[inst/extdata/asalmon_mcw/main.r:2:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/inst/extdata/asalmon_mcw/main.r#L13) *error:* **unexpected ')'**
```r
                                                                    )
                                                                    ^
```
[R/composite.R:2:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L17) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:20:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L25) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:27:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:28:26:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L28) *style:* **Put spaces around all infix operators.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                        ~^~
```
[R/matrix_retobj.R:28:93:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                                                                                ^
```
[R/matrix_retobj.R:30:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/matrix_retobj.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    MAT <- map2fit[[2]]$z
    ^~~
```
[R/matrix_retobj.R:32:15:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:32:86:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
                                                                                ^
```
[R/plotting_functions.R:38:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L70) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:72:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:81:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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/b5390309e3a4d8ef43204662e19a4989ac1ea060/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:104:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L104) *style:* **Lines should not be more than 80 characters.**
```r
        ## https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:110:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L110) *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:110:86:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L110) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",0,NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:113:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L113) *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:113:87:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L113) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",0,NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:121:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L121) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote markup file to ", output_path, "\n Ensure that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:131:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L131) *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:132:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L132) *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:136:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L136) *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:139:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L139) *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:140:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L140) *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:148:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L148) *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:152:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L152) *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:152:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L152) *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:156:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L156) *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:178:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L178) *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:178:59:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L178) *style:* **Variable or function name should be snake_case.**
```r
plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
                                                          ^~~~~~~~~~~
```
[R/plotting_functions.R:179:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L179) *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:179:85:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L179) *style:* **Trailing whitespace is superfluous.**
```r
    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)),
                                                                                ^
```
[R/plotting_functions.R:181:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L181) *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:181:95:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L181) *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:196:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L196) *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:203:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L203) *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:207:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L207) *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:217:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L217) *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:218:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L218) *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:218:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L218) *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:227:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L227) *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:234:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L234) *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:234:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L234) *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:234:83:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L234) *style:* **Trailing whitespace is superfluous.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
                                                                                ^
```
[R/plotting_functions.R:236:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L236) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    matrix_position_is_within_the_circle <- function() {
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:237:21:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L237) *style:* **Put spaces around all infix operators.**
```r
        !sqrt(markNA^2 + t(markNA)^2) < outer_radius
                   ~^~
```
[R/plotting_functions.R:237:35:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L237) *style:* **Put spaces around all infix operators.**
```r
        !sqrt(markNA^2 + t(markNA)^2) < outer_radius
                                 ~^~
```
[R/plotting_functions.R:239:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L239) *style:* **Variable or function name should be snake_case.**
```r
    markNA <- matrix(minitics, ncol = spatial_res, nrow = spatial_res)
    ^~~~~~
```
[R/plotting_functions.R:247:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L247) *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:252:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L252) *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:252:46:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L252) *style:* **Variable or function name should be snake_case.**
```r
compute_longitude_label_location <- function(axis.rads, outer_radius) {
                                             ^~~~~~~~~
```
[R/plotting_functions.R:253:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L253) *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:253:14:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L253) *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:262:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L262) *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:262:88:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L262) *style:* **Trailing whitespace is superfluous.**
```r
    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius,
                                                                                ^
```
[R/plotting_functions.R:264:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L264) *warning:* **no visible global function definition for ‘draw_line_segments’**
```r
    draw_line_segments(endpoints)
    ^~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:268:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L268) *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:275:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L275) *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:275:38:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L275) *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:276:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L276) *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:276:108:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L276) *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:286:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L286) *style:* **Variable or function name should be snake_case.**
