diff --git a/API b/API
index 7ab80fe95..bef9c6cd4 100644
--- a/API
+++ b/API
@@ -3,7 +3,7 @@
 ## Exported functions
 
 autoupdate(root = here::here())
-diff_requires_run_roxygenize(root = here::here())
+diff_requires_run_roxygenize(root = ".")
 dirs_R.cache(hook_id)
 install_precommit(force = FALSE)
 may_require_permanent_cache(temp_cache_is_enough = FALSE)
diff --git a/DESCRIPTION b/DESCRIPTION
index e065e2241..71e0f603d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -48,5 +48,5 @@ Roxygen: list(markdown = TRUE, roclets = c( "rd", "namespace", "collate",
     if (rlang::is_installed("pkgapi")) "pkgapi::api_roclet" else {
     warning("Please install r-lib/pkgapi to make sure the file API is kept
     up to date"); NULL} ) )
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 SystemRequirements: git
diff --git a/NEWS.md b/NEWS.md
index 7c325f0e4..c51c25794 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,10 +4,20 @@ editor_options:
     wrap: 72
 ---
 
+# precommit v0.3.2.9001 (Development version)
+-   `codemeta-description-updated`, `roxygenize`, and 
+    `use-tidy-description` now all support a `root` argument that 
+    specifies the directory in the git repo that contains the R package. 
+    Defaults to `.` since for most R package git repos, the git and R package 
+    root coincide.
+
 # precommit v0.3.2.9000
 
 -   `use_ci()` is now documented to take `NA`, not `NULL` for argument
     `ci` (#431).
+-   `deps-in-desc`supports a `root` argument that  specifies the directory in 
+    the git repo that contains the R package.  Defaults to `.` since for most R 
+    package git repos, the git and R package root coincide.
 
 # precommit v0.3.2
 
diff --git a/R/roxygen2.R b/R/roxygen2.R
index 2388570f0..19d2a5c9c 100644
--- a/R/roxygen2.R
+++ b/R/roxygen2.R
@@ -24,7 +24,7 @@ extract_diff_files <- function(files) {
 #' hook such as [roxygen2::roxygenize()] must run at all or not.
 #' @param root The root of project.
 #' @keywords internal
-extract_diff_root <- function(root = here::here()) {
+extract_diff_root <- function(root = ".") {
   assert_is_git_repo(root)
   repo <- git2r::repository(root)
   if (length(git2r::reflog(repo)) == 0) {
@@ -57,7 +57,7 @@ extract_diff_root <- function(root = here::here()) {
 #' diff_requires_run_roxygenize()
 #' }
 #' @export
-diff_requires_run_roxygenize <- function(root = here::here()) {
+diff_requires_run_roxygenize <- function(root = ".") {
   if (rlang::with_handlers(withr::with_namespace("git2r", FALSE), error = function(...) TRUE)) {
     generic <- paste0(
       " Please add the package as a dependency to ",
diff --git a/inst/hooks/exported/codemeta-description-updated.R b/inst/hooks/exported/codemeta-description-updated.R
index 313ba738a..eed0ad831 100755
--- a/inst/hooks/exported/codemeta-description-updated.R
+++ b/inst/hooks/exported/codemeta-description-updated.R
@@ -1,5 +1,21 @@
 #!/usr/bin/env Rscript
 
+"A hook to make sure DESCRIPTION hasn’t been edited more recently than
+codemeta.json.
+
+Usage:
+  codemeta-description-updated [--root=<root_>] <files>...
+
+Options:
+  --root=<root_>  Path relative to the git root that contains the R package
+                  root [default: .].
+
+" -> doc
+
+
+arguments <- docopt::docopt(doc)
+setwd(arguments$root)
+
 # adapted from https://github.com/lorenzwalthert/precommit/blob/f4413cfe6282c84f7176160d06e1560860c8bd3d/inst/hooks/exported/readme-rmd-rendered
 if (!file.exists("DESCRIPTION")) {
   rlang::abort("No `DESCRIPTION` found in repository.")
diff --git a/inst/hooks/exported/roxygenize.R b/inst/hooks/exported/roxygenize.R
index c0b30f421..e74a9eec6 100755
--- a/inst/hooks/exported/roxygenize.R
+++ b/inst/hooks/exported/roxygenize.R
@@ -14,13 +14,17 @@ This check should run *after* check that modify the files that are passed to
 them (like styler) because they will never modify their input .R files.
 
 Usage:
-  roxygenize [--no-warn-cache] <files>...
+  roxygenize [--no-warn-cache] [--root=<root_>] <files>...
 
 Options:
   --no-warn-cache  Suppress the warning about a missing permanent cache.
+  --root=<root_>  Path relative to the git root that contains the R package root [default: .].
 
