[inst/extdata/asalmon_mcw/main.r:2:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/inst/extdata/asalmon_mcw/main.r#L13) *error:* **unexpected ')'**
```r
                                                                    )
                                                                    ^
```
[R/composite.R:2:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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:9:14:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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/matrix_retobj.R:3:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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:20:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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:27:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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:28:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/matrix_retobj.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
    outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:28:22:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/matrix_retobj.R#L28) *style:* **Put spaces around all infix operators.**
```r
    outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                    ~^~
```
[R/matrix_retobj.R:30:3:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/matrix_retobj.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  MAT <- map2fit[[2]]$z
  ^~~
```
[R/matrix_retobj.R:32:13:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L10) *style:* **Use spaces to indent, not tabs.**
```r
	pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,]
^
```
[R/plotting_functions.R:10:78:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L10) *style:* **Commas should always have a space after.**
```r
	pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,]
                                                                             ^
```
[R/plotting_functions.R:11:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
	falciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:11:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L11) *style:* **Use spaces to indent, not tabs.**
```r
	falciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])
^
```
[R/plotting_functions.R:11:2:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L11) *warning:* **local variable ‘falciform_len’ assigned but may not be used**
```r
	falciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])
 ^~~~~~~~~~~~~
```
[R/plotting_functions.R:11:54:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L11) *style:* **Commas should always have a space after.**
```r
	falciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])
                                                     ^
```
[R/plotting_functions.R:11:87:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L11) *style:* **Commas should always have a space after.**
```r
	falciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])
                                                                                ^
```
[R/plotting_functions.R:12:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L12) *style:* **Use spaces to indent, not tabs.**
```r
	xy_len <- length(pixel_xy_positions[,1])
^
```
[R/plotting_functions.R:12:39:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L12) *style:* **Commas should always have a space after.**
```r
	xy_len <- length(pixel_xy_positions[,1])
                                      ^
```
[R/plotting_functions.R:13:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L13) *style:* **Use spaces to indent, not tabs.**
```r
	total_len <- length(datapoints_from_retistruct[,1])
^
```
[R/plotting_functions.R:13:50:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L13) *style:* **Commas should always have a space after.**
```r
	total_len <- length(datapoints_from_retistruct[,1])
                                                 ^
```
[R/plotting_functions.R:14:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L14) *style:* **Use spaces to indent, not tabs.**
```r
	falciform_coordinates <- datapoints_from_retistruct[(xy_len+1):total_len,]
^
```
[R/plotting_functions.R:14:61:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L14) *style:* **Put spaces around all infix operators.**
```r
	falciform_coordinates <- datapoints_from_retistruct[(xy_len+1):total_len,]
                                                           ~^~
```
[R/plotting_functions.R:14:75:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L14) *style:* **Commas should always have a space after.**
```r
	falciform_coordinates <- datapoints_from_retistruct[(xy_len+1):total_len,]
                                                                          ^
```
[R/plotting_functions.R:15:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L15) *style:* **Use spaces to indent, not tabs.**
```r
	return(list(pixel_xy_positions, falciform_coordinates))
^
```
[R/plotting_functions.R:20:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L20) *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:22:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L22) *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:26:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L26) *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:26:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L26) *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:26:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L26) *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:27:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L27) *style:* **Use spaces to indent, not tabs.**
```r
		falciform_xy_coordinates_transformed <- falciform_xy_coordinates #make a copy
^~
```
[R/plotting_functions.R:27:3:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L27) *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:28:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L28) *style:* **Use spaces to indent, not tabs.**
```r
		falc_y <- falciform_xy_coordinates[,2]
^~
```
[R/plotting_functions.R:28:39:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L28) *style:* **Commas should always have a space after.**
```r
		falc_y <- falciform_xy_coordinates[,2]
                                      ^
```
[R/plotting_functions.R:29:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L29) *style:* **Use spaces to indent, not tabs.**
```r
		half_of_vertical_pixels <- xy_img_dimensions[2]/2
^~
```
[R/plotting_functions.R:29:50:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L29) *style:* **Put spaces around all infix operators.**
```r
		half_of_vertical_pixels <- xy_img_dimensions[2]/2
                                                ~^~
```
[R/plotting_functions.R:30:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
		falciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:30:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L30) *style:* **Use spaces to indent, not tabs.**
```r
		falciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels
^~
```
[R/plotting_functions.R:30:55:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L30) *style:* **Put spaces around all infix operators.**
```r
		falciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels
                                                     ~^~
```
[R/plotting_functions.R:30:80:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L30) *style:* **Put spaces around all infix operators.**
```r
		falciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels
                                                                              ~^~
```
[R/plotting_functions.R:31:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L31) *style:* **Use spaces to indent, not tabs.**
```r
		return(falciform_xy_coordinates_transformed)
^~
```
[R/plotting_functions.R:35:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L35) *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:37:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L37) *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:38:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L38) *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:39:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L39) *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:42:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L42) *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:42:59:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L42) *style:* **Commas should always have a space after.**
```r
traditional_flatmount_plot <- function(pixel_xy_positions,z_vector, xy_outline_points){
                                                          ^
```
[R/plotting_functions.R:43:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L43) *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:43:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L43) *style:* **Use spaces to indent, not tabs.**
```r
	fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
^
```
[R/plotting_functions.R:43:9:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L43) *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:44:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L44) *style:* **Use spaces to indent, not tabs.**
```r
	set.panel(2,2)
^
```
[R/plotting_functions.R:44:2:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L44) *warning:* **no visible global function definition for ‘set.panel’**
```r
	set.panel(2,2)
 ^~~~~~~~~
```
[R/plotting_functions.R:44:14:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L44) *style:* **Commas should always have a space after.**
```r
	set.panel(2,2)
             ^
```
[R/plotting_functions.R:45:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L45) *style:* **Use spaces to indent, not tabs.**
```r
	plot(fit) # four diagnostic plots of  fit and residuals.