```r
RMat <- function(radians) {
^~~~
```
[R/plotting_functions.R:287:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L287) *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:291:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L291) *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:296:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L296) *warning:* **no visible global function definition for ‘plot_circle_radial_lines’**
```r
    plot_circle_radial_lines(radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:297:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L297) *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:298:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L298) *warning:* **no visible global function definition for ‘plot_radial_spokes_and_labels’**
```r
    plot_radial_spokes_and_labels(outer_radius)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:325:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L325) *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:325:71:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L325) *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:330:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L330) *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:338:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L338) *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:339:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L339) *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:339:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L339) *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:339:15:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L339) *style:* **Use <-, not =, for assignment.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
              ^
```
[R/plotting_functions.R:340:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L340) *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:340:10:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L340) *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:341:12:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L341) *warning:* **no visible global function definition for ‘predictSurface’**
```r
    tmp <- predictSurface(t, grid.list, extrap = extrapolate)
           ^~~~~~~~~~~~~~
```
[R/plotting_functions.R:342:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L342) *style:* **Variable or function name should be snake_case.**
```r
    Mat <- tmp$z
    ^~~
```
[R/plotting_functions.R:354:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *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:354:25:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *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:354:31:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *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:354:37:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *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:354:47:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *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:354:57:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L354) *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:355:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L355) *style:* **Variable or function name should be snake_case.**
```r
    r.labs <- c(90, 60, 30, 0, 330, 300)
    ^~~~~~
```
[R/plotting_functions.R:356:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L356) *style:* **Variable or function name should be snake_case.**
```r
    l.labs <- c(270, 240, 210, 180, 150, 120)
    ^~~~~~
```
[R/plotting_functions.R:358:9:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L358) *warning:* **no visible global function definition for ‘plot_longitudinal_lines’**
```r
        plot_longitudinal_lines(axis.rads[i], outer_radius)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:359:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L359) *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:359:83:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L359) *style:* **Trailing whitespace is superfluous.**
```r
        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i],
                                                                                ^
```
[R/plotting_functions.R:380:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L380) *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:381:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L381) *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:382:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L382) *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:389:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L389) *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:398:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L398) *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:402:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L402) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:410:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L410) *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:411:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L411) *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:412:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L412) *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:415:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L415) *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:417:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L417) *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:418:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L418) *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:426:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L426) *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:426:95:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L426) *style:* **Trailing whitespace is superfluous.**
```r
retinaplot <- function(retina_object, spatial_res = 1000, rotation = 0, inner_eye_view = TRUE,
                                                                                ^
```
[R/plotting_functions.R:428:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L428) *style:* **Variable or function name should be snake_case.**
```r
    AZx <- retina_object$azimuthal_data.datapoints[[1]]$x
    ^~~
```
[R/plotting_functions.R:429:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L429) *style:* **Variable or function name should be snake_case.**
```r
    AZy <- retina_object$azimuthal_data.datapoints[[1]]$y
    ^~~
```
[R/plotting_functions.R:430:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L430) *style:* **Variable or function name should be snake_case.**
```r
    AZz <- retina_object$azimuthal_data.datapoints[[1]]$z
    ^~~
```
[R/plotting_functions.R:432:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L432) *style:* **Variable or function name should be snake_case.**
```r
    rotAZ <- cartesian_rotation(AZx, AZy, rotation)
    ^~~~~
```
[R/plotting_functions.R:432:14:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L432) *warning:* **no visible global function definition for ‘cartesian_rotation’**
```r
    rotAZ <- cartesian_rotation(AZx, AZy, rotation)
             ^~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:433:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L433) *style:* **Variable or function name should be snake_case.**
```r
    AZx <- rotAZ$x
    ^~~
```
[R/plotting_functions.R:434:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    AZy <- rotAZ$y
    ^~~
```
[R/plotting_functions.R:435:1:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L435) *style:* **Lines should not be more than 80 characters.**
```r
    rotFALC <- cartesian_rotation(retina_object$azimuthal_data.falciform[[1]]$x,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:435:5:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rotFALC <- cartesian_rotation(retina_object$azimuthal_data.falciform[[1]]$x,
    ^~~~~~~
```
[R/plotting_functions.R:435:81:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L435) *style:* **Trailing whitespace is superfluous.**
```r
    rotFALC <- cartesian_rotation(retina_object$azimuthal_data.falciform[[1]]$x,
                                                                                ^
```
[R/plotting_functions.R:442:9:](https://github.com/bc/retina/blob/b5390309e3a4d8ef43204662e19a4989ac1ea060/R/plotting_functions.R#L442) *style:* **Variable or function name should be snake_case.**
```r
        AZx <- AZx * -1
        ^~~
```


Created multidev environment [attn-cms#ci-7](https://dashboard.pantheon.io/sites/59b8ccd3-dda4-48d3-8337-e687b7694b78#ci-7).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-7-attn-cms.pantheonsite.io/)


I am still getting this error: Java.lang.NullPointerException: Cannot set property 'clientid' on null object

Can you please take a look?  Thanks!


