[R/convertMsp2Spectra-data.R:23:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra-data.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
#' http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL/MSMS-GNPS-Curated-Neg.msp
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convertMsp2Spectra.R:33:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L33) *style:* **Variable and function name style should be camelCase.**
```r
    mzInd_1 <- grep("PRECURSORMZ:", msp[, 1])
    ^~~~~~~
```
[R/convertMsp2Spectra.R:34:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L34) *style:* **Variable and function name style should be camelCase.**
```r
    mzInd_2 <- grep("EXACTMASS:", msp[, 1])
    ^~~~~~~
```
[R/convertMsp2Spectra.R:47:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L47) *style:* **Variable and function name style should be camelCase.**
```r
    NAMES <- as.character(msp[nameInd,  2])
    ^~~~~
```
[R/convertMsp2Spectra.R:48:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L48) *style:* **Variable and function name style should be camelCase.**
```r
    MZ <- as.numeric(as.character(msp[mzInd, 2]))
    ^~
```
[R/convertMsp2Spectra.R:49:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L49) *style:* **Variable and function name style should be camelCase.**
```r
    NUMPEAKS <- as.numeric(as.character(msp[numpeaksInd, 2]))
    ^~~~~~~~
```
[R/convertMsp2Spectra.R:54:34:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L54) *style:* **Trailing whitespace is superfluous.**
```r
    if (numEntries != length(MZ))
                                 ^
```
[R/convertMsp2Spectra.R:58:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L58) *style:* **Variable and function name style should be camelCase.**
```r
    RT <- if (length(rtInd) == numEntries) {
    ^~
```
[R/convertMsp2Spectra.R:60:12:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L60) *warning:* **no visible global function definition for ‘Spectra’**
```r
    spl <- Spectra(spN_l, elementMetadata = DataFrame(names = NAMES))
           ^~~~~~~
```
[R/convertMsp2Spectra.R:60:45:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L60) *warning:* **no visible global function definition for ‘DataFrame’**
```r
    spl <- Spectra(spN_l, elementMetadata = DataFrame(names = NAMES))
                                            ^~~~~~~~~
```
[R/convertMsp2Spectra.R:64:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/convertMsp2Spectra.R#L64) *style:* **Variable and function name style should be camelCase.**
```r
    spN_l <- vector("list", numEntries)
    ^~~~~
```
[R/linkDf.R:91:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L91) *style:* **Variable and function name style should be camelCase.**
```r
    inds_cond <- lapply(seq_along(inds),
    ^~~~~~~~~
```
[R/linkDf.R:98:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L98) *style:* **Variable and function name style should be camelCase.**
```r
    inds_uniq <- unique(unlist(inds_cond))
    ^~~~~~~~~
```
[R/linkDf.R:100:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L100) *style:* **Variable and function name style should be camelCase.**
```r
    inds_uniq_combn <- combn(inds_uniq, 2)
    ^~~~~~~~~~~~~~~
```
[R/linkDf.R:103:19:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L103) *warning:* **Avoid 1:ncol(...) expressions, use seq_len.**
```r
    sim <- lapply(1:ncol(inds_uniq_combn), function(x) {
                  ^
```
[R/linkDf.R:104:9:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L104) *style:* **Variable and function name style should be camelCase.**
```r
        row_sim <- strsplit(inds_uniq_combn[1, x], split = "_")[[1]][2]
        ^~~~~~~
```
[R/linkDf.R:105:9:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L105) *style:* **Variable and function name style should be camelCase.**
```r
        col_sim <- strsplit(inds_uniq_combn[2, x], split = "_")[[1]][2]
        ^~~~~~~
```
[R/linkDf.R:138:65:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L138) *style:* **Trailing whitespace is superfluous.**
```r
#' lower `numeric`, threshold value for similarity values, below
                                                                ^
```
[R/linkDf.R:165:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L165) *style:* **Lines should not be more than 80 characters.**
```r
    if (!all(colnames(link0df) == c("group1", "spectrum1",  "group2", "spectrum2",  "similarity")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/linkDf.R:171:26:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L171) *style:* **Trailing whitespace is superfluous.**
```r
    if (lower > max(sim))
                         ^
```
[R/linkDf.R:226:66:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L226) *style:* **Trailing whitespace is superfluous.**
```r
    link0df <- createLink0df(similarityMatrix = similarityMatrix,
                                                                 ^
```
[R/linkDf.R:230:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L230) *style:* **Lines should not be more than 80 characters.**
```r
    thrLinkDf <- thresholdLinkDf(link0df = link0df, lower = lower, upper = upper)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/linkDf.R:278:40:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L278) *style:* **Commas should always have a space after.**
```r
        linkDf <- linkDf[which(linkDf[,"group1"] != linkDf[,"group2"]), ]
                                       ^
```
[R/linkDf.R:278:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L278) *style:* **Commas should always have a space after.**
```r
        linkDf <- linkDf[which(linkDf[,"group1"] != linkDf[,"group2"]), ]
                                                            ^
```
[R/linkDf.R:281:40:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L281) *style:* **Commas should always have a space after.**
```r
        linkDf <- linkDf[which(linkDf[,"group1"] == linkDf[,"group2"]), ]
                                       ^
```
[R/linkDf.R:281:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/linkDf.R#L281) *style:* **Commas should always have a space after.**
```r
        linkDf <- linkDf[which(linkDf[,"group1"] == linkDf[,"group2"]), ]
                                                            ^
```
[R/plottingFunctions.R:13:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L13) *warning:* **local variable ‘groupname_l’ assigned but may not be used**
```r
    groupname_l <- length(groupname)
    ^~~~~~~~~~~
```
[R/plottingFunctions.R:17:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L17) *warning:* **local variable ‘nameselected’ assigned but may not be used**
```r
    nameselected <- name[ind]
    ^~~~~~~~~~~~
```
[R/plottingFunctions.R:22:3:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plottingFunctions.R:24:20:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L24) *warning:* **no visible global function definition for ‘alpha’**
```r
        colours <- alpha(palette()[as.numeric(as.factor(group))[ind]+1], transparency)
                   ^~~~~
```
[R/plottingFunctions.R:26:20:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L26) *warning:* **no visible global function definition for ‘alpha’**
```r
        colours <- alpha(colour[as.numeric(as.factor(group))[ind]], transparency)
                   ^~~~~
```
[R/plottingFunctions.R:71:23:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L71) *warning:* **no visible global function definition for ‘alpha’**
```r
            colour <- alpha(colour, transparency)
                      ^~~~~
```
[R/plottingFunctions.R:82:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L82) *style:* **functions should have cyclomatic complexity of less than 15, this has 30.**
```r
plotCircos <- function(groupname, linkDf, initialize = c(TRUE, FALSE),
^
```
[R/plottingFunctions.R:93:63:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L93) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    name <- lapply(strsplit(groupname, split = "_"), function (x) x[length(x)])
                                                              ^
```
[R/plottingFunctions.R:97:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L97) *style:* **Variable and function name style should be camelCase.**
```r
    groupname_l <- length(groupname)
    ^~~~~~~~~~~
```
[R/plottingFunctions.R:107:11:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L107) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(!is.numeric(transparency)) stop("transparency is not numeric")
          ^
```
