# Getting started with spicy

    library(spicy)

spicy is an R package for descriptive statistics and data analysis, designed for data science and survey research workflows. It covers variable inspection, frequency tables, cross-tabulations with chi-squared tests and effect sizes, and publication-ready summary tables, offering functionality similar to Stata or SPSS but within a tidyverse-friendly R environment. This vignette walks through the core workflow using the bundled `sochealth` dataset, a simulated social-health survey with 1200 respondents and 24 variables.

## Inspect your data

`varlist()` (or its shortcut `vl()`) gives a compact overview of every variable in a data frame: name, label, representative values, class, number of distinct values, valid observations, and missing values. In RStudio or Positron, calling `varlist()` without arguments opens an interactive viewer - this is the most common usage in practice. Here we use `tbl = TRUE` to produce static output for the vignette:

    varlist(sochealth, tbl = TRUE)
    #> # A tibble: 24 × 7
    #>    Variable          Label                 Values Class N_distinct N_valid   NAs
    #>    <chr>             <chr>                 <chr>  <chr>      <int>   <int> <int>
    #>  1 sex               Sex                   Femal… fact…          2    1200     0
    #>  2 age               Age (years)           25, 2… nume…         51    1200     0
    #>  3 age_group         Age group             25-34… orde…          4    1200     0
    #>  4 education         Highest education le… Lower… orde…          3    1200     0
    #>  5 social_class      Subjective social cl… Lower… orde…          5    1200     0
    #>  6 region            Region of residence   Centr… fact…          6    1200     0
    #>  7 employment_status Employment status     Emplo… fact…          4    1200     0
    #>  8 income_group      Household income gro… Low, … orde…          4    1182    18
    #>  9 income            Monthly household in… 1000,… nume…       1052    1200     0
    #> 10 smoking           Current smoker        No, Y… fact…          2    1175    25
    #> # ℹ 14 more rows

You can also select specific columns with tidyselect syntax:

    varlist(sochealth, starts_with("bmi"), income, weight, tbl = TRUE)
    #> # A tibble: 4 × 7
    #>   Variable     Label                       Values Class N_distinct N_valid   NAs
    #>   <chr>        <chr>                       <chr>  <chr>      <int>   <int> <int>
    #> 1 bmi          Body mass index             16, 1… nume…        177    1188    12
    #> 2 bmi_category BMI category                Norma… orde…          3    1188    12
    #> 3 income       Monthly household income (… 1000,… nume…       1052    1200     0
    #> 4 weight       Survey design weight        0.294… nume…        794    1200     0

## Frequency tables

`freq()` produces frequency tables with counts, percentages, and (optionally) valid and cumulative percentages.

    freq(sochealth, education)
    #> Frequency table: education
    #>
    #>  Category │ Values           Freq.  Percent
    #> ──────────┼─────────────────────────────────
    #>  Valid    │ Lower secondary    261     21.8
    #>           │ Upper secondary    539     44.9
    #>           │ Tertiary           400     33.3
    #> ──────────┼─────────────────────────────────
    #>  Total    │                   1200    100.0
    #>
    #> Label: Highest education level
    #> Class: ordered, factor
    #> Data: sochealth

Weighted frequencies use the `weights` argument. With `rescale = TRUE`, the total weighted N matches the unweighted N:

    freq(sochealth, education, weights = weight, rescale = TRUE)
    #> Frequency table: education
    #>
    #>  Category │ Values            Freq.  Percent
    #> ──────────┼──────────────────────────────────
    #>  Valid    │ Lower secondary  258.62     21.6
    #>           │ Upper secondary  546.40     45.5
    #>           │ Tertiary         394.99     32.9
    #> ──────────┼──────────────────────────────────
    #>  Total    │                    1200    100.0
    #>
    #> Label: Highest education level
    #> Class: ordered, factor
    #> Data: sochealth
    #> Weight: weight (rescaled)

## Cross-tabulations

`cross_tab()` crosses two categorical variables. By default it shows counts, a chi-squared test, and Cramer’s V:

    cross_tab(sochealth, smoking, education)
    #> Crosstable: smoking x education (N)
    #>
    #>  Values      │      Lower secondary       Upper secondary       Tertiary
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  No          │                  179                   415            332
    #>  Yes         │                   78                   112             59
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  Total       │                  257                   527            391
    #>
    #>  Values      │      Total
    #> ─────────────┼────────────
    #>  No          │        926
    #>  Yes         │        249
    #> ─────────────┼────────────
    #>  Total       │       1175
    #>
    #> Chi-2(2) = 21.6, p < 0.001
    #> Cramer's V = 0.14