^
```
[R/plotting_functions.R:46:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L46) *style:* **Use spaces to indent, not tabs.**
```r
	set.panel()
^
```
[R/plotting_functions.R:46:2:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L46) *warning:* **no visible global function definition for ‘set.panel’**
```r
	set.panel()
 ^~~~~~~~~
```
[R/plotting_functions.R:47:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L47) *style:* **Use spaces to indent, not tabs.**
```r
	# summary of fit and estimates of lambda the smoothing parameter
^
```
[R/plotting_functions.R:48:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L48) *style:* **Use spaces to indent, not tabs.**
```r
	summary(fit)
^
```
[R/plotting_functions.R:49:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L49) *style:* **Use spaces to indent, not tabs.**
```r
	surface(fit) # Quick image/contour plot of GCV surface.
^
```
[R/plotting_functions.R:49:2:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L49) *warning:* **no visible global function definition for ‘surface’**
```r
	surface(fit) # Quick image/contour plot of GCV surface.
 ^~~~~~~
```
[R/plotting_functions.R:50:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L50) *style:* **Use spaces to indent, not tabs.**
```r
	return(fit)
^
```
[R/plotting_functions.R:58:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L58) *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:61:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L61) *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:62:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L62) *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:66:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L66) *style:* **Use spaces to indent, not tabs.**
```r
	roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
^
```
[R/plotting_functions.R:66:16:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L66) *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:69:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L69) *style:* **Use spaces to indent, not tabs.**
```r
		## ImageJ ROI format plots has the coordinate (0, 0) in the top
^~
```
[R/plotting_functions.R:70:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L70) *style:* **Use spaces to indent, not tabs.**
```r
		  ## left.  We have the coordinate (0, 0) in the bottom left. We need
^~
```
[R/plotting_functions.R:71:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L71) *style:* **Use spaces to indent, not tabs.**
```r
		  ## to transform P so that the outline appears in the correct
^~
```
[R/plotting_functions.R:72:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L72) *style:* **Use spaces to indent, not tabs.**
```r
		  ## orientation.
^~
```
[R/plotting_functions.R:73:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L73) *style:* **Use spaces to indent, not tabs.**
```r
			im <- NULL
^~~
```
[R/plotting_functions.R:74:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L74) *style:* **Use spaces to indent, not tabs.**
```r
		  roi_XY_coords <- roi_object$coords
^~
```
[R/plotting_functions.R:74:5:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L74) *style:* **Variable or function name should be snake_case.**
```r
		  roi_XY_coords <- roi_object$coords
    ^~~~~~~~~~~~~
```
[R/plotting_functions.R:75:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L75) *style:* **Use spaces to indent, not tabs.**
```r
		  offset <- ifelse(is.null(im), max(roi_XY_coords[,2]), nrow(im))
^~
```
[R/plotting_functions.R:75:54:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L75) *style:* **Commas should always have a space after.**
```r
		  offset <- ifelse(is.null(im), max(roi_XY_coords[,2]), nrow(im))
                                                     ^
```
[R/plotting_functions.R:76:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L76) *style:* **Use spaces to indent, not tabs.**
```r
		  roi_XY_coords[,2] <- offset - roi_XY_coords[,2]
^~
```
[R/plotting_functions.R:76:20:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L76) *style:* **Commas should always have a space after.**
```r
		  roi_XY_coords[,2] <- offset - roi_XY_coords[,2]
                   ^
```
[R/plotting_functions.R:76:50:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L76) *style:* **Commas should always have a space after.**
```r
		  roi_XY_coords[,2] <- offset - roi_XY_coords[,2]
                                                 ^
```
[R/plotting_functions.R:79:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:79:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Use spaces to indent, not tabs.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
^
```
[R/plotting_functions.R:79:26:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Put spaces around all infix operators.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                        ~^~
```
[R/plotting_functions.R:79:35:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Put spaces around all infix operators.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                                 ~^~
```
[R/plotting_functions.R:79:36:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Only use double-quotes.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                                   ^~~~~~~~~
```
[R/plotting_functions.R:79:50:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Put spaces around all infix operators.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                                                ~^~
```
[R/plotting_functions.R:79:58:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Put spaces around all infix operators.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                                                        ~^~
```
[R/plotting_functions.R:79:59:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Only use double-quotes.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                                                          ^~~~~~~~~~
```
[R/plotting_functions.R:79:75:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Put spaces around all infix operators.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                                                                         ~^~
```
[R/plotting_functions.R:79:76:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L79) *style:* **Only use double-quotes.**
```r
	plot(roi_XY_coords, type="l", col='#d3d3d3', asp=1, xlab='X Pixels', ylab='Y Pixels');
                                                                           ^~~~~~~~~~
```
[R/plotting_functions.R:80:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *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[,1]), cex=0.5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:80:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *style:* **Use spaces to indent, not tabs.**