[R/plottingFunctions.R:112:35:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L112) *style:* **Commas should always have a space after.**
```r
            xlim = matrix(rep(c(0,1), groupname_l), ncol = 2, byrow = TRUE))
                                  ^
```
[R/plottingFunctions.R:119:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L119) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/plottingFunctions.R:147:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L147) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/plottingFunctions.R:155:12:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L155) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for( i in 1:length(uniqueGroup)) {
           ^
```
[R/plottingFunctions.R:155:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L155) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        for( i in 1:length(uniqueGroup)) {
            ^
```
[R/plottingFunctions.R:155:19:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L155) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
        for( i in 1:length(uniqueGroup)) {
                  ^
```
[R/plottingFunctions.R:166:12:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L166) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for( i in 1:length(uniqueGroup)) {
           ^
```
[R/plottingFunctions.R:166:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L166) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        for( i in 1:length(uniqueGroup)) {
            ^
```
[R/plottingFunctions.R:166:19:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L166) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
        for( i in 1:length(uniqueGroup)) {
                  ^
```
[R/plottingFunctions.R:171:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L171) *style:* **Lines should not be more than 80 characters.**
```r
                sector.index = groupname[c(minInd:maxInd)[floor(length(minInd:maxInd) / 2)]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plottingFunctions.R:181:38:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L181) *style:* **Commas should always have a space after.**
```r
                circos.link(linkDf[i,]$"spectrum1", 0.5,
                                     ^
```
[R/plottingFunctions.R:182:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L182) *style:* **Commas should always have a space after.**
```r
                    linkDf[i,]$"spectrum2", 0.5,
                             ^
```
[R/plottingFunctions.R:186:43:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L186) *style:* **Commas should always have a space after.**
```r
                        max(0.5, linkDf[i,][["similarity"]])},
                                          ^
```
[R/plottingFunctions.R:273:63:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L273) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    name <- lapply(strsplit(groupname, split = "_"), function (x) x[length(x)])
                                                              ^
```
[R/plottingFunctions.R:277:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L277) *style:* **Variable and function name style should be camelCase.**
```r
    groupname_l <- length(groupname)
    ^~~~~~~~~~~
```
[R/plottingFunctions.R:284:28:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L284) *style:* **Commas should always have a space after.**
```r
    linkDfSpec1 <- linkDf[,"spectrum1"]
                           ^
```
[R/plottingFunctions.R:285:28:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L285) *style:* **Commas should always have a space after.**
```r
    linkDfSpec2 <- linkDf[,"spectrum2"]
                           ^
```
[R/plottingFunctions.R:288:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L288) *style:* **Lines should not be more than 80 characters.**
```r
        colours <- alpha(palette()[as.numeric(as.factor(group))[ind]+1], transparency)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plottingFunctions.R:288:69:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L288) *style:* **Put spaces around all infix operators.**
```r
        colours <- alpha(palette()[as.numeric(as.factor(group))[ind]+1], transparency)
                                                                   ~^~
```
[R/plottingFunctions.R:290:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L290) *style:* **Lines should not be more than 80 characters.**
```r
        colours <- alpha(colour[as.numeric(as.factor(group))[ind]], transparency)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plottingFunctions.R:293:15:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L293) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    for (h in 1:length(ind)) {
              ^
```
[R/plottingFunctions.R:301:12:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L301) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    } else {linkDfInd <- NULL}
           ^
```
[R/plottingFunctions.R:301:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L301) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    } else {linkDfInd <- NULL}
                             ^
```
[R/plottingFunctions.R:323:3:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L323) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plottingFunctions.R:325:3:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L325) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/plottingFunctions.R:330:65:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L330) *style:* **Trailing whitespace is superfluous.**
```r
#' groupname `character` vector containing "group" and "name" to
                                                                ^
```
[R/plottingFunctions.R:331:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L331) *style:* **Lines should not be more than 80 characters.**
```r
#' display, that is  a unique identifier of the features, "group" and "name" have
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plottingFunctions.R:331:82:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L331) *style:* **Trailing whitespace is superfluous.**
```r
#' display, that is  a unique identifier of the features, "group" and "name" have
                                                                                ^
```
[R/plottingFunctions.R:332:73:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L332) *style:* **Trailing whitespace is superfluous.**
```r
#' to be separated by `"_"` where "group" is the first and "name" is the
                                                                        ^
```
[R/plottingFunctions.R:339:70:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L339) *style:* **Trailing whitespace is superfluous.**
```r
#' colour `NULL` or `character`, colour defines the colours which are
                                                                     ^
```
[R/plottingFunctions.R:346:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L346) *style:* **Trailing whitespace is superfluous.**
```r
#' Internal use in `shinyCircos` or outside of `shinyCircos`
                                                            ^
```
[R/plottingFunctions.R:354:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L354) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/plottingFunctions.R:356:58:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L356) *style:* **Trailing whitespace is superfluous.**
```r
#' similarityMat <- compare_Spectra(spectra_tissue[1:10],
                                                         ^
```
[R/plottingFunctions.R:358:60:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L358) *style:* **Trailing whitespace is superfluous.**
```r
#' linkDf <- createLinkDf(similarityMatrix = similarityMat,
                                                           ^
```
[R/plottingFunctions.R:359:39:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L359) *style:* **Trailing whitespace is superfluous.**
```r
#'     spectra = spectra_tissue[1:10],
                                      ^
```
[R/plottingFunctions.R:360:74:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L360) *style:* **Trailing whitespace is superfluous.**
```r
#'     condition = c("SPL", "LIM", "ANT", "STY"), lower = 0.5, upper = 1)
                                                                         ^
```
[R/plottingFunctions.R:363:59:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L363) *style:* **Trailing whitespace is superfluous.**
```r
#' groupname <- c(as.character(linkDf_cut[, "spectrum1"]),
                                                          ^
```
