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Estimation statistics for categorical comparisons on a phyloseq object

Source: R/estim_pq.R
estim_diff_pq.Rd

Computes diversity metrics (Hill numbers by default) per sample and compares them across groups defined by a categorical variable using estimation statistics (effect sizes + bootstrap confidence intervals) via the dabestr package.

This approach replaces traditional p-value-based hypothesis testing with Gardner-Altman or Cumming estimation plots, following the estimation statistics framework (Ho et al. 2019).

Usage

estim_diff_pq(
  physeq,
  fact,
  q = c(0, 1, 2),
  custom_fn = NULL,
  effect_type = "cohens_d",
  idx = NULL,
  ci = 95,
  resamples = 5000,
  na_remove = TRUE,
  ...
)

Arguments

physeq

(phyloseq, required) A phyloseq object.

fact

(character, required) The name of a categorical column in sample_data to use as the grouping factor.

q

(numeric vector, default c(0, 1, 2)) The q values for Hill number computation: 0 = richness, 1 = Shannon exponential, 2 = inverse Simpson.

custom_fn

(function, default NULL) An optional custom diversity function. Must take a phyloseq object and return a named numeric vector (names = sample names) or a data.frame with one row per sample. If provided, q is ignored.

effect_type

(character, default "mean_diff") The type of effect size to compute. One of: "mean_diff", "median_diff", "cohens_d", "hedges_g", "cliffs_delta".

idx

(list or character vector, default NULL) The group ordering for comparisons. If NULL, uses factor levels with first level as control. For 2 groups: c("Control", "Treatment"). For 3+ groups: list(c("Ctrl", "T1", "T2")).

ci

(numeric, default 95) Confidence interval level (0-100).

resamples

(integer, default 5000) Number of bootstrap resamples.

na_remove

(logical, default TRUE) If TRUE, samples with NA in fact are removed before analysis.

...

Additional arguments passed to dabestr plotting functions.

Value

A list of class "estim_diff_pq_result" with components:

data

The diversity data.frame used for analysis

dabest_objects

A named list of dabestr objects (one per metric)

plots

A named list of dabestr plots (one per metric)

summary

A tibble summarizing all effect sizes and CIs with columns: metric, comparison, effect_size, ci_lower, ci_upper, pvalue_permtest, pvalue_welch, pvalue_mann_whitney

effect_type

The effect size type used

Details

lifecycle-experimental

The function uses the dabestr package to produce estimation plots. For two groups, Gardner-Altman plots are produced (float_contrast = TRUE). For three or more groups, Cumming plots are used (float_contrast = FALSE).

References

Ho, J., Tumkaya, T., Aryal, S., Choi, H., & Claridge-Chang, A. (2019). Moving beyond P values: data analysis with estimation graphics. Nature Methods, 16(7), 565-566.

See also

estim_cor_pq(), estim_diff_lpq(), adonis_lpq()

Examples

library(phyloseq)
data("data_fungi", package = "MiscMetabar")

# Subset to the 80 most abundant taxa to keep the example fast
# (the full data_fungi has 1420 taxa, which is slow for DA methods).
data_fungi_small <- prune_taxa(
  names(sort(taxa_sums(data_fungi), decreasing = TRUE))[1:80],
  data_fungi
)
data_fungi_small <- clean_pq(prune_samples(
  sample_sums(data_fungi_small) >= 500, data_fungi_small
))

pq <- subset_samples(data_fungi_small, !is.na(Height))
pq <- clean_pq(pq)
#> Cleaning suppress 3 taxa and 0 samples.

res <- estim_diff_pq(pq, fact = "Height")
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#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
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#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> ! Function arguments cannot be checked because the package divent is not attached.
#> → Add `CheckArguments=FALSE` to suppress this warning or run `library('divent')`.
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_boot_ci()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_boot_ci()`).
#> Warning: Removed 2 rows containing missing values or values outside the scale range
#> (`geom_boot_ci()`).
res
#> Estimation statistics: categorical comparison
#> Effect size type: cohens_d 
#> Metrics: Hill_0, Hill_1, Hill_2 
#> Comparisons: 2 
#> 
#> # A tibble: 6 × 8
#>   metric comparison   effect_size ci_lower ci_upper pvalue_permtest pvalue_welch
#>   <chr>  <chr>              <dbl>    <dbl>    <dbl>           <dbl>        <dbl>
#> 1 Hill_0 High vs Low       0.205        NA       NA           0.462        0.466
#> 2 Hill_0 High vs Mid…      0.136        NA       NA           0.601        0.618
#> 3 Hill_1 High vs Low      -0.315        NA       NA           0.25         0.247
#> 4 Hill_1 High vs Mid…      0.0312       NA       NA           0.905        0.908
#> 5 Hill_2 High vs Low      -0.306        NA       NA           0.263        0.261
#> 6 Hill_2 High vs Mid…      0.0837       NA       NA           0.747        0.757
#> # ℹ 1 more variable: pvalue_mann_whitney <dbl>
#> 
#> Note: P-values (permutation test, Welch t-test, Mann-Whitney U) are provided
#> for legacy purposes only. Focus on the effect size and its confidence interval
#> for interpretation. See Ho et al. (2019) Nature Methods 16:565-566.
res$plots$Hill_0

res$summary
#> # A tibble: 6 × 8
#>   metric comparison   effect_size ci_lower ci_upper pvalue_permtest pvalue_welch
#>   <chr>  <chr>              <dbl>    <dbl>    <dbl>           <dbl>        <dbl>
#> 1 Hill_0 High vs Low       0.205        NA       NA           0.462        0.466
#> 2 Hill_0 High vs Mid…      0.136        NA       NA           0.601        0.618
#> 3 Hill_1 High vs Low      -0.315        NA       NA           0.25         0.247
#> 4 Hill_1 High vs Mid…      0.0312       NA       NA           0.905        0.908
#> 5 Hill_2 High vs Low      -0.306        NA       NA           0.263        0.261
#> 6 Hill_2 High vs Mid…      0.0837       NA       NA           0.747        0.757
#> # ℹ 1 more variable: pvalue_mann_whitney <dbl>