[R/newCode.R:12:17:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L12) *style:* **Commas should never have a space before.**
```r
      sep = sep ,
               ~^
```
[R/newCode.R:49:16:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L49) *warning:* **Do not use absolute paths.**
```r
  filename <- "~/Desktop/Trinidad/LTT/fractionOfPopsize2.txt"
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:54:12:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L54) *warning:* **no visible global function definition for ‘readInputData’**
```r
  data <-  readInputData(file = filename, sep = separator)
           ^~~~~~~~~~~~~
```
[R/newCode.R:55:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L55) *warning:* **no visible global function definition for ‘addTimeScaleToData’**
```r
  data <- addTimeScaleToData(iT = itime, fT = ftime, data = data)
          ^~~~~~~~~~~~~~~~~~
```
[R/newCode.R:59:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L59) *style:* **Commented code should be removed.**
```r
  # source("~/Desktop/Trinidad/LTT/plotStackedAreas.R")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:77:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L77) *style:* **Commented code should be removed.**
```r
  #       install.packages("RColorBrewer")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:78:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L78) *style:* **Commented code should be removed.**
```r
  #       library(RColorBrewer)
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:82:4:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L82) *style:* **Commented code should be removed.**
```r
  #myColours= brewer.pal(8,"Set1")
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:83:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L83) *style:* **Use <-, not =, for assignment.**
```r
  myColours = (grDevices::rainbow(nDataCols, start = 0.11))
            ^
```
[R/newCode.R:96:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L96) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:112:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L112) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:113:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L113) *style:* **Use <-, not =, for assignment.**
```r
  myOrder = sample(1:nDataCols, nDataCols) #random selection of data columns
          ^
```
[R/newCode.R:131:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L131) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:149:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L149) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:169:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L169) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:193:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L193) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:223:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L223) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:224:32:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/newCode.R#L224) *style:* **Use <-, not =, for assignment.**
```r
  myColours[length(myColours)] = "white"
                               ^
```
[R/plotStackedAreas.R:47:3:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L47) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  legend.pt.cex=1,
  ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:52:4:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L52) *style:* **Use <-, not =, for assignment.**
```r
  X= data$time
   ^
```
[R/plotStackedAreas.R:52:4:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L52) *style:* **Put spaces around all infix operators.**
```r
  X= data$time
  ~^
```
[R/plotStackedAreas.R:54:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(stacked100){
    ^
```
[R/plotStackedAreas.R:55:16:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L55) *style:* **Put spaces around all infix operators.**
```r
    sumDataCols<- function(X){
              ~^
```
[R/plotStackedAreas.R:58:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L58) *style:* **Use <-, not =, for assignment.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
            ^
```
[R/plotStackedAreas.R:58:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L58) *style:* **Put spaces around all infix operators.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
           ~^
```
[R/plotStackedAreas.R:58:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L58) *style:* **Put spaces around all infix operators.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
                               ~^~
```
[R/plotStackedAreas.R:58:40:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L58) *style:* **Put spaces around all infix operators.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
                                      ~^~
```
[R/plotStackedAreas.R:59:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L59) *style:* **Use <-, not =, for assignment.**
```r
    Y= data[,2:ncol(data)]/dataSums
     ^
```
[R/plotStackedAreas.R:59:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L59) *style:* **Put spaces around all infix operators.**
```r
    Y= data[,2:ncol(data)]/dataSums
    ~^
```
[R/plotStackedAreas.R:59:14:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L59) *style:* **Commas should always have a space after.**
```r
    Y= data[,2:ncol(data)]/dataSums
             ^
```
[R/plotStackedAreas.R:59:27:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L59) *style:* **Put spaces around all infix operators.**
```r
    Y= data[,2:ncol(data)]/dataSums
                         ~^~
```
[R/plotStackedAreas.R:61:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L61) *style:* **Use <-, not =, for assignment.**
```r
    Y= data[,2:ncol(data)]
     ^
```
[R/plotStackedAreas.R:61:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L61) *style:* **Put spaces around all infix operators.**
```r
    Y= data[,2:ncol(data)]
    ~^
```
[R/plotStackedAreas.R:61:14:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L61) *style:* **Commas should always have a space after.**
```r
    Y= data[,2:ncol(data)]
             ^
```
[R/plotStackedAreas.R:63:12:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L63) *style:* **Use <-, not =, for assignment.**
```r
  ndatacols= ncol(Y)
           ^
```
[R/plotStackedAreas.R:63:12:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L63) *style:* **Put spaces around all infix operators.**
```r
  ndatacols= ncol(Y)
          ~^
```
[R/plotStackedAreas.R:66:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L66) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(sum(Y<0)>=1) stop("Data columns can not have negative values.")
    ^
```
[R/plotStackedAreas.R:66:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L66) *style:* **Put spaces around all infix operators.**
```r
  if(sum(Y<0)>=1) stop("Data columns can not have negative values.")
         ~^~
```
[R/plotStackedAreas.R:66:14:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L66) *style:* **Put spaces around all infix operators.**
```r
  if(sum(Y<0)>=1) stop("Data columns can not have negative values.")
            ~^~~
```
[R/plotStackedAreas.R:67:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L67) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(sum(X<0)>=1) stop("Time scale can not have negative values.")
    ^
```
[R/plotStackedAreas.R:67:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L67) *style:* **Put spaces around all infix operators.**
```r
  if(sum(X<0)>=1) stop("Time scale can not have negative values.")
         ~^~
```
[R/plotStackedAreas.R:67:14:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L67) *style:* **Put spaces around all infix operators.**
```r
  if(sum(X<0)>=1) stop("Time scale can not have negative values.")
            ~^~~
```
[R/plotStackedAreas.R:68:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(nrow(Y)==0) stop("Data columns appear to be empty.")
    ^
```
[R/plotStackedAreas.R:68:13:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L68) *style:* **Put spaces around all infix operators.**
```r
  if(nrow(Y)==0) stop("Data columns appear to be empty.")
           ~^~~
```
[R/plotStackedAreas.R:69:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(X)==0) stop("Time scale appears to be empty.")
    ^
```
[R/plotStackedAreas.R:69:15:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L69) *style:* **Put spaces around all infix operators.**
```r
  if(length(X)==0) stop("Time scale appears to be empty.")