```r
	text(roi_XY_coords[,1],roi_XY_coords[,2], labels=1:length(roi_XY_coords[,1]), cex=0.5)
^
```
[R/plotting_functions.R:80:22:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *style:* **Commas should always have a space after.**
```r
	text(roi_XY_coords[,1],roi_XY_coords[,2], labels=1:length(roi_XY_coords[,1]), cex=0.5)
                     ^
```
[R/plotting_functions.R:80:25:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *style:* **Commas should always have a space after.**
```r
	text(roi_XY_coords[,1],roi_XY_coords[,2], labels=1:length(roi_XY_coords[,1]), cex=0.5)
                        ^
```
[R/plotting_functions.R:80:40:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *style:* **Commas should always have a space after.**
```r
	text(roi_XY_coords[,1],roi_XY_coords[,2], labels=1:length(roi_XY_coords[,1]), cex=0.5)
                                       ^
```
[R/plotting_functions.R:80:50:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *style:* **Put spaces around all infix operators.**
```r
	text(roi_XY_coords[,1],roi_XY_coords[,2], labels=1:length(roi_XY_coords[,1]), cex=0.5)
                                                ~^~
```
[R/plotting_functions.R:80:75:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *style:* **Commas should always have a space after.**
```r
	text(roi_XY_coords[,1],roi_XY_coords[,2], labels=1:length(roi_XY_coords[,1]), cex=0.5)
                                                                          ^
```
[R/plotting_functions.R:80:83:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L80) *style:* **Put spaces around all infix operators.**
```r
	text(roi_XY_coords[,1],roi_XY_coords[,2], labels=1:length(roi_XY_coords[,1]), cex=0.5)
                                                                                ~^~
```
[R/plotting_functions.R:81:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L81) *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:81:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L81) *style:* **Use spaces to indent, not tabs.**
```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:81:11:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L81) *style:* **Only use double-quotes.**
```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:82:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L82) *style:* **Use spaces to indent, not tabs.**
```r
	return(roi_XY_coords)
^
```
[R/plotting_functions.R:89:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L89) *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:92:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L92) *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:93:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L93) *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:94:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L94) *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:96:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L96) *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, nasal_outline_index=NA) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:99:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L99) *style:* **Use spaces to indent, not tabs.**
```r
	firstup <- function(x) {
^
```
[R/plotting_functions.R:100:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
	##firstup function sourced from https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:100:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L100) *style:* **Use spaces to indent, not tabs.**
```r
	##firstup function sourced from https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
^
```
[R/plotting_functions.R:101:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L101) *style:* **Use spaces to indent, not tabs.**
```r
	   substr(x, 1, 1) <- toupper(substr(x, 1, 1))
^
```
[R/plotting_functions.R:102:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L102) *style:* **Use spaces to indent, not tabs.**
```r
	x
^
```
[R/plotting_functions.R:103:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L103) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/plotting_functions.R:104:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L104) *style:* **Use spaces to indent, not tabs.**
```r
	eye_side_string <- firstup(eye_left_or_right)
^
```
[R/plotting_functions.R:105:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L105) *style:* **Use spaces to indent, not tabs.**
```r
	if (is.na(dorsal_outline_index)){
^
```
[R/plotting_functions.R:106:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L106) *style:* **Use spaces to indent, not tabs.**
```r
	line2 <- paste0('NA,',
^
```
[R/plotting_functions.R:106:18:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L106) *style:* **Only use double-quotes.**
```r
	line2 <- paste0('NA,',
                 ^~~~~
```
[R/plotting_functions.R:107:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L107) *style:* **Use spaces to indent, not tabs.**
```r
									nasal_outline_index,
^~~~~~~~~
```
[R/plotting_functions.R:108:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L108) *style:* **Use spaces to indent, not tabs.**
```r
									',0,NA,TRUE,"',
^~~~~~~~~
```
[R/plotting_functions.R:109:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L109) *style:* **Use spaces to indent, not tabs.**
```r
									eye_side_string,
^~~~~~~~~
```
[R/plotting_functions.R:110:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L110) *style:* **Use spaces to indent, not tabs.**
```r
									'"')
^~~~~~~~~
```
[R/plotting_functions.R:111:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L111) *style:* **Use spaces to indent, not tabs.**
```r
	} else {
^
```
[R/plotting_functions.R:112:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L112) *style:* **Use spaces to indent, not tabs.**
```r
		line2 <- paste0(dorsal_outline_index,
^~
```
[R/plotting_functions.R:113:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L113) *style:* **Use spaces to indent, not tabs.**
```r
										',NA',
^~~~~~~~~~
```
[R/plotting_functions.R:113:11:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L113) *style:* **Only use double-quotes.**
```r
										',NA',
          ^~~~~
```
[R/plotting_functions.R:114:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L114) *style:* **Use spaces to indent, not tabs.**
```r
										',0,NA,TRUE,"',
^~~~~~~~~~
```
[R/plotting_functions.R:115:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L115) *style:* **Use spaces to indent, not tabs.**
```r
										eye_side_string,
^~~~~~~~~~
```
[R/plotting_functions.R:116:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L116) *style:* **Use spaces to indent, not tabs.**
```r
										'"')
^~~~~~~~~~
```
