[R/chisq_statistic.R:44:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/chisq_statistic.R#L44) *style:* **lines should not be more than 80 characters.**
```r
  if (length(maha)  != nrow(obj)) stop("length(mahalanobis distance) != nrow(obj)")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/correct.R:59:47:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(obj, !is.na(Entrez), !is.na(siRNAIDs)) %>%
                                              ^~~~~~~~
```
[R/correct.R:65:33:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L65) *style:* **Variable and function names should be all lowercase.**
```r
    res <- dplyr::group_by(res, GeneSymbol) %>%
                                ^~~~~~~~~~
```
[R/correct.R:72:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L72) *style:* **Variable and function names should be all lowercase.**
```r
  res <- .gespeR(res, path)
         ^~~~~~~
```
[R/correct.R:79:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L79) *style:* **Variable and function names should be all lowercase.**
```r
.gespeR <- function(obj, path)
^~~~~~~
```
[R/correct.R:83:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L83) *style:* **lines should not be more than 80 characters.**
```r
  # init the matrices so that all entrez id that are not in both matrices are discarded
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/correct.R:90:61:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L90) *style:* **Variable and function names should be all lowercase.**
```r
                               ids=as.character(pheno.frame$siRNAIDs),
                                                            ^~~~~~~~
```
[R/correct.R:104:45:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L104) *style:* **Variable and function names should be all lowercase.**
```r
                         dplyr::select(obj, GeneSymbol, Entrez) %>% unique,
                                            ^~~~~~~~~~
```
[R/correct.R:106:26:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L106) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(!is.na(GeneSymbol))
                         ^~~~~~~~~~
```
[R/correct.R:118:26:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(Virus, GeneSymbol, Entrez, siRNAIDs, Readout) %>%
                         ^~~~~~~~~~
```
[R/correct.R:118:46:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L118) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(Virus, GeneSymbol, Entrez, siRNAIDs, Readout) %>%
                                             ^~~~~~~~
```
[R/correct.R:119:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L119) *style:* **Variable and function names should be all lowercase.**
```r
    .[order(siRNAIDs)]
            ^~~~~~~~
```
[R/correct.R:122:44:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
  pheno.sirnas   <- as.character(pheno.mat$siRNAIDs)
                                           ^~~~~~~~
```
[R/correct.R:168:48:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L168) *style:* **Variable and function names should be all lowercase.**
```r
                            siRNAIDs=pheno.mat$siRNAIDs,
                                               ^~~~~~~~
```
[R/correct.R:175:43:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
  assertthat::assert_that(all(pheno.frame$siRNAIDs == rel.mat@siRNAs))
                                          ^~~~~~~~
```
[R/correct.R:176:43:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L176) *style:* **Variable and function names should be all lowercase.**
```r
  assertthat::assert_that(all(pheno.frame$siRNAIDs ==
                                          ^~~~~~~~
```
[R/correct.R:190:50:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L190) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(siRNAIDs=strsplit(as.character(siRNAIDs), ",")) %>%
                                                 ^~~~~~~~
```
[R/correct.R:191:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correct.R#L191) *style:* **Variable and function names should be all lowercase.**
```r
    tidyr::unnest(siRNAIDs)
                  ^~~~~~~~
```
[R/correlation.R:41:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/correlation.R#L41) *style:* **lines should not be more than 80 characters.**
```r
                                       method = c("pearson", "kendall", "spearman"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:57:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L57) *style:* **lines should not be more than 80 characters.**
```r
                                        path=NULL, graph=NULL, r=0.5, node.start.count=25,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:58:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L58) *style:* **lines should not be more than 80 characters.**
```r
                                        search.depth=5, delete.nodes.on.degree=1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:62:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(GeneSymbol, abs(Effect))
                  ^~~~~~~~~~
```
[R/diffuse.R:68:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::filter(GeneSymbol %in% hits$GeneSymbol) %>%
                    ^~~~~~~~~~
```
[R/diffuse.R:68:42:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::filter(GeneSymbol %in% hits$GeneSymbol) %>%
                                         ^~~~~~~~~~
```
[R/diffuse.R:69:22:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L69) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(-MeanBootstrap, -Pval, -FDR)