             ~^~~
```
[R/plotStackedAreas.R:72:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L72) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.na(areaBorderWidth)) areaBorderWidth<- 1
    ^
```
[R/plotStackedAreas.R:72:45:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L72) *style:* **Put spaces around all infix operators.**
```r
  if(is.na(areaBorderWidth)) areaBorderWidth<- 1
                                           ~^
```
[R/plotStackedAreas.R:73:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L73) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(colours)==1){
    ^
```
[R/plotStackedAreas.R:73:21:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L73) *style:* **Put spaces around all infix operators.**
```r
  if(length(colours)==1){
                   ~^~~
```
[R/plotStackedAreas.R:74:7:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L74) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.na(colours)) colours <- grDevices::rainbow(ndatacols)
      ^
```
[R/plotStackedAreas.R:76:56:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L76) *style:* **Put spaces around all infix operators.**
```r
  areaBorderCol <- as.vector(matrix(areaBorderCol, nrow=ndatacols, ncol=1))
                                                      ~^~
```
[R/plotStackedAreas.R:76:72:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L76) *style:* **Put spaces around all infix operators.**
```r
  areaBorderCol <- as.vector(matrix(areaBorderCol, nrow=ndatacols, ncol=1))
                                                                      ~^~
```
[R/plotStackedAreas.R:77:44:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L77) *style:* **Put spaces around all infix operators.**
```r
  colours <- as.vector(matrix(colours, nrow=ndatacols, ncol=1))
                                          ~^~
```
[R/plotStackedAreas.R:77:60:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L77) *style:* **Put spaces around all infix operators.**
```r
  colours <- as.vector(matrix(colours, nrow=ndatacols, ncol=1))
                                                          ~^~
```
[R/plotStackedAreas.R:78:60:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L78) *style:* **Put spaces around all infix operators.**
```r
  areaBorderWidth <- as.vector(matrix(areaBorderWidth, nrow=ndatacols, ncol=1))
                                                          ~^~
```
[R/plotStackedAreas.R:78:76:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L78) *style:* **Put spaces around all infix operators.**
```r
  areaBorderWidth <- as.vector(matrix(areaBorderWidth, nrow=ndatacols, ncol=1))
                                                                          ~^~
```
[R/plotStackedAreas.R:80:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L80) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(order)>1) {
    ^
```
[R/plotStackedAreas.R:80:19:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L80) *style:* **Put spaces around all infix operators.**
```r
  if(length(order)>1) {
                 ~^~
```
[R/plotStackedAreas.R:81:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L81) *style:* **lines should not be more than 80 characters.**
```r
    if(length(order)!=ndatacols) stop("Order array must be the length of data columns.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:81:7:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L81) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(order)!=ndatacols) stop("Order array must be the length of data columns.")
      ^
```
[R/plotStackedAreas.R:81:21:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L81) *style:* **Put spaces around all infix operators.**
```r
    if(length(order)!=ndatacols) stop("Order array must be the length of data columns.")
                   ~^~~
```
[R/plotStackedAreas.R:85:18:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L85) *style:* **Put spaces around all infix operators.**
```r
    areaBorderCol<- areaBorderCol[order]
                ~^
```
[R/plotStackedAreas.R:88:21:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L88) *style:* **Put spaces around all infix operators.**
```r
  upperPrevious <- X*0
                   ~^~
```
[R/plotStackedAreas.R:89:23:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L89) *style:* **Put spaces around all infix operators.**
```r
  areas <- vector(mode="list", ndatacols)
                     ~^~
```
[R/plotStackedAreas.R:90:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L90) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq(areas)){
     ^
```
[R/plotStackedAreas.R:91:37:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L91) *style:* **Commas should always have a space after.**
```r
    upperThis <- upperPrevious + Y[,i]
                                    ^
```
[R/plotStackedAreas.R:92:25:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L92) *style:* **Put spaces around all infix operators.**
```r
    areas[[i]] <- list(x=c(X, rev(X)), y=c(upperPrevious, rev(upperThis)))
                       ~^~
```
[R/plotStackedAreas.R:92:41:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L92) *style:* **Put spaces around all infix operators.**
```r
    areas[[i]] <- list(x=c(X, rev(X)), y=c(upperPrevious, rev(upperThis)))
                                       ~^~
```
[R/plotStackedAreas.R:96:7:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L96) *style:* **Use <-, not =, for assignment.**
```r
  xaxs="r"
      ^
```
[R/plotStackedAreas.R:96:7:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L96) *style:* **Put spaces around all infix operators.**
```r
  xaxs="r"
     ~^~
```
[R/plotStackedAreas.R:97:7:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L97) *style:* **Use <-, not =, for assignment.**
```r
  yaxs="r"
      ^
```
[R/plotStackedAreas.R:97:7:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L97) *style:* **Put spaces around all infix operators.**
```r
  yaxs="r"
     ~^~
```
[R/plotStackedAreas.R:98:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L98) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!addAxisSpace){
    ^
```
[R/plotStackedAreas.R:99:9:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L99) *style:* **Use <-, not =, for assignment.**
```r
    xaxs="i"
        ^
```
[R/plotStackedAreas.R:99:9:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L99) *style:* **Put spaces around all infix operators.**
```r
    xaxs="i"
       ~^~
```
[R/plotStackedAreas.R:100:9:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L100) *style:* **Use <-, not =, for assignment.**
```r
    yaxs="i"
        ^
```
[R/plotStackedAreas.R:100:9:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L100) *style:* **Put spaces around all infix operators.**
```r
    yaxs="i"
       ~^~
```
[R/plotStackedAreas.R:103:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L103) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.na(file)){
    ^
```
[R/plotStackedAreas.R:104:9:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L104) *style:* **Use <-, not =, for assignment.**
```r
    file=paste(file,".pdf",sep="")
        ^
```
[R/plotStackedAreas.R:104:9:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L104) *style:* **Put spaces around all infix operators.**
```r
    file=paste(file,".pdf",sep="")
       ~^~
```
[R/plotStackedAreas.R:104:21:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L104) *style:* **Commas should always have a space after.**
```r
    file=paste(file,".pdf",sep="")
                    ^
```
[R/plotStackedAreas.R:104:28:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L104) *style:* **Commas should always have a space after.**
```r
    file=paste(file,".pdf",sep="")
                           ^
```
[R/plotStackedAreas.R:104:31:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L104) *style:* **Put spaces around all infix operators.**
```r
    file=paste(file,".pdf",sep="")
                             ~^~
```
[R/plotStackedAreas.R:105:57:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L105) *style:* **Put spaces around all infix operators.**
```r
    grDevices::pdf(file, width = pdfW, height = pdfH, bg="white")
                                                       ~^~
```
[R/plotStackedAreas.R:108:34:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L108) *style:* **Put spaces around all infix operators.**
```r
  graphics::layout(matrix(1, ncol=1, byrow=TRUE))
                                ~^~
```
[R/plotStackedAreas.R:108:43:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L108) *style:* **Put spaces around all infix operators.**
```r
  graphics::layout(matrix(1, ncol=1, byrow=TRUE))
                                         ~^~
```
[R/plotStackedAreas.R:109:20:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L109) *style:* **Put spaces around all infix operators.**
```r
  graphics::par(mar=c(4, 4, 2, 2), cex=0.9)
                  ~^~
```
[R/plotStackedAreas.R:109:39:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L109) *style:* **Put spaces around all infix operators.**
```r
  graphics::par(mar=c(4, 4, 2, 2), cex=0.9)
                                     ~^~
```
[R/plotStackedAreas.R:111:59:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L111) *style:* **Put spaces around all infix operators.**
```r
  ylim <- range(sapply(areas, function(x) range(x$y, na.rm=TRUE)), na.rm=TRUE)
                                                         ~^~
```
[R/plotStackedAreas.R:111:73:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L111) *style:* **Put spaces around all infix operators.**
```r
  ylim <- range(sapply(areas, function(x) range(x$y, na.rm=TRUE)), na.rm=TRUE)
