diff --git a/.github/labeler.yml b/.github/labeler.yml
new file mode 100644
index 00000000000..58bb5ccb80f
--- /dev/null
+++ b/.github/labeler.yml
@@ -0,0 +1,57 @@
+#
+# Add project labels
+#
+
+# Add 'Documentation' label to any changes in the documentation
+
+'Documentation':
+  - book_source/**
+  - documentation/**
+  - CONTRIBUTING.md
+  - DEBUGING.md
+  - DEV-INTRO.md
+  - README.md
+
+# Add 'Dockerfile' label to any changes in the docker directory
+'Dockerfile':
+  - docker/**
+
+
+# Add 'Website' label to any changes in the web directory
+
+'Website':
+  - web/**
+
+# Add 'Base' label to any changes in the base directory
+
+'Base':
+  - base/**
+
+# Add 'Models' label to any changes in the models directory
+
+'Models':
+  - models/**
+
+# Add 'Modules' label to any changes in the modules directory
+
+'Modules':
+  - modules/**
+
+# Add 'GitHub Actions' label to any changes in the .github/workflows directory
+
+'GitHub Actions':
+  - .github/workflows/**
+
+# Add 'Scripts' label to any changes in the scripts directory
+
+'Scripts':
+  - scripts/**
+
+# Add 'Tests' label to any changes in the tests directory
+
+'Tests':
+  - tests/**
+  - '**/tests/**'
+  - '!**/tests/Rcheck_reference.log'
+
+
diff --git a/.github/settings.yml b/.github/settings.yml
new file mode 100644
index 00000000000..a7d87f7d2f9
--- /dev/null
+++ b/.github/settings.yml
@@ -0,0 +1,30 @@
+#Define the colour of labels over here
+
+labels:
+
+  - name: "Documentation"
+    color: a2dcf2
+
+  - name: "Dockerfile"
+    color: 0052CC
+
+  - name: "Website"
+    color: 84b6eb
+
+  - name: "Base"
+    color: 1ED626
+
+  - name: "Models"
+    color: C5DEF5
+
+  - name: "Modules"
+    color: FBCA04
+
+  - name: "GitHub Actions"
+    color: 84b6eb
+
+  - name: "Scripts"
+    color: 3B8924
+
+  - name: "Tests"
+    color: ff8c00
diff --git a/.github/workflows/prlabeler.yml b/.github/workflows/prlabeler.yml
new file mode 100644
index 00000000000..1a29e659168
--- /dev/null
+++ b/.github/workflows/prlabeler.yml
@@ -0,0 +1,22 @@
+# This workflow is based on github action official label action v4.
+# This workflow action is triggered on pull request event(on both fork & inside repo)
+# Labels will be applied based on filepath modification in PR.
+# This workflow uses a regex based labeling config file(.github/labeler.yml) to take labeling decision.
+
+name: "PR Labeler"
+on:
+  - pull_request_target
+jobs:
+  label:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/labeler@v4
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          configuration-path: ".github/labeler.yml"
+          sync-labels: false
+          dot: true
diff --git a/Makefile b/Makefile
index cda4ad6f72b..10fa7950f82 100644
--- a/Makefile
+++ b/Makefile
@@ -153,7 +153,8 @@ clean:
 	+ ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} \
 		-e "if (!requireNamespace('roxygen2', quietly = TRUE)" \
 		-e "    || packageVersion('roxygen2') != '7.2.3') {" \
-		-e "  devtools::install_github('r-lib/roxygen2@v7.2.3')" \
+		-e "  cran <- c(getOption('repos'), 'cloud.r-project.org')" \
+		-e "  remotes::install_version('roxygen2', '7.2.3', repos = cran, upgrade = FALSE)" \
 		-e "}"
 	$(eval INSTALLED_ROXYGEN_VERSION := 7.2.3)
 	echo `date` > $@
diff --git a/Makefile.depends b/Makefile.depends
index be631f3bfe1..bc5143e0671 100644
--- a/Makefile.depends
+++ b/Makefile.depends
@@ -30,7 +30,7 @@ $(call depends,models/template): | .install/base/db .install/base/logger .instal
 $(call depends,modules/allometry): | .install/base/db
 $(call depends,modules/assim.batch): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/workflow .install/modules/benchmark .install/modules/emulator .install/modules/meta.analysis .install/modules/uncertainty
 $(call depends,modules/assim.sequential): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/base/workflow .install/modules/benchmark .install/modules/data.land .install/modules/data.remote .install/modules/uncertainty
-$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
+$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/settings .install/base/utils .install/modules/data.land
 $(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils
 $(call depends,modules/data.hydrology): | .install/base/logger .install/base/utils
 $(call depends,modules/data.land): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/modules/benchmark .install/modules/data.atmosphere
diff --git a/base/all/DESCRIPTION b/base/all/DESCRIPTION
index ed96934ee9a..18f93be1bb3 100644
--- a/base/all/DESCRIPTION
+++ b/base/all/DESCRIPTION
@@ -64,6 +64,7 @@ Depends:
 Imports:
     utils
 Suggests:
+    mockery,
     PEcAn.ED2,
     PEcAn.SIPNET,
     PEcAn.BIOCRO,
@@ -71,6 +72,7 @@ Suggests:
     PEcAn.LINKAGES,
     PEcAn.allometry,
     PEcAn.photosynthesis,
+    sessioninfo,
     testthat
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
diff --git a/base/all/R/pecan_version.R b/base/all/R/pecan_version.R
index 51f983f0be9..85c9fc346db 100644
--- a/base/all/R/pecan_version.R
+++ b/base/all/R/pecan_version.R
@@ -16,13 +16,16 @@
 #'  locations in `.libPaths()`, or if you've loaded a new version into your
 #'  current session by loading it from its source directory without installing
 #'  it to the R library.
-#' If you see multiple rows unexpectedly, try `find.package(<pkgname>, verbose = TRUE)` to see where each version was found.
+#' If you see multiple rows unexpectedly, try
+#'  `find.package(<pkgname>, verbose = TRUE)` to see where each version was found.
 #'
 #' @param version PEcAn release number to use for expected package versions
 #' @param exact Show only tags that exactly match `version`,
 #'  or all tags that have it as a substring?
 #' @return data frame with columns for package name, expected version(s),
-#'  and installed version
+#'  and installed version.
+#'  If the `sessioninfo` package is installed, a fourth column reports where
+#'  each package was installed from: local, github, CRAN, etc.
 #'
 #' @examples
 #' pecan_version()
@@ -35,25 +38,6 @@
 #' @export
 pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
                           exact = FALSE) {
-  all_pkgs <- as.data.frame(utils::installed.packages())
-  our_pkgs <- all_pkgs[
-    grepl("PEcAn", all_pkgs$Package),
-    c("Package", "Version")
-  ]
-  colnames(our_pkgs) <- c("package", "installed")
-  our_pkgs$installed <- package_version(our_pkgs$installed)
-
-  # Check in currently loaded packages too,
-  # add rows for any that differ from installed versions
-  sess <- utils::sessionInfo()
-  sess <- c(sess$otherPkgs, sess$loadedOnly)
-  our_loaded <- sess[grepl("PEcAn", names(sess))]
-  our_loaded <- data.frame(
-    package = names(our_loaded),
-    installed = sapply(our_loaded, `[[`, "Version"))
-  our_loaded$installed <- package_version(our_loaded$installed)
-  our_pkgs <- merge(our_pkgs, our_loaded, all = TRUE)
-
   if (!exact) {
     version <- sapply(
       X = version,
@@ -62,9 +46,58 @@ pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
     )
     version <- unique(unlist(version))
   }
+  cols_to_return <- c("package", version, "installed")
+
+
+  if (requireNamespace("sessioninfo", quietly = TRUE)) {
+    cols_to_return <- c(cols_to_return, "source")
+
+    all_pkgs <- sessioninfo::package_info(pkgs = "installed", dependencies = FALSE)
+    our_pkgs <- all_pkgs[grepl("PEcAn", all_pkgs$package),]
+
+    all_loaded <- sessioninfo::package_info(pkgs = "loaded", dependencies = FALSE)
+    our_loaded <- all_loaded[grepl("PEcAn", all_loaded$package),]
+
+    unloaded <- our_pkgs[!our_pkgs$package %in% our_loaded$package,]
+    our_pkgs <- rbind(our_loaded, unloaded)
+    our_pkgs <- our_pkgs[order(our_pkgs$package),]
+
+
+    # TODO: consider using package_info's callouts of packages where loaded and
+    #   installed versions mismatch -- it's a more elegant version of what we
+    #   were trying for with the "multiple rows for packages with multiple
+    #   versions found" behavior.
+    our_pkgs$installed <- ifelse(
+      test = is.na(our_pkgs$loadedversion),
+      yes = our_pkgs$ondiskversion,
+      no = our_pkgs$loadedversion)
+    our_pkgs <- our_pkgs[, c("package", "installed", "source")]
+    our_pkgs$installed <- package_version(our_pkgs$installed)
+
+  } else {
+    all_pkgs <- as.data.frame(utils::installed.packages())
+    our_pkgs <- all_pkgs[
+      grepl("PEcAn", all_pkgs$Package),
+      c("Package", "Version")
+    ]
+    colnames(our_pkgs) <- c("package", "installed")
+    our_pkgs$installed <- package_version(our_pkgs$installed)
+    sess <- utils::sessionInfo()
+    sess <- c(sess$otherPkgs, sess$loadedOnly)
+    our_loaded <- sess[grepl("PEcAn", names(sess))]
+    our_loaded <- data.frame(
+      package = names(our_loaded),
+      installed = sapply(our_loaded, `[[`, "Version"))
+    our_loaded$installed <- package_version(our_loaded$installed)
+    our_pkgs <- merge(our_pkgs, our_loaded, all = TRUE)
+  }
+
 
-  res <- merge(our_pkgs, PEcAn.all::pecan_version_history, all = TRUE)
-  res <- res[, c("package", version, "installed")]
+  res <- merge(
+    x = our_pkgs,
+    y = PEcAn.all::pecan_version_history,
+    all = TRUE)
+  res <- res[, cols_to_return]
 
   drop_na_version_rows(res)
 }
diff --git a/base/all/man/pecan_version.Rd b/base/all/man/pecan_version.Rd
index e2ded17e8b1..a0275089a9a 100644
--- a/base/all/man/pecan_version.Rd
+++ b/base/all/man/pecan_version.Rd
@@ -14,7 +14,9 @@ or all tags that have it as a substring?}
 }
 \value{
 data frame with columns for package name, expected version(s),
-and installed version
+and installed version.
+If the \code{sessioninfo} package is installed, a fourth column reports where
+each package was installed from: local, github, CRAN, etc.
 }
 \description{
 Reports the currently installed or loaded version(s) of each PEcAn package,
@@ -34,7 +36,8 @@ This can occur if you have installed different versions to different
 locations in \code{.libPaths()}, or if you've loaded a new version into your
 current session by loading it from its source directory without installing
 it to the R library.
-If you see multiple rows unexpectedly, try \verb{find.package(<pkgname>, verbose = TRUE)} to see where each version was found.
+If you see multiple rows unexpectedly, try
+\verb{find.package(<pkgname>, verbose = TRUE)} to see where each version was found.
 }
 \examples{
 pecan_version()
diff --git a/base/all/tests/testthat/test-pecan_version.R b/base/all/tests/testthat/test-pecan_version.R
index 2a9100d4d7a..c1e45b0c267 100644
--- a/base/all/tests/testthat/test-pecan_version.R
+++ b/base/all/tests/testthat/test-pecan_version.R
@@ -26,7 +26,7 @@ test_that("pecan_version", {
   # tags substring matched only when exact = FALSE
   expect_named(
     pecan_version("v1.5"),
-    c("package", paste0("v1.5.", 0:3), "installed")
+    c("package", paste0("v1.5.", 0:3), "installed", "source")
   )
   expect_error(
     pecan_version("v1.5", exact = TRUE),
@@ -34,14 +34,14 @@ test_that("pecan_version", {
   )
   expect_named(
     pecan_version("v1.3", exact = TRUE),
-    c("package", "v1.3", "installed")
+    c("package", "v1.3", "installed", "source")
   )
 
   # returns current release if no args given
   noargs <- pecan_version()
   expected_tag <- tail(PEcAn.all::pecan_releases, 1)$tag
-  expect_length(noargs, 3)
-  expect_named(noargs, c("package", expected_tag, "installed"))
+  expect_length(noargs, 4)
+  expect_named(noargs, c("package", expected_tag, "installed", "source"))
 
   # Why the `any()`s below?
   # Because R CMD check runs tests with local test dir added to .libPaths,
@@ -67,3 +67,27 @@ test_that("pecan_version", {
     )
   )
 })
+
+
+test_that("pecan_version without sessioninfo", {
+
+  with_sessinfo <- pecan_version()
+
+  # make pecan_version think the sessioninfo package is unavailable
+  mockery::stub(pecan_version, 'requireNamespace', FALSE)
+  without_sessinfo <- pecan_version()
+
+  expect_length(with_sessinfo, 4)
+  expect_length(without_sessinfo, 3)
+  expect_equal(
+    with_sessinfo[, colnames(with_sessinfo) != "source"],
+    without_sessinfo)
+})
+
+# TODO: Would be nice to add a check here that will notice if the list of PEcAn
+# releases falls out of date, but it's not clear what other source of truth
+# to consult to determine that.
+#
+# The approach that failed just before I wrote this note:
+# No, the version of PEcAn.all (1.8.1.9000 today) is not reliably in sync with
+# the PEcAn version last tagged as a release (1.7.2 today).
diff --git a/base/workflow/DESCRIPTION b/base/workflow/DESCRIPTION
index efd8efabefd..137b9499eb8 100644
--- a/base/workflow/DESCRIPTION
+++ b/base/workflow/DESCRIPTION
@@ -31,20 +31,21 @@ Description: The Predictive Ecosystem Carbon Analyzer
     that can be used to run the major steps of a PEcAn analysis.
 License: BSD_3_clause + file LICENSE
 Imports:
-  dplyr,
-	PEcAn.data.atmosphere,
-	PEcAn.data.land,
-	PEcAn.DB,
-	PEcAn.logger,
-	PEcAn.remote,
-	PEcAn.settings,
-	PEcAn.uncertainty,
-	PEcAn.utils,
-	purrr (>= 0.2.3),
-	XML
+    dplyr,
+    PEcAn.data.atmosphere,
+    PEcAn.data.land,
+    PEcAn.DB,
+    PEcAn.logger,
+    PEcAn.remote,
+    PEcAn.settings,
+    PEcAn.uncertainty,
+    PEcAn.utils,
+    purrr (>= 0.2.3),
+    XML
 Suggests:
-	testthat,
-    mockery
+    mockery,
+    testthat,
+    withr
 Copyright: Authors
 Encoding: UTF-8
 RoxygenNote: 7.2.3
diff --git a/base/workflow/R/start_model_runs.R b/base/workflow/R/start_model_runs.R
index 37771d9bf2b..3c84d588180 100644
--- a/base/workflow/R/start_model_runs.R
+++ b/base/workflow/R/start_model_runs.R
@@ -23,7 +23,7 @@ start_model_runs <- function(settings, write = TRUE, stop.on.error = TRUE) {
   
   run_file <- file.path(settings$rundir, "runs.txt")
   # check if runs need to be done
-  if (!file.exists(file.path(settings$rundir, "runs.txt"))) {
+  if (!file.exists(run_file)) {
     PEcAn.logger::logger.warn(
       "runs.txt not found, assuming no runs need to be done")
     return()
diff --git a/base/workflow/tests/testthat/test.start_model_runs.R b/base/workflow/tests/testthat/test.start_model_runs.R
new file mode 100644
index 00000000000..052950e2c93
--- /dev/null
+++ b/base/workflow/tests/testthat/test.start_model_runs.R
@@ -0,0 +1,20 @@
+test_that("`start_model_runs` throws a warning if runs.txt not provided", {
+  withr::with_tempdir({
+    PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
+    on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE))
+    settings <- list(rundir = getwd())
+    expect_output(start_model_runs(settings), "runs.txt not found")
+  })
+})
+
+test_that("`start_model_runs` throws a warning if runs.txt is empty", {
+  withr::with_tempdir({
+    PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
+    on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE))
+    settings <- list(rundir = getwd())
+    file_path <- file.path(getwd(), "runs.txt")
+    file.create(file_path)
+    expect_output(start_model_runs(settings), "runs.txt found, but is empty")
+  })
+})
+
diff --git a/docker/depends/pecan.depends.R b/docker/depends/pecan.depends.R
index 64ef77eb10d..0f3057d896d 100644
--- a/docker/depends/pecan.depends.R
+++ b/docker/depends/pecan.depends.R
@@ -15,7 +15,7 @@ condense_version_requirements <- function(specs) {
   specs <- unique(specs[specs != "*"])
   versions <- package_version(
     gsub("[^[:digit:].-]+", "", specs))
-
+  
   if ((length(unique(versions)) > 1) && any(!grepl(">", specs))) {
     # Can't assume the latest version works for all, so give up.
     # We *could* write more to handle this case if needed, but it seems very rare:
@@ -39,30 +39,30 @@ condense_version_requirements <- function(specs) {
 # Install <version> or newer,
 # upgrading dependencies only if needed to satisfy stated version requirements
 ensure_version <- function(pkg, version) {
-    vers <- gsub('[^[:digit:].-]+', '', version)
-    cmp <- get(gsub('[^<>=]+', '', version))
-    ok <- requireNamespace(pkg, quietly = TRUE) &&
-        cmp(packageVersion(pkg), vers)
-    if (!ok) {
-        # install pkg and any *missing* dependencies
-        remotes::install_version(pkg, version, dependencies = TRUE, upgrade = FALSE)
-        # Now check for installed but *incompatible* dependencies
-        # (install_version doesn't resolve these when upgrade=FALSE)
-        dep <- desc::desc_get_deps(system.file("DESCRIPTION", package = pkg))
-        dep <- dep[
-            dep$type %in% c("Depends", "Imports", "LinkingTo")
-            & dep$version != "*"
-            & dep$package != "R",]
-        invisible(Map(ensure_version, dep$package, dep$version))
-    }
-
+  vers <- gsub('[^[:digit:].-]+', '', version)
+  cmp <- get(gsub('[^<>=]+', '', version))
+  ok <- requireNamespace(pkg, quietly = TRUE) &&
+    cmp(packageVersion(pkg), vers)
+  if (!ok) {
+    # install pkg and any *missing* dependencies
+    remotes::install_version(pkg, version, dependencies = TRUE, upgrade = FALSE)
+    # Now check for installed but *incompatible* dependencies
+    # (install_version doesn't resolve these when upgrade=FALSE)
+    dep <- desc::desc_get_deps(system.file("DESCRIPTION", package = pkg))
+    dep <- dep[
+      dep$type %in% c("Depends", "Imports", "LinkingTo")
+      & dep$version != "*"
+      & dep$package != "R",]
+    invisible(Map(ensure_version, dep$package, dep$version))
+  }
+  
 }
 
