From d7cca61bc0ba49fe8b3fe316a36dce37a007b9e6 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Mon, 13 Jul 2026 02:50:33 -0600
Subject: [PATCH 1/9] first draft of template-master.R, started testing

---
 template-config-renv.R | 226 +++++++++++++++++++++++++++++++++++++++++
 template-config.R      |  45 +++++---
 2 files changed, 259 insertions(+), 12 deletions(-)
 create mode 100644 template-config-renv.R

diff --git a/template-config-renv.R b/template-config-renv.R
new file mode 100644
index 0000000..37fb659
--- /dev/null
+++ b/template-config-renv.R
@@ -0,0 +1,226 @@
+#Template master.R
+
+# INSTRUCTIONS:
+# 
+# Step 1: Script Order
+#
+#At the end of this file, add "source("<filename>", echo = TRUE)" for each R script
+#provided by the author, in the order specified in the README. If the author provides
+#a main or master file, only that file must be added.
+
+#Step 2: Packages
+#
+# If the README specifies packages that need to be manually installed, add them 
+# once the renv is activated
+
+
+# Step 3: Generate log file
+# 
+# The following command works on Linux, MacOS, and on Windows
+# from the "Terminal" within Rstudio:
+#     R CMD BATCH master.R 
+# For alternative ways to do that, see 
+# https://github.com/labordynamicsinstitute/replicability-training/wiki/R-Tips
+
+#*================================================
+#* Let's do everything verbosely
+
+options(verbose=TRUE)
+
+#*================================================
+#* Let's capture the current working directory, so we can return to it later
+temphome <- getwd()
+
+#*================================================
+#* This lists the libraries that are to be installed to properly set up renv. Leave
+#* devtools and rprojroot here; if the authors want you to install others, wait
+#* until you've activated renv
+
+global.libraries <- c("devtools","rprojroot")
+install.packages(global.libraries)
+
+#*==============================================================================================*/
+#* This is specific to AEA replication environment. May not be needed if no confidential data   */
+#* are used in the reproducibility check.                                                       */
+#* Replicator should check the JIRA field "Working location of restricted data" for right path  */
+
+sdrive <- ""
+
+#*================================================
+#* This lists any paths, relative to the root directory, that are to be created.
+
+create.paths <- c("logs")
+# for instance, the following paths might be necessary
+#create.paths <- c("data/raw","data/interwrk","data/generated","results")
+
+################################################
+# Setup for automatic basepath detection       #
+################################################
+
+# Preferred:
+# in bash, go to the root directory and type
+# "touch .here". Then the following code will work cleanly.
+
+# Alternative:
+# There is already a "name_of_project.Rproj" file in the root directory.
+# No further action needed
+
+# If for some reason that does not work (and it always should)
+# manually override:
+
+# rootdir <- "path/to/root/directory"
+rootdir <- ""
+
+####################################
+# global libraries used everywhere #
+####################################
+
+posit.date <- Sys.Date() - 31
+# posit.date <- "2020-01-01" # uncomment and set manually if the above does not work
+
+# PPM only snapshots on weekdays (not sure why...)
+# Only check for weekday if posit.date is a Date object, not a string
+if (!is.character(posit.date) && weekdays(posit.date) %in% c("Saturday","Sunday")) {
+  posit.date <- posit.date - 2
+}
+
+# Check if running on Linux
+if (Sys.info()['sysname'] == "Linux") {
+  # Try to determine the Linux distribution and version using /etc/os-release
+  if (file.exists("/etc/os-release")) {
+    os_release <- system("grep -E '^(ID|VERSION_ID|VERSION_CODENAME|ID_LIKE)=' /etc/os-release", intern = TRUE)
+    
+    # Extract distribution ID (like ubuntu, debian, rocky)
+    distro_id <- gsub("ID=", "", grep("^ID=", os_release, value = TRUE))
+    distro_id <- gsub("[\"']", "", distro_id) # Remove quotes if present
+    
+    # Extract version ID (like 9.4 for Rocky Linux)
+    version_id <- gsub("VERSION_ID=", "", grep("^VERSION_ID=", os_release, value = TRUE))
+    version_id <- gsub("[\"']", "", version_id) # Remove quotes if present
+    
+    # Extract codename (like focal, jammy, bullseye)
+    codename <- gsub("VERSION_CODENAME=", "", grep("^VERSION_CODENAME=", os_release, value = TRUE))
+    
+    # Extract ID_LIKE (like rhel, centos, fedora)
+    id_like <- gsub("ID_LIKE=", "", grep("^ID_LIKE=", os_release, value = TRUE))
+    id_like <- gsub("[\"']", "", id_like) # Remove quotes if present
+    
+    # If we found Ubuntu or Debian
+    if (length(distro_id) > 0 && grepl("^(ubuntu|debian)$", distro_id)) {
+      # Set CRAN to binary PPM for Ubuntu/Debian
+      options(repos = c(CRAN = paste0("https://packagemanager.posit.co/cran/__linux__/", codename, "/", posit.date)))
+      message(paste0("Using binary PPM for Linux distribution: ", distro_id, " (", codename, ")"))
+    } else if (length(distro_id) > 0 && distro_id == "rocky" && grepl("^9", version_id)) {
+      # Set CRAN to binary PPM for Rocky Linux 9
+      options(repos = c(CRAN = paste0("https://packagemanager.posit.co/cran/__linux__/rhel9/", posit.date)))
+      message(paste0("Using binary PPM for Linux distribution: ", distro_id, " (version ", version_id, ")"))
+    } else if (length(distro_id) > 0 && distro_id == "opensuse-leap" && version_id == "15.6") {
+      # Set CRAN to binary PPM for opensuse-leap 15.6
+      options(repos = c(CRAN = paste0("https://packagemanager.posit.co/cran/__linux__/opensuse156/",posit.date)))
+      message(paste0("Using binary PPM for Linux distribution: ", distro_id, " (version ", version_id, ")"))
+    } else {
+      # Use standard PPM with date-based snapshot for other Linux
+      options(repos = c(CRAN = paste0("https://packagemanager.posit.co/cran/", posit.date)))
+    }
+  } else {
+    # Use standard PPM with date-based snapshot if os-release not available
+    options(repos = c(CRAN = paste0("https://packagemanager.posit.co/cran/", posit.date)))
+  }
+} else {
+  # Use standard PPM with date-based snapshot for non-Linux systems
+  options(repos = c(CRAN = paste0("https://packagemanager.posit.co/cran/", posit.date)))
+}
+
+
+
+# print option repos 
+message(paste0("Setting Posit Package Manager snapshot to ",posit.date))
+message("If this does not work, set the date manually in line 22")
+getOption("repos")
+
+# If any package in an renv lockfile is missing a recorded repository, renv::restore()
+# will use the PPM date from options("repos") <- your PPM date, not the author's
+
+
+####################################
+# Set path to root directory       #
+#                                  #
+####################################
+options(renv.consent = TRUE)
+
+if (!requireNamespace("here", quietly = TRUE)) install.packages("here")
+if ( rootdir == "" ) rootdir <- here::here()
+setwd(rootdir)
+
+
+# Main directories
+
+for ( dir in create.paths){
+	if (file.exists(file.path(rootdir,dir))){
+	} else {
+	dir.create(file.path(rootdir,dir))
+	}
+}
+
+
+# Setting project-specific library
+
+# Package management using author's renv when available
+
+if (file.exists(file.path(rootdir,"renv.lock"))) {
+  message("Detected renv.lock. Restoring author's renv environment.")
+  if (!requireNamespace("renv", quietly=TRUE)) install.packages("renv")
+  renv::restore(prompt=FALSE)
+} else {
+  message("No renv.lock found. Initializing project-local renv.")
+  if (!requireNamespace("renv", quietly=TRUE)) install.packages("renv")
+  if (!file.exists(file.path(rootdir,"renv"))) renv::init(bare=TRUE)
+
+  global.libraries <- unique(c(global.libraries,"here"))
+
+  pkgTest <- function(x){
+    if(!requireNamespace(x, quietly=TRUE))
+      install.packages(x, dependencies=TRUE)
+    library(x, character.only=TRUE)
+  }
+
+  invisible(lapply(global.libraries,pkgTest))
+  renv::snapshot(prompt=FALSE)
+}
+
+
+# Get information on the system we are running on
+Sys.info()
+R.version
+
+# Return to the directory we started in
+setwd(temphome)
+
+# keep these lines in the config file
+message("======================================================================================================")
+message(paste0(" Current working directory: ",getwd()))
+print(sessionInfo())
+message("Current libPaths:")
+message(.libPaths())
+message(print(list.files(.libPaths()[1])))
+
+message("Done with configuration.")
+
+
+####################################
+# Run author code                  #
+#                                  #
+####################################
+
+#* Add author's programs in the order listed in the README
+
+author.programs <- c(
+   "code/master.R"
+)
+
+for (prog in author.programs) {
+  message(paste0("---- Sourcing: ", prog, " ----"))
+  source(file.path(rootdir, prog), echo = TRUE)
+}
+
+
diff --git a/template-config.R b/template-config.R
index 3975deb..2b0c3f7 100644
--- a/template-config.R
+++ b/template-config.R
@@ -1,10 +1,17 @@
-#Template config.R
+#Template master.R
 