                                                                       ~^~
```
[R/plotStackedAreas.R:112:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **lines should not be more than 80 characters.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:112:20:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Commas should always have a space after.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                   ^
```
[R/plotStackedAreas.R:112:23:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Commas should always have a space after.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                      ^
```
[R/plotStackedAreas.R:112:31:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                             ~^~
```
[R/plotStackedAreas.R:112:42:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                        ~^~
```
[R/plotStackedAreas.R:112:53:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                   ~^~
```
[R/plotStackedAreas.R:112:61:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                           ~^~
```
[R/plotStackedAreas.R:112:71:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                                     ~^~
```
[R/plotStackedAreas.R:112:82:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                                                ~^~
```
[R/plotStackedAreas.R:112:93:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                                                ~^~
```
[R/plotStackedAreas.R:113:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L113) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq(areas)){
     ^
```
[R/plotStackedAreas.R:114:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L114) *style:* **lines should not be more than 80 characters.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:114:41:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L114) *style:* **Put spaces around all infix operators.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                       ~^~
```
[R/plotStackedAreas.R:114:63:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L114) *style:* **Put spaces around all infix operators.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                                             ~^~
```
[R/plotStackedAreas.R:114:79:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L114) *style:* **Put spaces around all infix operators.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                                                             ~^~
```
[R/plotStackedAreas.R:117:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L117) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.na(addLegend)){
    ^
```
[R/plotStackedAreas.R:118:10:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L118) *style:* **Use <-, not =, for assignment.**
```r
    names= colnames(Y)
         ^
```
[R/plotStackedAreas.R:118:10:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L118) *style:* **Put spaces around all infix operators.**
```r
    names= colnames(Y)
        ~^
```
[R/plotStackedAreas.R:119:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **lines should not be more than 80 characters.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:119:39:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                     ~^~
```
[R/plotStackedAreas.R:119:50:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                ~^~
```
[R/plotStackedAreas.R:119:58:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                        ~^~
```
[R/plotStackedAreas.R:119:73:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                       ~^~
```
[R/plotStackedAreas.R:119:89:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:90:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:119:111:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:118:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:125:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:137:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:144:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:159:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:122:20:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L122) *style:* **Put spaces around all infix operators.**
```r
  graphics::box(lwd=boxlwd)
                  ~^~
```
[R/plotStackedAreas.R:124:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L124) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.na(file)){
    ^
```
[R/plotStackedAreas.R:125:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/plotStackedAreas.R#L125) *warning:* **local variable ‘a’ assigned but may not be used**
```r
    a <- grDevices::dev.off()
    ^
```
[R/readBeast2Trees.R:6:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- readLines(file, n=2e3, warn = FALSE)
^
```
[R/readBeast2Trees.R:6:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- readLines(file, n=2e3, warn = FALSE)
    ^~~
```
[R/readBeast2Trees.R:7:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
^
```
[R/readBeast2Trees.R:7:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
    ^~~
```
[R/readBeast2Trees.R:8:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
	if(length(tmp)>1)
^
```
[R/readBeast2Trees.R:9:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L9) *style:* **Use two spaces to indent, never tabs.**
```r
	{
^
```
[R/readBeast2Trees.R:10:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
^~
```
[R/readBeast2Trees.R:11:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
^~
```
[R/readBeast2Trees.R:11:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
     ^~
```
[R/readBeast2Trees.R:12:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L12) *style:* **Use two spaces to indent, never tabs.**
```r
		system(cmd)
^~
```
[R/readBeast2Trees.R:13:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L13) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
^~
```
[R/readBeast2Trees.R:13:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L13) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
     ^~
```
[R/readBeast2Trees.R:14:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L14) *style:* **Use two spaces to indent, never tabs.**
```r
		system(cmd)
^~
```
[R/readBeast2Trees.R:15:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L15) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
^~
```
[R/readBeast2Trees.R:15:6:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L15) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
     ^~
```
[R/readBeast2Trees.R:16:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L16) *style:* **Use two spaces to indent, never tabs.**
```r
		cat(paste('\nrm files\n', paste(cmd, collapse='\n')))
^~
```
[R/readBeast2Trees.R:17:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L17) *style:* **Use two spaces to indent, never tabs.**
```r
		file.remove(cmd)
^~
```
[R/readBeast2Trees.R:18:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L18) *style:* **Use two spaces to indent, never tabs.**
```r
	}
^
```
[R/readBeast2Trees.R:19:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L19) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- ape::read.nexus(file)
^
```
[R/readBeast2Trees.R:19:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L19) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/readBeast2Trees.R:19:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L19) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- ape::read.nexus(file)
    ^~~
```
[R/readBeast2Trees.R:20:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L20) *style:* **Use two spaces to indent, never tabs.**
```r
	#	remove burn in
^
```
[R/readBeast2Trees.R:20:3:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L20) *style:* **Use two spaces to indent, never tabs.**
```r
	#	remove burn in
  ^
```
[R/readBeast2Trees.R:20:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L20) *style:* **Put spaces around all infix operators.**
```r
	tmp			<- readLines(file, n=2e3, warn = FALSE)
                               ~^~~
```
[R/readBeast2Trees.R:21:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L21) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
^
```
[R/readBeast2Trees.R:21:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L21) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
    ^~~
```
[R/readBeast2Trees.R:21:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L21) *style:* **Put spaces around all infix operators.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
                               ~^~~
```
[R/readBeast2Trees.R:21:49:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L21) *style:* **Only use double-quotes.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
                                                ^~~~~~~~
```
[R/readBeast2Trees.R:22:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L22) *style:* **Use two spaces to indent, never tabs.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
^
```
[R/readBeast2Trees.R:22:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	if(length(tmp)>1)
          ^
```
[R/readBeast2Trees.R:22:16:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L22) *style:* **Use two spaces to indent, never tabs.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
               ^
```
[R/readBeast2Trees.R:23:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L23) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- as.numeric( regmatches( names(mph), tmp) )
^
```
[R/readBeast2Trees.R:23:8:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L23) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- as.numeric( regmatches( names(mph), tmp) )
