Package 'tabxplor'

A tabxplor_grouped_tab object.

Indices

For matrices and arrays. If TRUE the result is coerced to the lowest possible dimension (see the examples). This only works for extracting elements, not for the replacement.

A tabxplor_grouped_tab object.

Indices

The new value.

A tabxplor_grouped_tab object.

Indices.

The new value.

A tabxplor_fmt object.

The name of the field to extract.

A tibble of class tabxplor_tab.

<data-masking> Variables, or functions of variables. Use desc() to sort a variable in descending order.

By default, will sort first by grouping variable. Set to FALSE to avoid this behaviour.

By default, will put totals at the end of their group. Set to FALSE to avoid this behaviour.

By default, only the rows with the same display than the first row are arranged : if the first row of the group displays percentages, rows with n or pvalues are kept at the same place (typically, at the end of the group). Rows with the text "row_pct", "n" or "pvalue" in the row_var name are also kept at the same place. Set to FALSE to avoid this behaviour.

The locale to sort character vectors in.

A table or data.framate containting tabxplor_fmt columns.

A data frame.

A named list used modify columns. A NULL value should remove an existing column.

A data frame.

Template to use for restoring attributes

A data frame.

A numeric or logical vector that indexes the rows of .data.

Future parameters.

The data frame.

<tidy-select> The variables to recode.

The name of the input data frame. Default to the expression given in data.

The name of the output data frame, if different from the input data frame.

Default is to use dplyr::mutate(). Set to base to use ⁠data$var <-⁠ style.

By default, a reminder of the syntax ("new" = "old") is printed. Set to FALSE to remove it.

By default the result is written in the console if there are less than 6 variables, written in a temporary file and opened otherwise. Set to false to get a data frame with a character variable instead.

The underlying count, as an integer vector of length n(). It is used to calculate confidence intervals.

The type of the column, which defines the type of background calculation to be made (as a single string, since it's not a field but an attribute) :

• "n": counts

• "mean": mean column (from numeric variables)

• "row": row percentages

• "col": column percentages

• "all": frequencies by subtable/group (i.e. by tab_vars)

• "all_tabs": frequencies for the whole table

The number of digits, as an integer, or an integer vector the length of n.

The display type : the name of the field you want to show when printing the vector. Among "n", "wn", "pct", "diff", "ctr", "mean", "var", "ci", "pct_ci" (percentages with visible confidence interval), "mean_ci" (means with visible confidence interval). As a single string, or a character vector the length of n.

The underlying weighted counts, as a double vector the length of n. It is used in certain operations on fmt, like means.

The percentages, as a double vector the length of n. Calculate with tab_pct.

The means, as a double vector the length of n.

The differences (from totals or first cells), as a double vector the length of n. Used to set colors for means and row or col percentages. Calculate with tab_pct.

The contributions of cells to (sub)tables variances, as a double vector the length of n. Used to print colors when color = "contrib". The mean contribution of each (sub)table is written on total rows (then, colors don't print well without total rows). Calculate with tab_chi2.

The cells variances, as a double vector the length of n. Used with type = "mean" to calculate confidence intervals. Calculate with tab_plain.

The confidence intervals, as a double vector the length of n. Used to print colors ("diff_ci", "after_ci"). Calculate with tab_ci.

The relative risk, as a double vector the length of n.

The odds ratio or relative risk ratio, as a double vector the length of n.

TRUE when the cell is part of a total row

TRUE when the cell is part of a total table

TRUE when the cell is part of a reference row (cf. ref)

FALSE when the comparison level is the subtable/group, TRUE when it is the whole table

The type of difference of the vector. Cf. tab.

The type of confidence intervals of the vector (calculate with tab_ci) :

• "" or "no": no ci have been calculated

• "cell": absolute confidence intervals of cells percentages.

• "diff": confidence intervals of the difference between a cell and the relative total cell (or relative first cell when ref = "first").

• "auto": "diff" for means and row/col percentages, "cell" for frequencies ("all", "all_tabs").

The name of the col_var used to calculate the vector

TRUE when the vector is a total column

TRUE when the vector is a reference column

The type of color to print :

• "no": no colors are printed.

• "diff": color percentages and means based on cells differences from totals (or from first cells when ref = "first").

• "diff_ci": color pct and means based on cells differences from totals or first cells, removing coloring when the confidence interval of this difference is higher than the difference itself.

• "after_ci": idem, but cut off the confidence interval from the difference first.

• "contrib": color cells based on their contribution to variance (except mean columns, from numeric variables).

The object to test, to get a field in, or to modify.

The value you want to inject in some fmt vector's vctrs::field or attribute using a given "set" function.

Used in methods to add arguments in the future.

By default, get_comp_all takes NA in comparison level to be a FALSE (=comparison at subtables/groups level). Set to FALSE to avoid this behavior.

The fmt vector to get the html color codes from.

The style type in set_color_style and get_color_style, "text" to color the text, "bg" to color the background.

For set_color_style and get_color_style, is your console or html table background "light" or "dark" ? Default to RStudio theme.

Use 24bits colors palettes for html tables : set to "green_red" or "blue_red". Only with mode = "color_code" (not mode = "crayon") and ⁠theme = "light⁠. Default to getOption("tabxplor.color_html_24_bit").

A fmt object.

Other parameters.

Should html tags be added (to print confidence intervals as subscripts) ?

How NAs should be printed. Default to NA.

Set to TRUE to print more verbose results, like indicating which is the reference row or col for differences.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

A tibble of class tabxplor_tab.

Variables or computations to group by.

When FALSE, the default, group_by() will override existing groups. To add to the existing groups, use .add = TRUE.

