Remove retistruct requirement and shorten documentation

inst/extdata/asalmon_mcw/main.r:2:1: style: Variable or function name should be snake_case.

LAMBDA_var <- 0.1 #Thin plate spline smoothing. Lambda=0 would be interpolation.
^~~~~~~~~~

inst/extdata/asalmon_mcw/main.r:3:1: style: Variable or function name should be snake_case.

RESOLUTION_var <- 500 #Plot width in pixels
^~~~~~~~~~~~~~

inst/extdata/asalmon_mcw/main.r:5:1: style: Lines should not be more than 80 characters.

#TODO change path. make sure this main.r script is just outside the diagram_retina folder.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/extdata/asalmon_mcw/main.r:8:1: style: Lines should not be more than 80 characters.

#todo verify these. see the tutorial here: https://github.com/bc/retina/blob/master/tutorial.md search for the part that starts with "#[V point of the tear,"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/extdata/asalmon_mcw/main.r:10:10: style: Commas should always have a space after.

    c(59,52,67),
         ^

inst/extdata/asalmon_mcw/main.r:10:13: style: Commas should always have a space after.

    c(59,52,67),
            ^

inst/extdata/asalmon_mcw/main.r:11:10: style: Commas should always have a space after.

    c(79,73,85),
         ^

inst/extdata/asalmon_mcw/main.r:11:13: style: Commas should always have a space after.

    c(79,73,85),
            ^

inst/extdata/asalmon_mcw/main.r:12:10: style: Commas should always have a space after.

    c(34,31,37))
         ^

inst/extdata/asalmon_mcw/main.r:12:13: style: Commas should always have a space after.

    c(34,31,37))
            ^

inst/extdata/asalmon_mcw/main.r:15:1: style: Lines should not be more than 80 characters.

assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/extdata/asalmon_mcw/main.r:15:22: style: Only use double-quotes.

assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
                     ^~~~~~

inst/extdata/asalmon_mcw/main.r:15:77: style: Put spaces around all infix operators.

assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
                                                                           ~^~

inst/extdata/asalmon_mcw/main.r:15:101: style: Put spaces around all infix operators.

assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
                                                                                                   ~^~

inst/extdata/asalmon_mcw/main.r:29:21: style: Commas should never have a space before.

        height = 45 ,# height of the counting frame in microns
                   ~^

inst/extdata/asalmon_mcw/main.r:29:22: style: Commas should always have a space after.

        height = 45 ,# height of the counting frame in microns
                     ^

inst/extdata/asalmon_mcw/main.r:34:28: style: Commas should never have a space before.

        extrapolate = TRUE ,          #Predicts densities to the equator.
                          ~^

inst/extdata/asalmon_mcw/main.r:36:1: style: Lines should not be more than 80 characters.

        rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/extdata/asalmon_mcw/main.r:37:22: style: Put spaces around all infix operators.

        plot_suppress=TRUE)
                    ~^~

inst/extdata/asalmon_mcw/main.r:39:29: style: Put spaces around all infix operators.

retinaplot(my_retina, lambda=0.001, polynomial_m=   2, rotation=0)
                           ~^~

inst/extdata/asalmon_mcw/main.r:39:49: style: Put spaces around all infix operators.

retinaplot(my_retina, lambda=0.001, polynomial_m=   2, rotation=0)
                                               ~^

inst/extdata/asalmon_mcw/main.r:39:64: style: Put spaces around all infix operators.

retinaplot(my_retina, lambda=0.001, polynomial_m=   2, rotation=0)
                                                              ~^~

inst/extdata/asalmon_mcw/main.r:40:10: style: Put spaces around all infix operators.

par(mfrow=c(2,2))
        ~^~

inst/extdata/asalmon_mcw/main.r:40:15: style: Commas should always have a space after.

par(mfrow=c(2,2))
              ^

R/composite.R:2:1: style: Lines should not be more than 80 characters.

##' @description This is a subfunction, that is useful when creating average maps.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/composite.R:3:1: style: Lines should not be more than 80 characters.

##' @param retina_list A list containing retina objects, with names(retina_list) all defined.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/composite.R:4:1: style: Lines should not be more than 80 characters.

##' @param rotation_indices Each value in this vector will correspond to the amount of rotation applied to each retina in the list.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/composite.R:5:1: style: Lines should not be more than 80 characters.

##' @param ... Arguments passed from other functions. You can access the thin plate spline interpolator here.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/composite.R:6:1: style: Lines should not be more than 80 characters.