                     ^~~~~~~~~~~~~
```
[R/diffuse.R:86:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L86) *style:* **lines should not be more than 80 characters.**
```r
                               path=NULL, graph=NULL, r=0.5, node.start.count=25,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:93:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, Readout) %>%
                    ^~~~~~~~~~
```
[R/diffuse.R:99:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, MeanEffect) %>%
                    ^~~~~~~~~~
```
[R/diffuse.R:99:33:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, MeanEffect) %>%
                                ^~~~~~~~~~
```
[R/diffuse.R:100:28:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L100) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::rename(Effect=MeanEffect)
                           ^~~~~~~~~~
```
[R/diffuse.R:104:35:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L104) *style:* **Variable and function names should be all lowercase.**
```r
    hits <- obj %>% dplyr::select(GeneSymbol, Effect)
                                  ^~~~~~~~~~
```
[R/diffuse.R:132:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L132) *style:* **lines should not be more than 80 characters.**
```r
         "neighbors"= .knn(hits, bootstrap.hits, adjm, node.start.count, search.depth, graph),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:153:44:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L153) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                           ^~~~~~~~~~
```
[R/diffuse.R:153:64:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L153) *style:* **Variable and function names should be all lowercase.**
```r
  li  <- list(diffusion=dplyr::select(res, GeneSymbol, Effect, DiffusionEffect),
                                                               ^~~~~~~~~~~~~~~
```
[R/diffuse.R:167:22:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
  diffuse.data$frame$DiffusionEffect <- mrw
                     ^~~~~~~~~~~~~~~
```
[R/diffuse.R:189:58:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L189) *style:* **Variable and function names should be all lowercase.**
```r
  boot.g <- tidyr::gather(bootstrap.hits, Boot, Effect, -GeneSymbol) %>%
                                                         ^~~~~~~~~~
```
[R/diffuse.R:201:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L201) *style:* **lines should not be more than 80 characters.**
```r
  # -> calculate means -> calculate alphas -> calculate variance -> calculate alpha_0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:202:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L202) *style:* **lines should not be more than 80 characters.**
```r
  flat.dat <- do.call("rbind", lapply(li, function(e) e)) %>% dplyr::select(-Effect)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:204:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::group_by(GeneSymbol) %>%
                    ^~~~~~~~~~
```
[R/diffuse.R:205:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L205) *style:* **lines should not be more than 80 characters.**
```r
    dplyr::summarise(MeanBootstrapDiffusionEffect=mean(DiffusionEffect, na.rm=T)) %>%
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:205:56:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L205) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::summarise(MeanBootstrapDiffusionEffect=mean(DiffusionEffect, na.rm=T)) %>%
                                                       ^~~~~~~~~~~~~~~
```
[R/diffuse.R:208:57:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L208) *style:* **Variable and function names should be all lowercase.**
```r
                          tidyr::spread(flat.dat, boot, DiffusionEffect),
                                                        ^~~~~~~~~~~~~~~
```
[R/diffuse.R:216:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L216) *style:* **lines should not be more than 80 characters.**
```r
.knn <- function(hits, bootstrap.hits, adjm, node.start.count, search.depth, graph)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/diffuse.R:226:56:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L226) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(Idx %in% as.integer(names(neighs))))$GeneSymbol
                                                       ^~~~~~~~~~
```
[R/diffuse.R:230:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L230) *style:* **Variable and function names should be all lowercase.**
```r
      dplyr::select(GeneSymbol, Effect)}
                    ^~~~~~~~~~
```
[R/diffuse.R:239:49:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/diffuse.R#L239) *style:* **Variable and function names should be all lowercase.**
```r
  genes.found <- dplyr::select(flat.dat, Start, GeneSymbol) %>%
                                                ^~~~~~~~~~
```
[R/effect_matrix.R:39:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/effect_matrix.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(GeneSymbol, Effect) %>%
                  ^~~~~~~~~~
```
[R/effect_matrix.R:43:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/effect_matrix.R#L43) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(GeneSymbol %in% gene.top$GeneSymbol) %>%
                  ^~~~~~~~~~
```
[R/effect_matrix.R:43:44:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/effect_matrix.R#L43) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::filter(GeneSymbol %in% gene.top$GeneSymbol) %>%
