v1.8.0 release

.github/workflows/R-CMD-check.yaml

@@ -4,7 +4,7 @@ name: R CI/CD test #R-CMD-check
 
 on:
   push:
-    # branches: [main, master, develop]
+    branches: [main, master, develop]
     paths-ignore:
       - '**.md'  # prevent md files (e.g., README.md) in any repo dir from trigering workflow
       - '**.bib'
@@ -37,10 +37,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
+          # - {os: macOS-latest,   r: 'release'}
+          # - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          # - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       #GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 

.gitignore

@@ -8,3 +8,4 @@ inst/doc/**/*.html
 renv/
 examples
 tests/*.xlsx
+.VSCodeCounter/*

DESCRIPTION

@@ -1,19 +1,19 @@
 Package: useeior
 Type: Package
 Title: USEEIO R modeling software
-Version: 1.7.2
-Date: 2025-7-28
+Version: 1.8.0
+Date: 2025-11-10
 Authors@R: c(
   person("Ben","Young", email="ben.young@erg.com", role="aut"),
   person("Jorge","Vendries", email="jvendries@gmail.com", role="aut"),
-  person("Wesley","Ingwersen", email="ingwersen.wesley@epa.gov", role= c("aut", "cre")))
+  person("Wesley","Ingwersen", email="ingwersw@stanford.edu", role= c("aut", "cre")))
 Description: The United States Environmentally-Extended Input-Output model
   is a model used to estimate potential environmental and economic impacts
   associated with the production and consumption of goods and services in the US.
   This package constructs a USEEIO model based on defined configuration parameters,
   calculates, validates, visualizes, and exports USEEIO models.
-URL: https://github.com/USEPA/useeior
-BugReports: https://github.com/USEPA/useeior/issues
+URL: https://github.com/cornerstone-data/useeior
+BugReports: https://github.com/cornerstone-data/useeior/issues
 Imports:
     arrow (>= 2.0.0),
     configr (>= 0.3.4),

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 U.S. EPA
+Copyright (c) 2025 Cornerstone Sustainability Data Initiative
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

R/DisaggregateFunctions.R

@@ -182,7 +182,7 @@ disaggregateSetup <- function (model, configpaths = NULL, setupType = "Disaggreg
     }
 
     if(!is.null(spec$SourceFile)) {
-      fbs <- getFlowbySector(spec$SourceFile)
+      fbs <- getFlowbySector(spec)
 
       # TODO: check if this if statement is necessary. 
       # That is, confirm that disaggregation cannot happen from SourceFile and thus this if statement would not be entered 

R/ExternalImportFactors.R

@@ -19,15 +19,13 @@ loadExternalImportFactors <- function(model, configpaths = NULL) {
 #' @return IFtable, dataframe of unprocessed import factors
 readImportFactorTable <- function(IFSpec, configpaths = NULL) {
   # Read in file with Import factors
-  if(is.null(IFSpec$FileLocation)){
+  if(is.null(IFSpec$FileLocation) || IFSpec$FileLocation == "useeior"){
     filename <- getInputFilePath(configpaths, folderPath = "extdata", filename = IFSpec$StaticFile)
-  } else if(IFSpec$FileLocation == "DataCommons") {
-    filename <- loadDataCommonsfile(IFSpec$StaticFile)    
-  } else if(IFSpec$FileLocation == "useeior") {
-    filename <- getInputFilePath(configpaths, folderPath = "extdata", filename = IFSpec$StaticFile)
-  }
-  IFTable <- utils::read.table(filename, sep = ",", header = TRUE,
+  } else {
+    filename <- loadDataFile(IFSpec$StaticFile, IFSpec$FileLocation, "ImportFactors")    
+    IFTable <- utils::read.table(filename, sep = ",", header = TRUE,
                                stringsAsFactors = FALSE)
+  }
   return(IFTable)
 }
 

R/FlowsaFunctions.R

@@ -21,7 +21,7 @@ getFlowbySectorCollapsed <- function(sat_spec) {
       }
     }
   } else {
-    f <- loadDataCommonsfile(sat_spec$StaticFile)
+    f <- loadDataFile(sat_spec$StaticFile, sat_spec$FileLocation, "SatelliteTable")
     fbs <- as.data.frame(arrow::read_parquet(f))
     # collapse the FBS sector columns into one column based on FlowType
     fbs$Sector <- NA
@@ -77,10 +77,10 @@ prepareFlowBySectorCollapsed <- function(fbsc, satellite=TRUE) {
 
