diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..619ef45
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,10 @@
+^.dockerignore$
+^.lintr$
+^.github/
+^Dockerfile$
+^LICENSE\.md$
+^docker-compose.yml$
+^input_dir/
+^output_dir/
+^run-pacta.sh$
+^workflow.pacta.Rproj$
diff --git a/.dockerignore b/.dockerignore
index 40160b5..70fe075 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -4,3 +4,8 @@
 **/Dockerfile
 **/*.md
 **/*.Rproj
+output_dir/**/*
+output_dir
+pacta-data/**/*
+pacta-data
+docker-compose.yml
diff --git a/.github/workflows/R.yml b/.github/workflows/R.yml
new file mode 100644
index 0000000..1023ad1
--- /dev/null
+++ b/.github/workflows/R.yml
@@ -0,0 +1,22 @@
+---
+# This example file will enable R language checks on push or PR to the main
+# branch.
+# It will also run the checks every weeknight at midnight UTC
+#
+# Note the @main in `uses:` on the last line. This will call the latest version
+# of the workflow from the `main` brnach in the RMI-PACTA/actions repo. You can
+# also specify a tag from that repo, or a commit SHA to pin action versions.
+on:
+  pull_request:
+  push:
+    branches: [main]
+  schedule:
+    - cron: '0 0 * * 1,2,3,4,5'
+  workflow_dispatch:
+
+name: R
+
+jobs:
+  R-package:
+    name: R Package Checks
+    uses: RMI-PACTA/actions/.github/workflows/R.yml@main
diff --git a/DESCRIPTION b/DESCRIPTION
index d81c081..c01b343 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,18 +1,41 @@
 Package: workflow.pacta
-Version: 0.0.0.9000
-Type: PACTA
-Description: Run PACTA.
-Depends:
-  dplyr,
-  jsonlite,
-  logger,
-  pacta.portfolio.allocate,
-  pacta.portfolio.audit,
-  pacta.portfolio.import,
-  pacta.portfolio.utils,
-  readr
+Title: Run PACTA
+Version: 0.0.0.9001
+Authors@R: 
+    c(person(given = "CJ",
+             family = "Yetman",
+             role = c("aut", "ctr"),
+             email = "cj@cjyetman.com",
+             comment = c(ORCID = "0000-0001-5099-9500")),
+      person(given = "Jackson", 
+             family = "Hoffart",
+             email = "jackson.hoffart@gmail.com", 
+             role = c("aut", "ctr"),
+             comment = c(ORCID = "0000-0002-8600-5042")),
+      person(given = "Alex",
+             family = "Axthelm",
+             role = c("aut", "cre", "ctr"),
+             email = "aaxthelm@rmi.org",
+             comment = c(ORCID = "0000-0001-8579-8565")),
+      person(given = "RMI",
+             role = c("cph", "fnd"),
+             email = "PACTA4investors@rmi.org"))
+Description: Run the PACTA Analysis.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Imports: 
+    dplyr,
+    jsonlite,
+    logger,
+    pacta.portfolio.allocate,
+    pacta.portfolio.audit, 
+    pacta.portfolio.import,
+    pacta.portfolio.utils,
+    readr
 Remotes:
-  RMI-PACTA/pacta.portfolio.allocate,
-  RMI-PACTA/pacta.portfolio.audit,
-  RMI-PACTA/pacta.portfolio.import,
-  RMI-PACTA/pacta.portfolio.utils
+    RMI-PACTA/pacta.portfolio.allocate,
+    RMI-PACTA/pacta.portfolio.audit,
+    RMI-PACTA/pacta.portfolio.import,
+    RMI-PACTA/pacta.portfolio.utils
diff --git a/Dockerfile b/Dockerfile
index dd9bec6..3f8d7de 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -76,8 +76,10 @@ RUN Rscript -e "\
   pak::pak(c(gh_pkgs)); \
   "
 
-COPY . /
+COPY . /workflow.pacta/
+
+RUN Rscript -e "pak::local_install(root = '/workflow.pacta')"
 
 # set default run behavior
-ENTRYPOINT ["/run-pacta.sh"]
-CMD ["input_dir/default_config.json"]
+ENTRYPOINT ["/workflow.pacta/run-pacta.sh"]
+CMD ["/workflow.pacta/input_dir/default_config.json"]
diff --git a/LICENSE b/LICENSE
index 844b42c..7ec6c95 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2023 RMI
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2024
+COPYRIGHT HOLDER: RMI
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..c3f0481
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 RMI
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..422078b
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,7 @@
+# Generated by roxygen2: do not edit by hand
+
+importFrom(logger,log_debug)
+importFrom(logger,log_error)
+importFrom(logger,log_info)
+importFrom(logger,log_trace)
+importFrom(logger,log_warn)
diff --git a/R/calc_weights_and_outputs.R b/R/calc_weights_and_outputs.R
new file mode 100644
index 0000000..d06b598
--- /dev/null
+++ b/R/calc_weights_and_outputs.R
@@ -0,0 +1,172 @@
+calc_weights_and_outputs <- function(
+  total_portfolio,
+  portfolio_type,
+  output_dir,
+  data_dir,
+  equity_market_list,
+  scenario_sources_list,
+  scenario_geographies_list,
+  sector_list,
+  has_map
+) {
+
+  log_info("Starting {portfolio_type} calculations.")