 # Read list of dependencies.
 # NOTE: These files are autogenerated --
 # use scripts/generate_dependencies.R to edit them.
 all_deps <- read.csv("pecan_package_dependencies.csv") |>
-    subset(!is_pecan)
+  subset(!is_pecan)
 gh_repos <- readLines("pecan_deps_from_github.txt")
 
 
@@ -74,9 +74,9 @@ remotes::install_github(gh_repos, lib = rlib)
 
 # For deps used by multiple packages, find a version that works for all
 uniq_deps <- tapply(
-        all_deps$version,
-        INDEX = all_deps$package,
-        FUN = condense_version_requirements)
+  all_deps$version,
+  INDEX = all_deps$package,
+  FUN = condense_version_requirements)
 
 
 # Install deps that declare no version restriction.
@@ -92,9 +92,8 @@ install.packages(missing, lib = rlib)
 # it can't fill the version req from snapshot versions.
 # (Assumes our CRAN uses the same URL scheme as Posit package manager)
 options(repos = c(
-    getOption('repos'),
-    sub(r'(\d{4}-\d{2}-\d{2})', 'latest', getOption('repos'))
+  getOption('repos'),
+  sub(r'(\d{4}-\d{2}-\d{2})', 'latest', getOption('repos'))
 ))
 versioned <- uniq_deps[uniq_deps != "*"]
-invisible(Map(ensure_version, names(versioned), versioned))
-
+invisible(Map(ensure_version, names(versioned), versioned))
\ No newline at end of file
diff --git a/docker/depends/pecan_package_dependencies.csv b/docker/depends/pecan_package_dependencies.csv
index 8345db18103..2ffb26841a7 100644
--- a/docker/depends/pecan_package_dependencies.csv
+++ b/docker/depends/pecan_package_dependencies.csv
@@ -39,7 +39,6 @@
 "datapack","*","modules/data.land","Imports",FALSE
 "DBI","*","base/db","Imports",FALSE
 "DBI","*","modules/data.remote","Imports",FALSE
-"dbplyr","*","modules/benchmark","Imports",FALSE
 "dbplyr",">= 2.4.0","base/db","Imports",FALSE
 "devtools","*","models/ed","Suggests",FALSE
 "doParallel","*","modules/data.atmosphere","Suggests",FALSE
@@ -184,6 +183,7 @@
 "mgcv","*","modules/data.atmosphere","Imports",FALSE
 "minpack.lm","*","modules/rtm","Suggests",FALSE
 "mlegp","*","modules/assim.batch","Imports",FALSE
+"mockery","*","base/all","Suggests",FALSE
 "mockery","*","base/qaqc","Suggests",FALSE
 "mockery","*","base/remote","Suggests",FALSE
 "mockery","*","base/settings","Suggests",FALSE
@@ -352,7 +352,6 @@
 "PEcAn.remote","*","models/stics","Imports",TRUE
 "PEcAn.remote","*","modules/assim.batch","Imports",TRUE
 "PEcAn.remote","*","modules/assim.sequential","Imports",TRUE
-"PEcAn.remote","*","modules/benchmark","Imports",TRUE
 "PEcAn.remote","*","modules/data.atmosphere","Imports",TRUE
 "PEcAn.remote","*","modules/data.land","Imports",TRUE
 "PEcAn.remote","*","modules/data.remote","Imports",TRUE
@@ -438,6 +437,7 @@
 "purrr",">= 0.2.3","modules/data.atmosphere","Imports",FALSE
 "pwr","*","modules/rtm","Suggests",FALSE
 "R.utils","*","base/db","Imports",FALSE
+"randomForest","*","modules/assim.sequential","Suggests",FALSE
 "randtoolbox","*","base/utils","Suggests",FALSE
 "randtoolbox","*","modules/uncertainty","Imports",FALSE
 "raster","*","base/visualization","Suggests",FALSE
@@ -446,6 +446,7 @@
 "raster","*","modules/data.land","Suggests",FALSE
 "raster","*","modules/data.remote","Suggests",FALSE
 "rcrossref","*","base/db","Suggests",FALSE
+"readr","*","modules/assim.sequential","Suggests",FALSE
 "REddyProc","*","modules/data.atmosphere","Imports",FALSE
 "redland","*","modules/data.land","Suggests",FALSE
 "reshape","*","modules/data.remote","Suggests",FALSE
@@ -528,6 +529,7 @@
 "RPostgreSQL","*","models/biocro","Suggests",FALSE
 "Rpreles","*","models/preles","Suggests",FALSE
 "RSQLite","*","base/db","Suggests",FALSE
+"sessioninfo","*","base/all","Suggests",FALSE
 "sf","*","modules/assim.sequential","Suggests",FALSE
 "sf","*","modules/data.atmosphere","Imports",FALSE
 "sf","*","modules/data.land","Imports",FALSE
@@ -554,6 +556,7 @@
 "stringr",">= 1.1.0","modules/data.atmosphere","Imports",FALSE
 "suntools","*","modules/data.atmosphere","Imports",FALSE
 "swfscMisc","*","modules/data.land","Imports",FALSE
+"terra","*","modules/assim.sequential","Suggests",FALSE
 "terra","*","modules/data.atmosphere","Imports",FALSE
 "terra","*","modules/data.land","Imports",FALSE
 "terra","*","modules/data.remote","Imports",FALSE
@@ -639,6 +642,7 @@
 "withr","*","base/settings","Suggests",FALSE
 "withr","*","base/utils","Suggests",FALSE
 "withr","*","base/visualization","Suggests",FALSE
+"withr","*","base/workflow","Suggests",FALSE
 "withr","*","models/ed","Suggests",FALSE
 "withr","*","models/sibcasa","Suggests",FALSE
 "withr","*","modules/allometry","Suggests",FALSE
diff --git a/modules/assim.sequential/DESCRIPTION b/modules/assim.sequential/DESCRIPTION
index b90f15a18cd..78641f263c6 100644
--- a/modules/assim.sequential/DESCRIPTION
+++ b/modules/assim.sequential/DESCRIPTION
@@ -47,11 +47,14 @@ Suggests:
     PEcAn.visualization,
     plotrix,
     plyr (>= 1.8.4),
+    randomForest,
     raster,
+    readr,
     reshape2 (>= 1.4.2),
     rlist,
     sf,
     stats,
+    terra,
     testthat,
     tictoc,
     tidyr,
diff --git a/modules/assim.sequential/R/Analysis_sda_block.R b/modules/assim.sequential/R/Analysis_sda_block.R
index 50a2046a773..f5bc2f634be 100644
--- a/modules/assim.sequential/R/Analysis_sda_block.R
+++ b/modules/assim.sequential/R/Analysis_sda_block.R
@@ -102,7 +102,6 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
   } else if (settings$state.data.assimilation$q.type == "wishart") {
     q.type <- 4
   }
-  
   #grab basic arguments based on X.
   site.ids <- unique(attributes(X)$Site)
   var.names <- unique(attributes(X)$dimnames[[2]])
@@ -112,7 +111,6 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
     diag(Pf)[which(diag(Pf)==0)] <- min(diag(Pf)[which(diag(Pf) != 0)])/5 #fixing det(Pf)==0
     PEcAn.logger::logger.warn("The zero variances in Pf is being replaced by one fifth of the minimum variance in those matrices respectively.")
   }
-  
   #distance calculations and localization
   site.locs <- settings$run %>% 
     purrr::map('site') %>% 
@@ -128,14 +126,16 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
     blocked.dis <- block_matrix(dis.matrix %>% as.numeric(), rep(length(var.names), length(site.ids)))
     Pf <- Localization.FUN(Pf, blocked.dis, settings$state.data.assimilation$scalef %>% as.numeric())
   }
-  
   #Handle observation
   #observation number per site
-  obs_per_site <- purrr::map_int(obs.mean[[t]], length)
+  #free run special case.
+  if (is.null(obs.mean[[t]])) {
+    obs_per_site <- rep(0, length(site.ids)) %>% purrr::set_names(site.ids)
+  } else {
+    obs_per_site <- purrr::map_int(obs.mean[[t]], length)
+  }
   #if we do free run or the current obs.mean are all NULL.
   if (as.logical(settings$state.data.assimilation$free.run) | all(is.null(unlist(obs.mean[[t]])))) {
-    obs.mean[[t]] <- vector("list", length(site.ids)) %>% `names<-`(site.ids)
-    obs.cov[[t]] <- vector("list", length(site.ids)) %>% `names<-`(site.ids)
     H <- list(ind = seq_along(rep(var.names, length(site.ids))))
     Y <- rep(NA, length(H$ind))
     R <- diag(1, length(H$ind))
@@ -174,8 +174,8 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
       #name matching between observation names and state variable names.
       f.2.y.ind <- obs.mean[[t]] %>% 
         purrr::map(\(x)which(var.names %in% names(x))) %>% 
-        base::unlist %>% 
-        base::unique
+        unlist %>% 
+        unique
       H <- list(ind = f.2.y.ind %>% purrr::map(function(start){
         seq(start, length(site.ids) * length(var.names), length(var.names))
       }) %>% unlist() %>% sort)
@@ -187,7 +187,6 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
                               by = "block_pft_var")
     }
   }
-  
   #start the blocking process
   #should we consider interactions between sites?
   if(as.numeric(settings$state.data.assimilation$scalef) == 0){
@@ -198,28 +197,32 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
       block.list[[i]]$sites.per.block <- i
       block.list[[i]]$site.ids <- site.ids[i]
       block.list[[i]]$t <- t
-      
       #fill in mu.f and Pf
       f.start <- (i - 1) * length(var.names) + 1
       f.end <- i * length(var.names)
       block.list[[i]]$data$muf <- mu.f[f.start:f.end]
       block.list[[i]]$data$pf <- Pf[f.start:f.end, f.start:f.end]
-      
+      #find indexs for Y.
+      y.start <- sum(obs_per_site[1:i])
+      y.end <- y.start + obs_per_site[i] - 1
       #fill in y and r
-      if (obs_per_site[i] == 0) {
-        y.start <- 1
-        y.end <- length(var.names)
-        block.list[[i]]$data$y.censored <- rep(NA, length(var.names))
-        block.list[[i]]$data$r <- diag(1, length(var.names))
-        block.h <- matrix(1, 1, length(var.names))
+      #if there is no observation for this site.
+      if (y.end < y.start) {
+        #if every site has zero observation/free run.
+        if (max(obs_per_site) == 0) {
+          block.list[[i]]$data$y.censored <- rep(NA, length(var.names))
+          block.list[[i]]$data$r <- diag(1, length(var.names))
+          block.h <- matrix(1, 1, length(var.names))
+        } else {
+          block.list[[i]]$data$y.censored <- rep(NA, max(obs_per_site))
+          block.list[[i]]$data$r <- diag(1, max(obs_per_site))
+          block.h <- matrix(1, 1, max(obs_per_site))
+        }
       } else {
-        y.start <- sum(obs_per_site[1:i-1]) + 1#obs_per_site[i] * (i - 1) + 1
-        y.end <- y.start + obs_per_site[i] - 1#obs_per_site[i] * i
         block.list[[i]]$data$y.censored <- y.censored[y.start:y.end]
         block.list[[i]]$data$r <- solve(R[y.start:y.end, y.start:y.end])
         block.h <- Construct.H.multisite(site.ids[i], var.names, obs.mean[[t]])
       }
-      
       #fill in constants.
       block.list[[i]]$H <- block.h
       block.list[[i]]$constant$H <- which(apply(block.h, 2, sum) == 1)
@@ -253,15 +256,9 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
       for (j in seq_along(ids)) {
         f.start <- (ids[j] - 1) * length(var.names) + 1
         f.end <- ids[j] * length(var.names)
-        # site.ind <- ids[j]
-        
         y.start <- sum(obs_per_site[1:ids[j]])
         y.end <- y.start + obs_per_site[ids[j]] - 1
-        # y.start <- obs_per_site[ids[j]] * (ids[j] - 1) + 1
-        # y.end <- obs_per_site[ids[j]] * ids[j]
-        
         f.ind <- c(f.ind, f.start:f.end)
-        
         #if the current site has greater or equal than 1 observation.
         if (y.end >= y.start) {
           # y.ind <- c(y.ind, y.start:y.end)
@@ -269,17 +266,28 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
           r.block <- c(r.block, diag(R)[y.start:y.end])
         } else {
           #if the current site has zero observation.
-          y.block <- c(y.block, rep(NA, max(obs_per_site)))
-          r.block <- c(r.block, rep(1, max(obs_per_site)))
+          #if for free run.
+          if (max(obs_per_site) == 0) {
+            y.block <- c(y.block, rep(NA, length(var.names)))
+            r.block <- c(r.block, rep(1, length(var.names)))
+          } else {
+            y.block <- c(y.block, rep(NA, max(obs_per_site)))
+            r.block <- c(r.block, rep(1, max(obs_per_site)))
+          }
         }
       }
-      # H
+      #if we have NA for y, we will build H differently.
       if (any(is.na(y.block))) {
-        block.h <- matrix(0, 1, length(ids)*length(var.names))#matrix(1, 1, length(var.names))
-        f.2.y.ind <- obs.mean[[t]] %>% 
-          purrr::map(\(x)which(var.names %in% names(x))) %>% 
-          base::unlist %>% 
-          base::unique
+        block.h <- matrix(0, 1, length(ids)*length(var.names))
+        #if for free run.
+        if (is.null(obs.mean[[t]])) {
+          f.2.y.ind <- seq_along(var.names)
+        } else {
+          f.2.y.ind <- obs.mean[[t]] %>% 
+            purrr::map(\(x)which(var.names %in% names(x))) %>% 
+            unlist %>% 
+            unique
+        }
         seq.ind <- f.2.y.ind %>% purrr::map(function(start){
           seq(start, dim(block.h)[2], length(var.names))
         }) %>% unlist()
@@ -287,29 +295,16 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
       } else {
         block.h <- Construct.H.multisite(site.ids[ids], var.names, obs.mean[[t]])
       }
-      
       #fill in  mu.f and Pf
       block.list[[i]]$data$muf <- mu.f[f.ind]
       block.list[[i]]$data$pf <- GrabFillMatrix(Pf, f.ind)
-      
       #fill in y and R
-      # y.block[which(is.na(y.block))] <- mu.f[f.ind[seq.ind[which(is.na(y.block))]]]
-      # r.block[which(is.na(r.block))] <- diag(Pf)[f.ind[seq.ind[which(is.na(r.block))]]]
-      block.list[[i]]$data$y.censored <- y.block#y.censored[y.ind]
+      block.list[[i]]$data$y.censored <- y.block
       if (length(r.block)  == 1) {
         block.list[[i]]$data$r <- 1/r.block
       } else {
-        block.list[[i]]$data$r <- solve(diag(r.block))#GrabFillMatrix(solve(R), y.ind)
+        block.list[[i]]$data$r <- solve(diag(r.block))
       }
-      
-      #fill in constants
-      # if (all(is.na(y.block))) {
-      #   block.h <- matrix(0, 1, length(ids)*length(var.names))#matrix(1, 1, length(var.names))
-      #   f.2.y.ind <- which(grepl(unique(names(unlist(obs.mean[[t]] %>% set_names(NULL)))), var.names, fixed = T))
-      #   block.h[1, seq(f.2.y.ind, dim(block.h)[2], length(var.names))] <- 1
-      # } else {
-      #   block.h <- Construct.H.multisite(site.ids[ids], var.names, obs.mean[[t]])
-      # }
       block.list[[i]]$H <- block.h
       block.list[[i]]$constant$H <- which(apply(block.h, 2, sum) == 1)
       block.list[[i]]$constant$N <- length(f.ind)
@@ -317,7 +312,36 @@ build.block.xy <- function(settings, block.list.all, X, obs.mean, obs.cov, t) {
       block.list[[i]]$constant$q.type <- q.type
     }
   }
-  
+  #if it's Wishart Q, we need to replace any NA Y with corresponding muf, and r with Pf.
+  #also, if length of observation is 1, the Wishart Q is not suitable for the MCMC.
+  #we will then need to change the Q type to 3, which is the vector Q.
+  if (q.type == 4) {
+    for (i in seq_along(block.list)) {
+      #check length.
+      if (block.list[[i]]$constant$YN == 1) {
+        block.list[[i]]$constant$q.type <- 3
+        next
+      }
+      # #check NAs.
+      # na.ind <- which(is.na(block.list[[i]]$data$y.censored))
+      # if (length(na.ind) > 0) {
+      #     block.list[[i]]$constant$YN <- block.list[[i]]$constant$YN - length(na.ind)
+      #     block.list[[i]]$constant$H <- block.list[[i]]$constant$H[-na.ind]
+      #     block.list[[i]]$data$y.censored <- block.list[[i]]$data$y.censored[-na.ind]
+      #     block.list[[i]]$data$r <- diag(diag(block.list[[i]]$data$r)[-na.ind])
+      # }
+      # na.site.ind <- which(obs_per_site[block.list[[i]]$site.ids] == 0)
+      # na.ind <- which(is.na(block.list[[i]]$data$y.censored))
+      # if (length(na.site.ind) > 0) {
+      #   site.inds <- block.list[[i]]$sites.per.block[na.site.ind]
+      #   y.2.muf.ind <- f.2.y.ind %>% purrr::map(function(start){
+      #     seq(start, length(mu.f), length(var.names))[site.inds]
+      #   }) %>% unlist() %>% sort()
+      #   block.list[[i]]$data$y.censored[na.ind] <- mu.f[y.2.muf.ind]
+      #   block.list[[i]]$data$r[na.ind, na.ind] <- Pf[y.2.muf.ind, y.2.muf.ind]
+      # }
+    }
+  }
   #return values.
   block.list.all[[t]] <- block.list
   return(list(block.list.all = block.list.all, H = H, Y = Y, R = R))
diff --git a/modules/assim.sequential/R/downscale_function.R b/modules/assim.sequential/R/downscale_function.R
new file mode 100644
index 00000000000..4a64beef645
--- /dev/null
+++ b/modules/assim.sequential/R/downscale_function.R
@@ -0,0 +1,93 @@
+##' @title North America Downscale Function
+##' @name NA_downscale
+##' @author Joshua Ploshay
+##'
+##' @param data  In quotes, file path for .rds containing ensemble data.
+##' @param focus_year In quotes, if SDA site run, format is yyyy/mm/dd, if NEON, yyyy-mm-dd. Restricted to years within file supplied to 'data'.
+##' @param C_pool In quotes, carbon pool of interest. Name must match carbon pool name found within file supplied to 'data'.
+##' @param covariates In quotes, file path of SpatRaster stack, used as predictors in randomForest. Layers within stack should be named.
+##' @param cords In quotes, file path for .csv file containing the site coordinates, columns named "lon" and "lat".
+##' @details This function will downscale forecast data to unmodeled locations using covariates and site locations
+##'
+##' @description This function uses the randomForest model.
+##'
+##' @return It returns the `downscale_output` list containing lists for the training and testing data sets, models, and predicted maps for each ensemble member.
+
+
+NA_downscale <- function(data, cords, covariates, focus_year, C_pool){
+  
+  # Read in the covariates and set CRS to EPSG:4326
+  covariates <- terra::rast(covariates) # ADD package to every function
+  terra::crs(covariates) <- "EPSG:4326"
+  
+  # Read the input data and site coordinates
+  input_data <- readRDS(data)
+  site_coordinates <- terra::vect(readr::read_csv(cords), geom=c("lon", "lat"), crs="EPSG:4326")
+  
+  # Extract the carbon data for the specified focus year
+  index <- which(names(input_data) == focus_year)
+  data <- input_data[[index]]
+  carbon_data <- as.data.frame(t(data[which(names(data) == C_pool)]))
+  names(carbon_data) <- paste0("ensemble",seq(1:ncol(carbon_data)))
+  
+  # Extract predictors from covariates raster using site coordinates
+  predictors <- as.data.frame(terra::extract(covariates, site_coordinates)) 
+  predictors <- dplyr::select(predictors, -1)
+  
+  # Combine each ensemble member with all predictors
+  ensembles <- list()
+  for (i in seq_along(carbon_data)) {
+    ensembles[[i]] <- cbind(carbon_data[[i]], predictors)
+  }
+  
+  # Rename the carbon_data column for each ensemble member
+  for (i in 1:length(ensembles)) {
+    ensembles[[i]] <- dplyr::rename(ensembles[[i]], "carbon_data" = "carbon_data[[i]]")
+  }
+  
+  # Split the observations in each data frame into two data frames based on the proportion of 3/4
+  ensembles <- lapply(ensembles, function(df) {
+    sample <- sample(1:nrow(df), size = round(0.75*nrow(df)))
+    train  <- df[sample, ]
+    test   <- df[-sample, ]
+    split_list <- list(train, test)
+    return(split_list)
+  })
+  
+  # Rename the training and testing data frames for each ensemble member
+  for (i in 1:length(ensembles)) {
+    # names(ensembles) <- paste0("ensemble",seq(1:length(ensembles)))
+    names(ensembles[[i]]) <- c("training", "testing")
+  }
+  
+  # Train a random forest model for each ensemble member using the training data
+  output <- list()
+  for (i in 1:length(ensembles)) {
+    output[[i]] <- randomForest::randomForest(ensembles[[i]][[1]][["carbon_data"]] ~ land_cover+tavg+prec+srad+vapr+nitrogen+phh2o+soc+sand,
+                                data = ensembles[[i]][[1]],
+                                ntree = 1000,
+                                na.action = stats::na.omit,
+                                keep.forest = T,
+                                importance = T)
+  }
+  
+  # Generate predictions (maps) for each ensemble member using the trained models
+  maps <- list(ncol(output))
+  for (i in 1:length(output)) {
+    maps[[i]] <- terra::predict(object = covariates,
+                         model = output[[i]],na.rm = T)
+  }
+  
+  # Organize the results into a single output list
+  downscale_output <- list(ensembles, output, maps)
+  
+  # Rename each element of the output list with appropriate ensemble numbers
+  for (i in 1:length(downscale_output)) {
+    names(downscale_output[[i]]) <- paste0("ensemble",seq(1:length(downscale_output[[i]])))
+  }
+  
+  # Rename the main components of the output list
+  names(downscale_output) <- c("data", "models", "maps")
+  
+  return(downscale_output)
+}
diff --git a/modules/assim.sequential/man/NA_downscale.Rd b/modules/assim.sequential/man/NA_downscale.Rd
new file mode 100644
index 00000000000..8ab6a5ea946
--- /dev/null
+++ b/modules/assim.sequential/man/NA_downscale.Rd
@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/downscale_function.R
+\name{NA_downscale}
+\alias{NA_downscale}
+\title{North America Downscale Function}
+\usage{
+NA_downscale(data, cords, covariates, focus_year, C_pool)
+}
+\arguments{
+\item{data}{In quotes, file path for .rds containing ensemble data.}
+
+\item{focus_year}{In quotes, if SDA site run, format is yyyy/mm/dd, if NEON, yyyy-mm-dd. Restricted to years within file supplied to 'data'.}
+
+\item{C_pool}{In quotes, carbon pool of interest. Name must match carbon pool name found within file supplied to 'data'.}
+
+\item{covariates}{In quotes, file path of SpatRaster stack, used as predictors in randomForest. Layers within stack should be named.}
+
+\item{cords}{In quotes, file path for .csv file containing the site coordinates, columns named "lon" and "lat".}
+}
+\value{
+It returns the `downscale_output` list containing lists for the training and testing data sets, models, and predicted maps for each ensemble member.
+}
+\description{
+This function uses the randomForest model.
+}
+\details{
+This function will downscale forecast data to unmodeled locations using covariates and site locations
+}
+\author{
+Joshua Ploshay
+}
diff --git a/modules/benchmark/DESCRIPTION b/modules/benchmark/DESCRIPTION
index 2cb70a15458..8ebd5bf11bc 100644
--- a/modules/benchmark/DESCRIPTION
+++ b/modules/benchmark/DESCRIPTION
@@ -19,7 +19,6 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation.
 Imports:
-    dbplyr,
     dplyr,
     ggplot2,
     gridExtra,
@@ -28,7 +27,6 @@ Imports:
     ncdf4 (>= 1.15),
     PEcAn.DB,
     PEcAn.logger,
-    PEcAn.remote,
     PEcAn.settings,
     PEcAn.utils,
     reshape2,
diff --git a/modules/benchmark/R/align_by_first_observation.R b/modules/benchmark/R/align_by_first_observation.R
index 38ee061c118..b1ae51afd0e 100644
--- a/modules/benchmark/R/align_by_first_observation.R
+++ b/modules/benchmark/R/align_by_first_observation.R
@@ -18,9 +18,11 @@
 #' table$plant_functional_type_two<- c('a','a','b', 'b') # PFT groupings
 #' table<-as.data.frame(table)
 #'
-#' aligned<-align_by_first_observation(observation_one = observation_one, observation_two = observation_two,
-#' custom_table = table)
-#' 
+#' aligned <- align_by_first_observation(
+#'   observation_one = observation_one,
+#'   observation_two = observation_two,
+#'   custom_table = table)
+#'
 #' # aligned should be a vector '[1] "AMCA3" "ARHY"  "AMCA3" "AMCA3"'
 #' @export
 align_by_first_observation<-function(observation_one, observation_two, custom_table){
diff --git a/modules/benchmark/R/align_data.R b/modules/benchmark/R/align_data.R
index 51169417e06..d3aee1468ac 100644
--- a/modules/benchmark/R/align_data.R
+++ b/modules/benchmark/R/align_data.R
@@ -1,13 +1,14 @@
-##' @name align_data
-##' @title Align timeseries data
-##' @export
+##' Align timeseries data
+##'
 ##' @param model.calc data.frame
 ##' @param obvs.calc data.frame
 ##' @param var data.frame
+##' @param align_method name of function to use for alignment
+##'
 ##' @importFrom rlang .data
 ##' @return dat
 ##' @author Betsy Cowdery
-
+##' @export
 