       ^~
```
[R/readBeast2Trees.R:23:9:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L23) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
	{
        ^
```
[R/readBeast2Trees.R:24:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
^
```
[R/readBeast2Trees.R:24:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L24) *style:* **lines should not be more than 80 characters.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:24:5:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
    ^~~
```
[R/readBeast2Trees.R:24:27:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L24) *style:* **Only use double-quotes.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:24:57:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                                                        ^
```
[R/readBeast2Trees.R:24:66:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                                                                 ^
```
[R/readBeast2Trees.R:24:68:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L24) *style:* **Only use double-quotes.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
                                                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:25:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L25) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
^
```
[R/readBeast2Trees.R:25:8:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L25) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
       ^~
```
[R/readBeast2Trees.R:25:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L25) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
                               ~^
```
[R/readBeast2Trees.R:25:40:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
                                       ^
```
[R/readBeast2Trees.R:25:82:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L25) *style:* **Only use double-quotes.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
                                                                                ^~~~
```
[R/readBeast2Trees.R:25:98:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L25) *style:* **Only use double-quotes.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
                                                                                ^~
```
[R/readBeast2Trees.R:26:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L26) *style:* **Use two spaces to indent, never tabs.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
^
```
[R/readBeast2Trees.R:26:12:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L26) *style:* **Use two spaces to indent, never tabs.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
           ^
```
[R/readBeast2Trees.R:27:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L27) *style:* **Use two spaces to indent, never tabs.**
```r
	mph
^
```
[R/readBeast2Trees.R:27:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L27) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
                               ~^~~
```
[R/readBeast2Trees.R:27:79:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L27) *style:* **Only use double-quotes.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
                                                                              ^~
```
[R/readBeast2Trees.R:29:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L29) *style:* **lines should not be more than 80 characters.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:29:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L29) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                               ~^~~
```
[R/readBeast2Trees.R:29:76:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L29) *style:* **Only use double-quotes.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                           ^~~
```
[R/readBeast2Trees.R:29:100:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L29) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ~^~
```
[R/readBeast2Trees.R:29:101:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L29) *style:* **Only use double-quotes.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ^~~
```
[R/readBeast2Trees.R:29:114:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L29) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ~^~
```
[R/readBeast2Trees.R:29:115:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L29) *style:* **Only use double-quotes.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ^~~~~~~
```
[R/readBeast2Trees.R:30:27:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L30) *style:* **Only use double-quotes.**
```r
		cat(paste('\nrm files\n', paste(cmd, collapse='\n')))
                          ^~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:30:63:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L30) *style:* **Only use double-quotes.**
```r
		cat(paste('\nrm files\n', paste(cmd, collapse='\n')))
                                                              ^~~~
```
[R/readBeast2Trees.R:35:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L35) *style:* **Put spaces around all infix operators.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
                               ~^~~
```
[R/readBeast2Trees.R:35:44:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L35) *style:* **Only use double-quotes.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
                                           ^~~~~~~~
```
[R/readBeast2Trees.R:36:11:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
          ^
```
[R/readBeast2Trees.R:36:19:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L36) *style:* **Put spaces around all infix operators.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
                 ~^~
```
[R/readBeast2Trees.R:36:30:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L36) *style:* **Only use double-quotes.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:37:25:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L37) *style:* **Put spaces around all infix operators.**
```r
	mph.it		<- as.numeric( regmatches( names(mph), tmp) )
                        ^~~
```
[R/readBeast2Trees.R:38:33:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L38) *style:* **Put spaces around all infix operators.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                               ~^~~
```
[R/readBeast2Trees.R:38:57:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L38) *style:* **Put spaces around all infix operators.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                                                       ~^~
```
[R/readBeast2Trees.R:39:25:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L39) *style:* **Put spaces around all infix operators.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
                       ~^
```
[R/readBeast2Trees.R:40:25:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L40) *style:* **Put spaces around all infix operators.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
                       ~^~~
```
[R/readBeast2Trees.R:40:34:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L40) *style:* **Only use double-quotes.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
                                 ^~~~~~~~
```
[R/readBeast2Trees.R:40:54:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/R/readBeast2Trees.R#L40) *style:* **Only use double-quotes.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
                                                     ^~
```
[tests/testthat/test-readBeast2Trees.R:2:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L2) *style:* **Use two spaces to indent, never tabs.**
```r
	trees_file <- system.file(
^
```
[tests/testthat/test-readBeast2Trees.R:3:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L3) *style:* **Use two spaces to indent, never tabs.**
```r
		"extdata", "readBeast2TreesExample.trees", package = "RBeast"
^~
```
[tests/testthat/test-readBeast2Trees.R:4:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L4) *style:* **Use two spaces to indent, never tabs.**
```r
	)
^
```
[tests/testthat/test-readBeast2Trees.R:4:20:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L4) *style:* **Put spaces around all infix operators.**
```r
	trees_file <- system.file(
                  ~^~~
```
[tests/testthat/test-readBeast2Trees.R:5:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L5) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_true(file.exists(trees_file))
^
```
[tests/testthat/test-readBeast2Trees.R:6:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	posterior <- readBeast2Trees(trees_file)
^
```
[tests/testthat/test-readBeast2Trees.R:7:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(length(posterior), 10)
^
```
[tests/testthat/test-readBeast2Trees.R:8:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(class(posterior[[1]]), "phylo")
^
```
[tests/testthat/test-readBeast2Trees.R:8:19:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L8) *style:* **Put spaces around all infix operators.**
```r
	posterior <- readBeast2Trees(trees_file)
                 ~^~~
```
[tests/testthat/test-readBeast2Trees.R:12:1:](https://github.com/beast-dev/RBeast/blob/31789fd10b76658be6ca61c03981fbcbc277dac1/tests/testthat/test-readBeast2Trees.R#L12) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Nice. 🐱


Thanks for running this :)


It's not the cleanest solution but it's quick and fixes probably most of issues with mixed owners. The reason we can't align all mixed owners by default is for example to prevent `=>` to align between lambdas and case arrows.