                                           ^~~~~~~~~~
```
[R/effect_matrix.R:44:26:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/effect_matrix.R#L44) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::select(Virus, GeneSymbol, Effect) %>%
                         ^~~~~~~~~~
```
[R/hist.R:35:27:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hist.R#L35) *style:* **Variable and function names should be all lowercase.**
```r
  ret <- dplyr::filter(x, ReadoutClass=="Readout")
                          ^~~~~~~~~~~~
```
[R/hist.R:58:5:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hist.R#L58) *style:* **Variable and function names should not use underscores.**
```r
    theme_bw() +
    ^~~~~~~~
```
[R/hist.R:59:18:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hist.R#L59) *style:* **Variable and function names should not use underscores.**
```r
    theme(text = element_text(size = 14, family = "Helvetica")) +
                 ^~~~~~~~~~~~
```
[R/hyperstatistics.R:75:59:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L75) *style:* **Variable and function names should be all lowercase.**
```r
  grp.indexes <- dplyr::group_indices(obj, Virus, Screen, ReadoutType,
                                                          ^~~~~~~~~~~
```
[R/hyperstatistics.R:76:39:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L76) *style:* **Variable and function names should be all lowercase.**
```r
                                      ScreenType, Library, Design, Cell)
                                      ^~~~~~~~~~
```
[R/hyperstatistics.R:92:50:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L92) *style:* **Variable and function names should be all lowercase.**
```r
                                         grp.dat$ScreenType[1],
                                                 ^~~~~~~~~~
```
[R/hyperstatistics.R:93:50:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
                                         grp.dat$ReadoutType[1],
                                                 ^~~~~~~~~~~
```
[R/hyperstatistics.R:98:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L98) *style:* **lines should not be more than 80 characters.**
```r
        fr <- .do.hyperstatistic(grp.dat, padjust, summ.method, do.summarization, level)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/hyperstatistics.R:115:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L115) *style:* **lines should not be more than 80 characters.**
```r
.do.hyperstatistic <- function(obj, padjust, summ.method, do.summarization, level)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/hyperstatistics.R:125:28:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
                           ScreenType, ReadoutType,
                           ^~~~~~~~~~
```
[R/hyperstatistics.R:125:40:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
                           ScreenType, ReadoutType,
                                       ^~~~~~~~~~~
```
[R/hyperstatistics.R:127:35:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L127) *style:* **Variable and function names should be all lowercase.**
```r
                           Plate, RowIdx, ColIdx,
                                  ^~~~~~
```
[R/hyperstatistics.R:127:43:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L127) *style:* **Variable and function names should be all lowercase.**
```r
                           Plate, RowIdx, ColIdx,
                                          ^~~~~~
```
[R/hyperstatistics.R:128:28:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L128) *style:* **Variable and function names should be all lowercase.**
```r
                           GeneSymbol, Entrez, siRNAIDs) %>%
                           ^~~~~~~~~~
```
[R/hyperstatistics.R:128:48:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L128) *style:* **Variable and function names should be all lowercase.**
```r
                           GeneSymbol, Entrez, siRNAIDs) %>%
                                               ^~~~~~~~
```
[R/hyperstatistics.R:145:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L145) *style:* **Variable and function names should be all lowercase.**
```r
                    ReadoutType, ScreenType,
                    ^~~~~~~~~~~
```
[R/hyperstatistics.R:145:34:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L145) *style:* **Variable and function names should be all lowercase.**
```r
                    ReadoutType, ScreenType,
                                 ^~~~~~~~~~
```
[R/hyperstatistics.R:147:35:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(HRes=.hypertest(GeneSymbol, siRNAIDs, Plate,
                                  ^~~~~~~~~~
```
[R/hyperstatistics.R:147:47:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
    dplyr::mutate(HRes=.hypertest(GeneSymbol, siRNAIDs, Plate,
                                              ^~~~~~~~
```
[R/hyperstatistics.R:148:35:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L148) *style:* **Variable and function names should be all lowercase.**
```r
                                  RowIdx, ColIdx, Readout, level)) %>%
                                  ^~~~~~
```
[R/hyperstatistics.R:148:43:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L148) *style:* **Variable and function names should be all lowercase.**
```r
                                  RowIdx, ColIdx, Readout, level)) %>%
