{"comment":{"url":"https://api.github.com/repos/bc/retina/comments/27479360","html_url":"https://github.com/bc/retina/commit/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d#commitcomment-27479360","id":27479360,"user":{"login":"lintr-bot","id":10925265,"avatar_url":"https://avatars3.githubusercontent.com/u/10925265?v=4","gravatar_id":"","url":"https://api.github.com/users/lintr-bot","html_url":"https://github.com/lintr-bot","followers_url":"https://api.github.com/users/lintr-bot/followers","following_url":"https://api.github.com/users/lintr-bot/following{/other_user}","gists_url":"https://api.github.com/users/lintr-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/lintr-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lintr-bot/subscriptions","organizations_url":"https://api.github.com/users/lintr-bot/orgs","repos_url":"https://api.github.com/users/lintr-bot/repos","events_url":"https://api.github.com/users/lintr-bot/events{/privacy}","received_events_url":"https://api.github.com/users/lintr-bot/received_events","type":"User","site_admin":false},"position":null,"line":null,"path":null,"commit_id":"5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d","created_at":"2018-02-11T00:09:33Z","updated_at":"2018-02-11T00:09:33Z","author_association":"NONE","body":"[inst/extdata/test_retinas/3hgbqg/main.r:4:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L4) *style:* **Lines should not be more than 80 characters.**\n```r\n​  LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:4:3:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L4) *style:* **Variable or function name should be snake_case.**\n```r\n​  LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n  ^~~~~~~~~~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:5:3:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L5) *style:* **Variable or function name should be snake_case.**\n```r\n​  RESOLUTION_var <- 500 #Plot width in pixels\n  ^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:9:3:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L9) *style:* **Variable or function name should be snake_case.**\n```r\n​  IJ <-data.frame(maxX = 1429,\n  ^~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:9:6:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L9) *style:* **Put spaces around all infix operators.**\n```r\n​  IJ <-data.frame(maxX = 1429,\n     ^~~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:13:33:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                  deltaX = (1429-108)/21,\n                               ~^~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:13:38:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                  deltaX = (1429-108)/21,\n                                    ~^~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:14:32:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L14) *style:* **Put spaces around all infix operators.**\n```r\n​                  deltaY = (989-85)/14)\n                              ~^~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:14:36:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L14) *style:* **Put spaces around all infix operators.**\n```r\n​                  deltaY = (989-85)/14)\n                                  ~^~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:26:23:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L26) *style:* **Commas should never have a space before.**\n```r\n​          height = 30 ,# height of the counting frame in microns\n                     ~^\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:26:24:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L26) *style:* **Commas should always have a space after.**\n```r\n​          height = 30 ,# height of the counting frame in microns\n                       ^\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:31:30:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L31) *style:* **Commas should never have a space before.**\n```r\n​          extrapolate = TRUE ,          #Predicts densities to the equator.\n                            ~^\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:33:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L33) *style:* **Lines should not be more than 80 characters.**\n```r\n​          rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:34:24:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L34) *style:* **Put spaces around all infix operators.**\n```r\n​          plot_suppress=TRUE,\n                      ~^~\n```\n[inst/extdata/test_retinas/3hgbqg/main.r:41:3:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/3hgbqg/main.r#L41) *warning:* **no visible global function definition for ‘retinaplot’**\n```r\n​  retinaplot(my_retina)\n  ^~~~~~~~~~\n```\n[inst/extdata/test_retinas/40oik5/main.r:2:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L2) *style:* **Lines should not be more than 80 characters.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/40oik5/main.r:2:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L2) *style:* **Variable or function name should be snake_case.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/40oik5/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L3) *style:* **Variable or function name should be snake_case.**\n```r\n​RESOLUTION_var <- 500 #Plot width in pixels\n^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/40oik5/main.r:5:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L5) *style:* **Variable or function name should be snake_case.**\n```r\n​IJ <-data.frame(maxX = 944,\n^~\n```\n[inst/extdata/test_retinas/40oik5/main.r:5:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L5) *style:* **Put spaces around all infix operators.**\n```r\n​IJ <-data.frame(maxX = 944,\n   ^~~\n```\n[inst/extdata/test_retinas/40oik5/main.r:21:15:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L21) *style:* **Commas should never have a space before.