diff --git a/.gitignore b/.gitignore
index 45b3942..2dfe3f5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,4 @@ inst/doc
 .ipynb
 animl-py/src/animl/__pycache__/**
 animl-py/src/animl/.ipynb_checkpoints/**
+examples/**
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index 6918ff7..3b262ef 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: animl
 Title: A Collection of ML Tools for Conservation Research
-Version: 3.1.1
+Version: 3.2.0
 Authors@R: c(person(given="Kyra", family="Swanson",email="tswanson@sdzwa.org", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1496-3217")), person(given="Mathias",family="Tobler",role = "aut"))
 Description: Functions required to classify subjects within camera trap field data. The package can handle both images and videos. The authors recommend a two-step approach using Microsoft's 'MegaDector' model and then a second model trained on the classes of interest.
diff --git a/NAMESPACE b/NAMESPACE
index 63dd3f3..7686fe6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export(WorkingDirectory)
 export(animl_install)
+export(animl_install_instructions)
 export(build_file_manifest)
 export(check_python)
 export(classify)
@@ -24,7 +25,7 @@ export(get_animals)
 export(get_empty)
 export(get_frame_as_image)
 export(list_models)
-export(load_animl_py)
+export(load_animl)
 export(load_class_list)
 export(load_classifier)
 export(load_data)
diff --git a/R/classification.R b/R/classification.R
index 415a10a..a16d74e 100644
--- a/R/classification.R
+++ b/R/classification.R
@@ -1,3 +1,22 @@
+#' Save model state weights
+#'
+#' @param model pytorch model
+#' @param out_dir directory to save model to
+#' @param epoch  current training epoch
+#' @param stats performance metrics of current epoch
+#' @param optimizer pytorch optimizer (optional)
+#' @param scheduler pytorch scheduler (optional)
+#'
+#' @returns None
+#' @export
+#'
+#' @examples
+#' \dontrun{save_classifier(model, 'models/', 10, list(acc = 0.85))}
+save_classifier <- function(model, out_dir, epoch, stats, optimizer=NULL, scheduler=NULL){
+  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py$save_classifier(model, out_dir, epoch, reticulate::r_to_py(stats), optimizer=optimizer, scheduler=scheduler)
+}
+
 #' Load a Classifier Model and Class_list
 #'
 #' @param model_path path to model
@@ -13,8 +32,7 @@
 #' classes <- load_class_list('sdzwa_andes_v1_classes.csv')
 #' andes <- load_classifier('andes_v1.pt', nrow(classes))}
 load_classifier <- function(model_path, classes, device=NULL, architecture="CTL"){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
-
+  animl_py <- .animl_internal$animl_py
   if(is.numeric(classes)){ classes = as.integer(classes)}
   animl_py$load_classifier(model_path, classes, device=device, architecture=architecture)
 }
@@ -35,7 +53,7 @@ load_classifier <- function(model_path, classes, device=NULL, architecture="CTL"
 #' @examples
 #' \dontrun{save_classifier(model, 'models/', 10, list(acc = 0.85))}
 save_classifier <- function(model, out_dir, epoch, stats, optimizer=NULL, scheduler=NULL){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$save_classifier(model, out_dir, epoch, reticulate::r_to_py(stats), optimizer=optimizer, scheduler=scheduler)
 }
 
@@ -78,7 +96,7 @@ classify <- function(model, detections,
                        batch_size=1, num_workers=1,
                        device=NULL, out_file=NULL){
   
-    animl_py <- get("animl_py", envir = parent.env(environment()))
+    animl_py <- .animl_internal$animl_py
     animl_py$classify(model, detections,
                       resize_width=as.integer(resize_width),
                       resize_height=as.integer(resize_height), 
@@ -95,13 +113,14 @@ classify <- function(model, detections,
 #' @param empty manifest of md human, vehicle and empty images
 #' @param predictions_raw softmaxed likelihoods from predict_species
 #' @param class_list list of class labels
+#' @param best whether to return one prediction per file
 #'
 #' @returns dataframe with prediction and confidence columns
 #' @export
 #'
 #' @examples
 #' \dontrun{animals <- single_classification(animals, empty, pred_raw, class_list)}
-single_classification <- function(animals, empty, predictions_raw, class_list){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
-  animl_py$single_classification(animals, empty, predictions_raw, class_list)
+single_classification <- function(animals, empty, predictions_raw, class_list, best=FALSE){
+  animl_py <- .animl_internal$animl_py
+  animl_py$single_classification(animals, empty, predictions_raw, class_list, best=best)
 }
diff --git a/R/detection.R b/R/detection.R
index 02e19fc..fe8d40c 100644
--- a/R/detection.R
+++ b/R/detection.R
@@ -11,7 +11,7 @@
 #' \dontrun{md_py <- megadetector("/mnt/machinelearning/megaDetector/md_v5a.0.0.pt", 
 #'                                model_type='mdv5', device='cuda:0')}
 load_detector <- function(model_path, model_type, device=NULL){
-  # first check if animl-py is loaded
+  animl_py <- .animl_internal$animl_py
   animl_py$load_detector(model_path, model_type=model_type, device=device)
 }
 
