Deploying to gh-pages from @ af9dec0 🚀

Author: adw96

articles/dilution-series.html

@@ -27,7 +27,6 @@ library(tidyverse)
 #> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
 library(tinyvamp)
 #> Loading required package: cir
-#> Loading required package: numDeriv
 #> Loading required package: parallel
 library(phyloseq) 
 # library(speedyseq)

articles/dilution-series.md

@@ -1,17 +1,28 @@
 # tinyvamp
 
+[![Coverage
+status](https://codecov.io/gh/statdivlab/tinyvamp/branch/main/graph/badge.svg)](https://codecov.io/github/statdivlab/tinyvamp?branch=main)
+
 `tinyvamp` is a package for estimation and removal of measurement error
 in high-throughput sequencing data.
 
+There are many use cases for `tinyvamp`; here are a few: - Estimating
+the detectability of different species using mock communities -
+Comparing experimental protocols (or batches) with respect to how they
+well they detect different species - Estimating “true” relative
+abundances after adjusting for differential detectability - Estimating
+“true” relative abundances after removing contamination relative
+abundance profiles - Estimating contamination relative abundances
+
+The online documentation is available
+[here](https://statdivlab.github.io/tinyvamp).
+
 Full details on the model and estimation method are available in the
 [preprint](https://arxiv.org/abs/2204.12733).
 
-**Documentation and vignettes are under construction - please check back
-soon!**
-
-**Needs something more urgently? File an
+Need something? File an
 [issue](https://github.com/statdivlab/tinyvamp/issues) or [send Amy an
-email](http://statisticaldiversitylab.com/team/amy-willis)!**
+email](http://statisticaldiversitylab.com/team/amy-willis)!
 
 ## Installation
 
@@ -23,6 +34,8 @@ You can install the development version of tinyvamp from
 remotes::install_github("statdivlab/tinyvamp")
 ```
 
+Are you using `tinyvamp`? We’d love to hear about it!
+
 ## Humans
 
 Authors: [David

index.html

@@ -1,17 +1,28 @@
 # tinyvamp
 
+[![Coverage
+status](https://codecov.io/gh/statdivlab/tinyvamp/branch/main/graph/badge.svg)](https://codecov.io/github/statdivlab/tinyvamp?branch=main)
+
 `tinyvamp` is a package for estimation and removal of measurement error
 in high-throughput sequencing data.
 
+There are many use cases for `tinyvamp`; here are a few: - Estimating
+the detectability of different species using mock communities -
+Comparing experimental protocols (or batches) with respect to how they
+well they detect different species - Estimating “true” relative
+abundances after adjusting for differential detectability - Estimating
+“true” relative abundances after removing contamination relative
+abundance profiles - Estimating contamination relative abundances
+
+The online documentation is available
+[here](https://statdivlab.github.io/tinyvamp).
+
 Full details on the model and estimation method are available in the
 [preprint](https://arxiv.org/abs/2204.12733).
 
-**Documentation and vignettes are under construction - please check back
-soon!**
-
-**Needs something more urgently? File an
+Need something? File an
 [issue](https://github.com/statdivlab/tinyvamp/issues) or [send Amy an
-email](http://statisticaldiversitylab.com/team/amy-willis)!**
+email](http://statisticaldiversitylab.com/team/amy-willis)!
 
 ## Installation
 
@@ -23,6 +34,8 @@ You can install the development version of tinyvamp from
 remotes::install_github("statdivlab/tinyvamp")
 ```
 
+Are you using `tinyvamp`? We’d love to hear about it!
+
 ## Humans
 
 Authors: [David
@@ -67,6 +80,8 @@ rather than responding to everyone individually.
   : karstens_phyloseq
 - [`meaninate()`](https://statdivlab.github.io/tinyvamp/reference/meaninate.md)
   : Calculate the mean given parameters
+- [`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)
   : Calculate derivative of mu_ij with respect to B
 - [`mu_d_gamma()`](https://statdivlab.github.io/tinyvamp/reference/mu_d_gamma.md)

index.md

@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   compare-experiments: compare-experiments.html
   dilution-series: dilution-series.html
-last_built: 2026-03-07T16:01Z
+last_built: 2026-03-07T16:20Z
 urls:
   reference: https://statdivlab.github.io/tinyvamp/reference
   article: https://statdivlab.github.io/tinyvamp/articles

llms.txt

@@ -27,6 +27,8 @@
   : karstens_phyloseq
 - [`meaninate()`](https://statdivlab.github.io/tinyvamp/reference/meaninate.md)
   : Calculate the mean given parameters
+- [`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)
   : Calculate derivative of mu_ij with respect to B
 - [`mu_d_gamma()`](https://statdivlab.github.io/tinyvamp/reference/mu_d_gamma.md)

pkgdown.yml

@@ -18,6 +18,7 @@
 <url><loc>https://statdivlab.github.io/tinyvamp/reference/index.html</loc></url>
 <url><loc>https://statdivlab.github.io/tinyvamp/reference/karstens_phyloseq.html</loc></url>
 <url><loc>https://statdivlab.github.io/tinyvamp/reference/meaninate.html</loc></url>
+<url><loc>https://statdivlab.github.io/tinyvamp/reference/mu_d_P.html</loc></url>
 <url><loc>https://statdivlab.github.io/tinyvamp/reference/mu_d_beta.html</loc></url>
 <url><loc>https://statdivlab.github.io/tinyvamp/reference/mu_d_gamma.html</loc></url>
 <url><loc>https://statdivlab.github.io/tinyvamp/reference/mu_d_gamma_tilde.html</loc></url>