**\n```r\n​  height = 25 ,# height of the counting frame in microns\n             ~^\n```\n[inst/extdata/test_retinas/40oik5/main.r:21:16:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L21) *style:* **Commas should always have a space after.**\n```r\n​  height = 25 ,# height of the counting frame in microns\n               ^\n```\n[inst/extdata/test_retinas/40oik5/main.r:26:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L26) *style:* **Commas should never have a space before.**\n```r\n​  extrapolate = TRUE ,          #Predicts densities to the equator.\n                    ~^\n```\n[inst/extdata/test_retinas/40oik5/main.r:28:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L28) *style:* **Lines should not be more than 80 characters.**\n```r\n​  rotation_ccw = 0, # when set to -90 degrees, the rotation is unaltered from the measured orientation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/40oik5/main.r:29:16:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L29) *style:* **Put spaces around all infix operators.**\n```r\n​  plot_suppress=TRUE,\n              ~^~\n```\n[inst/extdata/test_retinas/40oik5/main.r:34:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L34) *warning:* **no visible global function definition for ‘retinaplot’**\n```r\n​retinaplot(my_retina, rotation=115, col_breaks_source = c(0, 35000))\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/40oik5/main.r:34:31:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/40oik5/main.r#L34) *style:* **Put spaces around all infix operators.**\n```r\n​retinaplot(my_retina, rotation=115, col_breaks_source = c(0, 35000))\n                             ~^~\n```\n[inst/extdata/test_retinas/8pm223/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L3) *style:* **Lines should not be more than 80 characters.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/8pm223/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L3) *style:* **Variable or function name should be snake_case.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/8pm223/main.r:4:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L4) *style:* **Variable or function name should be snake_case.**\n```r\n​RESOLUTION_var <- 500 #Plot width in pixels\n^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/8pm223/main.r:6:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L6) *style:* **Variable or function name should be snake_case.**\n```r\n​IJ <-data.frame(maxX = 981,\n^~\n```\n[inst/extdata/test_retinas/8pm223/main.r:6:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L6) *style:* **Put spaces around all infix operators.**\n```r\n​IJ <-data.frame(maxX = 981,\n   ^~~\n```\n[inst/extdata/test_retinas/8pm223/main.r:22:15:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L22) *style:* **Commas should never have a space before.**\n```r\n​  height = 25 ,# height of the counting frame in microns\n             ~^\n```\n[inst/extdata/test_retinas/8pm223/main.r:22:16:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L22) *style:* **Commas should always have a space after.**\n```r\n​  height = 25 ,# height of the counting frame in microns\n               ^\n```\n[inst/extdata/test_retinas/8pm223/main.r:27:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L27) *style:* **Commas should never have a space before.**\n```r\n​  extrapolate = TRUE ,          #Predicts densities to the equator.\n                    ~^\n```\n[inst/extdata/test_retinas/8pm223/main.r:29:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L29) *style:* **Lines should not be more than 80 characters.**\n```r\n​  rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/8pm223/main.r:30:16:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L30) *style:* **Put spaces around all infix operators.**\n```r\n​  plot_suppress=TRUE,\n              ~^~\n```\n[inst/extdata/test_retinas/8pm223/main.r:34:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/8pm223/main.r#L34) *warning:* **no visible global function definition for ‘retinaplot’**\n```r\n​retinaplot(my_retina)\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L3) *style:* **Variable or function name should be snake_case.**\n```r\n​LAMBDA_var <- 0.1 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:4:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L4) *style:* **Variable or function name should be snake_case.**\n```r\n​RESOLUTION_var <- 500 #Plot width in pixels\n^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:8:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L8) *style:* **Variable or function name should be snake_case.**\n```r\n​IJ <-data.frame(maxX = 1210,\n^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:8:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L8) *style:* **Put spaces around all infix operators.**\n```r\n​IJ <-data.frame(maxX = 1210,\n   ^~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:12:31:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1210-72)/20,\n                             ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:12:35:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1210-72)/20,\n                                 ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:13:30:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (928-46)/15)\n                            ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:13:34:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (928-46)/15)\n                                ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:26:21:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L26) *style:* **Commas should never have a space before.**\n```r\n​        height = 45 ,# height of the counting frame in microns\n                   ~^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:26:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L26) *style:* **Commas should always have a space after.