Drop groups formed by factor levels that don't appear in the data? The default is TRUE except when .data has been previously grouped with .drop = FALSE.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

Should partial reference rows be counted as reference rows ? Default to FALSE.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

Should partial total rows be counted as total rows ? Default to FALSE.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

Should partial total tabs be counted as total tabs ? Default to FALSE.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

The object to test, to get a field in, or to modify.

Used in methods to add arguments in the future.

A data.frame.

The row variable, which will be printed with one level per line. If numeric, it will be converted to factor.

One column is printed for each level of each column variable. For numeric variables means are calculated, in a single column.

One subtable is made for each combination of levels of the tab variables. All tab variables are converted to factor. Leave empty to make a simple table.

A weight variable, of class numeric. Leave empty for unweighted results.

The type of percentages to calculate :

• "row": row percentages.

• "col": column percentages.

• "all": frequencies for each subtable/group, if there is tab_vars.

• "all_tabs": frequencies for the whole (set of) table(s).

The type of colors to print, as a single string. Vectorised over row_vars.

• "no": by default, no colors are printed.

• "diff": color percentages and means based on cells differences from totals (or from first cells when ref = "first").

• "diff_ci": color pct and means based on cells differences from totals or first cells, removing coloring when the confidence interval of this difference is higher than the difference itself.

• "after_ci": idem, but cut off the confidence interval from the difference first.

• "contrib": color cells based on their contribution to variance (except mean columns, from numeric variables).

• "OR": for pct == "col" or pct == "row", color based on odds ratios (or relative risks ratios)

Set to TRUE to make a Chi2 and add summary stats. Also useful to color cells based on their contribution to variance.

With pct = "row" or pct = "col", calculate and print odds ratios (for binary variables) or relative risks ratios (for variables with 3 levels or more).

• "no": by default, no OR are calculated.

• "OR": print OR (instead of percentages).

• "OR_pct": print OR, with percentages in bracket.

The policy to adopt with missing values. It must be a single string.

• na = "keep": by default, prints NA's as explicit "NA" level.

• na = "drop": removes NA levels before making each table (tabs made with different column variables may have a different number of observations, and won't exactly have the same total columns).

The levels of col_vars to keep.

• "all": by default, all levels are kept.

• "first": only keep the first level of each col_vars

• "auto": keep the first level when col_var is only two levels, keep all levels otherwise.

When set to a positive integer, levels with less count than that will be merged into an "Others" level.

By default, clean levels names, by removing prefix numbers like "1-", and text in parenthesis. Set to FALSE to avoid this behaviour.

The reference cell to calculate differences and ratios (used to print colors) :

• "auto": by default, cell difference from the corresponding total (rows or cols depending on pct = "row" or pct = "col") is used for diff ; cell ratio from the first line (or col) is use for OR (odds ratio/relative risks ratio).

• "tot": totals are always used.

• "first": calculate cell difference or ratio from the first cell of the row or column (useful to color temporal developments).

• n: when ref is an integer, the nth row (or column) is used for comparison.

• "regex": when ref is a string, it it used as a regular expression, to match with the names of the rows (or columns). Be precise enough to match only one column or row, otherwise you get a warning message.

• "no": not use ref and not calculate diffs to gain calculation time.

A second reference cell is needed to calculate odds ratios (or relative risks ratios). The first cell of the row or column is used by default. See ref for the full list of possible values.

The comparison level : by subtables/groups, or for the whole table.

The type of confidence intervals to calculate, passed to tab_ci.

• "cell": absolute confidence intervals of cells percentages.

• "diff": confidence intervals of the difference between a cell and the relative total cell (or relative first cell when ref = "first").

• "auto": ci = "diff" for means and row/col percentages, ci = "cell" for frequencies ("all", "all_tabs").

By default, for percentages, with ci = "cell" Wilson's method is used, and with ci = "diff" Wald's method along Agresti and Caffo's adjustment. Means use classic method.

The confidence level, as a single numeric between 0 and

1. Default to 0.95 (95\

By default confidence interval are printed with the interval display. Set to "moe" to use pct +- moe instead.

The total table, if there are subtables/groups (i.e. when tab_vars is provided). Vectorised over row_vars.

• "line": by default, add a general total line (necessary for calculations with comp = "all")

• "table": add a complete total table (i.e. row_var by col_vars without tab_vars).

• "no": not to draw any total table.

By default, rownames are wrapped when larger than 30 characters.

By default, colnames are wrapped when larger than 12 characters.

The information to display in the table.

For pct = "row" or pct = "col", set to FALSE not to add another column or row with unweighted counts (n).

Set to TRUE to add a column with the frequencies of the row variable (for pct = "row") or a row with the frequencies of the column variable (for pct = "col")

A character vector to print rows of legend under the table.

The number of digits to print, as a single integer, or an integer vector the same length as col_vars.

A data.frame.

The table caption. For formatting, you need to use a css with ⁠caption{}⁠in rmarkdown.

By default, a white table with black text, Set to "dark" for a black table with white text.

Should rows and cols with "Total" string be set in bold ?

Put a vertical border around each column ?

A string for HTML css font. By default, it uses '"DejaVu Sans", "Arial", arial, helvetica, sans-serif'. Set another default by setting options("tabxplor.kable_html_font" = ).

A TRUE or FALSE variable controlling whether the HTML table should have the preferable format for full_width. If not specified, a HTML table will have full width by default but this option will be set to FALSE for a LaTeX table.

By default, rownames are wrapped when larger than 30 characters.

By default, colnames are wrapped when larger than 12 characters.

Set to FALSE to wrap also on non whitespace characters.

A character vector to print rows of legend under the table.

Other arguments to pass to kableExtra::kable_styling.

A tabxplor_fmt column.

Name-value pairs. The name gives the name of the column in the output (do not change it).

The value can be:

• A vector of length 1, which will be recycled to the correct length.

• A vector the same length as the current group (or the whole data frame if ungrouped).

