factor_data_frame)] <- paste0("C", 1:(ncol(factor_data_frame)-1)) + if(summary_count) colnames(factor_data_frame)[ncol(factor_data_frame)] <- "Frequencies" + data_frame_list[[factor_data_frame_name]] <- factor_data_frame + self$import_data(data_frame_list) + factor_data_obj <- self$get_data_objects(factor_data_frame_name) + factor_data_obj$add_key(factor) + names(factor) <- factor + self$add_link(from_data_frame = data_name, to_data_frame = factor_data_frame_name, link_pairs = factor, type = keyed_link_label) + }, + + #' @title Split Date + #' @description Splits a date column into multiple date components in the specified data table. + #' @param data_name The name of the data table. + #' @param col_name The name of the date column. + #' @param year_val Boolean flag to include year value. Default is FALSE. + #' @param year_name Boolean flag to include year name. Default is FALSE. + #' @param leap_year Boolean flag to include leap year. Default is FALSE. + #' @param month_val Boolean flag to include month value. Default is FALSE. + #' @param month_abbr Boolean flag to include month abbreviation. Default is FALSE. + #' @param month_name Boolean flag to include month name. Default is FALSE. + #' @param week_val Boolean flag to include week value. Default is FALSE. + #' @param week_abbr Boolean flag to include week abbreviation. Default is FALSE. + #' @param week_name Boolean flag to include week name. Default is FALSE. + #' @param weekday_val Boolean flag to include weekday value. Default is FALSE. + #' @param weekday_abbr Boolean flag to include weekday abbreviation. Default is FALSE. + #' @param weekday_name Boolean flag to include weekday name. Default is FALSE. + #' @param day Boolean flag to include day value. Default is FALSE. + #' @param day_in_month Boolean flag to include day in month. Default is FALSE. + #' @param day_in_year Boolean flag to include day in year. Default is FALSE. + #' @param day_in_year_366 Boolean flag to include day in year (366). Default is FALSE. + #' @param pentad_val Boolean flag to include pentad value. Default is FALSE. + #' @param pentad_abbr Boolean flag to include pentad abbreviation. Default is FALSE. + #' @param dekad_val Boolean flag to include dekad value. Default is FALSE. + #' @param dekad_abbr Boolean flag to include dekad abbreviation. Default is FALSE. + #' @param quarter_val Boolean flag to include quarter value. Default is FALSE. + #' @param quarter_abbr Boolean flag to include quarter abbreviation. Default is FALSE. + #' @param with_year Boolean flag to include with year. Default is FALSE. + #' @param s_start_month The start month. Default is 1. + #' @param s_start_day_in_month The start day in month. Default is 1. + #' @param days_in_month Boolean flag to include days in month. Default is FALSE. + #' @return None + split_date = function(data_name, col_name = "", year_val = FALSE, year_name = FALSE, leap_year = FALSE, month_val = FALSE, month_abbr = FALSE, month_name = FALSE, week_val = FALSE, week_abbr = FALSE, week_name = FALSE, weekday_val = FALSE, weekday_abbr = FALSE, weekday_name = FALSE, day = FALSE, day_in_month = FALSE, day_in_year = FALSE, day_in_year_366 = FALSE, pentad_val = FALSE, pentad_abbr = FALSE, dekad_val = FALSE, dekad_abbr = FALSE, quarter_val = FALSE, quarter_abbr = FALSE, with_year = FALSE, s_start_month = 1, s_start_day_in_month = 1, days_in_month = FALSE) { + self$get_data_objects(data_name)$split_date(col_name = col_name , year_val = year_val, year_name = year_name, leap_year = leap_year, month_val = month_val, month_abbr = month_abbr, month_name = month_name, week_val = week_val, week_abbr = week_abbr, week_name = week_name, weekday_val = weekday_val, weekday_abbr = weekday_abbr, weekday_name = weekday_name, day = day, day_in_month = day_in_month, day_in_year = day_in_year, day_in_year_366 = day_in_year_366, pentad_val = pentad_val, pentad_abbr = pentad_abbr, dekad_val = dekad_val, dekad_abbr = dekad_abbr, quarter_val = quarter_val, quarter_abbr = quarter_abbr, with_year = with_year, s_start_month = s_start_month, s_start_day_in_month = s_start_day_in_month, days_in_month = days_in_month) + }, + + #' @title Import SST + #' @description Imports SST data and adds keys and links to the specified data tables. + #' @param dataset The SST dataset. + #' @param data_from The source of the data. Default is 5. + #' @param data_names A vector of data table names. + #' @return None + import_SST = function(dataset, data_from = 5, data_names = c()) { + data_list <- convert_SST(dataset, data_from) + if(length(data_list) != length(data_names)) stop("data_names vector should be of length 2") + names(data_list) = data_names + self$import_data(data_list) + self$add_key(data_names[1], c("Lon", "Lat", "Year", "Month", "Day"), "key1") + self$add_key(data_names[2], c("Lon", "Lat"), "key2") + link_pairs = c("Lon", "Lat") + names(link_pairs) = c("Lon", "Lat") + self$add_link(from_data_frame = data_names[1], to_data_frame = data_names[2], link_pairs = link_pairs, type = keyed_link_label) } + ), private = list( .data_sheets = list(), diff --git a/man/DataBook.Rd b/man/DataBook.Rd index 8d0a841..4b5f3e9 100644 --- a/man/DataBook.Rd +++ b/man/DataBook.Rd @@ -3,7 +3,7 @@ \docType{class} \name{DataBook} \alias{DataBook} -\title{DataBook Class} +\title{Append Property to Variables Metadata} \format{ An R6 class object. } @@ -17,11 +17,109 @@ DataBook$new(data_tables = list(), instat_obj_metadata = list(), messages = TRUE, convert = TRUE, create = TRUE) } \description{ -DataBook Class +Append Property to Variables Metadata -DataBook Class +Append Property to Variables Metadata + +Append Property to Dataframe Metadata + +Append Property to Metadata + +Add Metadata Field + +Reorder Dataframes + +Copy Columns + +Drop Unused Factor Levels + +Set Factor Levels + +Edit Factor Level + +Set Factor Reference Level + +Get Column Count + +Reorder Factor Levels + +Get Data Type + +Copy Data Frame + +Copy Column Metadata to Clipboard + +Copy Data Frame Metadata to Clipboard + +Copy to Clipboard + +Set Hidden Columns + +Unhide All Columns + +Set Hidden Data Frames + +Get Hidden Data Frames + +Set Row Names + +Get Row Names + +Set Protected Columns + +Get Metadata Fields + +Freeze Columns + +Unfreeze Columns + +Is Variables Metadata + +Data Frame Exists + +Add Key + +Is Key + +Has Key + +Get Keys + +Add New Comment + +Get Comments + +Get Links + +Set Structure Columns + +Add Dependent Columns + +Set Column Colours + +Has Colours + +Remove Column Colours + +Set Column Colours by Metadata + +Graph One Variable + +Make Date YearMonthDay + +Make Date YearDoY + +Set Contrasts of Factor + +Create Factor Data Frame + +Split Date + +Import SST } \details{ +DataBook Class + An R6 class to manage a collection of data tables along with their metadata and other associated properties. } \section{Methods}{ @@ -38,6 +136,188 @@ An R6 class to manage a collection of data tables along with their metadata and \item{\code{get_red_flag_column_names(data_name)}}{Gets the names of red flag columns in the specified data table.} \item{\code{get_CRI_column_names(data_name)}}{Gets the names of CRI columns in the specified data table.} \item{\code{get_corruption_column_name(data_name, type)}}{Gets the name of the corruption column in the specified data table.} +\item{\code{import_data(data_tables = list(), data_tables_variables_metadata = rep(list(data.frame()),length(data_tables)), data_tables_metadata = rep(list(list()),length(data_tables)), data_tables_filters = rep(list(list()),length(data_tables)), data_tables_column_selections = rep(list(list()),length(data_tables)), imported_from = as.list(rep("",length(data_tables))), data_names = NULL, messages=TRUE, convert=TRUE, create=TRUE, prefix=TRUE, add_to_graph_book = TRUE)}}{Imports data into the DataBook from a list of data tables and their metadata.} +\item{\code{replace_instat_object(new_instat_object)}}{Replaces the current instat object with a new one.} +\item{\code{set_data_objects(new_data_objects)}}{Sets the data objects for the DataBook.} +\item{\code{copy_data_object(data_name, new_name, filter_name = "", column_selection_name = "", reset_row_names = TRUE)}}{Copies a data object with optional filtering and column selection.} +\item{\code{import_RDS(data_RDS, keep_existing = TRUE, overwrite_existing = FALSE, include_objects = TRUE, include_metadata = TRUE, include_logs = TRUE, include_filters = TRUE, include_column_selections = TRUE, include_calculations = TRUE, include_comments = TRUE)}}{Imports data from an RDS file into the DataBook.} +\item{\code{clone_data_object(curr_data_object, include_objects = TRUE, include_metadata = TRUE, include_logs = TRUE, include_filters = TRUE, include_column_selections = TRUE, include_calculations = TRUE, include_comments = TRUE, ...)