**\n```r\n​        height = 45 ,# height of the counting frame in microns\n                     ^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:31:28:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L31) *style:* **Commas should never have a space before.**\n```r\n​        extrapolate = TRUE ,          #Predicts densities to the equator.\n                          ~^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:33:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L33) *style:* **Lines should not be more than 80 characters.**\n```r\n​        rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:34:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L34) *style:* **Put spaces around all infix operators.**\n```r\n​        plot_suppress=TRUE,\n                    ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:41:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L41) *warning:* **no visible global function definition for ‘retinaplot’**\n```r\n​retinaplot(my_retina)\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:43:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L43) *style:* **Variable or function name should be snake_case.**\n```r\n​findPeak <- function(my_retina){\n^~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:44:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L44) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tcoord <- my_retina$trimmed_data\n^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:45:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L45) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tpeak_temp <- coord[which.max(coord$z),]\n^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:45:40:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L45) *style:* **Commas should always have a space after.**\n```r\n​\tpeak_temp <- coord[which.max(coord$z),]\n                                       ^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Lines should not be more than 80 characters.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:29:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Put spaces around all infix operators.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n                           ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:45:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Commas should always have a space after.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n                                            ^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:59:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Put spaces around all infix operators.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n                                                         ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:71:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Commas should always have a space after.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n                                                                      ^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:79:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Put spaces around all infix operators.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n                                                                             ~^~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:46:91:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L46) *style:* **Commas should always have a space after.**\n```r\n​\tpeak <- data.frame(latitude=abs(peak_temp[,1]), longitude=peak_temp[,2], peak=peak_temp[,3])\n                                                                                          ^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:47:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L47) *style:* **Use spaces to indent, not tabs.**\n```r\n​\treturn(peak)\n^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:48:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L48) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t}\n^\n```\n[inst/extdata/test_retinas/bjii4t/main.r:53:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L53) *style:* **Commented code should be removed.**\n```r\n​  #lambda=0.001\n   ^~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:54:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L54) *style:* **Commented code should be removed.**\n```r\n​  #polynomial_m=2\n   ^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/bjii4t/main.r:55:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/bjii4t/main.r#L55) *style:* **Commented code should be removed.**\n```r\n​  #rotation=30\n   ^~~~~~~~~~~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L3) *style:* **Lines should not be more than 80 characters.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L3) *style:* **Variable or function name should be snake_case.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:4:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L4) *style:* **Variable or function name should be snake_case.**\n```r\n​RESOLUTION_var <- 500 #Plot width in pixels\n^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:8:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L8) *style:* **Variable or function name should be snake_case.**\n```r\n​IJ <-data.frame(maxX = 1084,\n^~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:8:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L8) *style:* **Put spaces around all infix operators.**\n```r\n​IJ <-data.frame(maxX = 1084,\n   ^~~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:12:31:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1084-100)/21,\n                             ~^~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:12:36:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1084-100)/21,\n                                  ~^~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:13:31:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (1022-36)/14)\n                             ~^~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:13:35:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (1022-36)/14)\n                                 ~^~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:26:21:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L26) *style:* **Commas should never have a space before.