 # INSTRUCTIONS:
 # 
 # Step 1: Add or modify code to install libraries
 #
-# If the author provides a setup or config file that installs packages, use it.
+# If the author provides a setup or config file that installs packages, list it 
+#first in the list of programs at the end of this file. If the README specifies 
+#packages that need to be manually installed, add them to line NUMBER of this file.
+
+
+
+
+
 # Then proceed to Step 2.
 # If not, then copy this code to "config.R", modify the lines after this comment block,
 # and add "source("config.R", echo = TRUE)" to the main file.
@@ -22,22 +29,19 @@
 # https://github.com/labordynamicsinstitute/replicability-training/wiki/R-Tips
 
 #*================================================
-#* Let's do everything verbosely.
+#* Let's do everything verbosely
 
 options(verbose=TRUE)
 
-
 #*================================================
-#* lets capture the current wd, so we can return to it later
+#* Let's capture the current working directory, so we can return to it later
 temphome <- getwd()
 
 #*================================================
-#* This lists the libraries that are to be installed.
-#* Adjust this by adding on additional ones identified by the authors as necessary
+#* This lists the libraries that are to be installed. Leave devtools and rprojroot
+#* here; add any additional ones identified by the authors as necessary
 
 global.libraries <- c("devtools","rprojroot")
-# For example, you can add on two additional ones:
-# global.libraries <- c("foreign","devtools","rprojroot","ggplot2","nonsenseR")
 
 #*==============================================================================================*/
 #* This is specific to AEA replication environment. May not be needed if no confidential data   */
@@ -188,11 +192,9 @@ pkgTest <- function(x)
 
 ## Add any libraries to this line, and uncomment it.
 
-
 results <- sapply(as.list(global.libraries), pkgTest)
 
-# lets get back to where we started
-
+# Return to the directory we started in
 setwd(temphome)
 
 # keep these lines in the config file
@@ -206,3 +208,22 @@ message(print(list.files(.libPaths()[1])))
 message("Done with configuration.")
 