}}{Clones a data object with options to include various components.} +\item{\code{clone_instat_calculation(curr_instat_calculation, ...)}}{Clones an instat calculation.} +\item{\code{import_from_ODK(username, form_name, platform)}}{Imports data from ODK (Open Data Kit).} +\item{\code{set_meta(new_meta)}}{Sets the metadata for the DataBook.} +\item{\code{set_objects(new_objects)}}{Sets the objects for the DataBook.} +\item{\code{append_data_object(name, obj, add_to_graph_book = TRUE)}}{Appends a data object to the DataBook.} +\item{\code{get_data_objects(data_name, as_list = FALSE, ...)}}{Gets data objects from the DataBook.} +\item{\code{get_data_frame(data_name, convert_to_character = FALSE, stack_data = FALSE, include_hidden_columns = TRUE, use_current_filter = TRUE, filter_name = "", use_column_selection = TRUE, column_selection_name = "", remove_attr = FALSE, retain_attr = FALSE, max_cols, max_rows, drop_unused_filter_levels = FALSE, start_row, start_col, ...)}}{Gets a data frame from the DataBook with various options.} +\item{\code{get_variables_metadata(data_name, data_type = "all", convert_to_character = FALSE, property, column, error_if_no_property = TRUE, direct_from_attributes = FALSE, use_column_selection = TRUE)}}{Gets the variables metadata for the specified data table.} +\item{\code{get_column_data_types(data_name, columns)}}{Gets the data types of the specified columns in the data table.} +\item{\code{get_column_labels(data_name, columns)}}{Gets the labels of the specified columns in the data table.} +\item{\code{get_data_frame_label(data_name, use_current_filter = FALSE)}}{Gets the label of the data frame.} +\item{\code{get_data_frame_metadata(data_name, label, include_calculated = TRUE, excluded_not_for_display = TRUE)}}{Gets the metadata of the data frame.} +\item{\code{get_combined_metadata(convert_to_character = FALSE)}}{Gets combined metadata from all data tables.} +\item{\code{get_metadata(name, ...)}}{Gets metadata for the specified name.} +\item{\code{get_data_names(as_list = FALSE, include, exclude, excluded_items, include_hidden = TRUE, ...)}}{Gets the names of the data tables in the DataBook.} +\item{\code{get_data_changed(data_name)}}{Checks if the data has changed.} +\item{\code{get_variables_metadata_changed(data_name)}}{Checks if the variables metadata has changed.} +\item{\code{get_metadata_changed(data_name)}}{Checks if the metadata has changed.} +\item{\code{get_calculations(data_name)}}{Gets the calculations for the specified data table.} +\item{\code{get_calculation_names(data_name, as_list = FALSE, excluded_items = c())}}{Gets the names of the calculations for the specified data table.} +\item{\code{dataframe_count()}}{Gets the count of data frames in the DataBook.} +\item{\code{set_data_frames_changed(data_name = "", new_val)}}{Sets the changed status for data frames.} +\item{\code{set_variables_metadata_changed(data_name = "", new_val)}}{Sets the changed status for variables metadata.} +\item{\code{set_metadata_changed(data_name = "", new_val)}}{Sets the changed status for metadata.} +\item{\code{add_columns_to_data(data_name, col_name = "", col_data, use_col_name_as_prefix = FALSE, hidden = FALSE, before, adjacent_column = "", num_cols, require_correct_length = TRUE, keep_existing_position = TRUE)}}{Adds columns to the specified data table.} +\item{\code{get_columns_from_data(data_name, col_names, from_stacked_data = FALSE, force_as_data_frame = FALSE, use_current_filter = TRUE, remove_labels = FALSE, drop_unused_filter_levels = FALSE)}}{Gets columns from the specified data table.} +\item{\code{create_graph_data_book()}}{Creates a graph data book.} +\item{\code{add_object(data_name = NULL, object_name = NULL, object_type_label, object_format, object)}}{Adds an object to the DataBook.} +\item{\code{get_object_names(data_name = NULL, object_type_label = NULL, as_list = FALSE, ...)}}{Gets the names of the objects in the DataBook.} +\item{\code{get_objects(data_name = NULL, object_type_label = NULL)}}{Gets the objects from the DataBook.} +\item{\code{get_object(data_name = NULL, object_name)}}{Gets a specific object from the DataBook.} +\item{\code{get_object_data(data_name = NULL, object_name, as_file = FALSE)}}{Gets the data of a specific object from the DataBook.} +\item{\code{get_objects_data(data_name = NULL, object_names = NULL, as_files = FALSE)}}{Gets the data of multiple objects from the DataBook.} +\item{\code{get_last_object_data(object_type_label, as_file = TRUE)}}{Gets the data of the last object of a specified type from the DataBook.} +\item{\code{rename_object(data_name, object_name, new_name, object_type = "object")}}{Renames an object in the DataBook.} +\item{\code{delete_objects(data_name, object_names, object_type = "object")}}{Deletes objects from the DataBook.} +\item{\code{reorder_objects(data_name, new_order)}}{Reorders the objects in the DataBook.} +\item{\code{get_from_object(data_name, object_name, value1, value2, value3)}}{Gets values from a specified object in the DataBook.} +\item{\code{add_filter(data_name, filter, filter_name = "", replace = TRUE, set_as_current_filter = FALSE, na.rm = TRUE, is_no_filter = FALSE, and_or = "&", inner_not = FALSE, outer_not = FALSE)}}{Adds a filter to the specified data table.} +\item{\code{add_filter_as_levels(data_name, filter_levels, column)}}{Adds filter levels to the specified column.} +\item{\code{current_filter(data_name)}}{Gets the current filter for the specified data table.} +\item{\code{set_current_filter(data_name, filter_name = "")}}{Sets the current filter for the specified data table.} +\item{\code{get_filter(data_name, filter_name)}}{Gets a filter by name from the specified data table.} +\item{\code{get_filter_as_logical(data_name, filter_name)}}{Gets a filter as a logical vector from the specified data table.} +\item{\code{get_current_filter(data_name)}}{Gets the current filter for the specified data table.} +\item{\code{get_filter_row_names(data_name, filter_name)}}{Gets the row names that match a specified filter in the data table.} +\item{\code{get_current_filter_name(data_name)}}{Gets the name of the current filter for the specified data table.} +\item{\code{get_filter_names(data_name, as_list = FALSE, include = list(), exclude = list(), excluded_items = c())}}{Gets the names of the filters in the specified data table.} +\item{\code{remove_current_filter(data_name)}}{Removes the current filter from the specified data table.} +\item{\code{filter_applied(data_name)}}{Checks if a filter is applied to the specified data table.} +\item{\code{filter_string(data_name, filter_name)}}{Gets the filter string for a specified filter in the data table.} +\item{\code{get_filter_as_instat_calculation(data_name, filter_name)}}{Gets a filter as an instat calculation from the specified data table.} +\item{\code{add_column_selection(data_name, column_selection, name = "", replace = TRUE, set_as_current = FALSE, is_everything = FALSE, and_or = "|")}}{Adds a column selection to the specified data table.} +\item{\code{current_column_selection(data_name)}}{Gets the current column selection for the specified data table.} +\item{\code{set_current_column_selection(data_name, name = "")}}{Sets the current column selection for the specified data table.} +\item{\code{get_column_selection(data_name, name)}}{Gets a column selection by name from the specified data table.} +\item{\code{get_column_selection_column_names(data_name, filter_name)}}{Gets the column names for a specified filter in the data table.} +\item{\code{get_column_selected_column_names(data_name, column_selection_name = "")}}{Gets the names of the selected columns in the specified data table.} +\item{\code{get_current_column_selection(data_name)}}{Gets the current column selection for the specified data table.} +\item{\code{get_current_column_selection_name(data_name)}}{Gets the name of the current column selection for the specified data table.} +\item{\code{get_column_selection_names(data_name, as_list = FALSE, include = list(), exclude = list(), excluded_items = c())}}{Gets the names of the column selections in the specified data table.} +\item{\code{remove_current_column_selection(data_name)}}{Removes the current column selection from the specified data table.} +\item{\code{column_selection_applied(data_name)}}{Checks if a column selection is applied to the specified data table.} +\item{\code{replace_value_in_data(data_name, col_names, rows, old_value, old_is_missing = FALSE, start_value = NA, end_value = NA, new_value, new_is_missing = FALSE, closed_start_value = TRUE, closed_end_value = TRUE, locf = FALSE, from_last = FALSE)}}{Replaces values in the specified columns and rows of the data table.} +\item{\code{paste_from_clipboard(data_name, col_names, start_row_pos = 1, first_clip_row_is_header = TRUE, clip_board_text)}}{Pastes data from the clipboard into the specified columns of the data table.