[inst/extdata/asalmon_mcw/main.r:2:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L2) *style:* **Variable or function name should be snake_case.**
```r
LAMBDA_var <- 0.1 #Thin plate spline smoothing. Lambda=0 would be interpolation.
^~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:3:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L3) *style:* **Variable or function name should be snake_case.**
```r
RESOLUTION_var <- 500 #Plot width in pixels
^~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:5:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L5) *style:* **Lines should not be more than 80 characters.**
```r
#TODO change path. make sure this main.r script is just outside the diagram_retina folder.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:8:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L8) *style:* **Lines should not be more than 80 characters.**
```r
#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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L10) *style:* **Commas should always have a space after.**
```r
    c(59,52,67),
         ^
```
[inst/extdata/asalmon_mcw/main.r:10:13:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L10) *style:* **Commas should always have a space after.**
```r
    c(59,52,67),
            ^
```
[inst/extdata/asalmon_mcw/main.r:11:10:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L11) *style:* **Commas should always have a space after.**
```r
    c(79,73,85),
         ^
```
[inst/extdata/asalmon_mcw/main.r:11:13:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L11) *style:* **Commas should always have a space after.**
```r
    c(79,73,85),
            ^
```
[inst/extdata/asalmon_mcw/main.r:12:10:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L12) *style:* **Commas should always have a space after.**
```r
    c(34,31,37))
         ^
```
[inst/extdata/asalmon_mcw/main.r:12:13:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L12) *style:* **Commas should always have a space after.**
```r
    c(34,31,37))
            ^
```
[inst/extdata/asalmon_mcw/main.r:13:69:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/inst/extdata/asalmon_mcw/main.r#L13) *error:* **unexpected ')'**
```r
                                                                    )
                                                                    ^
```
[R/composite.R:2:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
##' @description This is a subfunction, that is useful when creating average maps.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:3:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' @param retina_list A list containing retina objects, with names(retina_list) all defined.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:4:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
##' @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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' @param ... Arguments passed from other functions. You can access the thin plate spline interpolator here.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:6:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
##' @return sum_mat The sum of all retina objects in the list, with respect to the rotation indices.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:9:16:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L9) *warning:* **no visible global function definition for ‘mat_from_ret_obj’**
```r
    sum_mat <- mat_from_ret_obj(retina_list[[1]], rotation = 0, ...)
               ^~~~~~~~~~~~~~~~
```
[R/composite.R:12:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:12:85:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/composite.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i],
                                                                                ^
```
[R/matrix_retobj.R:3:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' 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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
##' @param n the number by which to divide the matrix by. Useful when generating partial averages.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:7:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
##' @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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:12:81:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE,
                                                                                ^
```
[R/matrix_retobj.R:17:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L17) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:20:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:20:87:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[,
                                                                                ^
```
[R/matrix_retobj.R:25:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L25) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:27:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:27:88:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE,
                                                                                ^
```
[R/matrix_retobj.R:28:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:28:26:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L28) *style:* **Put spaces around all infix operators.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                        ~^~
```
[R/matrix_retobj.R:28:93:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                                                                                ^
```
[R/matrix_retobj.R:30:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    MAT <- map2fit[[2]]$z
    ^~~
```
[R/matrix_retobj.R:32:15:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/matrix_retobj.R#L32) *style:* **Put spaces around all infix operators.**
```r
    return(MAT/n)
             ~^~
```
[R/plotting_functions.R:3:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' Extracts xy and falciform coordinates from datapoints collected from retistruct. Falc and Datapoints are stacked upon one another
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:5:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' @param datapoints_from_retistruct data structure that comes from the datapoints.csv, which is automatically generated by Retistruct.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:7:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
##' @return L list of pixel xy positions, and falciform coordinates in [1] and [2], respectively
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:9:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
extract_xy_and_falciform <- function(datapoints_from_retistruct, number_of_sampling_sites) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:10:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:10:81:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,
                                                                                ^
```
[R/plotting_functions.R:12:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:12:91:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[,
                                                                                ^
```
[R/plotting_functions.R:16:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_coordinates <- datapoints_from_retistruct[(xy_len + 1):total_len, ]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:22:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
##' 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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
##' @param falciform_xy_coordinates 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:29:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:29:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:31:52:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L31) *style:* **Put spaces around all infix operators.**
```r
    half_of_vertical_pixels <- xy_img_dimensions[2]/2
                                                  ~^~
```
[R/plotting_functions.R:32:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:32:86:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
                                                                                ^
```
[R/plotting_functions.R:38:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
##' Shows a visualization of the outline, as well as the location of each datapoint, with fit plot.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:40:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
##' @param pixel_xy_positions 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:41:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
##' @param z_vector numerical vector of density values for each of the coordinates
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:42:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
##' @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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
traditional_flatmount_plot <- function(pixel_xy_positions, z_vector, xy_outline_points) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:46:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:46:12:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L46) *warning:* **no visible global function definition for ‘Tps’, Did you mean 'Ops'?**
```r
    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
           ^~~
```
[R/plotting_functions.R:47:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L47) *warning:* **no visible global function definition for ‘set.panel’**
```r
    set.panel(2, 2)
    ^~~~~~~~~
```
[R/plotting_functions.R:49:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L49) *warning:* **no visible global function definition for ‘set.panel’**
```r
    set.panel()
    ^~~~~~~~~
```
[R/plotting_functions.R:52:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L52) *warning:* **no visible global function definition for ‘surface’**
```r
    surface(fit)  # Quick image/contour plot of GCV surface.
