rename package to pathviewr

ropensci · Jan 14, 2021 · 52e559c · 52e559c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: pathviewR
+Package: pathviewr
 Title: Wrangle, Analyze, and Visualize Animal Movement Data
 Version: 0.9.4.9000
 Authors@R: 
@@ -51,5 +51,5 @@ Suggests:
     testthat,
     covr
 VignetteBuilder: knitr
-URL: https://github.com/vbaliga/pathviewR
-BugReports: https://github.com/vbaliga/pathviewR/issues
+URL: https://github.com/vbaliga/pathviewr
+BugReports: https://github.com/vbaliga/pathviewr/issues
diff --git a/LICENSE.md b/LICENSE.md
@@ -573,7 +573,7 @@ Also add information on how to contact you by electronic and paper mail.
 If the program does terminal interaction, make it output a short notice like this
 when it starts in an interactive mode:
 
-    pathviewR Copyright (C) 2020 Melissa S. Armstrong; Vikram B. Baliga; Eric R. Press
+    pathviewr Copyright (C) 2020 Melissa S. Armstrong; Vikram B. Baliga; Eric R. Press
     This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type 'show c' for details.

diff --git a/R/all_in_one_functions.R b/R/all_in_one_functions.R
@@ -1,4 +1,4 @@
-## Part of the pathviewR package
+## Part of the pathviewr package
 ## Last updated: 2020-09-17 VBB
 
 
@@ -9,7 +9,7 @@
 #' For an imported viewr object, run through the cleaning pipeline as desired
 #'
 #' @param obj_name The input viewr object; a tibble or data.frame with attribute
-#'   \code{pathviewR_steps} that includes \code{"viewr"}
+#'   \code{pathviewr_steps} that includes \code{"viewr"}
 #' @param relabel_viewr_axes default TRUE, should axes be relabeled?
 #' @param gather_tunnel_data default TRUE, should tunnel data be gathered?
 #' @param trim_tunnel_outliers default TRUE, outliers be trimmed?
@@ -26,19 +26,19 @@
 #' @param ... Additional arguments passed to any of the corresponding functions
 #'
 #' @details Each argument corresponds to a standalone function in
-#'   \code{pathviewR}. E.g. the parameter \code{relabel_viewr_axes} allows a
-#'   user to choose whether \code{pathviewR::relabel_viewr_axes()} is run
+#'   \code{pathviewr}. E.g. the parameter \code{relabel_viewr_axes} allows a
+#'   user to choose whether \code{pathviewr::relabel_viewr_axes()} is run
 #'   internally. Should the user desire to use any non-default parameter values
 #'   for any functions included here, they should be supplied to this function
 #'   as additional arguments formatted exactly as they would appear in their
 #'   corresponding function(s). E.g. if the "autodetect" feature in
-#'   \code{pathviewR::separate_trajectories()} is desired, add an argument
+#'   \code{pathviewr::separate_trajectories()} is desired, add an argument
 #'   \code{max_frame_gap = "autodetect"} to the arguments supplied to this
 #'   function.
 #'
 #' @return A viewr object (tibble or data.frame with attribute
-#'   \code{pathviewR_steps} that includes \code{"viewr"}) that has passed
-#'   through several \code{pathviewR} functions as desired by the user,
+#'   \code{pathviewr_steps} that includes \code{"viewr"}) that has passed
+#'   through several \code{pathviewr} functions as desired by the user,
 #'   resulting in data that have been cleaned and ready for analyses.
 #'
 #' @author Vikram B. Baliga
@@ -48,12 +48,12 @@
 #' @export
 #'
 #' @examples
-#' library(pathviewR)
+#' library(pathviewr)
 #'
 #' ## Import the example Motive data included in the package
 #' motive_data <-
-#'   read_motive_csv(system.file("extdata", "pathviewR_motive_example_data.csv",
-#'                              package = 'pathviewR'))
+#'   read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
+#'                              package = 'pathviewr'))
 #'
 #' motive_full <-
 #'   motive_data %>%
@@ -65,8 +65,8 @@
 #' ## function to combine these steps
 #' motive_import_and_clean <-
 #'   import_and_clean_viewr(
-#'     file_name = system.file("extdata", "pathviewR_motive_example_data.csv",
-#'                             package = 'pathviewR'),
+#'     file_name = system.file("extdata", "pathviewr_motive_example_data.csv",
+#'                             package = 'pathviewr'),
 #'     desired_percent = 50,
 #'     max_frame_gap = "autodetect",
 #'     span = 0.95

diff --git a/R/analytical_functions.R b/R/analytical_functions.R
@@ -1,4 +1,4 @@
-## Part of the pathviewR package
+## Part of the pathviewr package
 ## Last updated: 2020-09-05 VBB
 