 
+####################################
+# Run author code                  #
+#                                  #
+####################################
+
+#* Add author's programs in the order listed in the README
+
+author.programs <- c(
+   "master.R",
+  # "code/01_clean_data.R",
+  # "code/02_analysis.R"
+)
+
+for (prog in author.programs) {
+  message(paste0("---- Sourcing: ", prog, " ----"))
+  source(file.path(rootdir, prog), echo = TRUE)
+}
+
+

From b03b3a4570c0b3a61e21eecff6251af0fc3b81cb Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Wed, 15 Jul 2026 01:36:34 -0600
Subject: [PATCH 2/9] fixed some bugs, turned off package installation prompts,
 added final screensho call

---
 template-config-renv.R | 49 +++++++++++++++++++++++++++++++++++++-----
 1 file changed, 44 insertions(+), 5 deletions(-)

diff --git a/template-config-renv.R b/template-config-renv.R
index 37fb659..4876d96 100644
--- a/template-config-renv.R
+++ b/template-config-renv.R
@@ -11,8 +11,8 @@
 #Step 2: Packages
 #
 # If the README specifies packages that need to be manually installed, add them 
-# once the renv is activated
-
+# to readme.libraries, NOT global.libraries to make sure they're part of the renv
+# snapshot.
 
 # Step 3: Generate log file
 # 
@@ -22,6 +22,12 @@
 # For alternative ways to do that, see 
 # https://github.com/labordynamicsinstitute/replicability-training/wiki/R-Tips
 
+# Step 4: Make sure this script carries over
+#
+# Check any author scripts you're running for lines like rm(list = ls(all = TRUE))
+# These will clear your environment and rootdir will no longer work. Comment these
+# lines out
+
 #*================================================
 #* Let's do everything verbosely
 
@@ -36,8 +42,17 @@ temphome <- getwd()
 #* devtools and rprojroot here; if the authors want you to install others, wait
 #* until you've activated renv
 
-global.libraries <- c("devtools","rprojroot")
-install.packages(global.libraries)
+# do we actually need devtools and rprojroot? testing but currently no
+global.libraries <- c()
+
+#global.libraries <- c("devtools","rprojroot")
+#install.packages(global.libraries)
+
+#*================================================
+#* If you're running this script in terminal, you may get a mirror error. This 
+#* line tells R where to install packages from to avoid this error
+
+options(repos = c(CRAN = "https://cloud.r-project.org"))
 
 #*==============================================================================================*/
 #* This is specific to AEA replication environment. May not be needed if no confidential data   */
@@ -165,6 +180,14 @@ for ( dir in create.paths){
 
 # Setting project-specific library
 
+
+# In order to make config.R run smoothly, turn off prompts asking if we want to
+# install packages
+
+options(renv.config.autoloader.enabled = TRUE)
+options(renv.config.install.prompt = FALSE)
+
+
 # Package management using author's renv when available
 
 if (file.exists(file.path(rootdir,"renv.lock"))) {
@@ -175,9 +198,17 @@ if (file.exists(file.path(rootdir,"renv.lock"))) {
   message("No renv.lock found. Initializing project-local renv.")
   if (!requireNamespace("renv", quietly=TRUE)) install.packages("renv")
   if (!file.exists(file.path(rootdir,"renv"))) renv::init(bare=TRUE)
-
+  source(file.path(rootdir, "renv", "activate.R"))
   global.libraries <- unique(c(global.libraries,"here"))
 
+#* If the README specifies additional packages that need to be installed,
+#* add them here. This runs AFTER renv has been activated, so they will be
+#* installed into the project-local renv library (not your base R library),
+#* and will be picked up correctly by renv::snapshot() below.
+  readme.libraries <- c()  # e.g. c("packagename1", "packagename2")
+  global.libraries <- c(global.libraries, readme.libraries)
+  
+  
   pkgTest <- function(x){
     if(!requireNamespace(x, quietly=TRUE))
       install.packages(x, dependencies=TRUE)
@@ -185,6 +216,12 @@ if (file.exists(file.path(rootdir,"renv.lock"))) {
   }
 
   invisible(lapply(global.libraries,pkgTest))
+  
+  #Install any remaining dependencies renv::dependencies() finds in scripts across
+  # the project.
+  missing <- setdiff(renv::dependencies(rootdir)$Package, rownames(installed.packages()))
+  if (length(missing) > 0) renv::install(missing, prompt=FALSE)
+  
   renv::snapshot(prompt=FALSE)
 }
 
@@ -223,4 +260,6 @@ for (prog in author.programs) {
   source(file.path(rootdir, prog), echo = TRUE)
 }
 
+#Final snapshot preserves the packages from a successful run
+renv::snapshot(prompt=FALSE)
 

From ee19e1b00ccc4db120b2ba21b355c9a41d7bd4e2 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Thu, 16 Jul 2026 03:08:49 -0600
Subject: [PATCH 3/9] fixed too many packages being installed, moved up Bash
 instructions

---
 template-config-renv.R | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/template-config-renv.R b/template-config-renv.R
index 4876d96..cf65aeb 100644
--- a/template-config-renv.R
+++ b/template-config-renv.R
@@ -1,7 +1,19 @@
 #Template master.R
 