**\n```r\n​        height = 35 ,# height of the counting frame in microns\n                   ~^\n```\n[inst/extdata/test_retinas/gv3igs/main.r:26:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L26) *style:* **Commas should always have a space after.**\n```r\n​        height = 35 ,# height of the counting frame in microns\n                     ^\n```\n[inst/extdata/test_retinas/gv3igs/main.r:31:28:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L31) *style:* **Commas should never have a space before.**\n```r\n​        extrapolate = TRUE ,          #Predicts densities to the equator.\n                          ~^\n```\n[inst/extdata/test_retinas/gv3igs/main.r:33:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L33) *style:* **Lines should not be more than 80 characters.**\n```r\n​        rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:34:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L34) *style:* **Put spaces around all infix operators.**\n```r\n​        plot_suppress=TRUE,\n                    ~^~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:41:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L41) *warning:* **no visible global function definition for ‘retinaplot’**\n```r\n​retinaplot(my_retina,rotation=270)\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/gv3igs/main.r:41:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L41) *style:* **Commas should always have a space after.**\n```r\n​retinaplot(my_retina,rotation=270)\n                     ^\n```\n[inst/extdata/test_retinas/gv3igs/main.r:41:30:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/gv3igs/main.r#L41) *style:* **Put spaces around all infix operators.**\n```r\n​retinaplot(my_retina,rotation=270)\n                            ~^~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L3) *style:* **Lines should not be more than 80 characters.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L3) *style:* **Variable or function name should be snake_case.**\n```r\n​LAMBDA_var <- 0.001 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:4:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L4) *style:* **Variable or function name should be snake_case.**\n```r\n​RESOLUTION_var <- 500 #Plot width in pixels\n^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:8:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L8) *style:* **Variable or function name should be snake_case.**\n```r\n​IJ <-data.frame(maxX = 1189,\n^~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:8:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L8) *style:* **Put spaces around all infix operators.**\n```r\n​IJ <-data.frame(maxX = 1189,\n   ^~~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:12:31:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1189-26)/19,\n                             ~^~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:12:35:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1189-26)/19,\n                                 ~^~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:13:30:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (986-81)/15)\n                            ~^~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:13:34:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (986-81)/15)\n                                ~^~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:26:21:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L26) *style:* **Commas should never have a space before.**\n```r\n​        height = 25 ,# height of the counting frame in microns\n                   ~^\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:26:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L26) *style:* **Commas should always have a space after.**\n```r\n​        height = 25 ,# height of the counting frame in microns\n                     ^\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:31:28:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L31) *style:* **Commas should never have a space before.**\n```r\n​        extrapolate = TRUE ,          #Predicts densities to the equator.\n                          ~^\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:33:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L33) *style:* **Lines should not be more than 80 characters.**\n```r\n​        rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:34:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L34) *style:* **Put spaces around all infix operators.**\n```r\n​        plot_suppress=TRUE,\n                    ~^~\n```\n[inst/extdata/test_retinas/jhvbwt/main.r:41:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/jhvbwt/main.r#L41) *warning:* **no visible global function definition for ‘retinaplot’**\n```r\n​retinaplot(my_retina)\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/raxp91/main.r:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L3) *style:* **Variable or function name should be snake_case.**\n```r\n​LAMBDA_var <- 0.1 #Thin plate spline smoothing. Lambda=0 would be interpolation.\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/raxp91/main.r:4:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L4) *style:* **Variable or function name should be snake_case.**\n```r\n​RESOLUTION_var <- 500 #Plot width in pixels\n^~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/raxp91/main.r:8:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L8) *style:* **Variable or function name should be snake_case.**\n```r\n​IJ <-data.frame(maxX = 1016,\n^~\n```\n[inst/extdata/test_retinas/raxp91/main.r:8:4:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L8) *style:* **Put spaces around all infix operators.