@@ -40,7 +40,8 @@ detect <- function(detector, image_file_names, resize_width, resize_height,
                    letterbox=TRUE, confidence_threshold=0.1, file_col='filepath',
                    batch_size=1, num_workers=1, device=NULL,
                    checkpoint_path=NULL, checkpoint_frequency=-1){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  
+  animl_py <- .animl_internal$animl_py
   animl_py$detect(detector, image_file_names, 
                   as.integer(resize_width), as.integer(resize_height),
                   letterbox=letterbox, confidence_threshold=confidence_threshold,
@@ -67,8 +68,7 @@ detect <- function(detector, image_file_names, resize_width, resize_height,
 #' mdresults <- parseMD(mdres)
 #' }
 parse_detections <- function(results, manifest=NULL, out_file=NULL, threshold=0, file_col="filepath") {
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$parse_detections(results, manifest=manifest, out_file=out_file,
                             threshold=threshold, file_col=file_col)
 }
-
diff --git a/R/export.R b/R/export.R
index c73c2ca..267b435 100644
--- a/R/export.R
+++ b/R/export.R
@@ -1,9 +1,9 @@
 #' Create SymLink Directories and Sort Classified Images
 #'
 #' @param manifest DataFrame of classified images 
-#' @param out_dir Destination directory for symlinks
+#' @param out_dir Destination directory for species folders
 #' @param out_file if provided, save the manifest to this file
-#' @param label_col (str): specify 'prediction' for species or 'category' for megadetector class
+#' @param label_col specify 'prediction' for species or 'category' for megadetector class
 #' @param file_col Colun containing file paths
 #' @param unique_name Unique image name identifier 
 #' @param copy Toggle to determine copy or hard link, defaults to link
@@ -18,7 +18,7 @@
 export_folders <- function(manifest, out_dir, out_file=NULL, 
                            label_col="prediction", file_col="filepath",
                            unique_name='uniquename', copy=FALSE) {
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   manifest <- animl_py$export_folders(manifest, out_dir, out_file,
                                       label_col=label_col, file_col=file_col,
                                       unique_name=unique_name, copy=copy)
@@ -49,7 +49,7 @@ remove_link <- function(manifest, link_col='link'){
 #'
 #' @param manifest dataframe containing file data and predictions
 #' @param export_dir directory to sort files into
-#' @param unique_name column name indicating a unique file name for each row
+#' @param unique_name column containing unique file names
 #'
 #' @return dataframe with new "Species" column that contains the verified species
 #' @export
@@ -87,7 +87,7 @@ update_labels_from_folders <- function(manifest, export_dir, unique_name='unique
 #' @examples
 #' \dontrun{export_megadetector(manifest, output_file= 'results.json', detector='MDv6')}
 export_coco <- function(manifest, class_list, out_file, info=NULL, licenses=NULL){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$export_coco(manifest, class_list, out_file, info=info, licenses=licenses)
 }
 
@@ -114,7 +114,7 @@ export_coco <- function(manifest, class_list, out_file, info=NULL, licenses=NULL
 export_camtrapR <- function(manifest, out_dir, out_file=NULL, label_col='prediction',
                             file_col="filepath", station_col='station', 
                             unique_name='uniquename', copy=FALSE){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$export_camtrapR(manifest, out_dir, out_file=out_file, label_col=label_col,
                            file_col=file_col, station_col=station_col,
                            unique_name=unique_name, copy=copy)
@@ -123,8 +123,8 @@ export_camtrapR <- function(manifest, out_dir, out_file=NULL, label_col='predict
 
 #' Converts the Manifests to a csv file that contains columns needed for TimeLapse conversion in later step
 #'
-#' @param results a DataFrame that has entries of anuimal classification
-#' @param image_dir location of root directory where all images are stored (can contain subdirectories)
+#' @param manifest a DataFrame that has entries of anuimal classification
+#' @param out_dir location of root directory where all images are stored (can contain subdirectories)
 #' @param only_animal A bool that confirms whether we want only animal detctions or all
 #'
 #' @returns animals.csv, non-anim.csv, csv_loc
@@ -132,9 +132,9 @@ export_camtrapR <- function(manifest, out_dir, out_file=NULL, label_col='predict
 #'
 #' @examples
 #' \dontrun{export_timelapse(animals, empty, '/path/to/images/')}
-export_timelapse <- function(results, image_dir, only_animal=TRUE){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
-  animl_py$export_timelapse(results, image_dir, only_animal=only_animal)
+export_timelapse <- function(manifest, out_dir, only_animal=TRUE){
+  animl_py <- .animl_internal$animl_py
+  animl_py$export_timelapse(manifest, out_dir, only_animal=only_animal)
 }
 
 
@@ -152,7 +152,7 @@ export_timelapse <- function(results, image_dir, only_animal=TRUE){
 #' \dontrun{export_megadetector(manifest, output_file= 'results.json', detector='MDv6')}
 export_megadetector <- function(manifest, out_file=NULL, 
                                 detector='MegaDetector v5a', prompt=TRUE){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$export_megadetector(manifest, out_file=out_file, 
                                detector=detector, prompt=prompt)
 }
diff --git a/R/file_management.R b/R/file_management.R
index 311321e..5f26c6c 100644
--- a/R/file_management.R
+++ b/R/file_management.R
@@ -22,7 +22,7 @@
 #' }
 build_file_manifest <- function(image_dir, exif=TRUE, out_file=NULL, 
                                 offset=0, recursive=TRUE) {
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   manifest <- animl_py$build_file_manifest(image_dir, exif=exif, out_file=out_file, offset=offset, recursive=recursive)
   return(manifest)
 }
@@ -145,7 +145,7 @@ check_file <- function(file, output_type) {
 #' save_json(mdresults, 'mdraw.json')
 #' }
 save_json <- function(data, out_file, prompt=TRUE){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$save_json(data, out_file, prompt=prompt)
 }
 
@@ -162,7 +162,7 @@ save_json <- function(data, out_file, prompt=TRUE){
 #' mdraw <- load_json('mdraw.json')
 #' }
 load_json <- function(file){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$load_json(file)
 }
 
@@ -181,7 +181,7 @@ load_json <- function(file){
 #'   download_model("https://models.com/path/to/model.pt", out_dir='models')
 #' }
 download_model <- function(model_url, out_dir='models'){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$download_model(model_url, out_dir = out_dir)
 }
 
