[R/plotting-colours.R:89:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L89) *style:* **Lines should not be more than 100 characters.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-colours.R:89:32:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L89) *style:* **Put spaces around all infix operators.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                              ~^~~
```
[R/plotting-colours.R:89:35:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L89) *style:* **Put spaces around all infix operators.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                                 ~^~~
```
[R/plotting-colours.R:89:41:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L89) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                                        ^
```
[R/plotting-colours.R:106:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L106) *style:* **Lines should not be more than 100 characters.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-colours.R:106:32:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L106) *style:* **Put spaces around all infix operators.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                              ~^~~
```
[R/plotting-colours.R:106:35:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L106) *style:* **Put spaces around all infix operators.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                                 ~^~~
```
[R/plotting-colours.R:106:41:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L106) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                                        ^
```
[R/plotting-colours.R:131:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L131) *style:* **Lines should not be more than 100 characters.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-colours.R:131:32:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L131) *style:* **Put spaces around all infix operators.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                              ~^~~
```
[R/plotting-colours.R:131:35:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L131) *style:* **Put spaces around all infix operators.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                                 ~^~~
```
[R/plotting-colours.R:131:41:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L131) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if (all(na.omit(object[])%%1==0)) { # some factor rasters are actually real number -- makes no sense
                                        ^
```
[R/plotting-colours.R:284:75:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L284) *style:* **Put spaces around all infix operators.**
```r
    isFac <- any(raster::is.factor(grobToPlot)) & all(na.omit(grobToPlot[]%%1)==0)
                                                                         ~^~~
```
[R/plotting-colours.R:284:79:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-colours.R#L284) *style:* **Put spaces around all infix operators.**
```r
    isFac <- any(raster::is.factor(grobToPlot)) & all(na.omit(grobToPlot[]%%1)==0)
                                                                             ~^~~
```
[R/plotting-helpers.R:1023:44:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L1023) *style:* **Commas should always have a space after.**
```r
          grobToPlot <- grobToPlot[polySeq,]
                                           ^
```
[R/plotting-helpers.R:1028:38:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L1028) *style:* **Commas should always have a space after.**
```r
        grobToPlot <- grobToPlot[a[1,],]
                                     ^
```
[R/plotting-helpers.R:1028:40:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L1028) *style:* **Commas should always have a space after.**
```r
        grobToPlot <- grobToPlot[a[1,],]
                                       ^
```
[R/plotting-helpers.R:1291:41:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L1291) *style:* **Put spaces around all infix operators.**
```r
            if (all(na.omit(grobToPlot[]%%1)==0)) {
                                       ~^~~
```
[R/plotting-helpers.R:1291:45:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L1291) *style:* **Put spaces around all infix operators.**
```r
            if (all(na.omit(grobToPlot[]%%1)==0)) {
                                           ~^~~
```
[R/plotting-helpers.R:1380:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L1380) *style:* **Lines should not be more than 100 characters.**
```r
    grid.rect(x = 0, height = unit(1 + needsNewTitle * inherits(grobToPlot, "Raster") * 0.20 / (nRows / 2), "npc"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2511:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2511) *style:* **Lines should not be more than 100 characters.**
```r
#'          jitter(sort(rbeta(nPoints, betaPar, betaPar) * (maxY - minY) + minY, decreasing = TRUE)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2589:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2589) *style:* **Variable or function name should be lowerCamelCase.**
```r
thin.SpatialPolygons <- function(x, tolerance = NULL, returnDataFrame = FALSE, minCoordsToThin = 0,
^~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2610:8:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2610) *style:* **Commented code should be removed.**
```r
      #xyOrd[["out"]] <- xyOrd[["out"]][thinRes, ]# thin line
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2633:50:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2633) *style:* **Commas should always have a space after.**
```r
            dat <- x@data[as.numeric(names1) + 1,]
                                                 ^
```
[R/plotting-helpers.R:2634:14:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2634) *style:* **Commented code should be removed.**
```r
            #row.names(dat) <- as.character(seq_len(length(xyOrd)))
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2666:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2666) *style:* **Variable or function name should be lowerCamelCase.**
```r
thin.default <- function(x, tolerance, returnDataFrame, minCoordsToThin, ...) {
^~~~~~~~~~~~
```
[R/plotting-helpers.R:2701:3:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2701) *style:* **Variable or function name should be lowerCamelCase.**
```r
  IDs <- tryCatch(unlist(lapply(ordSeq, function(xx) {
  ^~~
```
[R/plotting-helpers.R:2726:7:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2726) *style:* **Commented code should be removed.**
```r
    # Polygons <- rep(rep(seq(numPolygons), numPolygon), idLength$V1) # sequential numbering
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2727:5:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2727) *style:* **Variable or function name should be lowerCamelCase.**
```r
    Polygons <- rep(rep(IDs, numPolygon), idLength$V1) # actual ID labelling
    ^~~~~~~~
```
[R/plotting-helpers.R:2728:5:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2728) *style:* **Variable or function name should be lowerCamelCase.**
```r
    Polygon <- rep(unlist(lapply(numPolygon, seq)), idLength$V1)
    ^~~~~~~
```
[R/plotting-helpers.R:2735:36:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2735) *style:* **Commas should always have a space after.**
```r
    return(data.frame(lat = xyOrd[,1], long = xyOrd[,2], order = orders,
                                   ^
```
[R/plotting-helpers.R:2735:54:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2735) *style:* **Commas should always have a space after.**
```r
    return(data.frame(lat = xyOrd[,1], long = xyOrd[,2], order = orders,
                                                     ^
```
[R/plotting-helpers.R:2737:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2737) *style:* **Lines should not be more than 100 characters.**
```r
                      #group = paste0(as.character(Polygons), ".", as.character(Polygon)))) # the actual fortify
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2740:40:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2740) *style:* **Commas should always have a space after.**
```r
    out <- setDT(data.frame(x = xyOrd[,1], y = xyOrd[,2], groups = groups))
                                       ^
```
[R/plotting-helpers.R:2740:55:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2740) *style:* **Commas should always have a space after.**
```r
    out <- setDT(data.frame(x = xyOrd[,1], y = xyOrd[,2], groups = groups))
                                                      ^
```
[R/plotting-helpers.R:2755:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2755) *style:* **Lines should not be more than 100 characters.**
```r
    which(polygon@data$Shape_Area>(sort(polygon@data$Shape_Area, decreasing = TRUE)[maxNumPolygons]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting-helpers.R:2755:34:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2755) *style:* **Put spaces around all infix operators.**
```r
    which(polygon@data$Shape_Area>(sort(polygon@data$Shape_Area, decreasing = TRUE)[maxNumPolygons]))
                                ~^~
```
[R/plotting-helpers.R:2755:35:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2755) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    which(polygon@data$Shape_Area>(sort(polygon@data$Shape_Area, decreasing = TRUE)[maxNumPolygons]))
                                  ^
```
[R/plotting-helpers.R:2778:26:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-helpers.R#L2778) *style:* **Commas should always have a space after.**
```r
          totalAvailable," polygons in this view. See options('reproducuble.maxNumPolygons')")
                         ^
```
[R/plotting-other.R:202:48:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-other.R#L202) *style:* **Put spaces around all infix operators.**
```r
  if (any(raster::is.factor(ras1)) & all(ras1[]%%1==0)) {
                                              ~^~~
```
[R/plotting-other.R:202:51:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-other.R#L202) *style:* **Put spaces around all infix operators.**
```r
  if (any(raster::is.factor(ras1)) & all(ras1[]%%1==0)) {
                                                 ~^~~
```
[R/plotting-other.R:251:30:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-other.R#L251) *style:* **Commas should always have a space after.**
```r
    if (sum(corners$coords[1,] - corners$coords[2,]) %==% 0) {
                             ^
```
[R/plotting-other.R:251:51:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-other.R#L251) *style:* **Commas should always have a space after.**
```r
    if (sum(corners$coords[1,] - corners$coords[2,]) %==% 0) {
                                                  ^
```
[R/plotting-other.R:335:27:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-other.R#L335) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (length(row) == 0) { # above the plot
                          ^
```
[R/plotting-other.R:338:30:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting-other.R#L338) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (length(column) == 0) { # above the plot
                             ^
```
[R/plotting.R:308:6:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting.R#L308) *style:* **Commented code should be removed.**
```r
    #whFrame <- grep(scalls, pattern = "^Plot|^quickPlot::Plot")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting.R:318:8:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/R/plotting.R#L318) *style:* **Commented code should be removed.**
```r
      #dotObjs <- mget(dotNames[!noName], envir = plotFrame, inherits = TRUE)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-clickExtent.R:11:3:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-clickExtent.R#L11) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Sr1 <- Polygon(coords1)
  ^~~
```
[tests/testthat/test-clickExtent.R:12:3:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-clickExtent.R#L12) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Srs1 <- Polygons(list(Sr1), "s1")
  ^~~~
```
[tests/testthat/test-clickExtent.R:14:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-clickExtent.R#L14) *style:* **Lines should not be more than 100 characters.**
```r
  crs(shpEcozone) <- "+init=epsg:4326 +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-examples.R:11:15:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-examples.R#L11) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    setwd(owd)}
              ^
```
[tests/testthat/test-Plot-do-call.R:8:3:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-do-call.R#L8) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Sr1 <- Polygon(coords1)
  ^~~
```
[tests/testthat/test-Plot-do-call.R:9:3:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-do-call.R#L9) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Srs1 <- Polygons(list(Sr1), "s1")
  ^~~~
```
[tests/testthat/test-Plot-do-call.R:11:1:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-do-call.R#L11) *style:* **Lines should not be more than 100 characters.**
```r
  crs(shpEcozone) <- "+init=epsg:4326 +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-Plot-do-call.R:17:24:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-do-call.R#L17) *style:* **Commas should always have a space after.**
```r
  r <- raster(extent(0,10,0,10), res = 1, vals = 1:100)
                       ^
```
[tests/testthat/test-Plot-do-call.R:17:27:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-do-call.R#L17) *style:* **Commas should always have a space after.**
```r
  r <- raster(extent(0,10,0,10), res = 1, vals = 1:100)
                          ^
```
[tests/testthat/test-Plot-do-call.R:17:29:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-do-call.R#L17) *style:* **Commas should always have a space after.**
```r
  r <- raster(extent(0,10,0,10), res = 1, vals = 1:100)
                            ^
```
[tests/testthat/test-Plot-nonVisual.R:65:21:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-nonVisual.R#L65) *style:* **Commented code should be removed.**
```r
  library(raster); #on.exit(detach("package:raster"), add = TRUE)
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-Plot-nonVisual.R:70:3:](https://github.com/PredictiveEcology/quickPlot/blob/a56deb8655f93651bce833d3956f6df051421c0a/tests/testthat/test-Plot-nonVisual.R#L70) *style:* **Variable or function name should be lowerCamelCase.**
```r
  N <- ncol * nrow
  ^
```