**\n```r\n​IJ <-data.frame(maxX = 1016,\n   ^~~\n```\n[inst/extdata/test_retinas/raxp91/main.r:12:31:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1016-25)/18,\n                             ~^~\n```\n[inst/extdata/test_retinas/raxp91/main.r:12:35:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L12) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaX = (1016-25)/18,\n                                 ~^~\n```\n[inst/extdata/test_retinas/raxp91/main.r:13:30:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (923-48)/17)\n                            ~^~\n```\n[inst/extdata/test_retinas/raxp91/main.r:13:34:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L13) *style:* **Put spaces around all infix operators.**\n```r\n​                deltaY = (923-48)/17)\n                                ~^~\n```\n[inst/extdata/test_retinas/raxp91/main.r:26:21:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L26) *style:* **Commas should never have a space before.**\n```r\n​        height = 45 ,# height of the counting frame in microns\n                   ~^\n```\n[inst/extdata/test_retinas/raxp91/main.r:26:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L26) *style:* **Commas should always have a space after.**\n```r\n​        height = 45 ,# height of the counting frame in microns\n                     ^\n```\n[inst/extdata/test_retinas/raxp91/main.r:31:28:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L31) *style:* **Commas should never have a space before.**\n```r\n​        extrapolate = TRUE ,          #Predicts densities to the equator.\n                          ~^\n```\n[inst/extdata/test_retinas/raxp91/main.r:33:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L33) *style:* **Lines should not be more than 80 characters.**\n```r\n​        rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[inst/extdata/test_retinas/raxp91/main.r:34:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L34) *style:* **Put spaces around all infix operators.**\n```r\n​        plot_suppress=TRUE,\n                    ~^~\n```\n[inst/extdata/test_retinas/raxp91/main.r:41:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L41) *warning:* **no visible global function definition for ‘retinaplot’**\n```r\n​retinaplot(my_retina, lambda=0.001, polynomial_m=\t2, rotation=30)\n^~~~~~~~~~\n```\n[inst/extdata/test_retinas/raxp91/main.r:41:29:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L41) *style:* **Put spaces around all infix operators.**\n```r\n​retinaplot(my_retina, lambda=0.001, polynomial_m=\t2, rotation=30)\n                           ~^~\n```\n[inst/extdata/test_retinas/raxp91/main.r:41:49:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L41) *style:* **Put spaces around all infix operators.**\n```r\n​retinaplot(my_retina, lambda=0.001, polynomial_m=\t2, rotation=30)\n                                               ~^\n```\n[inst/extdata/test_retinas/raxp91/main.r:41:62:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/inst/extdata/test_retinas/raxp91/main.r#L41) *style:* **Put spaces around all infix operators.**\n```r\n​retinaplot(my_retina, lambda=0.001, polynomial_m=\t2, rotation=30)\n                                                            ~^~\n```\n[R/composite.R:2:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L2) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @description This is a subfunction, that is useful when creating average maps.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/composite.R:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L3) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param retina_list A list containing retina objects, with names(retina_list) all defined.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/composite.R:3:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L3) *style:* **Commented code should be removed.**\n```r\n​##' @param retina_list A list containing retina objects, with names(retina_list) all defined.\n ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/composite.R:4:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L4) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param rotation_indices Each value in this vector will correspond to the amount of rotation applied to each retina in the list.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/composite.R:5:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L5) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param ... Arguments passed from other functions. You can access the thin plate spline interpolator here.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/composite.R:6:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L6) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @return sum_mat The sum of all retina objects in the list, with respect to the rotation indices.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/composite.R:7:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L7) *style:* **Commented code should be removed.**\n```r\n​##' @author Brian Cohn \\email{brian.cohn@@usc.edu} and Lars Schmitz\n ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/composite.R:9:14:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/composite.R#L9) *warning:* **no visible global function definition for ‘mat_from_ret_obj’**\n```r\n​  sum_mat <- mat_from_ret_obj(retina_list[[1]], rotation = 0, ...)\n             ^~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L3) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' You can decide how much to rotate the retina before returning the matrix. You can also pass arguments to the polar plotter.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:6:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L6) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param n the number by which to divide the matrix by. Useful when generating partial averages.