[R/plotting_functions.R:117:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L117) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/plotting_functions.R:118:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L118) *style:* **Use spaces to indent, not tabs.**
```r
	line1 = '"iD","iN","phi0","iOD","DVflip","side"'
^
```
[R/plotting_functions.R:118:8:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L118) *style:* **Use <-, not =, for assignment.**
```r
	line1 = '"iD","iN","phi0","iOD","DVflip","side"'
       ^
```
[R/plotting_functions.R:119:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L119) *style:* **Use spaces to indent, not tabs.**
```r
	output_path <- file.path(path_to_retina_data_folder, "markup.csv")
^
```
[R/plotting_functions.R:120:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L120) *style:* **Use spaces to indent, not tabs.**
```r
	file.create(output_path)
^
```
[R/plotting_functions.R:121:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L121) *style:* **Use spaces to indent, not tabs.**
```r
	write(line1,file=output_path,append=TRUE)
^
```
[R/plotting_functions.R:121:14:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L121) *style:* **Commas should always have a space after.**
```r
	write(line1,file=output_path,append=TRUE)
             ^
```
[R/plotting_functions.R:121:18:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L121) *style:* **Put spaces around all infix operators.**
```r
	write(line1,file=output_path,append=TRUE)
                ~^~
```
[R/plotting_functions.R:121:31:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L121) *style:* **Commas should always have a space after.**
```r
	write(line1,file=output_path,append=TRUE)
                              ^
```
[R/plotting_functions.R:121:37:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L121) *style:* **Put spaces around all infix operators.**
```r
	write(line1,file=output_path,append=TRUE)
                                   ~^~
```
[R/plotting_functions.R:122:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L122) *style:* **Use spaces to indent, not tabs.**
```r
	write(line2, file=output_path, append=TRUE)
^
```
[R/plotting_functions.R:122:19:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L122) *style:* **Put spaces around all infix operators.**
```r
	write(line2, file=output_path, append=TRUE)
                 ~^~
```
[R/plotting_functions.R:122:39:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L122) *style:* **Put spaces around all infix operators.**
```r
	write(line2, file=output_path, append=TRUE)
                                     ~^~
```
[R/plotting_functions.R:123:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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:123:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L123) *style:* **Use spaces to indent, not tabs.**
```r
	message(paste('Wrote markup file to ',output_path, '\n Check that it exists beside your outline.roi file'))
^
```
[R/plotting_functions.R:123:16:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L123) *style:* **Only use double-quotes.**
```r
	message(paste('Wrote markup file to ',output_path, '\n Check that it exists beside your outline.roi file'))
               ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:123:40:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L123) *style:* **Commas should always have a space after.**
```r
	message(paste('Wrote markup file to ',output_path, '\n Check that it exists beside your outline.roi file'))
                                       ^
```
[R/plotting_functions.R:123:53:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L123) *style:* **Only use double-quotes.**
```r
	message(paste('Wrote markup file to ',output_path, '\n Check that it exists beside your outline.roi file'))
                                                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:124:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L124) *style:* **Use spaces to indent, not tabs.**
```r
	print(line1)
^
```
[R/plotting_functions.R:125:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L125) *style:* **Use spaces to indent, not tabs.**
```r
	print(line2)
^
```
[R/plotting_functions.R:126:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L126) *style:* **Use spaces to indent, not tabs.**
```r
	return(0)
^
```
[R/plotting_functions.R:134:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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:140:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L140) *style:* **Use spaces to indent, not tabs.**
```r
	output_path <- file.path(path_to_retina_data_folder, "T.csv")
^
```
[R/plotting_functions.R:141:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L141) *style:* **Use spaces to indent, not tabs.**
```r
	colnames(tear_coordinates_dataframe)<- c("V0","VB","VF")
^
```
[R/plotting_functions.R:141:38:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L141) *style:* **Put spaces around all infix operators.**
```r
	colnames(tear_coordinates_dataframe)<- c("V0","VB","VF")
                                    ~^
```
[R/plotting_functions.R:141:48:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L141) *style:* **Commas should always have a space after.**
```r
	colnames(tear_coordinates_dataframe)<- c("V0","VB","VF")
                                               ^
```
[R/plotting_functions.R:141:53:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L141) *style:* **Commas should always have a space after.**
```r
	colnames(tear_coordinates_dataframe)<- c("V0","VB","VF")
                                                    ^
```
[R/plotting_functions.R:142:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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:142:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L142) *style:* **Use spaces to indent, not tabs.**
```r
	write.table(tear_coordinates_dataframe, output_path, sep=',', row.names = FALSE)
^
```
[R/plotting_functions.R:142:58:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L142) *style:* **Put spaces around all infix operators.**
```r
	write.table(tear_coordinates_dataframe, output_path, sep=',', row.names = FALSE)
                                                        ~^~
```
[R/plotting_functions.R:142:59:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L142) *style:* **Only use double-quotes.**
```r
	write.table(tear_coordinates_dataframe, output_path, sep=',', row.names = FALSE)
                                                          ^~~
```
[R/plotting_functions.R:143:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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:143:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L143) *style:* **Use spaces to indent, not tabs.**
```r
	message(paste('Wrote tear file to ',output_path, '\n Check that it exists beside your outline.roi file'))
^
```
