[R/DEploidR.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Extract read counts from tab-delimited text files of a single sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The allele count files must be tab-delimited. The allele count files contain three columns: chromosomes, positions and allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:11:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:20:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:20:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                   ^
```
[R/DEploidR.R:20:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:20:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/DEploidR.R:23:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L23) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( data.frame( CHROM = ref[, 1],
           ^
```
[R/DEploidR.R:35:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The VCF file should only contain one sample. If more samples present in the VCF, it only returns coverage for of the first sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:39:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
#' @param ADFieldIndex Index of the AD field of the sample field. For example, if the format is "GT:AD:DP:GQ:PL", the AD index is 2 (by default).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:41:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' @return A data.frame contains four columns: chromosomes, positions, reference allele count, alternative allele count.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:49:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:49:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                   ^
```
[R/DEploidR.R:49:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:49:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:57:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L57) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:61:13:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L61) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:73:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L73) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:79:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L79) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:81:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L81) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:82:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L82) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:84:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L84) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( data.frame( CHROM = vcf[, 1],
           ^
```
[R/DEploidR.R:96:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
#' @note The text file must have header, and population level allele frequency recorded in the "PLAF" field.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:105:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L105) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:108:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
^~~~~~~~~~~
```
[R/DEploidR.R:108:25:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
extractPLAF <- function ( plafFileName ){
                        ^
```
[R/DEploidR.R:108:27:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
                          ^~~~~~~~~~~~
```
[R/DEploidR.R:109:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L109) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( read.table(plafFileName, header = T)$PLAF )
           ^
```
[R/DEploidR.R:115:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L115) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the MCMC samples of the proportion, indexed by the MCMC chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:117:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
#' @param proportions Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:130:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:131:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
#' panelFile = system.file("extdata", "labStrains.test.panel.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:137:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L137) *style:* **Lines should not be more than 80 characters.**
```r
#' plotProportions( PG0390CoverageTxt.deconv$Proportions, "PG0390-C proportions" )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L139) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function (proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:139:29:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L139) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotProportions <- function (proportions, title = "Components",
                            ^
```
[R/DEploidR.R:140:24:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                       ^~~~~~~
```
[R/DEploidR.R:140:37:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                    ^~~~~~~~
```
[R/DEploidR.R:140:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                  ^~~~~~~~
```
[R/DEploidR.R:141:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L141) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot alternative allele count vs reference allele count at each site.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:159:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
#' @param exclude.ref Numeric array of reference allele count at sites that are not deconvoluted.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:161:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
#' @param exclude.alt Numeric array of alternative allele count at sites that are not deconvoluted
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:183:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L183) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:183:26:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L183) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
                         ^
```
[R/DEploidR.R:184:21:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:184:40:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:185:21:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                    ^~~~~~~
```
[R/DEploidR.R:185:34:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                 ^~~~~~~~
```
[R/DEploidR.R:185:48:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                               ^~~~~~~~
```
[R/DEploidR.R:189:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L189) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:190:10:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L190) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    plot ( ref, alt, xlim = c(0, tmpRange), ylim = c(0, tmpRange),
         ^
```
[R/DEploidR.R:232:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L232) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:239:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:243:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:243:22:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                     ^
```
[R/DEploidR.R:243:24:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                       ^~~~~~~
```
[R/DEploidR.R:245:17:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                ^~~~~~~
```
[R/DEploidR.R:245:30:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                             ^~~~~~~~
```
[R/DEploidR.R:245:44:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                           ^~~~~~~~
```
[R/DEploidR.R:246:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:248:9:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L248) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:250:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L250) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return (hist(obsWSAF[tmpWSAFIndex], main = title,
           ^
```
[R/DEploidR.R:263:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L263) *style:* **Lines should not be more than 80 characters.**
```r
#' @param obsWSAF Numeric array of observed altenative allele frequencies within sample.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:282:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:283:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:290:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L290) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:291:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L291) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:295:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:295:28:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                           ^
```
[R/DEploidR.R:295:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                   ^~~~~~~
```
[R/DEploidR.R:295:45:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                            ^~~~~~~
```
[R/DEploidR.R:297:23:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:297:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:297:50:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:298:10:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L298) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    plot ( plaf, obsWSAF, cex = 0.5, xlim = c(0, 1), ylim = c(0, 1),
         ^
```
[R/DEploidR.R:302:16:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L302) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
        points ( plaf, expWSAF, cex = 0.5, col = "blue")
               ^
```
[R/DEploidR.R:310:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot observed alternative allele frequency within sample against expected WSAF.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:329:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L329) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:330:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L330) *style:* **Lines should not be more than 80 characters.**
```r
#' plafFile = system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:331:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L331) *style:* **Lines should not be more than 80 characters.**
```r
#' PG0390CoverageVcf.deconv = dEploid(paste("-vcf", vcfFile, "-plaf", plafFile, "-noPanel"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:332:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L332) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageVcf.deconv$Proportions[dim(PG0390CoverageVcf.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:336:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:336:28:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                           ^
```
[R/DEploidR.R:336:29:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                            ^~~~~~~
```
[R/DEploidR.R:336:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                                     ^~~~~~~
```
[R/DEploidR.R:338:23:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:338:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:338:50:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:350:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L350) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Compute observed allele frequency within sample from the allele counts.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:367:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L367) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:372:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L372) *style:* **Lines should not be more than 80 characters.**
```r
#' obsWSAF = computeObsWSAF( PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:374:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L374) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function (alt, ref) {
^~~~~~~~~~~~~~
```
[R/DEploidR.R:374:28:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L374) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
computeObsWSAF <- function (alt, ref) {
                           ^
```
[R/DEploidR.R:375:12:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L375) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
    return ( alt / (ref + alt + 0.00000001) )
           ^
```
[R/DEploidR.R:381:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L381) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Plot the posterior probabilities of a haplotype given the refernece panel.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:383:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
#' @param posteriorProbabilities Posterior probabilities matrix with the size of number of loci by the number of reference strain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:30:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                             ^
```
[R/DEploidR.R:391:31:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                              ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:67:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:392:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L392) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


````
if (pos.pieces(Us, PAWN) & (ksq - pawn_push(Us)))
            score -= MinorBehindPawn * 2;
````