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:7:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L7) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param reflect logical, by default it is TRUE, in order to view the retina from outside the eye (rather than from within.)\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:10:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L10) *style:* **Commented code should be removed.**\n```r\n​##' @author Brian Cohn \\email{brian.cohn@@usc.edu} and Lars Schmitz\n ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:20:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L20) *style:* **Lines should not be more than 80 characters.**\n```r\n​  az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:27:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L27) *style:* **Lines should not be more than 80 characters.**\n```r\n​  map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE,\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:28:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L28) *style:* **Lines should not be more than 80 characters.**\n```r\n​    outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/matrix_retobj.R:28:22:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L28) *style:* **Put spaces around all infix operators.**\n```r\n​    outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],\n                    ~^~\n```\n[R/matrix_retobj.R:30:3:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L30) *style:* **Variable or function name should be snake_case.**\n```r\n​  MAT <- map2fit[[2]]$z\n  ^~~\n```\n[R/matrix_retobj.R:32:13:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/matrix_retobj.R#L32) *style:* **Put spaces around all infix operators.**\n```r\n​  return(MAT/n)\n           ~^~\n```\n[R/plotting_functions.R:3:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L3) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' Extracts xy and falciform coordinates from datapoints collected from retistruct. Falc and Datapoints are stacked upon one another\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:5:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L5) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param datapoints_from_retistruct data structure that comes from the datapoints.csv, which is automatically generated by Retistruct.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:7:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L7) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @return L list of pixel xy positions, and falciform coordinates in [1] and [2], respectively\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:7:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L7) *style:* **Commented code should be removed.**\n```r\n​##' @return L list of pixel xy positions, and falciform coordinates in [1] and [2], respectively\n ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:9:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L9) *style:* **Lines should not be more than 80 characters.**\n```r\n​extract_xy_and_falciform <- function(datapoints_from_retistruct, number_of_sampling_sites) {\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:10:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L10) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tpixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,]\n^\n```\n[R/plotting_functions.R:10:78:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L10) *style:* **Commas should always have a space after.**\n```r\n​\tpixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,]\n                                                                             ^\n```\n[R/plotting_functions.R:11:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L11) *style:* **Lines should not be more than 80 characters.**\n```r\n​\tfalciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:11:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L11) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tfalciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])\n^\n```\n[R/plotting_functions.R:11:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L11) *warning:* **local variable ‘falciform_len’ assigned but may not be used**\n```r\n​\tfalciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])\n ^~~~~~~~~~~~~\n```\n[R/plotting_functions.R:11:54:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L11) *style:* **Commas should always have a space after.**\n```r\n​\tfalciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])\n                                                     ^\n```\n[R/plotting_functions.R:11:87:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L11) *style:* **Commas should always have a space after.**\n```r\n​\tfalciform_len <- length(datapoints_from_retistruct[,1]) - length(pixel_xy_positions[,1])\n                                                                                      ^\n```\n[R/plotting_functions.R:12:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L12) *style:* **Use spaces to indent, not tabs.**\n```r\n​\txy_len <- length(pixel_xy_positions[,1])\n^\n```\n[R/plotting_functions.R:12:39:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L12) *style:* **Commas should always have a space after.**\n```r\n​\txy_len <- length(pixel_xy_positions[,1])\n                                      ^\n```\n[R/plotting_functions.R:13:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L13) *style:* **Use spaces to indent, not tabs.**\n```r\n​\ttotal_len <- length(datapoints_from_retistruct[,1])\n^\n```\n[R/plotting_functions.R:13:50:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L13) *style:* **Commas should always have a space after.