 # INSTRUCTIONS:
+#
+# Step 0: Bash setup
 # 
+# In File Explorer, look for "name_of_project.Rproj" file in the root directory.
+# If one exists, go to Step 1. If not, open Git Bash.
+# In bash, set your working directory to the root directory (probably 123456/code
+#or similar) and type
+# "touch .here"
+
+# If for some reason that does not work (and it always should)
+# manually override in line XXX of this file.
+
+
 # Step 1: Script Order
 #
 #At the end of this file, add "source("<filename>", echo = TRUE)" for each R script
@@ -197,9 +209,8 @@ if (file.exists(file.path(rootdir,"renv.lock"))) {
 } else {
   message("No renv.lock found. Initializing project-local renv.")
   if (!requireNamespace("renv", quietly=TRUE)) install.packages("renv")
-  if (!file.exists(file.path(rootdir,"renv"))) renv::init(bare=TRUE)
+  if (!file.exists(file.path(rootdir,"renv"))) renv::init(bare=TRUE, restart = FALSE)
   source(file.path(rootdir, "renv", "activate.R"))
-  global.libraries <- unique(c(global.libraries,"here"))
 
 #* If the README specifies additional packages that need to be installed,
 #* add them here. This runs AFTER renv has been activated, so they will be
@@ -208,10 +219,10 @@ if (file.exists(file.path(rootdir,"renv.lock"))) {
   readme.libraries <- c()  # e.g. c("packagename1", "packagename2")
   global.libraries <- c(global.libraries, readme.libraries)
   
-  
+# dependencies = NA to prevent _all_ suggested packages from being downloaded
   pkgTest <- function(x){
     if(!requireNamespace(x, quietly=TRUE))
-      install.packages(x, dependencies=TRUE)
+      install.packages(x, dependencies=NA)
     library(x, character.only=TRUE)
   }
 

From 6e079c6b74e562a0ddcaa70fde2b4b99a0f3f210 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Sat, 18 Jul 2026 02:57:30 -0600
Subject: [PATCH 4/9] added renv.lock search in both directions, fixed snapshot
 overwriting, updated rootdir as necessary

---
 ...onfig-renv.R => NEW-template-config-renv.R | 166 +++++++++++-------
 1 file changed, 100 insertions(+), 66 deletions(-)
 rename template-config-renv.R => NEW-template-config-renv.R (62%)

diff --git a/template-config-renv.R b/NEW-template-config-renv.R
similarity index 62%
rename from template-config-renv.R
rename to NEW-template-config-renv.R
index cf65aeb..f9aef38 100644
--- a/template-config-renv.R
+++ b/NEW-template-config-renv.R
@@ -4,9 +4,7 @@
 #
 # Step 0: Bash setup
 # 
-# In File Explorer, look for "name_of_project.Rproj" file in the root directory.
-# If one exists, go to Step 1. If not, open Git Bash.
-# In bash, set your working directory to the root directory (probably 123456/code
+#In bash, set your working directory to the root directory (probably 123456/code
 #or similar) and type
 # "touch .here"
 
@@ -16,15 +14,14 @@
 
 # Step 1: Script Order
 #
-#At the end of this file, add "source("<filename>", echo = TRUE)" for each R script
-#provided by the author, in the order specified in the README. If the author provides
-#a main or master file, only that file must be added.
+#At the end of this file, add R scripts to author.programs in the order specified 
+#in the README. If the author provides a main or master file, likely only that 
+#file must be added.
 
 #Step 2: Packages
 #
 # If the README specifies packages that need to be manually installed, add them 
-# to readme.libraries, NOT global.libraries to make sure they're part of the renv
-# snapshot.
+# to readme.libraries further down.
 
 # Step 3: Generate log file
 # 
@@ -49,17 +46,6 @@ options(verbose=TRUE)
 #* Let's capture the current working directory, so we can return to it later
 temphome <- getwd()
 
-#*================================================
-#* This lists the libraries that are to be installed to properly set up renv. Leave
-#* devtools and rprojroot here; if the authors want you to install others, wait
-#* until you've activated renv
-
-# do we actually need devtools and rprojroot? testing but currently no
-global.libraries <- c()
-
-#global.libraries <- c("devtools","rprojroot")
-#install.packages(global.libraries)
-
 #*================================================
 #* If you're running this script in terminal, you may get a mirror error. This 
 #* line tells R where to install packages from to avoid this error
@@ -84,14 +70,6 @@ create.paths <- c("logs")
 # Setup for automatic basepath detection       #
 ################################################
 
-# Preferred:
-# in bash, go to the root directory and type
-# "touch .here". Then the following code will work cleanly.
-
-# Alternative:
-# There is already a "name_of_project.Rproj" file in the root directory.
-# No further action needed
-
 # If for some reason that does not work (and it always should)
 # manually override:
 
@@ -158,15 +136,14 @@ if (Sys.info()['sysname'] == "Linux") {
   options(repos = c(CRAN = paste0("https://packagemanager.posit.co/cran/", posit.date)))
 }
 
-
-
 # print option repos 
 message(paste0("Setting Posit Package Manager snapshot to ",posit.date))
 message("If this does not work, set the date manually in line 22")
 getOption("repos")
 
-# If any package in an renv lockfile is missing a recorded repository, renv::restore()
-# will use the PPM date from options("repos") <- your PPM date, not the author's
+# Note: if any package in an renv lockfile is missing a recorded repository, renv::restore()
+# will use the PPM date from options("repos"), meaning it will use _your_ PPM date,
+# not the author's
 
 
 ####################################
@@ -189,53 +166,103 @@ for ( dir in create.paths){
 	}
 }
 
-
-# Setting project-specific library
-
-
 # In order to make config.R run smoothly, turn off prompts asking if we want to
 # install packages
 
 options(renv.config.autoloader.enabled = TRUE)
 options(renv.config.install.prompt = FALSE)
 
