dCSTs for Vaginal Microbiome Data

Introduction

Community state types (CSTs) are the standard way to describe the structure of vaginal microbial communities. They were originally defined by hierarchical clustering of 16S rRNA data (Ravel et al. 2011) and later standardized by the VALENCIA nearest-centroid classifier (France et al. 2020).

Dominant Community State Types (dCSTs) group samples by their largest features and retain groups meeting a sample-support threshold. Fitting uses abundances rather than supplied CST labels; the retained states still depend on the fitting sample set. L-infinity normalization divides positive rows by their maximum at default tolerance, preserving their within-row rankings.

This vignette compares dCSTs with supplied Valencia labels on source training samples. It is a descriptive comparison, not held-out validation. See the function guide for fitting versus frozen transfer and the dataset guide for provenance and alignment.

Reference: Gajer, P. & Ravel, J. (2025). A New Approach to Compositional Data Analysis using \(L^\infty\)-normalization with Applications to Vaginal Microbiome. arXiv:2503.21543.

The Valencia 2k dataset

The valencia2k dataset is a stratified subsample of 2,000 vaginal samples from the Valencia CST-classifier training set (France et al. 2020). It contains species-level relative abundances for 178 taxa along with the original Valencia CST and sub-CST assignments.

data(valencia2k)

## Compositional matrix: 2000 samples x 178 taxa
dim(valencia2k$rel)
#> [1] 2000  178

## Valencia CST assignments
table(valencia2k$cst$Val_CST)
#> 
#>    I   II  III IV-A IV-B IV-C    V 
#>  557   69  582  141  454  117   80

## Top 10 most abundant taxa (by mean relative abundance)
means <- sort(colMeans(valencia2k$rel), decreasing = TRUE)
head(round(means, 4), 10)
#>     Lactobacillus_iners Lactobacillus_crispatus   Gardnerella_vaginalis 
#>                  0.2609                  0.2539                  0.1203 
#>  Lactobacillus_jensenii       Atopobium_vaginae                   BVAB1 
#>                  0.0418                  0.0370                  0.0297 
#>   Lactobacillus_gasseri   Sneathia_sanguinegens         g_Streptococcus 
#>                  0.0283                  0.0198                  0.0194 
#>           g_Megasphaera 
#>                  0.0158

The dominant taxa are familiar vaginal species: Lactobacillus iners, L. crispatus, Gardnerella vaginalis, and others. This is exactly the kind of data where dominant-feature assignments are most intuitive: most samples are dominated by a single species, and the identity of that species is biologically meaningful.

Reconstructing counts

The bundled matrix is compositional (rows sum to 1). For workflows that require count-like input (e.g., filter.asv()), we can reconstruct approximate counts using the per-sample read depths. These reconstructed and rounded values are not original observed counts:

count_mat <- sweep(valencia2k$rel, 1, valencia2k$reads, "*")
count_mat <- round(count_mat)
storage.mode(count_mat) <- "integer"

## Check: library sizes
summary(rowSums(count_mat))
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#>    3026   22281   47958   57111   74849  409411

The bundled Valencia matrix was already filtered upstream. The subset-building script takes that prepared matrix as input; we skip filter.asv() here and work directly with the compositional matrix.

\(L^\infty\) normalization

\(L^\infty\)-normalization divides each row by its maximum value. After normalization at default tolerance, every positive row has at least one coordinate equal to 1. Exact-zero rows remain zero, and rows at or below a positive tol remain unchanged. All rows in this example are positive.

Z <- normalize.linf(valencia2k$rel)

## Every row max should be 1
summary(apply(Z, 1, max))
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#>       1       1       1       1       1       1

Dominance sample sets: dominant species assignment

The dominant species is the column that achieves the maximum in each row. Samples with the same dominant species form a depth-1 dominance sample set. With the default first-column tie rule, dominant-feature assignment is deterministic and sample-independent: it depends only on the sample’s own abundance profile, never on other samples.

dominant.features <- linf.dominant.features(Z)

## How many distinct dominant taxa?
cat("Distinct dominant taxa:", length(dominant.features$observed.levels), "\n")
#> Distinct dominant taxa: 35