[R/plotting_functions.R:143:16:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L143) *style:* **Only use double-quotes.**
```r
	message(paste('Wrote tear file to ',output_path, '\n Check that it exists beside your outline.roi file'))
               ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:143:38:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L143) *style:* **Commas should always have a space after.**
```r
	message(paste('Wrote tear file to ',output_path, '\n Check that it exists beside your outline.roi file'))
                                     ^
```
[R/plotting_functions.R:143:51:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L143) *style:* **Only use double-quotes.**
```r
	message(paste('Wrote tear file to ',output_path, '\n Check that it exists beside your outline.roi file'))
                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:144:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L144) *style:* **Use spaces to indent, not tabs.**
```r
	return(tear_coordinates_dataframe)
^
```
[R/plotting_functions.R:151:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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/81cf21ca6b31da08f86aca07889b139dc56c61db/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:156:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L156) *style:* **Use spaces to indent, not tabs.**
```r
	output_path <- file.path(path_to_retina_data_folder, "P.csv")
^
```
[R/plotting_functions.R:157:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L157) *style:* **Use spaces to indent, not tabs.**
```r
	colnames(outline_coordinates)<- c("V1","V2")
^
```
[R/plotting_functions.R:157:31:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L157) *style:* **Put spaces around all infix operators.**
```r
	colnames(outline_coordinates)<- c("V1","V2")
                             ~^
```
[R/plotting_functions.R:157:41:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L157) *style:* **Commas should always have a space after.**
```r
	colnames(outline_coordinates)<- c("V1","V2")
                                        ^
```
[R/plotting_functions.R:158:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L158) *style:* **Use spaces to indent, not tabs.**
```r
	write.table(outline_coordinates, output_path, sep=',', row.names = F)
^
```
[R/plotting_functions.R:158:51:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L158) *style:* **Put spaces around all infix operators.**
```r
	write.table(outline_coordinates, output_path, sep=',', row.names = F)
                                                 ~^~
```
[R/plotting_functions.R:158:52:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L158) *style:* **Only use double-quotes.**
```r
	write.table(outline_coordinates, output_path, sep=',', row.names = F)
                                                   ^~~
```
[R/plotting_functions.R:159:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/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:159:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L159) *style:* **Use spaces to indent, not tabs.**
```r
	message(paste('Wrote coordinates file to ',output_path, '\n Check that it exists beside your outline.roi file'))
^
```
[R/plotting_functions.R:159:16:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L159) *style:* **Only use double-quotes.**
```r
	message(paste('Wrote coordinates file to ',output_path, '\n Check that it exists beside your outline.roi file'))
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:159:45:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L159) *style:* **Commas should always have a space after.**
```r
	message(paste('Wrote coordinates file to ',output_path, '\n Check that it exists beside your outline.roi file'))
                                            ^
```
[R/plotting_functions.R:159:58:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L159) *style:* **Only use double-quotes.**
```r
	message(paste('Wrote coordinates file to ',output_path, '\n Check that it exists beside your outline.roi file'))
                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:160:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L160) *style:* **Use spaces to indent, not tabs.**
```r
	return(outline_coordinates)
^
```
[R/plotting_functions.R:170:42:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L170) *style:* **Commas should always have a space after.**
```r
plot_original_xy_locations <- function(x,y) {
                                         ^
```
[R/plotting_functions.R:171:1:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L171) *style:* **Use spaces to indent, not tabs.**
```r
	points(x+0.005,y,pch=4, cex=0.5, col="gainsboro")
^
```
[R/plotting_functions.R:171:10:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L171) *style:* **Put spaces around all infix operators.**
```r
	points(x+0.005,y,pch=4, cex=0.5, col="gainsboro")
        ~^~
```
[R/plotting_functions.R:171:17:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L171) *style:* **Commas should always have a space after.**
```r
	points(x+0.005,y,pch=4, cex=0.5, col="gainsboro")
                ^
```
[R/plotting_functions.R:171:19:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L171) *style:* **Commas should always have a space after.**
```r
	points(x+0.005,y,pch=4, cex=0.5, col="gainsboro")
                  ^
```
[R/plotting_functions.R:171:22:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L171) *style:* **Put spaces around all infix operators.**
```r
	points(x+0.005,y,pch=4, cex=0.5, col="gainsboro")
                    ~^~
```
[R/plotting_functions.R:171:29:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L171) *style:* **Put spaces around all infix operators.**
```r
	points(x+0.005,y,pch=4, cex=0.5, col="gainsboro")
                           ~^~
```
[R/plotting_functions.R:171:38:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L171) *style:* **Put spaces around all infix operators.**
```r
	points(x+0.005,y,pch=4, cex=0.5, col="gainsboro")
                                    ~^~
```
[R/plotting_functions.R:172:12:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L172) *style:* **Commas should always have a space after.**
```r
  points(x,y,pch=4, cex=0.5, col="black")
           ^
```
[R/plotting_functions.R:172:14:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L172) *style:* **Commas should always have a space after.**
```r
  points(x,y,pch=4, cex=0.5, col="black")
             ^
```
[R/plotting_functions.R:172:17:](https://github.com/bc/retina/blob/81cf21ca6b31da08f86aca07889b139dc56c61db/R/plotting_functions.R#L172) *style:* **Put spaces around all infix operators.**
```r
  points(x,y,pch=4, cex=0.5, col="black")
               ~^~
```


@rob-Hitchens I dont understand completely how can i set owner without constructor?