} +\item{\code{rename_column_in_data(data_name, column_name = NULL, new_val = NULL, label = "", type = "single", .fn, .cols = everything(), new_column_names_df, new_labels_df, ...)}}{Renames a column in the specified data table.} +\item{\code{frequency_tables(data_name, x_col_names, y_col_name, n_column_factors = 1, store_results = TRUE, drop = TRUE, na.rm = FALSE, summary_name = NA, include_margins = FALSE, return_output = TRUE, treat_columns_as_factor = FALSE, page_by = "default", as_html = TRUE, signif_fig = 2, na_display = "", na_level_display = "NA", weights = NULL, caption = NULL, result_names = NULL, percentage_type = "none", perc_total_columns = NULL, perc_total_factors = c(), perc_total_filter = NULL, perc_decimal = FALSE, margin_name = "(All)", additional_filter, ...)}}{Creates frequency tables for the specified data table.} +\item{\code{anova_tables(data_name, x_col_names, y_col_name, signif.stars = FALSE, sign_level = FALSE, means = FALSE)}}{Creates ANOVA tables for the specified data table.} +\item{\code{cor(data_name, x_col_names, y_col_name, use = "everything", method = c("pearson", "kendall", "spearman"))}}{Calculates correlations for the specified columns in the data table.} +\item{\code{remove_columns_in_data(data_name, cols, allow_delete_all = FALSE)}}{Removes columns from the specified data table.} +\item{\code{remove_rows_in_data(data_name, row_names)}}{Removes rows from the specified data table.} +\item{\code{get_next_default_column_name(data_name, prefix)}}{Gets the next default column name for the specified data table.} +\item{\code{get_column_names(data_name, as_list = FALSE, include = list(), exclude = list(), excluded_items = c(), max_no, use_current_column_selection = TRUE)}}{Gets the column names in the specified data table.} +\item{\code{reorder_columns_in_data(data_name, col_order)}}{Reorders the columns in the specified data table.} +\item{\code{insert_row_in_data(data_name, start_row, row_data = c(), number_rows = 1, before = FALSE)}}{Inserts rows into the specified data table.} +\item{\code{get_data_frame_length(data_name, use_current_filter = FALSE)}}{Gets the length of the data frame in the specified data table.} +\item{\code{get_next_default_dataframe_name(prefix, include_index = TRUE, start_index = 1)}}{Gets the next default name for a data frame in the DataBook.} +\item{\code{delete_dataframes(data_names, delete_graph_book = TRUE)}}{Deletes data frames from the DataBook.} +\item{\code{remove_link(link_name)}}{Removes a link from the DataBook.} +\item{\code{get_column_factor_levels(data_name, col_name = "")}}{Gets the factor levels of a column in the specified data table.} +\item{\code{get_factor_data_frame(data_name, col_name = "", include_levels = TRUE, include_NA_level = FALSE)}}{Gets a factor data frame for the specified column in the data table.} +\item{\code{sort_dataframe(data_name, col_names = c(), decreasing = FALSE, na.last = TRUE, by_row_names = FALSE, row_names_as_numeric = TRUE)}}{Sorts the specified data table.} +\item{\code{rename_dataframe(data_name, new_value = "", label = "")}}{Renames the specified data table.} +\item{\code{convert_column_to_type(data_name, col_names = c(), to_type, factor_values = NULL, set_digits, set_decimals = FALSE, keep_attr = TRUE, ignore_labels = FALSE, keep.labels = TRUE)}}{Converts the specified columns to a different type in the data table.} +\item{\code{append_to_variables_metadata(data_name, col_names, property, new_val = "")}}{Appends a new value to the specified property in the variables metadata for the given columns in the specified data table.} +\item{\code{append_to_dataframe_metadata(data_name, property, new_val = "")}}{Appends a new value to the specified property in the dataframe metadata for the specified data table.} +\item{\code{append_to_metadata(property, new_val = "", allow_override_special = FALSE)}}{Appends a new value to the specified property in the overall metadata, with an option to override special properties.} +\item{\code{add_metadata_field(data_name, property, new_val = "")}}{Adds a new metadata field to the specified data table or to the overall metadata.} +\item{\code{reorder_dataframes(data_frames_order)}}{Reorders the data frames in the object based on the provided order.} +\item{\code{copy_columns(data_name, col_names = "", copy_to_clipboard = FALSE)}}{Copies the specified columns from the given data table, with an option to copy to the clipboard.} +\item{\code{drop_unused_factor_levels(data_name, col_name)}}{Drops unused factor levels from the specified column in the given data table.} +\item{\code{set_factor_levels(data_name, col_name, new_labels, new_levels, set_new_labels = TRUE)}}{Sets new factor levels and labels for the specified column in the given data table.} +\item{\code{edit_factor_level(data_name, col_name, old_level, new_level)}}{Edits an existing factor level in the specified column of the given data table.} +\item{\code{set_factor_reference_level(data_name, col_name, new_ref_level)}}{Sets a new reference level for the specified factor column in the given data table.} +\item{\code{get_column_count(data_name, use_column_selection = FALSE)}}{Returns the count of columns in the specified data table, with an option to use the current column selection.} +\item{\code{reorder_factor_levels(data_name, col_name, new_level_names)}}{Reorders the factor levels in the specified column of the given data table.} +\item{\code{get_data_type(data_name, col_name)}}{Returns the data type of the specified column in the given data table.} +\item{\code{copy_data_frame(data_name, new_name, label = "", copy_to_clipboard = FALSE)}}{Copies the specified data table to a new data table with an optional new name, label, and option to copy to the clipboard.} +\item{\code{copy_col_metadata_to_clipboard(data_name, property_names)}}{Copies the specified column metadata properties from the given data table to the clipboard.} +\item{\code{copy_data_frame_metadata_to_clipboard(data_name, property_names)}}{Copies the specified data frame metadata properties from the given data table to the clipboard.} +\item{\code{copy_to_clipboard(content)}}{Copies the given content to the clipboard.} +\item{\code{set_hidden_columns(data_name, col_names = c())}}{Sets the specified columns in the given data table to be hidden.} +\item{\code{unhide_all_columns(data_name)}}{Unhides all columns in the specified data table.} +\item{\code{set_hidden_data_frames(data_names = c())}}{Sets the specified data frames to be hidden.} +\item{\code{get_hidden_data_frames()}}{Returns the names of all hidden data frames.} +\item{\code{set_row_names(data_name, row_names)}}{Sets new row names for the specified data table.} +\item{\code{get_row_names(data_name)}}{Returns the row names of the specified data table.} +\item{\code{set_protected_columns(data_name, col_names)}}{Sets the specified columns in the given data table to be protected.} +\item{\code{get_metadata_fields(data_name, include_overall, as_list = FALSE, include, exclude, excluded_items = c())}}{Returns the metadata fields for the specified data table and overall metadata, with options to include or exclude specific fields.} +\item{\code{freeze_columns(data_name, column)}}{Freezes the specified columns in the given data table.} +\item{\code{unfreeze_columns(data_name)}}{Unfreezes all columns in the specified data table.} +\item{\code{is_variables_metadata(data_name, property, column, return_vector = FALSE)}}{Checks if the specified property is part of the variables metadata for the given column in the specified data table.} +\item{\code{data_frame_exists(data_name)}}{Checks if the specified data table exists in the object.} +\item{\code{add_key(data_name, col_names, key_name)}}{Adds a key to the specified data table using the given columns and key name.} +\item{\code{is_key(data_name, col_names)}}{Checks if the specified columns form a key in the given data table.} +\item{\code{has_key(data_name)}}{Checks if the specified data table has a key.} +\item{\code{get_keys(data_name, key_name)}}{Returns the keys for the specified data table and key name.} +\item{\code{add_new_comment(data_name, row = "", column = "", comment)}}{Adds a new comment to the specified data table, optionally specifying the row and column.} +\item{\code{get_comments(data_name, comment_id)}}{Returns the comments for the specified data table and comment ID.} +\item{\code{get_links(link_name, ...)}}{Returns the links for the specified link name or all links if no name is provided.} +\item{\code{set_structure_columns(data_name, struc_type_1 = c(), struc_type_2 = c(), struc_type_3 = c())}}{Sets the structure columns for the specified data table.