 " -> doc
 arguments <- docopt::docopt(doc)
+arguments$files <- normalizePath(arguments$files) # because working directory changes to root
+setwd(arguments$root)
+
 if (packageVersion("precommit") < "0.1.3.9010") {
   rlang::abort(paste(
     "This hooks only works with the R package {precommit} >= 0.1.3.9010",
diff --git a/inst/hooks/exported/use-tidy-description.R b/inst/hooks/exported/use-tidy-description.R
index e5903e054..f141afe05 100755
--- a/inst/hooks/exported/use-tidy-description.R
+++ b/inst/hooks/exported/use-tidy-description.R
@@ -1,4 +1,24 @@
 #!/usr/bin/env Rscript
+
+"A hook to run usethis::use_tidy_description() to ensure dependencies are
+ordered alphabetically and fields are in standard order.
+
+Usage:
+  use-tidy-description [--root=<root_>] <files>...
+
+Options:
+  --root=<root_>  Path relative to the git root that contains the R package root [default: .].
+
+" -> doc
+
+
+arguments <- docopt::docopt(doc)
+setwd(arguments$root)
+
+if (!file.exists("DESCRIPTION")) {
+  rlang::abort("No `DESCRIPTION` found in repository.")
+}
+
 description <- desc::description$new()
 description_old <- description$clone(deep = TRUE)
 deps <- description$get_deps()
diff --git a/man/diff_requires_run_roxygenize.Rd b/man/diff_requires_run_roxygenize.Rd
index ae71ad474..e6246fd5b 100644
--- a/man/diff_requires_run_roxygenize.Rd
+++ b/man/diff_requires_run_roxygenize.Rd
@@ -4,7 +4,7 @@
 \alias{diff_requires_run_roxygenize}
 \title{Check if we should run roxygen.}
 \usage{
-diff_requires_run_roxygenize(root = here::here())
+diff_requires_run_roxygenize(root = ".")
 }
 \arguments{
 \item{root}{The root of project.}
diff --git a/man/extract_diff_root.Rd b/man/extract_diff_root.Rd
index c9138fe81..30d775047 100644
--- a/man/extract_diff_root.Rd
+++ b/man/extract_diff_root.Rd
@@ -4,7 +4,7 @@
 \alias{extract_diff_root}
 \title{Extract old and new lines from \verb{git diff --cached}}
 \usage{
-extract_diff_root(root = here::here())
+extract_diff_root(root = ".")
 }
 \arguments{
 \item{root}{The root of project.}
diff --git a/man/git_init.Rd b/man/git_init.Rd
index 5ad97130f..10de1b6e1 100644
--- a/man/git_init.Rd
+++ b/man/git_init.Rd
@@ -6,6 +6,9 @@
 \usage{
 git_init(path = ".")
 }
+\arguments{
+\item{path}{A path to where to init a git repository}
+}
 \description{
 In particular, to avoid CRAN errors
 \href{https://github.com/lorenzwalthert/precommit/issues/320}{lorenzwalthert/precommit#320}.
diff --git a/tests/testthat/test-hooks.R b/tests/testthat/test-hooks.R
index de1fd9956..5cd3a4763 100644
--- a/tests/testthat/test-hooks.R
+++ b/tests/testthat/test-hooks.R
@@ -4,6 +4,26 @@
 # success
 run_test("use-tidy-description", "DESCRIPTION", suffix = "")
 
+# in sub directory with correct root
+run_test("use-tidy-description",
+  "DESCRIPTION",
+  suffix = "",
+  cmd_args = "--root=rpkg",
+  artifacts = c("rpkg/DESCRIPTION" = test_path("in/DESCRIPTION"))
+)
+
+
+
+# in sub directory with incorrect root
+# Need to generate the directoy `rpkg` but without DESCRIPTION file.
+run_test("use-tidy-description",
+  "DESCRIPTION",
+  suffix = "",
+  cmd_args = "--root=rpkg",
+  std_err = "No `DESCRIPTION` found in repository.",
+  artifacts = c("rpkg/README.md" = test_path("in/README.md"))
+)
+
 ### . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..
 ### style-files                                                             ####
 
@@ -373,8 +393,47 @@ run_test("roxygenize",
   }
 )
 
+# with outdated Rd present in correct root
+run_test("roxygenize",
+  file_name = c("rpkg/man/flie.Rd" = "flie.Rd"),
+  suffix = "",
+  std_err = NA,
+  cmd_args = "--root=rpkg",
+  std_out = "Writing NAMESPACE",
+  artifacts = c(
+    "rpkg/DESCRIPTION" = test_path("in/DESCRIPTION-no-deps.dcf"),
+    "rpkg/R/roxygenize.R" = test_path("in/roxygenize.R")
+  ),
+  file_transformer = function(files) {
+    withr::local_dir("rpkg")
+    git_init()
+    git2r::add(path = files)
+    # hack to add artifact to trigger diff_requires_roxygenize()
+    git2r::add(path = fs::path(fs::path_dir(fs::path_dir(files[1])), "R"))
+    files
+  }
+)
+
 