@@ -196,6 +196,6 @@ download_model <- function(model_url, out_dir='models'){
 #'   download_model("https://models.com/path/to/model.pt", out_dir='models')
 #' }
 list_models <- function(){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$list_models()
 }
\ No newline at end of file
diff --git a/R/install.R b/R/install.R
index e5916d8..3dcc22f 100644
--- a/R/install.R
+++ b/R/install.R
@@ -1,110 +1,175 @@
 # VARIABLE FOR VERSION
-ANIML_VERSION <- "3.1.1"
+ANIML_VERSION <- "3.2.0"
 
-#' Create a miniconda environment for animl and install animl-py
+#' Load animl-py if available
 #'
-#' @param py_env name of python environment
-#' @param animl_version version of animl to install
+#' @param envname name of python environment
 #' @param python_version version of python to install
-#' @param confirm allow user input
 #'
 #' @returns none
 #' @export
 #'
 #' @examples
-#' \dontrun{animl_install("animl_env", ANIML_VERSION, python_version="3.9", confirm=TRUE)}
-animl_install <- function(py_env = "animl_env",
-                          animl_version = ANIML_VERSION,
-                          python_version = "3.12",
-                          confirm=TRUE) {
+#' \dontrun{animl_install("animl_env", ANIML_VERSION, python_version="3.12")}
+load_animl <- function(envname = "animl_env",
+                          python_version = "3.12") {
   # 1. Load environment if exists
-  packageStartupMessage(sprintf("1. Loading Python Environment (%s)...", py_env))
-  try_error <- try(reticulate::use_condaenv(py_env, required = TRUE), silent=TRUE)
+  packageStartupMessage(sprintf("1. Loading Python Environment (%s)...", envname))
+  try_error <- try(reticulate::use_virtualenv(envname, required = TRUE), silent=TRUE)
   
   # 2. Install if not exists
   if (inherits(try_error, "try-error")) {
-    packageStartupMessage(try_error)
-    #packageStartupMessage(sprintf("%s not found \n", py_env))
-    # 2. Create new environment
-    packageStartupMessage("\n", sprintf("2. Creating a Python Environment (%s)", py_env))
-    animl_path <- tryCatch(expr = create_pyenv(python_version = python_version, py_env = py_env),
-                           error = function(e) stop(e, "An error occur when animl_install was creating the Python Environment.",
-                                                    "Check that you've accepted the conda TOS and restart the R session, before trying again."))
-    #print(animl_path)
-    # 3. Install animl-py
-    packageStartupMessage("\n3. Installing animl-py...")
-    package <- sprintf("animl==%s", animl_version)
-    reticulate::py_install(package, envname=py_env, pip=TRUE)
-    
-    packageStartupMessage("animl successfully installed. Restart R session to see changes.\n")
-    invisible(TRUE)
-    return(FALSE)
+    #packageStartupMessage(try_error)
+    msg <- sprintf(paste0("%s python environment not found. Run animl::animl_install().\n", 
+                          "See `?animl::animl_install_instructions` for more detail."), envname)
+    packageStartupMessage(msg)
   }
-  # conda env exists
+  # env exists
   else{
     # check animl-py installed
     packageStartupMessage("\n2. Checking animl-py version...")
     if(reticulate::py_module_available("animl")){
       animl_py <- reticulate::import("animl", delay_load = TRUE)
-      py_version <- animl_py$'__version__'
+      current_version <- animl_py$'__version__'
       # check version match
-      if (!identical(animl_version, py_version)){update_animl_py()}
+      if (!identical(ANIML_VERSION, current_version)){
+        # tell user to update animl-py
+        packageStartupMessage(paste0("animl-py version conflicts with current version.\n",
+                                     "To update animl-py, run animl::update_animl_py()."))
+      }
+      # correct version
+      else{
+        packageStartupMessage(paste0("animl successfully loaded."))
+        # assign to internal variable
+        assign("animl_py", animl_py, envir = .animl_internal)
+      }
     }
-    # animl-py not yet installed
+    # animl_env exists but animl-py not installed
     else{
-      packageStartupMessage("\n3. Installing animl-py...")
-      package <- sprintf("animl==%s", animl_version)
-      reticulate::use_condaenv(py_env)
-      reticulate::py_install(package, pip=TRUE)
+      packageStartupMessage(paste0("Python environment found but animl-py not installed.\n",
+                                   "See `?animl::animl_install_instructions`."))
     }
-    return(TRUE)
   }
+  invisible()
 }
 