 ## Align timeseries data using different functions
 
@@ -43,15 +44,19 @@ align_data <- function(model.calc, obvs.calc, var, align_method = "match_timeste
   coarse.unit <- compare$diff_units[coarse]
   
   # Round to the larger time step (experimental)
-  obvs.calc$round.posix  <- as.POSIXct(round(obvs.calc$posix,  units = coarse.unit))
-  model.calc$round.posix <- as.POSIXct(round(model.calc$posix, units = coarse.unit))
+  # Note: Oddly, the second argument to `round()` has to be unnamed here
+  #   because of an inconsistency in base R's rounding methods.
+  #   The generic `round()` expects the second arg to be called `digits`,
+  #   but then dispatches to `round.POSIXt`, which takes `units`.
+  obvs.calc$round.posix  <- as.POSIXct(round(obvs.calc$posix,  coarse.unit))
+  model.calc$round.posix <- as.POSIXct(round(model.calc$posix, coarse.unit))
   
   
   # Determine the overlaping range of dates
   # Compare the rounded dates because you can't compare dates of different units with range
   rng_obvs  <- range(unique(obvs.calc$round.posix))
   rng_model <- range(unique(model.calc$round.posix))
-  rng_dat   <- sort(c(rng_obvs, rng_model))[c(2, 3)] %>% lubridate::with_tz(., tzone = "UTC")
+  rng_dat   <- sort(c(rng_obvs, rng_model))[c(2, 3)] %>% lubridate::with_tz(tzone = "UTC")
   
   # Special case for annual timestep
   if(setequal(c(365,366), compare$diff_days[coarse]) | setequal(c(365), compare$diff_days[coarse]) | 
@@ -79,7 +84,7 @@ align_data <- function(model.calc, obvs.calc, var, align_method = "match_timeste
     filter(coarse_range_check[1] <= .data$round.posix)  %>% 
     filter(coarse_range_check[2] >= .data$round.posix)
   
-  out1 <- date_subsets[[compare$type[coarse]]] %>% dplyr::select(.,one_of(var))
+  out1 <- date_subsets[[compare$type[coarse]]] %>% dplyr::select(dplyr::one_of(var))
   colnames(out1) <- paste0(colnames(out1), ".", compare$type[coarse])
   
   
@@ -89,7 +94,7 @@ align_data <- function(model.calc, obvs.calc, var, align_method = "match_timeste
     date.coarse <- date_subsets[[compare$type[coarse]]]$round.posix
     date.fine   <- date_subsets[[compare$type[fine]]]$round.posix
     
-    data.fine   <- date_subsets[[compare$type[fine]]] %>% dplyr::select(.,one_of(var))
+    data.fine   <- date_subsets[[compare$type[fine]]] %>% dplyr::select(dplyr::one_of(var))
     colnames(data.fine) <- paste0(colnames(data.fine), ".", compare$type[fine])
     
     out2 <- apply(data.fine, 2, 
@@ -104,10 +109,10 @@ align_data <- function(model.calc, obvs.calc, var, align_method = "match_timeste
     
   } else if (mode.o == mode.m) { # here coarse and fine are just index values but but the time steps are the same size
     
-    out2 <- date_subsets[[compare$type[fine]]] %>% dplyr::select(.,one_of(var))
+    out2 <- date_subsets[[compare$type[fine]]] %>% dplyr::select(dplyr::one_of(var))
     colnames(out2) <- paste0(colnames(out2), ".", compare$type[fine])
     dat <- cbind(out1, out2)
-    dat$posix <- date_subsets[[compare$type[fine]]] %>% dplyr::select(.,one_of("round.posix")) %>% .[,1]
+    dat$posix <- date_subsets[[compare$type[fine]]] %>% dplyr::select(dplyr::one_of("round.posix")) %>% .[,1]
     
   }
   
diff --git a/modules/benchmark/R/align_pft.R b/modules/benchmark/R/align_pft.R
index 4bfebca9cff..e6d15f04ebe 100644
--- a/modules/benchmark/R/align_pft.R
+++ b/modules/benchmark/R/align_pft.R
@@ -1,7 +1,6 @@
-#################################################################
-#'align_pft
+#' Align vectors of Plant Functional Type and species.
+#'
 #'@details
-#' Aligns vectors of Plant Fucntional Typed and species.
 #' Can align: 
 #' - two vectors of plant fucntional types (pft's) if a custom map is provided
 #' - a list of species (usda, fia, or latin_name format) to a plant fucntional type
@@ -28,6 +27,9 @@
 #' @param format_two The output of query.format.vars() of observation two of the form output$vars$bety_names
 #' @param subset_is_ok When aligning two species lists, this allows for alignement when species lists aren't identical. 
 #' set to FALSE by default. 
+#' @param comparison_type one of "data_to_model", "data_to_data", or "model_to_model"
+#' @param ... other arguments, currently ignored
+#'
 #' @return \code{list} containing the following columns:
 #' \describe{
 #'  \item{\code{$original}}{Will spit back out original vectors pre-alignment}
diff --git a/modules/benchmark/R/bm_settings.R b/modules/benchmark/R/bm_settings.R
index 10ca924aa9f..0f679bd6dbe 100644
--- a/modules/benchmark/R/bm_settings.R
+++ b/modules/benchmark/R/bm_settings.R
@@ -26,12 +26,12 @@ read_settings_BRR <- function(settings){
     filter(.data$id == settings$benchmarking$reference_run_id) %>%
     collect()
 
-  BRR.settings <- BRR %>% pull(settings) %>% unlist() %>%
-    xmlToList(.,"pecan")
+  BRR.settings <- BRR %>% dplyr::pull(settings) %>% unlist() %>%
+    XML::xmlToList("pecan")
 
   PEcAn.logger::logger.debug(names(BRR.settings))
 
-  settings <- BRR.settings %>% append(settings,.) %>% PEcAn.settings::Settings()
+  settings <- append(settings, BRR.settings) %>% PEcAn.settings::Settings()
   invisible(settings)
 }
 
