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  "Title": "Clinical Publication",
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  "Description": "Accelerate the process from clinical data to medical\npublication, including clinical data cleaning, significant\nresult screening, and the generation of publish-ready tables\nand figures.",
  "Maintainer": "Yue Niu <niuyuesam@163.com>",
  "URL": "https://github.com/yotasama/clinpubr,\nhttps://gitee.com/yotasama/clinpubr",
  "BugReports": "https://github.com/yotasama/clinpubr/issues",
  "License": "MIT + file LICENSE",
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  "Collate": "'answer_check.R' 'baseline_table.R' 'calculate_index.R'\n'check_nonnum.R' 'classif_model_compare.R' 'combine_files.R'\n'cut_by.R' 'data_overview.R' 'data_screen.R'\n'exclusion_count.R' 'extract_num.R' 'get_valid.R'\n'get_valid_subset.R' 'importance_plot.R' 'initial_cleaning.R'\n'interactions.R' 'mark_outlier.R' 'merge.R' 'utils.R' 'misc.R'\n'multichoice.R' 'predictor_effect_plot.R' 'rcs_plot.R'\n'regressions.R' 'subgroup_forest.R' 'subject_standardize.R'\n'time_roc.R' 'to_date.R' 'unit_standardize.R'",
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  "Repository": "https://yotasama.r-universe.dev",
  "Date/Publication": "2026-05-25 11:51:08 UTC",
  "RemoteUrl": "https://github.com/yotasama/clinpubr",
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  "Author": "Yue Niu [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-6843-3548>),\nKeyun Wang [aut]",
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    "add_lists",
    "answer_check",
    "auto_encoding_repair",
    "baseline_table",
    "break_at",
    "calc_cindex",
    "calculate_index",
    "char_initial_cleaning",
    "check_nonnum",
    "classif_model_compare",
    "combine_files",
    "combine_multichoice",
    "common_prefix",
    "cut_by",
    "data_overview",
    "detect_outliers",
    "df_view_nonnum",
    "emp_colors",
    "exclusion_count",
    "extract_num",
    "fill_with_last",
    "filter_rcs_predictors",
    "first_mode",
    "format_pval",
    "formula_add_covs",
    "get_samples",
    "get_valid",
    "get_valid_subset",
    "get_var_types",
    "importance_plot",
    "indicate_duplicates",
    "interaction_p_value",
    "interaction_plot",
    "interaction_scan",
    "iqr_outlier",
    "keep_by_keyword",
    "mad_outlier",
    "max_missing_rates",
    "merge_by_range",
    "merge_by_substring",
    "merge_ordered_vectors",
    "na_max",
    "na_min",
    "na2false",
    "name2code",
    "predictor_effect_plot",
    "qq_show",
    "rcs_plot",
    "regression_basic_results",
    "regression_fit",
    "regression_forest",
    "regression_scan",
    "replace_elements",
    "screen_data_list",
    "split_multichoice",
    "str_match_replace",
    "subgroup_forest",
    "subject_view",
    "test_normality",
    "time_roc_plot",
    "to_date",
    "to_wide",
    "unit_standardize",
    "unit_view",
    "unmake_names",
    "value_initial_cleaning",
    "vec2code",
    "zscore_outlier"
  ],
  "_help": [
    {
      "page": "add_lists",
      "title": "Adding lists element-wise",
      "topics": [
        "add_lists"
      ]
    },
    {
      "page": "answer_check",
      "title": "Check answers of multiple choice questions",
      "topics": [
        "answer_check"
      ]
    },
    {
      "page": "baseline_table",
      "title": "Create a baseline table for a dataset.",
      "topics": [
        "baseline_table"
      ]
    },
    {
      "page": "break_at",
      "title": "Generate breaks for histogram",
      "topics": [
        "break_at"
      ]
    },
    {
      "page": "calc_cindex",
      "title": "Calculate C-index for survival data",
      "topics": [
        "calc_cindex"
      ]
    },
    {
      "page": "calculate_index",
      "title": "Calculate index based on conditions",
      "topics": [
        "calculate_index"
      ]
    },
    {
      "page": "check_nonnum",
      "title": "Check elements that are not numeric",
      "topics": [
        "check_nonnum"
      ]
    },
    {
      "page": "classif_model_compare",
      "title": "Performance comparison of classification models",
      "topics": [
        "classif_model_compare"
      ]
    },
    {
      "page": "combine_files",
      "title": "combine multiple data files into a single data frame",
      "topics": [
        "combine_files"
      ]
    },
    {
      "page": "combine_multichoice",
      "title": "Combine multi-choice columns into one",
      "topics": [
        "combine_multichoice"
      ]
    },
    {
      "page": "common_prefix",
      "title": "Get common prefix of a string vector",
      "topics": [
        "common_prefix"
      ]
    },
    {
      "page": "cut_by",
      "title": "Convert Numeric to Factor",
      "topics": [
        "cut_by"
      ]
    },
    {
      "page": "data_overview",
      "title": "Data Overview and Quality Check",
      "topics": [
        "data_overview"
      ]
    },
    {
      "page": "detect_outliers",
      "title": "Detect outliers in a numeric vector.",
      "topics": [
        "detect_outliers"
      ]
    },
    {
      "page": "df_view_nonnum",
      "title": "Show non-numeric elements in a data frame",
      "topics": [
        "df_view_nonnum"
      ]
    },
    {
      "page": "emp_colors",
      "title": "default color palette for 'clinpubr' plots",
      "topics": [
        "emp_colors"
      ]
    },
    {
      "page": "exclusion_count",
      "title": "Count the number of excluded samples at each step",
      "topics": [
        "exclusion_count"
      ]
    },
    {
      "page": "extract_num",
      "title": "Extract numbers from string.",