## Dominance sample-set size distribution (top 15)
dominance_tab <- sort(table(dominant.features$label), decreasing = TRUE)
head(dominance_tab, 15)
#> 
#>     Lactobacillus_iners Lactobacillus_crispatus   Gardnerella_vaginalis 
#>                     606                     564                     360 
#>                   BVAB1  Lactobacillus_jensenii   Lactobacillus_gasseri 
#>                      91                      67                      62 
#>       Atopobium_vaginae   Sneathia_sanguinegens         g_Streptococcus 
#>                      51                      40                      36 
#>       g_Bifidobacterium          g_Anaerococcus          g_Enterococcus 
#>                      26                      14                      13 
#>     g_Corynebacterium_1                BVAB_TM7        g_Staphylococcus 
#>                      11                       8                       7

We see the expected vaginal community structure: a few well-supported dominance sample sets (the Lactobacillus species, Gardnerella, BVAB1) and a long tail of rarer dominant taxa.

Depth-1 dCSTs

In practice, many provisional dominance sample sets contain very few samples. Dominant Community State Types (dCSTs) retain states at or above a minimum support threshold (\(n_0\)) and handle samples from low-support sets according to the selected policy.

The package supports two policies for handling low-support provisional sets:

“pure”: named dCSTs stay pure, and samples from low-support sets are labeled RARE_DOMINANT
“absorb”: samples from low-support sets are reassigned to a retained state by restricted argmax

dcst1 <- linf.csts(Z, n0 = 30, low.freq.policy = "pure")

## Retained depth-1 states
dcst1$retained.feature.labels
#> [1] "Lactobacillus_iners"     "Lactobacillus_crispatus"
#> [3] "Gardnerella_vaginalis"   "BVAB1"                  
#> [5] "Lactobacillus_jensenii"  "Lactobacillus_gasseri"  
#> [7] "Atopobium_vaginae"       "Sneathia_sanguinegens"  
#> [9] "g_Streptococcus"

## dCST assignment (pure policy)
dcst1_tab <- sort(table(dcst1$lineage.label), decreasing = TRUE)
dcst1_tab
#> 
#>     Lactobacillus_iners Lactobacillus_crispatus   Gardnerella_vaginalis 
#>                     606                     564                     360 
#>           RARE_DOMINANT                   BVAB1  Lactobacillus_jensenii 
#>                     123                      91                      67 
#>   Lactobacillus_gasseri       Atopobium_vaginae   Sneathia_sanguinegens 
#>                      62                      51                      40 
#>         g_Streptococcus 
#>                      36

Concordance with Valencia CSTs

The following cross-tabulation describes all 2,000 bundled rows, which were subsampled from the Valencia classifier training source. The dCST hierarchy was fitted on those same rows, without using their supplied CST labels. This overlap precludes interpreting agreement as held-out validation:

## Build concordance table: rows = dCSTs, columns = Valencia CSTs
dcst_labels <- dcst1$lineage.label.absorb  # use absorb view for clean comparison
metadata.order <- match(rownames(Z), valencia2k$cst$sample_id)
stopifnot(!anyNA(metadata.order), !anyDuplicated(valencia2k$cst$sample_id))
val_cst     <- valencia2k$cst$Val_CST[metadata.order]

concordance <- table(dCST = dcst_labels, Valencia = val_cst)

## Show as percentage: what fraction of each dCST falls in each Valencia CST?
pct <- round(100 * prop.table(concordance, margin = 1), 1)
pct
#>                          Valencia
#> dCST                          I    II   III  IV-A  IV-B  IV-C     V
#>   Atopobium_vaginae         0.0   0.0   0.0   4.9  88.5   3.3   3.3
#>   BVAB1                     0.0   0.0   0.0 100.0   0.0   0.0   0.0
#>   g_Streptococcus           0.0   0.0   0.0   0.0   0.0 100.0   0.0
#>   Gardnerella_vaginalis     0.0   1.3   0.3   8.2  86.9   3.3   0.0
#>   Lactobacillus_crispatus  95.9   0.0   1.0   0.2   0.0   2.9   0.0
#>   Lactobacillus_gasseri     0.0  98.4   0.0   0.0   0.0   1.6   0.0
#>   Lactobacillus_iners       0.0   0.2  91.4   0.6   4.0   2.1   1.8
#>   Lactobacillus_jensenii    0.0   0.0   0.0   0.0   0.0   4.3  95.7
#>   Sneathia_sanguinegens     0.0   0.0   2.3  13.6  81.8   2.3   0.0