 
 #' Load animl-py if available
 #'
+#' @param envname name of python environment
+#' @param python_version version of python to install
+#'
 #' @return animl-py module
 #' @export
 #'
 #' @examples
 #' \dontrun{animl_py <- load_animl_py()}
-load_animl_py <- function() {
-  if(reticulate::py_module_available("animl")){
-    animl_py <- reticulate::import("animl", delay_load = TRUE)
-    packageStartupMessage("animl-py loaded successfully.")
-    return(animl_py)
+animl_install <- function(envname = "animl_env", python_version = "3.12") {
+  if (!interactive()) {
+    stop("animl_install() must be run interactively.",call. = FALSE)
+  }
+  if (!requireNamespace("reticulate", quietly = TRUE)) {
+    stop("Please install the 'reticulate' package first: install.packages('reticulate')", call. = FALSE)
+  }
+  
+  # 1. Load environment if exists
+  packageStartupMessage(sprintf("1. Loading Python Environment (%s)...", envname))
+  try_error <- try(reticulate::use_virtualenv(envname, required = TRUE), silent=TRUE)
+  
+  # 2. Install if not exists
+  if (inherits(try_error, "try-error")) {
+    packageStartupMessage(try_error)
+    # 2. Create new environment
+    packageStartupMessage("\n", sprintf("2. Creating a Python Environment (%s)", envname))
+    animl_path <- tryCatch(expr = create_pyenv(python_version = python_version, envname = envname),
+                           error = function(e) stop(e, "An error occur when animl_install was creating the Python Environment."))
+    packageStartupMessage("animl successfully installed. Restart R session to see changes.\n")
   }
+  # animl_env exists
   else{
-    packageStartupMessage('Animl load failed')
-    packageStartupMessage(reticulate::py_config())
+    # check animl-py installed
+    packageStartupMessage("\n2. Checking animl-py version...")
+    if(reticulate::py_module_available("animl")){
+      animl_py <- reticulate::import("animl", delay_load = TRUE)
+      current_version <- animl_py$'__version__'
+      # check version match
+      if (!identical(ANIML_VERSION, current_version)){
+        update_animl_py()
+      }
+    }
+    # animl-py not yet installed
+    else{
+      packageStartupMessage("\n3. Installing animl-py...")
+      package <- sprintf("animl==%s", ANIML_VERSION)
+      reticulate::py_install(package, pip=TRUE)
+      packageStartupMessage("animl successfully installed. Restart R session to see changes.\n")
+    }
   }
+  invisible()
 }
 
 
-#' Update animl-py version
+#' Update animl-py version for the given environment
 #'
-#' @param py_env name of python environment
-#' @param animl_version version of animl to install
+#' @param envname name of python environment
 #'
 #' @returns None
 #' @export
 #'
 #' @examples
-#' \dontrun{update_animl_py(py_env = "animl_env", animl_version = ANIML_VERSION)}
-update_animl_py <- function(py_env = "animl_env",
-                            animl_version = ANIML_VERSION) {
+#' \dontrun{update_animl_py(py_env = "animl_env")}
+update_animl_py <- function(envname = "animl_env") {
+  if (!interactive()) {
+    stop(paste0("update_animl_py() must be run interactively.",
+                "For non-interactive/CI installs, use system installers or CI actions.",
+                call. = FALSE))
+  }
+  if (!requireNamespace("reticulate", quietly=TRUE)) {
+    stop("Please install the 'reticulate' package first: install.packages('reticulate')", call. = FALSE)
+  }
+  
   # load animl-py, check version
   packageStartupMessage("animl-py version mismatch, reinstalling...")
-  reticulate::use_condaenv(py_env)
-  reticulate::py_install(sprintf("animl==%s", animl_version), pip=TRUE)
+  reticulate::use_virtualenv(envname)
+  reticulate::py_install(sprintf("animl==%s", ANIML_VERSION), pip=TRUE)
+  packageStartupMessage("animl successfully installed. Restart R session to see changes.\n")
 }
 
 
+#' Install python if necessary and create the environment animl_env 
+#'
+#' @param envname name of the conda environment to create / use (default "animl-py")
+#' @param python_version python version to add to environment
+#' 
+#' @return invisible TRUE on success, otherwise stops or returns FALSE invisibly on failure
+#' @export
+create_pyenv <- function(envname = "animl_env", python_version = "3.12") {
+  if (!interactive()) {
+    stop(paste0("create_pyenv() must be run interactively.",
+                "For non-interactive/CI installs, use system installers or CI actions.",
+                call. = FALSE))
+  }
+  if (!requireNamespace("reticulate", quietly=TRUE)) {
+    stop("Please install the 'reticulate' package first: install.packages('reticulate')", call. = FALSE)
+  }
+  
+  # 1) Check is Python is installed and greater than 3.12
+  check_python(initialize=TRUE)
+  
+  # 2) Create venv
+  packageStartupMessage(paste0("Creating virtual environment '", envname, "' ..."))
+  reticulate::virtualenv_create(envname=envname, python_version=python_version)
+  
+  # 3) Install animl-py
+  packageStartupMessage("\n3. Installing animl-py...")
+  package <- sprintf("animl==%s", ANIML_VERSION)
+  reticulate::py_install(package, envname=envname, pip=TRUE)
+}
 
 
 #' Check that the python version is compatible with the current version of animl-py
 #'
+#' @param python_version version of python to install
 #' @param initialize load reticulate library if true
 #'
 #' @returns none
@@ -112,50 +177,76 @@ update_animl_py <- function(py_env = "animl_env",
 #'
 #' @examples
 #' \dontrun{check_python(initialize=FALSE)}
-check_python <- function(initialize = TRUE) {
+check_python <- function(python_version = "3.12", initialize = TRUE) {
+  if (!interactive()) {
+    stop(paste0("check_python() must be run interactively.",
+                "For non-interactive/CI installs, use system installers or CI actions.",
+                call. = FALSE))
+  }
+  if (!requireNamespace("reticulate", quietly=TRUE)) {
+    stop("Please install the 'reticulate' package first: install.packages('reticulate')", call. = FALSE)
+  }
+  # check if python is available
   python_test <- reticulate::py_available(initialize=initialize)
-  if (python_test) { py_version <- reticulate::py_discover_config()[["version"]]
+  if (python_test) { 
+    current_version <- reticulate::py_discover_config()[["version"]]
+    # check if correct version
+    if (!identical(as.character(current_version), "3.12")) {
+      packageStartupMessage(sprintf("Python %s not found, installing...", python_version))
+      reticulate::install_python(version=python_version)
+    }
+    # 3.12 installed
+    else{
+      packageStartupMessage(sprintf("Found Python version %s compatible with animl.", current_version))
+    }
   } 
-  else { stop("Unable to find a Python installation.",
-              "Please install Python befor running animl_initiaialzer().",
-              "For more details run reticulate::py_discover_config()")
+  # no python installed at all
+  else {
+    packageStartupMessage(sprintf("Python %s not found, installing...", python_version))
+    reticulate::install_python(version=python_version)
   }
-  if (utils::compareVersion(as.character(py_version), "3.12") == -1) {
-    stop("animl needs Python >=3.12")
-  }
-  packageStartupMessage(sprintf("Python version %s compatible with animl.", py_version))
+  invisible()
 }
 