 ################################## get_velocity ################################
@@ -9,7 +9,7 @@
 #' (see Details)
 #'
 #' @param obj_name The input viewr object; a tibble or data.frame with attribute
-#'   \code{pathviewR_steps} that includes \code{"viewr"}
+#'   \code{pathviewr_steps} that includes \code{"viewr"}
 #' @param time_col Name of the column containing time
 #' @param length_col Name of the column containing length dimension
 #' @param width_col Name of the column containing width dimension
@@ -20,7 +20,7 @@
 #'   the object? If so, enter a numeric. If not, keep NA.
 #' @param velocity_max Should data above a certain velocity be filtered out of
 #'   the object? If so, enter a numeric. If not, keep NA.
-#' @param ... Additional arguments passed to or from other pathviewR functions.
+#' @param ... Additional arguments passed to or from other pathviewr functions.
 #'
 #' @details Instantaneous velocity is not truly "instantaneous" but rather is
 #' approximated as the change in distance divided by change in time from one
@@ -44,8 +44,8 @@
 #' @examples
 #' ## Import the example Motive data included in the package
 #' motive_data <-
-#'   read_motive_csv(system.file("extdata", "pathviewR_motive_example_data.csv",
-#'                              package = 'pathviewR'))
+#'   read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
+#'                              package = 'pathviewr'))
 #'
 #' ## Clean the file. It is generally recommended to clean up to the
 #' ## "standarization" step before running get_velocity().
@@ -77,7 +77,7 @@ get_velocity <- function(obj_name,
                          ...) {
 
   # ## Check that it's a viewr object
-  # if (!any(attr(obj_name,"pathviewR_steps") == "viewr")) {
+  # if (!any(attr(obj_name,"pathviewr_steps") == "viewr")) {
   #   stop("This doesn't seem to be a viewr object")
   # }
 
@@ -141,8 +141,8 @@ Please check that you have entered the name of the height variable correctly.")
     obj_new <- dplyr::bind_cols(obj_name, res)
 
     ## Leave a note that we computed velocity via get_velocity()
-    attr(obj_new,"pathviewR_steps") <-
-      c(attr(obj_name,"pathviewR_steps"), "velocity_computed")
+    attr(obj_new,"pathviewr_steps") <-
+      c(attr(obj_name,"pathviewr_steps"), "velocity_computed")
 
   } else { ## if FALSE
     obj_new <- res
@@ -578,7 +578,7 @@ Please ensure there are only two columns, ordered x-axis first, y-axis second")
 #' experimental tunnel
 #'
 #' @param obj_name The input viewr object; a tibble or data.frame with attribute
-#'   \code{pathviewR_steps} that includes \code{"viewr"} and
+#'   \code{pathviewr_steps} that includes \code{"viewr"} and
 #'   \code{treatments_added}.
 #' @param simplify_output If TRUE, the returned object includes only the minimum
 #'   distance between the subject and the lateral/end walls. If FALSE, the
@@ -607,8 +607,8 @@ Please ensure there are only two columns, ordered x-axis first, y-axis second")
 #' @examples
 #'  ## Import sample data from package
 #' motive_data <-
-#'   read_motive_csv(system.file("extdata", "pathviewR_motive_example_data.csv",
-#'                               package = 'pathviewR'))
+#'   read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
+#'                               package = 'pathviewr'))
 #'
 #'  ## Process data up to and including insert_treatments()
 #' motive_data_full <-
@@ -640,12 +640,12 @@ calc_min_dist_v <- function(obj_name,
                             simplify_output = TRUE){
 
   ## Check that it's a viewr object
-  if (!any(attr(obj_name,"pathviewR_steps") == "viewr")){
+  if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
     stop("This doesn't seem to be a viewr object")
   }
 
   ## Check that insert_treatments() has been run
-  if (!any(attr(obj_name,"pathviewR_steps") == "treatments_added")){
+  if (!any(attr(obj_name,"pathviewr_steps") == "treatments_added")){
     stop("Please run insert_treatments() prior to use")
   }
 