Several dCSTs map predominantly to a single supplied Valencia CST in this source subset:

Lactobacillus crispatus dCST \(\to\) CST I (dominated by L. crispatus)
Lactobacillus iners dCST \(\to\) CST III (dominated by L. iners)
Gardnerella vaginalis dCST \(\to\) CST IV-B
BVAB1 dCST \(\to\) CST IV-A
Lactobacillus gasseri dCST \(\to\) CST II
Lactobacillus jensenii dCST \(\to\) CST V

## Reverse view: what fraction of each Valencia CST falls in each dCST?
pct_rev <- round(100 * prop.table(concordance, margin = 2), 1)
pct_rev
#>                          Valencia
#> dCST                          I    II   III  IV-A  IV-B  IV-C     V
#>   Atopobium_vaginae         0.0   0.0   0.0   2.1  11.9   1.7   2.5
#>   BVAB1                     0.0   0.0   0.0  67.4   0.0   0.0   0.0
#>   g_Streptococcus           0.0   0.0   0.0   0.0   0.0  57.3   0.0
#>   Gardnerella_vaginalis     0.0   7.2   0.2  22.7  74.7  11.1   0.0
#>   Lactobacillus_crispatus 100.0   0.0   1.0   0.7   0.0  14.5   0.0
#>   Lactobacillus_gasseri     0.0  91.3   0.0   0.0   0.0   0.9   0.0
#>   Lactobacillus_iners       0.0   1.4  98.6   2.8   5.5  11.1  13.8
#>   Lactobacillus_jensenii    0.0   0.0   0.0   0.0   0.0   2.6  83.8
#>   Sneathia_sanguinegens     0.0   0.0   0.2   4.3   7.9   0.9   0.0

The two tables describe overlap between different grouping rules on shared source samples. They do not estimate performance on an independent cohort.

Depth-2 refinement

Large dCSTs can be refined by dropping the dominant species and repeating the procedure on the remaining taxa. This produces a two-level hierarchy that reveals sub-community structure.

dcst2 <- refine.linf.csts(Z, dcst1, n0 = 15, refinement.factor = 2,
                           low.freq.policy = "pure", verbose = FALSE)

## Depth-2 dCST table
dcst2_tab <- sort(table(dcst2$lineage.label), decreasing = TRUE)
dcst2_tab
#> 
#>             Lactobacillus_iners__Gardnerella_vaginalis 
#>                                                    204 
#>        Lactobacillus_crispatus__Lactobacillus_jensenii 
#>                                                    151 
#>           Lactobacillus_crispatus__Lactobacillus_iners 
#>                                                    131 
#>                                          RARE_DOMINANT 
#>                                                    123 
#>                     Lactobacillus_iners__RARE_DOMINANT 
#>                                                    105 
#>            Lactobacillus_iners__Lactobacillus_jensenii 
#>                                                    102 
#>           Lactobacillus_iners__Lactobacillus_crispatus 
#>                                                    101 
#>                   Gardnerella_vaginalis__RARE_DOMINANT 
#>                                                     95 
#>               Gardnerella_vaginalis__Atopobium_vaginae 
#>                                                     94 
#>               Lactobacillus_crispatus__g_Lactobacillus 
#>                                                     88 
#>             Gardnerella_vaginalis__Lactobacillus_iners 
#>                                                     85 
#>                           BVAB1__Gardnerella_vaginalis 
#>                                                     63 
#>                 Lactobacillus_crispatus__RARE_DOMINANT 
#>                                                     63 
#>                                  Lactobacillus_gasseri 
#>                                                     62 
#>           Lactobacillus_crispatus__g_Corynebacterium_1 
#>                                                     42 
#>               Atopobium_vaginae__Gardnerella_vaginalis 
#>                                                     37 
#>                                        g_Streptococcus 
#>                                                     36 
#>           Gardnerella_vaginalis__Sneathia_sanguinegens 
#>                                                     33 
#>                           Gardnerella_vaginalis__BVAB1 
#>                                                     29 
#>                                   BVAB1__RARE_DOMINANT 
#>                                                     28 
#>               Lactobacillus_iners__g_Corynebacterium_1 
#>                                                     27 
#>                   Lactobacillus_iners__g_Streptococcus 
#>                                                     26 
#>                Gardnerella_vaginalis__g_Fastidiosipila 
#>                                                     24 
#>            Lactobacillus_jensenii__Lactobacillus_iners 
#>                                                     24 
#>                  Lactobacillus_jensenii__RARE_DOMINANT 
#>                                                     24 
#>                   Sneathia_sanguinegens__RARE_DOMINANT 
#>                                                     24 
#>                      Lactobacillus_iners__g_Finegoldia 
#>                                                     22 
#>         Lactobacillus_crispatus__Gardnerella_vaginalis 
#>                                                     21 
#>         Lactobacillus_crispatus__Lactobacillus_reuteri 
#>                                                     21 
#>             Lactobacillus_iners__Lactobacillus_gasseri 
#>                                                     19 
#>          Lactobacillus_jensenii__Gardnerella_vaginalis 
#>                                                     19 
#>         Lactobacillus_crispatus__Lactobacillus_gasseri 
#>                                                     17 
#>           Sneathia_sanguinegens__Gardnerella_vaginalis 
#>                                                     16 
#> Lactobacillus_crispatus__g_Clostridium_sensu_stricto_1 
#>                                                     15 
#>                  Lactobacillus_crispatus__g_Finegoldia 
#>                                                     15 
#>                       Atopobium_vaginae__RARE_DOMINANT 
#>                                                     14