##' @return sum_mat The sum of all retina objects in the list, with respect to the rotation indices.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/composite.R:9:16: warning: no visible global function definition for ‘mat_from_ret_obj’

    sum_mat <- mat_from_ret_obj(retina_list[[1]], rotation = 0, ...)
               ^~~~~~~~~~~~~~~~

R/composite.R:12:1: style: Lines should not be more than 80 characters.

        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i], 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/composite.R:12:85: style: Trailing whitespace is superfluous.

        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i], 
                                                                                    ^

R/matrix_retobj.R:3:1: style: Lines should not be more than 80 characters.

##' You can decide how much to rotate the retina before returning the matrix. You can also pass arguments to the polar plotter.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/matrix_retobj.R:6:1: style: Lines should not be more than 80 characters.

##' @param n the number by which to divide the matrix by. Useful when generating partial averages.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/matrix_retobj.R:7:1: style: Lines should not be more than 80 characters.

##' @param reflect logical, by default it is TRUE, in order to view the retina from outside the eye (rather than from within.)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/matrix_retobj.R:12:1: style: Lines should not be more than 80 characters.

mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/matrix_retobj.R:12:81: style: Trailing whitespace is superfluous.

mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE, 
                                                                                ^

R/matrix_retobj.R:17:1: style: Trailing whitespace is superfluous.

    
^~~~

R/matrix_retobj.R:20:1: style: Lines should not be more than 80 characters.

    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/matrix_retobj.R:20:87: style: Trailing whitespace is superfluous.

    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[, 
                                                                                      ^

R/matrix_retobj.R:25:1: style: Trailing whitespace is superfluous.

    
^~~~

R/matrix_retobj.R:27:1: style: Lines should not be more than 80 characters.

    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/matrix_retobj.R:27:88: style: Trailing whitespace is superfluous.

    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE, 
                                                                                       ^

R/matrix_retobj.R:28:1: style: Lines should not be more than 80 characters.

        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]], 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/matrix_retobj.R:28:26: style: Put spaces around all infix operators.

        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]], 
                        ~^~

R/matrix_retobj.R:28:93: style: Trailing whitespace is superfluous.

        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]], 
                                                                                            ^

R/matrix_retobj.R:30:5: style: Variable or function name should be snake_case.

    MAT <- map2fit[[2]]$z
    ^~~

R/matrix_retobj.R:32:15: style: Put spaces around all infix operators.

    return(MAT/n)
             ~^~

R/plotting_functions.R:3:1: style: Lines should not be more than 80 characters.

##' Extracts xy and falciform coordinates from datapoints collected from retistruct. Falc and Datapoints are stacked upon one another
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:5:1: style: Lines should not be more than 80 characters.

##' @param datapoints_from_retistruct data structure that comes from the datapoints.csv, which is automatically generated by Retistruct.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:7:1: style: Lines should not be more than 80 characters.

##' @return L list of pixel xy positions, and falciform coordinates in [1] and [2], respectively
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:9:1: style: Lines should not be more than 80 characters.

extract_xy_and_falciform <- function(datapoints_from_retistruct, number_of_sampling_sites) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:10:1: style: Lines should not be more than 80 characters.

    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:10:81: style: Trailing whitespace is superfluous.

    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites, 
                                                                                ^

R/plotting_functions.R:12:1: style: Lines should not be more than 80 characters.

    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:12:91: style: Trailing whitespace is superfluous.

    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[, 
                                                                                          ^

R/plotting_functions.R:16:1: style: Lines should not be more than 80 characters.

    falciform_coordinates <- datapoints_from_retistruct[(xy_len + 1):total_len, ]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:22:1: style: Lines should not be more than 80 characters.

##' ImageJ values don't always show up the right way, because Y values get larger and positive while moving down the image.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:24:1: style: Lines should not be more than 80 characters.

##' @param falciform_xy_coordinates 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:28:1: style: Lines should not be more than 80 characters.

reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:28:1: style: Variable and function names should not be longer than 30 characters.

reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:28:1: style: Variable or function name should be snake_case.

reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:29:1: style: Lines should not be more than 80 characters.

    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:29:5: style: Variable and function names should not be longer than 30 characters.

    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:31:52: style: Put spaces around all infix operators.

    half_of_vertical_pixels <- xy_img_dimensions[2]/2
                                                  ~^~

R/plotting_functions.R:32:1: style: Lines should not be more than 80 characters.

    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) * 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:32:86: style: Trailing whitespace is superfluous.

    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) * 
                                                                                     ^

R/plotting_functions.R:38:1: style: Lines should not be more than 80 characters.