[R/plottingFunctions.R:371:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L371) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:378:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L378) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:380:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L380) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:386:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L386) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:387:18:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L387) *style:* **Commas should always have a space after.**
```r
    plot(x = c(0,0.5), y = c(0,0.5), type = "n", xlab = "", ylab = "",
                 ^
```
[R/plottingFunctions.R:387:32:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L387) *style:* **Commas should always have a space after.**
```r
    plot(x = c(0,0.5), y = c(0,0.5), type = "n", xlab = "", ylab = "",
                               ^
```
[R/plottingFunctions.R:406:10:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L406) *style:* **Trailing whitespace is superfluous.**
```r
#' @param
         ^
```
[R/plottingFunctions.R:407:67:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L407) *style:* **Trailing whitespace is superfluous.**
```r
#' groupnameselected `character` vector with groupname of selected
                                                                  ^
```
[R/plottingFunctions.R:408:69:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L408) *style:* **Trailing whitespace is superfluous.**
```r
#' feature, vector containing "group" and "name" to display, that is
                                                                    ^
```
[R/plottingFunctions.R:412:10:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L412) *style:* **Trailing whitespace is superfluous.**
```r
#' @param
         ^
```
[R/plottingFunctions.R:413:63:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L413) *style:* **Trailing whitespace is superfluous.**
```r
#' linkDf `data.frame`, in each row there is information about
                                                              ^
```
[R/plottingFunctions.R:416:12:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L416) *style:* **Trailing whitespace is superfluous.**
```r
#' @details
           ^
```
[R/plottingFunctions.R:419:11:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L419) *style:* **Trailing whitespace is superfluous.**
```r
#' @return
          ^
```
[R/plottingFunctions.R:420:67:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L420) *style:* **Trailing whitespace is superfluous.**
```r
#' `getLinkDfIndices` returns indices concerning `linkDf` to which
                                                                  ^
```
[R/plottingFunctions.R:425:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L425) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/plottingFunctions.R:430:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L430) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:434:51:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L434) *style:* **Commas should always have a space after.**
```r
    linkDfInd <- lapply(linkDfInd, function(x) x[,1])
                                                  ^
```
[R/plottingFunctions.R:436:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L436) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:438:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L438) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:447:16:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L447) *style:* **Trailing whitespace is superfluous.**
```r
#' @description
               ^
```
[R/plottingFunctions.R:448:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L448) *style:* **Trailing whitespace is superfluous.**
```r
#' Calculates the nearest feature in polar coordinates given
                                                            ^
```
[R/plottingFunctions.R:457:12:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L457) *style:* **Trailing whitespace is superfluous.**
```r
#' @details
           ^
```
[R/plottingFunctions.R:458:60:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L458) *style:* **Trailing whitespace is superfluous.**
```r
#' `minFragCart2Polar` is employed to find the feature with
                                                           ^
```
[R/plottingFunctions.R:461:11:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L461) *style:* **Trailing whitespace is superfluous.**
```r
#' @return
          ^
```
[R/plottingFunctions.R:463:73:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L463) *style:* **Trailing whitespace is superfluous.**
```r
#' smallest distance to the given coordinates. As `minFragCart2Polar` is
                                                                        ^
```
[R/plottingFunctions.R:469:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L469) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/plottingFunctions.R:471:58:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L471) *style:* **Trailing whitespace is superfluous.**
```r
#' similarityMat <- compare_Spectra(spectra_tissue[1:10],
                                                         ^
```
[R/plottingFunctions.R:473:60:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L473) *style:* **Trailing whitespace is superfluous.**
```r
#' linkDf <- createLinkDf(similarityMatrix = similarityMat,
                                                           ^
```
[R/plottingFunctions.R:474:39:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L474) *style:* **Trailing whitespace is superfluous.**
```r
#'     spectra = spectra_tissue[1:10],
                                      ^
```
[R/plottingFunctions.R:475:74:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L475) *style:* **Trailing whitespace is superfluous.**
```r
#'     condition = c("SPL", "LIM", "ANT", "STY"), lower = 0.5, upper = 1)
                                                                         ^
```
[R/plottingFunctions.R:478:59:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L478) *style:* **Trailing whitespace is superfluous.**
```r
#' groupname <- c(as.character(linkDf_cut[, "spectrum1"]),
                                                          ^
```
[R/plottingFunctions.R:485:72:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L485) *style:* **Trailing whitespace is superfluous.**
```r
#' plotCircos(groupname, NULL, initialize = TRUE, featureNames = FALSE,
                                                                       ^
```
[R/plottingFunctions.R:489:39:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L489) *style:* **Trailing whitespace is superfluous.**
```r
#' degreeFeatures <- lapply(groupname,
                                      ^
```
[R/plottingFunctions.R:490:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L490) *style:* **Lines should not be more than 80 characters.**
```r
#'  function(x) mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plottingFunctions.R:506:16:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L506) *style:* **Trailing whitespace is superfluous.**
```r
#' @description
               ^
```
[R/plottingFunctions.R:514:63:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L514) *style:* **Trailing whitespace is superfluous.**
```r
#' `cart2Polar` is employed to translate cartesian coordinates
                                                              ^
```
[R/plottingFunctions.R:518:11:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L518) *style:* **Trailing whitespace is superfluous.**
```r
#' @return
          ^
```
[R/plottingFunctions.R:523:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L523) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/plottingFunctions.R:529:15:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L529) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    r <- sqrt( x ^ 2 + y ^ 2)
              ^
```
[R/plottingFunctions.R:530:20:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L530) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    thetaP <- atan( y/x ) * 180 / pi
                   ^
```
[R/plottingFunctions.R:530:22:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L530) *style:* **Put spaces around all infix operators.**
```r
    thetaP <- atan( y/x ) * 180 / pi
                    ~^~
```
[R/plottingFunctions.R:530:24:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L530) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    thetaP <- atan( y/x ) * 180 / pi
                       ^
```