Sounds good! I'll get rid of the test.


Yeah, I mistakenly included it... It was actually commented. The as.raw function is a builtin function. No need for it in the base library


at first blush, I'd rather than require a 1Gb package to use opencv though ...


comment 2


Is this from the generated client or added manually?


Chamo quejeso


I had proposed another fix, the source of record browses in the context being in base automation (use of ids and self.id). I saw with @rco-odoo it seemed that the fix did not prevent to end up with browse record in the context and therefore in the froozen options, which filled the cache for nothing (and it can quickly increase, and keep closed cursor). In fact the options for rendering must remain simple but as the list of options is not fixed, the idea is to fix them upstream. According to @rco-odoo the impact on performance (which we discussed during the fix) is negligible. I do not have any data on that.
I talked with @JKE-be about putting a white list for the contact json (with averwrite of the field in website and web_editor for additional keys). However, I come to the conclusion that the templates and actions can be modified, since nothing prevents a partner to have added information in the context and used by an overwrite on the contact template. The white list therefore seems a bad method.


docs: changes to documentation

We added the readme file in this repository

We have added the readme file in order to be able to explain the project more conveniently. In the README.md file you will see all the requirements to be able to run the project.


I'm surprised to here that the whole region is missing.  All of this should be in the stable/generated versions.  @deviprasad135 went through an exercise of comparing the manual and the generated versions.  Maybe these changes are in @deviprasad135 development branch.  @szymczdm was recently working on merging that branch.  @szymczdm is the missing content present in devi's branch?


Created multidev environment [therapyrealm-d8#pr-2](https://dashboard.pantheon.io/sites/1e2f72fb-b1d6-4944-b76a-de18b38c3d0c#pr-2).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-2-therapyrealm-d8.pantheonsite.io/)


issue-6790-VRP-D-term (EnergyArchmage) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: OK (2964 of 2969 tests passed, 11 test warnings)

Messages:

 * 11 tests had: AUD diffs.
 * 4 tests had: EIO diffs.
 * 2 tests had: ESO small diffs.
 * 2 tests had: MTR small diffs.
 * 5 tests had: SSZ big diffs.
 * 2 tests had: Table small diffs.

Failures:

regression Test Summary
 * Passed: 638
 * Failed: 5

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.83%25-yellow.png)


😄 This is the easy fix I was looking for! Thanks tested on Firefox.