A table, stored into a tibble data.frame. It is generally made with tab, tab_many or tab_plain.

A character vector to print legend lines under the table.

A tibble storing information about pvalues and variances, to fill with tab_chi2.

Needed to implement subclasses.

Needed to implement subclasses.

The grouping data.

A fmt object.

Other parameter.

A fmt object.

Other parameter.

Object to format or print.

Width of text output to generate.

Passed on to tbl_format_setup().

Number of rows to show.

Number of extra columns to print abbreviated information for, if the width is too small for the entire tibble.

Maximum number of footer lines.

Minimum number of characters for the row variable. Default to 30.

Set to TRUE to get the text as a character vector instead of a printed output.

Object to format or print.

Width of text output to generate.

Passed on to tbl_format_setup().

Number of rows to show.

Number of extra columns to print abbreviated information for, if the width is too small for the entire tibble.

Maximum number of footer lines.

Minimum number of characters for the row variable. Default to 30.

Set to TRUE to get the text as a character vector instead of a printed output.

A tibble of class tabxplor_tab.

Columns to move. will move columns to the left-hand side; specifying both is an error.

A tibble of class tabxplor_tab.

A function used to transform the selected .cols. Should return a character vector the same length as the input.

Columns to rename; defaults to all columns.

Additional arguments passed onto .fn.

A tibble of class tabxplor_tab.

Use new_name = old_name to rename selected variables.

A tibble of class tabxplor_tab.

Variables to be preserved when calling summarise(). This is typically a set of variables whose combination uniquely identify each row.

A tibble of class tabxplor_tab.

Variables to be preserved when calling summarise(). This is typically a set of variables whose combination uniquely identify each row.

A data.frame.

The name of the variable to create.

The list of the factors to count (only the first level is counted, as 1) ; as a character vector.

A tibble of class tabxplor_tab.

One or more unquoted expressions separated by commas. Variable names can be used as if they were positions in the data frame, so expressions like x:y can be used to select a range of variables.

The object to test, to get a field in, or to modify.

The value you want to inject in some fmt vector's vctrs::field or attribute using a given "set" function.

The object to test, to get a field in, or to modify.

The value you want to inject in some fmt vector's vctrs::field or attribute using a given "set" function.

The object to test, to get a field in, or to modify.

The value you want to inject in some fmt vector's vctrs::field or attribute using a given "set" function.

A tibble of class tabxplor_tab.

Name-value pairs of summary functions. The name will be the name of the variable in the result.

Grouping structure of the result.

A data frame.

The row variable, which will be printed with one level per line, and the column variable, which will be printed with one level per column. For numeric variables means are calculated, in a single column.

<tidy-select> Tab variables : a subtable is made for each combination of levels of the selected variables. Leave empty to make a simple cross-table. All tab_vars are converted to factor.

A weight variable, of class numeric. Leave empty for unweighted results.

<tidy-select> Supplementary columns variables, with only the first level printed, and row percentages (for numeric variables, a mean will be calculated for each row_var). To pass many variables you may use syntax sup_cols = c(sup_col1, sup_col2, ...). To keep all levels of other col_vars, or other types of percentages, use tab_many instead.

The type of percentages to calculate :

• "row": row percentages.

• "col": column percentages.

• "all": frequencies for each subtable/group, if there is tab_vars.

• "all_tabs": frequencies for the whole (set of) table(s).

The type of colors to print, as a single string :

• "no": by default, no colors are printed.

• "diff": color percentages and means based on cells differences from totals (or from first cells when ref = "first").

• "diff_ci": color pct and means based on cells differences from totals or first cells, removing coloring when the confidence interval of this difference is higher than the difference itself.

• "after_ci": idem, but cut off the confidence interval from the difference first.

• "contrib": color cells based on their contribution to variance (except mean columns, from numeric variables).

• "OR": for pct == "col" or pct == "row", color based on odds ratios (or relative risks ratios)

• "auto": frequencies (pct = "all", pct = "all_tabs") and counts are colored with "contrib". When ci = "diff", row and col percentages are colored with "after_ci" ; otherwise they are colored with "diff".

With pct = "row" or pct = "col", calculate and print odds ratios (for binary variables) or relative risks ratios (for variables with 3 levels or more).

• "no": by default, no OR are calculated.

• "OR": print OR (instead of percentages).

• "OR_pct": print OR, with percentages in bracket.

Set to TRUE to calculate Chi2 summaries with tab_chi2. Useful to print metadata, and to color cells based on their contribution to variance (color = "contrib"). Automatically added if needed for color.

The policy to adopt for missing values, as a single string :

• "keep": by default, NA's of row, col and tab variables are printed as an explicit "NA" level.

• "drop": remove NA's in row, col and tab variables before calculations are done. Supplementary columns are then calculated for observations with no NA in any of the row, col and tab variables.

Set to TRUE to clean levels names, by removing prefix numbers like "1-", and text in parenthesis. All data formatting arguments are passed to tab_prepare.

When set to a positive integer, levels with less count than it will be merged into an "Others" level.

The name of the "Other" level, as a single string.

The reference cell to calculate differences and ratios (used to print colors) :

• "auto": by default, cell difference from the corresponding total (rows or cols depending on pct = "row" or pct = "col") is used for diff ; cell ratio from the first line (or col) is use for OR (odds ratio/relative risks ratio).

• "tot": totals are always used.

• "first": calculate cell difference or ratio from the first cell of the row or column (useful to color temporal developments).

• n: when ref is an integer, the nth row (or column) is used for comparison.

• "regex": when ref is a string, it it used as a regular expression, to match with the names of the rows (or columns). Be precise enough to match only one column or row, otherwise you get a warning message.

• "no": not use ref and not calculate diffs to gain calculation time.

