diff --git a/DESCRIPTION b/DESCRIPTION index 1012ad6..456e7f9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: amR -Title: amR, an R package suite to predict AMR in bacterial pathogens (amRdata, amRml, amRshiny) +Title: amR, an R package suite to predict AMR in bacterial pathogens (amRdata, amRml, amRviz) Version: 0.0.0.9000 Authors@R: c( person("Janani", "Ravi", , "janani.ravi@cuanschutz.edu", role = c("aut", "cre"), @@ -12,7 +12,7 @@ Authors@R: c( person("Raymond", "Lesiyon", , "raymond.lesiyon@cuanschutz.edu", role = "ctb"), person("David", "Mayer", , "david.mayer@cuanschutz.edu", role = "ctb") ) -Description: amR is a metapackage aka package suite that lets users install the 3 packages, amRdata, amRml, and amRshiny with a single install function. +Description: amR is a metapackage aka package suite that lets users install the 3 packages, amRdata, amRml, and amRviz with a single install function. License: BSD_3_clause + file LICENSE Encoding: UTF-8 Roxygen: list(markdown = TRUE) diff --git a/R/install_amR.R b/R/install_amR.R index f0ae0dc..0bbec63 100644 --- a/R/install_amR.R +++ b/R/install_amR.R @@ -1,10 +1,10 @@ #' Install amR package suite #' #' Installs all packages in the amR suite for antimicrobial resistance -#' prediction: amRdata, amRml, and amRshiny. +#' prediction: amRdata, amRml, and amRviz. #' #' @param packages Character vector specifying which packages to install. -#' Options are "data", "ml", and "shiny". Default installs all three. +#' Options are "data", "ml", and "viz". Default installs all three. #' @param force Logical. If TRUE, forces reinstallation even if packages #' are already installed. Default is FALSE. #' @param upgrade Character. Controls whether to upgrade dependencies. @@ -31,13 +31,13 @@ #' # Install specific packages quietly #' installAMR(packages = c("data", "ml"), quiet = TRUE) #' } -installAMR <- function(packages = c("data", "ml", "shiny"), +installAMR <- function(packages = c("data", "ml", "viz"), force = FALSE, upgrade = "default", quiet = FALSE) { # Validate packages argument - valid_packages <- c("data", "ml", "shiny") + valid_packages <- c("data", "ml", "viz") packages <- match.arg(packages, valid_packages, several.ok = TRUE) @@ -46,7 +46,7 @@ installAMR <- function(packages = c("data", "ml", "shiny"), repo_map <- c( data = "JRaviLab/amRdata", ml = "JRaviLab/amRml", - shiny = "JRaviLab/amRshiny" + viz = "JRaviLab/amRviz" ) # Install each requested package diff --git a/README.Rmd b/README.Rmd index 54827f7..752d121 100644 --- a/README.Rmd +++ b/README.Rmd @@ -33,7 +33,7 @@ The amR suite consists of three packages that work together: |---------|-------------|------------| | **amRdata** | Data curation and feature extraction from bacterial genomes | [JRaviLab/amRdata](https://github.com/JRaviLab/amRdata) | | **amRml** | Machine learning models for AMR prediction | [JRaviLab/amRml](https://github.com/JRaviLab/amRml) | -| **amRshiny** | Interactive dashboard for exploring results | [JRaviLab/amRshiny](https://github.com/JRaviLab/amRshiny) | +| **amRviz** | Interactive dashboard for exploring results | [JRaviLab/amRviz](https://github.com/JRaviLab/amRviz) | ## Installation @@ -58,7 +58,7 @@ You can also install packages individually: ```r remotes::install_github("JRaviLab/amRdata") remotes::install_github("JRaviLab/amRml") -remotes::install_github("JRaviLab/amRshiny") +remotes::install_github("JRaviLab/amRviz") ``` ## Quick start @@ -67,7 +67,7 @@ remotes::install_github("JRaviLab/amRshiny") # Load all packages library(amRdata) library(amRml) -library(amRshiny) +library(amRviz) # 1. Prepare data with amRdata # features <- prepareFeatures(...) @@ -75,7 +75,7 @@ library(amRshiny) # 2. Train ML models with amRml # results <- runMLPipeline(...) -# 3. Explore results with amRshiny +# 3. Explore results with amRviz # launchDashboard(...) ``` @@ -83,7 +83,7 @@ library(amRshiny) ``` ┌─────────────┐ ┌─────────────┐ ┌─────────────┐ -│ amRdata │ --> │ amRml │ --> │ amRshiny │ +│ amRdata │ --> │ amRml │ --> │ amRviz │ │ │ │ │ │ │ │ - Genomes │ │ - Train LR │ │ - Dashboard │ │ - Features │ │ - Evaluate │ │ - Plots │ @@ -95,7 +95,7 @@ library(amRshiny) - [amRdata documentation](https://jravilab.github.io/amRdata) - [amRml documentation](https://jravilab.github.io/amRml) -- [amRshiny documentation](https://jravilab.github.io/amRshiny) +- [amRviz documentation](https://jravilab.github.io/amRviz) ## Citation diff --git a/README.md b/README.md index 03aa94a..86fee2c 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h the amR suite of packages for antimicrobial resistance (AMR) prediction in bacterial pathogens. - + ## The amR suite @@ -23,7 +23,7 @@ The amR suite consists of three packages that work together: |----|----|----| | **amRdata** | Data curation and feature extraction from bacterial genomes | [JRaviLab/amRdata](https://github.com/JRaviLab/amRdata) | | **amRml** | Machine learning models for AMR