+# Bulky renv.lock checks
 
-# Package management using author's renv when available
+# How many directory levels to search for an author-provided renv.lock,
+# relative to rootdir. Increase either if the author's renv.lock is more than 1
+# directory level up or down from rootdir
+lockfile.search.up   <- 1
+lockfile.search.down <- 1
 
-if (file.exists(file.path(rootdir,"renv.lock"))) {
-  message("Detected renv.lock. Restoring author's renv environment.")
-  if (!requireNamespace("renv", quietly=TRUE)) install.packages("renv")
-  renv::restore(prompt=FALSE)
-} else {
-  message("No renv.lock found. Initializing project-local renv.")
-  if (!requireNamespace("renv", quietly=TRUE)) install.packages("renv")
-  if (!file.exists(file.path(rootdir,"renv"))) renv::init(bare=TRUE, restart = FALSE)
-  source(file.path(rootdir, "renv", "activate.R"))
-
-#* If the README specifies additional packages that need to be installed,
-#* add them here. This runs AFTER renv has been activated, so they will be
-#* installed into the project-local renv library (not your base R library),
-#* and will be picked up correctly by renv::snapshot() below.
-  readme.libraries <- c()  # e.g. c("packagename1", "packagename2")
-  global.libraries <- c(global.libraries, readme.libraries)
+find_author_lockfile <- function(rootdir, up = 1, down = 1) {
   
-# dependencies = NA to prevent _all_ suggested packages from being downloaded
-  pkgTest <- function(x){
-    if(!requireNamespace(x, quietly=TRUE))
-      install.packages(x, dependencies=NA)
-    library(x, character.only=TRUE)
+  candidates <- data.frame(path = character(0), distance = integer(0))
+  
+  # rootdir itself
+  self_check <- file.path(rootdir, "renv.lock")
+  if (file.exists(self_check)) {
+    candidates <- rbind(candidates, data.frame(path = self_check, distance = 0))
   }
-
-  invisible(lapply(global.libraries,pkgTest))
   
-  #Install any remaining dependencies renv::dependencies() finds in scripts across
-  # the project.
-  missing <- setdiff(renv::dependencies(rootdir)$Package, rownames(installed.packages()))
-  if (length(missing) > 0) renv::install(missing, prompt=FALSE)
+  # check upwards from rootdir
+  current <- rootdir
+  for (i in seq_len(up)) {
+    parent <- dirname(current)
+    if (parent == current) break  # hit filesystem root
+    candidate <- file.path(parent, "renv.lock")
+    if (file.exists(candidate)) {
+      candidates <- rbind(candidates, data.frame(path = candidate, distance = i))
+    }
+    current <- parent
+  }
   
-  renv::snapshot(prompt=FALSE)
+  # check downwards from rootdir
+  if (down > 0) {
+    subdirs <- list.dirs(rootdir, recursive = TRUE, full.names = TRUE)
+    for (d in subdirs) {
+      depth <- length(strsplit(sub(paste0("^", rootdir), "", d), .Platform$file.sep)[[1]]) - 1
+      if (depth >= 1 && depth <= down) {
+        candidate <- file.path(d, "renv.lock")
+        if (file.exists(candidate)) {
+          candidates <- rbind(candidates, data.frame(path = candidate, distance = depth))
+        }
+      }
+    }
+  }
+  
+  if (nrow(candidates) == 0) return(NULL)
+  candidates <- candidates[order(candidates$distance), ]
+  candidates$path[1]
+}
+
+lockfile_path <- find_author_lockfile(rootdir, up = lockfile.search.up, down = lockfile.search.down)
+
+#if the author's renv.lock file was found, load their setup and switch rootdir to
+#what their code will likely expect
+if (!is.null(lockfile_path)) {
+  author_root <- dirname(lockfile_path)
+  message("Detected renv.lock at: ", lockfile_path)
+  rootdir <- author_root
+  setwd(rootdir)
+  if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
+  renv::restore(project = author_root, prompt = FALSE)
+  renv::load(project = author_root) #uses load not activate to prevent a popup asking to switch projects, which breaks the code
+
+#if no author renv.lock file was found, create a new blank renv project
+} else {
+  message("No renv.lock found within ", lockfile.search.up, " level(s) up / ",
+          lockfile.search.down, " level(s) down. Initializing project-local renv.")
+  if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
+  if (!file.exists(file.path(rootdir, "renv"))) renv::init(project = rootdir, bare = TRUE, restart = FALSE)
+  renv::load(project = rootdir) #uses load not activate to prevent a popup asking to switch projects, which breaks the code
 }
 
+#If you've run the setup and then the author's code breaks because they didn't
+#install some packages, or if the README specifies additional packages that need 
+#to be installed, add them here to install them into the project's renv library
+#(not base R library) and will be picked up correctly by renv::snapshot() below.
+
+readme.libraries <- c("paletteer", "viridis") #these are color packages for testing, delete 
+
+# Install packages from readme.libraries
+
+  pkgTest <- function(x)
+  {
+    if (!require(x,character.only = TRUE))
+    {
+      renv::install(x,prompt = FALSE)
+      if(!require(x,character.only = TRUE)) stop("Package not found")
+    }
+    return("OK")
+  }
+  
+invisible(lapply(readme.libraries,pkgTest))
 
 # Get information on the system we are running on
 Sys.info()
@@ -271,6 +298,13 @@ for (prog in author.programs) {
   source(file.path(rootdir, prog), echo = TRUE)
 }
 