A second reference cell is needed to calculate odds ratios (or relative risks ratios). The first cell of the row or column is used by default. See ref above for the full list of possible values.

The comparison level : by subtables/groups, or for the whole table.

• "tab": by default, contributions to variance, row differences from totals/first cells, and row confidence intervals for these differences, are calculated for each tab_vars group.

• "all": compare cells to the general total line (provided there is a total table with a total row), or with the first line of the total table when ref = "first".

The type of confidence intervals to calculate, passed to tab_ci (automatically added if needed for color).

• "cell": absolute confidence intervals of cells percentages.

• "diff": confidence intervals of the difference between a cell and the relative total cell (or relative first cell when ref = "first").

• "auto": ci = "diff" for means and row/col percentages, ci = "cell" for frequencies ("all", "all_tabs").

By default, for percentages, with Wilson's method is used, and with ci = "diff" Wald's method along Agresti and Caffo's adjustment. Means use classic method. This can be changed in tab_many. By default, with ci = "cell", the result is printed in the ⁠[inf;sup]⁠ form. Set options("tabxplor.ci_print" = "moe") to print pct +- moe instead.

The confidence level, as a single numeric between 0 and 1. Default to 0.95 (95%).

The total table, if there are subtables/groups (i.e. when tab_vars is provided) :

• "line": by default, add a general total line (necessary for calculations with comp = "all")

• "table": add a complete total table (i.e. row_var by col_vars without tab_vars).

• "no": not to draw any total table.

The name of the total table, as a single string.

The totals :

• c("col", "row") or "both" : by default, both total rows and total columns.

• "row": only total rows.

• "col": only total column.

• "no": remove all totals (after calculations if needed).

The names of the totals, as a character vector of length one or two. Use syntax of type c("Total row", "Total column") to set different names for rows and cols.

For pct = "row" or pct = "col", set to FALSE not to add another column or row with unweighted counts (n).

Set to TRUE to add a column with the frequencies of the row variable (for pct = "row") or a row with the frequencies of the column variable (for pct = "col").

A character vector to print rows of legend under the table.

The number of digits to print, as a single integer. To print a different number of digits for each sup_cols, an integer vector of length 1 + sup_cols (the first being the number of digits for the base table).

A dplyr::filter to apply to the data frame first, as a single string (which will be converted to code, i.e. to a call). Useful when printing multiples tabs with tibble::tribble, to use different filters for similar tables or simply make the field of observation more visible into the code.

A tibble of class tab, made with tab_plain or tab_many.

By default all elements of the Chi2 summary are calculated : contributions to variance, pvalue, variance and unweighted count. You can choose which are computed by selecting elements in the vector c("ctr", "p", "var", "counts").

Comparison level. When tab_vars are present, should the contributions to variance be calculated for each subtable/group (by default, comp = "tab") ? Should they be calculated for the whole table (comp = "all") ? comp must be set once and for all the first time you use tab_plain, tab_num or tab_chi2 with rows, or tab_ci.

The type of colors to print, as a single string.

• "no": by default, no colors are printed

• "all": color all cells based on their contribution to variance (except for mean columns, from numeric variables)

• "all_pct": color all percentages cells based on their contribution to variance

• "auto": only color columns with counts, pct = "all" or pct = "all_tabs"

A tibble of class tab made with tab_plain or tab_many.

The type of ci to calculate. Set to "cell" to calculate absolute confidence intervals. Set to "diff" to calculate the confidence intervals of the difference between a cell and the relative total cell (or the reference cell, when ref is not "tot" in tab_plain or tab_num). By default, "diff" ci are calculated for means and row and col percentages, "cell" ci for frequencies ("all", "all_tabs"). By default, with ci = "cell", the result is printed in the ⁠[inf;sup]⁠ form. Set options("tabxplor.ci_print" = "moe") to print pct +- moe instead.

Comparison level. When tab_vars are present, should the contributions to variance be calculated for each subtable/group (by default, comp = "tab") ? Should they be calculated for the whole table (comp = "all") ? comp must be set once and for all the first time you use tab_plain, tab_num or tab_chi2 with rows, or tab_ci.

The confidence level, as a single numeric between 0 and 1. Default to 0.95 (95%).

The type of colors to print, as a single string.

• "no": by default, no colors are printed

• "diff_ci": color pct and means based on cells differences from totals or first cells, removing coloring when the confidence interval of this difference is higher than the difference itself

• "after_ci": idem, but cut off the confidence interval from the difference

By default confidence intervals are calculated and used to set colors, but not printed. Set to TRUE to print them in the result.

Character string specifying which method to use with percentages for ci = "cell". This can be one out of: "wald", "wilson", "wilsoncc", "agresti-coull", "jeffreys", "modified wilson", "modified jeffreys", "clopper-pearson", "arcsine", "logit", "witting", "pratt", "midp", "lik" and "blaker". Defaults to "wilson". See BinomCI.

Character string specifying which method to use with percentages for ci = "diff". This can be one out of: "wald", "waldcc", "ac", "score", "scorecc", "mn", "mee", "blj", "ha", "hal", "jp". Defaults to "ac", Wald interval with the adjustment according to Agresti, Caffo for difference in proportions and independent samples. See BinomDiffCI.

A list of tabxplor_tab (or a tabxplor_tab)

A data.frame.

For data.frame of class tabxplor_tab, remove tab_vars.

Number of characters lengths between columns.

A table made with tab or tab_many, or a list of tab with the same col_vars and no tab_vars.

By default, a white table with black text, Set to "dark" for a black table with white text.

Set to "text" to color the text, "bg" to color the background. By default it takes getOption("tabxplor.color_style_type").

Use 24bits colors palettes for html tables : set to "green_red" or "blue_red". Only with mode = "color_code" (not mode = "crayon") and ⁠theme = "light⁠. Default to getOption("tabxplor.color_html_24_bit").