Leftover, ltr not here.


Leftover, should be removed.


another update Here Please


not been updated for 3 days , think this bot is over :/


Leftover, no ltr.


@TingPing ok sorry, I will try to avoid that next time.


This broke the website


[R/readBeast2Trees.R:6:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- readLines(file, n=2e3, warn = FALSE)
^
```
[R/readBeast2Trees.R:6:5:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- readLines(file, n=2e3, warn = FALSE)
    ^~~
```
[R/readBeast2Trees.R:7:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
^
```
[R/readBeast2Trees.R:7:5:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
    ^~~
```
[R/readBeast2Trees.R:8:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
	if(length(tmp)>1)
^
```
[R/readBeast2Trees.R:9:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L9) *style:* **Use two spaces to indent, never tabs.**
```r
	{
^
```
[R/readBeast2Trees.R:10:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L10) *style:* **Use two spaces to indent, never tabs.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
^~
```
[R/readBeast2Trees.R:11:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
^~
```
[R/readBeast2Trees.R:11:6:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L11) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
     ^~
```
[R/readBeast2Trees.R:12:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L12) *style:* **Use two spaces to indent, never tabs.**
```r
		system(cmd)
^~
```
[R/readBeast2Trees.R:13:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L13) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
^~
```
[R/readBeast2Trees.R:13:6:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L13) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
     ^~
```
[R/readBeast2Trees.R:14:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L14) *style:* **Use two spaces to indent, never tabs.**
```r
		system(cmd)
^~
```
[R/readBeast2Trees.R:15:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L15) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
^~
```
[R/readBeast2Trees.R:15:6:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L15) *style:* **Use two spaces to indent, never tabs.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
     ^~
```
[R/readBeast2Trees.R:16:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L16) *style:* **Use two spaces to indent, never tabs.**
```r
		cat(paste('\nrm files\n', paste(cmd, collapse='\n')))
^~
```
[R/readBeast2Trees.R:17:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L17) *style:* **Use two spaces to indent, never tabs.**
```r
		file.remove(cmd)
^~
```
[R/readBeast2Trees.R:18:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L18) *style:* **Use two spaces to indent, never tabs.**
```r
	}
^
```
[R/readBeast2Trees.R:19:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L19) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- ape::read.nexus(file)
^
```
[R/readBeast2Trees.R:19:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L19) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/readBeast2Trees.R:19:5:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L19) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- ape::read.nexus(file)
    ^~~
```
[R/readBeast2Trees.R:20:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L20) *style:* **Use two spaces to indent, never tabs.**
```r
	#	remove burn in
^
```
[R/readBeast2Trees.R:20:3:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L20) *style:* **Use two spaces to indent, never tabs.**
```r
	#	remove burn in
  ^
```
[R/readBeast2Trees.R:20:33:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L20) *style:* **Put spaces around all infix operators.**
```r
	tmp			<- readLines(file, n=2e3, warn = FALSE)
                               ~^~~
```
[R/readBeast2Trees.R:21:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L21) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
^
```
[R/readBeast2Trees.R:21:5:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L21) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
    ^~~
```
[R/readBeast2Trees.R:21:33:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L21) *style:* **Put spaces around all infix operators.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
                               ~^~~
```
[R/readBeast2Trees.R:21:49:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L21) *style:* **Only use double-quotes.**
```r
	tmp			<- which( grepl('#NEXUS', tmp) )
                                                ^~~~~~~~
```
[R/readBeast2Trees.R:22:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L22) *style:* **Use two spaces to indent, never tabs.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
^
```
[R/readBeast2Trees.R:22:11:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L22) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	if(length(tmp)>1)
          ^
```
[R/readBeast2Trees.R:22:16:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L22) *style:* **Use two spaces to indent, never tabs.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
               ^
```
[R/readBeast2Trees.R:23:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L23) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- as.numeric( regmatches( names(mph), tmp) )
^
```
[R/readBeast2Trees.R:23:8:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L23) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- as.numeric( regmatches( names(mph), tmp) )
       ^~
```
[R/readBeast2Trees.R:23:9:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L23) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
	{
        ^
```
[R/readBeast2Trees.R:24:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
^
```
[R/readBeast2Trees.R:24:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L24) *style:* **lines should not be more than 80 characters.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:24:5:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
    ^~~
```
[R/readBeast2Trees.R:24:27:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L24) *style:* **Only use double-quotes.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:24:57:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                                                        ^
```
[R/readBeast2Trees.R:24:66:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L24) *style:* **Use two spaces to indent, never tabs.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                                                                 ^
```
[R/readBeast2Trees.R:24:68:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L24) *style:* **Only use double-quotes.**
```r
		cat(paste('\nFound #NEXUS headers, n=',length(tmp),'.\nDiscard all lines before last entry on line', utils::tail(tmp,1)))
                                                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:25:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L25) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
^
```
[R/readBeast2Trees.R:25:8:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L25) *style:* **Use two spaces to indent, never tabs.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
       ^~
```
[R/readBeast2Trees.R:25:33:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L25) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
                               ~^
```
[R/readBeast2Trees.R:25:40:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
                                       ^
```
[R/readBeast2Trees.R:25:82:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L25) *style:* **Only use double-quotes.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
                                                                                ^~~~
```
[R/readBeast2Trees.R:25:98:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L25) *style:* **Only use double-quotes.**
```r
		cmd		<- paste('sed -i".bak" 1,', utils::tail(tmp,1)-1,'d ', file, sep='')
                                                                                ^~
```
[R/readBeast2Trees.R:26:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L26) *style:* **Use two spaces to indent, never tabs.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
^
```
