tabxplor

R-CMD-check

If R makes complex things simple, it can sometimes make simple things difficult. This is why tabxplor tries to make it easy to deal with multiple cross-tables: to create and manipulate them, but also to read them, using color helpers to highlight important informations. It would love to enhance your data exploration experience with simple yet powerful tools. All functions are propelled by tidyverse, pipe-friendly, and render tibble data frames which can be easily manipulated with dplyr. Tables can be exported to Excel and in html with formats and colors.

Installation

You can install tabxplor from CRAN with:

install.packages("tabxplor")

Or from github with :

# install.packages(devtools)
devtools::install_github("BriceNocenti/tabxplor")

Base usage: cross-tables with color helpers

The main functions are made to be user-friendly and time-saving is data analysis workflows.

tab makes a simple cross-table:

library(tabxplor)
tab(forcats::gss_cat, marital, race)
#> # A tabxplor tab: 7 x 5
#>   marital       Other Black  White  Total
#>   <fct>           <n>   <n>    <n>    <n>
#> 1 No answer         2     2     13     17
#> 2 Never married   633 1 305  3 478  5 416
#> 3 Separated       110   196    437    743
#> 4 Divorced        212   495  2 676  3 383
#> 5 Widowed          70   262  1 475  1 807
#> 6 Married         932   869  8 316 10 117
#> 7 Total         1 959 3 129 16 395 21 483

When one of the row or column variables is numeric, tab calculates means by category of the other variable.

tab comes with options to weight the table, print percentages, manage totals, digits and missing values, add legends, gather rare categories in a “Others” level.

tab(forcats::gss_cat, marital, race, pct = "row", na = "drop", subtext = gss,
rare_to_other = TRUE, n_min = 1000, other_level = "Custom_other_level_name")

When a third variable is provided, tab makes a table with as many subtables as it has levels. With several tab_vars, it makes a subtable for each combination of their levels. The result is grouped: in dplyr, operations like sum() or all() are done within each subtable, and not for the whole dataframe.

Colors may be added to highlight over-represented and under-represented cells, and therefore help the user read the table. By default, with color = "diff", colors are based on the differences between a cell and it’s related total (which only works with means and row or col pct). When a percentage is superior to the average percentage of the line or column, it appears with shades of green (or blue). When it’s inferior, it appears with shades of red/orange. A color legend is added below the table. In RStudio colors are adapted to the theme, light or dark.

data <- forcats::gss_cat %>% 
  dplyr::filter(year %in% c(2000, 2006, 2012), !marital %in% c("No answer", "Widowed"))
gss  <- "Source: General social survey 2000-2014"
gss2 <- "Source: General social survey 2000, 2006 and 2012"
tab(data, race, marital, year, subtext = gss2, pct = "row", color = "diff")

The sup_cols argument adds supplementary column variables to the table. With numeric variables, it calculates the mean for each category or the row variable. With text variables, only the first level is kept (you can choose which one to use by placing it first with forcats::fct_relevel). Use tab_many to keep all levels.

tab(dplyr::storms, category, status, sup_cols = c("pressure", "wind"))
#> # A tabxplor tab: 8 x 7
#>   category `tropical depressi~ `tropical storm` hurricane   Total pressure  wind
#>   <fct>              <n-mixed>        <n-mixed> <n-mixed> <n-mix>   <mean> <mea>
#> 1 -1                     2 545                0         0   2 545    1 008    27
#> 2 0                          0            4 373         0   4 373      999    46
#> 3 1                          0                1     1 684   1 685      982    71
#> 4 2                          0                0       628     628      967    89
#> 5 3                          0                0       363     363      954   105
#> 6 4                          0                0       348     348      940   122
#> 7 5                          0                0        68      68      916   145
#> 8 Total                  2 545            4 374     3 091     100      992    53

References and comparison levels for colors

By default, to calculate colors, each cell is compared to the subtable’s related total.