@@ -86,8 +86,8 @@ clean_settings_BRR <- function(inputfile){
 ##' @author Betsy Cowdery
 
 add_workflow_info <- function(settings, bety){
-  if (is.MultiSettings(settings)) {
-    return(papply(settings, add_workflow_id))
+  if (PEcAn.settings::is.MultiSettings(settings)) {
+    return(PEcAn.settings::papply(settings, add_workflow_id))
   }
   if(!as.logical(settings$benchmarking$new_run)){
     settings$workflow$id <- tbl(bety,"ensembles") %>%
@@ -109,8 +109,8 @@ add_workflow_info <- function(settings, bety){
 ##' @author Betsy Cowdery
 
 bm_settings2pecan_settings <- function(bm.settings){
-  if (is.MultiSettings(bm.settings)) {
-    return(papply(bm.settings, bm_settings2pecan_settings))
+  if (PEcAn.settings::is.MultiSettings(bm.settings)) {
+    return(PEcAn.settings::papply(bm.settings, bm_settings2pecan_settings))
   }
   out <- bm.settings["reference_run_id"]
   for(i in grep("benchmark", names(bm.settings))){
diff --git a/modules/benchmark/R/calc_benchmark.R b/modules/benchmark/R/calc_benchmark.R
index 72a36ef56ac..508f6c67b9c 100644
--- a/modules/benchmark/R/calc_benchmark.R
+++ b/modules/benchmark/R/calc_benchmark.R
@@ -1,10 +1,10 @@
-##-------------------------------------------------------------------------------------------------#
+##' Calculate benchmarking statistics
+##'
 ##' For each benchmark id, calculate metrics and update benchmarks_ensemble_scores
 ##'  
-##' @name calc_benchmark 
-##' @title Calculate benchmarking statistics
-##' @param bm.ensemble object, either from create_BRR or start.bm.ensemle
+##' @param settings settings object describing the run to calculate
 ##' @param bety database connection
+##' @param start_year,end_year time range to read. If NA, these are taken from `settings`
 ##' @export 
 ##' 
 ##' @author Betsy Cowdery 
@@ -135,9 +135,9 @@ calc_benchmark <- function(settings, bety, start_year = NA, end_year = NA) {
         var <- dplyr::filter(format$vars, .data$variable_id == bm$variable_id)[, "pecan_name"]
         var.list <- c(var.list, var)
         
-        obvs.calc <- obvs_full %>% dplyr::select(., dplyr::one_of(c("posix", var)))
+        obvs.calc <- obvs_full %>% dplyr::select(dplyr::one_of(c("posix", var)))
         obvs.calc[,var] <- as.numeric(obvs.calc[,var])
-        model.calc <- model_full %>% dplyr::select(., dplyr::one_of(c("posix", var)))
+        model.calc <- model_full %>% dplyr::select(dplyr::one_of(c("posix", var)))
         
         # Check that the variables actually got loaded, otherwise don't send to calc_metrics
         
@@ -157,7 +157,7 @@ calc_benchmark <- function(settings, bety, start_year = NA, end_year = NA) {
                                          bm_dir)
         
         for(metric.id in metrics$id){
-          metric.name <- filter(metrics,id == metric.id)[["name"]]
+          metric.name <- dplyr::filter(metrics,.data$id == metric.id)[["name"]]
           score <- out.calc_metrics[["benchmarks"]] %>% 
             dplyr::filter(.data$metric == metric.name) %>% 
             dplyr::select(score)
diff --git a/modules/benchmark/R/check_if_legal_table.R b/modules/benchmark/R/check_if_legal_table.R
index a0b3fe15b52..126b231b6b6 100644
--- a/modules/benchmark/R/check_if_legal_table.R
+++ b/modules/benchmark/R/check_if_legal_table.R
@@ -1,14 +1,16 @@
-#'  check_if_legal_table
+#' check_if_legal_table
+#'
 #' @details
 #' Checks if custom_table:
 #' 1. is formated correctly
 #' 2. is complete (has all of the species/pft's in both observations)
 #' 3. is condense-able (Could be represented as a hierachry)
 #' 
+#' @param table a table that either maps two pft's to one anouther or maps custom species codes to bety id codes.
+#'   In the second case, must be passable to match_species_id.
 #' @param observation_one a vector of plant functional types, or species
 #' @param observation_two anouther vector of plant functional types, or species
-#' @param custom_table a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-#' In the second case, must be passable to match_species_id. 
+#'
 #' @return \code{boolean} 
 #' @author Tempest McCabe
 check_if_legal_table<-function(table, observation_one, observation_two){
diff --git a/modules/benchmark/R/check_if_list_of_pfts.R b/modules/benchmark/R/check_if_list_of_pfts.R
index 0d2f8979db9..3b587240d94 100644
--- a/modules/benchmark/R/check_if_list_of_pfts.R
+++ b/modules/benchmark/R/check_if_list_of_pfts.R
@@ -1,9 +1,9 @@
 #' check_if_list_of_pfts
-#' @details Checks if format contains a variable named "plant_functional_type"
-#' @param observation_one a vector of plant fucntional types, or species
-#' @param observation_two anouther vector of plant fucntional types, or species
-#' @param custom_table a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-#' In the second case, must be passable to match_species_id. 
+#'
+#' Checks if format contains a variable named "plant_functional_type"
+#'
+#' @param vars names to check
+#'
 #' @return \code{boolean} 
 #' @author Tempest McCabe
 check_if_list_of_pfts<-function(vars){
diff --git a/modules/benchmark/R/check_if_species_list.R b/modules/benchmark/R/check_if_species_list.R
index 620f281c7e8..bbba2729af2 100644
--- a/modules/benchmark/R/check_if_species_list.R
+++ b/modules/benchmark/R/check_if_species_list.R
@@ -1,11 +1,12 @@
-#'@title check_if_species_list
+#' check_if_species_list
+#'
 #'@details
 #' Checks if format contains a species list in a known format, or a declared custom format. 
-#' 
-#' @param observation_one a vector of plant functional types, or species
-#' @param observation_two another vector of plant functional types, or species
+#'
+#' @param vars format
 #' @param custom_table a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
 #' In the second case, must be passable to match_species_id. 
+#'
 #' @return \code{boolean} 
 #' @author Tempest McCabe
 check_if_species_list<-function(vars,custom_table=NULL){
diff --git a/modules/benchmark/R/create_BRR.R b/modules/benchmark/R/create_BRR.R
index 8f4660faba4..d2e4d7f7e3b 100644
--- a/modules/benchmark/R/create_BRR.R
+++ b/modules/benchmark/R/create_BRR.R
@@ -1,10 +1,10 @@
-##-------------------------------------------------------------------------------------------------#
+##' Create benchmark reference run and ensemble
+##'
 ##' For each benchmark id, calculate metrics and update benchmarks_ensemble_scores
 ##'  
-##' @name create_BRR
-##' @title Create benchmark reference run and ensemble
 ##' @param ens_wf table made from joining ensemble and workflow tables 
 ##' @param con database connection
+##' @param user_id Optional user id to use for this record in reference_runs table
 ##' @export 
 ##' 
 ##' @author Betsy Cowdery 
@@ -36,7 +36,7 @@ create_BRR <- function(ens_wf, con, user_id = ""){
   }else if(dim(ref_run)[1] > 1){# There shouldn't be more than one reference run with the same settings
     PEcAn.logger::logger.error("There is more than one reference run in the database with these settings. Review for duplicates. ")
   }
-  BRR <- ref_run %>% dplyr::rename(.,reference_run_id = id)
+  BRR <- ref_run %>% dplyr::rename(reference_run_id = .data$id)
   return(BRR)
   # }else{logger.error(sprintf("Cannot create a benchmark reference run for a run on hostname: %s", 
   #                            ens_wf$hostname))}
diff --git a/modules/benchmark/R/define_benchmark.R b/modules/benchmark/R/define_benchmark.R
index 629828b9e4d..6178b942db0 100644
--- a/modules/benchmark/R/define_benchmark.R
+++ b/modules/benchmark/R/define_benchmark.R
@@ -1,16 +1,18 @@
+##' Benchmark Definition: Retrieve or Create Bety Benchmarking Records
+##'
 ##' Creates records for benchmarks, benchmarks_benchmarks_reference_runs, benchmarks_metrics
 ##'
-##' @name define_benchmark
-##' @title Benchmark Definition: Retrieve or Create Bety Benchmarking Records
-##' @param bm.settings settings list
+##' @param settings settings list
+##' @param bety database connection
+##'
 ##' @return updated settings list
 ##' @author Betsy Cowdery
-##' @export define_benchmark
 ##' @importFrom dplyr tbl filter rename collect select
+##' @export
 define_benchmark <- function(settings, bety){
   
-  if (is.MultiSettings(settings)) {
-    return(papply(settings, function(x) define_benchmark(x, bety)))
+  if (PEcAn.settings::is.MultiSettings(settings)) {
+    return(PEcAn.settings::papply(settings, function(x) define_benchmark(x, bety)))
   }
   bm.settings <- settings$benchmarking
   
@@ -22,18 +24,18 @@ define_benchmark <- function(settings, bety){
     if(!is.null(bm.settings$ensemble_id)){
       
       # check if there is already a BRR for ensemble.id, otherwise make one
-      bm_ens <- tbl(bety,"benchmarks_ensembles") %>% rename(bm_ensemble_id = id) %>% 
-        filter(ensemble_id == bm.settings$ensemble_id) %>% collect()
+      bm_ens <- dplyr::tbl(bety,"benchmarks_ensembles") %>% rename(bm_ensemble_id = .data$id) %>% 
+        filter(.data$ensemble_id == bm.settings$ensemble_id) %>% collect()
       
       if(length(bm_ens) == 0){
         # Get workflow id from ensemble id
-        ens_wf <- tbl(bety, 'ensembles') %>% filter(id == bm.settings$ensemble_id) %>% 
-          rename(ensemble_id = id) %>% 
-          left_join(.,tbl(bety, "workflows") %>% rename(workflow_id = id), by="workflow_id") %>% collect()
+        ens_wf <- dplyr::tbl(bety, 'ensembles') %>% filter(.data$id == bm.settings$ensemble_id) %>% 
+          rename(ensemble_id = .data$id) %>% 
+          dplyr::left_join(tbl(bety, "workflows") %>% rename(workflow_id = .data$id), by="workflow_id") %>% collect()
         BRR <- create_BRR(ens_wf, con = bety, user_id = settings$info$userid)
       }else if(dim(bm_ens)[1] == 1){
-        BRR <- tbl(bety,"reference_runs") %>% filter(id == bm_ens$reference_run_id) %>% 
-          rename(reference_run_id = id) %>% collect()
+        BRR <- tbl(bety,"reference_runs") %>% filter(.data$id == bm_ens$reference_run_id) %>% 
+          rename(reference_run_id = .data$id) %>% collect()
       }else if(dim(bm_ens)[1] > 1){ # There shouldn't be more than one reference run per run
         PEcAn.logger::logger.error("There is more than one reference run in the database for this ensemble id. Review for duplicates. ")
       }
@@ -41,8 +43,8 @@ define_benchmark <- function(settings, bety){
       bm.settings$reference_run_id <- BRR$reference_run_id
       # bm.settings$ensemble_id <- NULL
       
-    }else{logger.error("Cannot find or create benchmark reference run")}
-  }else{logger.debug("Reference run already created")}
+    }else{PEcAn.logger::logger.error("Cannot find or create benchmark reference run")}
+  }else{PEcAn.logger::logger.debug("Reference run already created")}
   
   
   # Retrieve/create benchmark entries
@@ -58,7 +60,7 @@ define_benchmark <- function(settings, bety){
     if(!is.null(benchmark$metrics)){
       metric_ids <- as.numeric(unlist(benchmark$metrics))
     }else{
-      metric_ids <- tbl(bety, 'metrics') %>% pull(id)
+      metric_ids <- tbl(bety, 'metrics') %>% dplyr::pull(.data$id)
     }
     
     # If site is not specified in benchmark settings (this may be unnecessary)
@@ -71,8 +73,8 @@ define_benchmark <- function(settings, bety){
     }
     
     bm <- tbl(bety, 'benchmarks') %>% 
-      filter(input_id == benchmark$input_id) %>%
-      filter(variable_id == benchmark$variable_id) %>%
+      filter(.data$input_id == benchmark$input_id) %>%
+      filter(.data$variable_id == benchmark$variable_id) %>%
       filter(site_id == site_id) %>% collect()
     
     # Retrieve/create benchmark record
@@ -81,27 +83,27 @@ define_benchmark <- function(settings, bety){
                             "VALUES ( %s, %s, %s, %s) RETURNING * ;"), 
                      benchmark$input_id, benchmark$variable_id,
                      site_id, settings$info$userid)
-      bm <- db.query(cmd, bety)
-      logger.debug(sprintf("Benchmark %.0f for input %.0f variable %.0f created", 
+      bm <- PEcAn.DB::db.query(cmd, bety)
+      PEcAn.logger::logger.debug(sprintf("Benchmark %.0f for input %.0f variable %.0f created", 
                            bm$id, bm$input_id, bm$variable_id))
     }else if(dim(bm)[1] >1){
       PEcAn.logger::logger.error(sprintf("DUPLICATE records exist for input %.0f variable %.0f", 
                                         as.numeric(benchmark$input_id), benchmark$variable_id))
     }else{
-      logger.debug(sprintf("Benchmark %.0f for input %.0f variable %.0f exists", 
+      PEcAn.logger::logger.debug(sprintf("Benchmark %.0f for input %.0f variable %.0f exists", 
                            bm$id, bm$input_id, bm$variable_id))      
     }
     
     # Retrieve/create benchmarks_benchmarks_reference_runs record
     bmBRR <- tbl(bety, 'benchmarks_benchmarks_reference_runs') %>% 
-      filter(benchmark_id == bm$id) %>%
-      filter(reference_run_id == bm.settings$reference_run_id)  %>% collect()
+      filter(.data$benchmark_id == bm$id) %>%
+      filter(.data$reference_run_id == bm.settings$reference_run_id)  %>% collect()
     
     if(dim(bmBRR)[1] == 0){
       cmd <- sprintf(paste0("INSERT INTO benchmarks_benchmarks_reference_runs",
                             " (benchmark_id, reference_run_id) VALUES (%s, %s)"),
                      bm$id, bm.settings$reference_run_id)
-      db.query(cmd, bety)
+      PEcAn.DB::db.query(cmd, bety)
     }else if(dim(bmBRR)[1] > 1){
       PEcAn.logger::logger.error("Duplicate record entries in benchmarks_benchmarks_reference_runs")
     }
@@ -109,13 +111,13 @@ define_benchmark <- function(settings, bety){
     # Retrieve/create benchmarks_metrics record
     for(k in seq_along(metric_ids)){
       bmmetric <- tbl(bety, 'benchmarks_metrics') %>% 
-        filter(benchmark_id == bm$id) %>%
-        filter(metric_id == metric_ids[[k]])  %>% collect()
+        filter(.data$benchmark_id == bm$id) %>%
+        filter(.data$metric_id == metric_ids[[k]])  %>% collect()
       
       if(dim(bmmetric)[1] == 0){
         cmd <- sprintf(paste0("INSERT INTO benchmarks_metrics (benchmark_id, metric_id) VALUES (%s, %s)"),
                        bm$id, metric_ids[[k]])
-        db.query(cmd, bety)
+        PEcAn.DB::db.query(cmd, bety)
       }else if(dim(bmmetric)[1] > 1){
         PEcAn.logger::logger.error("Duplicate record entries in benchmarks_metrics")
       }
diff --git a/modules/benchmark/R/format_wide2long.R b/modules/benchmark/R/format_wide2long.R
index 62dffbbd351..8ab93062e74 100644
--- a/modules/benchmark/R/format_wide2long.R
+++ b/modules/benchmark/R/format_wide2long.R
@@ -1,14 +1,12 @@
-##' @name format_wide2long
-##' @title format_wide2long
+##' Function to convert wide format to long format
 ##' 
 ##' @param out wide format data
 ##' @param format as returned by query.format.vars
-##' @param vars_used 
-##' @param time.row
+##' @param vars_used data frame mapping `input_name` to `bety_name`
+##' @param time.row ignored; value in output is set from `format$vars$storage_type`
 ##' @return list of updated values
 ##' @export
 ##' @author Istem Fer
-##' Function to convert wide format to long format
 format_wide2long <- function(out, format, vars_used, time.row){
   