**\n```r\n​\ttotal_len <- length(datapoints_from_retistruct[,1])\n                                                 ^\n```\n[R/plotting_functions.R:14:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L14) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tfalciform_coordinates <- datapoints_from_retistruct[(xy_len+1):total_len,]\n^\n```\n[R/plotting_functions.R:14:61:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L14) *style:* **Put spaces around all infix operators.**\n```r\n​\tfalciform_coordinates <- datapoints_from_retistruct[(xy_len+1):total_len,]\n                                                           ~^~\n```\n[R/plotting_functions.R:14:75:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L14) *style:* **Commas should always have a space after.**\n```r\n​\tfalciform_coordinates <- datapoints_from_retistruct[(xy_len+1):total_len,]\n                                                                          ^\n```\n[R/plotting_functions.R:15:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L15) *style:* **Use spaces to indent, not tabs.**\n```r\n​\treturn(list(pixel_xy_positions, falciform_coordinates))\n^\n```\n[R/plotting_functions.R:20:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L20) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' ImageJ values don't always show up the right way, because Y values get larger and positive while moving down the image.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:22:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L22) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param falciform_xy_coordinates 2 columns of coordinate (X,Y) data in ImageJ pixel format\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:23:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L23) *style:* **Commented code should be removed.**\n```r\n​##' @param xy_img_dimensions 2-cal list i.e. c(400,200)\n ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:26:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L26) *style:* **Lines should not be more than 80 characters.**\n```r\n​reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions){\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:26:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L26) *style:* **Variable and function names should not be longer than 30 characters.**\n```r\n​reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions){\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:26:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L26) *style:* **Variable or function name should be snake_case.**\n```r\n​reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions){\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:27:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L27) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\tfalciform_xy_coordinates_transformed <- falciform_xy_coordinates #make a copy\n^~\n```\n[R/plotting_functions.R:27:3:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L27) *style:* **Variable and function names should not be longer than 30 characters.**\n```r\n​\t\tfalciform_xy_coordinates_transformed <- falciform_xy_coordinates #make a copy\n  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L28) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\tfalc_y <- falciform_xy_coordinates[,2]\n^~\n```\n[R/plotting_functions.R:28:39:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L28) *style:* **Commas should always have a space after.**\n```r\n​\t\tfalc_y <- falciform_xy_coordinates[,2]\n                                      ^\n```\n[R/plotting_functions.R:29:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L29) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\thalf_of_vertical_pixels <- xy_img_dimensions[2]/2\n^~\n```\n[R/plotting_functions.R:29:50:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L29) *style:* **Put spaces around all infix operators.**\n```r\n​\t\thalf_of_vertical_pixels <- xy_img_dimensions[2]/2\n                                                ~^~\n```\n[R/plotting_functions.R:30:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L30) *style:* **Lines should not be more than 80 characters.**\n```r\n​\t\tfalciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:30:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L30) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\tfalciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels\n^~\n```\n[R/plotting_functions.R:30:55:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L30) *style:* **Put spaces around all infix operators.**\n```r\n​\t\tfalciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels\n                                                     ~^~\n```\n[R/plotting_functions.R:30:80:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L30) *style:* **Put spaces around all infix operators.**\n```r\n​\t\tfalciform_xy_coordinates_transformed$cyan <- (falc_y-half_of_vertical_pixels)*-1 + half_of_vertical_pixels\n                                                                              ~^~\n```\n[R/plotting_functions.R:31:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L31) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\treturn(falciform_xy_coordinates_transformed)\n^~\n```\n[R/plotting_functions.R:35:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L35) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' Shows a visualization of the outline, as well as the location of each datapoint, with fit plot.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:37:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L37) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param pixel_xy_positions 2 columns of coordinate (X,Y) data in ImageJ pixel format\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:38:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L38) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param z_vector numerical vector of density values for each of the coordinates\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:39:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L39) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param xy_outline_points 2 columns of coordinate(X,Y) data in ImageJ pixel format for the outline coordinates.