 
 #' Load flowsa's FlowBySector df
-#' @param filepath, a filepath to local parquet file
+#' @param sat_spec, a specification file
 #' @return A data frame for flowsa data in sector by region totals format
-getFlowbySector <- function(filepath) {
-  f <- loadDataCommonsfile(filepath)
+getFlowbySector <- function(sat_spec) {
+  f <- loadDataFile(sat_spec$StaticFile, sat_spec$FileLocation, "SatelliteTable")
   fbs <- as.data.frame(arrow::read_parquet(f))
   fbs <- prepareFlowBySectorCollapsed(fbs, satellite=FALSE)
   return(fbs)

R/LCIAfmtFunctions.R

@@ -37,7 +37,7 @@ getImpactMethod <- function(ind_spec) {
     imp_method <- lciafmt$get_mapped_method(method_id = parameters$method_id,
                                             indicators = indicators, methods = methods)
   } else {
-    f <- loadDataCommonsfile(ind_spec$StaticFile)
+    f <- loadDataFile(ind_spec$StaticFile, ind_spec$FileLocation, "Indicators")
     imp_method <- as.data.frame(arrow::read_parquet(f))
   }
 

R/LoadIndicators.R

@@ -21,7 +21,7 @@ loadIndicators <- function(model) {
    meta <- data.frame()
    factors <- data.frame()
    for (s in model$specs$Indicators) {
-      logging::loginfo(paste0("Getting ", s$Name, " indicator from ", s$FileLocation, "..."))
+      logging::loginfo(paste0("Loading ", s$Name, " indicator..."))
 
       # Populate metadata
       meta_fields <- c("Name","Code","Group","Unit","SimpleUnit","SimpleName")

R/LoadSatellites.R

@@ -41,7 +41,7 @@ loadSatTables <- function(model) {
     if(sat_spec$FileLocation == 'None'){
       logging::loginfo(paste0("Generating ", sat_spec$FullName, " flows..."))      
     } else {
-      logging::loginfo(paste0("Loading ", sat_spec$FullName, " flows from ", sat_spec$FileLocation, "..."))
+      logging::loginfo(paste0("Loading ", sat_spec$FullName, " flows..."))
     }
     if(sat_spec$SectorListSource == "NAICS" && sat_spec$SectorListYear != model$specs$BaseIOSchema) {
       logging::logwarn(paste0("SectorListYear of ", sat_spec$FullName," does not match the BaseIOSchema ",
@@ -117,12 +117,9 @@ generateTbSfromSatSpec <- function(sat_spec, model) {
       }
     }
     totals_by_sector <- do.call(eval(totalsgenfunction), list(params))
-  } else if (sat_spec$FileLocation == "DataCommons") {
-    f <- loadDataCommonsfile(sat_spec$StaticFile)
-    totals_by_sector <- utils::read.table(f, sep = ",", header = TRUE, stringsAsFactors = FALSE,
-                                          fileEncoding = 'UTF-8-BOM')
   } else {
-    totals_by_sector <- utils::read.table(sat_spec$StaticFile, sep = ",",
+    f <- loadDataFile(sat_spec$StaticFile, sat_spec$FileLocation, "SatelliteTable")
+    totals_by_sector <- utils::read.table(f, sep = ",",
                                           header = TRUE, stringsAsFactors = FALSE,
                                           fileEncoding = 'UTF-8-BOM')    
   }

R/StateiorFunctions.R

@@ -1,9 +1,9 @@
 # Functions for handling data from stateior, https://github.com/USEPA/stateior
 
 #' Load two-region IO data of model iolevel and year from user's local directory
-#' or the EPA Data Commons.
+#' or a specified file location.
 #' @description Load two-region IO data of model iolevel and year from user's
-#' local directory or the EPA Data Commons.
+#' local directory or specified file location.
 #' @param model An EEIO form USEEIO model object with model specs and IO meta data loaded.
 #' @param dataname Name of desired IO data, can be "Make", "Use", "DomesticUse",
 #' "UseTransactions", "FinalDemand", "InternationalTradeAdjustment,
@@ -35,7 +35,15 @@ getTwoRegionIOData <- function(model, dataname) {
   }
   # Load data
   logging::loginfo(paste0("Loading ", filename))
-  TwoRegionIOData <- readRDS(loadDataCommonsfile(paste0("stateio/", filename, ".rds")))
+  filename <-  paste0(filename, ".rds")
+  if (!is.null(model$specs$IOFileLocation)) {
+    f <- loadDataFile(filename, model$specs$IOFileLocation, "stateior")
+  } else {
+    #handle case where Data Commons files have subdirectory
+    f <- loadDataFile(paste0("stateio/",filename), "DataCommons", "stateior")
+  }
+
+  TwoRegionIOData <- readRDS(f)
   # Keep SoI and RoUS only
   TwoRegionIOData <- TwoRegionIOData[[state]]
   if(dataname %in% c("UseTransactions", "DomesticUseTransactions")) {