By default, html tooltips are used to display additional informations at mouse hover. Set to FALSE to discard.

By default, takes getOption("tabxplor.kable_popover"). When FALSE, html tooltips are of the base kind : they can't be used with floating table of content in rmarkdown documents. Set to TRUE to use kableExtra html popovers instead, which are compatible with floating toc. Remember to enable the popover module by copying the following code into your document : <script> $(document).ready(function(){ $('[data-toggle="popover"]').popover(); }); </script>

Print colors legend below the table ? You can then use a css chunk in rmarkdown to change popovers colors.

The table caption. For formatting, you need to use a css with ⁠caption{}⁠in rmarkdown.

A string for HTML css font. By default, it uses '"DejaVu Sans", "Arial", arial, helvetica, sans-serif'. Set another default by setting options("tabxplor.kable_html_font" = ).

Get the transformed data instead of the html table.

A TRUE or FALSE variable controlling whether the HTML table should have the preferable format for full_width. If not specified, a HTML table will have full width by default but this option will be set to FALSE for a LaTeX table.

By default, rownames are wrapped when larger than 30 characters.

By default, colnames are wrapped when larger than 12 characters.

Set to FALSE to wrap also on non whitespace characters.

Other arguments to pass to kableExtra::kable_styling.

A data frame.

The row variable, which will be printed with one level per line. If numeric, it will be converted to factor. If more than one row_var if provided, a different table is made for each of them.

<tidy-select> One column is printed for each level of each column variable. For numeric variables means are calculated, in a single column. To pass many variables you may use syntax col_vars = c(col_var1, col_var2, ...).

<tidy-select> One subtable is made for each combination of levels of the tab variables. To pass many variables you may use syntax tab_vars = c(tab_var1, tab_var2, ...). All tab variables are converted to factor. Leave empty to make a simple table.

A weight variable, of class numeric. Leave empty for unweighted results.

The type of percentages to calculate :

• "row": row percentages.

• "col": column percentages.

• "all": frequencies for each subtable/group, if there is tab_vars.

• "all_tabs": frequencies for the whole (set of) table(s).

The argument is vectorised over both row_vars and col_vars. You can then write as the following : pct = list(row_var1 = list("row", "col", "col"), row_var2 = list("col", "row", "row"))

The type of colors to print, as a single string. Vectorised over row_vars.

• "no": by default, no colors are printed.

• "diff": color percentages and means based on cells differences from totals (or from first cells when ref = "first").

• "diff_ci": color pct and means based on cells differences from totals or first cells, removing coloring when the confidence interval of this difference is higher than the difference itself.

• "after_ci": idem, but cut off the confidence interval from the difference first.

• "contrib": color cells based on their contribution to variance (except mean columns, from numeric variables).

• "OR": for pct == "col" or pct == "row", color based on odds ratios (or relative risks ratios)

• "auto": frequencies (pct = "all", pct = "all_tabs") and counts are colored with "contrib". When ci = "diff", row and col percentages are colored with "after_ci" ; otherwise they are colored with "diff".

With pct = "row" or pct = "col", calculate and print odds ratios (for binary variables) or relative risks ratios (for variables with 3 levels or more).

• "no": by default, no OR are calculated.

• "OR": print OR (instead of percentages).

• "OR_pct": print OR, with percentages in bracket.

Set to TRUE to calculate Chi2 summaries with tab_chi2. Useful to print metadata, and to color cells based on their contribution to variance (color = "contrib"). Vectorised over row_vars.

The policy to adopt with missing values. It must be a single string.

• na = "keep": by default, prints NA's as explicit "NA" level.

• na = "drop": removes NA levels before making each table (tabs made with different column variables may have a different number of observations, and won't exactly have the same total columns).

• "drop_all": remove NA's for all variables before making the tables.

The levels of col_vars to keep (for more complex selections use dplyr::select). The argument is vectorised over col_vars.

• "all": by default, all levels are kept.

• "first": only keep the first level of each col_vars

• "auto": keep the first level when col_var is only two levels, keep all levels otherwise

<tidy-select> Removes all observations with a NA in any of the chosen variables, for all tables (tabs for each column variable will have the same number of observations).

Set to TRUE to clean levels names, by removing prefix numbers like "1-", and text in parenthesis. All data formatting arguments are passed to tab_prepare.

With several row_vars, set to TRUE to bind all tables in a single tabxplor_tab.

When set to a positive integer, levels with less count than it will be merged into an "Others" level.

The name of the "Other" level, as a single string.

The reference cell to calculate differences and ratios (used to print colors) :

• "auto": by default, cell difference from the corresponding total (rows or cols depending on pct = "row" or pct = "col") is used for diff ; cell ratio from the first line (or col) is use for OR (odds ratio/relative risks ratio).

• "tot": totals are always used.

• "first": calculate cell difference or ratio from the first cell of the row or column (useful to color temporal developments).

• n: when ref is an integer, the nth row (or column) is used for comparison.

• "regex": when ref is a string, it it used as a regular expression, to match with the names of the rows (or columns). Be precise enough to match only one column or row, otherwise you get a warning message.

• "no": not use ref and not calculate diffs to gain calculation time.

A second reference cell is needed to calculate odds ratios (or relative risks ratios). The first cell of the row or column is used by default. See ref above for the full list of possible values.

The comparison level : by subtables/groups, or for the whole table. Vectorised over row_vars.

• "tab": by default, contributions to variance, row differences from totals/first cells, and row confidence intervals for these differences, are calculated for each tab_vars group.

• "all": compare cells to the general total line (provided there is a total table with a total row), or with the reference line of the total table when ref = "first", an integer or a regular expression.

The type of confidence intervals to calculate, passed to tab_ci. Vectorised over row_vars.

• "cell": absolute confidence intervals of cells percentages.