+
+  log_debug("Subsetting {portfolio_type} portfolio.")
+  port_raw_all <- pacta.portfolio.allocate::create_portfolio_subset(
+    portfolio = total_portfolio,
+    portfolio_type = portfolio_type
+  )
+
+  if (pacta.portfolio.utils::data_check(port_raw_all)) {
+    log_info(
+      "{portfolio_type} portfolio has data. ",
+      "Beginning {portfolio_type} calculations."
+    )
+
+    log_debug("Calculating {portfolio_type} portfolio weights.")
+    port <- pacta.portfolio.allocate::calculate_weights(
+      portfolio = port_raw_all,
+      portfolio_type = portfolio_type
+    )
+
+    log_debug(
+      "Merging ABCD data from database into {portfolio_type} portfolio."
+    )
+    if (portfolio_type == "Bonds") {
+      id_col <- "credit_parent_ar_company_id"
+    } else {
+      id_col <- "id"
+    }
+    id_col <- "credit_parent_ar_company_id"
+    port <- pacta.portfolio.allocate::merge_abcd_from_db(
+      portfolio = port,
+      portfolio_type = portfolio_type,
+      db_dir = data_dir,
+      equity_market_list = equity_market_list,
+      scenario_sources_list = scenario_sources_list,
+      scenario_geographies_list = scenario_geographies_list,
+      sector_list = sector_list,
+      id_col = id_col
+    )
+
+    # Portfolio weight methodology
+    log_info("Calculating portfolio weight methodology.")
+    log_debug("Calculating portfolio weight allocation.")
+    port_pw <- pacta.portfolio.allocate::port_weight_allocation(port)
+
+    log_debug("Aggregating companies for portfolio weight calculation.")
+    company_pw <- pacta.portfolio.allocate::aggregate_company(port_pw)
+
+    log_debug("Aggregating portfolio for portfolio weight calculation.")
+    port_pw <- pacta.portfolio.allocate::aggregate_portfolio(company_pw)
+
+    if (portfolio_type == "Bonds") {
+      log_info("Ownership weight calculation not defined for Bonds. Skipping.")
+      port_own <- NULL
+      company_own <- NULL
+    } else {
+      # Ownership weight methodology
+      log_info("Calculating ownership methodology.")
+      log_debug("Calculating ownership allocation.")
+      port_own <- pacta.portfolio.allocate::ownership_allocation(port)
+
+      log_debug("Aggregating companies for ownership calculation.")
+      company_own <- pacta.portfolio.allocate::aggregate_company(port_own)
+
+      log_debug("Aggregating portfolio for ownership calculation.")
+      port_own <- pacta.portfolio.allocate::aggregate_portfolio(company_own)
+    }
+
+    # Create combined outputs
+    log_debug("Creating combined {portfolio_type} company outputs.")
+    company_all <- dplyr::bind_rows(company_pw, company_own)
+
+    log_debug("Creating combined {portfolio_type} portfolio outputs.")
+    port_all <- dplyr::bind_rows(port_pw, port_own)
+
+    if (has_map && pacta.portfolio.utils::data_check(company_all)) {
+      log_debug("Creating {portfolio_type} map outputs.")
+      abcd_raw <- pacta.portfolio.allocate::get_abcd_raw(portfolio_type)
+      log_debug("Merging geography data into {portfolio_type} map outputs.")
+      map <- pacta.portfolio.allocate::merge_in_geography(
+        portfolio = company_all,
+        ald_raw = abcd_raw
+      )
+      log_trace("Removing abcd_raw object from memory.")
+      rm(abcd_raw)
+
+      log_debug("Aggregating {portfolio_type} map data.")
+      map <- pacta.portfolio.allocate::aggregate_map_data(map)
+    }
+
+    # Technology Share Calculation
+    if (nrow(port_all) > 0L) {
+      log_debug("Calculating {portfolio_type} portfolio technology share.")
+      port_all <- pacta.portfolio.allocate::calculate_technology_share(
+        df = port_all
+      )
+    }
+
+    if (nrow(company_all) > 0L) {
+      log_debug("Calculating {portfolio_type} company technology share.")
+      company_all <- pacta.portfolio.allocate::calculate_technology_share(
+        df = company_all
+      )
+    }
+
+    # Scenario alignment calculations
+    log_debug("Calculating {portfolio_type} portfolio scenario alignment.")
+    port_all <- pacta.portfolio.allocate::calculate_scenario_alignment(
+      df = port_all
+    )
+
+    log_debug("Calculating {portfolio_type} company scenario alignment.")
+    company_all <- pacta.portfolio.allocate::calculate_scenario_alignment(
+      df = company_all
+    )
+
+    results_company_filename <- file.path(
+      output_dir,
+      paste0(portfolio_type, "_results_company.rds")
+    )
+    if (pacta.portfolio.utils::data_check(company_all)) {
+      log_debug("Saving {portfolio_type} company results.")