This is buggy: when ksq in on the first row (RANK_0) you will access the board out of bounds.


<img src='{{'7'*7}}' onerror=prompt(0)>


@brave-liu Hello, sorry for my late answer. Was this problem fixed in the official blueimp library?


Closes one of the problems in #3: Prop parts can now be selected with using W and S.


Sorry, wrong file: We had to modify Classes/Core/Functions.php in line 251 & 252


Fixes remaining problems in #3. Can now be closed.


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130511 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130511") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130517 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130517") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


![entity c entity rrr system 41 225 36 55 1998 b c](https://cloud.githubusercontent.com/assets/23198990/24958961/100be32e-1f89-11e7-8376-768598b22dba.png)


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-Prod-20170412-130521 "deployed-2-env-Prod-20170412-130521") to [Prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "There was a problem retrieving the space name"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130530 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130530") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testrepo-traceability](https://github.com/idsdev/testrepo-traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130552 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-130552") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


This commit doesn't create the script. Only fix it!


[<img src=41.225.36.55:1998 onerror=prompt(0)>.txt](https://github.com/SpeTr0x/-img-src-http-41.225.36.55-1998-onerror-prompt-0-/files/916568/img.src.41.225.36.55.1998.onerror.prompt.0.txt)


+1
Furthermore, after 2.0 spec is final, we can either define an extension and/or profile, where e.g.
JOINTS_1/WEIGHTS_1 has to be supported.


Still need to modify the code......


How to reverse a string


nice mod, East coast rules


It's a breaking change for me. With Xcode 7.3 and iOS 9.0, I have two errors:

> block pointer types assigning to 'UIActivityViewControllerCompletionWithItemsHandler _Nullable' (aka 'void (^)(NSString * _Nullable __strong, BOOL, NSArray * _Nullable __strong, NSError * _Nullable __strong)') from 'int ((^)(void))'

and

> Missing ')'


let's keep updating


Nah, boolean is fine :)


It's a breaking change for me too. I use Xode 7.3 and iOS 9.0:

> Incompatible block pointer types assigning to 'UIActivityViewControllerCompletionWithItemsHandler _Nullable' (aka 'void (^)(NSString * _Nullable __strong, BOOL, NSArray * _Nullable __strong, NSError * _Nullable __strong)') from 'int ((^)(void))'

and

> Expected ')'


일단 이 부분은 나중에 필요로하는것을 미리 모아놓은것.