} +\item{\code{add_dependent_columns(data_name, columns, dependent_cols)}}{Adds dependent columns to the specified columns in the given data table.} +\item{\code{set_column_colours(data_name, columns, colours)}}{Sets the colors for the specified columns in the given data table.} +\item{\code{has_colours(data_name, columns)}}{Checks if the specified columns in the given data table have colors.} +\item{\code{remove_column_colours(data_name)}}{Removes colors from all columns in the specified data table.} +\item{\code{set_column_colours_by_metadata(data_name, columns, property)}}{Sets the colors for the specified columns in the given data table based on the specified metadata property.} +\item{\code{graph_one_variable(data_name, columns, numeric = "geom_boxplot", categorical = "geom_bar", character = "geom_bar", output = "facets", free_scale_axis = FALSE, ncol = NULL, coord_flip = FALSE, ... = ...)}}{Creates a graph for one variable in the specified data table with options for the type of graph, axis scaling, and other parameters.} +\item{\code{make_date_yearmonthday(data_name, year, month, day, f_year, f_month, f_day, year_format = "%Y", month_format = "%m")}}{Creates a date column from the specified year, month, and day columns in the given data table, with options for formatting.} + \item{\code{make_date_yeardoy(data_name, year, doy, base, doy_typical_length = "366")}}{Creates a date column from the specified year and day of year columns in the given data table.} + \item{\code{set_contrasts_of_factor(data_name, col_name, new_contrasts, defined_contr_matrix)}}{Sets the contrasts for the specified factor column in the given data table.} + \item{\code{create_factor_data_frame(data_name, factor, factor_data_frame_name, include_contrasts = FALSE, replace = FALSE, summary_count = TRUE)}}{Creates a new data frame for the specified factor column in the given data table, with options to include contrasts and summary counts.} + \item{\code{split_date(data_name, col_name = "", year_val = FALSE, year_name = FALSE, leap_year = FALSE, month_val = FALSE, month_abbr = FALSE, month_name = FALSE, week_val = FALSE, week_abbr = FALSE, week_name = FALSE, weekday_val = FALSE, weekday_abbr = FALSE, weekday_name = FALSE, day = FALSE, day_in_month = FALSE, day_in_year = FALSE, day_in_year_366 = FALSE, pentad_val = FALSE, pentad_abbr = FALSE, dekad_val = FALSE, dekad_abbr = FALSE, quarter_val = FALSE, quarter_abbr = FALSE, with_year = FALSE, s_start_month = 1, s_start_day_in_month = 1, days_in_month = FALSE)}}{Splits the specified date column into multiple components such as year, month, day, etc. in the given data table.} + \item{\code{import_SST(dataset, data_from = 5, data_names = c())}}{Imports SST data from the specified dataset and data source, creating data tables with the specified names.} + \item{\code{make_inventory_plot(data_name, date_col, station_col = NULL, year_col = NULL, doy_col = NULL, element_cols = NULL, add_to_data = FALSE, year_doy_plot = FALSE, coord_flip = FALSE, facet_by = NULL, graph_title = "Inventory Plot", graph_subtitle = NULL, graph_caption = NULL, title_size = NULL, subtitle_size = NULL, caption_size = NULL, labelXAxis, labelYAxis, xSize = NULL, ySize = NULL, Xangle = NULL, Yangle = NULL, scale_xdate, fromXAxis = NULL, toXAxis = NULL, byXaxis = NULL, date_ylabels, legend_position = NULL, xlabelsize = NULL, ylabelsize = NULL, scale = NULL, dir = "", row_col_number, nrow = NULL, ncol = NULL, key_colours = c("red", "grey"), display_rain_days = FALSE, facet_xsize = 9, facet_ysize = 9, facet_xangle = 90, facet_yangle = 90, scale_ydate = FALSE, date_ybreaks, step = 1, rain_cats = list(breaks = c(0, 0.85, Inf), labels = c("Dry", "Rain"), key_colours = c("tan3", "blue")))}}{Creates an inventory plot for the specified data table with various customization options.} + \item{\code{import_NetCDF(nc, path, name, only_data_vars = TRUE, keep_raw_time = TRUE, include_metadata = TRUE, boundary, lon_points = NULL, lat_points = NULL, id_points = NULL, show_requested_points = TRUE, great_circle_dist = FALSE)}}{Imports data from a NetCDF file, with options to specify the data variables, time format, metadata inclusion, and boundaries.} + \item{\code{infill_missing_dates(data_name, date_name, factors, start_month, start_date, end_date, resort = TRUE)}}{Infills missing dates in the specified data table using the provided date column and factors.} + \item{\code{get_key_names(data_name, include_overall = TRUE, include, exclude, include_empty = FALSE, as_list = FALSE, excluded_items = c())}}{Returns the key names for the specified data table, with options to include overall keys, exclude specific keys, and return as a list.} + \item{\code{remove_key(data_name, key_name)}}{Removes the specified key from the given data table.} + \item{\code{add_climdex_indices(data_name, climdex_output, freq = "annual", station, year, month)}}{Adds climdex indices to the specified data table, with options for frequency, station, year, and month.} + \item{\code{is_metadata(data_name, str)}}{Checks if the specified string is part of the metadata for the given data table.} + \item{\code{get_climatic_column_name(data_name, col_name)}}{Returns the climatic column name for the specified column in the given data table.} + \item{\code{merge_data(data_name, new_data, by = NULL, type = "left", match = "all")}}{Merges new data into the specified data table using the provided columns and merge type.} + \item{\code{get_corruption_data_names()}}{Returns the names of all data tables with corruption data.} + \item{\code{get_corruption_contract_data_names()}}{Returns the names of all data tables with corruption contract data.} + \item{\code{get_database_variable_names(query, data_name, include_overall = TRUE, include, exclude, include_empty = FALSE, as_list = FALSE, excluded_items = c())}}{Returns the database variable names for the specified query and data table, with options to include overall variables, exclude specific variables, and return as a list.} + \item{\code{get_nc_variable_names(file = "", as_list = FALSE, ...)}}{Returns the variable names from the specified NetCDF file, with an option to return as a list.} + \item{\code{has_database_connection()}}{Checks if there is a database connection.} + \item{\code{database_connect(dbname, user, host, port, drv = RMySQL::MySQL())}}{Connects to a database using the provided credentials and driver.} + \item{\code{get_database_connection()}}{Returns the current database connection.} + \item{\code{set_database_connection(dbi_connection)}}{Sets the database connection to the specified DBI connection object.} + \item{\code{database_disconnect()}}{Disconnects from the current database.} + \item{\code{import_from_climsoft(stationfiltercolumn = "stationId", stations = c(), elementfiltercolumn = "elementId", elements = c(), include_observation_data = FALSE, include_observation_flags = FALSE, unstack_data = FALSE, include_elements_info = FALSE, start_date = NULL, end_date = NULL)}}{Imports data from CLIMSOFT using the specified filters and options for observation data, flags, and unstacking.} + \item{\code{import_from_iri(download_from, data_file, data_frame_name, location_data_name, path, X1, X2 = NA, Y1, Y2 = NA, get_area_point = "area")}}{Imports data from IRI using the specified parameters for download, file path, coordinates, and area type.} + \item{\code{export_workspace(data_names, file, include_graphs = TRUE, include_models = TRUE, include_metadata = TRUE)}}{Exports the workspace to a file, including the specified data tables, graphs, models, and metadata.} + \item{\code{set_links(new_links)}}{Sets the links in the object to the specified new links.} + \item{\code{display_daily_graph(data_name, date_col = NULL, station_col = NULL, year_col = NULL, doy_col = NULL, climatic_element = NULL, upper_limit = 100, bar_colour = "blue", rug_colour = "red")}}{Displays a daily graph for the specified data table with options for columns, element, colors, and limits.} + \item{\code{create_variable_set(data_name, set_name, columns)}}{Creates a variable set with the specified name and columns in the given data table.} + \item{\code{update_variable_set(data_name, set_name, columns, new_set_name)}}{Updates the specified variable set with new columns and optionally a new name in the given data table.} + \item{\code{delete_variable_sets(data_name, set_names)}}{Deletes the specified variable sets from the given data table.} + \item{\code{get_variable_sets_names(data_name, include_overall = TRUE, include, exclude, include_empty = FALSE, as_list = FALSE, excluded_items = c())}}{Returns the names of variable sets for the specified data table, with options to include overall sets, exclude specific sets, and return as a list.} + \item{\code{get_variable_sets(data_name, set_names, force_as_list = FALSE)}}{Returns the specified variable sets from the given data table, with an option to force the result as a list.