Deploying to gh-pages from @ 558d154 🚀

Author: adw96

llms.txt

@@ -49,16 +49,22 @@ rather than responding to everyone individually.
 - [`calculate_log_penalty()`](https://statdivlab.github.io/tinyvamp/reference/calculate_log_penalty.md)
   : Calculate barrier penalty to add to objective function inside
   barrier algorithm
+- [`costea2017_metaphlan2_profiles`](https://statdivlab.github.io/tinyvamp/reference/costea2017_metaphlan2_profiles.md)
+  : MetaPhlAn2 taxonomic profiles from the Costea 2017 study.
 - [`costea2017_mock_composition`](https://statdivlab.github.io/tinyvamp/reference/costea2017_mock_composition.md)
   : The composition of 10 spike-in taxa in 19 samples observed from flow
   cytometry.
+- [`costea2017_sample_data`](https://statdivlab.github.io/tinyvamp/reference/costea2017_sample_data.md)
+  : costea2017_sample_data
 - [`dataframes_to_parameters()`](https://statdivlab.github.io/tinyvamp/reference/dataframes_to_parameters.md)
   : Convert parameter values stored in data frame format to matrix
   format
 - [`estimate_parameters()`](https://statdivlab.github.io/tinyvamp/reference/estimate_parameters.md)
   : Fit tinyvamp model to HTS microbiome data
 - [`evaluate_criterion_lr()`](https://statdivlab.github.io/tinyvamp/reference/evaluate_criterion_lr.md)
   : Criterion Evaluation Function
+- [`karstens_phyloseq`](https://statdivlab.github.io/tinyvamp/reference/karstens_phyloseq.md)
+  : karstens_phyloseq
 - [`mu_d_P()`](https://statdivlab.github.io/tinyvamp/reference/mu_d_P.md)
   : Calculate derivative of mu_ij with respect to an entry of P
 - [`mu_d_beta()`](https://statdivlab.github.io/tinyvamp/reference/mu_d_beta.md)

pkgdown.yml

@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   compare-experiments: compare-experiments.html
   dilution-series: dilution-series.html
-last_built: 2026-03-06T21:01Z
+last_built: 2026-03-07T00:27Z
 urls:
   reference: https://statdivlab.github.io/tinyvamp/reference
   article: https://statdivlab.github.io/tinyvamp/articles

reference/costea2017_metaphlan2_profiles.html

@@ -0,0 +1,18 @@
+# MetaPhlAn2 taxonomic profiles from the Costea 2017 study.
+
+MetaPhlAn2 taxonomic profiles from the Costea 2017 study.
+
+## Usage
+
+``` r
+costea2017_metaphlan2_profiles
+```
+
+## Format
+
+A data frame with the observed relative abundances (from MetaPhlAn2) of
+taxa (rows) in each sample (columns)
+
+## Source
+
+<https://doi.org/10.1038/nbt.3960>

reference/costea2017_metaphlan2_profiles.md

@@ -0,0 +1,17 @@
+# costea2017_sample_data
+
+Sample metadata for the Costea 2017 study.
+
+## Usage
+
+``` r
+costea2017_sample_data
+```
+
+## Format
+
+A data frame mapping samples to protocols and individuals
+
+## Source
+
+<https://doi.org/10.1038/nbt.3960>

reference/costea2017_sample_data.html

@@ -156,6 +156,14 @@ estimate_parameters(
 
   Maximum value of barrier_t. Defaults to 1e12.
 
+- initial_conv_tol:
+
+  Are we flat enough in the likelihood yet? Where to start.
+
+- final_conv_tol:
+
+  Are we flat enough in the likelihood yet? Where to end.
+
 - constraint_tolerance:
 
   The tolerance for the augmented Lagrangian algorithm. Final estimates