      "topics": [
        "extract_num"
      ]
    },
    {
      "page": "fill_with_last",
      "title": "Fill NA values with the last valid value",
      "topics": [
        "fill_with_last"
      ]
    },
    {
      "page": "filter_rcs_predictors",
      "title": "Filter predictors for RCS",
      "topics": [
        "filter_rcs_predictors"
      ]
    },
    {
      "page": "first_mode",
      "title": "Calculate the first mode",
      "topics": [
        "first_mode"
      ]
    },
    {
      "page": "format_pval",
      "title": "Format p-value for publication",
      "topics": [
        "format_pval"
      ]
    },
    {
      "page": "formula_add_covs",
      "title": "Add covariates to a formula",
      "topics": [
        "formula_add_covs"
      ]
    },
    {
      "page": "get_samples",
      "title": "Generate a sample of values from a vector and collapse them.",
      "topics": [
        "get_samples"
      ]
    },
    {
      "page": "get_valid",
      "title": "Get one valid value from vector.",
      "topics": [
        "get_valid"
      ]
    },
    {
      "page": "get_valid_subset",
      "title": "Get the subset that satisfies the missing rate condition.",
      "topics": [
        "get_valid_subset"
      ]
    },
    {
      "page": "get_var_types",
      "title": "Get variable types for baseline table",
      "topics": [
        "get_var_types"
      ]
    },
    {
      "page": "importance_plot",
      "title": "Importance plot",
      "topics": [
        "importance_plot"
      ]
    },
    {
      "page": "indicate_duplicates",
      "title": "Determine duplicate elements including their first occurrence.",
      "topics": [
        "indicate_duplicates"
      ]
    },
    {
      "page": "interaction_p_value",
      "title": "Calculate interaction p-value",
      "topics": [
        "interaction_p_value"
      ]
    },
    {
      "page": "interaction_plot",
      "title": "Plot interactions",
      "topics": [
        "interaction_plot"
      ]
    },
    {
      "page": "interaction_scan",
      "title": "Scan for interactions between variables",
      "topics": [
        "interaction_scan"
      ]
    },
    {
      "page": "keep_by_keyword",
      "title": "Keep string segment by regex keyword position",
      "topics": [
        "keep_by_keyword"
      ]
    },
    {
      "page": "mad_outlier",
      "title": "Mark possible outliers using different methods.",
      "topics": [
        "iqr_outlier",
        "mad_outlier",
        "zscore_outlier"
      ]
    },
    {
      "page": "max_missing_rates",
      "title": "Get the maximum missing rate of rows and columns.",
      "topics": [
        "max_missing_rates"
      ]
    },
    {
      "page": "merge_by_range",
      "title": "Merge Data Frames by Exact Keys and Value Range",
      "topics": [
        "merge_by_range"
      ]
    },
    {
      "page": "merge_by_substring",
      "title": "Merge Data Frame by String Key Matching",
      "topics": [
        "merge_by_substring"
      ]
    },
    {
      "page": "merge_ordered_vectors",
      "title": "Merging vectors while maintaining order",
      "topics": [
        "merge_ordered_vectors"
      ]
    },
    {
      "page": "na_max",
      "title": "Safe min and max functions that return NA if all values are NA",
      "topics": [
        "na_max",
        "na_min"
      ]
    },
    {
      "page": "na2false",
      "title": "Replace NA values with FALSE",
      "topics": [
        "na2false"
      ]
    },
    {
      "page": "predictor_effect_plot",
      "title": "Plot the effect of a predictor variable",
      "topics": [
        "predictor_effect_plot"
      ]
    },
    {
      "page": "qq_show",
      "title": "QQ plot",
      "topics": [
        "qq_show"
      ]
    },
    {
      "page": "rcs_plot",
      "title": "Plot restricted cubic spline",
      "topics": [
        "rcs_plot"
      ]
    },
    {
      "page": "regression_basic_results",
      "title": "Basic results of logistic or Cox regression.",
      "topics": [
        "regression_basic_results"
      ]
    },
    {
      "page": "regression_fit",
      "title": "Obtain regression results",
      "topics": [
        "regression_fit"
      ]
    },
    {
      "page": "regression_forest",
      "title": "Forest plot of regression results",
      "topics": [
        "regression_forest"
      ]
    },
    {
      "page": "regression_scan",
      "title": "Scan for significant regression predictors",
      "topics": [
        "regression_scan"
      ]
    },
    {
      "page": "replace_elements",
      "title": "Replacing elements in a vector",
      "topics": [
        "replace_elements"
      ]
    },
    {
      "page": "screen_data_list",
      "title": "Screen and Join Multi-Table Clinical Data by Expression",
      "topics": [
        "screen_data_list"
      ]
    },
    {
      "page": "split_multichoice",
      "title": "Split multi-choice data into columns",
      "topics": [
        "split_multichoice"
      ]
    },
    {
      "page": "str_match_replace",
      "title": "Match string and replace with corresponding value",
      "topics": [
        "str_match_replace"
      ]
    },
    {
      "page": "subgroup_forest",
      "title": "Create subgroup forest plot.",
      "topics": [
        "subgroup_forest"
      ]
    },
    {
      "page": "subject_view",
      "title": "Get an overview of different subjects in data.",
      "topics": [
        "subject_view"
      ]
    },
    {
      "page": "test_normality",
      "title": "Test normality of a numeric variable",
      "topics": [
        "test_normality"
      ]
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