Concordance with Valencia sub-CSTs

dcst2_labels <- dcst2$lineage.label.absorb
val_subcst   <- valencia2k$cst$Val_subCST[metadata.order]

concordance2 <- table(dCST = dcst2_labels, Valencia = val_subcst)

## Percentage by dCST (row-wise)
pct2 <- round(100 * prop.table(concordance2, margin = 1), 1)

## Show only dCSTs with at least 20 samples for readability
dcst2_sizes <- rowSums(concordance2)
pct2[dcst2_sizes >= 20, , drop = FALSE]
#>                                                  Valencia
#> dCST                                                I-A   I-B    II III-A III-B
#>   Atopobium_vaginae__Gardnerella_vaginalis          0.0   0.0   0.0   0.0   0.0
#>   BVAB1__Gardnerella_vaginalis                      0.0   0.0   0.0   0.0   0.0
#>   g_Streptococcus                                   0.0   0.0   0.0   0.0   0.0
#>   Gardnerella_vaginalis                             0.0   0.0   0.0   0.0   0.0
#>   Gardnerella_vaginalis__Atopobium_vaginae          0.0   0.0   0.7   0.0   0.0
#>   Gardnerella_vaginalis__BVAB1                      0.0   0.0   0.0   0.0   0.0
#>   Gardnerella_vaginalis__g_Fastidiosipila           0.0   0.0   0.0   0.0   0.0
#>   Gardnerella_vaginalis__Lactobacillus_iners        0.0   0.0   3.3   0.0   0.8
#>   Gardnerella_vaginalis__Sneathia_sanguinegens      0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Corynebacterium_1     58.0  42.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Finegoldia            60.0  40.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Lactobacillus         90.2   9.8   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Gardnerella_vaginalis   41.7  54.2   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_iners     44.4  51.1   0.0   0.0   4.5
#>   Lactobacillus_crispatus__Lactobacillus_jensenii  82.0  18.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_reuteri   74.2  25.8   0.0   0.0   0.0
#>   Lactobacillus_gasseri                             0.0   0.0  98.4   0.0   0.0
#>   Lactobacillus_iners                               0.0   0.0   0.0   4.5  18.2
#>   Lactobacillus_iners__g_Corynebacterium_1          0.0   0.0   0.0  91.3   8.7
#>   Lactobacillus_iners__g_Finegoldia                 0.0   0.0   0.0  81.6  18.4
#>   Lactobacillus_iners__g_Streptococcus              0.0   0.0   0.0  67.7  29.0
#>   Lactobacillus_iners__Gardnerella_vaginalis        0.0   0.0   0.0  39.0  51.0
#>   Lactobacillus_iners__Lactobacillus_crispatus      0.0   0.0   0.0  48.7  51.3
#>   Lactobacillus_iners__Lactobacillus_gasseri        0.0   0.0   5.0  80.0  15.0
#>   Lactobacillus_iners__Lactobacillus_jensenii       0.0   0.0   0.0  77.6  13.1
#>   Lactobacillus_jensenii__Gardnerella_vaginalis     0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_jensenii__Lactobacillus_iners       0.0   0.0   0.0   0.0   0.0
#>   Sneathia_sanguinegens__Gardnerella_vaginalis      0.0   0.0   0.0   0.0   2.5
#>                                                  Valencia
#> dCST                                               IV-A  IV-B IV-C0 IV-C1 IV-C2
#>   Atopobium_vaginae__Gardnerella_vaginalis          3.9  92.2   0.0   0.0   0.0
#>   BVAB1__Gardnerella_vaginalis                    100.0   0.0   0.0   0.0   0.0
#>   g_Streptococcus                                   0.0   0.0   9.0  58.2   3.0
#>   Gardnerella_vaginalis                            10.0  46.7  23.3   0.0   0.0
#>   Gardnerella_vaginalis__Atopobium_vaginae          0.0  99.3   0.0   0.0   0.0
#>   Gardnerella_vaginalis__BVAB1                     75.8  24.2   0.0   0.0   0.0
#>   Gardnerella_vaginalis__g_Fastidiosipila           3.4  96.6   0.0   0.0   0.0
#>   Gardnerella_vaginalis__Lactobacillus_iners        1.7  94.2   0.0   0.0   0.0