##' Shows a visualization of the outline, as well as the location of each datapoint, with fit plot.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:40:1: style: Lines should not be more than 80 characters.

##' @param pixel_xy_positions 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:41:1: style: Lines should not be more than 80 characters.

##' @param z_vector numerical vector of density values for each of the coordinates
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:42:1: style: Lines should not be more than 80 characters.

##' @param xy_outline_points 2 columns of coordinate(X,Y) data in ImageJ pixel format for the outline coordinates.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:45:1: style: Lines should not be more than 80 characters.

traditional_flatmount_plot <- function(pixel_xy_positions, z_vector, xy_outline_points) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:46:1: style: Lines should not be more than 80 characters.

    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:46:12: warning: no visible global function definition for ‘Tps’, Did you mean 'Ops'?

    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
           ^~~

R/plotting_functions.R:47:5: warning: no visible global function definition for ‘set.panel’

    set.panel(2, 2)
    ^~~~~~~~~

R/plotting_functions.R:49:5: warning: no visible global function definition for ‘set.panel’

    set.panel()
    ^~~~~~~~~

R/plotting_functions.R:52:5: warning: no visible global function definition for ‘surface’

    surface(fit)  # Quick image/contour plot of GCV surface.
    ^~~~~~~

R/plotting_functions.R:61:1: style: Lines should not be more than 80 characters.

##' Shows a visualization of the outline, as well as the location of each datapoint so the user can identify where the tears are.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:64:1: style: Lines should not be more than 80 characters.

##' @param path_to_retina_data_folder The path to the folder that contains the outline.roi file.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:65:1: style: Lines should not be more than 80 characters.

##' @return roi_coordinates XY vals of pixel coordinates of the outline points, in order.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:69:1: style: Lines should not be more than 80 characters.

    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:69:19: warning: no visible global function definition for ‘read.ijroi’

    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
                  ^~~~~~~~~~

R/plotting_functions.R:70:1: style: Trailing whitespace is superfluous.

    
^~~~

R/plotting_functions.R:72:1: style: Lines should not be more than 80 characters.

    # format plots has the coordinate (0, 0) in the top left.  We have the coordinate
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:73:1: style: Lines should not be more than 80 characters.

    # (0, 0) in the bottom left. We need to transform P so that the outline appears
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:76:5: style: Variable or function name should be snake_case.

    roi_XY_coords <- roi_object$coords
    ^~~~~~~~~~~~~

R/plotting_functions.R:80:1: style: Trailing whitespace is superfluous.

    
^~~~

R/plotting_functions.R:81:1: style: Lines should not be more than 80 characters.

    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels", 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:81:81: style: Trailing whitespace is superfluous.

    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels", 
                                                                                ^

R/plotting_functions.R:83:1: style: Lines should not be more than 80 characters.

    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:83:83: style: Trailing whitespace is superfluous.

    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[, 
                                                                                  ^

R/plotting_functions.R:85:1: style: Lines should not be more than 80 characters.

    message("If you are getting this message, you are using a special feature. Contact me at brian.cohn@usc.edu and I will happily teach you how to use it.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:93:1: style: Lines should not be more than 80 characters.

##' @description Creates a markup.csv file. One of the dorsal_outline_index or nasal_outline_index must be filled in. Not both.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:96:1: style: Lines should not be more than 80 characters.

##' @param dorsal_outline_index The index of the point that points toward dorsal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:97:1: style: Lines should not be more than 80 characters.

##' @param nasal_outline_index The index of the opint that points toward nasal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:98:1: style: Lines should not be more than 80 characters.

##' @param path_to_retina_data_folder The path where the markup.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:100:1: style: Lines should not be more than 80 characters.

assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:100:107: style: Trailing whitespace is superfluous.

assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA, 
                                                                                                          ^

R/plotting_functions.R:103:1: style: Lines should not be more than 80 characters.

        ## https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:109:1: style: Lines should not be more than 80 characters.

        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:109:57: style: Commas should always have a space after.

        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string, 
                                                        ^

R/plotting_functions.R:109:62: style: Commas should always have a space after.

        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string, 
                                                             ^

R/plotting_functions.R:109:93: style: Trailing whitespace is superfluous.

        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string, 
                                                                                            ^

R/plotting_functions.R:112:1: style: Lines should not be more than 80 characters.

        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:112:58: style: Commas should always have a space after.

        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string, 
                                                         ^

R/plotting_functions.R:112:63: style: Commas should always have a space after.

        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string, 
                                                              ^

R/plotting_functions.R:112:94: style: Trailing whitespace is superfluous.