   # GapMacro example:
diff --git a/modules/benchmark/R/get_species_list_standard.R b/modules/benchmark/R/get_species_list_standard.R
index e1bae78078b..d7872a31f96 100644
--- a/modules/benchmark/R/get_species_list_standard.R
+++ b/modules/benchmark/R/get_species_list_standard.R
@@ -1,13 +1,11 @@
 #' get_species_list_standard
-#' @details 
+#'
 #' Returns the format type for convience of use with match_species_id
-#' @param observation_one a vector of plant fucntional types, or species
-#' @param observation_two anouther vector of plant fucntional types, or species
-#' @param custom_table a table that either maps two pft's to one another or maps custom species codes to bety id codes. 
-#' In the second case, must be passable to match_species_id. 
+#'
+#' @param vars format to be matched
 #' @return \code{character} Returns "usda", "latin_name", "fia" or "custom"
 #' @author Tempest McCabe
-get_species_list_standard<-function(vars){
+get_species_list_standard <- function(vars) {
   
   if(any(c("species_id", "species_USDA_symbol") %in% vars)){
     return("usda")
@@ -15,11 +13,11 @@ get_species_list_standard<-function(vars){
     return('latin_name')
   }else if("species_FIA_symbol" %in% vars){
     return('fia')
-  }else if(!is.null(custom_table)){
-    if("bety_species_id" %in% names(custom_table)){
+  }else if(!is.null(vars)){
+    if("bety_species_id" %in% names(vars)){
       return("custom")
     }else{
-      logger.warn("Note: custom_table does not have column named 'bety_species_id' and cannot be used with match_species_id(). This prohibits species-level mapping, but allows PFT level mapping.")
+      PEcAn.logger::logger.warn("Note: `vars` does not have column named 'bety_species_id' and cannot be used with match_species_id(). This prohibits species-level mapping, but allows PFT level mapping.")
     }
   }else{
     return(FALSE)
diff --git a/modules/benchmark/R/load_csv.R b/modules/benchmark/R/load_csv.R
index 2b0ff3486b6..28c9bdea4ef 100644
--- a/modules/benchmark/R/load_csv.R
+++ b/modules/benchmark/R/load_csv.R
@@ -1,31 +1,30 @@
-##' @name load_csv
-##' @title load_csv
-##' @export
+##' load_csv
+##'
 ##' @param data.path character
 ##' @param format list
-##' @param start_year numeric
-##' @param end_year numeric
 ##' @param site list
+##' @param vars column names to return. If NULL, returns all columns
 ##' 
 ##' @author Betsy Cowdery
+##' @export
 load_csv <- function(data.path, format, site, vars = NULL) {
   
   data.path <- sapply(data.path, function(x) dir(dirname(x), basename(x), full.names = TRUE))
   
   if (format$header == 0 | format$header == 1) {
-    dat <- read.csv(data.path, skip = format$skip, na.strings = format$na.strings, 
+    dat <- utils::read.csv(data.path, skip = format$skip, na.strings = format$na.strings, 
                     as.is = TRUE, check.names = FALSE, header = as.logical(format$header))
   } else if (format$header > 1) {
-    dat <- read.csv(data.path, skip = format$skip, na.strings = format$na.strings,
+    dat <- utils::read.csv(data.path, skip = format$skip, na.strings = format$na.strings,
                     as.is = TRUE, check.names = FALSE, header = TRUE)
-    dat <- dat[-c(1:header - 1), ]
+    dat <- dat[-c(1:format$header - 1), ]
   } else {
-    dat <- read.csv(data.path, skip = format$skip, na.strings = format$na.strings,
+    dat <- utils::read.csv(data.path, skip = format$skip, na.strings = format$na.strings,
                     as.is = TRUE, check.names = FALSE)
   }
   
   if(!is.null(vars)){
-    return(dplyr::select(dat, one_of(vars)))
+    return(dplyr::select(dat, dplyr::one_of(vars)))
   }else{
     return(dat)
   }
diff --git a/modules/benchmark/R/load_data.R b/modules/benchmark/R/load_data.R
index 10289ae9898..3f72ad3d3ea 100644
--- a/modules/benchmark/R/load_data.R
+++ b/modules/benchmark/R/load_data.R
@@ -1,15 +1,19 @@
-##' @name load_data
-##' @title load_data
-##' @export
-##' @param data.path character
-##' @param format list
-##' @param start_year numeric
-##' @param end_year numeric
-##' @param site list
-##' @author Betsy Cowdery, Istem Fer, Joshua Mantooth
-##' Generic function to convert input files containing observational data to 
-##' a common PEcAn format. 
+#' load data
+#'
+#' Generic function to convert input files containing observational data to
+#' a common PEcAn format.
+#'
+#' @param data.path character
+#' @param format list
+#' @param start_year numeric
+#' @param end_year numeric
+#' @param site list
+#' @param vars.used.index which variables to use? If NULL, these are taken from `format`
+#' @param ... further arguments, currently ignored
+#'
+#' @author Betsy Cowdery, Istem Fer, Joshua Mantooth
 #' @importFrom magrittr %>%
+#' @export
 
 load_data <- function(data.path, format, start_year = NA, end_year = NA, site = NA, 
                       vars.used.index=NULL, ...) {
@@ -128,13 +132,13 @@ load_data <- function(data.path, format, start_year = NA, end_year = NA, site =
   # This was part of the arguments but never implemented
   if(!is.na(start_year)){
     out$year <- lubridate::year(out$posix)
-    out <- out %>% filter(.,year >= as.numeric(start_year))
+    out <- out %>% filter(.data$year >= as.numeric(start_year))
     print("subsetting by start year")
   }
   
   if(!is.na(end_year)){
     out$year <- lubridate::year(out$posix)
-    out <- out %>% filter(.,year <= as.numeric(end_year))
+    out <- out %>% filter(.data$year <= as.numeric(end_year))
     print("subsetting by end year")
   }
   
diff --git a/modules/benchmark/R/load_netcdf.R b/modules/benchmark/R/load_netcdf.R
index 629ee006f36..2e956ffee85 100644
--- a/modules/benchmark/R/load_netcdf.R
+++ b/modules/benchmark/R/load_netcdf.R
@@ -1,13 +1,11 @@
-##' @name load_x_netcdf
-##' @title load_x_netcdf
-##' @export
+##' Load from netCDF
+##'
 ##' @param data.path character vector or list
 ##' @param format list
-##' @param start_year numeric
-##' @param end_year numeric
 ##' @param site list
 ##' @param vars character
 ##' @author Istem Fer
+##' @export
 load_x_netcdf <- function(data.path, format, site, vars = NULL) {
   data.path <- sapply(data.path, function(x) dir(dirname(x), basename(x), full.names = TRUE))
   nc <- lapply(data.path, ncdf4::nc_open)
diff --git a/modules/benchmark/R/load_rds.R b/modules/benchmark/R/load_rds.R
index f7b81c49cda..7fb82daa5b8 100644
--- a/modules/benchmark/R/load_rds.R
+++ b/modules/benchmark/R/load_rds.R
@@ -4,7 +4,7 @@
 ##' @param data.path character
 ##' @param format list, not used, for compatibility
 ##' @param site not used, for compatibility
-##' @param vars 
+##' @param vars optional variable names to load. if NULL, returns all variables in file
 ##' 
 ##' @author Istem Fer
 load_rds <- function(data.path, format, site, vars = NULL) {
@@ -14,7 +14,7 @@ load_rds <- function(data.path, format, site, vars = NULL) {
   dat <- readRDS(data.path)
 
   if(!is.null(vars)){
-    return(dplyr::select(dat, one_of(vars)))
+    return(dplyr::select(dat, dplyr::one_of(vars)))
   }else{
     return(dat)
   }
diff --git a/modules/benchmark/R/load_tab.R b/modules/benchmark/R/load_tab.R
index 6b13ee6c278..4f95eca6413 100644
--- a/modules/benchmark/R/load_tab.R
+++ b/modules/benchmark/R/load_tab.R
@@ -1,36 +1,34 @@
-##' @name load_tab_separated_values
-##' @title load_tab_separated_values
-##' @export
+##' Load files with mime-type 'text/tab-separated-values'
+##'
 ##' @param data.path character
 ##' @param format list
-##' @param start_year numeric
-##' @param end_year numeric
 ##' @param site list
+##' @param vars variable names to load. If NULL, loads all columns
 ##' 
 ##' @author Betsy Cowdery, Mike Dietze
+##' @export
 load_tab_separated_values <- function(data.path, format, site=NULL, vars = NULL) {
-  ## load's mime-type = text/tab-separated-values
   
   data.path <- sapply(data.path, function(x) dir(dirname(x), basename(x), full.names = TRUE))
   
   if (format$header == 0) {
-    dat <- read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings, 
+    dat <- utils::read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings, 
                       as.is = TRUE, check.names = FALSE, header = FALSE)
     colnames(dat)[format$vars$column_number] <- format$vars$input_name
   } else if (format$header == 1) {
-    dat <- read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings, 
+    dat <- utils::read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings, 
                     as.is = TRUE, check.names = FALSE, header = TRUE)
   } else if (format$header > 1) {
-    dat <- read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings,
+    dat <- utils::read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings,
                     as.is = TRUE, check.names = FALSE, header = TRUE)
-    dat <- dat[-c(1:header - 1), ]
+    dat <- dat[-c(1:format$header - 1), ]
   } else {
-    dat <- read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings,
+    dat <- utils::read.table(data.path, sep="\t",skip = format$skip, na.strings = format$na.strings,
                     as.is = TRUE, check.names = FALSE)
   }
   
   if(!is.null(vars)){
-    return(dplyr::select(dat, one_of(vars)))
+    return(dplyr::select(dat, dplyr::one_of(vars)))
   }else{
     return(dat)
   }
diff --git a/modules/benchmark/R/match_timestep.R b/modules/benchmark/R/match_timestep.R
index 8f59533a338..bb030ed447f 100644
--- a/modules/benchmark/R/match_timestep.R
+++ b/modules/benchmark/R/match_timestep.R
@@ -8,7 +8,7 @@
 ##' @author Istem Fer
 match_timestep <- function(date.coarse, date.fine, data.fine) {
   
-  midpoints <- c(-Inf, head(as.numeric(date.fine), -1)) + c(0, diff(as.numeric(date.fine)) / 2)
+  midpoints <- c(-Inf, utils::head(as.numeric(date.fine), -1)) + c(0, diff(as.numeric(date.fine)) / 2)
   
   return(data.fine[findInterval(date.coarse, midpoints)])
 } # match_timestep
diff --git a/modules/benchmark/R/metric_AME.R b/modules/benchmark/R/metric_AME.R
index 805d54dcbf8..cd5950bac97 100644
--- a/modules/benchmark/R/metric_AME.R
+++ b/modules/benchmark/R/metric_AME.R
@@ -1,9 +1,10 @@
-##' @name metric_AME
-##' @title Absolute Maximum Error
-##' @export
+##' Absolute Maximum Error
+##'
 ##' @param dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Betsy Cowdery
+##' @export
 
 metric_AME <- function(dat, ...) {
   PEcAn.logger::logger.info("Metric: Absolute Maximum Error")
diff --git a/modules/benchmark/R/metric_Frechet.R b/modules/benchmark/R/metric_Frechet.R
index 3a11cb96a77..e79014c6450 100644
--- a/modules/benchmark/R/metric_Frechet.R
+++ b/modules/benchmark/R/metric_Frechet.R
@@ -2,12 +2,13 @@
 ##' @title Frechet Distance
 ##' @export
 ##' @param metric_dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Betsy Cowdery
 
 metric_Frechet <- function(metric_dat, ...) {
-  logger.info("Metric: Frechet Distance")
-  dat.no.na <- na.omit(metric_dat)
+  PEcAn.logger::logger.info("Metric: Frechet Distance")
+  dat.no.na <- stats::na.omit(metric_dat)
   Fdist <- SimilarityMeasures::Frechet(as.matrix(dat.no.na$obvs), as.matrix(dat.no.na$model))
   return(Fdist)
 } # metric_Frechet
diff --git a/modules/benchmark/R/metric_MAE.R b/modules/benchmark/R/metric_MAE.R
index 03229d1f0b5..06fa9577a4e 100644
--- a/modules/benchmark/R/metric_MAE.R
+++ b/modules/benchmark/R/metric_MAE.R
@@ -1,10 +1,10 @@
-##' @name metric_MAE
-##' @title Mean Absolute Error
-##' @export
+##' Mean Absolute Error
 ##' @param dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Betsy Cowdery
 ##' 
+##' @export
 metric_MAE <- function(dat, ...) {
   PEcAn.logger::logger.info("Metric: Mean Absolute Error")
   return(mean(abs(dat$model - dat$obvs),na.rm=TRUE))
diff --git a/modules/benchmark/R/metric_MSE.R b/modules/benchmark/R/metric_MSE.R
index 1ace772a42f..a3d91a14764 100644
--- a/modules/benchmark/R/metric_MSE.R
+++ b/modules/benchmark/R/metric_MSE.R
@@ -2,6 +2,7 @@
 ##' @title Mean Square Error
 ##' @export
 ##' @param dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Betsy Cowdery
 
diff --git a/modules/benchmark/R/metric_PPMC.R b/modules/benchmark/R/metric_PPMC.R
index 6c3d7a55dd9..53ec1151c84 100644
--- a/modules/benchmark/R/metric_PPMC.R
+++ b/modules/benchmark/R/metric_PPMC.R
@@ -2,6 +2,7 @@
 ##' @title Pearson Product Moment Correlation
 ##' @export
 ##' @param metric_dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Betsy Cowdery
 
@@ -10,5 +11,5 @@ metric_PPMC <- function(metric_dat, ...) {
   # numer <- sum((metric_dat$obvs - mean(metric_dat$obvs)) * (metric_dat$model - mean(metric_dat$model)))
   # denom <- sqrt(sum((metric_dat$obvs - mean(metric_dat$obvs)) ^ 2)) * sqrt(sum((metric_dat$model - mean(metric_dat$model)) ^ 2))
   # return(numer / denom)
-  return(cor(metric_dat$obvs, metric_dat$model))
+  return(stats::cor(metric_dat$obvs, metric_dat$model))
 } # metric_PPMC
diff --git a/modules/benchmark/R/metric_R2.R b/modules/benchmark/R/metric_R2.R
index 8de8b497bd5..94e5df7677b 100644
--- a/modules/benchmark/R/metric_R2.R
+++ b/modules/benchmark/R/metric_R2.R
@@ -2,6 +2,7 @@
 ##' @title Coefficient of Determination (R2)
 ##' @export
 ##' @param metric_dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Betsy Cowdery
 
@@ -13,7 +14,7 @@ metric_R2 <- function(metric_dat, ...) {
   out <- (numer / denom) ^ 2
   
   if(is.na(out)){
-    fit <- lm(metric_dat$model ~ metric_dat$obvs)
+    fit <- stats::lm(metric_dat$model ~ metric_dat$obvs)
     out <- summary(fit)$r.squared
   }
   
diff --git a/modules/benchmark/R/metric_RAE.R b/modules/benchmark/R/metric_RAE.R
index 77e4b9004c2..b644aabb56a 100644
--- a/modules/benchmark/R/metric_RAE.R
+++ b/modules/benchmark/R/metric_RAE.R
@@ -2,12 +2,13 @@
 ##' @title Relative Absolute Error
 ##' @export
 ##' @param metric_dat dataframe
-##' 
+##' @param ... ignored
+##'
 ##' @author Betsy Cowdery
 
 metric_RAE <- function(metric_dat, ...) {
   PEcAn.logger::logger.info("Metric: Relative Absolute Error")
-  metric_dat <- na.omit(metric_dat)
+  metric_dat <- stats::na.omit(metric_dat)
   numer <- mean(abs(metric_dat$obvs - metric_dat$model))
   denom <- mean(abs(metric_dat$obvs - mean(metric_dat$obvs)))
   return(numer/denom)
diff --git a/modules/benchmark/R/metric_RMSE.R b/modules/benchmark/R/metric_RMSE.R
index 6ae45498b82..ebd02fc89c2 100644
--- a/modules/benchmark/R/metric_RMSE.R
+++ b/modules/benchmark/R/metric_RMSE.R
@@ -2,6 +2,7 @@
 ##' @title Root Mean Square Error
 ##' @export
 ##' @param dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Betsy Cowdery
 
diff --git a/modules/benchmark/R/metric_cor.R b/modules/benchmark/R/metric_cor.R
index 26780eb757a..cf3bfa026f3 100644
--- a/modules/benchmark/R/metric_cor.R
+++ b/modules/benchmark/R/metric_cor.R
@@ -2,10 +2,11 @@
 ##' @title Correlation Coefficient
 ##' @export
 ##' @param dat dataframe
+##' @param ... ignored
 ##' 
 ##' @author Mike Dietze
 
 metric_cor <- function(dat, ...) {
   PEcAn.logger::logger.info("Metric: Correlation Coefficient")
-  return(cor(dat$model,dat$obvs,use ="pairwise.complete.obs"))
+  return(stats::cor(dat$model,dat$obvs,use ="pairwise.complete.obs"))
 } # metric_cor
diff --git a/modules/benchmark/R/metric_lmDiag_plot.R b/modules/benchmark/R/metric_lmDiag_plot.R
index 5519f4f6ec6..2be6f50d951 100644
--- a/modules/benchmark/R/metric_lmDiag_plot.R
+++ b/modules/benchmark/R/metric_lmDiag_plot.R
@@ -2,14 +2,17 @@
 ##' @title Linear Regression Diagnostic Plot
 ##' @export
 ##' @param metric_dat data.frame
+##' @param var ignored
+##' @param filename path to save plot, or NA to not save
+##' @param draw.plot logical: return plot object?
 ##' 
 ##' @author Betsy Cowdery
 metric_lmDiag_plot <- function(metric_dat, var, filename = NA, draw.plot = FALSE) {
   PEcAn.logger::logger.info("Metric: Linear Regression Diagnostic Plot")
   
-  fit <- lm(metric_dat[, 1] ~ metric_dat[, 2])
+  fit <- stats::lm(metric_dat[, 1] ~ metric_dat[, 2])
 
-  p1 <- ggplot2::ggplot(fit, aes(.fitted, .resid))
+  p1 <- ggplot2::ggplot(fit, ggplot2::aes(.data$.fitted, .data$.resid))
   p1 <- p1 + ggplot2::geom_point()
   p1 <- p1 + ggplot2::stat_smooth(method = "loess") 
   p1 <- p1 + ggplot2::geom_hline(yintercept = 0, col = "red", linetype = "dashed")
@@ -18,15 +21,15 @@ metric_lmDiag_plot <- function(metric_dat, var, filename = NA, draw.plot = FALSE
   p1 <- p1 + ggplot2::ggtitle("Residual vs Fitted Plot") 
   p1 <- p1 + ggplot2::theme_bw()
   