[R/default_param_doc.R:45:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/default_param_doc.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  N0,
  ^~
```
[R/default_param_doc.R:46:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/default_param_doc.R#L46) *style:* **Variable or function name should be snake_case.**
```r
  Nsims,
  ^~~~~
```
[R/default_param_doc.R:61:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/default_param_doc.R#L61) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/functions_likelihood.R:7:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L7) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
lik_pt  <- function (lambda, mu, time){
                    ^
```
[R/functions_likelihood.R:8:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L8) *style:* **Variable or function name should be snake_case.**
```r
  Lambda <- exp((mu-lambda)*(time))
  ^~~~~~
```
[R/functions_likelihood.R:8:20:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L8) *style:* **Put spaces around all infix operators.**
```r
  Lambda <- exp((mu-lambda)*(time))
                  ~^~
```
[R/functions_likelihood.R:8:28:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L8) *style:* **Put spaces around all infix operators.**
```r
  Lambda <- exp((mu-lambda)*(time))
                          ~^~
```
[R/functions_likelihood.R:8:29:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L8) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  Lambda <- exp((mu-lambda)*(time))
                            ^
```
[R/functions_likelihood.R:9:20:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                  ~^~~
```
[R/functions_likelihood.R:9:25:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                       ~^~
```
[R/functions_likelihood.R:9:26:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                         ^
```
[R/functions_likelihood.R:9:27:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                          ^
```
[R/functions_likelihood.R:9:29:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                           ~^~
```
[R/functions_likelihood.R:9:30:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                             ^
```
[R/functions_likelihood.R:9:32:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                              ~^~
```
[R/functions_likelihood.R:9:39:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                                     ~^~
```
[R/functions_likelihood.R:9:40:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                                       ^
```
[R/functions_likelihood.R:9:47:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L9) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  out    <- (lambda==mu)*( 1/(1+lambda*(time)) ) +
                                              ^
```
[R/functions_likelihood.R:10:12:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
          ~^~~
```
[R/functions_likelihood.R:10:17:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
               ~^~
```
[R/functions_likelihood.R:10:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                 ^
```
[R/functions_likelihood.R:10:19:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                  ^
```
[R/functions_likelihood.R:10:27:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                         ~^~
```
[R/functions_likelihood.R:10:31:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                             ~^~
```
[R/functions_likelihood.R:10:32:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                               ^
```
[R/functions_likelihood.R:10:39:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                                     ~^~
```
[R/functions_likelihood.R:10:42:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                                        ~^~
```
[R/functions_likelihood.R:10:49:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                                               ~^~
```
[R/functions_likelihood.R:10:50:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                                                 ^
```
[R/functions_likelihood.R:10:57:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                                                       ~^~~
```
[R/functions_likelihood.R:10:63:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    (lambda!=mu)*( (lambda-mu)/(lambda-mu*Lambda*(lambda!=mu)) )
                                                              ^
```
[R/functions_likelihood.R:18:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L18) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
lik_ut  <- function (lambda, mu, time){
                    ^
```
[R/functions_likelihood.R:19:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  Lambda <- exp((mu-lambda)*(time))
  ^~~~~~
```
[R/functions_likelihood.R:19:20:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L19) *style:* **Put spaces around all infix operators.**
```r
  Lambda <- exp((mu-lambda)*(time))
                  ~^~
```
[R/functions_likelihood.R:19:28:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L19) *style:* **Put spaces around all infix operators.**
```r
  Lambda <- exp((mu-lambda)*(time))
                          ~^~
```
[R/functions_likelihood.R:19:29:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L19) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  Lambda <- exp((mu-lambda)*(time))
                            ^
```
[R/functions_likelihood.R:20:20:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                  ~^~~
```
[R/functions_likelihood.R:20:25:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                       ~^~
```
[R/functions_likelihood.R:20:26:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                         ^
```
[R/functions_likelihood.R:20:27:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                          ^
```
[R/functions_likelihood.R:20:34:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                ~^~
```
[R/functions_likelihood.R:20:35:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                  ^
```
[R/functions_likelihood.R:20:41:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                       ~^~
```
[R/functions_likelihood.R:20:42:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                         ^
```
[R/functions_likelihood.R:20:44:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                          ~^~
```
[R/functions_likelihood.R:20:51:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Put spaces around all infix operators.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                                 ~^~
```
[R/functions_likelihood.R:20:52:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                                   ^
```
[R/functions_likelihood.R:20:59:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L20) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  out    <- (lambda==mu)*( lambda*(time)/(1+lambda*(time)) ) +
                                                          ^
```
[R/functions_likelihood.R:21:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:21:12:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
          ~^~~
```
[R/functions_likelihood.R:21:17:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
               ~^~
```
[R/functions_likelihood.R:21:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                 ^
```
[R/functions_likelihood.R:21:19:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                  ^
```
[R/functions_likelihood.R:21:36:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                                  ~^~
```
[R/functions_likelihood.R:21:59:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                                                         ~^~
```
[R/functions_likelihood.R:21:66:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                                                                ~^~
```
[R/functions_likelihood.R:21:67:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                                                                  ^
```
[R/functions_likelihood.R:21:74:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Put spaces around all infix operators.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                                                                        ~^~~
```
[R/functions_likelihood.R:21:80:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    (lambda!=mu)*( (lambda - lambda*Lambda) / (lambda - mu*Lambda*(lambda!=mu)) )
                                                                               ^
```
[R/functions_likelihood.R:29:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L29) *style:* **Variable or function name should be snake_case.**
```r
lik_Pi  <- function (lambda, mu, time){
^~~~~~
```
[R/functions_likelihood.R:29:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L29) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
lik_Pi  <- function (lambda, mu, time){
                    ^
```
[R/functions_likelihood.R:30:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
  out <- lik_pt(lambda = lambda, mu = mu, time = time)*(1-lik_ut(lambda = lambda, mu = mu, time = time))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:30:10:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L30) *warning:* **no visible global function definition for ‘lik_pt’**
```r
  out <- lik_pt(lambda = lambda, mu = mu, time = time)*(1-lik_ut(lambda = lambda, mu = mu, time = time))
         ^~~~~~
```
[R/functions_likelihood.R:30:55:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L30) *style:* **Put spaces around all infix operators.**
```r
  out <- lik_pt(lambda = lambda, mu = mu, time = time)*(1-lik_ut(lambda = lambda, mu = mu, time = time))
                                                     ~^~
```
[R/functions_likelihood.R:30:56:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L30) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  out <- lik_pt(lambda = lambda, mu = mu, time = time)*(1-lik_ut(lambda = lambda, mu = mu, time = time))
                                                       ^
```
[R/functions_likelihood.R:30:58:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L30) *style:* **Put spaces around all infix operators.**
```r
  out <- lik_pt(lambda = lambda, mu = mu, time = time)*(1-lik_ut(lambda = lambda, mu = mu, time = time))
                                                        ~^~
```
[R/functions_likelihood.R:30:59:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L30) *warning:* **no visible global function definition for ‘lik_ut’**
```r
  out <- lik_pt(lambda = lambda, mu = mu, time = time)*(1-lik_ut(lambda = lambda, mu = mu, time = time))