R/UtilityFunctions.R

@@ -150,51 +150,98 @@ writeMatrixasBinFile <- function(matrix, path) {
   close(out)
 }
 
-#' downloads files from the Data Commons and stores in a local temporary data directory
+#' Downloads files from a given source and stores in a local data directory
 #' @param source The name of the source file (e.g. "TRACI_2.1_v1.parquet")
-#' @param subdirectory The name of the package where the source file is stored on
-#' Data Commons including any subfolders (e.g. "lciafmt/traci_2_1")
-#' @param debug_url The Data Commons base url, including directory and subdirectories
-downloadDataCommonsfile <- function(source, subdirectory, debug_url) {
+#' @param subdirectory The name of the subdirectory where the source file is stored on
+#' remote location including any subfolders (e.g. "lciafmt/traci_2_1"). May be empty.
+#' @param url The url of the data storage location
+#' @param query_string A string for URLs where query string is present after file name.
+#' e.g. "?download=1". May be empty.
+#' @param localpath A string value looked up from LocalStorageConfig with a path for local storage
+#'  like "flowsa/FlowBySector"
+#' @return NULL if successful
+downloadDataFile <- function(source, subdirectory, url, query_string, localpath) {
   # Define file directory
-  directory <- paste0(rappdirs::user_data_dir(), "/", subdirectory)
+  directory <- paste0(rappdirs::user_data_dir(), "/", localpath)
   # Check for and create subdirectory if necessary
   if(!file.exists(directory)){
     dir.create(directory, recursive = TRUE)
   }
 
   # Download file
-  utils::download.file(paste0(debug_url, "/", source),
-                       paste0(directory, "/", source),
+  utils::download.file(paste0(file.path(url, source), query_string),
+                       file.path(directory, source),
                        mode = "wb", quiet = TRUE)
 }
 
-#' Load the static file originating from Data Commons either by loading from local directory
-#' or downloading from Data Commons and 
-#' saving to local directory
+#' Load the file originating from a remote location
 #' @param static_file The name of a static file, including the subdirectories
-#' @return The static file originating from Data Commons
-loadDataCommonsfile <- function(static_file) {
+#' @param location The name of the data store location, which is used to look up the URL in RemoteLocationConfig.yml 
+#' @param type A string that matches a key value in LocalStorageConfig.yml
+#' @return The static file loaded from the location or local cache
+loadDataFile <- function(static_file, location, type) {
   # load method name
   method_name <- static_file
   # define symbol to split method name
   pat <- "(.*)/(.*)"
   # subdirectory is the string of the method name prior to the last "/"
-  subdirectory <- sub(pat, "\\1", method_name)
+
+  if (grepl(pat,method_name)) {
+    remotesubdirectory <- sub(pat, "\\1", method_name)  
+  } else {
+    remotesubdirectory <- ""
+  }
+
   # file name is the string of the method name after the last "/"
   file_name <- sub(pat, "\\2", method_name)
 
-  # url for data commons
-  debug_url <- paste0("https://dmap-data-commons-ord.s3.amazonaws.com/", subdirectory)
-
-  directory <- paste0(rappdirs::user_data_dir(), "/", subdirectory)
+  #If file name has a query string strip it off
+  query_string <- ""
+  if(grepl("\\?",file_name)) {
+    name_parts <- strsplit(method_name,"\\?")
+    file_name <- name_parts[[1]][1]
+    query_string <- paste0("?",name_parts[[1]][2])
+  }
+
+  #Load location config
+  configpath <- system.file("extdata/RemoteLocationConfig.yml", package = "useeior")
+  remoteconfig <- configr::read.config(configpath)
+  #Load local storage config
+  configpath <- system.file("extdata/LocalStorageConfig.yml", package = "useeior")
+  localconfig <- configr::read.config(configpath)
+
+  #Use local storage info for local storage path
+  #Local cache
+  localpath <- ""
+  if(remotesubdirectory != "") {
+    localpath <- remotesubdirectory
+  } else if(!is.null(localconfig[[type]])) {
+    localpath <- localconfig[[type]]
+  }
+  directory <- file.path(rappdirs::user_data_dir(), localpath)
 