• "diff": confidence intervals of the difference between a cell and the relative total cell (or relative first cell when ref = "first").

• "auto": ci = "diff" for means and row/col percentages, ci = "cell" for frequencies ("all", "all_tabs").

By default, for percentages, with ci = "cell" Wilson's method is used, and with ci = "diff" Wald's method along Agresti and Caffo's adjustment. Means use classic method. This can be changed with method_cell and method_diff. By default, with ci = "cell", the result is printed in the ⁠[inf;sup]⁠ form. Set options("tabxplor.ci_print" = "moe") to print pct +- moe instead.

The confidence level, as a single numeric between 0 and 1. Default to 0.95 (95%).

Character string specifying which method to use with percentages for ci = "cell". This can be one out of: "wald", "wilson", "wilsoncc", "agresti-coull", "jeffreys", "modified wilson", "modified jeffreys", "clopper-pearson", "arcsine", "logit", "witting", "pratt", "midp", "lik" and "blaker". Defaults to "wilson". See BinomCI.

Character string specifying which method to use with percentages for ci = "diff". This can be one out of: "wald", "waldcc", "ac", "score", "scorecc", "mn", "mee", "blj", "ha", "hal", "jp". Defaults to "ac", Wald interval with the adjustment according to Agresti, Caffo for difference in proportions and independent samples. See BinomDiffCI.

The total table, if there are subtables/groups (i.e. when tab_vars is provided). Vectorised over row_vars.

• "line": by default, add a general total line (necessary for calculations with comp = "all")

• "table": add a complete total table (i.e. row_var by col_vars without tab_vars).

• "no": not to draw any total table.

The name of the total table, as a single string.

By default, total rows are printed. Set to FALSE to remove them (after calculations if needed). Vectorised over row_vars.

The policy with total columns. Vectorised over col_vars.

• "last": by default, only prints a total column for the last column variable (of class factor, not numeric).

• "each": print a total column for each column variable.

• "no": remove all total columns (after calculations if needed).

The names of the totals, as a character vector of length one or two. Use syntax of type c("Total row", "Total column") to set different names for rows and cols.

For pct = "row" or pct = "col", set to FALSE not to add another column or row with unweighted counts (n).

Set to TRUE to add a column with the frequencies of the row variable (for pct = "row") or a row with the frequencies of the column variable (for pct = "col").

The number of digits to print, as a single integer, or an integer vector the same length as col_vars. The argument is vectorisez over col_vars.

A character vector to print rows of legend under the table.

A dplyr::filter to apply to the data frame first, as a single string (which will be converted to code, i.e. to a call). Useful when printing multiples tabs with tibble::tribble, to use different filters for similar tables or simply make the field of observation more visible into the code.

A tibble of class tab, made with tab, tab_many or tab_plain.

In tab_get_vars, a character vector containing the wanted vars names: "row_var", "col_vars" or "tab_vars".

A object to test with is_tab.

Default to "positive", which just print breaks for positive spreads. Set to all to get breaks for negative spreads as well.

For set_color_style and get_color_style, is your console or html table background "light" or "dark" ? Default to RStudio theme.

Use 24bits colors palettes for html tables : set to "green_red" or "blue_red". Only with mode = "color_code" (not mode = "crayon") and ⁠theme = "light⁠. Default to getOption("tabxplor.color_html_24_bit").

Possibility to provide a custom color styles, as a character vector of 10 html color codes (the five first for over-represented numbers, the five last for under-represented ones). The result is saved to options("tabxplor.color_style"). To discard, relaunch the function with custom_palette = NULL.

By default, get_color_style returns a list of crayon coloring functions. Set to "color_code" to return html color codes.

If they are to be changed, the breaks used for percentages. Default to c(0.05, 0.1, 0.2, 2, 0.3) : first color used when the pct of a cell is +5% superior to the pct of the related total ; second color used when it is +10% superior ; third +20% superior ; fourth *2 superior ; fifth +30% superior. When > 1, it does not take differences but ratio. The opposite for cells inferior to the total (without the *2 rule). With color = "after_ci", the first break is subtracted from all breaks (default becomes c(0, 0.05, 0.15, 2, 0.25) : +0%, +5%, +15%, *2, +25%).

If they are to be changed, the breaks used for means. Default to c(1.15, 1.5, 2, 4) : first color used when the mean of a cell is superior to 1.15 times the mean of the related total row ; second color used when it is superior to 1.5 times ; etc. The opposite for cells inferior to the total. With color = "after_ci", the first break is divided from all breaks (default becomes c(1, 1.3, 1.7, 3.5)).

If they are to be changed, the breaks used for contributions to variance. Default to c(1, 2, 5, 10) : first color used when the contribution of a cell is superior to the mean contribution ; second color used when it is superior to 2 times the mean contribution ; etc. The global color (for example green or red/orange) is given by the sign of the spread.

When missing, return all color breaks. Specify to return a given color break, among "pct", "mean", "contrib", "pct_ci" and "mean_ci".

A data frame.

The row variable, which will be printed with one level per line. If numeric, it will be used as a factor.

The numeric variables, which will appear in columns : means and standard deviation are calculated for each levels of row_var and tab_vars.

<tidy-select> Tab variables : a subtable is made for each combination of levels of the selected variables. Leave empty to make a simple cross-table. All tab variables are converted to factor.

A weight variable, of class numeric. Leave empty for unweighted results.

TRUE print the color percentages and means based on cells differences from totals or reference cell, as provided by ref. Default to FALSE, no colors.

The policy to adopt for missing values in row and tab variables (factors), as a single string.

• "keep": by default, NA's of row and tab variables are printed as an explicit "NA" level.

• "drop": remove NA's in row and tab variables.