        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string, 
                                                                                             ^

R/plotting_functions.R:120:1: style: Lines should not be more than 80 characters.

    message(paste("Wrote markup file to ", output_path, "\n Ensure that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:130:1: style: Lines should not be more than 80 characters.

##' @param tear_coordinates_dataframe the dataframe of 3 columns, with c('V0','VB','VF'), and n columns, where n= number of tears
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:131:1: style: Lines should not be more than 80 characters.

##' @param path_to_retina_data_folder The path where the T.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:135:1: style: Lines should not be more than 80 characters.

assemble_tear_file <- function(tear_coordinates_dataframe, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:138:1: style: Lines should not be more than 80 characters.

    write.table(tear_coordinates_dataframe, output_path, sep = ",", row.names = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:139:1: style: Lines should not be more than 80 characters.

    message(paste("Wrote tear file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:147:1: style: Lines should not be more than 80 characters.

##' @param path_to_retina_data_folder The path where the P.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:151:1: style: Lines should not be more than 80 characters.

assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:151:1: style: Variable and function names should not be longer than 30 characters.

assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:155:1: style: Lines should not be more than 80 characters.

    message(paste("Wrote coordinates file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:177:1: style: Variable and function names should not be longer than 30 characters.

plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:177:59: style: Variable or function name should be snake_case.

plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
                                                          ^~~~~~~~~~~

R/plotting_functions.R:178:1: style: Lines should not be more than 80 characters.

    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)), 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:178:85: style: Trailing whitespace is superfluous.

    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)), 
                                                                                    ^

R/plotting_functions.R:180:1: style: Lines should not be more than 80 characters.

    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:180:95: style: Trailing whitespace is superfluous.

    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads, 
                                                                                              ^

R/plotting_functions.R:195:1: style: Lines should not be more than 80 characters.

    fields::image.plot(legend.only = TRUE, col = col, zlim = zlim, family = "Palatino")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:202:1: style: Lines should not be more than 80 characters.

##' @param endpoints a 4 element numeric vector describing the xy and x'y' for the line segment.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:206:1: style: Lines should not be more than 80 characters.

    segments(endpoints[1], endpoints[2], endpoints[3], endpoints[4], col = color_hex)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:216:1: style: Lines should not be more than 80 characters.

##' @param endpoints vector of 4 numerics, x,y and x',y' defining the line segment
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:217:1: style: Lines should not be more than 80 characters.

write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:217:1: style: Variable and function names should not be longer than 30 characters.

write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:226:1: style: Lines should not be more than 80 characters.

##' @description We do not need points plotted in the corners of the plotted circle.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:233:1: style: Lines should not be more than 80 characters.

nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:233:1: style: Variable and function names should not be longer than 30 characters.

nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:233:83: style: Trailing whitespace is superfluous.

nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix, 
                                                                                  ^

R/plotting_functions.R:235:5: style: Variable and function names should not be longer than 30 characters.

    matrix_position_is_within_the_circle <- function() {
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:238:5: style: Variable or function name should be snake_case.

    markNA <- matrix(minitics, ncol = spatial_res, nrow = spatial_res)
    ^~~~~~

R/plotting_functions.R:246:1: style: Lines should not be more than 80 characters.

##' @description Find the location to put the label around the circle at each of the lines
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:251:1: style: Variable and function names should not be longer than 30 characters.

compute_longitude_label_location <- function(axis.rads, outer_radius) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:251:46: style: Variable or function name should be snake_case.

compute_longitude_label_location <- function(axis.rads, outer_radius) {
                                             ^~~~~~~~~

R/plotting_functions.R:252:1: style: Lines should not be more than 80 characters.

    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:252:14: warning: no visible global function definition for ‘RMat’, Did you mean 'hat'?

    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
             ^~~~

R/plotting_functions.R:261:1: style: Lines should not be more than 80 characters.

    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:261:88: style: Trailing whitespace is superfluous.

    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius, 
                                                                                       ^

R/plotting_functions.R:263:5: warning: no visible global function definition for ‘draw_line_segments’

    draw_line_segments(endpoints)
    ^~~~~~~~~~~~~~~~~~

R/plotting_functions.R:267:1: style: Lines should not be more than 80 characters.

##' @description put a degree label at the ends of the endpoints for each longitude
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:274:1: style: Lines should not be more than 80 characters.

plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:274:38: style: Variable or function name should be snake_case.

plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
                                     ^~~~~~~~

R/plotting_functions.R:275:1: style: Lines should not be more than 80 characters.

    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad, 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:275:108: style: Trailing whitespace is superfluous.