+      saveRDS(
+        company_all,
+        results_company_filename
+      )
+    }
+
+    results_portfolio_filename <- file.path(
+      output_dir,
+      paste0(portfolio_type, "_results_portfolio.rds")
+    )
+    if (pacta.portfolio.utils::data_check(port_all)) {
+      log_debug("Saving {portfolio_type} portfolio results.")
+      saveRDS(
+        port_all,
+        results_portfolio_filename
+      )
+    }
+
+    if (has_map && pacta.portfolio.utils::data_check(map)) {
+      log_debug("Saving {portfolio_type} map results.")
+      results_map_filename <- file.path(
+        output_dir,
+        paste0(portfolio_type, "_results_map.rds")
+      )
+      saveRDS(
+        map,
+        results_map_filename
+      )
+    }
+
+  } else {
+    log_trace(
+      "{portfolio_type} portfolio has no rows. ",
+      "Skipping {portfolio_type} calculations."
+    )
+  }
+
+}
diff --git a/R/run_analysis.R b/R/run_analysis.R
new file mode 100644
index 0000000..bec1a0a
--- /dev/null
+++ b/R/run_analysis.R
@@ -0,0 +1,59 @@
+run_analysis <- function(
+  data_dir,
+  output_dir,
+  equity_market_list,
+  scenario_sources_list,
+  scenario_geographies_list,
+  sector_list,
+  has_map
+) {
+
+  # defaulting to WARN to maintain current (silent) behavior.
+  logger::log_threshold(Sys.getenv("LOG_LEVEL", "WARN"))
+  logger::log_formatter(logger::formatter_glue)
+
+  # -------------------------------------------------------------------------
+
+  log_info("Starting PACTA calculations.")
+
+  # quit if there's no relevant PACTA assets --------------------------------
+
+  total_portfolio_path <- file.path(output_dir, "total_portfolio.rds")
+  if (file.exists(total_portfolio_path)) {
+    total_portfolio <- readRDS(total_portfolio_path)
+    log_trace(
+      "Checking for PACTA relevant data in file: \"{total_portfolio_path}\"."
+    )
+    pacta.portfolio.utils::quit_if_no_pacta_relevant_data(total_portfolio)
+  } else {
+    log_warn("file \"{total_portfolio_path}\" does not exist.")
+    warning("File \"total_portfolio.rds\" file does not exist.")
+  }
+
+
+  calc_weights_and_outputs(
+    total_portfolio = total_portfolio,
+    portfolio_type = "Equity",
+    output_dir = output_dir,
+    data_dir = data_dir,
+    equity_market_list = equity_market_list,
+    scenario_sources_list = scenario_sources_list,
+    scenario_geographies_list = scenario_geographies_list,
+    sector_list = sector_list,
+    has_map = has_map
+  )
+
+  calc_weights_and_outputs(
+    total_portfolio = total_portfolio,
+    portfolio_type = "Bonds",
+    output_dir = output_dir,
+    data_dir = data_dir,
+    equity_market_list = equity_market_list,
+    scenario_sources_list = scenario_sources_list,
+    scenario_geographies_list = scenario_geographies_list,
+    sector_list = sector_list,
+    has_map = has_map
+  )
+
+  log_info("Finished PACTA calculations.")
+}
diff --git a/R/run_audit.R b/R/run_audit.R
new file mode 100644
index 0000000..36f55ba
--- /dev/null
+++ b/R/run_audit.R
@@ -0,0 +1,140 @@
+run_audit <- function(
+  data_dir,
+  portfolio_path,
+  output_dir
+) {
+
+  log_info("Starting portfolio audit")
+
+  # load necessary input data -------------------------------------------------
+  log_info("Loading input data.")
+
+  log_debug("Loading currencies.")
+  currencies <- readRDS(file.path(data_dir, "currencies.rds"))
+
+  log_debug("Loading fund data.")
+  fund_data <- readRDS(file.path(data_dir, "fund_data.rds"))
+  log_debug("Loading fund list data.")
+  total_fund_list <- readRDS(
+    file.path(data_dir, "total_fund_list.rds")
+  )
+  log_debug("Loading ISIN to fund table.")
+  isin_to_fund_table <- readRDS(
+    file.path(data_dir, "isin_to_fund_table.rds")
+  )
+
+  log_debug("Loading financial data.")
+  fin_data <- readRDS(file.path(data_dir, "financial_data.rds"))
+
+  log_debug("Loading entity info.")
+  entity_info <- pacta.portfolio.audit::get_entity_info(dir = data_dir)
+
+  log_debug("Loading Equity ABCD flags.")
+  abcd_flags_equity <- readRDS(
+    file.path(data_dir, "abcd_flags_equity.rds")
+  )
+  log_debug("Loading Bonds ABCD flags.")
+  abcd_flags_bonds <- readRDS(
+    file.path(data_dir, "abcd_flags_bonds.rds")
+  )
+
+  log_debug("Loading entity emission intensities.")