NAs in numeric variables are always removed when calculating means. For that reason the n field of each resulting fmt column, used to calculate confidence intervals, only takes into account the complete observations (without NA). To drop all rows with NA in any numeric variable first, use tab_prepare or tab_many with the na_drop_all argument.

The reference cell to calculate differences and ratios (used to print colors) :

• "auto": by default, cell difference from the corresponding total (rows or cols depending on pct = "row" or pct = "col") is used for diff ; cell ratio from the first line (or col) is use for OR (odds ratio/relative risks ratio).

• "tot": totals are always used.

• "first": calculate cell difference or ratio from the first cell of the row or column (useful to color temporal developments).

• n: when ref is an integer, the nth row (or column) is used for comparison.

• "regex": when ref is a string, it it used as a regular expression, to match with the names of the rows (or columns). Be precise enough to match only one column or row, otherwise you get a warning message.

• "no": not use ref and not calculate diffs to gain calculation time.

Comparison level. When tab_vars are present, should the contributions to variance be calculated for each subtable/group (by default, comp = "tab") ? Should they be calculated for the whole table (comp = "all") ? comp must be set once and for all the first time you use tab_plain, tab_num or tab_chi2 with rows, or tab_ci.

The type of confidence intervals to calculate, passed to tab_ci (automatically added if needed for color).

• "cell": absolute confidence intervals of cells percentages.

• "diff": confidence intervals of the difference between a cell and the relative total cell (or relative first cell when ref = "first").

• "auto": ci = "diff" for means and row/col percentages, ci = "cell" for frequencies ("all", "all_tabs").

The confidence level for the confidence intervals, as a single numeric between 0 and 1. Default to 0.95 (95%).

The total table, if there are subtables/groups (i.e. when tab_vars is provided) :

• "line": by default, add a general total line (necessary for calculations with comp = "all")

• "table": add a complete total table (i.e. row_var by col_vars without tab_vars).

• "no": not to draw any total table.

The name of the total table, as a single string.

The totals :

• c("col", "row") or "both" : by default, both total rows and total columns.

• "row": only total rows.

• "col": only total column.

• "no": remove all totals (after calculations if needed).

The names of the totals, as a character vector of length one or two. Use syntax of type c("Total row", "Total column") to set different names for rows and cols.

A character vector to print rows of legend under the table.

The number of digits to print, as a single integer.

Set to TRUE to obtain a table with normal numeric vectors (not fmt).

Set to TRUE to obtain a plain data.frame (not a tibble), with normal numeric vectors (not fmt). Useful, for example, to pass the table to correspondence analysis with FactoMineR.

A tibble of class tab made with tab_plain or tab_many.

The type of percentages to calculate. "row" draw row percentages. Set to "col" for column percentages. Set to "all" for frequencies (based on each subtable/group if tab_vars is provided). Set to "all_tabs" to calculate frequencies based on the whole (set of) table(s).

The number of digits to print for percentages. As a single integer, or an integer vector the same length than col_vars.

The reference cell to calculate differences and ratios (used to print colors) :

• "auto": by default, cell difference from the corresponding total (rows or cols depending on pct = "row" or pct = "col") is used for diff ; cell ratio from the first line (or col) is use for OR (odds ratio/relative risks ratio).

• "tot": totals are always used.

• "first": calculate cell difference or ratio from the first cell of the row or column (useful to color temporal developments).

• n: when ref is an integer, the nth row (or column) is used for comparison.

• "regex": when ref is a string, it it used as a regular expression, to match with the names of the rows (or columns). Be precise enough to match only one column or row, otherwise you get a warning message.

• "no": not use ref and not calculate diffs to gain calculation time.

Comparison level. When tab_vars are present, should the row differences be calculated for each subtable/group (by default comp = "tab" : comparison of each cell to the relative total row) ? Should they be calculated for the whole table (comp = "all" : comparison of each cell to the total row of the total table) ? When comp = "all" and ref = "first", cells are compared to the first cell of the total table instead. This parameter doesn't affect column percentages. comp must be set once and for all the first time you use tab_chi2, tab_pct with rows, or tab_ci.

Set to TRUE to color the resulting tab based on differences (from totals or from the first cell).

If percentages are already calculated and you just want to recalculate differences.

A data frame.

The row variable, which will be printed with one level per line, and the column variable, which will be printed with one level per column. Numeric variables will be used as factors. To calculate means, use tab_num.

<tidy-select> Tab variables : a subtable is made for each combination of levels of the selected variables. Leave empty to make a simple cross-table. All tab variables are converted to factor.

A weight variable, of class numeric. Leave empty for unweighted results.

The type of percentages to calculate :

• "row": row percentages.

• "col": column percentages.

• "all": frequencies for each subtable/group, if there is tab_vars.

• "all_tabs": frequencies for the whole (set of) table(s).

The type of colors to print, as a single string :

• "no": by default, no colors are printed.

• "diff": color percentages and means based on cells differences from totals (or from first cells when ref = "first").

• "OR": for pct == "col" or pct == "row", color based on odds ratios (or relative risks ratios)

With pct = "row" or pct = "col", calculate and print odds ratios (for binary variables) or relative risks ratios (for variables with 3 levels or more).

• "no": by default, no OR are calculated.

• "OR": print OR (instead of percentages).

• "OR_pct": print OR, with percentages in bracket.

The policy to adopt with missing values, as a single string.

• "keep": by default, NA's of row, col and tab variables are printed as explicit "NA" level.

• "drop": removes NA of row, col and tab variables.

The reference cell to calculate differences and ratios (used to print colors) :

• "auto": by default, cell difference from the corresponding total (rows or cols depending on pct = "row" or pct = "col") is used for diff ; cell ratio from the first line (or col) is use for OR (odds ratio/relative risks ratio).

• "tot": totals are always used.

• "first": calculate cell difference or ratio from the first cell of the row or column (useful to color temporal developments).

