parameters: Parameters
In Thewhey-Brian/ADTools: Alzheimer Disease Data Tools

parameters

R Documentation

Parameters

Description

List of function parameters in the ADTool package

Arguments

`path`	Directory of the BIOCARD data files. Default value is the working directory,
`reference_time`	A data frame contains patients' ID and corresponding reference time for each patient. The cognitive time is set to be the default reference time (if NULL). Use can also specify reference time used. For example, "COG" represents the cognitive time, and "DIAG" represent the diagnosis time.
`window_setting`	A list contains a integer (unit of days) indicating the maximum acceptable gap time for merging each biomarker test to base data and a logical value indicating whether the time window should overlap. The default value is 730 days and FALSE. For most data, the time windows are calculated from the baseline time (left window = the midpoint between current and the previous time point; right window = the midpoint between current and the next time point). If the time windows are longer than the maximum acceptable length, then force to select biomarkers within the maximum window length we set. For the first and last baseline time, since there is no "previous" or "next" time point available, use the maximum acceptable window length instead. For the overlap setting, ff TRUE, all time windows will set from 1/2 "window" days before the baseline time to the 1/2 "window" days after baseline. In this case, the time windows may overlap, which means some biomarkers may be merged into multiple baseline data. If FALSE, the windows will be calculated from the baseline times. The left window is set to be the midpoint between the current and the previous time point. The right window is set to be the midpoint between the current and the next time point. For the first and last baseline time, since there is no "previous" or "next" time point available, use the maximum acceptable window length instead.
`pattern`	A string indicating the pattern of all the data files. Default is "*.xls" (should work for both .xls and .xlsx). This pattern is used to read all table names from the path. It can also be other file formats, such as ".csv".
`src_files`	Updated dictionary file for source file features. See `dict_src_files` for more details.
`src_tables`	Updated dictionary file for source table features. See `dict_src_tables` for more details.
`verbose`	A logical value indicating weather printing out process information.
`vec_name`	A character string indicating the vector needed to be removed special characters.
`lower_case`	A logical value indicating the lower case setting. Default "False." If true, all characters will to convert to lower cases.
`src_type`	A string indicating the source of data. Options include "BIOCARD", "NACC" and "ADNI"
`col_name`	A string indicating a column name in the source data file.
`dict_src_tables`	A dictionary file for the parameters. The default dictionary is appended in the package. Since the parameters in tables may vary, it could be modified by using a costomized parameter dictionary. The format can refer to the appended dictionary. See `dict_src_tables` for more details.
`table_code`	Code of subtables ("Cognitive" as "COG"), which can be mapped to the source data files and is used for internal data manipulation. The options are "COG" (Cognitive), "DIAG" (Diagnosis), "CSF" (FINAL_CSF), "DEMO" (Demographics), "HIPPO" (Hippocampus), "AMY" (Amygdala), "EC" (Entorhinal), "GE" (Genetics), "LIST_A" (list of patients not enrolled), "LIST_B" (list of patients impaired).
`file_names`	List the names of all subtables in the path (all tables should from the same path).
`dict_src_files`	A path of data file (.csv) of the parameters dictionary. The default dictionary is appended in the package. Since the parameters in tables may vary, it could be modified by using a costomized parameter dictionary. The format can refer to the appended dictionary. See `dict_src_files` for more details.
`dat`	The baseline time dataset.
`v_date`	A string indicating the date name of the baseline time.
`v_id`	A string indicating the id name of baseline dateset. Default is "subject_id" (may varied if using customized column names dictionary).
`dat_se`	A dataset that will be merged.
`dat_marker`	A data set including new biomarker that will be merged.
`m_date`	A string indicating the name of measure date in dat_marker.
`rst_dict`	A dataset that waiting to be updated.
`csv_dict`	A dataset with updated information.
`cur_dat`	A dataset indicating current loaded subtable.
`data`	A dataset. Possible choices are "dict_tbl": the dictionary for the structure of tables, "dict_cil_name": the dictionary maps the original column names (old_col_name) to the column names of generated analysis dataset, "dict_data": This dictionary includes all the variables names in the analysis dataset. This dictionary could be used to check the location and description of each variable.
`str`	String to search. Default value is NULL. If NULL, this function is used to check the entire dictionary. If input a string (the variable name of the analysis dataset), this function is used to check the location and description of the variable.
`csv_fname`	A string indicating the CSV filename to be saved (saved to the default location). Default is NULL. The saved file is in .scv format. If changes of default dictionaries needed, then the costomized dictionary could be added here. However, the format of the costomized dictionary should follow the default one.
`dict`	A string indicating the name of the dictionary. The available options are: "src_files": the dictionary for table structure, "src_tables": the dictionary for mapping column names, "ana_data": the dictionary for query, "adni": the dictionary for ADNI data.
`apoecode`	A string indicating the APOE. The available options are: 3.4, 4.4, 2.4
`par_apoe`	A list indicating the map for apoecode. Default value is list(levels = c(3.4, 4.4, 2.4),labels = c(1, 2, NA))).
`ad_ana_data`	The analysis data get from adt_biocard() function.
`...`
`vars`	A list of strings indicating categorical variables name.
`x`	The analysis data set
`var`	A string indicating the queried variable
`stack_by`	A string indicating the way to group data. Options are "sex" and "diagnosis".
`distn`	A string indicating the interested distribution. Options are "age", "visit", and "yar"
`pat_sub`	A data set contains needed information for ploting