-  p2 <- ggplot2::ggplot(fit, aes(qqnorm(.stdresid)[[1]], .stdresid)) 
+  p2 <- ggplot2::ggplot(fit, ggplot2::aes(stats::qqnorm(.data$.stdresid)[[1]], .data$.stdresid)) 
   p2 <- p2 + ggplot2::geom_point(na.rm = TRUE)
-  p2 <- p2 + ggplot2::geom_abline(aes(qqline(.stdresid))) 
+  p2 <- p2 + ggplot2::geom_abline(ggplot2::aes(stats::qqline(.data$.stdresid))) 
   p2 <- p2 + ggplot2::xlab("Theoretical Quantiles") 
   p2 <- p2 + ggplot2::ylab("Standardized Residuals")
   p2 <- p2 + ggplot2::ggtitle("Normal Q-Q") 
   p2 <- p2 + ggplot2::theme_bw()
   
-  p3 <- ggplot2::ggplot(fit, aes(.fitted, sqrt(abs(.stdresid)))) 
+  p3 <- ggplot2::ggplot(fit, ggplot2::aes(.data$.fitted, sqrt(abs(.data$.stdresid))))
   p3 <- p3 + ggplot2::geom_point(na.rm = TRUE)
   p3 <- p3 + ggplot2::stat_smooth(method = "loess", na.rm = TRUE) 
   p3 <- p3 + ggplot2::xlab("Fitted Value")
@@ -34,15 +37,15 @@ metric_lmDiag_plot <- function(metric_dat, var, filename = NA, draw.plot = FALSE
   p3 <- p3 + ggplot2::ggtitle("Scale-Location") 
   p3 <- p3 + ggplot2::theme_bw()
   
-  p4 <- ggplot2:: ggplot(fit, aes(seq_along(.cooksd), .cooksd)) 
+  p4 <- ggplot2:: ggplot(fit, ggplot2::aes(seq_along(.data$.cooksd), .data$.cooksd)) 
   p4 <- p4 + ggplot2::geom_bar(stat = "identity", position = "identity")
   p4 <- p4 + ggplot2::xlab("Obs. Number") 
   p4 <- p4 + ggplot2::ylab("Cook's distance")
   p4 <- p4 + ggplot2::ggtitle("Cook's distance") 
   p4 <- p4 + ggplot2::theme_bw()
   
-  p5 <- ggplot2::ggplot(fit, aes(.hat, .stdresid)) 
-  p5 <- p5 + ggplot2::geom_point(aes(size = .cooksd), na.rm = TRUE)
+  p5 <- ggplot2::ggplot(fit, ggplot2::aes(.data$.hat, .data$.stdresid)) 
+  p5 <- p5 + ggplot2::geom_point(ggplot2::aes(size = .data$.cooksd), na.rm = TRUE)
   p5 <- p5 + ggplot2::stat_smooth(method = "loess", na.rm = TRUE)
   p5 <- p5 + ggplot2::xlab("Leverage") 
   p5 <- p5 + ggplot2::ylab("Standardized Residuals")
@@ -51,7 +54,7 @@ metric_lmDiag_plot <- function(metric_dat, var, filename = NA, draw.plot = FALSE
   p5 <- p5 + ggplot2::theme_bw() 
   p5 <- p5 + ggplot2::theme(legend.position = "bottom")
   
-  p6 <- ggplot2::ggplot(fit, aes(.hat, .cooksd)) 
+  p6 <- ggplot2::ggplot(fit, ggplot2::aes(.data$.hat, .data$.cooksd)) 
   p6 <- p6 + ggplot2::geom_point(na.rm = TRUE) 
   p6 <- p6 + ggplot2::stat_smooth(method = "loess", na.rm = TRUE)
   p6 <- p6 + ggplot2::xlab("Leverage hii") 
@@ -63,9 +66,9 @@ metric_lmDiag_plot <- function(metric_dat, var, filename = NA, draw.plot = FALSE
   p <- gridExtra::grid.arrange(p1, p2, p3, p4, p5, p6, nrow = 3)
   
     if (!is.na(filename)) {
-      pdf(filename, width = 10, height = 6)
+      grDevices::pdf(filename, width = 10, height = 6)
       plot(p)
-      dev.off()
+      grDevices::dev.off()
     }
   
   if (draw.plot) {
diff --git a/modules/benchmark/R/metric_residual_plot.R b/modules/benchmark/R/metric_residual_plot.R
index e7f4b624183..38a20a65125 100644
--- a/modules/benchmark/R/metric_residual_plot.R
+++ b/modules/benchmark/R/metric_residual_plot.R
@@ -1,28 +1,28 @@
-##' @name metric_residual_plot
-##' @title Residual Plot
-##' @export
-##' @param metric_dat
-##' @param var
-##' @param filename
-##' @param draw.plot
+##' Residual Plot
+##'
+##' @param metric_dat dataframe to plot, with at least columns `time`, `model`, `obvs`
+##' @param var variable name, used as plot title
+##' @param filename path to save plot, or NA to not save
+##' @param draw.plot logical: Return the plot object?
 ##' 
 ##' @author Betsy Cowdery
+##' @export
 metric_residual_plot <- function(metric_dat, var, filename = NA, draw.plot = is.na(filename)) {
   PEcAn.logger::logger.info("Metric: Residual Plot")
   
   metric_dat$time <- lubridate::year(as.Date(as.character(metric_dat$time), format = "%Y"))
   metric_dat$diff <- abs(metric_dat$model - metric_dat$obvs)
-  metric_dat$zeros <- rep(0, length(time))
+  metric_dat$zeros <- rep(0, length(metric_dat$time))
   
-  p <- ggplot2::ggplot(data = metric_dat, aes(x = time)) 
-  p <- p + ggplot2::geom_path(aes(y = zeros), colour = "#666666", size = 2, linetype = 2, lineend = "round") 
-  p <- p + ggplot2::geom_point(aes(y = diff), size = 4, colour = "#619CFF") 
+  p <- ggplot2::ggplot(data = metric_dat, ggplot2::aes(x = .data$time)) 
+  p <- p + ggplot2::geom_path(ggplot2::aes(y = .data$zeros), colour = "#666666", size = 2, linetype = 2, lineend = "round") 
+  p <- p + ggplot2::geom_point(ggplot2::aes(y = .data$diff), size = 4, colour = "#619CFF") 
   p <- p + ggplot2::labs(title = var, x = "years", y = "abs(model - observation)")
   
   if (!is.na(filename)) {
-    pdf(filename, width = 10, height = 6)
+    grDevices::pdf(filename, width = 10, height = 6)
     plot(p)
-    dev.off()
+    grDevices::dev.off()
   }
   
   if (draw.plot) {
diff --git a/modules/benchmark/R/metric_run.R b/modules/benchmark/R/metric_run.R
index 5b07163eef4..40183a872e8 100644
--- a/modules/benchmark/R/metric_run.R
+++ b/modules/benchmark/R/metric_run.R
@@ -1,9 +1,9 @@
-##' @name metric_run
-##' @title Model Run Check
-##' @export
+##' Model Run Check
+##'
 ##' @param settings list
 ##' 
 ##' @author Betsy Cowdery
+##' @export
 metric_run <- function(settings){
 
   # The goal of this function is to determine if a model run has been successfully completed. 
diff --git a/modules/benchmark/R/metric_scatter_plot.R b/modules/benchmark/R/metric_scatter_plot.R
index 3e285f7d71d..751d08e53b4 100644
--- a/modules/benchmark/R/metric_scatter_plot.R
+++ b/modules/benchmark/R/metric_scatter_plot.R
@@ -1,25 +1,25 @@
-##' @name metric_scatter_plot
-##' @title Scatter Plot
-##' @export
-##' @param metric_dat
-##' @param var
-##' @param filename
-##' @param draw.plot
+##' Scatter Plot
+##'
+##' @param metric_dat dataframe to plot, with at least columns `model` and `obvs`
+##' @param var ignored
+##' @param filename path to save plot, or NA to not save
+##' @param draw.plot logical: Return the plot object?
 ##' 
 ##' @author Betsy Cowdery
+##' @export
 
 metric_scatter_plot <- function(metric_dat, var, filename = NA, draw.plot = is.na(filename)) {
   PEcAn.logger::logger.info("Metric: Scatter Plot")
   
   p <- ggplot2::ggplot(data = metric_dat) 
-  p <- p + ggplot2::geom_point(aes(x = model, y = obvs), size = 4) 
+  p <- p + ggplot2::geom_point(ggplot2::aes(x = .data$model, y = .data$obvs), size = 4) 
   p <- p + ggplot2::geom_abline(slope = 1, intercept = 0, colour = "#666666", 
                        size = 2, linetype = 2)
   
   if (!is.na(filename)) {
-    pdf(filename, width = 10, height = 6)
+    grDevices::pdf(filename, width = 10, height = 6)
     plot(p)
-    dev.off()
+    grDevices::dev.off()
   }
   
   if (draw.plot) {
diff --git a/modules/benchmark/R/metric_timeseries_plot.R b/modules/benchmark/R/metric_timeseries_plot.R
index a35dc007c3f..ca879b95648 100644
--- a/modules/benchmark/R/metric_timeseries_plot.R
+++ b/modules/benchmark/R/metric_timeseries_plot.R
@@ -1,12 +1,13 @@
-##' @name metric_timeseries_plot
-##' @title Timeseries Plot
-##' @export
-##' @param metric_dat
-##' @param var
-##' @param filename
-##' @param draw.plot
-##' @importFrom ggplot2 ggplot labs geom_path geom_point
+##' Timeseries Plot
+##'
+##' @param metric_dat dataframe to plot, with at least columns `time`, `model`, `obvs`
+##' @param var variable name, used as plot title
+##' @param filename path to save plot, or NA to not save
+##' @param draw.plot logical: Return the plot object?
+##'
 ##' @author Betsy Cowdery
+##' @importFrom ggplot2 ggplot labs geom_path geom_point
+##' @export
 
 metric_timeseries_plot <- function(metric_dat, var, filename = NA, draw.plot = is.na(filename)) {
   PEcAn.logger::logger.info("Metric: Timeseries Plot")
@@ -19,17 +20,17 @@ metric_timeseries_plot <- function(metric_dat, var, filename = NA, draw.plot = i
     metric_dat$time <- date.time
   }
   
-  p <- ggplot(data = metric_dat, aes(x = time)) 
+  p <- ggplot(data = metric_dat, ggplot2::aes(x = .data$time)) 
   p <- p + labs(title = var, y = "") 
-  p <- p + geom_path(aes(y = model, colour = "Model"), size = 2) 
-  p <- p + geom_point(aes(y = model, colour = "Model"), size = 4) 
-  p <- p + geom_path(aes(y = obvs, colour = "Observed"), size = 2) 
-  p <- p + geom_point(aes(y = obvs, colour = "Observed"), size = 4)
+  p <- p + geom_path(ggplot2::aes(y = .data$model, colour = "Model"), size = 2) 
+  p <- p + geom_point(ggplot2::aes(y = .data$model, colour = "Model"), size = 4) 
+  p <- p + geom_path(ggplot2::aes(y = .data$obvs, colour = "Observed"), size = 2) 
+  p <- p + geom_point(ggplot2::aes(y = .data$obvs, colour = "Observed"), size = 4)
   
   if (!is.na(filename)) {
-    pdf(filename, width = 10, height = 6)
+    grDevices::pdf(filename, width = 10, height = 6)
     plot(p)
-    dev.off()
+    grDevices::dev.off()
   }
   
   if (draw.plot) {
diff --git a/modules/benchmark/R/pecan_bench.R b/modules/benchmark/R/pecan_bench.R
index 85441429869..598a25c4260 100644
--- a/modules/benchmark/R/pecan_bench.R
+++ b/modules/benchmark/R/pecan_bench.R
@@ -51,7 +51,7 @@ pecan_bench <- function(comp_run, bench_id, imp_limit, high_limit) {
   # more than one site, more than one variable we want to track) so we need flexibility.  More
   # generally, files should never be hardcoded since these tests will run on many different machines
   
-  obs_file <- read.table("Location of the data table")
+  obs_file <- utils::read.table("Location of the data table")
   obs_value <- obs_file$value
   N <- size(obs_value)
   
@@ -70,7 +70,7 @@ pecan_bench <- function(comp_run, bench_id, imp_limit, high_limit) {
   # purpose of that run was recorded elsewhere.  seems like it would be much better to have all that
   # in one place
   
-  bench_file <- read.table("Location of the data table", bench_id)
+  bench_file <- utils::read.table("Location of the data table", bench_id)
   bench_value <- bench_file$value
   
   # First calculate the differences between the current benchmark run and the observed values
@@ -179,8 +179,8 @@ pecan_bench <- function(comp_run, bench_id, imp_limit, high_limit) {
   # calculate the
   
   if (bench_ratio_mean < imp_limit & bench_ratio_count > 0.8) {
-    Set_Bench(...)  #Subroutine which sets the current run to be the new benchmark comparison run as well as saves the previous benchmark comparison run a database
-    Compare_Bench(...)  #Subroutine which calculates a new vector of values which are essentially the benchmark ratios between old runs and the current comparison run.
+    #Set_Bench(...)  #Subroutine which sets the current run to be the new benchmark comparison run as well as saves the previous benchmark comparison run a database
+    #Compare_Bench(...)  #Subroutine which calculates a new vector of values which are essentially the benchmark ratios between old runs and the current comparison run.
   }
   ## MCD: I wonder if this should be automatic (i.e. every time the model does better it becomes the
   ## new benchmark) or whether it should be something where the user is prompted to confirm that we
diff --git a/modules/benchmark/man/align_by_first_observation.Rd b/modules/benchmark/man/align_by_first_observation.Rd
index dba4cf7e7f9..4bc3c0efca8 100644
--- a/modules/benchmark/man/align_by_first_observation.Rd
+++ b/modules/benchmark/man/align_by_first_observation.Rd
@@ -30,8 +30,10 @@ table$plant_functional_type_one<- c("AMCA3","AMCA3","ARHY", "ARHY")
 table$plant_functional_type_two<- c('a','a','b', 'b') # PFT groupings
 table<-as.data.frame(table)
 
-aligned<-align_by_first_observation(observation_one = observation_one, observation_two = observation_two,
-custom_table = table)
+aligned <- align_by_first_observation(
+  observation_one = observation_one,
+  observation_two = observation_two,
+  custom_table = table)
 
 # aligned should be a vector '[1] "AMCA3" "ARHY"  "AMCA3" "AMCA3"'
 }
diff --git a/modules/benchmark/man/align_data.Rd b/modules/benchmark/man/align_data.Rd
index 5ab6125b9e2..c62f819314d 100644
--- a/modules/benchmark/man/align_data.Rd
+++ b/modules/benchmark/man/align_data.Rd
@@ -12,6 +12,8 @@ align_data(model.calc, obvs.calc, var, align_method = "match_timestep")
 \item{obvs.calc}{data.frame}
 
 \item{var}{data.frame}
+
+\item{align_method}{name of function to use for alignment}
 }
 \value{
 dat
diff --git a/modules/benchmark/man/align_pft.Rd b/modules/benchmark/man/align_pft.Rd
index 407af6a61bd..71a24566e2f 100644
--- a/modules/benchmark/man/align_pft.Rd
+++ b/modules/benchmark/man/align_pft.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/align_pft.R
 \name{align_pft}
 \alias{align_pft}
-\title{align_pft}
+\title{Align vectors of Plant Functional Type and species.}
 \usage{
 align_pft(
   con,
@@ -32,6 +32,10 @@ In the second case, must be passable to match_species_id.}
 
 \item{subset_is_ok}{When aligning two species lists, this allows for alignement when species lists aren't identical. 
 set to FALSE by default.}
+
+\item{comparison_type}{one of "data_to_model", "data_to_data", or "model_to_model"}
+
+\item{...}{other arguments, currently ignored}
 }
 \value{
 \code{list} containing the following columns:
@@ -43,10 +47,9 @@ set to FALSE by default.}
 }
 }
 \description{
-align_pft
+Align vectors of Plant Functional Type and species.
 }
 \details{
-Aligns vectors of Plant Fucntional Typed and species.
 Can align: 
 - two vectors of plant fucntional types (pft's) if a custom map is provided
 - a list of species (usda, fia, or latin_name format) to a plant fucntional type
diff --git a/modules/benchmark/man/calc_benchmark.Rd b/modules/benchmark/man/calc_benchmark.Rd
index 9d988bfc72a..0b970147d80 100644
--- a/modules/benchmark/man/calc_benchmark.Rd
+++ b/modules/benchmark/man/calc_benchmark.Rd
@@ -7,9 +7,11 @@
 calc_benchmark(settings, bety, start_year = NA, end_year = NA)
 }
 \arguments{
+\item{settings}{settings object describing the run to calculate}
+
 \item{bety}{database connection}
 