[R/plottingFunctions.R:536:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L536) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plottingFunctions.R:563:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L563) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/plottingFunctions.R:576:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L576) *style:* **Variable and function name style should be camelCase.**
```r
    mz_sub <- spectra[subject]@listData[[1]]@mz
    ^~~~~~
```
[R/plottingFunctions.R:577:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L577) *style:* **Variable and function name style should be camelCase.**
```r
    int_sub <- spectra[subject]@listData[[1]]@intensity
    ^~~~~~~
```
[R/plottingFunctions.R:578:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L578) *style:* **Variable and function name style should be camelCase.**
```r
    mz_que <- spectra[query]@listData[[1]]@mz
    ^~~~~~
```
[R/plottingFunctions.R:579:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L579) *style:* **Variable and function name style should be camelCase.**
```r
    int_que <- spectra[query]@listData[[1]]@intensity
    ^~~~~~~
```
[R/plottingFunctions.R:581:25:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L581) *style:* **Trailing whitespace is superfluous.**
```r
    ## normalize to 100%
                        ^
```
[R/plottingFunctions.R:582:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L582) *style:* **Variable and function name style should be camelCase.**
```r
    int_sub <- int_sub / max(int_sub) * 100
    ^~~~~~~
```
[R/plottingFunctions.R:583:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L583) *style:* **Variable and function name style should be camelCase.**
```r
    int_que <- int_que / max(int_que) * 100
    ^~~~~~~
```
[R/plottingFunctions.R:585:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L585) *style:* **Variable and function name style should be camelCase.**
```r
    df_sub <- data.frame(mz = mz_sub, int = -int_sub, is = "MS/MS #1")
    ^~~~~~
```
[R/plottingFunctions.R:586:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L586) *style:* **Variable and function name style should be camelCase.**
```r
    df_que <- data.frame(mz = mz_que, int = int_que, is = "MS/MS #2")
    ^~~~~~
```
[R/plottingFunctions.R:590:17:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L590) *style:* **Trailing whitespace is superfluous.**
```r
    ggplot(df) +
                ^
```
[R/plottingFunctions.R:591:43:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/plottingFunctions.R#L591) *style:* **Put spaces around all infix operators.**
```r
        geom_segment(aes(x = mz, xend = mz+0.001, y = int, yend = 0, col = is),
                                         ~^~
```
[R/sd01_outputXCMS-data.R:5:16:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/sd01_outputXCMS-data.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#' @description
               ^
```
[R/sd01_outputXCMS-data.R:7:69:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/sd01_outputXCMS-data.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' `XCMS` using the data from Li et al. (2015). See Li et al. (2015)
                                                                    ^
```
[R/sd02_deconvoluted-data.R:5:16:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/sd02_deconvoluted-data.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
#' @description
               ^
```
[R/sd02_deconvoluted-data.R:6:58:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/sd02_deconvoluted-data.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#' `sd02_deconvoluted` contains MS/MS data from Li et al.
                                                         ^
```
[R/sd02_deconvoluted-data.R:7:72:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/sd02_deconvoluted-data.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#' (2015). It is a `data.frame` which hosts m/z values, retention time,
                                                                       ^
```
[R/shinyApp.R:8:16:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L8) *warning:* **no visible global function definition for ‘createLink0df’**
```r
    link0df <- createLink0df(simMat, spectra = spectra, condition = condition)
               ^~~~~~~~~~~~~
```
[R/shinyApp.R:10:60:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
#' Visualise the similarity of MS/MS features in a reactive
                                                           ^
```
[R/shinyApp.R:11:78:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L11) *style:* **Trailing whitespace is superfluous.**
```r
#' context. See `Details` the vignette for further descriptions on how to use
                                                                             ^
```
[R/shinyApp.R:15:58:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L15) *style:* **Trailing whitespace is superfluous.**
```r
#' similarityMatrix `matrix`, `similarityMatrix` contains
                                                         ^
```
[R/shinyApp.R:16:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
#' pair-wise similarity coefficients which give information about the similarity
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:16:81:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L16) *style:* **Trailing whitespace is superfluous.**
```r
#' pair-wise similarity coefficients which give information about the similarity
                                                                                ^
```
[R/shinyApp.R:19:16:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L19) *warning:* **no visible global function definition for ‘highlight’**
```r
        return(highlight(type_match, inds, linkDf))
               ^~~~~~~~~
```
[R/shinyApp.R:20:48:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
#' spectra an S4 object of class `Spectra`, the
                                               ^
```
[R/shinyApp.R:21:75:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L21) *style:* **Trailing whitespace is superfluous.**
```r
#' `Spectra` object will be used to display information about the selected
                                                                          ^
```
[R/shinyApp.R:26:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L26) *warning:* **local variable ‘rt’ assigned but may not be used**
```r
    rt <- unlist(lapply(spectra@listData, function(x) x@rt))
    ^~
```
[R/shinyApp.R:27:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L27) *warning:* **local variable ‘prec_mz’ assigned but may not be used**
```r
    prec_mz <- unlist(lapply(spectra@listData, function(x) x@precursorMz))
    ^~~~~~~
```
[R/shinyApp.R:29:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L29) *warning:* **local variable ‘groupname’ assigned but may not be used**
```r
    groupname <- rownames(similarityMatrix)
    ^~~~~~~~~
```
[R/shinyApp.R:29:55:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L29) *style:* **Trailing whitespace is superfluous.**
```r
#' ... further arguments passed to `shinyCircos`, e.g.
                                                      ^
```
[R/shinyApp.R:30:65:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L30) *style:* **Trailing whitespace is superfluous.**
```r
#' `cexFeatureNames` to pass to `plotCircos` to set font size in
                                                                ^
```
[R/shinyApp.R:34:64:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L34) *style:* **Trailing whitespace is superfluous.**
```r
#' The function is based on the `shiny` and `circlize` package.
                                                               ^
```
[R/shinyApp.R:35:75:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L35) *style:* **Trailing whitespace is superfluous.**
```r
#' The user can choose interactively thresholds, type of links (between or
                                                                          ^
```
[R/shinyApp.R:36:80:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L36) *style:* **Trailing whitespace is superfluous.**
```r
#' within groups), display information about MS/MS features, permanently select
                                                                               ^
```
[R/shinyApp.R:38:77:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L38) *style:* **Trailing whitespace is superfluous.**
```r
#' stores annotation information about the MS/MS features. Names of features
                                                                            ^
```