   # file must be saved in the local directory
   f <- paste0(directory,'/', file_name)
 
   if(!file.exists(f)){
-    logging::loginfo(paste0("file not found, downloading from ", debug_url))
-    downloadDataCommonsfile(file_name, subdirectory, debug_url)
+    if (grepl("Zenodo", location)) {
+      # Extract the entry ID from the model spec for use in url
+      id <- sub("Zenodo", "", location)
+      location <- "Zenodo"
+    } else {
+      id <- ""
+    }
+    if (is.null(remoteconfig[[location]])) {
+      logging::logerror(paste("The location", location," does not have a URL associated with it. ",
+                              "Ensure it is listed in RemoteLocationConfig.yml"))
+      return(NULL)
+    } else {
+      url <- file.path(sub("__ID__", id, remoteconfig[[location]]),
+                       remotesubdirectory)
+    }
+    logging::loginfo(paste0("file not found, downloading from ", url))
+    downloadDataFile(file_name, remotesubdirectory, url, query_string=query_string,
+                     localpath=localpath)
   }
   return(f)
 }

README.md

@@ -1,6 +1,6 @@
 # useeior <img src="inst/img/logo.png" align="right" width="240" />
 <!-- badges: start -->
-[![R CI/CD test](https://github.com/USEPA/useeior/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/USEPA/useeior/actions/workflows/R-CMD-check.yaml)
+[![R CI/CD test](https://github.com/cornerstone-data/useeior/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cornerstone-data/useeior/actions/workflows/R-CMD-check.yaml)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 [![useeior DOI](http://img.shields.io/badge/useeior%20DOI-10.5281/zenodo.7020213-blue.svg)](https://doi.org/10.5281/zenodo.7020213)
 [![useeior paper](http://img.shields.io/badge/useeior%20paper-10.3390/app12094469-blue.svg)](https://doi.org/10.3390/app12094469)
@@ -12,8 +12,8 @@ The [model object](format_specs/Model.md) is the primary output that is built ac
 [Model specifications](inst/extdata/modelspecs) and associated hybridization specifications, e.g. [disaggregation](inst/extdata/disaggspecs), for EPA-validated models are included in the package.
 
 `useeior` offers various functions for validating, calculating, visualizing, and writing out models and/or their components.
-`useeior` is a core component of the [USEEIO Modeling Framework](https://github.com/USEPA/useeio) and is in a stable development state.
-Users intending to use the package for production purposes and applications should use [Releases](https://github.com/USEPA/useeior/releases).
+`useeior` is a core component of the [USEEIO Modeling Framework](https://github.com/cornerstone-data/useeio) and is in a stable development state.
+Users intending to use the package for production purposes and applications should use [Releases](https://github.com/cornerstone-data/useeior/releases).
 `useeior` v1.0.0 was peer-reviewed internally at USEPA and published at Zenodo.
 
 An peer-reviewed article describing `useeior` was published in the journal Applied Sciences in April 2022.
@@ -37,22 +37,22 @@ Li, M., Ingwersen, W.W., Young, B., Vendries, J. and Birney, C., 2022. useeior:
 
 See the following sections for installation and basic usage of `useeior`.
 
-See [Wiki](https://github.com/USEPA/useeior/wiki) for advanced uses, details about built-in data and metadata and how to contribute to `useeior`.
+<!-- See [Wiki](https://github.com/USEPA/useeior/wiki) for advanced uses, details about built-in data and metadata and how to contribute to `useeior`. -->
 
 ## Installation
 
 ```r
 # Install development version from GitHub
 install.packages("devtools")
-devtools::install_github("USEPA/useeior")
+devtools::install_github("cornerstone-data/useeior")
 ```
 
 ```r
 # Install a previously released version (e.g. v1.0.0) from GitHub
-devtools::install_github("USEPA/useeior@v1.0.0")
+devtools::install_github("cornerstone-data/useeior@v1.7.0")
 ```
 
-See [Releases](https://github.com/USEPA/useeior/releases) for all previously released versions.
+See [Releases](https://github.com/cornerstone-data/useeior/releases) for all previously released versions.
 
 ## Usage
 
@@ -225,7 +225,3 @@ Currently, it only compares flow totals between two models. More comparisons wil
 ### Additional Information
 
 A complete list of available functions for calculating, validating, exporting and visualizing model can be found [here](https://github.com/USEPA/useeior/wiki/Using-useeior#calculate-validate-export-visualize-model) in the Wiki.
-
-## Disclaimer
-
-The United States Environmental Protection Agency (EPA) GitHub project code is provided on an "as is" basis and the user assumes responsibility for its use.  EPA has relinquished control of the information and no longer has responsibility to protect the integrity , confidentiality, or availability of the information.  Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA.  The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.