Add percentages with `percent`:

    cross_tab(sochealth, smoking, education, percent = "col")
    #> Crosstable: smoking x education (Column %)
    #>
    #>  Values      │      Lower secondary       Upper secondary       Tertiary
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  No          │                 69.6                  78.7           84.9
    #>  Yes         │                 30.4                  21.3           15.1
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  Total       │                100.0                 100.0          100.0
    #>  N           │                  257                   527            391
    #>
    #>  Values      │      Total
    #> ─────────────┼────────────
    #>  No          │       78.8
    #>  Yes         │       21.2
    #> ─────────────┼────────────
    #>  Total       │      100.0
    #>  N           │       1175
    #>
    #> Chi-2(2) = 21.6, p < 0.001
    #> Cramer's V = 0.14

Group by a third variable with `by`:

    cross_tab(sochealth, smoking, education, by = sex)
    #> Crosstable: smoking x education (N) | sex = Female
    #>
    #>  Values      │      Lower secondary       Upper secondary       Tertiary
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  No          │                   95                   220            160
    #>  Yes         │                   38                    62             31
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  Total       │                  133                   282            191
    #>
    #>  Values      │      Total
    #> ─────────────┼────────────
    #>  No          │        475
    #>  Yes         │        131
    #> ─────────────┼────────────
    #>  Total       │        606
    #>
    #> Chi-2(2) = 7.1, p = 0.029
    #> Cramer's V = 0.11
    #>
    #> Crosstable: smoking x education (N) | sex = Male
    #>
    #>  Values      │      Lower secondary       Upper secondary       Tertiary
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  No          │                   84                   195            172
    #>  Yes         │                   40                    50             28
    #> ─────────────┼───────────────────────────────────────────────────────────
    #>  Total       │                  124                   245            200
    #>
    #>  Values      │      Total
    #> ─────────────┼────────────
    #>  No          │        451
    #>  Yes         │        118
    #> ─────────────┼────────────
    #>  Total       │        569
    #>
    #> Chi-2(2) = 15.6, p < 0.001
    #> Cramer's V = 0.17

When both variables are ordered factors, `cross_tab()` automatically selects an ordinal measure (Kendall’s Tau-b) instead of Cramer’s V:

    cross_tab(sochealth, self_rated_health, education)
    #> Crosstable: self_rated_health x education (N)
    #>
    #>  Values         │      Lower secondary       Upper secondary       Tertiary
    #> ────────────────┼───────────────────────────────────────────────────────────
    #>  Poor           │                   28                    28              5
    #>  Fair           │                   86                   118             62
    #>  Good           │                  102                   263            193
    #>  Very good      │                   44                   118            133
    #> ────────────────┼───────────────────────────────────────────────────────────
    #>  Total          │                  260                   527            393
    #>
    #>  Values         │      Total
    #> ────────────────┼────────────
    #>  Poor           │         61
    #>  Fair           │        266
    #>  Good           │        558
    #>  Very good      │        295
    #> ────────────────┼────────────
    #>  Total          │       1180
    #>
    #> Chi-2(6) = 73.2, p < 0.001
    #> Kendall's Tau-b = 0.20

## Association measures

For a quick overview of all available association statistics, pass a contingency table to `assoc_measures()`:

    tbl <- xtabs(~ smoking + education, data = sochealth)
    assoc_measures(tbl)
    #> Measure                            Estimate     SE  CI lower  CI upper        p
    #> Cramer's V                            0.136     --     0.079     0.191  < 0.001
    #> Contingency Coefficient               0.134     --        --        --  < 0.001
    #> Lambda symmetric                      0.000  0.000     0.000     0.000       --
    #> Lambda R|C                            0.000  0.000     0.000     0.000       --
    #> Lambda C|R                            0.000  0.000     0.000     0.000       --
    #> Goodman-Kruskal's Tau R|C             0.018  0.008     0.003     0.034    0.023
    #> Goodman-Kruskal's Tau C|R             0.008  0.003     0.001     0.014    0.022
    #> Uncertainty Coefficient symmetric     0.011  0.005     0.002     0.021    0.021
    #> Uncertainty Coefficient R|C           0.018  0.008     0.003     0.032    0.021
    #> Uncertainty Coefficient C|R           0.009  0.004     0.001     0.016    0.021
    #> Goodman-Kruskal Gamma                -0.268  0.056    -0.378    -0.158  < 0.001
    #> Kendall's Tau-b                      -0.126  0.027    -0.180    -0.073  < 0.001
    #> Kendall's Tau-c                      -0.117  0.026    -0.167    -0.067  < 0.001
    #> Somers' D R|C                        -0.091  0.020    -0.131    -0.052  < 0.001
    #> Somers' D C|R                        -0.175  0.038    -0.249    -0.101  < 0.001

