Moves code from amRdash to amR_shiny.

.Rbuildignore

@@ -1,5 +1,6 @@
 \.Rproj$
 ^\.Rproj\.user$
+^.*\.Rproj$
 ^LICENSE\.md$
 ^README\.Rmd$
 ^cran-comments\.md$

.gitignore

@@ -5,3 +5,7 @@
 .DS_Store
 .quarto
 inst/doc
+# docs
+docs
+# Rmd/qmd artifacts
+inst/notebooks/*.html

DESCRIPTION

@@ -1,24 +1,65 @@
-Package: NewShinyPackage
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
-Authors@R: 
-    person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = c("aut", "cre"))
-Description: What the package does (one paragraph).
-License: MIT + file LICENSE
-Imports: 
-    config,
-    golem,
-    shiny
-Suggests: 
+Package: amRshiny
+Title: Interactive dashboard for AMR data and model visualization | pkg 3 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("Emily", "Boyer", , "emily.boyer@cuanschutz.edu", role = "ctb"),
+    person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb"),
+    person("Raymond", "Lesiyon", , "raymond.lesiyon@cuanschutz.edu", role = "ctb"),
+    person("Abhirupa", "Ghosh", , "abhirupa.ghosh@cuanschutz.edu", role = "ctb"),
+    person("Evan", "Brenner", , "evan.brenner@cuanschutz.edu", role = "ctb"),
+    person("Charmie", "Vang", , "charmie.vang@cuanschutz.edu", role = "ctb")
+  )
+Description: Interactive Shiny dashboard for exploring antimicrobial resistance
+    (AMR) data and machine learning model results from the AMR package suite.
+    Provides intuitive visualization of metadata (e.g., geographic, temporal, host),
+    model performance comparisons across species, drugs, and molecular scales,
+    important features, and cross-model analyses. Includes modular UI
+    components and publication-quality plot export. Can operate independently
+    with pre-computed data files or integrate with amR_data and amR_ml packages.
+License: BSD_3_clause + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends:
+    R (>= 4.1.0)
+Imports:
+    arrow,
+    circlize,
+    ComplexHeatmap,
+    countrycode,
+    DBI,
+    dplyr,
+    DT,
+    duckdb,
+    ggplot2,
+    glue,
+    grid,
+    here,
+    networkD3,
+    plotly,
+    purrr,
+    readr,
+    rlang,
+    shiny,
+    shinycssloaders,
+    shinydashboard,
+    shinyjs,
+    stringr,
+    tibble,
+    tidyr
+Suggests:
     knitr,
     rmarkdown,
-    spelling,
     testthat (>= 3.0.0)
-Config/testthat/edition: 3
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
-URL: https://github.com/JRaviLab/NewShinyPackage
-BugReports: https://github.com/JRaviLab/NewShinyPackage/issues
 VignetteBuilder: knitr
-Language: en-US
+biocViews:
+    AMR,
+    GUI,
+    MicrobialGenomics,
+    Pathogen,
+    Visualization
+URL: https://github.com/jravilab/amR_shiny
+BugReports: https://github.com/jravilab/amR_shiny/issues

LICENSE

@@ -1,3 +1,3 @@
-YEAR: 2024
-COPYRIGHT HOLDER: NewShinyPackage authors
+YEAR: 2026
+COPYRIGHT HOLDER: JRaviLab
 ORGANIZATION: JRaviLab

LICENSE.md

@@ -1,6 +1,6 @@
 # BSD 3-clause License
 
-Copyright (c) 2024 NewShinyPackage authors
+Copyright (c) 2026 JRaviLab
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