+  entity_emission_intensities <- readRDS(
+    file.path(data_dir, "iss_entity_emission_intensities.rds")
+  )
+  log_debug("Loading average sector emission intensities.")
+  avg_sector_eis <- readRDS(
+    file.path(data_dir, "iss_average_sector_emission_intensities.rds")
+  )
+
+
+  # Portfolios --------------------------------------------------------------
+
+  log_info("Reading portfolio from file: \"{portfolio_path}\".")
+  portfolio_raw <- pacta.portfolio.import::read_portfolio_csv(
+    filepaths = portfolio_path
+  )
+
+  log_info("Processing raw portfolio.")
+  portfolio <- pacta.portfolio.audit::process_raw_portfolio(
+    portfolio_raw = portfolio_raw,
+    fin_data = fin_data,
+    fund_data = fund_data,
+    entity_info = entity_info,
+    currencies = currencies,
+    total_fund_list = total_fund_list,
+    isin_to_fund_table = isin_to_fund_table
+  )
+
+  # this is necessary because pacta.portfolio.allocate::add_revenue_split() was
+  # removed in #142, but later we realized that it had a sort of hidden
+  # behavior where if there is no revenue data it maps the
+  # security_mapped_sector column of the portfolio data to financial_sector,
+  # which is necessary later
+  portfolio[["has_revenue_data"]] <- FALSE
+  portfolio[["financial_sector"]] <- portfolio[["security_mapped_sector"]]
+
+  log_debug("Adding ABCD flags to portfolio.")
+  portfolio <- pacta.portfolio.audit::create_ald_flag(
+    portfolio,
+    comp_fin_data = abcd_flags_equity,
+    debt_fin_data = abcd_flags_bonds
+  )
+
+  log_debug("Adding portfolio flags to portfolio.")
+  portfolio_total <- pacta.portfolio.audit::add_portfolio_flags(
+    portfolio = portfolio,
+    currencies = currencies
+  )
+
+  log_debug("Summarizing portfolio.")
+  portfolio_overview <- pacta.portfolio.audit::portfolio_summary(
+    portfolio_total = portfolio_total
+  )
+
+  log_debug("Creating audit file.")
+  audit_file <- pacta.portfolio.audit::create_audit_file(
+    portfolio_total = portfolio_total,
+    has_revenue = FALSE
+  )
+
+  log_debug("Calculating financed emissions.")
+  emissions_totals <-
+    pacta.portfolio.audit::calculate_portfolio_financed_emissions(
+      portfolio_total,
+      entity_info,
+      entity_emission_intensities,
+      avg_sector_eis
+    )
+
+  # Saving -------------------------------------------------------------------
+
+  log_info("Saving output.")
+  log_debug("output directory: \"{output_dir}\".")
+
+  log_debug("Exporting audit information.")
+  pacta.portfolio.audit::export_audit_information_data(
+    audit_file_ = audit_file,
+    portfolio_total_ = portfolio_total,
+    folder_path = output_dir
+  )
+
+  log_debug("Exporting portfolio total.")
+  saveRDS(
+    portfolio_total,
+    file.path(output_dir, "total_portfolio.rds")
+  )
+  log_debug("Exporting portfolio overview.")
+  saveRDS(
+    portfolio_overview,
+    file.path(output_dir, "overview_portfolio.rds")
+  )
+  log_debug("Exporting audit file RDS.")
+  saveRDS(audit_file, file.path(output_dir, "audit_file.rds"))
+  log_debug("Exporting audit file CSV.")
+  readr::write_csv(audit_file, file.path(output_dir, "audit_file.csv"))
+  log_debug("Exporting emissions.")
+  saveRDS(emissions_totals, file.path(output_dir, "emissions.rds"))
+
+  log_info("Portfolio audit finished.")
+}
diff --git a/R/run_pacta.R b/R/run_pacta.R
new file mode 100644
index 0000000..c8241ec
--- /dev/null
+++ b/R/run_pacta.R
@@ -0,0 +1,30 @@
+run_pacta <- function(
+  cfg_path = commandArgs(trailingOnly = TRUE)
+) {
+  log_info("Running PACTA")
+
+  # Read Params
+  log_trace("Determining configuration file path")
+  if (length(cfg_path) == 0L || cfg_path == "") {
+    log_warn("No configuration file specified, using default")
+    cfg_path <- file.path("input_dir", "default_config.json")
+  }
+  log_debug("Loading configuration from file: \"{cfg_path}\".")
+  cfg <- jsonlite::fromJSON(cfg_path)
+
+  run_audit(
+    data_dir = cfg[["data_dir"]],
+    portfolio_path = cfg[["portfolio_path"]],
+    output_dir = cfg[["output_dir"]]
+  )
+  run_analysis(
+    data_dir = cfg[["data_dir"]],
+    output_dir = cfg[["output_dir"]],
+    equity_market_list = cfg[["equity_market_list"]],
+    scenario_sources_list = cfg[["scenario_sources_list"]],
+    scenario_geographies_list = cfg[["scenario_geographies_list"]],
+    sector_list = cfg[["sector_list"]],
+    has_map = cfg[["has_map"]]
+  )
+  log_info("PACTA run complete.")