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:39:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L39) *style:* **Commented code should be removed.**\n```r\n​##' @param xy_outline_points 2 columns of coordinate(X,Y) data in ImageJ pixel format for the outline coordinates.\n ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:42:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L42) *style:* **Lines should not be more than 80 characters.**\n```r\n​traditional_flatmount_plot <- function(pixel_xy_positions,z_vector, xy_outline_points){\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:42:59:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L42) *style:* **Commas should always have a space after.**\n```r\n​traditional_flatmount_plot <- function(pixel_xy_positions,z_vector, xy_outline_points){\n                                                          ^\n```\n[R/plotting_functions.R:43:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L43) *style:* **Lines should not be more than 80 characters.**\n```r\n​\tfit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:43:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L43) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tfit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.\n^\n```\n[R/plotting_functions.R:43:9:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L43) *warning:* **no visible global function definition for ‘Tps’, Did you mean 'nls'?**\n```r\n​\tfit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.\n        ^~~\n```\n[R/plotting_functions.R:44:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L44) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tset.panel(2,2)\n^\n```\n[R/plotting_functions.R:44:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L44) *warning:* **no visible global function definition for ‘set.panel’**\n```r\n​\tset.panel(2,2)\n ^~~~~~~~~\n```\n[R/plotting_functions.R:44:14:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L44) *style:* **Commas should always have a space after.**\n```r\n​\tset.panel(2,2)\n             ^\n```\n[R/plotting_functions.R:45:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L45) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tplot(fit) # four diagnostic plots of  fit and residuals.\n^\n```\n[R/plotting_functions.R:46:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L46) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tset.panel()\n^\n```\n[R/plotting_functions.R:46:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L46) *warning:* **no visible global function definition for ‘set.panel’**\n```r\n​\tset.panel()\n ^~~~~~~~~\n```\n[R/plotting_functions.R:47:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L47) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t# summary of fit and estimates of lambda the smoothing parameter\n^\n```\n[R/plotting_functions.R:48:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L48) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tsummary(fit)\n^\n```\n[R/plotting_functions.R:49:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L49) *style:* **Use spaces to indent, not tabs.**\n```r\n​\tsurface(fit) # Quick image/contour plot of GCV surface.\n^\n```\n[R/plotting_functions.R:49:2:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L49) *warning:* **no visible global function definition for ‘surface’**\n```r\n​\tsurface(fit) # Quick image/contour plot of GCV surface.\n ^~~~~~~\n```\n[R/plotting_functions.R:50:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L50) *style:* **Use spaces to indent, not tabs.**\n```r\n​\treturn(fit)\n^\n```\n[R/plotting_functions.R:58:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L58) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' Shows a visualization of the outline, as well as the location of each datapoint so the user can identify where the tears are.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:61:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L61) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @param path_to_retina_data_folder The path to the folder that contains the outline.roi file.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:62:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L62) *style:* **Lines should not be more than 80 characters.**\n```r\n​##' @return roi_coordinates XY vals of pixel coordinates of the outline points, in order.\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[R/plotting_functions.R:66:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L66) *style:* **Use spaces to indent, not tabs.**\n```r\n​\troi_object <- read.ijroi(file.path(path_to_retina_data_folder, \"outline.roi\"))\n^\n```\n[R/plotting_functions.R:66:16:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L66) *warning:* **no visible global function definition for ‘read.ijroi’**\n```r\n​\troi_object <- read.ijroi(file.path(path_to_retina_data_folder, \"outline.roi\"))\n               ^~~~~~~~~~\n```\n[R/plotting_functions.R:69:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L69) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\t## ImageJ ROI format plots has the coordinate (0, 0) in the top\n^~\n```\n[R/plotting_functions.R:70:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L70) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\t  ## left.  We have the coordinate (0, 0) in the bottom left. We need\n^~\n```\n[R/plotting_functions.R:71:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L71) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\t  ## to transform P so that the outline appears in the correct\n^~\n```\n[R/plotting_functions.R:72:1:](https://github.com/bc/retina/blob/5b3a4f85f09c1443bdf9d0fb2a254fcaa2bede5d/R/plotting_functions.R#L72) *style:* **Use spaces to indent, not tabs.**\n```r\n​\t\t  ## orientation.\n^~\n```\n"}}
{"actor":{"display_login":"lintr-bot"}}