I don't know if I understood your question correctly, but EdiEntry is a struct thus it cannot be assigned the null value. So each time you check for pass it around it allocates by default as the empty path. This is not in the cache its like the zero value inside an int32 allocation.


isWhitelistedNetworkConnection should be isWhitelistedWifiConnection


Изменил.


I used my own in time when disabling checkers wasn't working properly. I can surely update now, or al least test it :)


Are you passing in the value manually? You could raise PR to not do the above if a value is set?


Спасибо.


Поменял решение.


Code style pls: the max line length: 80


Good, thanks.


Hello, you've done a good job!
You mentioned
> You may wonder why a keyboard layout containing all of Unicode is not devised then? The limited number of keycode available through USB simply disallow such a thing.

While in Chapter 10 “Keyboard/Keypad Page (0x07)” of [Hut1_12v2.pdf](http://www.usb.org/developers/hidpage/Hut1_12v2.pdf), at the last row of Table 12, it is clearly written that Usage ID (Dec) 232-65535 / (Hex) E8-FFFF is reserved. Although that is not enough for all code points in all planes of Unicode, it is almost enough for 1 plane of characters, which can satisfy a number of requirements.
Am I correct? I am going to make a big USB keyboard containing 500 to 600 keys for desktops. This is one of the key issues determining whether this is possible.


Is this the right place? I am not sure any action like this should be done on startServer


that means
process.env.mypostingkey
process.env.sadbin
like this?

and where put discord bot token?


@Nadahar thanks for letting me know. I'm just updating it and some dependencies, that's what happens while updates are happening


why did u do this ?
![man-on-stairs-going-down-symbol-vector_145794281](https://user-images.githubusercontent.com/39866063/40909657-26c325c6-67fb-11e8-9202-026b529d90bf.jpg)


Commit de base


We want the view to be launch when the server a .dk is launch. But I agree
with. For the moment it is just a workaround. I will implement it in a
clean way

On Mon, 4 Jun 2018, 11:27 Emilio Jesús Gallego Arias, <
notifications@github.com> wrote:

> Is this the right place? I am not sure any action like this should be done
> on startServer
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/lachhebo/dedukti-editor/commit/50be14a20320aeb34616c04dc1e33302e8afaeaf#commitcomment-29230135>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AeudjnQPgxKPKQxoi4eoKrV5kMs_1qztks5t5P2OgaJpZM4UYvs9>
> .
>


Why did u do this ?
![43598](https://user-images.githubusercontent.com/39866063/40909726-53e9f0de-67fb-11e8-897e-216e40aa7ef1.png)


@VinaLx
( 抱拳


This was needed to compile bra in K computer with C++03 option.


We want the view to be launch when a .dk file is launch. But I agree with
you, for the moment, it is just a workaround. I will implement it in a
clean way

On Mon, 4 Jun 2018, 11:29 Ismail lachheb, <ismaellachheb@gmail.com> wrote:

>
>
> On Mon, 4 Jun 2018, 11:27 Emilio Jesús Gallego Arias, <
> notifications@github.com> wrote:
>
>> Is this the right place? I am not sure any action like this should be
>> done on startServer
>>
>> —
>> You are receiving this because you authored the thread.
>> Reply to this email directly, view it on GitHub
>> <https://github.com/lachhebo/dedukti-editor/commit/50be14a20320aeb34616c04dc1e33302e8afaeaf#commitcomment-29230135>,
>> or mute the thread
>> <https://github.com/notifications/unsubscribe-auth/AeudjnQPgxKPKQxoi4eoKrV5kMs_1qztks5t5P2OgaJpZM4UYvs9>
>> .
>>
>


Why ?
![canstock22249256](https://user-images.githubusercontent.com/39866063/40909753-678fb2c2-67fb-11e8-93be-3a7383ba711a.jpg)


another ques can you send me a details instruction  how deploy this in heroku and run 24/7 hour??
If then i send you 3 sbd as a gift and for good work


增家


Do you want core_reg_stall?


@yutakuroda こんにちは。おそらく別のkotaさんにメンションしてると思いますのでご注意ください。


thankyou


Thank you @Juba19 for suggestions


boi is there a way the sizes of the canvas can be obtained, if they can then width/2 and height/2 could be used.. I remember both java and swift had this feature..


This breaks vim-airline https://github.com/vim-airline/vim-airline/issues/605#issuecomment-394293794

What would be the prefered fix for this?


Pls. add a small notice about function intentions, at least about its input and output.


Since the static MG and AT thing can take damage, we should consider to decrease the price by a bit. Maybe 500 or 600?


I think you should locate that in the constructor, keep in mind that the server can be started many times as the client can decide to shut it down, so start server should only do server business itself.