#>   Gardnerella_vaginalis__Sneathia_sanguinegens      2.4  97.6   0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Corynebacterium_1      0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Finegoldia             0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Lactobacillus          0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Gardnerella_vaginalis    4.2   0.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_iners      0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_jensenii   0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_reuteri    0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_gasseri                             0.0   0.0   0.0   0.0   1.6
#>   Lactobacillus_iners                               4.5  13.6  27.3   0.0   9.1
#>   Lactobacillus_iners__g_Corynebacterium_1          0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_iners__g_Finegoldia                 0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_iners__g_Streptococcus              0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_iners__Gardnerella_vaginalis        1.2   8.8   0.0   0.0   0.0
#>   Lactobacillus_iners__Lactobacillus_crispatus      0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_iners__Lactobacillus_gasseri        0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_iners__Lactobacillus_jensenii       0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_jensenii__Gardnerella_vaginalis     0.0   0.0   0.0   0.0   0.0
#>   Lactobacillus_jensenii__Lactobacillus_iners       0.0   0.0   0.0   0.0   0.0
#>   Sneathia_sanguinegens__Gardnerella_vaginalis     15.0  82.5   0.0   0.0   0.0
#>                                                  Valencia
#> dCST                                              IV-C3 IV-C4     V
#>   Atopobium_vaginae__Gardnerella_vaginalis          0.0   0.0   3.9
#>   BVAB1__Gardnerella_vaginalis                      0.0   0.0   0.0
#>   g_Streptococcus                                  28.4   1.5   0.0
#>   Gardnerella_vaginalis                             3.3  16.7   0.0
#>   Gardnerella_vaginalis__Atopobium_vaginae          0.0   0.0   0.0
#>   Gardnerella_vaginalis__BVAB1                      0.0   0.0   0.0
#>   Gardnerella_vaginalis__g_Fastidiosipila           0.0   0.0   0.0
#>   Gardnerella_vaginalis__Lactobacillus_iners        0.0   0.0   0.0
#>   Gardnerella_vaginalis__Sneathia_sanguinegens      0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Corynebacterium_1      0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Finegoldia             0.0   0.0   0.0
#>   Lactobacillus_crispatus__g_Lactobacillus          0.0   0.0   0.0
#>   Lactobacillus_crispatus__Gardnerella_vaginalis    0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_iners      0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_jensenii   0.0   0.0   0.0
#>   Lactobacillus_crispatus__Lactobacillus_reuteri    0.0   0.0   0.0
#>   Lactobacillus_gasseri                             0.0   0.0   0.0
#>   Lactobacillus_iners                              18.2   4.5   0.0
#>   Lactobacillus_iners__g_Corynebacterium_1          0.0   0.0   0.0
#>   Lactobacillus_iners__g_Finegoldia                 0.0   0.0   0.0
#>   Lactobacillus_iners__g_Streptococcus              0.0   0.0   3.2
#>   Lactobacillus_iners__Gardnerella_vaginalis        0.0   0.0   0.0
#>   Lactobacillus_iners__Lactobacillus_crispatus      0.0   0.0   0.0
#>   Lactobacillus_iners__Lactobacillus_gasseri        0.0   0.0   0.0
#>   Lactobacillus_iners__Lactobacillus_jensenii       0.0   0.0   9.3
#>   Lactobacillus_jensenii__Gardnerella_vaginalis     0.0   0.0 100.0
#>   Lactobacillus_jensenii__Lactobacillus_iners       0.0   0.0 100.0
#>   Sneathia_sanguinegens__Gardnerella_vaginalis      0.0   0.0   0.0

