Package: anumaan
Type: Package
Title: Antimicrobial Resistance Surveillance Preprocessing and Burden
        Estimation
Version: 0.1.0.9037
Authors@R: c(
    person(
      "Nilanjana", "Dey",
      email = "nilanjanadey276@gmail.com",
      role = c("aut")
    ),
    person(
      "Nima", "Jijo",
      email = "nimajijopallath@gmail.com",
      role = c("aut")
    ),
    person(
      "Namrata", "Kharat",
      email = "namratak.ndmc@gmail.com",
      role = c("aut")
    ),
    person(
      "Saket", "Choudhary",
      email = "saketc@iitb.ac.in",
      role = c("aut", "cre")
    )
  )
Description: Provides a preprocessing pipeline for antimicrobial
        resistance (AMR) surveillance data, exploratory data analysis
        (EDA) tools for reviewing cohorts prior to modelling, and
        burden estimation. Supports polymicrobial weighting,
        multidrug-resistant (MDR) and extensively drug-resistant (XDR)
        classification, resistance profile estimation, and
        disability-adjusted life year (DALY) calculations.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: dplyr (>= 1.0.0), tidyr (>= 1.0.0), stringr (>= 1.4.0),
        stringdist (>= 0.9.0), lubridate (>= 1.7.0), magrittr (>=
        2.0.0), readr (>= 2.0.0), readxl (>= 1.3.0), tibble (>= 3.0.0),
        rlang (>= 0.4.0), ggplot2 (>= 3.4.0), scales (>= 1.2.0),
        fitdistrplus (>= 1.1.0), RColorBrewer (>= 1.1.0), ggridges (>=
        0.5.0), tidytext (>= 0.3.0)
SystemRequirements: Python (>= 3.8) with the 'alethia' package for
        ICD-10 semantic embedding (optional; only needed when
        prep_map_diagnosis_to_icd() is called with method =
        "python_embedding"). CmdStan (>= 2.33) for Pathway 2 Bayesian
        estimation (optional; install via cmdstanr::install_cmdstan()
        after installing the 'cmdstanr' package).
Suggests: bayesplot (>= 1.10.0), cmdstanr (>= 0.7.0), testthat (>=
        3.0.0), knitr, rmarkdown, pkgdown, ggpubr (>= 0.4.0),
        reticulate (>= 1.28), Matrix, osqp, quadprog, posterior (>=
        1.0.0), pbivnorm, ComplexHeatmap, circlize
Additional_repositories: https://stan-dev.r-universe.dev
VignetteBuilder: knitr
URL: https://saketlab.github.io/anumaan/,
        https://github.com/saketlab/anumaan
BugReports: https://github.com/saketlab/anumaan/issues
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: libicu-dev python3 libx11-dev
Repository: https://saketlab.r-universe.dev
Date/Publication: 2026-10-20 05:05:24 UTC
RemoteUrl: https://github.com/saketlab/anumaan
RemoteRef: HEAD
RemoteSha: d6c34fce57a87de98e49c62702303eddcf8de610
NeedsCompilation: no
Packaged: 2026-10-20 06:04:03 UTC; root
Author: Nilanjana Dey [aut],
  Nima Jijo [aut],
  Namrata Kharat [aut],
  Saket Choudhary [aut, cre]
Maintainer: Saket Choudhary <saketc@iitb.ac.in>