                                          ^~~~~~
```
[R/hyperstatistics.R:157:27:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L157) *style:* **Variable and function names should be all lowercase.**
```r
  data.table::setDT(res)[,HyperRank := cumsum(res$Hit)]
                          ^~~~~~~~~
```
[R/hyperstatistics.R:158:36:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L158) *style:* **Variable and function names should be all lowercase.**
```r
  data.table::setDT(res)[Hit == 0, HyperRank := NA_integer_]
                                   ^~~~~~~~~
```
[R/hyperstatistics.R:179:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L179) *style:* **lines should not be more than 80 characters.**
```r
  ## if we do the hypergeometric test on genes we need another grouping as for siRNAs
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/hyperstatistics.R:187:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L187) *style:* **lines should not be more than 80 characters.**
```r
  # (the siRNA SHOULD be identical to grouping by plate/row/col; so the last grouping should be redundant)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/hyperstatistics.R:213:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/hyperstatistics.R#L213) *style:* **lines should not be more than 80 characters.**
```r
    prob <- stats::phyper(i - 1, ranks[i], N - ranks[i], ndrawn, lower.tail = F, log.p=F)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:43:49:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
       gene.pathogen.matrix=gene.pathogen.matrix )
                                                ^
```
[R/lmm-locfdr.R:84:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L84) *style:* **Use <-, not =, for assignment.**
```r
  call = match.call()
       ^
```
[R/lmm-locfdr.R:101:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L101) *style:* **Use <-, not =, for assignment.**
```r
        med = median(zz)
            ^
```
[R/lmm-locfdr.R:102:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L102) *style:* **Use <-, not =, for assignment.**
```r
        ra = med + (1 - pct) * (range(zz) - med)
           ^
```
[R/lmm-locfdr.R:103:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L103) *style:* **Use <-, not =, for assignment.**
```r
        lo = ra[1]
           ^
```
[R/lmm-locfdr.R:104:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L104) *style:* **Use <-, not =, for assignment.**
```r
        up = ra[2]
           ^
```
[R/lmm-locfdr.R:141:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L141) *style:* **Use <-, not =, for assignment.**
```r
    fp0 = matrix(NA, 6, 4)
        ^
```
[R/lmm-locfdr.R:142:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L142) *style:* **Use <-, not =, for assignment.**
```r
    colnames(fp0) = c("delta", "sigleft", "p0", "sigright")
                  ^
```
[R/lmm-locfdr.R:145:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L145) *style:* **Use <-, not =, for assignment.**
```r
    fp0 = matrix(NA, 6, 3)
        ^
```
[R/lmm-locfdr.R:146:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L146) *style:* **Use <-, not =, for assignment.**
```r
    colnames(fp0) = c("delta", "sigma", "p0")
                  ^
```
[R/lmm-locfdr.R:148:17:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L148) *style:* **Use <-, not =, for assignment.**
```r
  rownames(fp0) = c("thest", "theSD", "mlest", "mleSD", "cmest",  "cmeSD")
                ^
```
[R/lmm-locfdr.R:149:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L149) *style:* **Use <-, not =, for assignment.**
```r
  fp0["thest", 1:2] = c(0, 1)
                    ^
```
[R/lmm-locfdr.R:150:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L150) *style:* **Use <-, not =, for assignment.**
```r
  fp0["theSD", 1:2] = 0
                    ^
```
[R/lmm-locfdr.R:176:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L176) *style:* **Use <-, not =, for assignment.**
```r
    cmerror = I(is.na(co[3]) | is.na(co[2]))
            ^
```
[R/lmm-locfdr.R:178:15:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L178) *style:* **Use <-, not =, for assignment.**
```r
      cmerror = I(co[2] >= 0 | co[2] + co[3] >= 0)
              ^
```
[R/lmm-locfdr.R:181:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L181) *style:* **Use <-, not =, for assignment.**
```r
    cmerror = is.na(co[3])
            ^
```
[R/lmm-locfdr.R:183:15:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L183) *style:* **Use <-, not =, for assignment.**
```r
      cmerror = I(co[3] >= 0)
              ^
```
[R/lmm-locfdr.R:213:5:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L213) *style:* **Use <-, not =, for assignment.**
```r
  b = 4.3 * exp(-0.26 * log(N, 10))
    ^
```
[R/lmm-locfdr.R:215:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L215) *style:* **Use <-, not =, for assignment.**
```r
    med = median(zz)
        ^
```
[R/lmm-locfdr.R:216:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L216) *style:* **Use <-, not =, for assignment.**
```r
    sc = diff(quantile(zz)[c(2, 4)])/(2 * stats::qnorm(0.75))
       ^
```
[R/lmm-locfdr.R:217:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L217) *style:* **Use <-, not =, for assignment.**
```r
    mlests = locmle(zz, xlim = c(med, b * sc))
           ^
```
[R/lmm-locfdr.R:219:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L219) *style:* **lines should not be more than 80 characters.**
```r