@OrganicCoder -- It all makes sense now... today... thank you. Miss you guys! Hope you're well!


This deprecation warning is already annoying the heck out of me. Maybe there's a way to only show it if you actually use this constant?


The file CalciumDependencePaper.svg has the actual figure for the paper


@githwxi should I add these changes to the build-release notes or automate it? I didn't notice if this caused problems in the build.


Executing 8d68b015-0196-4745-a8b8-69cf02b87f41


Task Execution in Progress


Execution completed.


### Results for event id: 8d68b015-0196-4745-a8b8-69cf02b87f41
Docker : run env in latest alpine1a (eb6203) Execution completed.

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

```
...
HOME=/root
1=var2=val2
0=myvar=myval
HOSTNAME=3eda1fdcb389
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

```

https://github.com/apocas/dockerode


Completed 8d68b015-0196-4745-a8b8-69cf02b87f41


Closes #4


Typo in issue keyword. Should be: QubesOS/qubes-issues#3957


Closes #3


This commit breaks my installation on the Pi2. to test. git checkout the one before this, reset the image and reboot. All works. When this commit is used, after an image reset, php-fpm, rune_PL_wrk, mpd, etc are not running at boot.


Make a separate Makefile for the windows builds, as these changes break the linux build; it's a small extra step but if people want to build on Windows they can do make -f Makefile.win  (or similar).

Could also just have a ./build.bat  (or sh) though it's not overly mattering.


Create CCO-License


哇 那太感谢了。So kind of you! 我的那个验证问题嘛， 随便写一个我就可以看到您的请求了🤗


Thank you for the comment, @ahundt. I think that this commit is better to be called "a correction" rather than "a breaking change". When using `app(weights='imagenet', include_top=False)`, users expect 16x or 32x down-sampled feature maps and all the apps except `ResNet50` return a 32x map (7x7 for a 224x224 input) correctly. The current `ResNet50` results in a 224x down-sampled map (1x1) which is apparently weird. Anyway I think the idea printing a warning is good as you pointed out.

Please note that the results of `model = ResNet50(weights='imagenet', include_top=False, input_shape=(224, 224, 3)); model.summary()` are:

Before this commit:
```
add_16 (Add)                    (None, 7, 7, 2048)   0           bn5c_branch2c[0][0]
                                                                 activation_46[0][0]
__________________________________________________________________________________________________
activation_49 (Activation)      (None, 7, 7, 2048)   0           add_16[0][0]
__________________________________________________________________________________________________
avg_pool (AveragePooling2D)     (None, 1, 1, 2048)   0           activation_49[0][0]
==================================================================================================
```
After this commit:
```
add_16 (Add)                    (None, 7, 7, 2048)   0           bn5c_branch2c[0][0]
                                                                 activation_46[0][0]
__________________________________________________________________________________________________
activation_49 (Activation)      (None, 7, 7, 2048)   0           add_16[0][0]
==================================================================================================
```


I think you can point to the directory instead of adding file by file


@hideaki216 いいですね！一行あたりのコードの長さを気にできるとなお良いですね。


Were these tests deleted on purpose?


What is this?


Install python and PyCharm CE, install requests library.
Write to the text file the counter of successful queries executed with the command 'script'


@hideaki216       <%= render 'books_list', books: @books %>
books_listはどこにありましたっけ？


Executing 9341117b-da40-4a65-a4ee-83f9e6715732


Task Execution in Progress