} + \item{\code{crops_definitions(data_name, year, station, rain, day, rain_totals, plant_days, plant_lengths, start_check = TRUE, season_data_name, start_day, end_day, definition_props = TRUE, print_table = TRUE)}}{Defines crop parameters for the specified data table using the provided columns and options for seasons, days, and properties.} + \item{\code{tidy_climatic_data(x, format, stack_cols, day, month, year, stack_years, station, element, element_name="value", ignore_invalid = FALSE, silent = FALSE, unstack_elements = TRUE, new_name)}}{Converts wide-format daily climatic data to long format using the specified columns and options for format, elements, and validation.} + \item{\code{get_geometry(data)}}{Returns the geometry column for the specified data table.} + \item{\code{package_check(package)}}{Checks if the specified package is installed and returns information about its version and availability.} + \item{\code{download_from_IRI(source, data, path = tempdir(), min_lon, max_lon, min_lat, max_lat, min_date, max_date, name, download_type = "Point", import = TRUE)}}{Downloads data from IRI using the specified source, data, coordinates, date range, and options for download type and import.} + \item{\code{patch_climate_element(data_name, date_col_name = "", var = "", vars = c(), max_mean_bias = NA, max_stdev_bias = NA, time_interval = "month", column_name, station_col_name = station_col_name)}}{Patches the specified climate element in the given data table using the provided columns and options for bias, time interval, and station.} + \item{\code{visualize_element_na(data_name, element_col_name, element_col_name_imputed, station_col_name, x_axis_labels_col_name, ncol = 2, type = "distribution", xlab = NULL, ylab = NULL, legend = TRUE, orientation = "horizontal", interval_size = interval_size, x_with_truth = NULL, measure = "percent")}}{Visualizes missing data for the specified element in the given data table using the provided columns and options for labels, legend, orientation, and measure.} + \item{\code{get_data_entry_data(data_name, station, date, elements, view_variables, station_name, type, start_date, end_date)}}{Returns data entry data for the specified data table using the provided columns and options for date range, variables, and type.} + \item{\code{save_data_entry_data(data_name, new_data, rows_changed, comments_list = list(), add_flags = FALSE, ...)}}{Saves data entry data to the specified data table with options for adding comments, flags, and rows changed.} + \item{\code{import_from_cds(user, dataset, elements, start_date, end_date, lon, lat, path, import = FALSE, new_name)}}{Imports data from CDS using the specified user, dataset, elements, date range, coordinates, and options for file path and import.} + \item{\code{add_flag_fields(data_name, col_names, key_column_names)}}{Adds flag fields to the specified columns in the given data table, using the provided key columns.} + \item{\code{remove_empty(data_name, which = c("rows","cols"))}}{Removes empty rows or columns from the specified data table.} + \item{\code{replace_values_with_NA(data_name, row_index, column_index)}}{Replaces values with NA in the specified rows and columns of the given data table.} + \item{\code{has_labels(data_name, col_names)}}{Checks if the specified columns in the given data table have labels.} + \item{\code{wrap_or_unwrap_data(data_name, col_name, column_data, width, wrap = TRUE)}}{Wraps or unwraps the specified column data in the given data table to the specified width.} } } @@ -62,6 +342,55 @@ An R6 class to manage a collection of data tables along with their metadata and \item \href{#method-DataBook-get_red_flag_column_names}{\code{DataBook$get_red_flag_column_names()}} \item \href{#method-DataBook-get_CRI_column_names}{\code{DataBook$get_CRI_column_names()}} \item \href{#method-DataBook-get_corruption_column_name}{\code{DataBook$get_corruption_column_name()}} +\item \href{#method-DataBook-append_to_variables_metadata}{\code{DataBook$append_to_variables_metadata()}} +\item \href{#method-DataBook-append_to_dataframe_metadata}{\code{DataBook$append_to_dataframe_metadata()}} +\item \href{#method-DataBook-append_to_metadata}{\code{DataBook$append_to_metadata()}} +\item \href{#method-DataBook-add_metadata_field}{\code{DataBook$add_metadata_field()}} +\item \href{#method-DataBook-reorder_dataframes}{\code{DataBook$reorder_dataframes()}} +\item \href{#method-DataBook-copy_columns}{\code{DataBook$copy_columns()}} +\item \href{#method-DataBook-drop_unused_factor_levels}{\code{DataBook$drop_unused_factor_levels()}} +\item \href{#method-DataBook-set_factor_levels}{\code{DataBook$set_factor_levels()}} +\item \href{#method-DataBook-edit_factor_level}{\code{DataBook$edit_factor_level()}} +\item \href{#method-DataBook-set_factor_reference_level}{\code{DataBook$set_factor_reference_level()}} +\item \href{#method-DataBook-get_column_count}{\code{DataBook$get_column_count()}} +\item \href{#method-DataBook-reorder_factor_levels}{\code{DataBook$reorder_factor_levels()}} +\item \href{#method-DataBook-get_data_type}{\code{DataBook$get_data_type()}} +\item \href{#method-DataBook-copy_data_frame}{\code{DataBook$copy_data_frame()}} +\item \href{#method-DataBook-copy_col_metadata_to_clipboard}{\code{DataBook$copy_col_metadata_to_clipboard()}} +\item \href{#method-DataBook-copy_data_frame_metadata_to_clipboard}{\code{DataBook$copy_data_frame_metadata_to_clipboard()}} +\item \href{#method-DataBook-copy_to_clipboard}{\code{DataBook$copy_to_clipboard()}} +\item \href{#method-DataBook-set_hidden_columns}{\code{DataBook$set_hidden_columns()}} +\item \href{#method-DataBook-unhide_all_columns}{\code{DataBook$unhide_all_columns()}} +\item \href{#method-DataBook-set_hidden_data_frames}{\code{DataBook$set_hidden_data_frames()}} +\item \href{#method-DataBook-get_hidden_data_frames}{\code{DataBook$get_hidden_data_frames()}} +\item \href{#method-DataBook-set_row_names}{\code{DataBook$set_row_names()}} +\item \href{#method-DataBook-get_row_names}{\code{DataBook$get_row_names()}} +\item \href{#method-DataBook-set_protected_columns}{\code{DataBook$set_protected_columns()}} +\item \href{#method-DataBook-get_metadata_fields}{\code{DataBook$get_metadata_fields()}} +\item \href{#method-DataBook-freeze_columns}{\code{DataBook$freeze_columns()}} +\item \href{#method-DataBook-unfreeze_columns}{\code{DataBook$unfreeze_columns()}} +\item \href{#method-DataBook-is_variables_metadata}{\code{DataBook$is_variables_metadata()}} +\item \href{#method-DataBook-data_frame_exists}{\code{DataBook$data_frame_exists()}} +\item \href{#method-DataBook-add_key}{\code{DataBook$add_key()}} +\item \href{#method-DataBook-is_key}{\code{DataBook$is_key()}} +\item \href{#method-DataBook-has_key}{\code{DataBook$has_key()}} +\item \href{#method-DataBook-get_keys}{\code{DataBook$get_keys()}} +\item \href{#method-DataBook-add_new_comment}{\code{DataBook$add_new_comment()}} +\item \href{#method-DataBook-get_comments}{\code{DataBook$get_comments()}} +\item \href{#method-DataBook-get_links}{\code{DataBook$get_links()}} +\item \href{#method-DataBook-set_structure_columns}{\code{DataBook$set_structure_columns()}} +\item \href{#method-DataBook-add_dependent_columns}{\code{DataBook$add_dependent_columns()}} +\item \href{#method-DataBook-set_column_colours}{\code{DataBook$set_column_colours()}} +\item \href{#method-DataBook-has_colours}{\code{DataBook$has_colours()}} +\item \href{#method-DataBook-remove_column_colours}{\code{DataBook$remove_column_colours()}} +\item \href{#method-DataBook-set_column_colours_by_metadata}{\code{DataBook$set_column_colours_by_metadata()}} +\item \href{#method-DataBook-graph_one_variable}{\code{DataBook$graph_one_variable()}} +\item \href{#method-DataBook-make_date_yearmonthday}{\code{DataBook$make_date_yearmonthday()}} +\item \href{#method-DataBook-make_date_yeardoy}{\code{DataBook$make_date_yeardoy()}} +\item \href{#method-DataBook-set_contrasts_of_factor}{\code{DataBook$set_contrasts_of_factor()}} +\item \href{#method-DataBook-create_factor_data_frame}{\code{DataBook$create_factor_data_frame()}} +\item \href{#method-DataBook-split_date}{\code{DataBook$split_date()}} +\item \href{#method-DataBook-import_SST}{\code{DataBook$import_SST()}} \item \href{#method-DataBook-clone}{\code{DataBook$clone()}} } } @@ -336,6 +665,1320 @@ The name of the corruption column. } } \if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-append_to_variables_metadata}{}}} +\subsection{Method \code{append_to_variables_metadata()}}{ +Appends a new property and its value to the metadata of specified columns in a data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$append_to_variables_metadata( + data_name, + col_names, + property, + new_val = "" +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_names}}{A vector of column names to which the property should be appended.