      warning("length(zz) > 500,000: For ML estimation, a wider interval than optimal was used.  To use the optimal interval, rerun with mlests = c(",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:221:14:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L221) *style:* **Use <-, not =, for assignment.**
```r
      mlests = locmle(zz, xlim = c(med, sc))
             ^
```
[R/lmm-locfdr.R:226:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L226) *style:* **Use <-, not =, for assignment.**
```r
      b = 1
        ^
```
[R/lmm-locfdr.R:228:14:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L228) *style:* **Use <-, not =, for assignment.**
```r
      Cov.in = list(x = x, X = X, f = f, sw = sw)
             ^
```
[R/lmm-locfdr.R:229:14:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L229) *style:* **Use <-, not =, for assignment.**
```r
      ml.out = locmle(zz, xlim = c(mlests[1], b * mlests[2]),
             ^
```
[R/lmm-locfdr.R:231:14:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L231) *style:* **Use <-, not =, for assignment.**
```r
      mlests = ml.out$mle
             ^
```
[R/lmm-locfdr.R:233:17:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L233) *style:* **Use <-, not =, for assignment.**
```r
    else mlests = locmle(zz, xlim = c(mlests[1], b * mlests[2]),
                ^
```
[R/lmm-locfdr.R:235:23:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L235) *style:* **Use <-, not =, for assignment.**
```r
    fp0["mlest", 1:3] = mlests[1:3]
                      ^
```
[R/lmm-locfdr.R:236:23:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L236) *style:* **Use <-, not =, for assignment.**
```r
    fp0["mleSD", 1:3] = mlests[4:6]
                      ^
```
[R/lmm-locfdr.R:240:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L240) *style:* **lines should not be more than 80 characters.**
```r
                                                              2]/mlests[2])) > 0.05)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:241:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L241) *style:* **lines should not be more than 80 characters.**
```r
      warning("Discrepancy between central matching and maximum likelihood estimates.\nConsider rerunning with nulltype = 1")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:251:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L251) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
           ^
```
[R/lmm-locfdr.R:251:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L251) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
                  ^
```
[R/lmm-locfdr.R:251:27:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L251) *style:* **Use <-, not =, for assignment.**
```r
    delhat = xmax = xmaxx = mlests[1]
                          ^
```
[R/lmm-locfdr.R:252:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L252) *style:* **Use <-, not =, for assignment.**
```r
    sighat = mlests[2]
           ^
```
[R/lmm-locfdr.R:253:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L253) *style:* **Use <-, not =, for assignment.**
```r
    p0 = mlests[3]
       ^
```
[R/lmm-locfdr.R:254:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L254) *style:* **Use <-, not =, for assignment.**
```r
    f0 = stats::dnorm(x, delhat, sighat)
       ^
```
[R/lmm-locfdr.R:255:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L255) *style:* **Use <-, not =, for assignment.**
```r
    f0 = (sum(f) * f0)/sum(f0)
       ^
```
[R/lmm-locfdr.R:257:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L257) *style:* **Use <-, not =, for assignment.**
```r
  fdr = pmin((p0 * f0)/f, 1)
      ^
```
[R/lmm-locfdr.R:261:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L261) *style:* **Use <-, not =, for assignment.**
```r
  fp0["thest", 3] = p0theo
                  ^
```
[R/lmm-locfdr.R:273:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L273) *style:* **Use <-, not =, for assignment.**
```r
  else xxlo = xmax
            ^
```
[R/lmm-locfdr.R:276:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L276) *style:* **Use <-, not =, for assignment.**
```r
  else xxhi = xmax
            ^
```
[R/lmm-locfdr.R:281:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L281) *style:* **Use <-, not =, for assignment.**
```r
  else xxlo = xmax
            ^
```
[R/lmm-locfdr.R:284:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L284) *style:* **Use <-, not =, for assignment.**
```r
  else xxhi = xmax
            ^
```
[R/lmm-locfdr.R:288:66:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L288) *style:* **Use <-, not =, for assignment.**
```r
    fdr[x >= mlests[1] - mlests[2] & x <= mlests[1] + mlests[2]] = 1
                                                                 ^
```
[R/lmm-locfdr.R:289:67:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L289) *style:* **Use <-, not =, for assignment.**
```r
    fdr0[x >= mlests[1] - mlests[2] & x <= mlests[1] + mlests[2]] = 1
                                                                  ^
```
[R/lmm-locfdr.R:300:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L300) *style:* **lines should not be more than 80 characters.**
```r
                                                             fdr[ido]) * fall[ido])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:302:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L302) *style:* **lines should not be more than 80 characters.**
```r