[R/shinyApp.R:39:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L39) *style:* **Trailing whitespace is superfluous.**
```r
#' within the `similarityMatrix` have to be found as entries
                                                            ^
```
[R/shinyApp.R:40:62:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L40) *style:* **Trailing whitespace is superfluous.**
```r
#' in `Spectra`. `names(Spectra)` are used as identifiers and
                                                             ^
```
[R/shinyApp.R:41:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L41) *style:* **Trailing whitespace is superfluous.**
```r
#' `colnames`/`rownames` from `similarityMatrix` are cleaved
                                                            ^
```
[R/shinyApp.R:44:70:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L44) *style:* **Trailing whitespace is superfluous.**
```r
#' "adduct" in the slot `elementMetadata` of `spectra`. After exiting
                                                                     ^
```
[R/shinyApp.R:46:72:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L46) *style:* **Trailing whitespace is superfluous.**
```r
#' in the slot `elementMetadata`. If one or several of these columns is
                                                                       ^
```
[R/shinyApp.R:47:75:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L47) *style:* **Trailing whitespace is superfluous.**
```r
#' already present in `elementMetadata`, the column(s) will be used as the
                                                                          ^
```
[R/shinyApp.R:51:68:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L51) *style:* **Trailing whitespace is superfluous.**
```r
#' `character`, `shinyCircos` returns a `character` vector with the
                                                                   ^
```
[R/shinyApp.R:57:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L57) *style:* **Trailing whitespace is superfluous.**
```r
#' @examples
            ^
```
[R/shinyApp.R:62:49:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L62) *style:* **Trailing whitespace is superfluous.**
```r
#' shinyCircos(similarityMatrix = similarityMat,
                                                ^
```
[R/shinyApp.R:66:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L66) *style:* **functions should have cyclomatic complexity of less than 15, this has 46.**
```r
shinyCircos <- function(similarityMatrix, spectra, condition, ...) {
^
```
[R/shinyApp.R:92:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L92) *style:* **Variable and function name style should be camelCase.**
```r
    prec_mz <- unlist(lapply(spectra@listData, function(x) x@precursorMz))
    ^~~~~~~
```
[R/shinyApp.R:98:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L98) *style:* **Variable and function name style should be camelCase.**
```r
    RT <- MetCirc:::typeMatch_link0(similarityMatrix = similarityMatrix,
    ^~
```
[R/shinyApp.R:101:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L101) *style:* **Variable and function name style should be camelCase.**
```r
    rt_match <- RT[["type_match"]]
    ^~~~~~~~
```
[R/shinyApp.R:108:64:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L108) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    nameRT <- lapply(strsplit(rt_match, split = "_"), function (x) x[length(x)])
                                                               ^
```
[R/shinyApp.R:120:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L120) *style:* **Variable and function name style should be camelCase.**
```r
    MZ <- MetCirc:::typeMatch_link0(similarityMatrix = similarityMatrix,
    ^~
```
[R/shinyApp.R:123:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L123) *style:* **Variable and function name style should be camelCase.**
```r
    mz_match <- MZ[["type_match"]]
    ^~~~~~~~
```
[R/shinyApp.R:130:64:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L130) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    nameMZ <- lapply(strsplit(mz_match, split = "_"), function (x) x[length(x)])
                                                               ^
```
[R/shinyApp.R:142:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L142) *style:* **Variable and function name style should be camelCase.**
```r
    Clust <- MetCirc:::typeMatch_link0(similarityMatrix = similarityMatrix,
    ^~~~~
```
[R/shinyApp.R:145:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L145) *style:* **Variable and function name style should be camelCase.**
```r
    clust_match <- Clust[["type_match"]]
    ^~~~~~~~~~~
```
[R/shinyApp.R:152:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L152) *style:* **Lines should not be more than 80 characters.**
```r
    nameClust <- lapply(strsplit(clust_match, split = "_"), function (x) x[length(x)])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:152:70:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L152) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    nameClust <- lapply(strsplit(clust_match, split = "_"), function (x) x[length(x)])
                                                                     ^
```
[R/shinyApp.R:164:5:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L164) *style:* **Variable and function name style should be camelCase.**
```r
    plot_l <- list(highlightMz = highlightMZ, fillMz = fillMZ,
    ^~~~~~
```
[R/shinyApp.R:166:16:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L166) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        spe <- reactiveValues(spectra = spectra)
               ^~~~~~~~~~~~~~
```
[R/shinyApp.R:183:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L183) *style:* **Lines should not be more than 80 characters.**
```r
                            choices = c("all" = "all", "inter-class links" = "inter",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:184:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L184) *style:* **Lines should not be more than 80 characters.**
```r
                                "intra-class links" = "intra"), selected = "all"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:189:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L189) *style:* **Lines should not be more than 80 characters.**
```r
                            choices = c("clustering" = "clustering", "m/z" = "mz",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:190:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L190) *style:* **Lines should not be more than 80 characters.**
```r
                              "retention time" = "retentionTime"), selected = "mz"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:197:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L197) *style:* **Lines should not be more than 80 characters.**
```r
                        actionButton("stop", "Stop and export \n selected features")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:204:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L204) *style:* **Trailing whitespace is superfluous.**
```r
                        sliderInput("plotSize", "plot size",
                                                            ^
```
[R/shinyApp.R:210:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L210) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~
```
[R/shinyApp.R:214:19:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L214) *warning:* **no visible global function definition for ‘eventReactive’**
```r
        indAnn <- eventReactive(input$annotate, {ind()})
                  ^~~~~~~~~~~~~
```
[R/shinyApp.R:217:41:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L217) *style:* **Trailing whitespace is superfluous.**
```r
                plotOutput("plotSpec")),
                                        ^
```
[R/shinyApp.R:222:28:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L222) *warning:* **no visible global function definition for ‘eventReactive’**
```r
        annotateClasses <- eventReactive(input$annotate, {input$classes})
                           ^~~~~~~~~~~~~
```
[R/shinyApp.R:229:27:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L229) *warning:* **no visible global function definition for ‘eventReactive’**
```r
        annotateAdduct <- eventReactive(input$annotate, {input$adduct})
                          ^~~~~~~~~~~~~
```
[R/shinyApp.R:235:51:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L235) *style:* **Trailing whitespace is superfluous.**
```r
                textInput("names", label = "name",
                                                  ^
```