    ^~~~~~~
```
[R/plotting_functions.R:61:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
##' 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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path to the folder that contains the outline.roi file.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:65:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
##' @return roi_coordinates XY vals of pixel coordinates of the outline points, in order.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:69:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:69:19:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L69) *warning:* **no visible global function definition for ‘read.ijroi’**
```r
    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
                  ^~~~~~~~~~
```
[R/plotting_functions.R:70:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L70) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:72:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L72) *style:* **Lines should not be more than 80 characters.**
```r
    # format plots has the coordinate (0, 0) in the top left.  We have the coordinate
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:73:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
    # (0, 0) in the bottom left. We need to transform P so that the outline appears
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:76:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L76) *style:* **Variable or function name should be snake_case.**
```r
    roi_XY_coords <- roi_object$coords
    ^~~~~~~~~~~~~
```
[R/plotting_functions.R:80:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:81:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L81) *style:* **Lines should not be more than 80 characters.**
```r
    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:81:81:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L81) *style:* **Trailing whitespace is superfluous.**
```r
    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels",
                                                                                ^
```
[R/plotting_functions.R:83:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:83:83:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L83) *style:* **Trailing whitespace is superfluous.**
```r
    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[,
                                                                                ^
```
[R/plotting_functions.R:85:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
    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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
##' @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:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
##' @param dorsal_outline_index The index of the point that points toward dorsal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:97:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L97) *style:* **Lines should not be more than 80 characters.**
```r
##' @param nasal_outline_index The index of the opint that points toward nasal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:98:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L98) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the markup.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:100:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:100:107:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L100) *style:* **Trailing whitespace is superfluous.**
```r
assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA,
                                                                                ^
```
[R/plotting_functions.R:102:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L102) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:103:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L103) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:106:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L106) *style:* **Lines should not be more than 80 characters.**
```r
        ## https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:112:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L112) *style:* **Lines should not be more than 80 characters.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",0,NA,TRUE,\"", eye_side_string,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:112:86:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L112) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",0,NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:115:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L115) *style:* **Lines should not be more than 80 characters.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",0,NA,TRUE,\"", eye_side_string,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:115:87:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L115) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",0,NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:118:11:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L118) *style:* **Use <-, not =, for assignment.**
```r
    line1 = "\"iD\",\"iN\",\"phi0\",\"iOD\",\"DVflip\",\"side\""
          ^
```
[R/plotting_functions.R:123:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L123) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote markup file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:127:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L127) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:134:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L134) *style:* **Lines should not be more than 80 characters.**
```r
##' @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:135:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L135) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the T.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:139:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L139) *style:* **Lines should not be more than 80 characters.**
```r
assemble_tear_file <- function(tear_coordinates_dataframe, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:142:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
    write.table(tear_coordinates_dataframe, output_path, sep = ",", row.names = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:143:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote tear file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:151:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the P.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:155:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L155) *style:* **Lines should not be more than 80 characters.**
```r
assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:155:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L155) *style:* **Variable and function names should not be longer than 30 characters.**
```r
assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:159:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote coordinates file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:181:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L181) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:181:59:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L181) *style:* **Variable or function name should be snake_case.**
```r
plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
                                                          ^~~~~~~~~~~