+}
diff --git a/R/workflow.pacta-package.R b/R/workflow.pacta-package.R
new file mode 100644
index 0000000..e181405
--- /dev/null
+++ b/R/workflow.pacta-package.R
@@ -0,0 +1,11 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom logger log_debug
+#' @importFrom logger log_error
+#' @importFrom logger log_info
+#' @importFrom logger log_trace
+#' @importFrom logger log_warn
+## usethis namespace: end
+NULL
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 0000000..52e3491
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,23 @@
+---
+services:
+  workflow.pacta:
+    build: .
+    # stdin_open: true
+    # tty: true
+    # entrypoint: ["R", "--args"]
+    command: '/input_dir/default_config.json'
+    environment:
+      LOG_LEVEL: TRACE
+    volumes:
+      - type: bind
+        source: ${data_dir:-./pacta-data}
+        target: /pacta-data
+        read_only: true
+      - type: bind
+        source: ${output_dir:-./output_dir}
+        target: /output_dir
+        read_only: false
+      - type: bind
+        source: ${input_dir:-./input_dir}
+        target: /input_dir
+        read_only: true
diff --git a/man/workflow.pacta-package.Rd b/man/workflow.pacta-package.Rd
new file mode 100644
index 0000000..7059e0e
--- /dev/null
+++ b/man/workflow.pacta-package.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/workflow.pacta-package.R
+\docType{package}
+\name{workflow.pacta-package}
+\alias{workflow.pacta}
+\alias{workflow.pacta-package}
+\title{workflow.pacta: Run PACTA}
+\description{
+Run the PACTA Analysis.
+}
+\author{
+\strong{Maintainer}: Alex Axthelm \email{aaxthelm@rmi.org} (\href{https://orcid.org/0000-0001-8579-8565}{ORCID}) [contractor]
+
+Authors:
+\itemize{
+  \item CJ Yetman \email{cj@cjyetman.com} (\href{https://orcid.org/0000-0001-5099-9500}{ORCID}) [contractor]
+  \item Jackson Hoffart \email{jackson.hoffart@gmail.com} (\href{https://orcid.org/0000-0002-8600-5042}{ORCID}) [contractor]
+}
+
+Other contributors:
+\itemize{
+  \item RMI \email{PACTA4investors@rmi.org} [copyright holder, funder]
+}
+
+}
+\keyword{internal}
diff --git a/pacta_01.R b/pacta_01.R
deleted file mode 100644
index aad1dc5..0000000
--- a/pacta_01.R
+++ /dev/null
@@ -1,130 +0,0 @@
-suppressPackageStartupMessages({
-  library(pacta.portfolio.utils)
-  library(pacta.portfolio.import)
-  library(pacta.portfolio.audit)
-  library(dplyr)
-  library(readr)
-  library(jsonlite)
-})
-
-# defaulting to WARN to maintain current (silent) behavior.
-logger::log_threshold(Sys.getenv("LOG_LEVEL", "WARN"))
-logger::log_formatter(logger::formatter_glue)
-
-# -------------------------------------------------------------------------
-
-logger::log_info("Starting portfolio audit")
-
-logger::log_trace("Determining configuration file path")
-cfg_path <- commandArgs(trailingOnly = TRUE)
-if (length(cfg_path) == 0 || cfg_path == "") {
-  logger::log_warn("No configuration file specified, using default")
-  cfg_path <- "input_dir/default_config.json"
-}
-logger::log_debug("Loading configuration from file: \"{cfg_path}\".")
-cfg <- fromJSON(cfg_path)
-
-# load necessary input data ----------------------------------------------------
-
-logger::log_info("Loading input data.")
-
-logger::log_debug("Loading currencies.")
-currencies <- readRDS(file.path(cfg$data_dir, "currencies.rds"))
-
-logger::log_debug("Loading fund data.")
-fund_data <- readRDS(file.path(cfg$data_dir, "fund_data.rds"))
-logger::log_debug("Loading fund list data.")
-total_fund_list <- readRDS(file.path(cfg$data_dir, "total_fund_list.rds"))
-logger::log_debug("Loading ISIN to fund table.")
-isin_to_fund_table <- readRDS(file.path(cfg$data_dir, "isin_to_fund_table.rds"))
-
-logger::log_debug("Loading financial data.")
-fin_data <- readRDS(file.path(cfg$data_dir, "financial_data.rds"))
-
-logger::log_debug("Loading entity info.")
-entity_info <- get_entity_info(dir = cfg$data_dir)
-
-logger::log_debug("Loading Equity ABCD flags.")
-abcd_flags_equity <- readRDS(file.path(cfg$data_dir, "abcd_flags_equity.rds"))
-logger::log_debug("Loading Bonds ABCD flags.")
-abcd_flags_bonds <- readRDS(file.path(cfg$data_dir, "abcd_flags_bonds.rds"))
-
-logger::log_debug("Loading entity emission intensities.")