The depth-2 refinement recovers sub-CST structure. For example, the Lactobacillus crispatus dCST splits based on the second-most-abundant taxon, and these sub-dCSTs align with Valencia sub-CSTs I-A and I-B.

The full pipeline

For convenience, linf.dcst.landmark.pipeline() runs the entire workflow in one call: normalization, depth-1 dCSTs, depth-2 refinement, and landmark computation.

out <- linf.dcst.landmark.pipeline(
  valencia2k$rel,
  feature.ids    = colnames(valencia2k$rel),
  feature.labels = colnames(valencia2k$rel),
  n0.depth1      = 30,
  n0.depth2      = 15,
  refinement.factor = 2,
  low.freq.policy   = "pure",
  landmark.view     = "absorb",
  verbose           = FALSE
)

names(out)
#> [1] "linf.rel"         "dcst.depth1"      "dcst.depth2"      "landmarks.depth1"
#> [5] "landmarks.depth2" "params"

Landmark points

All four landmark methods select observed rows by the lineage’s leaf-feature value: its maximum, minimum, or the observation nearest its mean or median. They do not construct averaged community profiles. The pipeline supplies L-infinity-normalized values, so these measurements are relative to the sample maximum, not proportions of total community abundance.

## Depth-1 landmarks
lm1 <- out$landmarks.depth1$landmarks

## Show landmarks for a few key dCST dominance-lineages
key_lineages <- c("Lactobacillus_crispatus", "Lactobacillus_iners",
                  "Gardnerella_vaginalis")
key_lm <- lm1[lm1$lineage.id %in% key_lineages, ]

## For each dCST, show the endpoint.max landmark's target value
## (target-feature abundance relative to the row maximum)
ep_max <- key_lm[key_lm$landmark.type == "endpoint.max",
                 c("lineage.label", "point.name", "target.value")]
ep_max
#>             lineage.label point.name target.value
#> 1 Lactobacillus_crispatus         s1            1
#> 5   Gardnerella_vaginalis         s6            1
#> 9     Lactobacillus_iners         s7            1

## And the endpoint.min (lowest target value among assigned rows)
ep_min <- key_lm[key_lm$landmark.type == "endpoint.min",
                 c("lineage.label", "point.name", "target.value")]
ep_min
#>              lineage.label point.name target.value
#> 2  Lactobacillus_crispatus       s658   0.00504737
#> 6    Gardnerella_vaginalis       s577   0.01120848
#> 10     Lactobacillus_iners       s312   0.00000000

A depth-1 pure dominant feature has normalized value one in every positive member, so endpoint selection can consist entirely of ties. Absorbed samples may have a smaller target value because their assigned feature is not their original maximum. Neither endpoint establishes near-total or marginal unit-sum dominance. Inspect unit-sum relative abundances for that question.

Summary

This workflow fits supported dominance groups, refines selected parents and selects observed landmark rows. Its concordance tables describe overlap with Valencia labels on source training samples. To assign separate samples while preserving the fitted states, use transfer.dcsts() and inspect unassigned (NA) depths; fitting on new samples would learn a different hierarchy. The function guide explains these contracts and the dataset guide gives a disjoint reference/query demonstration.

References

France, M. T., Ma, B., Gajer, P., et al. (2020). VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. Microbiome, 8(1), 166.
Gajer, P. & Ravel, J. (2025). A New Approach to Compositional Data Analysis using \(L^\infty\)-normalization with Applications to Vaginal Microbiome. arXiv:2503.21543.
Ravel, J., Gajer, P., Abdo, Z., et al. (2011). Vaginal microbiome of reproductive-age women. PNAS, 108(Suppl 1), 4680–4687.