    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad, 
                                                                                                           ^

R/plotting_functions.R:285:1: style: Variable or function name should be snake_case.

RMat <- function(radians) {
^~~~

R/plotting_functions.R:286:1: style: Lines should not be more than 80 characters.

    return(matrix(c(cos(radians), sin(radians), -sin(radians), cos(radians)), ncol = 2))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:290:1: style: Lines should not be more than 80 characters.

##' @description plots radial lines, degree label for latitudes, and plots radial spokes with labels
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:295:5: warning: no visible global function definition for ‘plot_circle_radial_lines’

    plot_circle_radial_lines(radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:296:5: warning: no visible global function definition for ‘plot_degree_label_for_latitudes’

    plot_degree_label_for_latitudes(outer_radius, radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:297:5: warning: no visible global function definition for ‘plot_radial_spokes_and_labels’

    plot_radial_spokes_and_labels(outer_radius)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:324:1: style: Variable and function names should not be longer than 30 characters.

define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:324:71: style: Variable or function name should be snake_case.

define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
                                                                      ^~~

R/plotting_functions.R:329:1: style: Lines should not be more than 80 characters.

    } else if ((length(col_breaks_source) == 2) & (is.numeric(col_breaks_source))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:346:1: style: Lines should not be more than 80 characters.

##' @param extrapolate whether to predict out to the equator of the eye, even if no data exists nearby.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:347:1: style: Lines should not be more than 80 characters.

interpolate_input_data <- function(minitics, x, y, z, lambda, polynomial_m, extrapolate) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:348:1: style: Lines should not be more than 80 characters.

    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:348:5: style: Variable or function name should be snake_case.

    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
    ^~~~~~~~~

R/plotting_functions.R:348:15: style: Use <-, not =, for assignment.

    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
              ^

R/plotting_functions.R:349:1: style: Lines should not be more than 80 characters.

    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:349:10: warning: no visible global function definition for ‘Tps’, Did you mean 'Ops'?

    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
         ^~~

R/plotting_functions.R:350:12: warning: no visible global function definition for ‘predictSurface’

    tmp <- predictSurface(t, grid.list, extrap = extrapolate)
           ^~~~~~~~~~~~~~

R/plotting_functions.R:351:5: style: Variable or function name should be snake_case.

    Mat <- tmp$z
    ^~~

R/plotting_functions.R:363:5: style: Variable or function name should be snake_case.

    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
    ^~~~~~~~~

R/plotting_functions.R:363:25: style: Put spaces around all infix operators.

    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                       ~^~

R/plotting_functions.R:363:31: style: Put spaces around all infix operators.

    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                             ~^~

R/plotting_functions.R:363:37: style: Put spaces around all infix operators.

    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                   ~^~

R/plotting_functions.R:363:47: style: Put spaces around all infix operators.

    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                             ~^~

R/plotting_functions.R:363:57: style: Put spaces around all infix operators.

    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                                       ~^~

R/plotting_functions.R:364:5: style: Variable or function name should be snake_case.

    r.labs <- c(90, 60, 30, 0, 330, 300)
    ^~~~~~

R/plotting_functions.R:365:5: style: Variable or function name should be snake_case.

    l.labs <- c(270, 240, 210, 180, 150, 120)
    ^~~~~~

R/plotting_functions.R:367:9: warning: no visible global function definition for ‘plot_longitudinal_lines’

        plot_longitudinal_lines(axis.rads[i], outer_radius)
        ^~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:368:1: style: Lines should not be more than 80 characters.

        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i], 
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:368:83: style: Trailing whitespace is superfluous.

        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i], 
                                                                                  ^

R/plotting_functions.R:389:1: style: Lines should not be more than 80 characters.

##' @description Useful for making the falciform process look more smooth and refined. This is purely aesthetic.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:390:1: style: Lines should not be more than 80 characters.

##' @details enhance the resolution of a polygon vertices dataframe by creating a spline along each vertex.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:391:1: style: Lines should not be more than 80 characters.

##' @param xy vertices in dataframe with x and y columns, in order (not all are used).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:398:1: style: Lines should not be more than 80 characters.

##' @references http://gis.stackexchange.com/questions/24827/how-to-smooth-the-polygons-in-a-contour-map
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting_functions.R:407:5: style: Variable or function name should be snake_case.

    data.spline <- spline(1:(n + 2 * k), data[, 1], n = vertices, ...)
    ^~~~~~~~~~~

R/plotting_functions.R:411:1: style: Trailing whitespace is superfluous.

    
^~~~

bc / retina

Remove retistruct requirement and shorten documentation #29