[R/shinyApp.R:237:24:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L237) *style:* **Trailing whitespace is superfluous.**
```r
            } else NULL
                       ^~
```
[R/shinyApp.R:244:24:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L244) *style:* **Trailing whitespace is superfluous.**
```r
            } else NULL
                       ^
```
[R/shinyApp.R:251:1:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L251) *style:* **Lines should not be more than 80 characters.**
```r
                    value = isolate(spe$spectra@elementMetadata$information[ind()]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/shinyApp.R:252:24:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L252) *style:* **Trailing whitespace is superfluous.**
```r
            } else NULL
                       ^~
```
[R/shinyApp.R:259:24:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L259) *style:* **Trailing whitespace is superfluous.**
```r
            } else NULL
                       ^~
```
[R/shinyApp.R:278:25:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L278) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        coordsNewSgl <- reactiveValues(X = 0, Y = 0)
                        ^~~~~~~~~~~~~~
```
[R/shinyApp.R:279:25:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L279) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        coordsOldSgl <- reactiveValues(X = 0, Y = 0)
                        ^~~~~~~~~~~~~~
```
[R/shinyApp.R:279:49:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L279) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        indAnn <- eventReactive(input$annotate, {ind()})
                                                ^
```
[R/shinyApp.R:287:58:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L287) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        annotateClasses <- eventReactive(input$annotate, {input$classes})
                                                         ^
```
[R/shinyApp.R:290:61:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L290) *style:* **Trailing whitespace is superfluous.**
```r
        annotateInformation <- eventReactive(input$annotate,
                                                            ^
```
[R/shinyApp.R:291:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L291) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
            {input$information})
            ^
```
[R/shinyApp.R:294:21:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L294) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        onCircle <- reactiveValues(is = NULL)
                    ^~~~~~~~~~~~~~
```
[R/shinyApp.R:294:57:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L294) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        annotateAdduct <- eventReactive(input$annotate, {input$adduct})
                                                        ^
```
[R/shinyApp.R:307:19:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L307) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        indSgl <- reactiveValues(ind = NULL)
                  ^~~~~~~~~~~~~~
```
[R/shinyApp.R:307:65:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L307) *style:* **Trailing whitespace is superfluous.**
```r
            spe$spectra@elementMetadata$information[indAnn()] <-
                                                                ^
```
[R/shinyApp.R:315:25:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L315) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        coordsNewDbl <- reactiveValues(X = 0, Y = 0)
                        ^~~~~~~~~~~~~~
```
[R/shinyApp.R:316:25:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L316) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        coordsOldDbl <- reactiveValues(X = 0, Y = 0)
                        ^~~~~~~~~~~~~~
```
[R/shinyApp.R:318:9:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L318) *style:* **Variable and function name style should be camelCase.**
```r
        GN <- reactive({
        ^~
```
[R/shinyApp.R:332:19:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L332) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        indDbl <- reactiveValues(ind = NULL, new = NULL)
                  ^~~~~~~~~~~~~~
```
[R/shinyApp.R:334:9:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L334) *style:* **Variable and function name style should be camelCase.**
```r
        linkDf_cut <- reactive(
        ^~~~~~~~~~
```
[R/shinyApp.R:338:9:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L338) *style:* **Variable and function name style should be camelCase.**
```r
        linkDf_threshold <- reactive(
        ^~~~~~~~~~~~~~~~
```
[R/shinyApp.R:348:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L348) *style:* **Variable and function name style should be camelCase.**
```r
                coordsNewSgl$X <- input$circosSgl$x
                             ^
```
[R/shinyApp.R:349:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L349) *style:* **Variable and function name style should be camelCase.**
```r
                coordsNewSgl$Y <- input$circosSgl$y
                             ^
```
[R/shinyApp.R:350:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L350) *style:* **Variable and function name style should be camelCase.**
```r
                coordsOldSgl$X <- coordsNewSgl$X
                             ^
```
[R/shinyApp.R:351:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L351) *style:* **Variable and function name style should be camelCase.**
```r
                coordsOldSgl$Y <- coordsNewSgl$Y
                             ^
```
[R/shinyApp.R:353:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L353) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(indDblMZ$ind <- NULL)
            ^~~~~~~
```
[R/shinyApp.R:353:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L353) *style:* **Variable and function name style should be camelCase.**
```r
                coordsNewSgl$X <- coordsOldSgl$X
                             ^
```
[R/shinyApp.R:354:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L354) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(indDblRT$ind <- NULL)
            ^~~~~~~
```
[R/shinyApp.R:354:30:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L354) *style:* **Variable and function name style should be camelCase.**
```r
                coordsNewSgl$Y <- coordsOldSgl$Y
                             ^
```
[R/shinyApp.R:355:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L355) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(indDblCluster$ind <- NULL)
            ^~~~~~~
```
[R/shinyApp.R:356:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L356) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(indDbl$new <- NULL)
            ^~~~~~~
```
[R/shinyApp.R:357:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L357) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(onCircle$is <- FALSE)
            ^~~~~~~
```
[R/shinyApp.R:358:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L358) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(indSgl$ind <- NULL)
            ^~~~~~~
```
[R/shinyApp.R:364:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L364) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(onCircle$is <- FALSE)
            ^~~~~~~
```
[R/shinyApp.R:365:13:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L365) *warning:* **no visible global function definition for ‘isolate’**
```r
            isolate(indSgl$ind <- NULL)
            ^~~~~~~
```
[R/shinyApp.R:370:21:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L370) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        indDblMZ <- reactiveValues(ind = NULL)
                    ^~~~~~~~~~~~~~
```
[R/shinyApp.R:377:41:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L377) *warning:* **no visible global function definition for ‘isolate’**
```r
                        indDblMZ$ind <- isolate(indDblMZ$ind[-which(newIndMZ == indDblMZ$ind)])
                                        ^~~~~~~
```
[R/shinyApp.R:378:45:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L378) *warning:* **no visible global function definition for ‘isolate’**
```r
                    } else {indDblMZ$ind <- isolate(c(indDblMZ$ind, newIndMZ))}
                                            ^~~~~~~
```
[R/shinyApp.R:383:21:](https://github.com/tnaake/MetCirc/blob/4826bcab6c1b0e0fbc494a9c41f2c651c8cf66dd/R/shinyApp.R#L383) *warning:* **no visible global function definition for ‘reactiveValues’**
```r
        indDblRT <- reactiveValues(ind = NULL)
                    ^~~~~~~~~~~~~~
```