-entity_emission_intensities <- readRDS(file.path(cfg$data_dir, "iss_entity_emission_intensities.rds"))
-logger::log_debug("Loading average sector emission intensities.")
-average_sector_emission_intensities <- readRDS(
-  file.path(cfg$data_dir, "iss_average_sector_emission_intensities.rds")
-)
-
-
-# Portfolios -------------------------------------------------------------------
-
-logger::log_info("Reading portfolio from file: \"{cfg$portfolio_path}\".")
-portfolio_raw <- read_portfolio_csv(cfg$portfolio_path)
-
-logger::log_info("Processing raw portfolio.")
-portfolio <- process_raw_portfolio(
-  portfolio_raw = portfolio_raw,
-  fin_data = fin_data,
-  fund_data = fund_data,
-  entity_info = entity_info,
-  currencies = currencies,
-  total_fund_list = total_fund_list,
-  isin_to_fund_table = isin_to_fund_table
-)
-
-# FIXME: this is necessary because pacta.portfolio.allocate::add_revenue_split()
-#  was removed in #142, but later we realized that it had a sort of hidden
-#  behavior where if there is no revenue data it maps the security_mapped_sector
-#  column of the portfolio data to financial_sector, which is necessary later
-portfolio <-
-  portfolio %>%
-  mutate(
-    has_revenue_data = FALSE,
-    financial_sector = .data$security_mapped_sector
-  )
-
-logger::log_debug("Adding ABCD flags to portfolio.")
-portfolio <- create_ald_flag(portfolio, comp_fin_data = abcd_flags_equity, debt_fin_data = abcd_flags_bonds)
-
-logger::log_debug("Adding portfolio flags to portfolio.")
-portfolio_total <- add_portfolio_flags(portfolio)
-
-logger::log_debug("Summarizing portfolio.")
-portfolio_overview <- portfolio_summary(portfolio_total)
-
-logger::log_debug("Creating audit file.")
-audit_file <- create_audit_file(portfolio_total, has_revenue = FALSE)
-
-logger::log_debug("Calculating financed emissions.")
-emissions_totals <- calculate_portfolio_financed_emissions(
-  portfolio_total,
-  entity_info,
-  entity_emission_intensities,
-  average_sector_emission_intensities
-)
-
-# Saving -----------------------------------------------------------------------
-
-logger::log_info("Saving output.")
-logger::log_debug("output directory: \"{cfg$output_dir}\".")
-
-logger::log_debug("Exporting audit information.")
-export_audit_information_data(
-  audit_file_ = audit_file,
-  portfolio_total_ = portfolio_total,
-  folder_path = cfg$output_dir
-)
-
-logger::log_debug("Exporting portfolio total.")
-saveRDS(portfolio_total, file.path(cfg$output_dir, "total_portfolio.rds"))
-logger::log_debug("Exporting portfolio overview.")
-saveRDS(portfolio_overview, file.path(cfg$output_dir, "overview_portfolio.rds"))
-logger::log_debug("Exporting audit file RDS.")
-saveRDS(audit_file, file.path(cfg$output_dir, "audit_file.rds"))
-logger::log_debug("Exporting audit file CSV.")
-write_csv(audit_file, file.path(cfg$output_dir, "audit_file.csv"))
-logger::log_debug("Exporting emissions.")
-saveRDS(emissions_totals, file.path(cfg$output_dir, "emissions.rds"))
-
-logger::log_info("Portfolio audit finished.")
diff --git a/pacta_02.R b/pacta_02.R
deleted file mode 100644
index cee4e05..0000000
--- a/pacta_02.R
+++ /dev/null
@@ -1,261 +0,0 @@
-suppressPackageStartupMessages({
-  library(pacta.portfolio.utils)
-  library(pacta.portfolio.allocate)
-  library(dplyr)
-  library(jsonlite)
-})
-
-# defaulting to WARN to maintain current (silent) behavior.
-logger::log_threshold(Sys.getenv("LOG_LEVEL", "WARN"))
-logger::log_formatter(logger::formatter_glue)
-
-# ------------------------------------------------------------------------------
-
-logger::log_info("Starting PACTA calculations.")
-
-logger::log_trace("Determining configuration file path")
-cfg_path <- commandArgs(trailingOnly = TRUE)
-if (length(cfg_path) == 0 || cfg_path == "") {
-  logger::log_warn("No configuration file specified, using default")
-  cfg_path <- "input_dir/default_config.json"
-}
-logger::log_debug("Loading configuration from file: \"{cfg_path}\".")
-cfg <- fromJSON(cfg_path)
-
-# quit if there's no relevant PACTA assets -------------------------------------
-
-total_portfolio_path <- file.path(cfg$output_dir, "total_portfolio.rds")
-if (file.exists(total_portfolio_path)) {
-  total_portfolio <- readRDS(total_portfolio_path)
-  logger::log_trace("Checking for PACTA relevant data in file: \"{total_portfolio_path}\".")
-  quit_if_no_pacta_relevant_data(total_portfolio)
-} else {
-  logger::log_warn("file \"{total_portfolio_path}\" does not exist.")