Individual functions such as `cramer_v()`, `gamma_gk()`, or `kendall_tau_b()` return a scalar by default. Pass `detail = TRUE` for the confidence interval and p-value:

    cramer_v(tbl, detail = TRUE)
    #> Estimate  CI lower  CI upper        p
    #>    0.136     0.079     0.191  < 0.001

## Summary tables

`table_categorical()` covers grouped or one-way summary tables for categorical variables:

    table_categorical(
      sochealth,
      select = c(smoking, physical_activity, dentist_12m),
      by = education,
      output = "tinytable"
    )

`table_continuous()` summarizes continuous variables, either overall or by a categorical `by` variable, and can also add group-comparison tests:

    table_continuous(
      sochealth,
      select = c(bmi, life_sat_health),
      by = education
    )
    #> Descriptive statistics
    #>
    #>  Variable                       │ Group              M     SD    Min    Max
    #> ────────────────────────────────┼────────────────────────────────────────────
    #>  Body mass index                │ Lower secondary  28.09  3.47  18.20  38.90
    #>                                 │ Upper secondary  26.02  3.43  16.00  37.10
    #>                                 │ Tertiary         24.39  3.52  16.00  33.00
    #> ╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌
    #>  Satisfaction with health (1-5) │ Lower secondary  2.71   1.20  1.00   5.00
    #>                                 │ Upper secondary  3.53   1.19  1.00   5.00
    #>                                 │ Tertiary         4.11   1.04  1.00   5.00
    #>
    #>  Variable                       │ Group            95% CI LL  95% CI UL    n
    #> ────────────────────────────────┼────────────────────────────────────────────
    #>  Body mass index                │ Lower secondary    27.66      28.51    260
    #>                                 │ Upper secondary    25.73      26.31    534
    #>                                 │ Tertiary           24.04      24.74    394
    #> ╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌
    #>  Satisfaction with health (1-5) │ Lower secondary    2.57       2.86     259
    #>                                 │ Upper secondary    3.43       3.63     534
    #>                                 │ Tertiary           4.01       4.21     399

`table_continuous_lm()` covers the same reporting territory when you want to stay in a linear-model framework, for example with robust standard errors or case weights:

    table_continuous_lm(
      sochealth,
      select = c(wellbeing_score, bmi),
      by = sex,
      vcov = "HC3"
    )
    #> Continuous outcomes by Sex
    #>
    #>  Variable                      │ M (Female)  M (Male)  Δ (Male - Female)
    #> ───────────────────────────────┼─────────────────────────────────────────
    #>  WHO-5 wellbeing index (0-100) │   67.16      71.05          3.89
    #>  Body mass index               │   25.69      26.20          0.51
    #>
    #>  Variable                      │ 95% CI LL  95% CI UL      p   R²      n
    #> ───────────────────────────────┼─────────────────────────────────────────
    #>  WHO-5 wellbeing index (0-100) │   2.12       5.65     <.001  0.02  1200
    #>  Body mass index               │   0.09       0.93      .018  0.00  1188

For detailed guidance, see the dedicated articles on `table_categorical()`, `table_continuous()`, `table_continuous_lm()`, and the final reporting overview for APA-style summary tables.

## Row-wise summaries

`mean_n()`, `sum_n()`, and `count_n()` compute row-wise statistics across selected columns, with automatic handling of missing values.

    sochealth |>
      dplyr::mutate(
        mean_sat  = mean_n(select = starts_with("life_sat")),
        sum_sat   = sum_n(select = starts_with("life_sat"), min_valid = 2),
        n_missing = count_n(select = starts_with("life_sat"), special = "NA")
      ) |>
      dplyr::select(starts_with("life_sat"), mean_sat, sum_sat, n_missing) |>
      head() |>
      as.data.frame()
    #>   life_sat_health life_sat_work life_sat_relationships life_sat_standard
    #> 1               5             3                      5                 5
    #> 2               4             4                      5                 5
    #> 3               3             2                      5                 3
    #> 4               3             4                      3                 2
    #> 5               4             5                      4                 4
    #> 6               5             5                      5                 3
    #>   mean_sat sum_sat n_missing
    #> 1     4.50      18         0
    #> 2     4.50      18         0
    #> 3     3.25      13         0
    #> 4     3.00      12         0
    #> 5     4.25      17         0
    #> 6     4.50      18         0

## Learn more

- See `?varlist` to inspect variables, labels, values, and missing data.
- See `?cross_tab` for the full list of arguments (weights, simulation, association measures).
- See `?table_categorical` for grouped or one-way categorical tables.
- See `?table_continuous` for continuous summaries and group comparisons.
- See `?table_continuous_lm` for model-based mean-comparison tables with robust standard errors or case weights.
- See `?assoc_measures` for the complete list of association statistics.
- See `?code_book` to generate an interactive HTML codebook.