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Basic structure using all settings for good code: eslint, prettier and editor config.


`public `


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`public let remoteDevices`


У тебя переменная `instances` нигде неиспользуется, поэтому ее можно не создавать. А в функцию `init` ты передаешь `options`, а такой переменной нет вообще (поэтому кстати и ошибка в консоли висит). Нужно просто оставить `M.Materialbox.init(elems);`


自动构建 [auto-dragalia-b293204c.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/826/artifacts/0/home/circleci/project/artifacts/auto-dragalia-b293204c.zip)


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Deep Neural Network


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@JanVerderber Boljša opcija je, če uporabiš DateTimeProperty in mu nastaviš parameter auto_now_add, kar pomeni da se bo avtomatično zabeležil datum, ko bo objekt ustvarjen. Poglej, kako je to narejeno v User modelu in najbolje da kar od tam kopiraš polja: created, updated ter deleted (glej vrstice 53-55): https://github.com/JanVerderber/ninjatodo/blob/master/models/user.py


Jeśli używasz importu z * to musisz być pewien, ze sobie poradzisz z rozwiązywaniem konfliktów nazw klas pomiędzy pakietami. Generalnie przez jednych to jest zalecana metoda, przez innych uważane jest za złą praktykę. Ja osobiście preferuję import do każdej klasy osobno.