[R/readBeast2Trees.R:26:12:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L26) *style:* **Use two spaces to indent, never tabs.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
           ^
```
[R/readBeast2Trees.R:27:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L27) *style:* **Use two spaces to indent, never tabs.**
```r
	mph
^
```
[R/readBeast2Trees.R:27:33:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L27) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
                               ~^~~
```
[R/readBeast2Trees.R:27:79:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L27) *style:* **Only use double-quotes.**
```r
		cmd		<- paste('sed -i".bak2" 1s/\\;// ', file, sep='')
                                                                              ^~
```
[R/readBeast2Trees.R:29:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L29) *style:* **lines should not be more than 80 characters.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:29:33:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L29) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                               ~^~~
```
[R/readBeast2Trees.R:29:76:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L29) *style:* **Only use double-quotes.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                           ^~~
```
[R/readBeast2Trees.R:29:100:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L29) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ~^~
```
[R/readBeast2Trees.R:29:101:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L29) *style:* **Only use double-quotes.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ^~~
```
[R/readBeast2Trees.R:29:114:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L29) *style:* **Put spaces around all infix operators.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ~^~
```
[R/readBeast2Trees.R:29:115:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L29) *style:* **Only use double-quotes.**
```r
		cmd		<- list.files(paste(rev(rev(strsplit(file, '/')[[1]])[-1]),collapse='/'), pattern='*bak*', full.names=TRUE)
                                                                                ^~~~~~~
```
[R/readBeast2Trees.R:30:27:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L30) *style:* **Only use double-quotes.**
```r
		cat(paste('\nrm files\n', paste(cmd, collapse='\n')))
                          ^~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:30:63:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L30) *style:* **Only use double-quotes.**
```r
		cat(paste('\nrm files\n', paste(cmd, collapse='\n')))
                                                              ^~~~
```
[R/readBeast2Trees.R:35:33:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L35) *style:* **Put spaces around all infix operators.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
                               ~^~~
```
[R/readBeast2Trees.R:35:44:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L35) *style:* **Only use double-quotes.**
```r
	tmp			<- regexpr('[0-9]+',names(mph))
                                           ^~~~~~~~
```
[R/readBeast2Trees.R:36:11:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
          ^
```
[R/readBeast2Trees.R:36:19:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L36) *style:* **Put spaces around all infix operators.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
                 ~^~
```
[R/readBeast2Trees.R:36:30:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L36) *style:* **Only use double-quotes.**
```r
	if(any(tmp<0))	stop('unexpected nexus file without STATE iteration numbers')
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/readBeast2Trees.R:37:25:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L37) *style:* **Put spaces around all infix operators.**
```r
	mph.it		<- as.numeric( regmatches( names(mph), tmp) )
                        ^~~
```
[R/readBeast2Trees.R:38:33:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L38) *style:* **Put spaces around all infix operators.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                               ~^~~
```
[R/readBeast2Trees.R:38:57:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L38) *style:* **Put spaces around all infix operators.**
```r
	mph			<- lapply( which( mph.it>opt.burnin), function(j)	mph[[j]]	)
                                                       ~^~
```
[R/readBeast2Trees.R:39:25:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L39) *style:* **Put spaces around all infix operators.**
```r
	mph.it		<- mph.it[ mph.it > opt.burnin ]
                       ~^
```
[R/readBeast2Trees.R:40:25:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L40) *style:* **Put spaces around all infix operators.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
                       ~^~~
```
[R/readBeast2Trees.R:40:34:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L40) *style:* **Only use double-quotes.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
                                 ^~~~~~~~
```
[R/readBeast2Trees.R:40:54:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/R/readBeast2Trees.R#L40) *style:* **Only use double-quotes.**
```r
	names(mph)	<- paste('STATE_',mph.it,sep='')
                                                     ^~
```
[tests/testthat/test-readBeast2Trees.R:2:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L2) *style:* **Use two spaces to indent, never tabs.**
```r
	trees_file <- system.file(
^
```
[tests/testthat/test-readBeast2Trees.R:3:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L3) *style:* **Use two spaces to indent, never tabs.**
```r
		"extdata", "readBeast2TreesExample.trees", package = "RBeast"
^~
```
[tests/testthat/test-readBeast2Trees.R:4:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L4) *style:* **Use two spaces to indent, never tabs.**
```r
	)
^
```
[tests/testthat/test-readBeast2Trees.R:4:20:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L4) *style:* **Put spaces around all infix operators.**
```r
	trees_file <- system.file(
                  ~^~~
```
[tests/testthat/test-readBeast2Trees.R:5:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L5) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_true(file.exists(trees_file))
^
```
[tests/testthat/test-readBeast2Trees.R:6:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	posterior <- readBeast2Trees(trees_file)
^
```
[tests/testthat/test-readBeast2Trees.R:7:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(length(posterior), 10)
^
```
[tests/testthat/test-readBeast2Trees.R:8:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L8) *style:* **Use two spaces to indent, never tabs.**
```r
	expect_equal(class(posterior[[1]]), "phylo")
^
```
[tests/testthat/test-readBeast2Trees.R:8:19:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L8) *style:* **Put spaces around all infix operators.**
```r
	posterior <- readBeast2Trees(trees_file)
                 ~^~~
```
[tests/testthat/test-readBeast2Trees.R:12:1:](https://github.com/beast-dev/RBeast/blob/0b83e747bce8a680667925190e9eb74cdc7029a5/tests/testthat/test-readBeast2Trees.R#L12) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Sad...


Omg that was dumb of me :+1:


Was this intentional?


I didn't recognized...
but it's ok since these both styles are mixed everywhere in the project, it will be difficult to get every single developer to use only one of them xD


Bad idea you broke any plugin using addWindow($inv,null);
!!!!!!!!!!'n


@Pub4Game Why did you add line 326? It seems it is done at https://github.com/Nukkit/Nukkit/blob/master/src/main/java/cn/nukkit/level/Level.java#L1460


Was working on the template too, should we add a `umurmur` user and service?


这是什么鬼？ 非法字符？


awesome!
thanks a lot


just realised, this was what I have been using all this time. Not 100% accurate.

Let's assume a standard WiFi router with a ethernet cable plugged into it. If someone pulls off that cable, the WiFi router will still stay powered on and your phone will be connected to WiFi, but won't have any internet access. doing a

```
Runtime runtime=getRuntime();
runtime.exec('ping 8.8.8.8');
````

and parsing the output and/or return code will work around this limitation.