copy/paste Du weißt schon :-)


OKay!! Link enabled :)
https://mega.nz/#!xI5QHb6D!yMrUjL3DTgzYs8d4sjZ83RPSPelBO3qwrC0eIiBILYo


I see

If that remains, just report a bug on Symplify: https://github.com/symplify/symplify/issues/new

I'll give it prirority


Looks like a very old test. We haven't worked on `ElasticsearchRepositoryTest` really for a long time. This is for the reason that all of its test scope is also covered by BaseRepositoryTest. So one could argue just to drop these tests. But there's not really a need to do so. I assume that this test has more resources indexed than inserted just because the internal processing order has changed. Should I still check this?


@pranaymedatwal  There is still indention issue in some files. it should be 2 spaces.


I'm fine with aiming at 80 chars, and aiming at 100 chars if we can't make
that and an extreme of 120 chars, although I also don't mind occasional
scrolling horizontally.
Most of all I don't want to waste time with reformatting working code,
especially when it takes it into what I see as a negative direction...the
styles that were there are very common throughout the codebase so *if* we
are to change those then it should be discussed/agreed/documented/made
consistent throughout & I for one am very loathe to embark on such a
project...I would rather just leave it alone

On 4 June 2018 at 09:43, Dominic König <notifications@github.com> wrote:

> I've tried a variety of screen settings - but the only way to cope with
> excessively long lines would be to use a (much) smaller font, which isn't
> acceptable for long screen hours and aging eyes though.
>
> The most I can handle is around 102 chars, everything beyond that requires
> horizontal scrolling hiding the left parts of the code, thus obscuring the
> flow.
>
> So, if this is not a Fran-only code base now, then I think you should take
> practical aspects of other coders into consideration. I don't insist on 80
> chars, but I can't handle 120 either - half way in-between would be a good
> compromise.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/nursix/eden/commit/d54f5ec71f77d09884a6cddcf86f1a4e80e1d8d8#commitcomment-29229484>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAXx2MSpmS8NgIVP0MaZICOM2O4fPAGDks5t5PNJgaJpZM4UYjLG>
> .
>


@leseb what about checking the ceph socket a/o ceph processes ?


TODO: must improve broadcasting, making it easier without having to go through an entire layer.
Perhaps a folder just for broadcasted messages.


> changed to 'tr1'

Interestingly enough, on master branches it was [switched to std](https://github.com/rakshasa/rtorrent/commit/3b39f37f49d4e439b81f6828f78316f8b61a48c0#diff-c625cf3c4e2b6574677c76e3910f33afL317) again. That's why I use [this](https://github.com/chros73/rtorrent-ps-ch/blob/a160a83ba6fa8bc25ed852dc2e2aa611d921dcf6/patches/command_pyroscope.cc#L49).


When will this go low?


ne oldu ne olacak bilmiyorum


Hi,
Yes, it works now but there is another one issue - urllib.error.URLError: <urlopen error timed out>
It occurs when I try to get list of tags from the repo which has more the 5 tags.


嗯嗯


The canvas size is defined in `gg.NewContext(w,h)`, but do you mean after it has been defined?
This can be obtained by using `gg.Width()` and `gg.Height()`!


Hi @twinaphex
I didn't see the problem you mention in my reicast PR comments but I had to add a `glEnable(GL_STENCIL_TEST)`at line 1530 to make ModVolMode 3 work. (It should probably be enabled all the time except for TR btw.)
Also, the two glBindBuffer at line 1607-8 are not needed AFAIK and might be responsible for the Soulcalibur crash you mention in an earlier commit (applying shadows after PT polys)


Should this be core_reg_stall? How can you assign to a parameter?  Maybe I don't know system verlog?


It was a quick fix I guess. Thanks for the finding, I've pushed the cleanup.


@TomasVotruba One more thing. I can't use yours because of `indentation: tab`. I am using different indentation per project (more customers with different habbits), so I need it not defined.


No Remove process.env.STEEMKEY fully and then put ypur posting key similarly remove process.env.STEEMAUTHOR and put sadbin.

Similarly replace process.env.DISCORDTOKEN with your discord token.
client.connect({
        token: process.env.DISCORDTOKEN
    });

To deploy on Heroku you just have to push the changes and run it by node upvote.js. But in the free plan, it will not run 24 hours, for that you need to buy the basic plan.


Tag abschließen!


It's back up now but something went wrong with the update so it's in limbo between 3.2.1 and 3.2.2... *shrugs* seems to be working though


Tag abschließen


![](https://github.trello.services/images/mini-trello-icon.png) [T111: Neues Intro](https://trello.com/c/5HvlYbXu/128-t111-neues-intro)


Can you try to make sure this compiles with iverilog or something? It should be easy with fusesoc.


Are you sure about that? XD


Stephen


Consider adding docstrings for the class and its methods.


IMHO checking for a ceph process is enough.


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Wieso hast du den Titel entfernt?


Look at other cores like mam. They have tests and the fusesoc .core file.


Turns out Gef and some of the pharma set ups with long-running Chaste installs were still using PETSc 3.0 quite happily until this commit(!).

As a general rule, if it isn't hurting us we might as well leave logic for old versions in. Makes code a bit untidier I know, but doesn't even get compiled so doesn't really do any harm...