                                                                fdr0[ido]) * fall[ido])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:304:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L304) *style:* **lines should not be more than 80 characters.**
```r
                                                              fdr[iup]) * fall[iup])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:306:1:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L306) *style:* **lines should not be more than 80 characters.**
```r
                                                                 fdr0[iup]) * fall[iup])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/lmm-locfdr.R:308:28:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L308) *style:* **Use <-, not =, for assignment.**
```r
  Efdr[which(is.na(Efdr))] = 1
                           ^
```
[R/lmm-locfdr.R:315:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L315) *style:* **Use <-, not =, for assignment.**
```r
    mul = c(1, mult)
        ^
```
[R/lmm-locfdr.R:316:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L316) *style:* **Use <-, not =, for assignment.**
```r
    EE = rep(0, length(mul))
       ^
```
[R/lmm-locfdr.R:318:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L318) *style:* **Use <-, not =, for assignment.**
```r
      xe = sqrt(mul[m]) * x
         ^
```
[R/lmm-locfdr.R:319:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L319) *style:* **Use <-, not =, for assignment.**
```r
      f1e = approx(xe, f1, x, rule = 2, ties = mean)$y
          ^
```
[R/lmm-locfdr.R:320:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L320) *style:* **Use <-, not =, for assignment.**
```r
      f1e = (f1e * sum(f1))/sum(f1e)
          ^
```
[R/lmm-locfdr.R:321:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L321) *style:* **Use <-, not =, for assignment.**
```r
      f0e = f0
          ^
```
[R/lmm-locfdr.R:322:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L322) *style:* **Use <-, not =, for assignment.**
```r
      p0e = p0
          ^
```
[R/lmm-locfdr.R:324:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L324) *style:* **Use <-, not =, for assignment.**
```r
        f0e = f00
            ^
```
[R/lmm-locfdr.R:325:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L325) *style:* **Use <-, not =, for assignment.**
```r
        p0e = p0theo
            ^
```
[R/lmm-locfdr.R:327:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L327) *style:* **Use <-, not =, for assignment.**
```r
      fdre = (p0e * f0e)/(p0e * f0e + f1e)
           ^
```
[R/lmm-locfdr.R:328:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L328) *style:* **Use <-, not =, for assignment.**
```r
      EE[m] = sum(f1e * fdre)/sum(f1e)
            ^
```
[R/lmm-locfdr.R:330:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L330) *style:* **Use <-, not =, for assignment.**
```r
    EE = EE/EE[1]
       ^
```
[R/lmm-locfdr.R:331:15:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L331) *style:* **Use <-, not =, for assignment.**
```r
    names(EE) = mul
              ^
```
[R/lmm-locfdr.R:333:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L333) *style:* **Use <-, not =, for assignment.**
```r
  Cov2.out = loccov2(X, X0, i0, f, fp0["cmest", ], N)
           ^
```
[R/lmm-locfdr.R:334:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L334) *style:* **Use <-, not =, for assignment.**
```r
  Cov0.out = loccov2(X, matrix(1, length(x), 1), i0, f, fp0["thest",
           ^
```
[R/lmm-locfdr.R:338:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L338) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = Cov0.out$Ilfdr
            ^
```
[R/lmm-locfdr.R:340:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L340) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = ml.out$Ilfdr
            ^
```
[R/lmm-locfdr.R:342:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L342) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = Cov2.out$Ilfdr
            ^
```
[R/lmm-locfdr.R:347:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L347) *style:* **Use <-, not =, for assignment.**
```r
    Cov = Cov0.out$Cov
        ^
```
[R/lmm-locfdr.R:349:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L349) *style:* **Use <-, not =, for assignment.**
```r
    Cov = ml.out$Cov.lfdr
        ^
```
[R/lmm-locfdr.R:350:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L350) *style:* **Use <-, not =, for assignment.**
```r
  else Cov = Cov2.out$Cov
           ^
```
[R/lmm-locfdr.R:352:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L352) *style:* **Use <-, not =, for assignment.**
```r
  fp0["cmeSD", 1:3] = Cov2.out$stdev[c(2, 3, 1)]
                    ^
```
[R/lmm-locfdr.R:354:21:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L354) *style:* **Use <-, not =, for assignment.**
```r
    fp0["cmeSD", 4] = fp0["cmeSD", 2]
                    ^
```
[R/lmm-locfdr.R:355:19:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L355) *style:* **Use <-, not =, for assignment.**
```r
  fp0["theSD", 3] = Cov0.out$stdev[1]
                  ^
```
[R/lmm-locfdr.R:358:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L358) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["thest", c(3, 1, 2)]
          ^
```
[R/lmm-locfdr.R:359:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L359) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["theSD", c(3, 1, 2)]
            ^
```
[R/lmm-locfdr.R:360:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L360) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(Cov0.out$pds.)