 
-
-#' Create the miniconda environment animl_env 
+#' Delete the animl_env environment
 #'
-#' @param python_version python version for new environment
-#' @param py_env name of python environment
+#' @param envname python environment to remove
 #'
-#' @returns python path for new environment
+#' @returns none
 #' @export
 #'
 #' @examples
-#' \dontrun{create_env("3.12", py_env='animl_env')}
-create_pyenv <- function(python_version, py_env = "animl_env") {
-  #Check is Python is greather than 3.9
-  check_python(initialize=TRUE)
-  pyenv_path <- reticulate::conda_create(py_env, python_version = python_version)
-  print(pyenv_path)
-  pyenv_path
+#' \dontrun{delete_pyenv('animl_env')}
+delete_pyenv <- function(envname = "animl_env") {
+  if (!interactive()) {
+    stop(paste0("delete_pyenv() must be run interactively.",
+                "For non-interactive/CI installs, use system installers or CI actions.",
+                call. = FALSE))
+  }
+  if (!requireNamespace("reticulate", quietly=TRUE)) {
+    stop("Please install the 'reticulate' package first: install.packages('reticulate')", call. = FALSE)
+  }
+  
+  try(reticulate::virtualenv_remove(envname), silent = TRUE)
 }
 
 
-#' Delete the animl_env environment
-#'
-#' @param py_env python environment to remove
-#'
-#' @returns none
+#' Installation Instructions for animl-r Python dependencies
+#' 
+#' 
 #' @export
-#'
-#' @examples
-#' \dontrun{delete_pyenv('animl_env')}
-delete_pyenv <- function(py_env = "animl_env") {
-  try(reticulate::conda_remove(py_env), silent = TRUE)
+animl_install_instructions <- function() {
+  cat(
+    "animl: instructions to prepare a Python environment for optional features\n\n",
+    "Run animl::animl_install() to set up Python 3.12 environment and install animl-py dependency.\n\n",
+    "Virtualenv/pip alternative (requires python 3.12 installed):\n",
+    "  python -m venv ~/venvs/animl_env\n",
+    "  source ~/venvs/animl_env/bin/activate\n",
+    "  pip install --upgrade pip\n",
+    "  pip install animl\n\n",
+    "Restart R session and reload animl library.",
+    sep = ""
+  )
+  invisible(NULL)
 }
diff --git a/R/reid.R b/R/reid.R
index f995b1f..e3ff548 100644
--- a/R/reid.R
+++ b/R/reid.R
@@ -9,7 +9,7 @@
 #' @examples
 #' \dontrun{miew = load_miewid("miewid_v3.bin")}
 load_miew <- function(file_path, device=NULL){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$load_miew(file_path, device=device)
 }
 
@@ -30,7 +30,7 @@ load_miew <- function(file_path, device=NULL){
 #' \dontrun{embeddings = extract_embeddings(miew, manifest)}
 extract_miew_embeddings <- function(miew_model, manifest, file_col="filepath", 
                                     batch_size=1, num_workers=1, device=NULL){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$extract_miew_embeddings(miew_model, manifest, file_col=file_col,
                                    batch_size=as.integer(batch_size), 
                                    num_workers=as.integer(num_workers),
@@ -48,7 +48,7 @@ extract_miew_embeddings <- function(miew_model, manifest, file_col="filepath",
 #' @examples
 #' \dontrun{cleaned_dist <- remove_diagonal(dist_matrix)}
 remove_diagonal <- function(A){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$remove_diagonal(A)
 }
 
@@ -63,7 +63,7 @@ remove_diagonal <- function(A){
 #' @examples
 #' \dontrun{dist_matrix <- euclidean_squared_distance(embeddings, embeddings)}
 euclidean_squared_distance <- function(input1, input2){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$euclidean_squared_distance(input1, input2)
 }
 
@@ -78,7 +78,7 @@ euclidean_squared_distance <- function(input1, input2){
 #' @examples
 #' \dontrun{dist_matrix <- cosine_distance(embeddings, embeddings)}
 cosine_distance <- function(input1, input2){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$cosine_distance(input1, input2)
 }
 
@@ -96,7 +96,7 @@ cosine_distance <- function(input1, input2){
 #' @examples
 #' \dontrun{dist_matrix <- compute_distance_matrix(embeddings, embeddings, metric='cosine')}
 compute_distance_matrix <- function(input1, input2, metric='euclidean'){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$compute_distance_matrix(input1, input2, metric=metric)
 }
 
@@ -115,6 +115,6 @@ compute_distance_matrix <- function(input1, input2, metric='euclidean'){
 #' dist_matrix <- compute_batched_distance_matrix(query_embeddings, database_embeddings, 
 #'                                                metric='cosine', batch_size=12)}
 compute_batched_distance_matrix <- function(input1, input2, metric='cosine', batch_size=10){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$compute_batched_distance_matrix(input1, input2, metric=metric, batch_size=batch_size)
 }  
\ No newline at end of file
diff --git a/R/split.R b/R/split.R
index 13f86c9..c223e51 100644
--- a/R/split.R
+++ b/R/split.R
@@ -77,7 +77,7 @@ get_animals <- function(manifest){
 train_val_test <- function(manifest, label_col="class", file_col='filepath', 
                            conf_col = 'confidence', out_dir=NULL,
                            val_size= 0.1, test_size = 0.1, seed=42){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$train_val_test(manifest, label_col="class", file_col='filepath', 
                           conf_col = 'confidence', out_dir=NULL,
                           val_size= 0.1, test_size = 0.1, seed=42)
diff --git a/R/train.R b/R/train.R
index 1a86f1d..ccc5b32 100644
--- a/R/train.R
+++ b/R/train.R
@@ -16,7 +16,7 @@
 #' @examples
 #' \dontrun{train_main('training_cfg.yml')}
 train_main <- function(cfg){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$train_main(cfg)
 }
 