                                                          ^~~~~~
```
[R/functions_likelihood.R:36:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
#' Basic denominator likelihood module. If squared yields branching contribution, otherwise is shift contribution.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:40:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
lik_single_event <- function(lambda, mu, time1, time2){ #if squared describes the linkage between two consecutives full lines, if its exponent is one it describes instead a single-lineage shift.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:40:55:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L40) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
lik_single_event <- function(lambda, mu, time1, time2){ #if squared describes the linkage between two consecutives full lines, if its exponent is one it describes instead a single-lineage shift.
                                                      ^
```
[R/functions_likelihood.R:45:14:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  lik <- lik^(-1)
             ^
```
[R/functions_likelihood.R:55:38:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L55) *style:* **Variable or function name should be snake_case.**
```r
lik_custom      <- function(dataset, N0 = 1, input_check = 1){
                                     ^~
```
[R/functions_likelihood.R:60:19:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L60) *warning:* **no visible global function definition for ‘times_matrix2t_coordinates’**
```r
  coords       <- times_matrix2t_coordinates(times_matrix = times_matrix)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:61:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L61) *warning:* **local variable ‘ti’ assigned but may not be used**
```r
  ti           <- coords$ti
  ^~
```
[R/functions_likelihood.R:65:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L65) *style:* **Variable or function name should be snake_case.**
```r
  Ntimepoints  <- ncol(times_matrix)
  ^~~~~~~~~~~
```
[R/functions_likelihood.R:68:23:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L68) *warning:* **no visible global function definition for ‘check_input_data_coherence’**
```r
    coherent_input <- check_input_data_coherence(dataset = dataset, N0 = N0)
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:69:29:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L69) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (coherent_input == 0){stop("Input data are incoherent")}
                            ^
```
[R/functions_likelihood.R:69:63:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L69) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if (coherent_input == 0){stop("Input data are incoherent")}
                                                              ^
```
[R/functions_likelihood.R:72:26:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L72) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!is.null(ncol(tb))){ rownames(tb) <- c("time", "who") }
                         ^
```
[R/functions_likelihood.R:72:61:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L72) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!is.null(ncol(tb))){ rownames(tb) <- c("time", "who") }
                                                            ^
```
[R/functions_likelihood.R:73:26:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L73) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!is.null(ncol(ts))){ rownames(ts) <- c("time", "who") }
                         ^
```
[R/functions_likelihood.R:73:61:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L73) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!is.null(ncol(ts))){ rownames(ts) <- c("time", "who") }
                                                            ^
```
[R/functions_likelihood.R:74:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L74) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  nbranches <- 0; if(!is.null(ncol(tb))){nbranches <- ncol(tb)};
                    ^
```
[R/functions_likelihood.R:74:41:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L74) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  nbranches <- 0; if(!is.null(ncol(tb))){nbranches <- ncol(tb)};
                                        ^
```
[R/functions_likelihood.R:74:63:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L74) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  nbranches <- 0; if(!is.null(ncol(tb))){nbranches <- ncol(tb)};
                                                              ^
```
[R/functions_likelihood.R:75:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L75) *style:* **Variable or function name should be snake_case.**
```r
  Ntips   <-  N0 + nbranches
  ^~~~~
```
[R/functions_likelihood.R:76:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L76) *warning:* **local variable ‘fathers’ assigned but may not be used**
```r
  fathers <- unname( c(rep(0, N0), tb[2,]) ); sons <- 1:Ntips
  ^~~~~~~
```
[R/functions_likelihood.R:76:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fathers <- unname( c(rep(0, N0), tb[2,]) ); sons <- 1:Ntips
                    ^
```
[R/functions_likelihood.R:76:41:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L76) *style:* **Commas should always have a space after.**
```r
  fathers <- unname( c(rep(0, N0), tb[2,]) ); sons <- 1:Ntips
                                        ^
```
[R/functions_likelihood.R:76:43:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L76) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fathers <- unname( c(rep(0, N0), tb[2,]) ); sons <- 1:Ntips
                                          ^
```
[R/functions_likelihood.R:76:47:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L76) *warning:* **local variable ‘sons’ assigned but may not be used**
```r
  fathers <- unname( c(rep(0, N0), tb[2,]) ); sons <- 1:Ntips
                                              ^~~~
```
[R/functions_likelihood.R:77:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
  lik_den <- 1; r <- rep(regime <- 1, Ntips); n <- 1; t <- 2; shift <- branch <- 0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:79:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L79) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/functions_likelihood.R:80:36:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L80) *style:* **Commas should always have a space after.**
```r
    shift  <- (sign(times_matrix[2,t]) < 0)
                                   ^
```
[R/functions_likelihood.R:81:36:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L81) *style:* **Commas should always have a space after.**
```r
    branch <- (sign(times_matrix[2,t]) > 0)
                                   ^
```
[R/functions_likelihood.R:83:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
    lineages_affected_by_the_event <- rep(0,n); lineages_affected_by_the_event[abs(times_matrix[2,t])] <- 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:83:45:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L83) *style:* **Commas should always have a space after.**
```r
    lineages_affected_by_the_event <- rep(0,n); lineages_affected_by_the_event[abs(times_matrix[2,t])] <- 1
                                            ^
```
[R/functions_likelihood.R:83:99:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L83) *style:* **Commas should always have a space after.**
```r
    lineages_affected_by_the_event <- rep(0,n); lineages_affected_by_the_event[abs(times_matrix[2,t])] <- 1
                                                                                ^
```
[R/functions_likelihood.R:85:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L85) *style:* **Commented code should be removed.**
```r
    # print(lineages_affected_by_the_event)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:87:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:87:38:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L87) *style:* **Commas should always have a space after.**
```r
    time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                     ^
```
[R/functions_likelihood.R:87:58:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L87) *style:* **Commas should always have a space after.**
```r
    time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                                         ^
```
[R/functions_likelihood.R:87:59:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L87) *style:* **Put spaces around all infix operators.**
```r
    time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                                         ~^~
```
[R/functions_likelihood.R:87:102:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L87) *style:* **Commas should always have a space after.**
```r
    time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                                                                ^
```
[R/functions_likelihood.R:88:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    per_lineage_outcome <- lik_single_event(time1 = time_interval1, time2 = time_interval2, lambda = lambdas[r[1:n]], mu = mus[r[1:n]])^expo
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:88:28:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L88) *warning:* **no visible global function definition for ‘lik_single_event’**
```r
    per_lineage_outcome <- lik_single_event(time1 = time_interval1, time2 = time_interval2, lambda = lambdas[r[1:n]], mu = mus[r[1:n]])^expo
                           ^~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:92:5:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L92) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/functions_likelihood.R:93:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
      updated <- update_regimes(t = t, regime = regime, times_matrix = times_matrix, r = r, n = n)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:93:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L93) *warning:* **no visible global function definition for ‘update_regimes’**
```r
      updated <- update_regimes(t = t, regime = regime, times_matrix = times_matrix, r = r, n = n)
                 ^~~~~~~~~~~~~~
```
[R/functions_likelihood.R:98:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L98) *style:* **Commented code should be removed.**
```r
    # t <- t + 1; t #remember to comment this
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:99:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L99) *style:* **Commented code should be removed.**
```r
    # print(r); #remember to comment this
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:107:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L107) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/functions_likelihood.R:108:36:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L108) *style:* **Commas should always have a space after.**