prediction | [JRaviLab/amRml](https://github.com/JRaviLab/amRml) | -| **amRshiny** | Interactive dashboard for exploring results | [JRaviLab/amRshiny](https://github.com/JRaviLab/amRshiny) | +| **amRviz** | Interactive dashboard for exploring results | [JRaviLab/amRviz](https://github.com/JRaviLab/amRviz) | ## Installation @@ -48,7 +48,7 @@ You can also install packages individually: ``` r remotes::install_github("JRaviLab/amRdata") remotes::install_github("JRaviLab/amRml") -remotes::install_github("JRaviLab/amRshiny") +remotes::install_github("JRaviLab/amRviz") ``` ## Quick start @@ -57,7 +57,7 @@ remotes::install_github("JRaviLab/amRshiny") # Load all packages library(amRdata) library(amRml) -library(amRshiny) +library(amRviz) # 1. Prepare data with amRdata # features <- prepareFeatures(...) @@ -65,14 +65,14 @@ library(amRshiny) # 2. Train ML models with amRml # results <- runMLPipeline(...) -# 3. Explore results with amRshiny +# 3. Explore results with amRviz # launchDashboard(...) ``` ## Workflow overview ┌─────────────┐ ┌─────────────┐ ┌─────────────┐ - │ amRdata │ --> │ amRml │ --> │ amRshiny │ + │ amRdata │ --> │ amRml │ --> │ amRviz │ │ │ │ │ │ │ │ - Genomes │ │ - Train LR │ │ - Dashboard │ │ - Features │ │ - Evaluate │ │ - Plots │ @@ -83,7 +83,7 @@ library(amRshiny) - [amRdata documentation](https://jravilab.github.io/amRdata) - [amRml documentation](https://jravilab.github.io/amRml) -- [amRshiny documentation](https://jravilab.github.io/amRshiny) +- [amRviz documentation](https://jravilab.github.io/amRviz) ## Citation diff --git a/amR.Rproj b/amR.Rproj index 69fafd4..d2a1afc 100644 --- a/amR.Rproj +++ b/amR.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: 6761cf5b-842c-4498-aaa3-1f6bf1b396a4 RestoreWorkspace: No SaveWorkspace: No diff --git a/man/figures/README-amR.png b/man/figures/README-amR.png index 6ec434d..d2ababe 100644 Binary files a/man/figures/README-amR.png and b/man/figures/README-amR.png differ diff --git a/man/installAMR.Rd b/man/installAMR.Rd index 3dcdb6a..047b57f 100644 --- a/man/installAMR.Rd +++ b/man/installAMR.Rd @@ -5,7 +5,7 @@ \title{Install amR package suite} \usage{ installAMR( - packages = c("data", "ml", "shiny"), + packages = c("data", "ml", "viz"), force = FALSE, upgrade = "default", quiet = FALSE @@ -13,7 +13,7 @@ installAMR( } \arguments{ \item{packages}{Character vector specifying which packages to install. -Options are "data", "ml", and "shiny". Default installs all three.} +Options are "data", "ml", and "viz". Default installs all three.} \item{force}{Logical. If TRUE, forces reinstallation even if packages are already installed. Default is FALSE.} @@ -29,7 +29,7 @@ Invisible NULL. Called for side effects (package installation). } \description{ Installs all packages in the amR suite for antimicrobial resistance -prediction: amRdata, amRml, and amRshiny. +prediction: amRdata, amRml, and amRviz. } \examples{ \dontrun{ diff --git a/tests/testthat/test-install.R b/tests/testthat/test-install.R index 620d00f..d653846 100644 --- a/tests/testthat/test-install.R +++ b/tests/testthat/test-install.R @@ -2,13 +2,13 @@ test_that("installAMR validates package arguments", { # Valid packages should not error expect_no_error( - match.arg(c("data", "ml"), c("data", "ml", "shiny"), several.ok = TRUE) + match.arg(c("data", "ml"), c("data", "ml", "viz"), several.ok = TRUE) ) # Invalid package should error expect_error( - match.arg("invalid", c("data", "ml", "shiny"), several.ok = TRUE) + match.arg("invalid", c("data", "ml", "viz"), several.ok = TRUE) ) }) @@ -28,7 +28,7 @@ test_that("installAMR has correct default arguments", { args <- formals(installAMR) # Check default values - expect_equal(eval(args$packages), c("data", "ml", "shiny")) + expect_equal(eval(args$packages), c("data", "ml", "viz")) expect_false(eval(args$force)) expect_equal(eval(args$upgrade), "default") expect_false(eval(args$quiet)) diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd index 69e32ce..c355961 100644 --- a/vignettes/intro.Rmd +++ b/vignettes/intro.Rmd @@ -19,7 +19,7 @@ The amR package suite provides tools for antimicrobial resistance (AMR) predicti - **amRdata**: Data curation and feature extraction from bacterial genomes - **amRml**: Machine learning models for AMR prediction -- **amRshiny**: Interactive dashboard for exploring results +- **amRviz**: Interactive dashboard for exploring results ## Installation @@ -30,7 +30,7 @@ library(amR) installAMR() ``` -This will install amRdata, amRml, and amRshiny from GitHub. +This will install amRdata, amRml, and amRviz from GitHub. ### Installing specific packages @@ -64,6 +64,6 @@ installAMR(upgrade = "never") A typical amR workflow involves: 1. Preparing genomic feature data with **amRdata** 2. Training ML models with **amRml** -3. Exploring results with **amRshiny** +3. Exploring results with **amRviz** See the individual package vignettes for detailed usage instructions.