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num**3 another way of doing it


removed test files from branch 1stclass


but if someone specified the argument, why don't we still handle it? Yes someone may subscribe pyblox in javablox, but he still sent the command anyways, the message will still be in javablox channel


TeamCity MAS / MAS [Build 1.1.0.561-MAS-150-WeeklyEmailN](https://teamcity.nice.org.uk/viewLog.html?buildId=64414&buildTypeId=Mas_Mas) outcome was **SUCCESS**
Summary: Tests passed: 12 Build time: 00:01:56


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

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Project | Plan | Build
---|---|---
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### Deployments updated

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|Deployment project |
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strive to avoid inline styling, it can lead to performance issues. add classname


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


action


k


Привет, спасибо за карту Ала-Арчи, очень помогла.
Вопрос: вот ты удалил .img из репы, а откуда его теперь можно скачать? Не все умеют/хотят osm рендерить.


TeamCity MAS / MAS [Build 1.1.0.562](https://teamcity.nice.org.uk/viewLog.html?buildId=64417&buildTypeId=Mas_Mas) outcome was **FAILURE**
Summary: Artifacts size 0 B is 100% different from 3.6 MB in build #1.1.0.557-r893BC73; exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:15


I suggest passing the film prop, for code concise


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
# @param    current                 vector       Current parameter combination for which we are determining the weight
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:12:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                   scalar       standard deviation of the perturbation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:13:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function  function     Function to calculate the prior probability of a set of parameters
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:36:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
# @brief apply the ABC routine used in our Methods in Ecology and Evolution Paper
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:43:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
# @param    statistics                    vector      A vector containing functions that take a tree as an argument and return a single scalar value (the statistic).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:44:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
# @param    simulation_function           vector      A function that implements the diversification model and returns an object of class phylo
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:45:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
# @param    init_epsilon_values           vector      A vector containing the initial threshold values for the summary statistics from the vector statistics.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:46:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_generating_function     function    Function to generate parameters from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:47:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function        function    Function to calculate the prior probability of a set of parameters (should match prior_generating_function in shape)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:48:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
# @param    number_of_particles           scalar      Number of particles to be used per iteration of the ABC-SMC algorithm.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:49:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                         scalar      Standard deviation of the perturbance distribution (perturbance distribution is a gaussian with mean 0).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:50:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
# @param    stop_rate                     scalar      If the acceptance rate drops below \code{stopRate}, stop the ABC-SMC algorithm  and assume convergence.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:51:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
# @return                                 matrix      A matrix with n columns, where n is the number of parameters you are trying to estimate.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:75:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:126:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L301) *style:* **Lines should not be more than 80 characters.**
```r
# @brief Estimate the likelihood of a given tree, provided a likelihood function, using a Monte Carlo Markov Chain
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:308:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L308) *style:* **Lines should not be more than 80 characters.**
```r
# @param    likelihood_function   function    Function that calculates the likelihood of our diversification model, given the tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:309:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L311) *style:* **Lines should not be more than 80 characters.**
```r
# @param    logtransforms         scalar      Whether to perform jumps on logtransformed parameters (TRUE) or not (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:313:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L313) *style:* **Lines should not be more than 80 characters.**
```r
# @param    burnin                scalar      Length of the burnin, default is 30% of iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:315:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                 scalar      Standard deviation of the jumping distribution, which is N(0, sigma).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:316:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L316) *style:* **Lines should not be more than 80 characters.**
```r
# @return                         mcmc        An MCMC object, as used by the package "coda".
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:320:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/get_norm_brts.R:22:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L186) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:274:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L274) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:275:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L344) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:345:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                           ^
```
[R/plot_nLTT.R:51:33:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                                ^
```
[R/plot_nLTT.R:52:28:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/plot_nLTT.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] / max( xy[, 1])      #normalize time
                           ^
```
[R/plot_nLTT.R:94:32:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/plot_nLTT.R#L94) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs(min( xy[, 1])) #make sure time runs from 0..T
                               ^
```
[R/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-abc_smc_nltt.R#L30) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-abc_smc_nltt.R:35:3:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:55:3:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-get_average_nltt.R#L10) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_average_nltt.R:41:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:14:3:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:58:3:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:40:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_brts.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    regexp = "branching times must be negative, for example -3 time units since the present"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:54:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_brts.R#L54) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:77:16:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_extinct.R#L77) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:78:16:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_extinct.R#L78) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


En regardant plus en détail, votre utilisation de `kvs_`et `kvs` fait un peu peur... rapellez vous que vous les avez déclaré comme des `KVS *`soit un  `struct element **`. Attention à la manipulation de pointeurs !!
Vous devriez revenir en arrière. Considérez la variable `kvs` que vous aviez avant comme variable globale, ca devrait suffire.


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@paluh The reason I moved is that psc-ide-vim is dependent on Syntastic plugin, which is synchronous. I work on very large PureScript projects daily, some have more than 100 modules with some modules having more than 1000 lines. It started lagging to me whenever I save because after saving every time, psc-ide-vim will launch Syntastic, which will cause a wait time of 2-3 seconds.

LanguageClient-NeoVim, on the other hand, works asynchronously. I also use Deoplete extension which is used by LanguageClient-NeoVim.  It's been a year since I made this change and since then my life with PureScript became a lot easier.

If you decide to use this commit, please update the LanguageClient-NeoVim plugin to the newer version as I have found some bugs in it and got them fixed. Also, take [this](https://github.com/sriharshachilakapati/dotfiles/commit/135230d19822fcd822b85e1b5c93d667cf29d295) commit as reference for the newer configuration. This allows you to work with multiple projects with different PureScript versions.

Let me know your feelings once you make the switch.


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@JensWehner why is this changed?
@gtirimbo and @wscharpach is this something that was discussed with you guys too?


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e1323beで対応されました


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