When a third variable or more are provided, it’s possible to compare with the general total line instead, by setting comp = "all". Here, only the last total row is highlighted (TOTAL ENSEMBLE appears in white but other total rows in grey).

tab(data, race, marital, year, subtext = gss2, pct = "row", color = "diff", comp = "all")

With diff = "first", each row (or column) is compared to the first row (or column), which is particularly helpful to highlight historical evolutions. The first rows then appears in white (while totals are themselves colored like normal lines).

data <- data %>% dplyr::mutate(year = as.factor(year))
tab(data, year, marital, race, pct = "row", color = "diff", diff = "first", tot = "col",
    totaltab = "table")

Confidence intervals

It it possible to print confidence intervals for each cell:

tab(forcats::gss_cat, race, marital, pct = "row", ci = "cell")
#> # A tabxplor tab: 4 x 8
#>   race   `No answer` `Never married` Separated Divorced Widowed Married  Total
#>   <fct>       <row%>          <row%>    <row%>   <row%>  <row%>  <row%> <row%>
#> 1 Other       0%±0.3         32%±2.1    6%±1.1  11%±1.5  4%±0.9 48%±2.2   100%
#> 2 Black       0%±0.2         42%±1.7    6%±0.9  16%±1.3  8%±1.0 28%±1.6   100%
#> 3 White       0%±0.1         21%±0.6    3%±0.3  16%±0.6  9%±0.4 51%±0.8   100%
#> 4 Total       0%             25%        3%      16%      8%     47%       100%

It is also possible to use confidence intervals to enhance colors helpers. With color = "diff_ci", the cells are only colored if the confidence interval of the difference between them and their reference cell (in total or first row/col) is superior to the difference itself. Otherwise, it means the cell is not significantly different from it’s reference in the total (or first) row: it turns grey, and the reader is not anymore tempted to over-interpret the difference.

tab(forcats::gss_cat, race, marital, pct = "row", color = "diff_ci")

Finally, another calculation appears helpful: the difference between the cell and the total, minus the confidence interval of this difference (or in other word, what remains of that difference after having subtracted the confidence interval). ci = "after_ci" highligths all the cells whose value is significantly different from the relative total (or first cell). This is particularly useful when working on small populations: we can see at a glance which numbers we have right to read and interpret.

tab(forcats::gss_cat, race, marital, subtext = gss, pct = "row", color = "after_ci")

Chi2 stats and contributions of cells to variance

chi2 = TRUE add summary statistics made in the chi2 metric: degrees of freedom (df), unweighted count, pvalue and (sub)table’s variance. Chi2 pvalue is colored in green when inferior to 5%, and in red when superior or equal to 5%, meaning that the table is not significantly different from the independent hypothesis (the two variables may be independent).

tab(forcats::gss_cat, race, marital, chi2 = TRUE)
#> chi2 stats     marital
#> df                  12
#> variance        0.0464
#> pvalue              0%
#> count           21 483
#> 
#> # A tabxplor tab: 4 x 8
#>   race   `No answer` `Never married` Separated Divorced Widowed Married  Total
#>   <fct>          <n>             <n>       <n>      <n>     <n>     <n>    <n>
#> 1 Other            2             633       110      212      70     932  1 959
#> 2 Black            2           1 305       196      495     262     869  3 129
#> 3 White           13           3 478       437    2 676   1 475   8 316 16 395
#> 4 Total           17           5 416       743    3 383   1 807  10 117 21 483

Chi2 stats can also be used to color cells based on their contributions to the variance of the (sub)table, with color = "contrib". By default, only the cells whose contribution is superior to the mean contribution are colored. It highlights the cells which would stand out in a correspondence analysis (the two related categories would be located at the edges of the first axes ; here, being black is associated with never married and being separated).

tab(forcats::gss_cat, race, marital, color = "contrib")

Combine tabxplor and dplyr

The result of tab is a tibble::tibble data frame with class tab. It gets it’s own printing methods but, in the same time, can be transformed using most dplyr verbs, like a normal tibble.

library(dplyr)
tab(storms, category, status, sup_cols = c("pressure", "wind")) %>%
  filter(category != "-1") %>%
dplyr::select(-`tropical depression`)
  arrange(is_totrow(.), desc(category)) # use is_totrow to keep total rows

With dplyr::arrange, don’t forget to keep the order of tab variables and total rows:

tab(data, race, marital, year, pct = "row") %>%
  arrange(year, is_totrow(.), desc(Married))

Draw more complex tables with tab_many

tab is a wrapper around the more powerful function tab_many, which can be used to customize your tables.