```
[R/plotting_functions.R:182:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L182) *style:* **Lines should not be more than 80 characters.**
```r
    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:182:85:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L182) *style:* **Trailing whitespace is superfluous.**
```r
    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)),
                                                                                ^
```
[R/plotting_functions.R:184:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L184) *style:* **Lines should not be more than 80 characters.**
```r
    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:184:95:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L184) *style:* **Trailing whitespace is superfluous.**
```r
    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads,
                                                                                ^
```
[R/plotting_functions.R:199:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L199) *style:* **Lines should not be more than 80 characters.**
```r
    fields::image.plot(legend.only = TRUE, col = col, zlim = zlim, family = "Palatino")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:206:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L206) *style:* **Lines should not be more than 80 characters.**
```r
##' @param endpoints a 4 element numeric vector describing the xy and x'y' for the line segment.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:210:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
    segments(endpoints[1], endpoints[2], endpoints[3], endpoints[4], col = color_hex)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:220:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
##' @param endpoints vector of 4 numerics, x,y and x',y' defining the line segment
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:221:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L221) *style:* **Lines should not be more than 80 characters.**
```r
write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:221:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L221) *style:* **Variable and function names should not be longer than 30 characters.**
```r
write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:230:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L230) *style:* **Lines should not be more than 80 characters.**
```r
##' @description We do not need points plotted in the corners of the plotted circle.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:237:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L237) *style:* **Lines should not be more than 80 characters.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:237:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L237) *style:* **Variable and function names should not be longer than 30 characters.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:237:83:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L237) *style:* **Trailing whitespace is superfluous.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
                                                                                ^
```
[R/plotting_functions.R:239:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L239) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    matrix_position_is_within_the_circle <- function() {
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:240:21:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L240) *style:* **Put spaces around all infix operators.**
```r
        !sqrt(markNA^2 + t(markNA)^2) < outer_radius
                   ~^~
```
[R/plotting_functions.R:240:35:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L240) *style:* **Put spaces around all infix operators.**
```r
        !sqrt(markNA^2 + t(markNA)^2) < outer_radius
                                 ~^~
```
[R/plotting_functions.R:242:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L242) *style:* **Variable or function name should be snake_case.**
```r
    markNA <- matrix(minitics, ncol = spatial_res, nrow = spatial_res)
    ^~~~~~
```
[R/plotting_functions.R:250:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Find the location to put the label around the circle at each of the lines
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:255:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L255) *style:* **Variable and function names should not be longer than 30 characters.**
```r
compute_longitude_label_location <- function(axis.rads, outer_radius) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:255:46:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L255) *style:* **Variable or function name should be snake_case.**
```r
compute_longitude_label_location <- function(axis.rads, outer_radius) {
                                             ^~~~~~~~~
```
[R/plotting_functions.R:256:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L256) *style:* **Lines should not be more than 80 characters.**
```r
    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:256:14:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L256) *warning:* **no visible global function definition for ‘RMat’, Did you mean 'hat'?**
```r
    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
             ^~~~
```
[R/plotting_functions.R:265:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L265) *style:* **Lines should not be more than 80 characters.**
```r
    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:265:88:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L265) *style:* **Trailing whitespace is superfluous.**
```r
    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius,
                                                                                ^
```
[R/plotting_functions.R:267:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L267) *warning:* **no visible global function definition for ‘draw_line_segments’**
```r
    draw_line_segments(endpoints)
    ^~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:271:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L271) *style:* **Lines should not be more than 80 characters.**
```r
##' @description put a degree label at the ends of the endpoints for each longitude
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:278:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L278) *style:* **Lines should not be more than 80 characters.**
```r
plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:278:38:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L278) *style:* **Variable or function name should be snake_case.**
```r
plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
                                     ^~~~~~~~
```
[R/plotting_functions.R:279:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:279:108:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L279) *style:* **Trailing whitespace is superfluous.**
```r
    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad,
                                                                                ^
```
[R/plotting_functions.R:289:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L289) *style:* **Variable or function name should be snake_case.**
```r
RMat <- function(radians) {
^~~~
```
[R/plotting_functions.R:290:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L290) *style:* **Lines should not be more than 80 characters.**