 # without Rd present
+run_test("roxygenize",
+  file_name = c("rpkg1/R/roxygenize.R" = "roxygenize.R"),
+  suffix = "",
+  cmd_args = "--root=rpkg1",
+  std_err = "Please commit the new `.Rd` files",
+  artifacts = c(
+    "rpkg1/DESCRIPTION" = test_path("in/DESCRIPTION-no-deps.dcf"),
+    "rpkg2/R/roxygenize.R" = test_path("in/roxygenize.R")
+  ),
+  file_transformer = function(files) {
+    withr::local_dir("rpkg1")
+    git_init()
+    git2r::add(path = files)
+    files
+  }
+)
+
+# with Rd present in wrong root
 run_test("roxygenize",
   file_name = c("R/roxygenize.R" = "roxygenize.R"),
   suffix = "",
@@ -458,6 +517,46 @@ run_test("codemeta-description-update",
   }
 )
 
+# succeed in correct root
+run_test("codemeta-description-update",
+  file_name = c(
+    "rpkg/DESCRIPTION" = "DESCRIPTION",
+    "rpkg/codemeta.json" = "codemeta.json"
+  ),
+  cmd_args = "--root=rpkg",
+  suffix = "",
+  file_transformer = function(files) {
+    if (length(files) > 1) {
+      # transformer is called once on all files and once per file
+      content_2 <- readLines(files[2])
+      Sys.sleep(2)
+      writeLines(content_2, files[2])
+    }
+    files
+  }
+)
+
+# # fail in wrong root
+run_test("codemeta-description-update",
+  file_name = c(
+    "rpkg/DESCRIPTION" = "DESCRIPTION",
+    "rpkg/codemeta.json" = "codemeta.json",
+    "rpkg2/codemeta.json" = "README.md"
+  ),
+  cmd_args = "--root=rpkg2",
+  std_err = "No `DESCRIPTION` found in repository.",
+  suffix = "",
+  file_transformer = function(files) {
+    if (length(files) > 1) {
+      # transformer is called once on all files and once per file
+      content_2 <- readLines(files[2])
+      Sys.sleep(2)
+      writeLines(content_2, files[2])
+    }
+    files
+  }
+)
+
 ### . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..
 ### readme-rmd-rendered                                                     ####
 if (has_git()) {
diff --git a/vignettes/available-hooks.Rmd b/vignettes/available-hooks.Rmd
index 37735f0f5..083f0ce54 100644
--- a/vignettes/available-hooks.Rmd
+++ b/vignettes/available-hooks.Rmd
@@ -223,6 +223,22 @@ This hook does not modify input files, but writes to `.Rd` files in
 `man/`, `NAMESPACE` and potentially others depending on which roxygen
 roclets you specified in `DESCRIPTION`.
 
+
+**Arguments**
+
+<!-- -->
+
+    id: roxygenize
+    args: [--root=<R package root>] 
+
+
+-   Argument `root` specifies the directory in the git repo that
+    contains the R package. Defaults to `.` since for most R package git
+    repos, the git and R package root coincide. Added in version
+    0.3.3.00000.
+
+
+
 ## `deps-in-desc`
 
 Checks if packages used with the `pkgname::fun()` syntax are listed in
@@ -248,7 +264,7 @@ your DESCRIPTION file. Note that `README.Rmd` is never checked.
 <!-- -->
 
     id: deps-in-desc 
-      args: [--root=<R package root>] 
+    args: [--root=<R package root>] 
 
 This hook does not modify the file `DESCRIPTION` because the user should
 decide for each package if it should go to `Imports:` or `Suggests:`,
@@ -261,6 +277,19 @@ are ordered alphabetically and fields are in standard order.
 
 This hook does modify the file `DESCRIPTION`.
 
+**Arguments**
+
+<!-- -->
+
+    id: use-tidy-description
+    args: [--root=<R package root>] 
+
+
+-   Argument `root` specifies the directory in the git repo that
+    contains the R package. Defaults to `.` since for most R package git
+    repos, the git and R package root coincide. Added in version
+    0.3.3.00000.
+    
 ## `lintr`
 
 A hook to run `lintr::lint()` to check that R files are lint free.
@@ -288,3 +317,16 @@ i.e. remind you to run `codemetar::write_codemeta()` in order to keep
 `codemeta.json` in sync with `DESCRIPTION`.
 
 This hook does not modify any file.
+
+**Arguments**
+
+<!-- -->
+
+    id: codemeta-description-updated
+    args: [--root=<R package root>] 
+
+
+-   Argument `root` specifies the directory in the git repo that
+    contains the R package. Defaults to `.` since for most R package git
+    repos, the git and R package root coincide. Added in version
+    0.3.3.00000.