P.S. This specific niggle only happens for us Indians with shitty connections lol


Yeah, the initialization has been done in `__init__` method


Yeah, i've removed in the commit pushed after this


yesssss, would love to see this released.


I have fixed spacing issue in the attribute.


To compare how long it takes to optimize one node. I thought we could apply this commit over the current master and then profile to compare the time spent in optimizing each nodes


Oops .. sorry! :)
I don't know if umurmurd is meant to be run as a service, but probably yes.
If you like, you can take the package ownership and modify as you think may fit.


Uses \\n and \\r, it will print \n and \r on string


\\n and \\r


Why the fuck would anyone minify code that is suppose to be handed in to a professor?


DAMM GITHUB CELLPHONE WEBSITE
use Double \r and Double \n


You are correct. Path.join should not be used on URL, only file paths. With that said, URLs are the same across all operating systems and can be structured with '/'. I will revert my change on this one line and the issue "should" still be resolved <crosses fingers>.


Perhaps we should add another label similar to WIP to indicate that someone is taking care of a request?


I think you need a `variable=this_unit` line.


Could you explain more?


Please finally stop breaking plugins


Yea i guess we could just assignee issues if we work on them, forgot about it.
But no problem at all, this package was easy enough no real work involved.


Great work assigning the same class to the "job titles"!  For readability, I would suggest using a class name of "job-title" instead of "jobtitle" next time.


The changes:

1. First tries to match `$__fish...` variables, only then other `$_...`
2. Matches 2 or more underscores between `$` and `fish`. Very helpful in files like __fish_git_prompt.fish that has stuff like
```fish
printf "%s$format%s" "$___fish_git_prompt_color_prefix" "$___fish_git_prompt_color_prefix_done$c$b$f$r$p$informative_status$___fish_git_prompt_color_suffix" "$___git_ps_color_suffix_done"
```


And a new SIPCheck.command that compatible with 10.12 should be added :)
[SIPCheck.command.zip](https://github.com/linzhouyu/OS-X-Lenovo-Y450/files/405048/SIPCheck.command.zip)
And it seems that cannot get kernel log in 10.12... i.e. Should use a new command if the system version is 10.12.


Forgot `variable=this_unit`


You need `variable=this_unit` in this foreach block, I think.


Looks like you want `variable=second_this_item` in this foreach loop.


I am sitting here waiting for another qt5 build, that's why I hacked up the template instead of twiddling my thumbs. Yea, now that you say it, assignee is perfect for this...
Will you take the package or should I go and try to add user and service?


Closes #1


lol Neurotic


I am about to make a pr to this file.


Say there was code like:

    String s = other_string + GetSomething();

And you refactored it so GetSomething() returns a number instead of string. Compiler will not be able to catch this mistake and you end up with improper string that you will only notice later.

Or how about arrays.

    String s1[10];
    String s2;

    // <...>

    some_print(s1 + 2);
    some_print(s2 + 2);

Easy to get confused there. Both print lines are exactly the same. It is not clear at all what print lines do from looking only at them. The only hint would be variable name and programmers do not always give meaningful names.

And lastly this is very counter-intuitive. Adding string to another string is intuitive. But we can argue what adding a number to a string could mean. Convert number to a string and concatenate? Extend string container to contain extra characters? Pad string with spaces? It really is a matter of opinion here and people have different opinions..

I realize this makes writing fancy short code easier but at the same time this code will be confusing to anyone else who is not familiar with this non-standard behaviour or is new to the which makes use of this.

A good benchmark of feature validity is this. Ask yourself if such operators would ever have a chance ending up in stdlib. If answer is like "never ever in a million years" then its probably not a good idea to do.. Notice how [constructors](https://github.com/urho3d/Urho3D/blob/fafd921f32629de88d031e24f6f16552886b3ebc/Source/Urho3D/Container/Str.h#L113) that convert other types to string are `explicit`. It is a safeguard against unintended effect. You just negated that safeguard with this patch..

@cadaver wont you agree?


You're welcome - and thanks for writing the script in the first place. :)

Testing is always appreciated, of course. Not sure what is would take to add this to your list of tested platforms?


This function does not exist, so it's filling the logs with errors.


Don't merge until we merge God damn it


Nitpicking?!


Well if u interested u can help..
https://github.com/ArchRPG/ARCore


Totally sorry about this....this was supposed to be in test branch!
Removing it now

On Sat, Aug 6, 2016, 8:24 PM Davor Bertovic <notifications@github.com>
wrote:

> Don't merge until we merge God damn it
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/Zephyr-OS/platform_frameworks_base/commit/843c7db793d19fe153d1197c51296d4d52fe3962#commitcomment-18548698>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AJqWEy8dn2W6EYOf1FWIhVsNjHQ2vYYyks5qdKAIgaJpZM4JeSzq>
> .
>


<!DOCTYPE html>
<html lang="en">
<head>
	<meta charset="UTF-8">
	<title>Document</title>
</head>
<body>

</body>
</html>


Fish


Missing `[do]`


And no body is going to add minions to the base branch, want them, add them yourself.


Empty lines with spaces lol


Arrgghh i hate git


2091-WrappedHPWH (kbenne) - Win64-Windows-7-VisualStudio-12: OK (2416 of 2447 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-98.73%25-yellow.svg)


It seems to be fine. Doesn't affect my changes.


I'd prefer using `[break][/break]` here. (Note that this kind of exit strategy wouldn't work in `[foreach]`.)


@tohojo   Is it possible to run openwrt in a VM or in docker?


With the removal of the Accuracy class, it makes sense to simply rewrite this section entirely.  A solid hierarchy for types needs to be created, not just stuffed into conditional logic.


BTW, you can do overall testing via here:  https://github.com/Neilpang/acmetest#how-to-run-tests


This latest changes to #adjustColumn(...) will return a new column instance instead of updating what was passed in.


These tests will qualify the proposed type hierarchy; type changes and precision/scale updates


CNAME init


Oups ! The orientation was already commited...


Ой, лишний комментарий, забыл удалить, не обращай внимания

"<!--За это (секшн вместо дивов), сказали, наставники могут ругать, но так можно :D-->"


Why did you change back from `column.name` to `column.propertyName`?