NAMESPACE

@@ -1,10 +1,121 @@
 # Generated by roxygen2: do not edit by hand
 
-export(run_app)
-import(shiny)
-importFrom(golem,activate_js)
-importFrom(golem,add_resource_path)
-importFrom(golem,bundle_resources)
-importFrom(golem,favicon)
-importFrom(golem,with_golem_options)
+export(launchAMRDashboard)
+export(launch_amr_dashboard)
+importFrom(ComplexHeatmap,Heatmap)
+importFrom(ComplexHeatmap,draw)
+importFrom(DBI,dbConnect)
+importFrom(DBI,dbGetQuery)
+importFrom(DBI,dbWriteTable)
+importFrom(DT,dataTableOutput)
+importFrom(DT,datatable)
+importFrom(DT,renderDataTable)
+importFrom(arrow,read_parquet)
+importFrom(arrow,write_parquet)
+importFrom(circlize,colorRamp2)
+importFrom(dplyr,all_of)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,c_across)
+importFrom(dplyr,collect)
+importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,n)
+importFrom(dplyr,pull)
+importFrom(dplyr,rowwise)
+importFrom(dplyr,select)
+importFrom(dplyr,slice_head)
+importFrom(dplyr,slice_max)
+importFrom(dplyr,summarize)
+importFrom(dplyr,ungroup)
+importFrom(duckdb,duckdb)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_boxplot)
+importFrom(ggplot2,geom_col)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,position_jitterdodge)
+importFrom(ggplot2,scale_color_brewer)
+importFrom(ggplot2,scale_fill_brewer)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,theme_minimal)
+importFrom(glue,glue)
+importFrom(grid,gpar)
+importFrom(grid,unit)
+importFrom(here,here)
+importFrom(plotly,colorbar)
+importFrom(plotly,layout)
+importFrom(plotly,plot_ly)
+importFrom(plotly,plotlyOutput)
+importFrom(plotly,renderPlotly)
+importFrom(purrr,map_dfr)
+importFrom(readr,read_csv)
+importFrom(readr,read_tsv)
+importFrom(rlang,.data)
+importFrom(rlang,sym)
+importFrom(shiny,actionButton)
+importFrom(shiny,br)
+importFrom(shiny,column)
+importFrom(shiny,conditionalPanel)
+importFrom(shiny,downloadHandler)
+importFrom(shiny,fluidPage)
+importFrom(shiny,fluidRow)
+importFrom(shiny,h2)
+importFrom(shiny,h3)
+importFrom(shiny,h4)
+importFrom(shiny,icon)
+importFrom(shiny,includeCSS)
+importFrom(shiny,isolate)
+importFrom(shiny,mainPanel)
+importFrom(shiny,navbarPage)
+importFrom(shiny,observe)
+importFrom(shiny,observeEvent)
+importFrom(shiny,plotOutput)
+importFrom(shiny,radioButtons)
+importFrom(shiny,reactive)
+importFrom(shiny,reactiveVal)
+importFrom(shiny,renderPlot)
+importFrom(shiny,renderUI)
+importFrom(shiny,req)
+importFrom(shiny,selectInput)
 importFrom(shiny,shinyApp)
+importFrom(shiny,sliderInput)
+importFrom(shiny,tabPanel)
+importFrom(shiny,tabsetPanel)
+importFrom(shiny,tagList)
+importFrom(shiny,tags)
+importFrom(shiny,uiOutput)
+importFrom(shiny,updateSelectInput)
+importFrom(shiny,updateSelectizeInput)
+importFrom(shiny,wellPanel)
+importFrom(shinydashboard,box)
+importFrom(shinydashboard,tabBox)
+importFrom(shinyjs,useShinyjs)
+importFrom(stats,setNames)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_extract_all)
+importFrom(stringr,str_flatten)
+importFrom(stringr,str_glue)
+importFrom(stringr,str_match)
+importFrom(stringr,str_remove)
+importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split_i)
+importFrom(stringr,str_to_lower)
+importFrom(stringr,str_to_sentence)
+importFrom(stringr,str_trunc)
+importFrom(tibble,column_to_rownames)
+importFrom(tibble,tibble)
+importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate)
+importFrom(utils,packageVersion)