```r
    return(matrix(c(cos(radians), sin(radians), -sin(radians), cos(radians)), ncol = 2))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:294:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L294) *style:* **Lines should not be more than 80 characters.**
```r
##' @description plots radial lines, degree label for latitudes, and plots radial spokes with labels
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:299:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L299) *warning:* **no visible global function definition for ‘plot_circle_radial_lines’**
```r
    plot_circle_radial_lines(radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:300:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L300) *warning:* **no visible global function definition for ‘plot_degree_label_for_latitudes’**
```r
    plot_degree_label_for_latitudes(outer_radius, radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:301:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L301) *warning:* **no visible global function definition for ‘plot_radial_spokes_and_labels’**
```r
    plot_radial_spokes_and_labels(outer_radius)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:328:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L328) *style:* **Variable and function names should not be longer than 30 characters.**
```r
define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:328:71:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L328) *style:* **Variable or function name should be snake_case.**
```r
define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
                                                                      ^~~
```
[R/plotting_functions.R:333:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L333) *style:* **Lines should not be more than 80 characters.**
```r
    } else if ((length(col_breaks_source) == 2) & (is.numeric(col_breaks_source))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:341:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L341) *style:* **Lines should not be more than 80 characters.**
```r
interpolate_input_data <- function(minitics, x, y, z, lambda, polynomial_m, extrapolate) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:342:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L342) *style:* **Lines should not be more than 80 characters.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:342:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L342) *style:* **Variable or function name should be snake_case.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
    ^~~~~~~~~
```
[R/plotting_functions.R:342:15:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L342) *style:* **Use <-, not =, for assignment.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
              ^
```
[R/plotting_functions.R:343:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L343) *style:* **Lines should not be more than 80 characters.**
```r
    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:343:10:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L343) *warning:* **no visible global function definition for ‘Tps’, Did you mean 'Ops'?**
```r
    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
         ^~~
```
[R/plotting_functions.R:344:12:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L344) *warning:* **no visible global function definition for ‘predictSurface’**
```r
    tmp <- predictSurface(t, grid.list, extrap = extrapolate)
           ^~~~~~~~~~~~~~
```
[R/plotting_functions.R:345:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L345) *style:* **Variable or function name should be snake_case.**
```r
    Mat = tmp$z
    ^~~
```
[R/plotting_functions.R:345:9:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L345) *style:* **Use <-, not =, for assignment.**
```r
    Mat = tmp$z
        ^
```
[R/plotting_functions.R:357:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L357) *style:* **Variable or function name should be snake_case.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
    ^~~~~~~~~
```
[R/plotting_functions.R:357:25:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L357) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                       ~^~
```
[R/plotting_functions.R:357:31:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L357) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                             ~^~
```
[R/plotting_functions.R:357:37:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L357) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                   ~^~
```
[R/plotting_functions.R:357:47:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L357) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                             ~^~
```
[R/plotting_functions.R:357:57:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L357) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                                       ~^~
```
[R/plotting_functions.R:358:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L358) *style:* **Variable or function name should be snake_case.**
```r
    r.labs <- c(90, 60, 30, 0, 330, 300)
    ^~~~~~
```
[R/plotting_functions.R:359:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L359) *style:* **Variable or function name should be snake_case.**
```r
    l.labs <- c(270, 240, 210, 180, 150, 120)
    ^~~~~~
```
[R/plotting_functions.R:361:9:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L361) *warning:* **no visible global function definition for ‘plot_longitudinal_lines’**
```r
        plot_longitudinal_lines(axis.rads[i], outer_radius)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:362:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L362) *style:* **Lines should not be more than 80 characters.**
```r
        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:362:83:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L362) *style:* **Trailing whitespace is superfluous.**
```r
        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i],
                                                                                ^
```
[R/plotting_functions.R:383:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Useful for making the falciform process look more smooth and refined. This is purely aesthetic.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:384:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L384) *style:* **Lines should not be more than 80 characters.**
```r
##' @details enhance the resolution of a polygon vertices dataframe by creating a spline along each vertex.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:385:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L385) *style:* **Lines should not be more than 80 characters.**
```r
##' @param xy vertices in dataframe with x and y columns, in order (not all are used).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:392:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L392) *style:* **Lines should not be more than 80 characters.**
```r
##' @references http://gis.stackexchange.com/questions/24827/how-to-smooth-the-polygons-in-a-contour-map
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:401:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L401) *style:* **Variable or function name should be snake_case.**
```r
    data.spline <- spline(1:(n + 2 * k), data[, 1], n = vertices, ...)