That said, for boost serialization I'm considering a 'wipe' of unsupported versions as that really is adding confusion trying to cope with all the old versions!


Bitte lies die Aufgabe nochmal: Header mit Navigation.


Quick question ... As more and more providers add support for auto-discover to their old packages; is there any way of auto-detecting which packages are doing this so you know which/when to remove them from app.php ? Something in the logs, something about packages loaded twice or something like that? Curious to see if I've missed any in my own "spring cleaning". :)


Yes, I will try compiling it with iverilog. Other modules have the cocotb-based unit tests which currently require Synopsys VCS. Since I don't have access to Synopsys VCS, it will not be possible to test using those unit tests.


This method could be a private member, or belong to a different Util class.


System.out.println("Binary number:"+n);


so if I understand `dc.DrawCircle(dc.width()/2,dc.height()/2,400)` would also hit the centre..
why do you use semi colons? i though go added them _'well virtually added them'_ by default at compile time.. 🤔


`ok==True` is redundant. (Also, you don't *need* to use parens in python conditionals.)


We don't open firewall ports by default. Please add a separate option to do so.


@emmjaykay Mind filing an issue? You're comment on an old commit. Thanks!


How does this support username password authentication?
Can you provide an example?


Humm... Acho q eu tinha entendido errado oq vc disse então :(


Inconsistent style. Chỗ có dấu `;`, chỗ không có. Em cần chọn 1 style cho 1 project và follow.

Project ở 4handy thường không có dấu `;`


@permission_classes((IsAuthenticated,)) add ","


test


Created multidev environment [pm-portal#ci-2](https://dashboard.pantheon.io/sites/8b0b6fe0-30fe-45c6-8bbd-e777ebae0ca8#ci-2).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-2-pm-portal.pantheonsite.io/)


static in a builder omg please fix this!


Hình như không có option `upset` mà chỉ có option `upsert`?


ah.  thx.


Created multidev environment [dgreat#pr-foot](https://dashboard.pantheon.io/sites/41cad7fe-472d-43a9-a470-d391b9622376#pr-foot).

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


True. However, IMHO, the code would be easier to follow with the define (of course we would need to explicitly ask for ARM32 and ARM64). Otherwise the coder might get confused about x86-regs in the ARM code. It is, however, your call, Tamas.


Same defines as above.


Thermal sensors are OK


Can you add "then" in there, too?

GET BOX THEN OPEN IT


APB framework already defines `cluster` to be `kubernetes` or `openshift`. Suggest defining affirmative boolean value 'clustered' instead of frequent use of `not singlenode`, especially since I would suspect most test and prod environments to use `clustered` or `secure-clustered` plan by default.


var myvar;


var myvar = 10;


Created multidev environment [attn-cms#ci-3](https://dashboard.pantheon.io/sites/59b8ccd3-dda4-48d3-8337-e687b7694b78#ci-3).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-3-attn-cms.pantheonsite.io/)


var soma = 15 + 8;


Agree. This is, however, not a functional change that should be in this patch. Please, create a separate patch if you would like to change style issues. Besides, if you would like to adjust the spacing issue, please consider the coding style of LibVMI and change the function so that it does not contain the extra space before and after the '('. Consistency is key :)


Thanks; I'll leave it out of Android Studio for now.


Please remove this extra line.


var soma += 24


Are you sure you got this the right way around?  This is for an output stream, so the slave interface should match the stream depth, and the master interface should be 2 (the way it was before). I think it's the other one that's backwards --- it has the master interface (which the dwidth converter is driving into the HLS module) fixed at 2 bytes.

Or I might just be really confused. :-)


g


ok


`yarn add reset-css`


>I'll be reverting this commit after testing and establishing it is the cause.

It seems that this is not the commit responsible for the behaviour being experienced. Sorry for the false alarm.


Please remove the extra line.


var soma = 24 * 3;


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Instalación **`index.php?route=account/cron_indepi2`**


Small nitpick but this assertion is not necessary since the next assertion would fail if site_setting is not present.


/"loadatomneutronprotonelectronroute"
/"loadnehtechnineissuegoldatomfussiocode"


Given that I don't do Python, can you please clarify what the setting 'backup_keep_count_by_number' actually does? I did a test with it set to 1 and it did a new backup but left the previous one as well, whereas I had expected it to keep only the 1 backup. Thanks.


Hi,
  I have a question about this commit.
  Can you explain why you implement the function "aligned_alloc" instead of using the predefined api in stdlib?
  Thank you very much.

Best Regards
HC


> It seems that this is not the commit responsible for the behaviour being experienced.

Thanks for letting us know.

Nevertheless, it should avoid using services with parental control set on them anyway. if it doesn't have that check, it has the potential to cause the kind of problem you encountered.


I am confused. Do we really need the lower two events for handling priv calls? :)


holy files batman!


C<SC<SC


function divisao(x, y){
return x + y;
}
divisao(15, 8);
23


lol


divisao(10, 2);
12