} + +\item{\code{property}}{The name of the property to append.} + +\item{\code{new_val}}{The value of the property to append. Default is an empty string.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-append_to_dataframe_metadata}{}}} +\subsection{Method \code{append_to_dataframe_metadata()}}{ +Appends a new property and its value to the metadata of a data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$append_to_dataframe_metadata(data_name, property, new_val = "")}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{property}}{The name of the property to append.} + +\item{\code{new_val}}{The value of the property to append. Default is an empty string.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-append_to_metadata}{}}} +\subsection{Method \code{append_to_metadata()}}{ +Appends a new property and its value to the metadata of the current object. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$append_to_metadata( + property, + new_val = "", + allow_override_special = FALSE +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{property}}{The name of the property to append.} + +\item{\code{new_val}}{The value of the property to append. Default is an empty string.} + +\item{\code{allow_override_special}}{Boolean flag to allow overriding special properties. Default is FALSE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-add_metadata_field}{}}} +\subsection{Method \code{add_metadata_field()}}{ +Adds a new metadata field and its value to the specified data table or all data tables. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$add_metadata_field(data_name, property, new_val = "")}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table. Use overall_label to apply to all data tables.} + +\item{\code{property}}{The name of the property to append.} + +\item{\code{new_val}}{The value of the property to append. Default is an empty string.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-reorder_dataframes}{}}} +\subsection{Method \code{reorder_dataframes()}}{ +Reorders the dataframes in the object according to the specified order. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$reorder_dataframes(data_frames_order)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_frames_order}}{A vector specifying the new order of dataframes.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-copy_columns}{}}} +\subsection{Method \code{copy_columns()}}{ +Copies specified columns from a data table to another location or clipboard. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$copy_columns(data_name, col_names = "", copy_to_clipboard = FALSE)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_names}}{A vector of column names to copy.} + +\item{\code{copy_to_clipboard}}{Boolean flag to copy to clipboard. Default is FALSE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-drop_unused_factor_levels}{}}} +\subsection{Method \code{drop_unused_factor_levels()}}{ +Drops unused levels from a factor column in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$drop_unused_factor_levels(data_name, col_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the column.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_factor_levels}{}}} +\subsection{Method \code{set_factor_levels()}}{ +Sets new levels for a factor column in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_factor_levels( + data_name, + col_name, + new_labels, + new_levels, + set_new_labels = TRUE +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the column.} + +\item{\code{new_labels}}{A vector of new labels for the factor levels.} + +\item{\code{new_levels}}{A vector of new levels.} + +\item{\code{set_new_labels}}{Boolean flag to set new labels. Default is TRUE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-edit_factor_level}{}}} +\subsection{Method \code{edit_factor_level()}}{ +Edits a level in a factor column in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$edit_factor_level(data_name, col_name, old_level, new_level)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the column.} + +\item{\code{old_level}}{The old level to replace.} + +\item{\code{new_level}}{The new level to set.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_factor_reference_level}{}}} +\subsection{Method \code{set_factor_reference_level()}}{ +Sets the reference level for a factor column in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_factor_reference_level(data_name, col_name, new_ref_level)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the column.} + +\item{\code{new_ref_level}}{The new reference level.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_column_count}{}}} +\subsection{Method \code{get_column_count()}}{ +Returns the number of columns in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_column_count(data_name, use_column_selection = FALSE)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{use_column_selection}}{Boolean flag to use column selection. Default is FALSE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +The number of columns. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-reorder_factor_levels}{}}} +\subsection{Method \code{reorder_factor_levels()}}{ +Reorders the levels of a factor column in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$reorder_factor_levels(data_name, col_name, new_level_names)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the column.} + +\item{\code{new_level_names}}{A vector specifying the new order of factor levels.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_data_type}{}}} +\subsection{Method \code{get_data_type()}}{ +Returns the data type of the specified column in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_data_type(data_name, col_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the column.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +The data type of the column. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-copy_data_frame}{}}} +\subsection{Method \code{copy_data_frame()}}{ +Copies a data frame to a new name or clipboard. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$copy_data_frame( + data_name, + new_name, + label = "", + copy_to_clipboard = FALSE +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{new_name}}{The new name for the copied data frame.} + +\item{\code{label}}{A label for the new data frame. Default is an empty string.} + +\item{\code{copy_to_clipboard}}{Boolean flag to copy to clipboard. Default is FALSE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-copy_col_metadata_to_clipboard}{}}} +\subsection{Method \code{copy_col_metadata_to_clipboard()}}{ +Copies the metadata of specified columns to the clipboard. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$copy_col_metadata_to_clipboard(data_name, property_names)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{property_names}}{A vector of property names to copy. Default is all properties.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-copy_data_frame_metadata_to_clipboard}{}}} +\subsection{Method \code{copy_data_frame_metadata_to_clipboard()}}{ +Copies the metadata of the specified data table to the clipboard. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$copy_data_frame_metadata_to_clipboard(data_name, property_names)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{property_names}}{A vector of property names to copy. Default is all properties.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-copy_to_clipboard}{}}} +\subsection{Method \code{copy_to_clipboard()}}{ +Copies the specified content to the clipboard. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$copy_to_clipboard(content)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{content}}{The content to copy to the clipboard.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_hidden_columns}{}}} +\subsection{Method \code{set_hidden_columns()}}{ +Sets the specified columns as hidden in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_hidden_columns(data_name, col_names = c())}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_names}}{A vector of column names to set as hidden.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-unhide_all_columns}{}}} +\subsection{Method \code{unhide_all_columns()}}{ +Unhides all columns in the specified data table or all data tables if data_name is missing. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$unhide_all_columns(data_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table. If missing, applies to all data tables.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_hidden_data_frames}{}}} +\subsection{Method \code{set_hidden_data_frames()}}{ +Sets the specified data tables as hidden. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_hidden_data_frames(data_names = c())}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_names}}{A vector of data table names to set as hidden.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_hidden_data_frames}{}}} +\subsection{Method \code{get_hidden_data_frames()}}{ +Returns a list of hidden data tables. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_hidden_data_frames()}\if{html}{\out{