```r
    shift  <- (sign(times_matrix[2,t]) < 0)
                                   ^
```
[R/functions_likelihood.R:109:36:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L109) *style:* **Commas should always have a space after.**
```r
    branch <- (sign(times_matrix[2,t]) > 0)
                                   ^
```
[R/functions_likelihood.R:111:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L111) *style:* **Commented code should be removed.**
```r
    # print(r[1:n])
      ^~~~~~~~~~~~~
```
[R/functions_likelihood.R:112:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L112) *style:* **Commented code should be removed.**
```r
    # print(lambdas[r[1:n]])
      ^~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:113:37:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L113) *style:* **Commas should always have a space after.**
```r
    time_interval <- times_matrix[1,t] - times_matrix[1,t-1]
                                    ^
```
[R/functions_likelihood.R:113:57:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L113) *style:* **Commas should always have a space after.**
```r
    time_interval <- times_matrix[1,t] - times_matrix[1,t-1]
                                                        ^
```
[R/functions_likelihood.R:113:58:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L113) *style:* **Put spaces around all infix operators.**
```r
    time_interval <- times_matrix[1,t] - times_matrix[1,t-1]
                                                        ~^~
```
[R/functions_likelihood.R:114:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
    per_lineage_outcome <- lik_Pi(lambda = lambdas[r[1:n]], mu = mus[r[1:n]], time = time_interval)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:114:28:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L114) *warning:* **no visible global function definition for ‘lik_Pi’**
```r
    per_lineage_outcome <- lik_Pi(lambda = lambdas[r[1:n]], mu = mus[r[1:n]], time = time_interval)
                           ^~~~~~
```
[R/functions_likelihood.R:117:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L117) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(shift)
      ^
```
[R/functions_likelihood.R:118:5:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L118) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/functions_likelihood.R:119:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
      updated <- update_regimes(t = t, regime = regime, times_matrix = times_matrix, r = r, n = n)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:119:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L119) *warning:* **no visible global function definition for ‘update_regimes’**
```r
      updated <- update_regimes(t = t, regime = regime, times_matrix = times_matrix, r = r, n = n)
                 ^~~~~~~~~~~~~~
```
[R/functions_likelihood.R:124:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L124) *style:* **Commented code should be removed.**
```r
    # t <- t + 1; #remember to comment this
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:125:7:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L125) *style:* **Commented code should be removed.**
```r
    # print(r); #remember to comment this
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:133:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L133) *style:* **Lines should not be more than 80 characters.**
```r
#' Custom likelihood function that applies the procedure after tree splitting. It uses lik_custom for each lineages.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:138:39:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L138) *style:* **Variable or function name should be snake_case.**
```r
lik_custom_split <- function(dataset, N0 = 1, input_check = 1){
                                      ^~
```
[R/functions_likelihood.R:144:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L144) *warning:* **no visible global function definition for ‘split_times_matrix’**
```r
  split_matrices <- split_times_matrix(times_matrix)
                    ^~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:145:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L145) *style:* **Variable or function name should be snake_case.**
```r
  Ntips <- length(split_matrices)
  ^~~~~
```
[R/functions_likelihood.R:148:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L148) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/functions_likelihood.R:149:35:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L149) *style:* **Commas should always have a space after.**
```r
    ti_i <- split_matrices[[i]][1,1]
                                  ^
```
[R/functions_likelihood.R:153:12:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L153) *style:* **Commas should always have a space after.**
```r
    ts_i[2,] <- 1
           ^
```
[R/functions_likelihood.R:154:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L154) *style:* **Put spaces around all infix operators.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                   ~^~~
```
[R/functions_likelihood.R:154:25:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L154) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                        ^
```
[R/functions_likelihood.R:154:30:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L154) *style:* **Use <-, not =, for assignment.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                             ^
```
[R/functions_likelihood.R:154:30:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L154) *style:* **Put spaces around all infix operators.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                            ~^~
```
[R/functions_likelihood.R:154:35:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L154) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                                  ^
```
[R/functions_likelihood.R:155:48:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L155) *style:* **Commas should always have a space after.**
```r
    lambdas_i <- lambdas[split_matrices[[i]][3,]]
                                               ^
```
[R/functions_likelihood.R:156:44:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L156) *style:* **Commas should always have a space after.**
```r
    mus_i     <- mus[split_matrices[[i]][3,]]
                                           ^
```
[R/functions_likelihood.R:157:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L157) *style:* **Lines should not be more than 80 characters.**
```r
    tm_i      <- arrange_times_matrix(ti = ti_i, tf = tf_i, tb = tb_i, ts = ts_i)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:157:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L157) *warning:* **no visible global function definition for ‘arrange_times_matrix’**
```r
    tm_i      <- arrange_times_matrix(ti = ti_i, tf = tf_i, tb = tb_i, ts = ts_i)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:159:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L159) *warning:* **no visible global function definition for ‘lik_custom’**
```r
    lik[i]    <- lik_custom(dataset = dataset_i, N0 = 1)
                 ^~~~~~~~~~
```
[R/functions_likelihood.R:164:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L164) *style:* **Lines should not be more than 80 characters.**
```r
#' Custom likelihood function for single lineages. You can use it after you apply split_times_matrix.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:169:50:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L169) *style:* **Variable or function name should be snake_case.**
```r
lik_custom_single_lineage   <- function(dataset, N0 = 1, input_check = 1){
                                                 ^~
```
[R/functions_likelihood.R:174:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L174) *style:* **Variable or function name should be snake_case.**
```r
  Ntimepoints  <- ncol(times_matrix)
  ^~~~~~~~~~~
```
[R/functions_likelihood.R:175:19:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L175) *warning:* **no visible global function definition for ‘times_matrix2t_coordinates’**
```r
  tf           <- times_matrix2t_coordinates(times_matrix = times_matrix)$tf
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:180:5:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L180) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/functions_likelihood.R:181:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L181) *style:* **Lines should not be more than 80 characters.**
```r
      time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:181:40:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L181) *style:* **Commas should always have a space after.**
```r
      time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                       ^
```
[R/functions_likelihood.R:181:60:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L181) *style:* **Commas should always have a space after.**
```r
      time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                                           ^
```
[R/functions_likelihood.R:181:61:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L181) *style:* **Put spaces around all infix operators.**
```r
      time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                                           ~^~
```
[R/functions_likelihood.R:181:104:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L181) *style:* **Commas should always have a space after.**
```r
      time_interval1 <- times_matrix[1,t] - times_matrix[1,t-1]; time_interval2 <- tf - times_matrix[1,t]
                                                                                ^
```
[R/functions_likelihood.R:182:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L182) *style:* **Lines should not be more than 80 characters.**
```r
      den_term <- lik_single_event(time1 = time_interval1, time2 = time_interval2, lambda = lambdas[regime], mu = mus[regime])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:182:19:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L182) *warning:* **no visible global function definition for ‘lik_single_event’**
```r
      den_term <- lik_single_event(time1 = time_interval1, time2 = time_interval2, lambda = lambdas[regime], mu = mus[regime])
                  ^~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:190:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L190) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/functions_likelihood.R:191:37:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L191) *style:* **Commas should always have a space after.**
```r
    time_interval <- times_matrix[1,t] - times_matrix[1,t-1]
                                    ^
```