• n: when ref is an integer, the nth row (or column) is used for comparison.

• "regex": when ref is a string, it it used as a regular expression, to match with the names of the rows (or columns). Be precise enough to match only one column or row, otherwise you get a warning message.

• "no": not use ref and not calculate diffs to gain calculation time.

A second reference cell is needed to calculate odds ratios (or relative risks ratios). The first cell of the row or column is used by default. See ref above for the full list of possible values.

Comparison level. When tab_vars are present, should the contributions to variance be calculated for each subtable/group (by default, comp = "tab") ? Should they be calculated for the whole table (comp = "all") ? comp must be set once and for all the first time you use tab_plain, tab_num or tab_chi2 with rows, or tab_ci.

The total table, if there are subtables/groups (i.e. when tab_vars is provided) :

• "line": by default, add a general total line (necessary for calculations with comp = "all")

• "table": add a complete total table (i.e. row_var by col_vars without tab_vars).

• "no": not to draw any total table.

The name of the total table, as a single string.

The totals :

• c("col", "row") or "both" : by default, both total rows and total columns.

• "row": only total rows.

• "col": only total column.

• "no": remove all totals (after calculations if needed).

The names of the totals, as a character vector of length one or two. Use syntax of type c("Total row", "Total column") to set different names for rows and cols.

A character vector to print rows of legend under the table.

The number of digits to print, as a single integer.

Set to TRUE to obtain a table with normal numeric vectors (not fmt).

Set to TRUE to obtain a plain data.frame (not a tibble), with normal numeric vectors (not fmt). Useful, for example, to pass the table to correspondence analysis with FactoMineR.

A table made with tab or tab_many.

By default, a white table with black text, Set to "dark" for a black table with white text.

Set to "text" to color the text, "bg" to color the background. By default it takes getOption("tabxplor.color_style_type").

Use 24bits colors palettes for html tables : set to "green_red" or "blue_red". Only with mode = "color_code" (not mode = "crayon") and ⁠theme = "light⁠. Default to getOption("tabxplor.color_html_24_bit").

Print colors legend below the table ?

The table caption.

By default, rownames are wrapped when larger than 30 characters.

By default, colnames are wrapped when larger than 12 characters.

Set to FALSE to wrap also on non whitespace characters.

A dataframe.

Variables then to be passed in tab_plain.

<tidy-select> Removes all observation with a NA in any of the chosen variables.

Set to TRUE to clean levels names, by removing prefix numbers like "1-", and text in parentheses.

When set to a positive integer, levels with less count than it will be merged into an "Others" level.

The name of the "Other" level, as a character vector of length one.

A tabxplor_tab (with chi2 table as attribute).

A tibble of class tab, made with tab, tab_many or tab_plain.

<tidy-select> The tab variables to pass to column, with a syntax of type c(var1, var2, ...).

String added to the start of every variable name.

If no names_prefix is given, new names takes the form spread_var_col_var_level. Should then the column names be sorted ? If FALSE, the default, column names are ordered by first appearance.

The new name of the total rows, as a single string.

A tibble of class tab, made with tab_plain or tab_many.

c("col", "row") and "both" print total rows and total columns. Set to "row" or "col" to print only one type. Set to "no" to remove all totals.

The names of the totals, as a character vector of length one or two. Use c("Total_row", "Total_column") to set different names for rows and cols.

"last" only prints a total column for the last factor column variable. Set to "each" to print a total column for each column variable.

The original database used to calculate the tab : it is only useful for mean columns (of numeric variables), in order to calculate the variances of total rows, necessary to calculate confidence intervals with tab_ci.

A tibble of class tab, made with tab_plain or tab_many.

If there are subtables, corresponding to the levels of tab_vars, totaltab = "table" add a complete total table. totaltab = "line" add a total table of only one row with the general total. totaltab = "no" remove any existing total table.

The name of the total table, as a single string.

The original database used to calculate the tab : it is only useful for mean columns (of numeric variables), in order to calculate the variances necessary to calculate confidence intervals with tab_ci.

A tabxplor_tab or a tibble .

By default, rownames are wrapped when larger than 30 characters.

By default, colnames are wrapped when larger than 12 characters.

On the second lines or more, the number or characters to use for indentation.

Set to FALSE to wrap also on non whitespace characters.

Set to FALSE to keep normal spaces in text (auto-break).

The string to use for linebreak : ⁠\n⁠ in text, but ⁠<br>⁠ in html.

A table made with tab, tab_many or tab_plain, or a list of such tables.

The name, and possibly the path, of the Excel file to create (possibly without the .xlsx extension). Default path to temporary directory. Set global option "tabxplor.export_dir" with link[base:options]{options} to change default directory. By default replace is TRUE when path is provided, FALSE when path is not provided. Use replace = TRUE to overwrite existing files. Use open = FALSE if you don't want to automatically open the tables in Excel (or another software associated with .xlsx files).

Rotate the names of columns to an angle (in degrees).

By default, tab_vars columns are removed to gain space. Set to FALSE to keep them.

The standard width for numeric columns, as a number. Set to "auto" to let Excel choose.

Should the color legends be printed with the subtexts ?

The Excel sheets options :

• "tabs": a new sheet is created for each table

• "unique": all tables are on the same sheet

• "auto": subsequent tables with the same column vars are printed on the same sheets

The total count under which a column or row is turned pale grey because there is not enough observation for it to be significant. Default to 0 (not used).

The titles of the different tables, as a character vector. When missing titles are given based on the names of the variables.

Font for text and for numbers.

Font sizes of text elements.

By default all cells displayed as 0 (even rounded) turn pale grey, to make the distribution of empty cells (and other cells) more visible. Provide a number to turn grey every cell below it. Set to Inf not to use this feature.

By default, the text is colored. Set to "bg" to color the background instead.