}} +} + +\subsection{Returns}{ +A vector of hidden data table names. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_row_names}{}}} +\subsection{Method \code{set_row_names()}}{ +Sets the row names for the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_row_names(data_name, row_names)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{row_names}}{A vector of row names to set.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_row_names}{}}} +\subsection{Method \code{get_row_names()}}{ +Returns the row names of the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_row_names(data_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A vector of row names. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_protected_columns}{}}} +\subsection{Method \code{set_protected_columns()}}{ +Sets the specified columns as protected in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_protected_columns(data_name, col_names)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_names}}{A vector of column names to set as protected.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_metadata_fields}{}}} +\subsection{Method \code{get_metadata_fields()}}{ +Returns the metadata fields of the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_metadata_fields( + data_name, + include_overall, + as_list = FALSE, + include, + exclude, + excluded_items = c() +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{include_overall}}{Boolean flag to include overall metadata fields. Default is TRUE.} + +\item{\code{as_list}}{Boolean flag to return the result as a list. Default is FALSE.} + +\item{\code{include}}{A vector of metadata fields to include. Default is all fields.} + +\item{\code{exclude}}{A vector of metadata fields to exclude. Default is none.} + +\item{\code{excluded_items}}{A vector of metadata fields to exclude. Default is an empty vector.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A vector or list of metadata fields. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-freeze_columns}{}}} +\subsection{Method \code{freeze_columns()}}{ +Freezes the specified columns in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$freeze_columns(data_name, column)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{column}}{A vector of column names to freeze.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-unfreeze_columns}{}}} +\subsection{Method \code{unfreeze_columns()}}{ +Unfreezes all columns in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$unfreeze_columns(data_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-is_variables_metadata}{}}} +\subsection{Method \code{is_variables_metadata()}}{ +Checks if the specified property is metadata for the given columns in the data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$is_variables_metadata( + data_name, + property, + column, + return_vector = FALSE +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{property}}{The name of the property to check.} + +\item{\code{column}}{The name of the column.} + +\item{\code{return_vector}}{Boolean flag to return the result as a vector. Default is FALSE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A boolean value indicating if the property is metadata for the columns. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-data_frame_exists}{}}} +\subsection{Method \code{data_frame_exists()}}{ +Checks if the specified data table exists. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$data_frame_exists(data_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A boolean value indicating if the data table exists. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-add_key}{}}} +\subsection{Method \code{add_key()}}{ +Adds a key to the specified columns in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$add_key(data_name, col_names, key_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_names}}{A vector of column names to add as keys.} + +\item{\code{key_name}}{The name of the key.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-is_key}{}}} +\subsection{Method \code{is_key()}}{ +Checks if the specified columns are keys in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$is_key(data_name, col_names)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_names}}{A vector of column names to check.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A boolean value indicating if the columns are keys. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-has_key}{}}} +\subsection{Method \code{has_key()}}{ +Checks if the specified data table has a key. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$has_key(data_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A boolean value indicating if the data table has a key. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_keys}{}}} +\subsection{Method \code{get_keys()}}{ +Returns the keys of the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_keys(data_name, key_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{key_name}}{The name of the key. Default is all keys.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A list of keys. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-add_new_comment}{}}} +\subsection{Method \code{add_new_comment()}}{ +Adds a new comment to the specified row and column in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$add_new_comment(data_name, row = "", column = "", comment)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{row}}{The name of the row.} + +\item{\code{column}}{The name of the column.} + +\item{\code{comment}}{The comment text.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_comments}{}}} +\subsection{Method \code{get_comments()}}{ +Returns the comments for the specified data table and comment ID. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_comments(data_name, comment_id)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{comment_id}}{The ID of the comment.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A data frame of comments. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-get_links}{}}} +\subsection{Method \code{get_links()}}{ +Returns the links for the specified link name or all links. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$get_links(link_name, ...)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{link_name}}{The name of the link. Default is all links.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A list of links. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_structure_columns}{}}} +\subsection{Method \code{set_structure_columns()}}{ +Sets the structure columns for the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_structure_columns( + data_name, + struc_type_1 = c(), + struc_type_2 = c(), + struc_type_3 = c() +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{struc_type_1}}{A vector of column names for the first structure type.} + +\item{\code{struc_type_2}}{A vector of column names for the second structure type.} + +\item{\code{struc_type_3}}{A vector of column names for the third structure type.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-add_dependent_columns}{}}} +\subsection{Method \code{add_dependent_columns()}}{ +Adds dependent columns to the specified columns in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$add_dependent_columns(data_name, columns, dependent_cols)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{columns}}{A vector of column names to add dependents to.} + +\item{\code{dependent_cols}}{A vector of dependent column names.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_column_colours}{}}} +\subsection{Method \code{set_column_colours()}}{ +Sets the colours for the specified columns in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_column_colours(data_name, columns, colours)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{columns}}{A vector of column names to set colours for.} + +\item{\code{colours}}{A vector of colours.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-has_colours}{}}} +\subsection{Method \code{has_colours()}}{ +Checks if the specified columns have colours in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$has_colours(data_name, columns)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{columns}}{A vector of column names to check.