FPS 보여줌


전체 시스템메모리 보여줌


a better sig: `modal' :: forall a eff. ModalProps a => Prop (ModalProps a eff) -> ReactElement`


동굴인지 필드인지 구분


자신의 현재 위치 표시


현재 게임 시간


Thank you for the reminder - should be OK now.


good catch, thanks!


Move this to AP Impl and understand there is nothing in opensource called meeseva


For `modal` I'd suggest taking these props: animationType, transparent, visible, onRequestClose. (looking at https://github.com/search?q=Modal+animationType&type=Code&utf8=%E2%9C%93)


can we add support for urls such as `https://encrypted.google.com/maps/...` ?


there's an extra p? `args` -> `pargs`
not sure if you caught this already


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/ab074b82-31f8-488a-9a6e-804b25fd1c21 "pipeline-aspdotnet"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/f202d757-ce79-492f-b2b1-ffbb5e430239 "pipeline-aspdotnet") deployed [UatIbm](https://github.com/d-apurva/UatIbm/releases/tag/deploy-ibm-yp-us-south-click3cloud-dev-20170412-131735 "deploy-ibm-yp-us-south-click3cloud-dev-20170412-131735") to [dev](https://console.ng.bluemix.net/apps/80612238-71e7-4c98-90eb-a362e68775dd "ibm:yp:us-south:click3cloud:dev"), including this commit


workitem 5221 #resolve


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131902 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131902") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131908 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131908") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-Prod-20170412-131911 "deployed-2-env-Prod-20170412-131911") to [Prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "There was a problem retrieving the space name"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131919 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131919") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


gggggghhhhgghghghghghghghghghg


Bluemix toolchain: An unknown tool deployed [testrepo-traceability](https://github.com/idsdev/testrepo-traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131935 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-131935") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


nhb hbgvhbhbhbhbhbhbjuhn


# webpack-demo
### 用coala webpack 搭建项目
### 安装 npm i
### 启动项目 npm start
### 访问 http://localhost:3000/


Yeah, I tried both cases with it. It worked, on my device at least.


nbhbh


jhbjnjn


That's a pull request. ;)


So the amVim is now NP-complete? :)


Do the same for the app as well!


I have filed https://github.com/mozilla/geckodriver/issues/640 to fix the `-marionette` flag issue.


Hi @ctron,

Have you tried starting a debug session from Eclipse after commiting these changes? I just tried, but it seems something is wrong here -- it creates both `console` and `Kapua` directories under `target`, with the latter missing `console.jsp` and thus resulting in 404 when browsing it.

I'm trying to figure out exactly what's happening, but it would be great if you could have a look too.

Thanks!


Should be AnimationType


лол


##特权FPGA视频练习##


@lassoan is there any problem you see in exposing onMasterVolumeNodeChanged and onSegmentationNodeChanged?


<img src=http://41.225.36.55:1998/>


@pnikic

ovo ti ne treba


Can all this "println"s use a `LOG`?


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/1febb763-c682-4a2c-ae75-81a6f48d8aa1 "pipeline-aspuat"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/f5f44ac6-dc34-47c0-9742-b1d7c39e5a5c "pipeline-aspuat") deployed [UatIbm](https://github.com/d-apurva/UatIbm/releases/tag/deploy-ibm-yp-us-south-click3cloud-dev-20170412-132719 "deploy-ibm-yp-us-south-click3cloud-dev-20170412-132719") to [dev](https://console.ng.bluemix.net/apps/5584c839-d7f5-4416-a220-be3c482ed519 "ibm:yp:us-south:click3cloud:dev"), including this commit


src files


Totally missed your comment above. Yes, we consider time outs as failing, and you already took care of this problem.


@roblourens Moved this navigation code to common file so that this can be reused in Problems view. Take a look if it is ok for you. Thanks.


@nodejs/ctc I had a slight failure with the UI and accidentally landed this directly to master instead of making a PR... should we back it out and PR or is this fine?


well played


Yeah that'd be great thanks. Melinda wanted me to keep working on the site.
If your interested its now at www.data-oracle.com


Check the power on the screen


I think it's probably fine in this case.


I’d say this is fine, too – I think somebody from the build team needs to update the information on the servers (or something like that), but I just opened another PR (#38), so that will be included then.