-  warning("This is weird... the `total_portfolio.rds` file does not exist in the `30_Processed_inputs` directory.")
-}
-
-
-# Equity -----------------------------------------------------------------------
-
-logger::log_info("Starting equity calculations.")
-
-logger::log_debug("Subsetting equity portfolio.")
-port_raw_all_eq <- create_portfolio_subset(total_portfolio, "Equity")
-
-if (inherits(port_raw_all_eq, "data.frame") && nrow(port_raw_all_eq) > 0) {
-  logger::log_info("Equity portfolio has data. Beginning equity calculations.")
-  map_eq <- NA
-  company_all_eq <- NA
-  port_all_eq <- NA
-
-  logger::log_debug("Calculating quity portfolio weights.")
-  port_eq <- calculate_weights(port_raw_all_eq, "Equity")
-
-  logger::log_debug("Merging ABCD data from database into equity portfolio.")
-  port_eq <- merge_abcd_from_db(
-    portfolio = port_eq,
-    portfolio_type= "Equity",
-    db_dir = cfg$data_dir,
-    equity_market_list = cfg$equity_market_list,
-    scenario_sources_list = cfg$scenario_sources_list,
-    scenario_geographies_list = cfg$scenario_geographies_list,
-    sector_list = cfg$sector_list,
-    id_col = "id"
-  )
-
-  # Portfolio weight methodology
-  logger::log_info("Calculating portfolio weight methodology.")
-  logger::log_debug("Calculating portfolio weight allocation.")
-  port_pw_eq <- port_weight_allocation(port_eq)
-
-  logger::log_debug("Aggregating companies for portfolio weight calculation.")
-  company_pw_eq <- aggregate_company(port_pw_eq)
-
-  logger::log_debug("Aggregating portfolio for portfolio weight calculation.")
-  port_pw_eq <- aggregate_portfolio(company_pw_eq)
-
-  # Ownership weight methodology
-  logger::log_info("Calculating ownership methodology.")
-  logger::log_debug("Calculating ownership allocation.")
-  port_own_eq <- ownership_allocation(port_eq)
-
-  logger::log_debug("Aggregating companies for ownership calculation.")
-  company_own_eq <- aggregate_company(port_own_eq)
-
-  logger::log_debug("Aggregating portfolio for ownership calculation.")
-  port_own_eq <- aggregate_portfolio(company_own_eq)
-
-  # Create combined outputs
-  logger::log_debug("Creating combined equity company outputs.")
-  company_all_eq <- bind_rows(company_pw_eq, company_own_eq)
-
-  logger::log_debug("Creating combined equity portfolio outputs.")
-  port_all_eq <- bind_rows(port_pw_eq, port_own_eq)
-
-  if (cfg$has_map) {
-    logger::log_debug("Creating equity map outputs.")
-    abcd_raw_eq <- get_abcd_raw("Equity")
-    logger::log_debug("Merging geography data into equity map outputs.")
-    map_eq <- merge_in_geography(company_all_eq, abcd_raw_eq)
-    logger::log_trace("Removing abcd_raw_eq object from memory.")
-    rm(abcd_raw_eq)
-
-    logger::log_debug("Aggregating equity map data.")
-    map_eq <- aggregate_map_data(map_eq)
-  }
-
-  # Technology Share Calculation
-  logger::log_debug("Calculating equity portfolio technology share.")
-  port_all_eq <- calculate_technology_share(port_all_eq)
-
-  logger::log_debug("Calculating equity company technology share.")
-  company_all_eq <- calculate_technology_share(company_all_eq)
-
-  # Scenario alignment calculations
-  logger::log_debug("Calculating equity portfolio scenario alignment.")
-  port_all_eq <- calculate_scenario_alignment(port_all_eq)
-
-  logger::log_debug("Calculating equity company scenario alignment.")
-  company_all_eq <- calculate_scenario_alignment(company_all_eq)
-
-  if (data_check(company_all_eq)) {
-    logger::log_debug("Saving equity company results.")
-    saveRDS(company_all_eq, file.path(cfg$output_dir, "Equity_results_company.rds"))
-  }
-
-  if (data_check(port_all_eq)) {
-    logger::log_debug("Saving equity portfolio results.")
-    saveRDS(port_all_eq, file.path(cfg$output_dir, "Equity_results_portfolio.rds"))
-  }
-
-  if (cfg$has_map) {
-    if (data_check(map_eq)) {
-      logger::log_debug("Saving equity map results.")
-      saveRDS(map_eq, file.path(cfg$output_dir, "Equity_results_map.rds"))
-    }
-  }
-
-  logger::log_trace("Removing equity portfolio objects from memory.")
-  rm(port_raw_all_eq)
-  rm(port_eq)
-  rm(port_pw_eq)
-  rm(port_own_eq)
-  rm(port_all_eq)
-  rm(company_pw_eq)
-  rm(company_own_eq)
-  rm(company_all_eq)
-} else {
-  logger::log_trace(
-    "Equity portfolio has no rows. Skipping equity calculations."