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +A boolean value indicating if the columns have colours. +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-remove_column_colours}{}}} +\subsection{Method \code{remove_column_colours()}}{ +Removes the colours from all columns in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$remove_column_colours(data_name)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_column_colours_by_metadata}{}}} +\subsection{Method \code{set_column_colours_by_metadata()}}{ +Sets the colours for the specified columns based on metadata in the given data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_column_colours_by_metadata(data_name, columns, property)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{columns}}{A vector of column names to set colours for.} + +\item{\code{property}}{The metadata property to use for setting colours.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-graph_one_variable}{}}} +\subsection{Method \code{graph_one_variable()}}{ +Creates a graph for a single variable in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$graph_one_variable( + data_name, + columns, + numeric = "geom_boxplot", + categorical = "geom_bar", + character = "geom_bar", + output = "facets", + free_scale_axis = FALSE, + ncol = NULL, + coord_flip = FALSE, + ... +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{columns}}{A vector of column names to graph.} + +\item{\code{numeric}}{The type of graph for numeric columns. Default is "geom_boxplot".} + +\item{\code{categorical}}{The type of graph for categorical columns. Default is "geom_bar".} + +\item{\code{character}}{The type of graph for character columns. Default is "geom_bar".} + +\item{\code{output}}{The output type for the graph. Default is "facets".} + +\item{\code{free_scale_axis}}{Boolean flag to allow free scaling of axes. Default is FALSE.} + +\item{\code{ncol}}{The number of columns in the output. Default is NULL.} + +\item{\code{coord_flip}}{Boolean flag to flip coordinates. Default is FALSE.} + +\item{\code{...}}{Additional arguments passed to the graph function.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-make_date_yearmonthday}{}}} +\subsection{Method \code{make_date_yearmonthday()}}{ +Creates a date column from year, month, and day columns in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$make_date_yearmonthday( + data_name, + year, + month, + day, + f_year, + f_month, + f_day, + year_format = "\%Y", + month_format = "\%m" +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{year}}{The name of the year column.} + +\item{\code{month}}{The name of the month column.} + +\item{\code{day}}{The name of the day column.} + +\item{\code{f_year}}{The format for the year column.} + +\item{\code{f_month}}{The format for the month column.} + +\item{\code{f_day}}{The format for the day column.} + +\item{\code{year_format}}{The format for the year. Default is "\%Y".} + +\item{\code{month_format}}{The format for the month. Default is "\%m".} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-make_date_yeardoy}{}}} +\subsection{Method \code{make_date_yeardoy()}}{ +Creates a date column from year and day of year columns in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$make_date_yeardoy( + data_name, + year, + doy, + base, + doy_typical_length = "366" +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{year}}{The name of the year column.} + +\item{\code{doy}}{The name of the day of year column.} + +\item{\code{base}}{The base date for the day of year.} + +\item{\code{doy_typical_length}}{The typical length of the day of year. Default is "366".} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-set_contrasts_of_factor}{}}} +\subsection{Method \code{set_contrasts_of_factor()}}{ +Sets the contrasts for a factor column in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$set_contrasts_of_factor( + data_name, + col_name, + new_contrasts, + defined_contr_matrix +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the column.} + +\item{\code{new_contrasts}}{A vector of new contrasts.} + +\item{\code{defined_contr_matrix}}{A defined contrast matrix.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-create_factor_data_frame}{}}} +\subsection{Method \code{create_factor_data_frame()}}{ +Creates a new data frame for a factor column in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$create_factor_data_frame( + data_name, + factor, + factor_data_frame_name, + include_contrasts = FALSE, + replace = FALSE, + summary_count = TRUE +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{factor}}{The name of the factor column.} + +\item{\code{factor_data_frame_name}}{The name of the new data frame.} + +\item{\code{include_contrasts}}{Boolean flag to include contrasts. Default is FALSE.} + +\item{\code{replace}}{Boolean flag to replace the existing factor data frame. Default is FALSE.} + +\item{\code{summary_count}}{Boolean flag to include summary count. Default is TRUE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-split_date}{}}} +\subsection{Method \code{split_date()}}{ +Splits a date column into multiple date components in the specified data table. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$split_date( + data_name, + col_name = "", + year_val = FALSE, + year_name = FALSE, + leap_year = FALSE, + month_val = FALSE, + month_abbr = FALSE, + month_name = FALSE, + week_val = FALSE, + week_abbr = FALSE, + week_name = FALSE, + weekday_val = FALSE, + weekday_abbr = FALSE, + weekday_name = FALSE, + day = FALSE, + day_in_month = FALSE, + day_in_year = FALSE, + day_in_year_366 = FALSE, + pentad_val = FALSE, + pentad_abbr = FALSE, + dekad_val = FALSE, + dekad_abbr = FALSE, + quarter_val = FALSE, + quarter_abbr = FALSE, + with_year = FALSE, + s_start_month = 1, + s_start_day_in_month = 1, + days_in_month = FALSE +)}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{data_name}}{The name of the data table.} + +\item{\code{col_name}}{The name of the date column.} + +\item{\code{year_val}}{Boolean flag to include year value. Default is FALSE.} + +\item{\code{year_name}}{Boolean flag to include year name. Default is FALSE.} + +\item{\code{leap_year}}{Boolean flag to include leap year. Default is FALSE.} + +\item{\code{month_val}}{Boolean flag to include month value. Default is FALSE.} + +\item{\code{month_abbr}}{Boolean flag to include month abbreviation. Default is FALSE.} + +\item{\code{month_name}}{Boolean flag to include month name. Default is FALSE.} + +\item{\code{week_val}}{Boolean flag to include week value. Default is FALSE.} + +\item{\code{week_abbr}}{Boolean flag to include week abbreviation. Default is FALSE.} + +\item{\code{week_name}}{Boolean flag to include week name. Default is FALSE.} + +\item{\code{weekday_val}}{Boolean flag to include weekday value. Default is FALSE.} + +\item{\code{weekday_abbr}}{Boolean flag to include weekday abbreviation. Default is FALSE.} + +\item{\code{weekday_name}}{Boolean flag to include weekday name. Default is FALSE.} + +\item{\code{day}}{Boolean flag to include day value. Default is FALSE.} + +\item{\code{day_in_month}}{Boolean flag to include day in month. Default is FALSE.} + +\item{\code{day_in_year}}{Boolean flag to include day in year. Default is FALSE.} + +\item{\code{day_in_year_366}}{Boolean flag to include day in year (366). Default is FALSE.} + +\item{\code{pentad_val}}{Boolean flag to include pentad value. Default is FALSE.} + +\item{\code{pentad_abbr}}{Boolean flag to include pentad abbreviation. Default is FALSE.} + +\item{\code{dekad_val}}{Boolean flag to include dekad value. Default is FALSE.} + +\item{\code{dekad_abbr}}{Boolean flag to include dekad abbreviation. Default is FALSE.} + +\item{\code{quarter_val}}{Boolean flag to include quarter value. Default is FALSE.} + +\item{\code{quarter_abbr}}{Boolean flag to include quarter abbreviation. Default is FALSE.} + +\item{\code{with_year}}{Boolean flag to include with year. Default is FALSE.} + +\item{\code{s_start_month}}{The start month. Default is 1.} + +\item{\code{s_start_day_in_month}}{The start day in month. Default is 1.} + +\item{\code{days_in_month}}{Boolean flag to include days in month. Default is FALSE.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-DataBook-import_SST}{}}} +\subsection{Method \code{import_SST()}}{ +Imports SST data and adds keys and links to the specified data tables. +\subsection{Usage}{ +\if{html}{\out{
}}\preformatted{DataBook$import_SST(dataset, data_from = 5, data_names = c())}\if{html}{\out{
}} +} + +\subsection{Arguments}{ +\if{html}{\out{
}} +\describe{ +\item{\code{dataset}}{The SST dataset.} + +\item{\code{data_from}}{The source of the data. Default is 5.} + +\item{\code{data_names}}{A vector of data table names.} +} +\if{html}{\out{
}} +} +\subsection{Returns}{ +None +} +} +\if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-DataBook-clone}{}}} \subsection{Method \code{clone()}}{