-\item{bm.ensemble}{object, either from create_BRR or start.bm.ensemle}
+\item{start_year, end_year}{time range to read. If NA, these are taken from `settings`}
 }
 \description{
 For each benchmark id, calculate metrics and update benchmarks_ensemble_scores
diff --git a/modules/benchmark/man/check_if_legal_table.Rd b/modules/benchmark/man/check_if_legal_table.Rd
index d31609148f6..c9c62085ff3 100644
--- a/modules/benchmark/man/check_if_legal_table.Rd
+++ b/modules/benchmark/man/check_if_legal_table.Rd
@@ -7,12 +7,12 @@
 check_if_legal_table(table, observation_one, observation_two)
 }
 \arguments{
+\item{table}{a table that either maps two pft's to one anouther or maps custom species codes to bety id codes.
+In the second case, must be passable to match_species_id.}
+
 \item{observation_one}{a vector of plant functional types, or species}
 
 \item{observation_two}{anouther vector of plant functional types, or species}
-
-\item{custom_table}{a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.}
 }
 \value{
 \code{boolean}
diff --git a/modules/benchmark/man/check_if_list_of_pfts.Rd b/modules/benchmark/man/check_if_list_of_pfts.Rd
index ed2fa46c778..f515eb38a14 100644
--- a/modules/benchmark/man/check_if_list_of_pfts.Rd
+++ b/modules/benchmark/man/check_if_list_of_pfts.Rd
@@ -7,20 +7,12 @@
 check_if_list_of_pfts(vars)
 }
 \arguments{
-\item{observation_one}{a vector of plant fucntional types, or species}
-
-\item{observation_two}{anouther vector of plant fucntional types, or species}
-
-\item{custom_table}{a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.}
+\item{vars}{names to check}
 }
 \value{
 \code{boolean}
 }
 \description{
-check_if_list_of_pfts
-}
-\details{
 Checks if format contains a variable named "plant_functional_type"
 }
 \author{
diff --git a/modules/benchmark/man/check_if_species_list.Rd b/modules/benchmark/man/check_if_species_list.Rd
index 02637b73657..60357127e67 100644
--- a/modules/benchmark/man/check_if_species_list.Rd
+++ b/modules/benchmark/man/check_if_species_list.Rd
@@ -7,12 +7,10 @@
 check_if_species_list(vars, custom_table = NULL)
 }
 \arguments{
+\item{vars}{format}
+
 \item{custom_table}{a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
 In the second case, must be passable to match_species_id.}
-
-\item{observation_one}{a vector of plant functional types, or species}
-
-\item{observation_two}{another vector of plant functional types, or species}
 }
 \value{
 \code{boolean}
diff --git a/modules/benchmark/man/create_BRR.Rd b/modules/benchmark/man/create_BRR.Rd
index df6d1b4988c..a0c26b7e6bf 100644
--- a/modules/benchmark/man/create_BRR.Rd
+++ b/modules/benchmark/man/create_BRR.Rd
@@ -10,6 +10,8 @@ create_BRR(ens_wf, con, user_id = "")
 \item{ens_wf}{table made from joining ensemble and workflow tables}
 
 \item{con}{database connection}
+
+\item{user_id}{Optional user id to use for this record in reference_runs table}
 }
 \description{
 For each benchmark id, calculate metrics and update benchmarks_ensemble_scores
diff --git a/modules/benchmark/man/define_benchmark.Rd b/modules/benchmark/man/define_benchmark.Rd
index 5f7c4451650..f93a799506d 100644
--- a/modules/benchmark/man/define_benchmark.Rd
+++ b/modules/benchmark/man/define_benchmark.Rd
@@ -7,7 +7,9 @@
 define_benchmark(settings, bety)
 }
 \arguments{
-\item{bm.settings}{settings list}
+\item{settings}{settings list}
+
+\item{bety}{database connection}
 }
 \value{
 updated settings list
diff --git a/modules/benchmark/man/format_wide2long.Rd b/modules/benchmark/man/format_wide2long.Rd
index ee1250fe320..c5a985f7cba 100644
--- a/modules/benchmark/man/format_wide2long.Rd
+++ b/modules/benchmark/man/format_wide2long.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/format_wide2long.R
 \name{format_wide2long}
 \alias{format_wide2long}
-\title{format_wide2long}
+\title{Function to convert wide format to long format}
 \usage{
 format_wide2long(out, format, vars_used, time.row)
 }
@@ -11,15 +11,16 @@ format_wide2long(out, format, vars_used, time.row)
 
 \item{format}{as returned by query.format.vars}
 
-\item{vars_used}{}
+\item{vars_used}{data frame mapping `input_name` to `bety_name`}
+
+\item{time.row}{ignored; value in output is set from `format$vars$storage_type`}
 }
 \value{
 list of updated values
 }
 \description{
-format_wide2long
+Function to convert wide format to long format
 }
 \author{
 Istem Fer
-Function to convert wide format to long format
 }
diff --git a/modules/benchmark/man/get_species_list_standard.Rd b/modules/benchmark/man/get_species_list_standard.Rd
index 944f8492026..f1e26ffa981 100644
--- a/modules/benchmark/man/get_species_list_standard.Rd
+++ b/modules/benchmark/man/get_species_list_standard.Rd
@@ -7,20 +7,12 @@
 get_species_list_standard(vars)
 }
 \arguments{
-\item{observation_one}{a vector of plant fucntional types, or species}
-
-\item{observation_two}{anouther vector of plant fucntional types, or species}
-
-\item{custom_table}{a table that either maps two pft's to one another or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.}
+\item{vars}{format to be matched}
 }
 \value{
 \code{character} Returns "usda", "latin_name", "fia" or "custom"
 }
 \description{
-get_species_list_standard
-}
-\details{
 Returns the format type for convience of use with match_species_id
 }
 \author{
diff --git a/modules/benchmark/man/load_csv.Rd b/modules/benchmark/man/load_csv.Rd
index 1b9dcd7c089..fdf055ac6bd 100644
--- a/modules/benchmark/man/load_csv.Rd
+++ b/modules/benchmark/man/load_csv.Rd
@@ -13,9 +13,7 @@ load_csv(data.path, format, site, vars = NULL)
 
 \item{site}{list}
 
-\item{start_year}{numeric}
-
-\item{end_year}{numeric}
+\item{vars}{column names to return. If NULL, returns all columns}
 }
 \description{
 load_csv
diff --git a/modules/benchmark/man/load_data.Rd b/modules/benchmark/man/load_data.Rd
index 70bfbd5993e..c1a993f314b 100644
--- a/modules/benchmark/man/load_data.Rd
+++ b/modules/benchmark/man/load_data.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/load_data.R
 \name{load_data}
 \alias{load_data}
-\title{load_data}
+\title{load data}
 \usage{
 load_data(
   data.path,
@@ -24,12 +24,15 @@ load_data(
 \item{end_year}{numeric}
 
 \item{site}{list}
+
+\item{vars.used.index}{which variables to use? If NULL, these are taken from `format`}
+
+\item{...}{further arguments, currently ignored}
 }
 \description{
-load_data
+Generic function to convert input files containing observational data to
+a common PEcAn format.
 }
 \author{
 Betsy Cowdery, Istem Fer, Joshua Mantooth
-Generic function to convert input files containing observational data to 
-a common PEcAn format.
 }
diff --git a/modules/benchmark/man/load_rds.Rd b/modules/benchmark/man/load_rds.Rd
index e684a796cf2..a1e1e552bbd 100644
--- a/modules/benchmark/man/load_rds.Rd
+++ b/modules/benchmark/man/load_rds.Rd
@@ -13,7 +13,7 @@ load_rds(data.path, format, site, vars = NULL)
 
 \item{site}{not used, for compatibility}
 
-\item{vars}{}
+\item{vars}{optional variable names to load. if NULL, returns all variables in file}
 }
 \description{
 load_rds
diff --git a/modules/benchmark/man/load_tab_separated_values.Rd b/modules/benchmark/man/load_tab_separated_values.Rd
index 22a307047c8..1f7d4eba7cc 100644
--- a/modules/benchmark/man/load_tab_separated_values.Rd
+++ b/modules/benchmark/man/load_tab_separated_values.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/load_tab.R
 \name{load_tab_separated_values}
 \alias{load_tab_separated_values}
-\title{load_tab_separated_values}
+\title{Load files with mime-type 'text/tab-separated-values'}
 \usage{
 load_tab_separated_values(data.path, format, site = NULL, vars = NULL)
 }
@@ -13,12 +13,10 @@ load_tab_separated_values(data.path, format, site = NULL, vars = NULL)
 
 \item{site}{list}
 
-\item{start_year}{numeric}
-
-\item{end_year}{numeric}
+\item{vars}{variable names to load. If NULL, loads all columns}
 }
 \description{
-load_tab_separated_values
+Load files with mime-type 'text/tab-separated-values'
 }
 \author{
 Betsy Cowdery, Mike Dietze
diff --git a/modules/benchmark/man/load_x_netcdf.Rd b/modules/benchmark/man/load_x_netcdf.Rd
index 7534f711a7d..c02d2b55229 100644
--- a/modules/benchmark/man/load_x_netcdf.Rd
+++ b/modules/benchmark/man/load_x_netcdf.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/load_netcdf.R
 \name{load_x_netcdf}
 \alias{load_x_netcdf}
-\title{load_x_netcdf}
+\title{Load from netCDF}
 \usage{
 load_x_netcdf(data.path, format, site, vars = NULL)
 }
@@ -14,13 +14,9 @@ load_x_netcdf(data.path, format, site, vars = NULL)
 \item{site}{list}
 