@@ -732,12 +732,12 @@ calc_min_dist_v <- function(obj_name,
 
   ## return object and add note that minimum distaces were calculated
   if(simplify_output == TRUE){
-    attr(obj_simplify, "pathviewR_steps") <-
-      c(attr(obj_name, "pathviewR_steps"), "min_dist_calculated")
+    attr(obj_simplify, "pathviewr_steps") <-
+      c(attr(obj_name, "pathviewr_steps"), "min_dist_calculated")
     return(obj_simplify)
   } else {
-    attr(obj_name, "pathviewR_steps") <-
-      c(attr(obj_name, "pathviewR_steps"), "min_dist_calculated")
+    attr(obj_name, "pathviewr_steps") <-
+      c(attr(obj_name, "pathviewr_steps"), "min_dist_calculated")
     return(obj_name)
   }
 }
@@ -749,7 +749,7 @@ calc_min_dist_v <- function(obj_name,
 #' experimental tunnel
 #'
 #' @param obj_name The input viewr object; a tibble or data.frame with attribute
-#'   \code{pathviewR_steps} that include \code{"viewr"} and
+#'   \code{pathviewr_steps} that include \code{"viewr"} and
 #'   \code{treatments_added}.
 #'
 #' @return A tibble or data.frame with added variables for
@@ -769,8 +769,8 @@ calc_min_dist_v <- function(obj_name,
 #' @examples
 #' ## Import sample data from package
 #'  flydra_data <-
-#'  read_flydra_mat(system.file("extdata", "pathviewR_flydra_example_data.mat",
-#'                                package = 'pathviewR'),
+#'  read_flydra_mat(system.file("extdata", "pathviewr_flydra_example_data.mat",
+#'                                package = 'pathviewr'),
 #'                                subject_name = "birdie_sanders")
 #'
 #'    ## Process data up to and including insert_treatments()
@@ -802,12 +802,12 @@ calc_min_dist_v <- function(obj_name,
 calc_min_dist_box <- function(obj_name){
 
   ## Check that it's a viewr object
-  if (!any(attr(obj_name,"pathviewR_steps") == "viewr")) {
+  if (!any(attr(obj_name,"pathviewr_steps") == "viewr")) {
     stop("This doesn't seem to be a viewr object")
   }
 
   ## Check that insert_treatments() has been run
-  if (!any(attr(obj_name,"pathviewR_steps") == "treatments_added")){
+  if (!any(attr(obj_name,"pathviewr_steps") == "treatments_added")){
     stop("Please run insert_treatments() prior to use")
   }
 
@@ -823,7 +823,7 @@ calc_min_dist_box <- function(obj_name){
            obj_name$tunnel_length/2 + obj_name$position_length)
 
   ## Leave note that minimum distances were calculated
-  attr(obj_name, "pathviewR_steps") <- c(attr(obj_name, "pathviewR_steps"),
+  attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
                                          "min_dist_calculated")
 
 
@@ -836,15 +836,15 @@ calc_min_dist_box <- function(obj_name){
 #' Estimate visual angles from a subject's perspective in an experimental tunnel
 #'
 #' @param obj_name The input viewr object; a tibble or data.frame with
-#' attributes \code{pathviewR_steps} that include \code{"viewr"}
+#' attributes \code{pathviewr_steps} that include \code{"viewr"}
 #' and \code{min_dist_calculated}.
 #'
 #' @details \code{get_vis_angle()} assumes the following:
 #' - The subject's gaze is fixed at the point on the either side of the tunnel
 #' that minimizes the distance to visual stimuli and therefore maximizes visual
 #' angles.
 #' - The subject's head is facing parallel to the length axis of the tunnel.
-#' Visual perception functions in future versions of pathviewR will integrate
+#' Visual perception functions in future versions of pathviewr will integrate
 #' head orientation coordinates.
 #' Angles are reported in radians/cycle (\code{vis_angle_pos_rad}) and
 #' degrees/cycle (\code{vis_angle_pos_deg}).
@@ -863,11 +863,11 @@ calc_min_dist_box <- function(obj_name){
 #' @examples
 #'  ## Import sample data from package
 #' motive_data <-
-#'   read_motive_csv(system.file("extdata", "pathviewR_motive_example_data.csv",
-#'                               package = 'pathviewR'))
+#'   read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
+#'                               package = 'pathviewr'))
 #' flydra_data <-
-#'   read_flydra_mat(system.file("extdata", "pathviewR_flydra_example_data.mat",
-#'                               package = 'pathviewR'),
+#'   read_flydra_mat(system.file("extdata", "pathviewr_flydra_example_data.mat",
+#'                               package = 'pathviewr'),
 #'                               subject_name = "birdie_sanders")
 #'
 #'  ## Process data up to and including get_min_dist()
@@ -918,12 +918,12 @@ calc_min_dist_box <- function(obj_name){
 get_vis_angle <- function(obj_name){
 
