Fix Title typo, add contributors, and correct stale package links

DESCRIPTION

@@ -1,13 +1,17 @@
 Package: amRml
-Title: Machile learning framework to predict AMR across molecular scales | pkg 2 of 3-pkg amR suite
+Title: Machine learning framework to predict AMR across molecular scales | pkg 2 of 3-pkg amR suite
 Version: 0.99.0
 Authors@R: c(
     person("Janani", "Ravi", , "janani.ravi@cuanschutz.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7443-925X")),
     person("Ethan", "Wolfe", , "ethan.wolfe@cuanschutz.edu", role = "ctb"),
     person("Evan", "Brenner", , "evan.brenner@cuanschutz.edu", role = "ctb"),
     person("Abhirupa", "Ghosh", , "abhirupa.ghosh@cuanschutz.edu", role = "ctb"),
-    person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb")
+    person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb"),
+    person("Emily", "Boyer", , "emily.boyer@cuanschutz.edu", role = "ctb"),
+    person("Charmie", "Vang", , "charmie.vang@cuanschutz.edu", role = "ctb"),
+    person("Alexander", "McKim", , "alexander.mckim@cuanschutz.edu", role = "ctb",
+           comment = c(ORCID = "0000-0002-7802-7591"))
   )
 Description: Comprehensive machine learning (ML) pipeline for predicting antimicrobial
     resistance (AMR) in ESKAPE pathogens across molecular scales (gene, protein,
@@ -16,7 +20,7 @@ Description: Comprehensive machine learning (ML) pipeline for predicting antimic
     (geographic, temporal, species). Includes model evaluation, feature importance
     analysis, cross-scale performance comparison, and functional characterization
     of top features. Designed to work with data from amRdata package and generate
-    results for amRshiny visualization. Can work independently with example
+    results for amRviz visualization. Can work independently with example
     ESKAPE pathogen datasets, too.
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8

README.Rmd

@@ -115,7 +115,7 @@ amRml is designed to work seamlessly with other amR packages:
 ```r
 library(amRdata)
 library(amRml)
-library(amRshiny)
+library(amRviz)
 
 # 1. Curate data
 prepareGenomes("Shigella flexneri")
@@ -130,18 +130,19 @@ launchAMRDashboard()
 
 ## Related packages
 - [amR](https://github.com/JRaviLab/amR): Suite metapackage
-- [amRdata](https://github.com/JRaviLab/amRml): Data preparation for AMR prediction
-- [amRshiny](https://github.com/JRaviLab/amRshiny): Interactive dashboard
+- [amRdata](https://github.com/JRaviLab/amRdata): Data preparation for AMR prediction
+- [amRviz](https://github.com/JRaviLab/amRviz): Interactive dashboard
 
 ## Citation
 If you use `amRml` in your research, please cite:
 
-```
-Brenner E, Ghosh A, Wolfe E, Boyer E, Vang C, Lesiyon R, Mayer D, Ravi J. (2026).
-amR: an R package suite to predict antimicrobial resistance in bacterial pathogens.
-R package version 0.99.0.
-https://github.com/JRaviLab/amR
-```
+> Ghosh A^, Brenner EP^, Boyer EA, McKim AP, Vang CK, Wolfe EP, Mayer D, Lesiyon RL, Ravi J.
+>
+> amR: an R package suite to predict antimicrobial resistance in bacterial pathogens.
+>
+> bioRxiv. 2026. DOI: [10.64898/2026.07.10.734579](https://doi.org/10.64898/2026.07.10.734579).
+
+^ Co-first authors
 
 ## Contributing
 

README.md

@@ -144,7 +144,7 @@ amRml is designed to work seamlessly with other amR packages:
 ``` r
 library(amRdata)
 library(amRml)
-library(amRshiny)
+library(amRviz)
 
 # 1. Curate data
 prepareGenomes("Shigella flexneri")
@@ -160,19 +160,24 @@ launchAMRDashboard()
 ## Related packages
 
 - [amR](https://github.com/JRaviLab/amR): Suite metapackage
-- [amRdata](https://github.com/JRaviLab/amRml): Data preparation for AMR
-  prediction
-- [amRshiny](https://github.com/JRaviLab/amRshiny): Interactive
-  dashboard
+- [amRdata](https://github.com/JRaviLab/amRdata): Data preparation for
+  AMR prediction
+- [amRviz](https://github.com/JRaviLab/amRviz): Interactive dashboard
 
 ## Citation
 
 If you use `amRml` in your research, please cite:
 
-    Brenner E, Ghosh A, Wolfe E, Boyer E, Vang C, Lesiyon R, Mayer D, Ravi J. (2026).
-    amR: an R package suite to predict antimicrobial resistance in bacterial pathogens.
-    R package version 0.99.0.
-    https://github.com/JRaviLab/amR
+> Ghosh A^, Brenner EP^, Boyer EA, McKim AP, Vang CK, Wolfe EP, Mayer D,
+> Lesiyon RL, Ravi J.
+>
+> amR: an R package suite to predict antimicrobial resistance in
+> bacterial pathogens.
+>
+> bioRxiv. 2026. DOI:
+> [10.64898/2026.07.10.734579](https://doi.org/10.64898/2026.07.10.734579).
+
+^ Co-first authors
 
 ## Contributing