    ^~~~~~~~~~~
```
[R/plotting_functions.R:405:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L405) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:413:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L413) *style:* **Lines should not be more than 80 characters.**
```r
##' \code{retinaplot} Generates an Azimuthal Equidistant plot projection of a retina object.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:414:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L414) *style:* **Lines should not be more than 80 characters.**
```r
##' You can also set lambda(floating point number) and polynomial_m(integer), as well as extrapolate (TRUE, FALSE).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:415:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L415) *style:* **Lines should not be more than 80 characters.**
```r
##' @param inner_eye_view boolean, default is TRUE. If set to false, the plotted view of the retina will have the viewpoint within the skull looking at the rear of the eye. inner_eye_view has the same view as the traditional wholemount.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:418:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L418) *style:* **Lines should not be more than 80 characters.**
```r
##' @param return_fit logical, whether or not to return the interpolation fit data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:420:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L420) *style:* **Lines should not be more than 80 characters.**
```r
##' @param retina_object A list containing an element \code{azimuthal_data.datapoints} with
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:421:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L421) *style:* **Lines should not be more than 80 characters.**
```r
##' \code{x,y,z} datapoints. File must also include \code{azimuthal_data.falciform}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:429:1:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L429) *style:* **Lines should not be more than 80 characters.**
```r
retinaplot <- function(retina_object, spatial_res = 1000, rotation = 0, inner_eye_view = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:429:95:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L429) *style:* **Trailing whitespace is superfluous.**
```r
retinaplot <- function(retina_object, spatial_res = 1000, rotation = 0, inner_eye_view = TRUE,
                                                                                ^
```
[R/plotting_functions.R:431:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L431) *style:* **Variable or function name should be snake_case.**
```r
    AZx <- retina_object$azimuthal_data.datapoints[[1]]$x
    ^~~
```
[R/plotting_functions.R:432:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L432) *style:* **Variable or function name should be snake_case.**
```r
    AZy <- retina_object$azimuthal_data.datapoints[[1]]$y
    ^~~
```
[R/plotting_functions.R:433:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L433) *style:* **Variable or function name should be snake_case.**
```r
    AZz <- retina_object$azimuthal_data.datapoints[[1]]$z
    ^~~
```
[R/plotting_functions.R:435:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rotAZ <- cartesian_rotation(AZx, AZy, rotation)
    ^~~~~
```
[R/plotting_functions.R:435:14:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L435) *warning:* **no visible global function definition for ‘cartesian_rotation’**
```r
    rotAZ <- cartesian_rotation(AZx, AZy, rotation)
             ^~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:436:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L436) *style:* **Variable or function name should be snake_case.**
```r
    AZx <- rotAZ$x
    ^~~
```
[R/plotting_functions.R:437:5:](https://github.com/bc/retina/blob/6595cf2d393687eec656ff6f650a165757e790be/R/plotting_functions.R#L437) *style:* **Variable or function name should be snake_case.**
```r
    AZy <- rotAZ$y
    ^~~
```


## Jenkins Build Summary

Built from [this commit](https://github.com/ripple/rippled/commit/66f1c044eead6cdf01194aff4cefe8325514fb09)

Built at __20180605 - 00:31:57__

### Test Results

Build Type | Log | Result | Status
---------- | --- | ------ | ------
docs | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/docs.txt) | 1 cases, 0 failed, t: 2s | PASS :white_check_mark:
clang.debug.unity | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/clang.debug.unity.txt) | 1030 cases, 0 failed, t: 281s | PASS :white_check_mark:
clang.debug.unity,
PARALLEL_TESTS=false | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/clang.debug.unity_PARALLEL_TESTS_false.txt) | no test results, t: 2s | FAIL :red_circle:
clang.debug.nounity | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/clang.debug.nounity.txt) | no test results, t: 2s | FAIL :red_circle:
msvc.debug | [console](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//console) | no test results, t: n/a | FAIL :red_circle:
msvc.debug,
PROJECT_NAME=rippled_classic | [console](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//console) | no test results, t: n/a | FAIL :red_circle:
msvc.release | [console](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//console) | no test results, t: n/a | FAIL :red_circle:
gcc.debug.unity | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/gcc.debug.unity.txt) | 1030 cases, 0 failed, t: 263s | PASS :white_check_mark:
gcc.debug.nounity | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/gcc.debug.nounity.txt) | no test results, t: 1s | FAIL :red_circle:
clang.release.unity | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/clang.release.unity.txt) | no test results, t: 8s | FAIL :red_circle:
gcc.release.unity | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/gcc.release.unity.txt) | no test results, t: 7s | FAIL :red_circle:
gcc.debug.unity
-Dstatic=true | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/gcc.debug.unity_Dstatic_true.txt) | no test results, t: 3s | FAIL :red_circle:
coverage | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/shard_transfer/1//artifact/coverage.txt) | 1030 cases, 0 failed, t: 641s | PASS :white_check_mark:


I think you're right. I didn't double check with vivado build after changing the script. Can you change the script to what it should be?