@@ -31,6 +31,6 @@ train_main <- function(cfg){
 #' @examples
 #' \dontrun{test_main('training_cfg.yml')}
 test_main <- function(cfg){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$test_main(cfg)
 }
\ No newline at end of file
diff --git a/R/video_processing.R b/R/video_processing.R
index ca6aa48..a6640c3 100644
--- a/R/video_processing.R
+++ b/R/video_processing.R
@@ -7,7 +7,7 @@
 #' @param out_dir directory to save frames to if not null
 #' @param file_col string value indexing which column contains file paths
 #' @param parallel Toggle for parallel processing, defaults to FALSE
-#' @param num_workers number of processors to use if parallel, defaults to 1
+#' @param num_workers number of processors to use if parallel, defaults to 4
 #'
 #' @return dataframe of still frames for each video
 #' @export
@@ -17,10 +17,10 @@
 #' frames <- extract_frames(manifest, out_dir = "C:\\Users\\usr\\Videos\\", frames = 5)
 #' }
 extract_frames <- function(files, frames=5, fps=NULL, out_file=NULL, out_dir=NULL,
-                           file_col="filepath", parallel=FALSE, num_workers=1){
+                           file_col="filepath", parallel=TRUE, num_workers=4){
   if (!is.null(fps)){ fps <- as.integer(fps) }
   if (!is.null(frames)){ frames <- as.integer(frames) }
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$extract_frames(files, frames=frames, fps=fps, out_file=out_file, out_dir=out_dir,
                           file_col=file_col, parallel=parallel, num_workers=as.integer(num_workers))
 }
@@ -38,6 +38,6 @@ extract_frames <- function(files, frames=5, fps=NULL, out_file=NULL, out_dir=NUL
 #' @examples
 #' \dontrun{get_frame_as_image('/example/path/to/video.mp4', frame=213)}
 get_frame_as_image <- function(video_path, frame=0){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
-  animl_py$get_frame_as_image(video_path, frame=frame)
+  animl_py <- .animl_internal$animl_py
+  animl_py$get_frame_as_image(video_path, frame=as.integer(frame))
 }
\ No newline at end of file
diff --git a/R/visualization.R b/R/visualization.R
index 72290df..768c1a7 100644
--- a/R/visualization.R
+++ b/R/visualization.R
@@ -20,7 +20,7 @@
 plot_box <- function(rows, file_col='filepath', min_conf=0, label_col=NULL,
                      show_confidence=FALSE, colors=NULL, detector_labels=NULL,
                      return_img=FALSE) {
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$plot_box(rows, file_col=file_col, min_conf=min_conf, label_col=label_col,
                     show_confidence=show_confidence, colors=colors, detector_labels=detector_labels,
                     return_img=return_img)
@@ -50,7 +50,7 @@ plot_box <- function(rows, file_col='filepath', min_conf=0, label_col=NULL,
 plot_all_bounding_boxes <- function(manifest, out_dir, file_col='filepath', min_conf=0.1, 
                                     label_col=FALSE, show_confidence=FALSE,
                                     colors=NULL, detector_labels=NULL){
-  animl_py <- get("animl_py", envir = parent.env(environment()))
+  animl_py <- .animl_internal$animl_py
   animl_py$plot_all_bounding_boxes(manifest, out_dir, file_col=file_col, min_conf=min_conf, 
                                    label_col=label_col, show_confidence=show_confidence,
                                    colors=colors, detector_labels=detector_labels)
diff --git a/R/zzz.R b/R/zzz.R
index 299c8e6..498e708 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,19 +1,27 @@
+.animl_internal <- new.env(parent = emptyenv())
+.animl_internal$animl_py <- NULL
+
 .onLoad <- function(libname, pkgname) {
-  animl_env_avail <- animl_install()
-  if (animl_env_avail) {
-    animl_py <- load_animl_py()
-    assign("animl_py", animl_py, envir = parent.env(environment()))
-  }
-  else{
-    .stop_animl_failed()
-  }
+  animl_py <- load_animl()
+  invisible()
 }
 
-.stop_animl_failed <- function(){
+
+.onAttach <- function(libname, pkgname) {
+  # Only give a very small hint to interactive users (not required)
   if (interactive()) {
-    warning('animl_env load failed')
-  } else {
-    # non-interactive / scripts should get a clean error
-    stop('animl_env load failed', call. = FALSE)
+    if (requireNamespace("reticulate", quietly = TRUE)) {
+      pkgmsg <- paste0(
+        "animl: requires Python 3.12 and animl-py 3.2.0. If animl fails to load, ",
+        "see `?animl::animl_install_instructions`."
+      )
+    } else {
+      pkgmsg <- paste0(
+        "animl: For all features install the 'reticulate' package ",
+        "(install.packages('reticulate')) and follow `?animl::animl_install_instructions`."
+      )
+    }
+    packageStartupMessage(pkgmsg)
   }
+  invisible()
 }
\ No newline at end of file
diff --git a/examples/Workflow_animl.R b/examples/Workflow_animl.R
index 8f6c46d..6a9cb92 100644
--- a/examples/Workflow_animl.R
+++ b/examples/Workflow_animl.R
@@ -75,8 +75,7 @@ manifest <- sequence_classification(animals, empty=empty, pred_raw, classes=clas
 #===============================================================================
 