-  )
-}
-
-# Bonds ------------------------------------------------------------------------
-
-logger::log_info("Starting bonds calculations.")
-port_raw_all_cb <- create_portfolio_subset(total_portfolio, "Bonds")
-
-if (inherits(port_raw_all_cb, "data.frame") && nrow(port_raw_all_cb) > 0) {
-  logger::log_info("Bonds portfolio has data. Beginning bonds calculations.")
-  map_cb <- NA
-  company_all_cb <- NA
-  port_all_cb <- NA
-
-  logger::log_debug("Calculating bonds portfolio weights.")
-  port_cb <- calculate_weights(port_raw_all_cb, "Bonds")
-
-  logger::log_debug("Merging ABCD data from database into bonds portfolio.")
-  port_cb <- merge_abcd_from_db(
-    portfolio = port_cb,
-    portfolio_type = "Bonds",
-    db_dir = cfg$data_dir,
-    equity_market_list = cfg$equity_market_list,
-    scenario_sources_list = cfg$scenario_sources_list,
-    scenario_geographies_list = cfg$scenario_geographies_list,
-    sector_list = cfg$sector_list,
-    id_col = "credit_parent_ar_company_id"
-  )
-
-  # Portfolio weight methodology
-  logger::log_info("Calculating bonds portfolio weight methodology.")
-  logger::log_debug("Calculating bonds portfolio weight allocation.")
-  port_pw_cb <- port_weight_allocation(port_cb)
-
-  logger::log_debug(
-    "Aggregating companies for bonds portfolio weight calculation."
-  )
-  company_pw_cb <- aggregate_company(port_pw_cb)
-
-  logger::log_debug(
-    "Aggregating portfolio for bonds portfolio weight calculation."
-  )
-  port_pw_cb <- aggregate_portfolio(company_pw_cb)
-
-  # Create combined outputs
-  logger::log_debug("Creating combined bonds company outputs.")
-  company_all_cb <- company_pw_cb
-
-  logger::log_debug("Creating combined bonds portfolio outputs.")
-  port_all_cb <- port_pw_cb
-
-  if (cfg$has_map) {
-    if (data_check(company_all_cb)) {
-      logger::log_debug("Creating bonds map outputs.")
-      abcd_raw_cb <- get_abcd_raw("Bonds")
-      logger::log_debug("Merging geography data into bonds map outputs.")
-      map_cb <- merge_in_geography(company_all_cb, abcd_raw_cb)
-      logger::log_trace("Removing abcd_raw_cb object from memory.")
-      rm(abcd_raw_cb)
-
-      logger::log_debug("Aggregating bonds map data.")
-      map_cb <- aggregate_map_data(map_cb)
-    }
-  }
-
-  # Technology Share Calculation
-  if (nrow(port_all_cb) > 0) {
-    logger::log_debug("Calculating bonds portfolio technology share.")
-    port_all_cb <- calculate_technology_share(port_all_cb)
-  }
-
-  if (nrow(company_all_cb) > 0) {
-    logger::log_debug("Calculating bonds company technology share.")
-    company_all_cb <- calculate_technology_share(company_all_cb)
-  }
-
-  # Scenario alignment calculations
-  logger::log_debug("Calculating bonds portfolio scenario alignment.")
-  port_all_cb <- calculate_scenario_alignment(port_all_cb)
-
-  logger::log_debug("Calculating bonds company scenario alignment.")
-  company_all_cb <- calculate_scenario_alignment(company_all_cb)
-
-  if (data_check(company_all_cb)) {
-    logger::log_debug("Saving bonds company results.")
-    saveRDS(company_all_cb, file.path(cfg$output_dir, "Bonds_results_company.rds"))
-  }
-
-  if (data_check(port_all_cb)) {
-    logger::log_debug("Saving bonds portfolio results.")
-    saveRDS(port_all_cb, file.path(cfg$output_dir, "Bonds_results_portfolio.rds"))
-  }
-  
-  if (cfg$has_map) {
-    if (data_check(map_cb)) {
-      logger::log_debug("Saving bonds map results.")
-      saveRDS(map_cb, file.path(cfg$output_dir, "Bonds_results_map.rds"))
-    }
-  }
-
-  logger::log_trace("Removing bonds portfolio objects from memory.")
-  rm(port_raw_all_cb)
-  rm(port_cb)
-  rm(port_pw_cb)
-  rm(port_all_cb)
-  rm(company_pw_cb)
-  rm(company_all_cb)
-} else {
-  logger::log_trace("Bonds portfolio has no rows. Skipping bonds calculations.")
-}
-
-logger::log_info("Finished PACTA calculations.")
diff --git a/run-pacta.sh b/run-pacta.sh
index f13fe59..00138df 100755
--- a/run-pacta.sh
+++ b/run-pacta.sh
@@ -3,5 +3,4 @@
 # Set permissions so that new files can be deleted/overwritten outside docker
 umask 000
 
-Rscript --vanilla pacta_01.R "${1}" \
-  && Rscript --vanilla pacta_02.R "${1}"
+Rscript --vanilla -e 'workflow.pacta:::run_pacta()' "${1}"