It’s possible, for example, to make a summary table of as many columns variables as you want (showing all levels, or showing only one specific level like here):

first_lvs <- c("Married", "$25000 or more", "Strong republican", "Protestant")
data <- forcats::gss_cat %>% mutate(across(
  where(is.factor),
  ~ forcats::fct_relevel(., first_lvs[first_lvs %in% levels(.)])
))
tab_many(data, race, c(marital, rincome, partyid, relig, age, tvhours),
         levels = "first", pct = "row", chi2 = TRUE, color = "auto")

Using tab or tab_many with purrr::map and tibble::tribble, you can program several tables with different parameters all at once, in a readable way:

tabs <-
  purrr::pmap(
    tibble::tribble(
      ~row_var, ~col_vars       , ~pct , ~filter              , ~subtext               ,
      "race"  , "marital"       , "no" , NULL                 , "Source: GSS 2000-2014",
      "race"  , "marital"       , "row", NULL                 , "Source: GSS 2000-2014",
      "race"  , "marital"       , "col", NULL                 , "Source: GSS 2000-2014",
      "relig" , c("race", "age"), "row", "year %in% 2000:2010", "Source: GSS 2000-2010",
      "relig" , c("race", "age"), "row", "year %in% 2010:2014", "Source: GSS 2010-2014",
      NA_character_, "race"     , "no" , NULL                 , "Source: GSS 2000-2014",
    ),
    .f = tab_many,
    data = forcats::gss_cat, color = "auto", chi2 = TRUE)

Export to html or Excel

To export a table to html with colors, tabxplor uses knitr::kable and kableExtra. In this format differences from totals, confidence intervals, contribution to variance, and unweighted counts, are available in a tooltip at cells hover.

tabs <- tab(forcats::gss_cat, race, marital, subtext = "Source: GSS 2000-2014", 
            pct = "row", color = "diff")
tabs %>% tab_kable()

To print an html table by default (for example, in RStudio viewer), use tabxplor options:

options(tabxplor.print = "kable") # default to options(tabxplor.print = "console")

tab_xl exports any table or list of tables to Excel, with all colors, chi2 stats and formatting. On Excel, it is still possible to do calculations on raw numbers.

tabs %>% tab_xl(replace = TRUE, sheets = "unique")

Programming with tabxplor

When not doing data analysis but writing functions, you can use the sub-functions of tab_many step by step to attain more flexibility or speed. That way, it’s possible to write new functions to customize your tables even more.

data <- dplyr::starwars %>%
  tab_prepare(sex, hair_color, gender, rare_to_other = TRUE,
              n_min = 5, na = "keep")

data %>%
  tab_plain(sex, hair_color, gender) %>%
  tab_totaltab("line")  %>%
  tab_tot()  %>%
  tab_pct(comp = "all")  %>%
  tab_ci("diff", color = "after_ci")  %>%
  tab_chi2(calc = "p")

The whole architecture of tabxplor is powered by a special vector class, named fmt for formatted numbers. As a vctrs::record, it stores behind the scenes all the data necessary to calculate printed results, formats and colors. A set of functions are available to access or transform this data, like is_totrow, is_totcol or is_tottab. ?fmt to get more information.

The simple way to recover the underlying numbers as numeric vectors is get_num:

tab(data, race, marital, year, pct = "row") %>%
  mutate(across(where(is_fmt), get_num))

To render character vectors (without colors), use format:

tab(data, race, marital, year, pct = "row") %>%
  mutate(across(where(is_fmt), format))

For the simplest table, with only numeric counts (no fmt), or even as normal data.frame (not a tibble):

# combine with `tab_prepare` to handle missing values
tab_plain(data, race, marital, num = TRUE) # counts as numeric vector
tab_plain(data, race, marital, df = TRUE)  # same, with unique class = "data.frame"