-#Final snapshot preserves the packages from a successful run
-renv::snapshot(prompt=FALSE)
+#Final snapshot preserves the packages from a successful run but won't overwrite
+#the author's original. Not forced, may change later. Select option 1 so you don't
+#include `here` in the snapshot, but make sure no other packages are listed.
+renv::snapshot(
+  project  = rootdir,
+  lockfile = file.path(rootdir, "renv.lock.replicator_snapshot"),
+  packages = c(renv::dependencies(rootdir)$Package, readme.libraries),
+  prompt   = FALSE
+)
 

From 112b433e2103e485d0b6bf5a3fa48dd88e59eb09 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Sun, 19 Jul 2026 02:14:42 -0600
Subject: [PATCH 5/9] added note about logs; successfully tested in 3 repos on
 personal laptop

---
 NEW-template-config-renv.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEW-template-config-renv.R b/NEW-template-config-renv.R
index f9aef38..cb8fe14 100644
--- a/NEW-template-config-renv.R
+++ b/NEW-template-config-renv.R
@@ -25,7 +25,8 @@
 
 # Step 3: Generate log file
 # 
-# The following command works on Linux, MacOS, and on Windows
+# Once the code runs successfully, run this to get a log file: 
+#The following command works on Linux, MacOS, and on Windows
 # from the "Terminal" within Rstudio:
 #     R CMD BATCH master.R 
 # For alternative ways to do that, see 

From aa9f96044c6cc0930648180e9193a68e2cc48c98 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Tue, 21 Jul 2026 02:05:44 -0600
Subject: [PATCH 6/9] tested successfully on CCSS Cloud

---
 NEW-template-config-renv.R => template-Main.R | 84 +++++++++----------
 1 file changed, 42 insertions(+), 42 deletions(-)
 rename NEW-template-config-renv.R => template-Main.R (80%)

diff --git a/NEW-template-config-renv.R b/template-Main.R
similarity index 80%
rename from NEW-template-config-renv.R
rename to template-Main.R
index cb8fe14..124bb2e 100644
--- a/NEW-template-config-renv.R
+++ b/template-Main.R
@@ -4,34 +4,37 @@
 #
 # Step 0: Bash setup
 # 
-#In bash, set your working directory to the root directory (probably 123456/code
-#or similar) and type
+# In bash, set your working directory to where you're running this (probably 123456/code
+# or similar) and type
 # "touch .here"
 
 # If for some reason that does not work (and it always should)
-# manually override in line XXX of this file.
+# manually override in line 79 of this file.
 
 
 # Step 1: Script Order
 #
-#At the end of this file, add R scripts to author.programs in the order specified 
-#in the README. If the author provides a main or master file, likely only that 
-#file must be added.
+# At the end of this file, add R scripts to author.programs in the order specified 
+# in the README. If the author provides a main or master file, likely only that 
+# file must be added.
 
-#Step 2: Packages
+
+# Step 2: Packages
 #
 # If the README specifies packages that need to be manually installed, add them 
-# to readme.libraries further down.
+# to readme.libraries on line 251.
+
 
 # Step 3: Generate log file
 # 
-# Once the code runs successfully, run this to get a log file: 
-#The following command works on Linux, MacOS, and on Windows
+# Once the code runs successfully, or if you need a log, run this to get a log file: 
+# The following command works on Linux, MacOS, and on Windows
 # from the "Terminal" within Rstudio:
 #     R CMD BATCH master.R 
 # For alternative ways to do that, see 
 # https://github.com/labordynamicsinstitute/replicability-training/wiki/R-Tips
 
+
 # Step 4: Make sure this script carries over
 #
 # Check any author scripts you're running for lines like rm(list = ls(all = TRUE))
@@ -48,32 +51,30 @@ options(verbose=TRUE)
 temphome <- getwd()
 
 #*================================================
-#* If you're running this script in terminal, you may get a mirror error. This 
-#* line tells R where to install packages from to avoid this error
+#* If you're running this script in terminal, you may get an  error about trying
+#* to use CRAN without setting a mirror. This line tells R where to install 
+#* packages from to avoid this error
 
 options(repos = c(CRAN = "https://cloud.r-project.org"))
 
 #*==============================================================================================*/
-#* This is specific to AEA replication environment. May not be needed if no confidential data   */
-#* are used in the reproducibility check.                                                       */
-#* Replicator should check the JIRA field "Working location of restricted data" for right path  */
+#* This is specific to AEA replication environment. May not be needed if no 
+#* confidential data are used in the reproducibility check. Replicator should
+#* check the JIRA field "Working location of restricted data" for right path  */
 
 sdrive <- ""
 
 #*================================================
-#* This lists any paths, relative to the root directory, that are to be created.
+#* This lists any paths, relative to the root directory, that are to be created
 
 create.paths <- c("logs")
-# for instance, the following paths might be necessary
-#create.paths <- c("data/raw","data/interwrk","data/generated","results")
+# For instance, the following paths might be necessary
+# create.paths <- c("data/raw","data/interwrk","data/generated","results")
 
 ################################################
 # Setup for automatic basepath detection       #
 ################################################
 
-# If for some reason that does not work (and it always should)
-# manually override:
-
 # rootdir <- "path/to/root/directory"
 rootdir <- ""
 
@@ -142,22 +143,21 @@ message(paste0("Setting Posit Package Manager snapshot to ",posit.date))
 message("If this does not work, set the date manually in line 22")
 getOption("repos")
 
-# Note: if any package in an renv lockfile is missing a recorded repository, renv::restore()
-# will use the PPM date from options("repos"), meaning it will use _your_ PPM date,
-# not the author's
-
+# Note: if any package in an renv lockfile is missing a recorded repository, 
+# renv::restore() will use the PPM date from options("repos"), meaning it will 
+# use *your* PPM date, not the author's
 