[R/functions_likelihood.R:191:57:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L191) *style:* **Commas should always have a space after.**
```r
    time_interval <- times_matrix[1,t] - times_matrix[1,t-1]
                                                        ^
```
[R/functions_likelihood.R:191:58:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L191) *style:* **Put spaces around all infix operators.**
```r
    time_interval <- times_matrix[1,t] - times_matrix[1,t-1]
                                                        ~^~
```
[R/functions_likelihood.R:192:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L192) *style:* **Lines should not be more than 80 characters.**
```r
    num_term <- lik_Pi(lambda = lambdas[regime], mu = mus[regime], time = time_interval)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:192:17:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L192) *warning:* **no visible global function definition for ‘lik_Pi’**
```r
    num_term <- lik_Pi(lambda = lambdas[regime], mu = mus[regime], time = time_interval)
                ^~~~~~
```
[R/functions_likelihood.R:201:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L201) *style:* **Lines should not be more than 80 characters.**
```r
#' Custom likelihood function that applies the procedure after tree splitting. It uses lik_custom_single_lineage for each lineages.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:206:40:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L206) *style:* **Variable or function name should be snake_case.**
```r
lik_custom_split2 <- function(dataset, N0 = 1, input_check = 1){
                                       ^~
```
[R/functions_likelihood.R:212:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L212) *warning:* **no visible global function definition for ‘split_times_matrix’**
```r
  split_matrices <- split_times_matrix(times_matrix)
                    ^~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:213:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L213) *style:* **Variable or function name should be snake_case.**
```r
  Ntips <- length(split_matrices)
  ^~~~~
```
[R/functions_likelihood.R:215:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L215) *warning:* **local variable ‘ds’ assigned but may not be used**
```r
  ds <- vector("list", Ntips)
  ^~
```
[R/functions_likelihood.R:217:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L217) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/functions_likelihood.R:218:35:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L218) *style:* **Commas should always have a space after.**
```r
    ti_i <- split_matrices[[i]][1,1]
                                  ^
```
[R/functions_likelihood.R:222:12:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L222) *style:* **Commas should always have a space after.**
```r
    ts_i[2,] <- 1
           ^
```
[R/functions_likelihood.R:223:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L223) *style:* **Put spaces around all infix operators.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                   ~^~~
```
[R/functions_likelihood.R:223:25:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L223) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                        ^
```
[R/functions_likelihood.R:223:30:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L223) *style:* **Use <-, not =, for assignment.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                             ^
```
[R/functions_likelihood.R:223:30:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L223) *style:* **Put spaces around all infix operators.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                            ~^~
```
[R/functions_likelihood.R:223:35:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L223) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                                  ^
```
[R/functions_likelihood.R:224:48:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L224) *style:* **Commas should always have a space after.**
```r
    lambdas_i <- lambdas[split_matrices[[i]][3,]]
                                               ^
```
[R/functions_likelihood.R:225:44:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L225) *style:* **Commas should always have a space after.**
```r
    mus_i     <- mus[split_matrices[[i]][3,]]
                                           ^
```
[R/functions_likelihood.R:226:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L226) *style:* **Lines should not be more than 80 characters.**
```r
    tm_i      <- arrange_times_matrix(ti = ti_i, tf = tf_i, tb = tb_i, ts = ts_i)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:226:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L226) *warning:* **no visible global function definition for ‘arrange_times_matrix’**
```r
    tm_i      <- arrange_times_matrix(ti = ti_i, tf = tf_i, tb = tb_i, ts = ts_i)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:228:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L228) *warning:* **no visible global function definition for ‘lik_custom_single_lineage’**
```r
    lik[i]    <- lik_custom_single_lineage(dataset = dataset_i, N0 = 1)
                 ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:233:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L233) *style:* **Lines should not be more than 80 characters.**
```r
#' Custom likelihood function that applies the procedure after tree splitting. It uses lik_custom_single_lineage for each lineages.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:238:40:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L238) *style:* **Variable or function name should be snake_case.**
```r
lik_custom_split3 <- function(dataset, N0 = 1, input_check = 1){
                                       ^~
```
[R/functions_likelihood.R:245:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L245) *warning:* **no visible global function definition for ‘split_times_matrix3’**
```r
  split_matrices <- split_times_matrix3(times_matrix)
                    ^~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:246:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L246) *style:* **Variable or function name should be snake_case.**
```r
  Ntips <- length(split_matrices)
  ^~~~~
```
[R/functions_likelihood.R:249:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L249) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/functions_likelihood.R:250:35:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L250) *style:* **Commas should always have a space after.**
```r
    ti_i <- split_matrices[[i]][1,1]
                                  ^
```
[R/functions_likelihood.R:254:12:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L254) *style:* **Commas should always have a space after.**
```r
    ts_i[2,] <- 1
           ^
```
[R/functions_likelihood.R:255:21:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L255) *style:* **Put spaces around all infix operators.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                   ~^~~
```
[R/functions_likelihood.R:255:25:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L255) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                        ^
```
[R/functions_likelihood.R:255:30:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L255) *style:* **Use <-, not =, for assignment.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                             ^
```
[R/functions_likelihood.R:255:30:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L255) *style:* **Put spaces around all infix operators.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                            ~^~
```
[R/functions_likelihood.R:255:35:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L255) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if (length(ts_i)==0){ts_i=NULL}
                                  ^
```
[R/functions_likelihood.R:256:48:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L256) *style:* **Commas should always have a space after.**
```r
    lambdas_i <- lambdas[split_matrices[[i]][3,]]
                                               ^
```
[R/functions_likelihood.R:257:44:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L257) *style:* **Commas should always have a space after.**
```r
    mus_i     <- mus[split_matrices[[i]][3,]]
                                           ^
```
[R/functions_likelihood.R:258:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L258) *style:* **Lines should not be more than 80 characters.**
```r
    tm_i      <- arrange_times_matrix(ti = ti_i, tf = tf_i, tb = tb_i, ts = ts_i)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:258:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L258) *warning:* **no visible global function definition for ‘arrange_times_matrix’**
```r
    tm_i      <- arrange_times_matrix(ti = ti_i, tf = tf_i, tb = tb_i, ts = ts_i)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:260:18:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L260) *warning:* **no visible global function definition for ‘lik_custom_single_lineage3’**
```r
    lik[i]    <- lik_custom_single_lineage3(dataset = dataset_i, N0 = 1)
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:265:1:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L265) *style:* **Lines should not be more than 80 characters.**
```r
#' Custom likelihood function for single lineages. You can use it after you apply split_times_matrix.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:270:51:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L270) *style:* **Variable or function name should be snake_case.**
```r
lik_custom_single_lineage3   <- function(dataset, N0 = 1, input_check = 1){
                                                  ^~
```
[R/functions_likelihood.R:275:3:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L275) *style:* **Variable or function name should be snake_case.**
```r
  Ntimepoints  <- ncol(times_matrix)
  ^~~~~~~~~~~
```
[R/functions_likelihood.R:276:19:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L276) *warning:* **no visible global function definition for ‘times_matrix2t_coordinates’**
```r
  tf           <- times_matrix2t_coordinates(times_matrix = times_matrix)$tf
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/functions_likelihood.R:281:5:](https://github.com/Giappo/sls/blob/09e25a7fdf657c1cdd4f0e4c2f85d762331c84fe/R/functions_likelihood.R#L281) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```


No, I had it wrong. You want `domain=bool`.


Especially so in full-blown Perl 6 code, because there we also [try to figure out if we're in a `Promise` that has dynamic scoped stashed away for us](https://github.com/rakudo/rakudo/blob/a167e6cca926389caaf7348f8faa9a436d10cfe4/src/core/stubs.pm6#L33-L58)