How about using another flag, such as "cors_allow_origin_regex" for this?


Mainline Xen does not yet implement XEN_DOMCTL_MONITOR_EVENT_SINGLESTEP for ARM. However, I tend to agree on leaving this check here. Please add a comment above stating that single-stepping is not  yet implemented in Xen :)


Please remove this line.


CameraActor needs to be CameraActorBehaviour


I think the rationale is to catch newly introduced deprecations earlier than later and force devs to fix them.


Style issue. Please add a ' ' before the '('


Same here.


How about adding fail task like https://github.com/automationbroker/automation-broker-apb/blob/a6f1779189964d92aec0de8600830bb8775ebb19/tasks/main.yml#L20 when elasticsearch serviceaccount does not already exist in namespace with appropriate privileges?


Executing 86a202c8-7bd4-4360-8fa2-de213ad60c23


Task Execution in Progress


Behavior should be Behaviour


Execution completed.


You know it ;)


Created multidev environment [attn-cms#ci-5](https://dashboard.pantheon.io/sites/59b8ccd3-dda4-48d3-8337-e687b7694b78#ci-5).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-5-attn-cms.pantheonsite.io/)


Beyond, we mention the issue with arm_regs and x86_regs pointing to the same memory. Please be consistent with the final solution.


Executing 335151a9-179b-4007-9b1b-a922fc32a3b3


Working state (except Android O) before adding JobScheduler.


### Results for event id: 86a202c8-7bd4-4360-8fa2-de213ad60c23
Docker : run env in latest alpine1a (eb6203) Execution completed.

**output tail (5 lines total):**

```
...
HOME=/root
1=var2=val2
0=myvar=myval
HOSTNAME=1a86aa09f17c
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

```

https://github.com/apocas/dockerode


Completed 86a202c8-7bd4-4360-8fa2-de213ad60c23


### Results for event id: 335151a9-179b-4007-9b1b-a922fc32a3b3
Docker : run env in latest alpine1a (eb6203) Execution completed.

**output tail (5 lines total):**

```
...
HOME=/root
1=var2=val2
0=myvar=myval
HOSTNAME=0ab9c64298ac
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

```

https://github.com/apocas/dockerode


Completed 335151a9-179b-4007-9b1b-a922fc32a3b3


Executing 6aa8d0a5-299b-420a-9a8f-4b1d4deeb545


### Results for event id: 6aa8d0a5-299b-420a-9a8f-4b1d4deeb545
Docker : run env in latest alpine1a (eb6203) Execution completed.

**output tail (5 lines total):**

```
...
HOME=/root
1=var2=val2
0=myvar=myval
HOSTNAME=4b2dc26516a8
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

```

https://github.com/apocas/dockerode


Completed 6aa8d0a5-299b-420a-9a8f-4b1d4deeb545


When I run this in Postman, I do not get these error messages when editing a Friend. Be sure to check _where_ you are checking this data against. :)


开发者好像解散了所有QQ群，我像开发者要过火狐的可以使用的插件，但是不小心弄丢了，开发者能再发一下吗！谢谢你。


Adjusted level mod to match findings. Fixed with 74e52cc


回退到初始化版本