 ####################################
 # Set path to root directory       #
 #                                  #
 ####################################
+
 options(renv.consent = TRUE)
 
 if (!requireNamespace("here", quietly = TRUE)) install.packages("here")
 if ( rootdir == "" ) rootdir <- here::here()
 setwd(rootdir)
 
-
 # Main directories
 
 for ( dir in create.paths){
@@ -173,11 +173,12 @@ for ( dir in create.paths){
 options(renv.config.autoloader.enabled = TRUE)
 options(renv.config.install.prompt = FALSE)
 
-# Bulky renv.lock checks
+# renv.lock checks
 
 # How many directory levels to search for an author-provided renv.lock,
-# relative to rootdir. Increase either if the author's renv.lock is more than 1
-# directory level up or down from rootdir
+# relative to rootdir. Increase if you can see the author's renv.lock is more than
+# 1 directory level up or down from rootdir
+
 lockfile.search.up   <- 1
 lockfile.search.down <- 1
 
@@ -185,7 +186,7 @@ find_author_lockfile <- function(rootdir, up = 1, down = 1) {
   
   candidates <- data.frame(path = character(0), distance = integer(0))
   
-  # rootdir itself
+  # check rootdir itself
   self_check <- file.path(rootdir, "renv.lock")
   if (file.exists(self_check)) {
     candidates <- rbind(candidates, data.frame(path = self_check, distance = 0))
@@ -224,8 +225,8 @@ find_author_lockfile <- function(rootdir, up = 1, down = 1) {
 
 lockfile_path <- find_author_lockfile(rootdir, up = lockfile.search.up, down = lockfile.search.down)
 
-#if the author's renv.lock file was found, load their setup and switch rootdir to
-#what their code will likely expect
+# If the author's renv.lock file was found, load their setup and switch rootdir
+# to what their code will likely expect
 if (!is.null(lockfile_path)) {
   author_root <- dirname(lockfile_path)
   message("Detected renv.lock at: ", lockfile_path)
@@ -235,7 +236,7 @@ if (!is.null(lockfile_path)) {
   renv::restore(project = author_root, prompt = FALSE)
   renv::load(project = author_root) #uses load not activate to prevent a popup asking to switch projects, which breaks the code
 
-#if no author renv.lock file was found, create a new blank renv project
+# If no author renv.lock file was found, create a new blank renv project
 } else {
   message("No renv.lock found within ", lockfile.search.up, " level(s) up / ",
           lockfile.search.down, " level(s) down. Initializing project-local renv.")
@@ -244,12 +245,10 @@ if (!is.null(lockfile_path)) {
   renv::load(project = rootdir) #uses load not activate to prevent a popup asking to switch projects, which breaks the code
 }
 
-#If you've run the setup and then the author's code breaks because they didn't
-#install some packages, or if the README specifies additional packages that need 
-#to be installed, add them here to install them into the project's renv library
-#(not base R library) and will be picked up correctly by renv::snapshot() below.
+# If missing packages, add them here to install into the project's renv library
+#(not base R library) so they will be picked up correctly by renv::snapshot() below
 
-readme.libraries <- c("paletteer", "viridis") #these are color packages for testing, delete 
+readme.libraries <- c() #ex: c("paletteer", "viridis")
 
 # Install packages from readme.libraries
 
@@ -272,7 +271,7 @@ R.version
 # Return to the directory we started in
 setwd(temphome)
 
-# keep these lines in the config file
+# Keep these lines in the config file
 message("======================================================================================================")
 message(paste0(" Current working directory: ",getwd()))
 print(sessionInfo())
@@ -299,9 +298,10 @@ for (prog in author.programs) {
   source(file.path(rootdir, prog), echo = TRUE)
 }
 
-#Final snapshot preserves the packages from a successful run but won't overwrite
-#the author's original. Not forced, may change later. Select option 1 so you don't
-#include `here` in the snapshot, but make sure no other packages are listed.
+# Final snapshot preserves the packages from a successful run but won't overwrite
+# the author's original. Not forced, may change later. Select option 1 so you don't
+# include `here` in the snapshot, but make sure no other packages are listed in 
+# the warning
 renv::snapshot(
   project  = rootdir,
   lockfile = file.path(rootdir, "renv.lock.replicator_snapshot"),

From 759ccf2e4aaa224f63ea2163327bf6aae91727e3 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Tue, 21 Jul 2026 22:37:01 -0600
Subject: [PATCH 7/9] revert changes to template-config.R, all new work is
 separate in template-Main.R

---
 template-config.R | 45 ++++++++++++---------------------------------
 1 file changed, 12 insertions(+), 33 deletions(-)

diff --git a/template-config.R b/template-config.R
index 2b0c3f7..3975deb 100644
--- a/template-config.R
+++ b/template-config.R
@@ -1,17 +1,10 @@
-#Template master.R
+#Template config.R
 
 # INSTRUCTIONS:
 # 
 # Step 1: Add or modify code to install libraries
 #
-# If the author provides a setup or config file that installs packages, list it 
-#first in the list of programs at the end of this file. If the README specifies 
-#packages that need to be manually installed, add them to line NUMBER of this file.
-
-
-
-
-
+# If the author provides a setup or config file that installs packages, use it.
 # Then proceed to Step 2.
 # If not, then copy this code to "config.R", modify the lines after this comment block,
 # and add "source("config.R", echo = TRUE)" to the main file.
@@ -29,19 +22,22 @@
 # https://github.com/labordynamicsinstitute/replicability-training/wiki/R-Tips
 
 #*================================================
-#* Let's do everything verbosely
+#* Let's do everything verbosely.
 
 options(verbose=TRUE)
 