```
# Rakudo, uncached
$ time perl6 -e 'class Foo { method a() { self.b }; method b() { self.c }; method c() { self.d }; method d() { my int $x; my $z; my $y := $*Y; while $x++ < 3_000_0000 { $z := $*Y + $*Y } } }; { my $*Y = 42; Foo.new.a }'

real  0m22.060s
user  0m21.101s
sys 0m0.172s

# Rakudo, cached
$ time perl6 -e 'class Foo { method a() { self.b }; method b() { self.c }; method c() { self.d }; method d() { my int $x; my $z; my $y := $*Y; while $x++ < 3_000_0000 { $z := $y + $y } } }; { my $*Y = 42; Foo.new.a }'

real  0m4.971s
user  0m4.620s
sys 0m0.064s
```

```
# NQP, uncached
$ time nqp -e 'class Foo { method a() { self.b }; method b() { self.c }; method c() { self.d }; method d() { my int $x; my $z; my $y := $*Y; while $x++ < 3_000_0000 { $z := $*Y + $*Y } } }; { my $*Y := 42; Foo.new.a }'

real  0m4.263s
user  0m4.088s
sys 0m0.048s

# NQP, cached
$ time nqp -e 'class Foo { method a() { self.b }; method b() { self.c }; method c() { self.d }; method d() { my int $x; my $z; my $y := $*Y; while $x++ < 3_000_0000 { $z := $y + $y } } }; { my $*Y := 42; Foo.new.a }'