 \item{vars}{character}
-
-\item{start_year}{numeric}
-
-\item{end_year}{numeric}
 }
 \description{
-load_x_netcdf
+Load from netCDF
 }
 \author{
 Istem Fer
diff --git a/modules/benchmark/man/metric_AME.Rd b/modules/benchmark/man/metric_AME.Rd
index b7b8c539163..76564fc901e 100644
--- a/modules/benchmark/man/metric_AME.Rd
+++ b/modules/benchmark/man/metric_AME.Rd
@@ -8,6 +8,8 @@ metric_AME(dat, ...)
 }
 \arguments{
 \item{dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Absolute Maximum Error
diff --git a/modules/benchmark/man/metric_Frechet.Rd b/modules/benchmark/man/metric_Frechet.Rd
index ab81bcb5044..86136671b42 100644
--- a/modules/benchmark/man/metric_Frechet.Rd
+++ b/modules/benchmark/man/metric_Frechet.Rd
@@ -8,6 +8,8 @@ metric_Frechet(metric_dat, ...)
 }
 \arguments{
 \item{metric_dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Frechet Distance
diff --git a/modules/benchmark/man/metric_MAE.Rd b/modules/benchmark/man/metric_MAE.Rd
index 8bcf95b9509..e19e885e814 100644
--- a/modules/benchmark/man/metric_MAE.Rd
+++ b/modules/benchmark/man/metric_MAE.Rd
@@ -8,6 +8,8 @@ metric_MAE(dat, ...)
 }
 \arguments{
 \item{dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Mean Absolute Error
diff --git a/modules/benchmark/man/metric_MSE.Rd b/modules/benchmark/man/metric_MSE.Rd
index 2c2ad1600e2..aea5795eeb6 100644
--- a/modules/benchmark/man/metric_MSE.Rd
+++ b/modules/benchmark/man/metric_MSE.Rd
@@ -8,6 +8,8 @@ metric_MSE(dat, ...)
 }
 \arguments{
 \item{dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Mean Square Error
diff --git a/modules/benchmark/man/metric_PPMC.Rd b/modules/benchmark/man/metric_PPMC.Rd
index 413340bcd5c..31c6a43abf4 100644
--- a/modules/benchmark/man/metric_PPMC.Rd
+++ b/modules/benchmark/man/metric_PPMC.Rd
@@ -8,6 +8,8 @@ metric_PPMC(metric_dat, ...)
 }
 \arguments{
 \item{metric_dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Pearson Product Moment Correlation
diff --git a/modules/benchmark/man/metric_R2.Rd b/modules/benchmark/man/metric_R2.Rd
index cd047b5183a..65b1feb7fea 100644
--- a/modules/benchmark/man/metric_R2.Rd
+++ b/modules/benchmark/man/metric_R2.Rd
@@ -8,6 +8,8 @@ metric_R2(metric_dat, ...)
 }
 \arguments{
 \item{metric_dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Coefficient of Determination (R2)
diff --git a/modules/benchmark/man/metric_RAE.Rd b/modules/benchmark/man/metric_RAE.Rd
index 69195ce87c6..a062ff76839 100644
--- a/modules/benchmark/man/metric_RAE.Rd
+++ b/modules/benchmark/man/metric_RAE.Rd
@@ -8,6 +8,8 @@ metric_RAE(metric_dat, ...)
 }
 \arguments{
 \item{metric_dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Relative Absolute Error
diff --git a/modules/benchmark/man/metric_RMSE.Rd b/modules/benchmark/man/metric_RMSE.Rd
index e6b0b608aee..0335f86187e 100644
--- a/modules/benchmark/man/metric_RMSE.Rd
+++ b/modules/benchmark/man/metric_RMSE.Rd
@@ -8,6 +8,8 @@ metric_RMSE(dat, ...)
 }
 \arguments{
 \item{dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Root Mean Square Error
diff --git a/modules/benchmark/man/metric_cor.Rd b/modules/benchmark/man/metric_cor.Rd
index b2ea61b01d0..a8e84fd9743 100644
--- a/modules/benchmark/man/metric_cor.Rd
+++ b/modules/benchmark/man/metric_cor.Rd
@@ -8,6 +8,8 @@ metric_cor(dat, ...)
 }
 \arguments{
 \item{dat}{dataframe}
+
+\item{...}{ignored}
 }
 \description{
 Correlation Coefficient
diff --git a/modules/benchmark/man/metric_lmDiag_plot.Rd b/modules/benchmark/man/metric_lmDiag_plot.Rd
index 56628c76ad2..a73af4e12af 100644
--- a/modules/benchmark/man/metric_lmDiag_plot.Rd
+++ b/modules/benchmark/man/metric_lmDiag_plot.Rd
@@ -8,6 +8,12 @@ metric_lmDiag_plot(metric_dat, var, filename = NA, draw.plot = FALSE)
 }
 \arguments{
 \item{metric_dat}{data.frame}
+
+\item{var}{ignored}
+
+\item{filename}{path to save plot, or NA to not save}
+
+\item{draw.plot}{logical: return plot object?}
 }
 \description{
 Linear Regression Diagnostic Plot
diff --git a/modules/benchmark/man/metric_residual_plot.Rd b/modules/benchmark/man/metric_residual_plot.Rd
index 9583f352ab7..ff80b0c547d 100644
--- a/modules/benchmark/man/metric_residual_plot.Rd
+++ b/modules/benchmark/man/metric_residual_plot.Rd
@@ -12,7 +12,13 @@ metric_residual_plot(
 )
 }
 \arguments{
-\item{draw.plot}{}
+\item{metric_dat}{dataframe to plot, with at least columns `time`, `model`, `obvs`}
+
+\item{var}{variable name, used as plot title}
+
+\item{filename}{path to save plot, or NA to not save}
+
+\item{draw.plot}{logical: Return the plot object?}
 }
 \description{
 Residual Plot
diff --git a/modules/benchmark/man/metric_scatter_plot.Rd b/modules/benchmark/man/metric_scatter_plot.Rd
index 46f8a6d22f0..93da2a3db5e 100644
--- a/modules/benchmark/man/metric_scatter_plot.Rd
+++ b/modules/benchmark/man/metric_scatter_plot.Rd
@@ -12,7 +12,13 @@ metric_scatter_plot(
 )
 }
 \arguments{
-\item{draw.plot}{}
+\item{metric_dat}{dataframe to plot, with at least columns `model` and `obvs`}
+
+\item{var}{ignored}
+
+\item{filename}{path to save plot, or NA to not save}
+
+\item{draw.plot}{logical: Return the plot object?}
 }
 \description{
 Scatter Plot
diff --git a/modules/benchmark/man/metric_timeseries_plot.Rd b/modules/benchmark/man/metric_timeseries_plot.Rd
index 89b647ff561..e5a7b1d9604 100644
--- a/modules/benchmark/man/metric_timeseries_plot.Rd
+++ b/modules/benchmark/man/metric_timeseries_plot.Rd
@@ -11,6 +11,15 @@ metric_timeseries_plot(
   draw.plot = is.na(filename)
 )
 }
+\arguments{
+\item{metric_dat}{dataframe to plot, with at least columns `time`, `model`, `obvs`}
+
+\item{var}{variable name, used as plot title}
+
+\item{filename}{path to save plot, or NA to not save}
+
+\item{draw.plot}{logical: Return the plot object?}
+}
 \description{
 Timeseries Plot
 }
diff --git a/modules/benchmark/tests/Rcheck_reference.log b/modules/benchmark/tests/Rcheck_reference.log
index 3675e758938..825ed0601a0 100644
--- a/modules/benchmark/tests/Rcheck_reference.log
+++ b/modules/benchmark/tests/Rcheck_reference.log
@@ -1,5 +1,5 @@
-* using log directory ‘/home/tanishq010/pecan/modules/PEcAn.benchmark.Rcheck’
-* using R version 4.2.1 (2022-06-23)
+* using log directory ‘/tmp/Rtmps3SFpV/PEcAn.benchmark.Rcheck’
+* using R version 4.1.3 (2022-03-10)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-manual --as-cran’
@@ -7,49 +7,6 @@
 * checking extension type ... Package
 * this is package ‘PEcAn.benchmark’ version ‘1.7.2’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... WARNING
-Maintainer: ‘Mike Dietze <dietze@bu.edu>’
-
-New submission
-
-License components with restrictions and base license permitting such:
-  BSD_3_clause + file LICENSE
-File 'LICENSE':
-  University of Illinois/NCSA Open Source License
-
-  Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-  Permission is hereby granted, free of charge, to any person obtaining
-  a copy of this software and associated documentation files (the
-  "Software"), to deal with 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:
-
-  - Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimers.
-  - Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimers in the
-    documentation and/or other materials provided with the distribution.
-  - Neither the names of University of Illinois, NCSA, nor the names
-    of its contributors may be used to endorse or promote products
-    derived from this Software without specific prior written permission.
-
-  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 CONTRIBUTORS 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 WITH THE SOFTWARE.
-
-Strong dependencies not in mainstream repositories:
-  PEcAn.DB, PEcAn.logger, PEcAn.remote, PEcAn.settings, PEcAn.utils
-Suggests or Enhances not in mainstream repositories:
-  PEcAn.data.land
-
-The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -63,11 +20,7 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-Author field differs from that derived from Authors@R
-  Author:    ‘Michael Dietze, David LeBauer, Rob Kooper, Toni Viskari’
-  Authors@R: ‘Mike Dietze [aut, cre], David LeBauer [aut], Rob Kooper [aut], Toni Viskari [aut], University of Illinois, NCSA [cph]’
-
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK
@@ -80,117 +33,20 @@ Author field differs from that derived from Authors@R
 * checking whether the namespace can be loaded with stated dependencies ... OK
 * checking whether the namespace can be unloaded cleanly ... OK
 * checking loading without being on the library search path ... OK
-* checking use of S3 registration ... OK
-* checking dependencies in R code ... NOTE
-Namespaces in Imports field not imported from:
-  ‘PEcAn.remote’ ‘XML’ ‘dbplyr’
-  All declared Imports should be used.
+* checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
 * checking R code for possible problems ... NOTE
-Warning: <anonymous>: ... may be used in an incorrect context: ‘Set_Bench(...)’
-
-Warning: <anonymous>: ... may be used in an incorrect context: ‘Compare_Bench(...)’
-
-add_workflow_info: no visible global function definition for
-  ‘is.MultiSettings’
-add_workflow_info: no visible global function definition for ‘papply’
 add_workflow_info: no visible binding for global variable
   ‘add_workflow_id’
 add_workflow_info: no visible binding for global variable ‘.’
-align_data: possible error in round(obvs.calc$posix, units =
-  coarse.unit): unused argument (units = coarse.unit)
-align_data: possible error in round(model.calc$posix, units =
-  coarse.unit): unused argument (units = coarse.unit)
 align_data: no visible binding for global variable ‘.’
-align_data: no visible global function definition for ‘one_of’
-bm_settings2pecan_settings: no visible global function definition for
-  ‘is.MultiSettings’
-bm_settings2pecan_settings: no visible global function definition for
-  ‘papply’
-calc_benchmark: no visible binding for global variable ‘.’
-calc_benchmark: no visible binding for global variable ‘id’
-create_BRR: no visible binding for global variable ‘.’
-create_BRR: no visible binding for global variable ‘id’
-define_benchmark: no visible global function definition for
-  ‘is.MultiSettings’
-define_benchmark: no visible global function definition for ‘papply’
-define_benchmark: no visible binding for global variable ‘id’
-define_benchmark: no visible binding for global variable ‘ensemble_id’
-define_benchmark: no visible global function definition for ‘left_join’
-define_benchmark: no visible binding for global variable ‘.’
-define_benchmark: no visible global function definition for
-  ‘logger.error’
-define_benchmark: no visible global function definition for
-  ‘logger.debug’
-define_benchmark: no visible global function definition for ‘pull’
-define_benchmark: no visible binding for global variable ‘input_id’
-define_benchmark: no visible binding for global variable ‘variable_id’
-define_benchmark: no visible global function definition for ‘db.query’
-define_benchmark: no visible binding for global variable ‘benchmark_id’
-define_benchmark: no visible binding for global variable
-  ‘reference_run_id’
-define_benchmark: no visible binding for global variable ‘metric_id’
-get_species_list_standard: no visible binding for global variable
-  ‘custom_table’
-get_species_list_standard: no visible global function definition for
-  ‘logger.warn’
-load_csv: no visible global function definition for ‘read.csv’
-load_csv: no visible binding for global variable ‘header’
-load_csv: no visible global function definition for ‘one_of’
 load_data: no visible binding for global variable ‘username’
 load_data: no visible binding for global variable ‘password’
 load_data: no visible binding for global variable ‘output_path’
-load_data: no visible binding for global variable ‘.’
-load_data: no visible binding for global variable ‘year’
-load_rds: no visible global function definition for ‘one_of’
-load_tab_separated_values: no visible global function definition for
-  ‘read.table’
-load_tab_separated_values: no visible binding for global variable
-  ‘header’
-load_tab_separated_values: no visible global function definition for
-  ‘one_of’
-match_timestep: no visible global function definition for ‘head’
-metric_Frechet: no visible global function definition for ‘logger.info’
-metric_Frechet: no visible global function definition for ‘na.omit’
-metric_PPMC: no visible global function definition for ‘cor’
-metric_R2: no visible global function definition for ‘lm’
-metric_RAE: no visible global function definition for ‘na.omit’
-metric_cor: no visible global function definition for ‘cor’
-metric_lmDiag_plot: no visible global function definition for ‘lm’
-metric_lmDiag_plot: no visible global function definition for ‘aes’
-metric_lmDiag_plot: no visible binding for global variable ‘.fitted’
-metric_lmDiag_plot: no visible binding for global variable ‘.resid’
-metric_lmDiag_plot: no visible global function definition for ‘qqnorm’
-metric_lmDiag_plot: no visible binding for global variable ‘.stdresid’
-metric_lmDiag_plot: no visible global function definition for ‘qqline’
-metric_lmDiag_plot: no visible binding for global variable ‘.cooksd’
-metric_lmDiag_plot: no visible binding for global variable ‘.hat’
-metric_lmDiag_plot: no visible global function definition for ‘pdf’
-metric_lmDiag_plot: no visible global function definition for ‘dev.off’
-metric_residual_plot: no visible binding for global variable ‘time’
-metric_residual_plot: no visible global function definition for ‘aes’
-metric_residual_plot: no visible binding for global variable ‘zeros’
-metric_residual_plot: no visible global function definition for ‘pdf’
-metric_residual_plot: no visible global function definition for
-  ‘dev.off’
-metric_scatter_plot: no visible global function definition for ‘aes’
-metric_scatter_plot: no visible binding for global variable ‘model’
-metric_scatter_plot: no visible binding for global variable ‘obvs’
-metric_scatter_plot: no visible global function definition for ‘pdf’
-metric_scatter_plot: no visible global function definition for
-  ‘dev.off’
-metric_timeseries_plot: no visible global function definition for ‘aes’
-metric_timeseries_plot: no visible binding for global variable ‘time’
-metric_timeseries_plot: no visible binding for global variable ‘model’
-metric_timeseries_plot: no visible binding for global variable ‘obvs’
-metric_timeseries_plot: no visible global function definition for ‘pdf’
-metric_timeseries_plot: no visible global function definition for
-  ‘dev.off’
 pecan_bench: no visible global function definition for
   ‘validation_check’
-pecan_bench: no visible global function definition for ‘read.table’
 pecan_bench: no visible global function definition for ‘size’
 pecan_bench: no visible binding for global variable ‘comp_value’
 pecan_bench: no visible binding for global variable
@@ -198,169 +54,24 @@ pecan_bench: no visible binding for global variable
 pecan_bench: no visible binding for global variable
   ‘ratio_dif_uncertainty’
 pecan_bench: no visible binding for global variable ‘ratio_dif’
-pecan_bench: no visible global function definition for ‘Set_Bench’
-pecan_bench: ... may be used in an incorrect context: ‘Set_Bench(...)’
-pecan_bench: no visible global function definition for ‘Compare_Bench’
-pecan_bench: ... may be used in an incorrect context:
-  ‘Compare_Bench(...)’
-read_settings_BRR: no visible global function definition for ‘pull’
-read_settings_BRR: no visible global function definition for
-  ‘xmlToList’
-read_settings_BRR: no visible binding for global variable ‘.’
 Undefined global functions or variables:
-  . .cooksd .fitted .hat .resid .stdresid Compare_Bench Set_Bench
-  add_workflow_id aes benchmark_id comp_dif_uncertainty comp_value cor
-  custom_table db.query dev.off ensemble_id head header id input_id
-  is.MultiSettings left_join lm logger.debug logger.error logger.info
-  logger.warn metric_id model na.omit obvs one_of output_path papply
-  password pdf pull qqline qqnorm ratio_dif ratio_dif_uncertainty
-  read.csv read.table reference_run_id size time username
-  validation_check variable_id xmlToList year zeros
-Consider adding
-  importFrom("grDevices", "dev.off", "pdf")
-  importFrom("stats", "cor", "lm", "na.omit", "qqline", "qqnorm", "time")
-  importFrom("utils", "head", "read.csv", "read.table")
-to your NAMESPACE file.
-
-Warning: <anonymous>: ... may be used in an incorrect context: ‘Set_Bench(...)’
-
-Warning: <anonymous>: ... may be used in an incorrect context: ‘Compare_Bench(...)’
-
+  . add_workflow_id comp_dif_uncertainty comp_value output_path
+  password ratio_dif ratio_dif_uncertainty size username
+  validation_check
 * checking Rd files ... OK
 * checking Rd metadata ... OK
-* checking Rd line widths ... NOTE
-Rd file 'align_by_first_observation.Rd':
-  \examples lines wider than 100 characters:
-     aligned<-align_by_first_observation(observation_one = observation_one, observation_two = observation_two,
-
-These lines will be truncated in the PDF manual.
+* checking Rd line widths ... OK
 * checking Rd cross-references ... OK
 * checking for missing documentation entries ... OK
 * checking for code/documentation mismatches ... OK
-* checking Rd \usage sections ... WARNING
-Undocumented arguments in documentation object 'align_data'
-  ‘align_method’
-
-Undocumented arguments in documentation object 'align_pft'
-  ‘comparison_type’ ‘...’
-
-Undocumented arguments in documentation object 'calc_benchmark'
-  ‘settings’ ‘start_year’ ‘end_year’
-Documented arguments not in \usage in documentation object 'calc_benchmark':
-  ‘bm.ensemble’
-
-Undocumented arguments in documentation object 'check_if_legal_table'
-  ‘table’
-Documented arguments not in \usage in documentation object 'check_if_legal_table':
-  ‘custom_table’
-
-Undocumented arguments in documentation object 'check_if_list_of_pfts'
-  ‘vars’
-Documented arguments not in \usage in documentation object 'check_if_list_of_pfts':
-  ‘observation_one’ ‘observation_two’ ‘custom_table’
-
-Undocumented arguments in documentation object 'check_if_species_list'
-  ‘vars’
-Documented arguments not in \usage in documentation object 'check_if_species_list':
-  ‘observation_one’ ‘observation_two’
-
-Undocumented arguments in documentation object 'create_BRR'
-  ‘user_id’
-
-Undocumented arguments in documentation object 'define_benchmark'
-  ‘settings’ ‘bety’
-Documented arguments not in \usage in documentation object 'define_benchmark':
-  ‘bm.settings’
-
-Undocumented arguments in documentation object 'format_wide2long'
-  ‘time.row’
-
-Undocumented arguments in documentation object 'get_species_list_standard'
-  ‘vars’
-Documented arguments not in \usage in documentation object 'get_species_list_standard':
-  ‘observation_one’ ‘observation_two’ ‘custom_table’
-
-Undocumented arguments in documentation object 'load_csv'
-  ‘vars’
-Documented arguments not in \usage in documentation object 'load_csv':
-  ‘start_year’ ‘end_year’
-
-Undocumented arguments in documentation object 'load_data'
-  ‘vars.used.index’ ‘...’
-
-Undocumented arguments in documentation object 'load_tab_separated_values'
-  ‘vars’
-Documented arguments not in \usage in documentation object 'load_tab_separated_values':
-  ‘start_year’ ‘end_year’
-
-Documented arguments not in \usage in documentation object 'load_x_netcdf':
-  ‘start_year’ ‘end_year’
-
-Undocumented arguments in documentation object 'metric_AME'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_Frechet'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_MAE'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_MSE'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_PPMC'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_R2'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_RAE'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_RMSE'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_cor'
-  ‘...’
-
-Undocumented arguments in documentation object 'metric_lmDiag_plot'
-  ‘var’ ‘filename’ ‘draw.plot’
-
-Undocumented arguments in documentation object 'metric_residual_plot'
-  ‘metric_dat’ ‘var’ ‘filename’
-
-Undocumented arguments in documentation object 'metric_scatter_plot'
-  ‘metric_dat’ ‘var’ ‘filename’
-
-Undocumented arguments in documentation object 'metric_timeseries_plot'
-  ‘metric_dat’ ‘var’ ‘filename’ ‘draw.plot’
-
-Functions with \usage entries need to have the appropriate \alias
-entries, and all their arguments documented.
-The \usage entries must correspond to syntactically valid R code.
-See chapter ‘Writing R documentation files’ in the ‘Writing R
-Extensions’ manual.
-* checking Rd contents ... WARNING
-Argument items with no description in Rd object 'format_wide2long':
-  ‘vars_used’
-
-Argument items with no description in Rd object 'load_rds':
-  ‘vars’
-
-Argument items with no description in Rd object 'metric_residual_plot':
-  ‘draw.plot’
-
-Argument items with no description in Rd object 'metric_scatter_plot':
-  ‘draw.plot’
-
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
 * checking examples ... OK
 * checking for unstated dependencies in ‘tests’ ... OK
-* checking tests ...
+* checking tests ... OK
   Running ‘testthat.R’
- OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
-
-Status: 3 WARNINGs, 4 NOTEs
+Status: 1 NOTE
diff --git a/modules/data.atmosphere/R/temporal.downscaling.R b/modules/data.atmosphere/R/temporal.downscaling.R
index 76600f91420..4032fe61135 100644
--- a/modules/data.atmosphere/R/temporal.downscaling.R
+++ b/modules/data.atmosphere/R/temporal.downscaling.R
@@ -120,7 +120,7 @@ cfmet.downscale.subdaily <- function(subdailymet, output.dt = 1) {
 cfmet.downscale.daily <- function(dailymet, output.dt = 1, lat) {
   
   tint <- 24/output.dt
-  tseq <- 0:(23 * output.dt)/output.dt
+  tseq <- seq(from = 0, to = 23, by = output.dt)
   
   data.table::setkeyv(dailymet, c("year", "doy"))
   
diff --git a/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R b/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R
index 2d3d34be2f7..2b514f84b6a 100644
--- a/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R
+++ b/modules/data.atmosphere/tests/testthat/test.cf-downscaling.R
@@ -21,6 +21,32 @@ test_that(
   expect_equal(b[,signif(range(wind), 2)], c(0.066, 6.60))
 })
 
+test_that("downscaling with timestep", {
+  df <- data.table::data.table(
+    year = 2020, doy = 100,
+    air_temperature_min = 293.15, air_temperature_max = 303.15, air_temperature = 298.15,
+    surface_downwelling_shortwave_flux_in_air = 1000,
+    air_pressure = 1030,
+    wind_speed = 0,
+    relative_humidity = 0.5,
+    precipitation_flux = 2 / (60 * 60)) # units: mm/sec
+
+  r1 <- cfmet.downscale.daily(df, output.dt = 1, lat = 40)
+  r6 <- cfmet.downscale.daily(df, output.dt = 6, lat = 40)
+  r12 <- cfmet.downscale.daily(df, output.dt = 12, lat = 40)
+
+  expect_equal(nrow(r1), 24)
+  expect_equal(nrow(r6), 4)
+  expect_equal(nrow(r12), 2)
+
+  list(r1, r6,r12) %>%
+  purrr::walk(~{
+    expect_equal(mean(.$air_temperature), (df$air_temperature - 273.15)) # input is K, output is C
+    expect_equal(sum(.$precipitation_flux), df$precipitation_flux)
+    expect_true(all(.$air_pressure == df$air_pressure))
+  })
+
+})
 
 test_that("get.ncvector works",{
   run.dates <- data.table::data.table(index = 1:2, date = c(lubridate::ymd("1951-01-01 UTC"), lubridate::ymd("1951-01-02 UTC")))
diff --git a/web/workflow.R b/web/workflow.R
index 1fab4b6062a..ea5ae7d9510 100755
--- a/web/workflow.R
+++ b/web/workflow.R
@@ -31,6 +31,10 @@ options(error = quote({
 # ----------------------------------------------------------------------
 # PEcAn Workflow
 # ----------------------------------------------------------------------
+
+# Report package versions for provenance
+PEcAn.all::pecan_version()
+
 # Open and read in settings file for PEcAn run.
 settings <- PEcAn.settings::read.settings(args$settings)