+
 #*================================================
-#* Let's capture the current working directory, so we can return to it later
+#* lets capture the current wd, so we can return to it later
 temphome <- getwd()
 
 #*================================================
-#* This lists the libraries that are to be installed. Leave devtools and rprojroot
-#* here; add any additional ones identified by the authors as necessary
+#* This lists the libraries that are to be installed.
+#* Adjust this by adding on additional ones identified by the authors as necessary
 
 global.libraries <- c("devtools","rprojroot")
+# For example, you can add on two additional ones:
+# global.libraries <- c("foreign","devtools","rprojroot","ggplot2","nonsenseR")
 
 #*==============================================================================================*/
 #* This is specific to AEA replication environment. May not be needed if no confidential data   */
@@ -192,9 +188,11 @@ pkgTest <- function(x)
 
 ## Add any libraries to this line, and uncomment it.
 
+
 results <- sapply(as.list(global.libraries), pkgTest)
 
-# Return to the directory we started in
+# lets get back to where we started
+
 setwd(temphome)
 
 # keep these lines in the config file
@@ -208,22 +206,3 @@ message(print(list.files(.libPaths()[1])))
 message("Done with configuration.")
 
 
-####################################
-# Run author code                  #
-#                                  #
-####################################
-
-#* Add author's programs in the order listed in the README
-
-author.programs <- c(
-   "master.R",
-  # "code/01_clean_data.R",
-  # "code/02_analysis.R"
-)
-
-for (prog in author.programs) {
-  message(paste0("---- Sourcing: ", prog, " ----"))
-  source(file.path(rootdir, prog), echo = TRUE)
-}
-
-

From 350209b70a9f861eee1db45198f2028abf4c0b83 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Thu, 23 Jul 2026 02:12:10 -0600
Subject: [PATCH 8/9] fixed log file creation command

---
 template-Main.R | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/template-Main.R b/template-Main.R
index 124bb2e..46cb790 100644
--- a/template-Main.R
+++ b/template-Main.R
@@ -9,7 +9,7 @@
 # "touch .here"
 
 # If for some reason that does not work (and it always should)
-# manually override in line 79 of this file.
+# manually override in line 76 of this file.
 
 
 # Step 1: Script Order
@@ -22,25 +22,22 @@
 # Step 2: Packages
 #
 # If the README specifies packages that need to be manually installed, add them 
-# to readme.libraries on line 251.
+# to readme.libraries on line 248.
 
 
-# Step 3: Generate log file
-# 
-# Once the code runs successfully, or if you need a log, run this to get a log file: 
-# The following command works on Linux, MacOS, and on Windows
-# from the "Terminal" within Rstudio:
-#     R CMD BATCH master.R 
-# For alternative ways to do that, see 
-# https://github.com/labordynamicsinstitute/replicability-training/wiki/R-Tips
-
-
-# Step 4: Make sure this script carries over
+# Step 3: Make sure this script carries over
 #
 # Check any author scripts you're running for lines like rm(list = ls(all = TRUE))
 # These will clear your environment and rootdir will no longer work. Comment these
 # lines out
 
+# Step 4: Run code and generate log files
+# 
+# From the Terminal (not Console) tab within Rstudio:
+#     R CMD BATCH --verbose --vanilla main.R main.$(date +%F_%H-%M-%S).Rout 
+# For alternative ways to do that, see 
+# https://github.com/labordynamicsinstitute/replicability-training/wiki/R-Tips
+
 #*================================================
 #* Let's do everything verbosely
 

From 79aae49f5916ac7533209c2efdbd6d5d8b19fef8 Mon Sep 17 00:00:00 2001
From: unknown <ansu1338@colorado.edu>
Date: Fri, 24 Jul 2026 01:22:42 -0600
Subject: [PATCH 9/9] updated file name, fixed rootdir instructions

---
 template-Main.R => template-main.R | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)
 rename template-Main.R => template-main.R (96%)

diff --git a/template-Main.R b/template-main.R
similarity index 96%
rename from template-Main.R
rename to template-main.R
index 46cb790..1ecd0f7 100644
--- a/template-Main.R
+++ b/template-main.R
@@ -2,36 +2,36 @@
 
 # INSTRUCTIONS:
 #
-# Step 0: Bash setup
+# Step 1: Packages
+#
+# If the README specifies packages that need to be manually installed, add them 
+# to readme.libraries on line 248.
+
+# Step 2: rootdir setup
 # 
-# In bash, set your working directory to where you're running this (probably 123456/code
-# or similar) and type
+# Identify the base directory of your replication package. If the author has an 
+#rproj file or a .here file, rootdir will be set there. Otherwise, in bash, set 
+# your working directory to the base directory, and type
 # "touch .here"
-
+#
 # If for some reason that does not work (and it always should)
 # manually override in line 76 of this file.
 
 
-# Step 1: Script Order
+# Step 3: Script order
 #
 # At the end of this file, add R scripts to author.programs in the order specified 
 # in the README. If the author provides a main or master file, likely only that 
 # file must be added.
 
 
-# Step 2: Packages
-#
-# If the README specifies packages that need to be manually installed, add them 
-# to readme.libraries on line 248.
-
-
-# Step 3: Make sure this script carries over
+# Step 4: Make sure this script carries over
 #
 # Check any author scripts you're running for lines like rm(list = ls(all = TRUE))
 # These will clear your environment and rootdir will no longer work. Comment these
 # lines out
 
-# Step 4: Run code and generate log files
+# Step 5: Run code and generate log files
 # 
 # From the Terminal (not Console) tab within Rstudio:
 #     R CMD BATCH --verbose --vanilla main.R main.$(date +%F_%H-%M-%S).Rout