real  0m2.938s
user  0m2.724s
sys 0m0.032s
```


I tested it it in a seperate then because getContractBalance returns a promise. If I changed like you suggested (correct me if I am wrong):

it("should put 100000000000 wei in the Splitter contract", function() {
        return Splitter.deployed().then(function(instance) {
          splitter = instance;
          return splitter.activate({ from: accounts[0] });
        }).then(function() {
          return splitter.split(accounts[1], accounts[2], {from: accounts[0], value: totalAmount, gasPrice: gasPrice});
        }).then(function(txObj) {
          assert.strictEqual(getContractBalance().toString(10), totalAmount.toString(10),
                          totalAmount + " wasn't in the Splitter contract");
        });
      });
    });

... then it throws the error:

 Contract: Splitter
       Splitting the money
         should put 100000000000 wei in the Splitter contract:
     AssertionError: 10000000000000000 wasn't in the Splitter contract: expected '[object Promise]' to equal '10000000000000000'
      at test/splitter.js:55:18
      at <anonymous>
      at process._tickDomainCallback (internal/process/next_tick.js:2

Don't I need to do it in a different then to resolve the promise ?


issue-6790-VRP-D-term (EnergyArchmage) - x86_64-Linux-Ubuntu-14.04-cppcheck-1.61: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


You accidentaly assigned the whole argentinia shape to the local source sources/south-america/ar/IGNorthophotoPosadas(WMTS).geojson. It was wrong in JOSM too, I just fixed it there, you can copy the shape. (I'll not fix it here myself as selecting so much lines is not possible in github.)


ลองใช้ arrow function


por si acaso es un get, set en string


ลองใช้ state แบบของจิ๋ว


issue #2


Ah, lovely, thank you! :)


ลองเก็บ value ด้วย mobx


@MikeIbberson Few things:
1) Importing list into component - Would this just be the products' post archive object?
2) In list.twig (List in product page), are the sublabels the post category?

list-downloads.twig is specifically for /downloads archive. Will need to customize it to direct download instead of an anchor link. Should I just throw that component inside the /product template? (Or a 2nd reusable list component)


cc @TysonAndre


ใช้ this.timer โอเคแล้ว เป็นการเรียกตัวแปรของตัวคลาสเอง


@meentastic I added the immigration justice reference in this list, and the list from Sophshep in the SI channel. As you come across other ops, would you mind adding here? This can serve as an initial list and we can iterate as we go. There is probably a similar list in #policy, but thinking this will be specific to pro bono.


พรุ่งนี้ก่อนเที่ยงอยากได้คำตอบว่า event.preventDefault ไว้ทำอะไร


TeamCity LCM :: liblcm-win32-master Continuous [Build 224](http://build.palaso.org/viewLog.html?buildId=122998&buildTypeId=Liblcm_LiblcmWin32masterContinuous) outcome was **FAILURE**
Summary: Compilation error: src\SIL.LCModel.Core\SIL.LCModel.Core.csproj (new) Build time: 00:00:29


Can you elaborate on the bug that was fixed here? Cursory review suggests you've refactored to make liysession.py concise and made python names configurable. I don't see a logical error from the previous version that got addressed here. Thanks for your clarifications.


Created multidev environment [sfgov#pr-79](https://dashboard.pantheon.io/sites/91d50373-c4cf-40e4-a646-cb73e16a140c#pr-79).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-79-sfgov.pantheonsite.io/)


Just set the property for the builds where you want it to run.  Here it’s configured to run on libraries that are in the shared framework for the best configuration for netcoreapp.

Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: Dan Moseley <notifications@github.com>
Sent: Wednesday, June 20, 2018 12:25:10 PM
To: dotnet/corefx
Cc: Eric St. John; Author
Subject: Re: [dotnet/corefx] Update ILLinkTrimAssembly condition (145762c)

We should have enough test coverage of the Windows compat pack assemblies. What would the change be if I wanted to include those?

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdotnet%2Fcorefx%2Fcommit%2F145762c865b67f0bf1292b4fa30ce1c0142e742f%23commitcomment-29438684&data=02%7C01%7CEric.St.John%40microsoft.com%7C44d4f7f1ed844708ad8508d5d6e38a39%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636651195121108602&sdata=sc4Chyoiq5YsaBNhZiIXbNFKqM96G8mJ9NwAu1O3fa0%3D&reserved=0>, or mute the thread<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAIgUXJ2vKVrDPrMtJdIK80JOnsxcv5T0ks5t-qGWgaJpZM4UugHW&data=02%7C01%7CEric.St.John%40microsoft.com%7C44d4f7f1ed844708ad8508d5d6e38a39%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C636651195121118607&sdata=%2BZulZf8mHGKygK02Ztw4MsRZTGFq5mi5PAY1HHPbehI%3D&reserved=0>.


You misunderstood my suggestion. I didn't want to say that MATE should follow GNOME's HIG. But dropping menu items has some adventages.

1. You don't have to maintain reimplementation of GtkImageMenuItem. Just placing image before label is not good solution: you have to add ability to disable icon, you have to deal with margins and various themes, you have to maintain separate library for it or separate copies of code.

2. Consistence. GNOME applications (like gnome-disks or dconf-editor), Firefox, nm-applet and a lot of apps are using plain menu items without icon. When MATE will continue to use icons for *every* menu items, it will be inconsistent with other world. Sorry, this is the reality — when GNOME is saying that menu icons are bad, a lot of apps is going to remove it.


@ivan2340 I think the lines to specify a default file name are still useful. Some images could have really weird url names so it's nice to have a fallback.


TeamCity LCM :: liblcm-win64-master Continuous [Build 187](http://build.palaso.org/viewLog.html?buildId=122999&buildTypeId=Liblcm_LiblcmWin64masterContinuous) outcome was **FAILURE**
Summary: Compilation error: src\SIL.LCModel.Core\SIL.LCModel.Core.csproj (new) Build time: 00:00:41


Half of the regressions *were* caught by tests (the build's currently failing) - I was just derelict, and didn't run them. But more tests is always good.


This is all generated code.


Thanks, fixed


Fixed


Yeah I remember I changed it but not sure why. In this PR I was also trying to fix the failing specs in accounting gem so it may be a fix for a failing test. Don't think it's related to Accept.js feature.


You shouldn't have to unlink the old file before renaming the temp file in its place.  That runs the risk of losing the file permanently if the client crashes in this window.  Instead, this should just rename the temp file over the old filename and it will be atomically replaced.


TeamCity LCM :: liblcm-linux64-master Continuous [Build 192](http://build.palaso.org/viewLog.html?buildId=123000&buildTypeId=Liblcm_LiblcmLinux64masterContinuous) outcome was **SUCCESS**
Summary: Tests passed: 2620, ignored: 32 Build time: 00:01:48


TeamCity LCM :: liblcm-win64-master Continuous [Build 188](http://build.palaso.org/viewLog.html?buildId=123007&buildTypeId=Liblcm_LiblcmWin64masterContinuous) outcome was **FAILURE**
Summary: Compilation error: src\SIL.LCModel.Core\SIL.LCModel.Core.csproj (new) Build time: 00:00:40


TeamCity LCM :: liblcm-win32-master Continuous [Build 225](http://build.palaso.org/viewLog.html?buildId=123009&buildTypeId=Liblcm_LiblcmWin32masterContinuous) outcome was **FAILURE**
Summary: Compilation error: src\SIL.LCModel.Core\SIL.LCModel.Core.csproj (new) Build time: 00:00:20


Emm, care to release?


(Project initialized with [create-react-app](https://github.com/facebook/create-react-app))


I missed this one. @fmichonneau it looks like you committed merge conflict markers, I will fix.


TeamCity LCM :: liblcm-win32-master Continuous [Build 226](http://build.palaso.org/viewLog.html?buildId=123010&buildTypeId=Liblcm_LiblcmWin32masterContinuous) outcome was **SUCCESS**
Summary: Tests passed: 2608, ignored: 44 Build time: 00:01:22


will do and thanks @brookienoodle !


hummm....


Any register you write needs to be either and output operand or a clobber for the ASM statement. The C compiler might be using it, while you overwrite it with a value. See https://gcc.gnu.org/onlinedocs/gcc/Extended-Asm.html


TeamCity LCM :: liblcm-win64-master Continuous [Build 189](http://build.palaso.org/viewLog.html?buildId=123011&buildTypeId=Liblcm_LiblcmWin64masterContinuous) outcome was **FAILURE**
Summary: Compilation error: src\SIL.LCModel.Core\SIL.LCModel.Core.csproj Build time: 00:00:45


@msmalik681 Yes, though it will probably introduce a bunch of new bugs at the same time...


Created multidev environment [composer-digital-initiatives#pr-41](https://dashboard.pantheon.io/sites/3d35643a-2d94-44d8-ac78-4f1526e12dcf#pr-41).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-41-composer-digital-initiatives.pantheonsite.io/)


TeamCity LCM :: liblcm-win64-master Continuous [Build 190](http://build.palaso.org/viewLog.html?buildId=123012&buildTypeId=Liblcm_LiblcmWin64masterContinuous) outcome was **FAILURE**
Summary: Compilation error: src\SIL.LCModel.Core\SIL.LCModel.Core.csproj Build time: 00:00:37


The TI linker file could be removed. I don't see rules to build with TI CGT, and pru-gcc has its own linker configuration files.