Using a left join in a one-to-many relation where the many-entity has "aliased" properties, this property are not loaded from db in the join result.


There are x86 builds which should run in a VM: https://downloads.lede-project.org/snapshots/targets/x86/ - not sure about docker.

I'll look into what it takes to do automated testing when I have some time to spare :)


C# also support String + number


Dadel


In old variant String + number also no cause any warnings, just spoiling String (Visual studio)


Forgot to change to `this_item`


Hi!
I've heard you were looking for that stuff for   a long time, so I finally found it for you, read more here <http://best.johnsonfenceonline.com/e3ceclrz>

Looking forward, afenna


I don't see this as a large problem. AngelScript string class used in Urho also has string + number operators, so this allows to use similar constructs in AS & C++.


It seems that a new connection uses a new local port. This causes the NAT assigning a new external port. Therefore, the response for this test will always be false, which doesn't make sense.


31c064bf178c1dfc63ccd47e4c820122b86fa7cf でrevert。


This fixes IPv6 issue, since we need 16 bytes for IPv6 addresses. Moreover, RCF says the 16 bytes has to be random -- the previous implementation makes the first 4 bytes constant and rest 12 bytes random.

I didn't understand why RFC5389 introduces xorMappedAddr. Maybe for security issue? I just implemented it, and use xorMappedAddr if it present, otherwise use mappedAddr.

Any hints?


It should work now. I did away with the C99 style initializers.


First attempt at Gitproject


Not sure about this. Do you feel we should include this .js under engine package? Do you feel it weird just lying around at background.js level?


love this change :)


Are you sure this is correct? My SNES emulation stopped to worked today, and I suspect this commit.


aaa


xorMappedAddr is needed when routers blindly rewrite addresses, essentially search replace in the whole packet, not just IP header.

Which RFC says that the 16 bytes should be random?
I remember clearly reading that the first 4 bytes should be the magic cookie, and the rest should be ID.

S


I didn't see an infinite loop in my review, are you sure? Changing the loop index variable in `[for]` works, but not in `[foreach]`.


Should we move this to background.js? If not let us change the function name from validate to something else. It does not feel right that the validate function is also handling menu redesign.


/cc @peti I'm not sure how we can upstream this patch, since upstream currently does not depend on any GLUT implementation at build-time right now. Also freeglut only provides pkg-config files in recentish versions (~2014 or so), upstream might want to support older versions and different GLUT implementations. Is it ok to just leave this patch in nixpkgs?


Yep. There are also some event listeners in the custom tags on the DOM that link to Riot code.
<img width="1046" alt="sample" src="https://cloud.githubusercontent.com/assets/1953194/17457504/9a56404c-5bd0-11e6-9c33-04f24386a2e8.png">

Not sure why `riot`or `riot$1` still comes up as "undefined" when typed in the console, but anyways, the page definitely uses Riot.


The reason this wasn't being called is because `0` (actually `nullptr`) is being passed to `NativeInitGraphics`.  See here:

https://github.com/hrydgard/ppsspp/blob/b39206f922cd27e37f6126393a9c583f0d7f2e78/ios/ViewController.mm#L37-L43

`GraphicsContext` has methods which you can override to update vsync, handle init/shutdown, and control swapping.  It's more important for Vulkan, which I suppose isn't so much a thing on Mac...

-[Unknown]


Ah yes, you are right, we should only change remote addresses, not local.


Oh sorry, did not see the response in time, I already tested and added a user and a service script.


Update emoncms.org fingerprint


Hmm, this just means the user can no longer configure it in the ini?  The default configuration will be:

For iOS, depends on jailbreak/64-bit detection.  Otherwise, true on armv6/armv7/armv8/x86_32/x86_64.  `_M_X64` must be defined on Intel 64-bit platforms for here and many other places.  It's automatically defined if `__x86_64__` is, which gets defined by gcc/clang.

So it's strange if this isn't already defaulting on.

-[Unknown]


I am not removing the cookie. Just changed 4 bytes cookie + 12 bytes id to 16 bytes id. The latter case is the same as the protocol described in the RFC 5389. From the server's view, nothing is changed except the first 4 bytes becomes completely random.


I have made this change on your behalf.


This covers some of issue #18


crap typo fix coming ... I **Tested** it somehow the PR does not match what I tested.


:+1:  thx


Issue #15 work


ah, my fault. I looked at both RFCs back and forth, and messed it up. rfc3489 says the 16 bytes has to be random, but rfc5389 says 4 bytes magic cookie + 12 bytes transaction id. I will fix that later today.


Because I specifically use the cookie to filter STUN packets from other non-stun packets.


EMS (brianlball) - i386-Windows-7-VisualStudio-12: Build Failed

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-20.25%25-red.svg)


It is correct I think, but I need to rebuild binaries (in the meantime you can do a source install of the emulator and it should be fine)


#16 and #17 are in this commit... Didn't know I already did this


Неа, мы все блоки кода всегда пишем в полной версии, то есть else {return} - об этом написано критерия оценки


Soon! :)


no logic in variable naming. Most uses format `${something-something}.verions` and this `something.something.version`


И давай таки уберём else if и оставим только if.


No, it shouldn't. Block coordinates are taken from the bottom left corner. This is incorrect.


Hi, there is no tag on this release.


Тут достаточно только return, else не нужен, так как он следует из кода блока: если а тру, то делай это, а во всех иных случаях верни 'я никуда не попал'


Should be `slf4j.version`


Java Programming Lesson 1 (29.06.2016)/src/com/company/Main.java

This is Java...Test


No clue how to interpret your notes/what to correct

No new line e at end of file? What does that mean and when we were told to/how to do this


А тут этот else даже и не нужен, можно по аналогии с первой проверкой просто сделать после всех if return


@wullxz This mistake is the reason not to push directly to master ;)


I dont think highly of some  automated tools, but isnt there something to clean these all out? It was a pita to clear the C++ includes and Im sure these are pretty much all the same state.


I'm going to go through them all when I'm done with the refactor.


Yeah, the large asteroids look awesome!


hows that going?


Eae


here you broke it


and you fixed it incorrectly


#16 related