 #symlink species predictions
-alldata <- export_folders(manifest, linkdir)
-write.csv(alldata, results)
+alldata <- export_folders(manifest, linkdir, out_file = results_file)
 
 
 #===============================================================================
diff --git a/man/animl_install.Rd b/man/animl_install.Rd
index b8c10eb..cbf548d 100644
--- a/man/animl_install.Rd
+++ b/man/animl_install.Rd
@@ -2,30 +2,21 @@
 % Please edit documentation in R/install.R
 \name{animl_install}
 \alias{animl_install}
-\title{Create a miniconda environment for animl and install animl-py}
+\title{Load animl-py if available}
 \usage{
-animl_install(
-  py_env = "animl_env",
-  animl_version = ANIML_VERSION,
-  python_version = "3.12",
-  confirm = TRUE
-)
+animl_install(envname = "animl_env", python_version = "3.12")
 }
 \arguments{
-\item{py_env}{name of python environment}
-
-\item{animl_version}{version of animl to install}
+\item{envname}{name of python environment}
 
 \item{python_version}{version of python to install}
-
-\item{confirm}{allow user input}
 }
 \value{
-none
+animl-py module
 }
 \description{
-Create a miniconda environment for animl and install animl-py
+Load animl-py if available
 }
 \examples{
-\dontrun{animl_install("animl_env", ANIML_VERSION, python_version="3.9", confirm=TRUE)}
+\dontrun{animl_py <- load_animl_py()}
 }
diff --git a/man/animl_install_instructions.Rd b/man/animl_install_instructions.Rd
new file mode 100644
index 0000000..f902f94
--- /dev/null
+++ b/man/animl_install_instructions.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/install.R
+\name{animl_install_instructions}
+\alias{animl_install_instructions}
+\title{Installation Instructions for animl-r Python dependencies}
+\usage{
+animl_install_instructions()
+}
+\description{
+Installation Instructions for animl-r Python dependencies
+}
diff --git a/man/check_python.Rd b/man/check_python.Rd
index 299c2c7..a2172b7 100644
--- a/man/check_python.Rd
+++ b/man/check_python.Rd
@@ -4,9 +4,11 @@
 \alias{check_python}
 \title{Check that the python version is compatible with the current version of animl-py}
 \usage{
-check_python(initialize = TRUE)
+check_python(python_version = "3.12", initialize = TRUE)
 }
 \arguments{
+\item{python_version}{version of python to install}
+
 \item{initialize}{load reticulate library if true}
 }
 \value{
diff --git a/man/create_pyenv.Rd b/man/create_pyenv.Rd
index cbaa398..64aa95e 100644
--- a/man/create_pyenv.Rd
+++ b/man/create_pyenv.Rd
@@ -2,21 +2,18 @@
 % Please edit documentation in R/install.R
 \name{create_pyenv}
 \alias{create_pyenv}
-\title{Create the miniconda environment animl_env}
+\title{Install python if necessary and create the environment animl_env}
 \usage{
-create_pyenv(python_version, py_env = "animl_env")
+create_pyenv(envname = "animl_env", python_version = "3.12")
 }
 \arguments{
-\item{python_version}{python version for new environment}
+\item{envname}{name of the conda environment to create / use (default "animl-py")}
 
-\item{py_env}{name of python environment}
+\item{python_version}{python version to add to environment}
 }
 \value{
-python path for new environment
+invisible TRUE on success, otherwise stops or returns FALSE invisibly on failure
 }
 \description{
-Create the miniconda environment animl_env
-}
-\examples{
-\dontrun{create_env("3.12", py_env='animl_env')}
+Install python if necessary and create the environment animl_env
 }
diff --git a/man/delete_pyenv.Rd b/man/delete_pyenv.Rd
index 6bd522d..bb0af3a 100644
--- a/man/delete_pyenv.Rd
+++ b/man/delete_pyenv.Rd
@@ -4,10 +4,10 @@
 \alias{delete_pyenv}
 \title{Delete the animl_env environment}
 \usage{
-delete_pyenv(py_env = "animl_env")
+delete_pyenv(envname = "animl_env")
 }
 \arguments{
-\item{py_env}{python environment to remove}
+\item{envname}{python environment to remove}
 }
 \value{
 none
diff --git a/man/export_folders.Rd b/man/export_folders.Rd
index 3b2e750..62d05f1 100644
--- a/man/export_folders.Rd
+++ b/man/export_folders.Rd
@@ -17,11 +17,11 @@ export_folders(
 \arguments{
 \item{manifest}{DataFrame of classified images}
 
-\item{out_dir}{Destination directory for symlinks}
+\item{out_dir}{Destination directory for species folders}
 
 \item{out_file}{if provided, save the manifest to this file}
 
-\item{label_col}{(str): specify 'prediction' for species or 'category' for megadetector class}
+\item{label_col}{specify 'prediction' for species or 'category' for megadetector class}
 
 \item{file_col}{Colun containing file paths}
 
diff --git a/man/export_timelapse.Rd b/man/export_timelapse.Rd
index afc89d5..69173c7 100644
--- a/man/export_timelapse.Rd
+++ b/man/export_timelapse.Rd
@@ -4,12 +4,12 @@
 \alias{export_timelapse}
 \title{Converts the Manifests to a csv file that contains columns needed for TimeLapse conversion in later step}
 \usage{
-export_timelapse(results, image_dir, only_animal = TRUE)
+export_timelapse(manifest, out_dir, only_animal = TRUE)
 }
 \arguments{
-\item{results}{a DataFrame that has entries of anuimal classification}
+\item{manifest}{a DataFrame that has entries of anuimal classification}
 