   ## Check that it's a viewr object
-  if (!any(attr(obj_name,"pathviewR_steps") == "viewr")){
+  if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
     stop("This doesn't seem to be a viewr object")
   }
 
   ## Check that calc_min_dist() has been run
-  if (!any(attr(obj_name, "pathviewR_steps") == "min_dist_calculated")){
+  if (!any(attr(obj_name, "pathviewr_steps") == "min_dist_calculated")){
     stop("Please run calc_min_dist_v() or calc_min_dist_box() prior to use")
   }
 
@@ -947,7 +947,7 @@ get_vis_angle <- function(obj_name){
   obj_name$vis_angle_end_deg <- rad_2_deg(obj_name$vis_angle_end_rad)
 
   ## Leave a note that visual angles were calculated
-  attr(obj_name, "pathviewR_steps") <- c(attr(obj_name, "pathviewR_steps"),
+  attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
                                          "vis_angles_calculated")
   return(obj_name)
 }
@@ -959,15 +959,15 @@ get_vis_angle <- function(obj_name){
 #' perspective in an experimental tunnel.
 #'
 #' @param obj_name The input viewr object; a tibble or data.frame with attribute
-#' \code{pathviewR_steps} that includes \code{"viewr"} and
+#' \code{pathviewr_steps} that includes \code{"viewr"} and
 #' \code{vis_angles_calculated}.
 #'
 #' @details \code{get_sf()} assumes the following:
 #' - The subject's gaze is fixed at the point on the either side of the tunnel
 #' that minimizes the distance to visual stimuli and therefore maximizes visual
 #' angles.
 #' - The subject's head is facing parallel to the length axis of the tunnel.
-#' Visual perception functions in future versions of pathviewR will integrate
+#' Visual perception functions in future versions of pathviewr will integrate
 #' head orientation coordinates.
 #' Spatial frequency is reported in cycles/degree and is the inverse of visual
 #' angle (degrees/cycle).
@@ -985,11 +985,11 @@ get_vis_angle <- function(obj_name){
 #' @examples
 #'  ## Import sample data from package
 #' motive_data <-
-#'   read_motive_csv(system.file("extdata", "pathviewR_motive_example_data.csv",
-#'                               package = 'pathviewR'))
+#'   read_motive_csv(system.file("extdata", "pathviewr_motive_example_data.csv",
+#'                               package = 'pathviewr'))
 #' flydra_data <-
-#'   read_flydra_mat(system.file("extdata", "pathviewR_flydra_example_data.mat",
-#'                               package = 'pathviewR'),
+#'   read_flydra_mat(system.file("extdata", "pathviewr_flydra_example_data.mat",
+#'                               package = 'pathviewr'),
 #'                               subject_name = "birdie_sanders")
 #'
 #'  ## Process data up to and including get_vis_angle()
@@ -1042,12 +1042,12 @@ get_vis_angle <- function(obj_name){
 get_sf <- function(obj_name){
 
   ## Check that it's a viewr object
-  if (!any(attr(obj_name,"pathviewR_steps") == "viewr")){
+  if (!any(attr(obj_name,"pathviewr_steps") == "viewr")){
     stop("This doesn't seem to be a viewr object")
   }
 
   ## Check that get_vis_angle() has been run
-  if (!any(attr(obj_name,"pathviewR_steps") == "vis_angles_calculated")){
+  if (!any(attr(obj_name,"pathviewr_steps") == "vis_angles_calculated")){
     stop("Please run get_vis_angle() prior to use")
   }
 
@@ -1057,7 +1057,7 @@ get_sf <- function(obj_name){
   obj_name$sf_end <- 1/obj_name$vis_angle_end_deg
 
   ## Leave a note that visual angles were calculated
-  attr(obj_name, "pathviewR_steps") <- c(attr(obj_name, "pathviewR_steps"),
+  attr(obj_name, "pathviewr_steps") <- c(attr(obj_name, "pathviewr_steps"),
                                          "sf_calculated")