-\item{image_dir}{location of root directory where all images are stored (can contain subdirectories)}
+\item{out_dir}{location of root directory where all images are stored (can contain subdirectories)}
 
 \item{only_animal}{A bool that confirms whether we want only animal detctions or all}
 }
diff --git a/man/extract_frames.Rd b/man/extract_frames.Rd
index 850511f..f7af8c1 100644
--- a/man/extract_frames.Rd
+++ b/man/extract_frames.Rd
@@ -11,8 +11,8 @@ extract_frames(
   out_file = NULL,
   out_dir = NULL,
   file_col = "filepath",
-  parallel = FALSE,
-  num_workers = 1
+  parallel = TRUE,
+  num_workers = 4
 )
 }
 \arguments{
@@ -30,7 +30,7 @@ extract_frames(
 
 \item{parallel}{Toggle for parallel processing, defaults to FALSE}
 
-\item{num_workers}{number of processors to use if parallel, defaults to 1}
+\item{num_workers}{number of processors to use if parallel, defaults to 4}
 }
 \value{
 dataframe of still frames for each video
diff --git a/man/load_animl.Rd b/man/load_animl.Rd
new file mode 100644
index 0000000..b12422e
--- /dev/null
+++ b/man/load_animl.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/install.R
+\name{load_animl}
+\alias{load_animl}
+\title{Load animl-py if available}
+\usage{
+load_animl(envname = "animl_env", python_version = "3.12")
+}
+\arguments{
+\item{envname}{name of python environment}
+
+\item{python_version}{version of python to install}
+}
+\value{
+none
+}
+\description{
+Load animl-py if available
+}
+\examples{
+\dontrun{animl_install("animl_env", ANIML_VERSION, python_version="3.12")}
+}
diff --git a/man/load_animl_py.Rd b/man/load_animl_py.Rd
deleted file mode 100644
index 27664fa..0000000
--- a/man/load_animl_py.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/install.R
-\name{load_animl_py}
-\alias{load_animl_py}
-\title{Load animl-py if available}
-\usage{
-load_animl_py()
-}
-\value{
-animl-py module
-}
-\description{
-Load animl-py if available
-}
-\examples{
-\dontrun{animl_py <- load_animl_py()}
-}
diff --git a/man/save_classifier.Rd b/man/save_classifier.Rd
index c7d1ecb..3effba3 100644
--- a/man/save_classifier.Rd
+++ b/man/save_classifier.Rd
@@ -4,6 +4,15 @@
 \alias{save_classifier}
 \title{Save model state weights}
 \usage{
+save_classifier(
+  model,
+  out_dir,
+  epoch,
+  stats,
+  optimizer = NULL,
+  scheduler = NULL
+)
+
 save_classifier(
   model,
   out_dir,
@@ -27,11 +36,16 @@ save_classifier(
 \item{scheduler}{pytorch scheduler (optional)}
 }
 \value{
+None
+
 None
 }
 \description{
+Save model state weights
+
 Save model state weights
 }
 \examples{
 \dontrun{save_classifier(model, 'models/', 10, list(acc = 0.85))}
+\dontrun{save_classifier(model, 'models/', 10, list(acc = 0.85))}
 }
diff --git a/man/single_classification.Rd b/man/single_classification.Rd
index 1ddd9a9..3c66b95 100644
--- a/man/single_classification.Rd
+++ b/man/single_classification.Rd
@@ -4,7 +4,13 @@
 \alias{single_classification}
 \title{Get Maximum likelihood label for each Detection}
 \usage{
-single_classification(animals, empty, predictions_raw, class_list)
+single_classification(
+  animals,
+  empty,
+  predictions_raw,
+  class_list,
+  best = FALSE
+)
 }
 \arguments{
 \item{animals}{manifest of animal detections}
@@ -14,6 +20,8 @@ single_classification(animals, empty, predictions_raw, class_list)
 \item{predictions_raw}{softmaxed likelihoods from predict_species}
 
 \item{class_list}{list of class labels}
+
+\item{best}{whether to return one prediction per file}
 }
 \value{
 dataframe with prediction and confidence columns
diff --git a/man/update_animl_py.Rd b/man/update_animl_py.Rd
index c4a4743..b2a5160 100644
--- a/man/update_animl_py.Rd
+++ b/man/update_animl_py.Rd
@@ -2,21 +2,19 @@
 % Please edit documentation in R/install.R
 \name{update_animl_py}
 \alias{update_animl_py}
-\title{Update animl-py version}
+\title{Update animl-py version for the given environment}
 \usage{
-update_animl_py(py_env = "animl_env", animl_version = ANIML_VERSION)
+update_animl_py(envname = "animl_env")
 }
 \arguments{
-\item{py_env}{name of python environment}
-
-\item{animl_version}{version of animl to install}
+\item{envname}{name of python environment}
 }
 \value{
 None
 }
 \description{
-Update animl-py version
+Update animl-py version for the given environment
 }
 \examples{
-\dontrun{update_animl_py(py_env = "animl_env", animl_version = ANIML_VERSION)}
+\dontrun{update_animl_py(py_env = "animl_env")}
 }
diff --git a/man/update_labels_from_folders.Rd b/man/update_labels_from_folders.Rd
index d47133c..806ddd9 100644
--- a/man/update_labels_from_folders.Rd
+++ b/man/update_labels_from_folders.Rd
@@ -11,7 +11,7 @@ update_labels_from_folders(manifest, export_dir, unique_name = "uniquename")
 
 \item{export_dir}{directory to sort files into}
 
-\item{unique_name}{column name indicating a unique file name for each row}
+\item{unique_name}{column containing unique file names}
 }
 \value{
 dataframe with new "Species" column that contains the verified species