           ^
```
[R/lmm-locfdr.R:363:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L363) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["mlest", c(3, 1, 2)]
          ^
```
[R/lmm-locfdr.R:364:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L364) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["mleSD", c(3, 1, 2)]
            ^
```
[R/lmm-locfdr.R:365:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L365) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(ml.out$pds.)
           ^
```
[R/lmm-locfdr.R:368:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L368) *style:* **Use <-, not =, for assignment.**
```r
      pds = fp0["cmest", c(3, 1, 2)]
          ^
```
[R/lmm-locfdr.R:369:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L369) *style:* **Use <-, not =, for assignment.**
```r
      stdev = fp0["cmeSD", c(3, 1, 2)]
            ^
```
[R/lmm-locfdr.R:370:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L370) *style:* **Use <-, not =, for assignment.**
```r
      pds. = t(Cov2.out$pds.)
           ^
```
[R/lmm-locfdr.R:373:20:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L373) *style:* **Use <-, not =, for assignment.**
```r
    colnames(pds.) = names(pds) = c("p0", "delhat", "sighat")
                   ^
```
[R/lmm-locfdr.R:373:33:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L373) *style:* **Use <-, not =, for assignment.**
```r
    colnames(pds.) = names(pds) = c("p0", "delhat", "sighat")
                                ^
```
[R/lmm-locfdr.R:374:18:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L374) *style:* **Use <-, not =, for assignment.**
```r
    names(stdev) = c("sdp0", "sddelhat", "sdsighat")
                 ^
```
[R/lmm-locfdr.R:391:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L391) *style:* **Use <-, not =, for assignment.**
```r
  z.2 = rep(NA, 2)
      ^
```
[R/lmm-locfdr.R:392:5:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L392) *style:* **Use <-, not =, for assignment.**
```r
  m = order(fd)[nx]
    ^
```
[R/lmm-locfdr.R:394:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L394) *style:* **Use <-, not =, for assignment.**
```r
    z.2[2] = stats::approx(fd[m:nx], x[m:nx], 0.2, ties = mean)$y
           ^
```
[R/lmm-locfdr.R:397:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L397) *style:* **Use <-, not =, for assignment.**
```r
    z.2[1] = stats::approx(fd[1:m], x[1:m], 0.2, ties = mean)$y
           ^
```
[R/lmm-locfdr.R:411:6:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L411) *style:* **Use <-, not =, for assignment.**
```r
  vl = list(fdr = ffdr, fp0 = fp0, Efdr = Efdr, cdf1 = cdf1,
     ^
```
[R/lmm-locfdr.R:414:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L414) *style:* **Use <-, not =, for assignment.**
```r
    vl$mult = EE
            ^
```
[R/lmm-locfdr.R:415:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L415) *style:* **Use <-, not =, for assignment.**
```r
  vl$call = call
          ^
```
[R/lmm-locfdr.R:426:5:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L426) *style:* **Use <-, not =, for assignment.**
```r
  N = length(z)
    ^
```
[R/lmm-locfdr.R:429:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L429) *style:* **Use <-, not =, for assignment.**
```r
      b = 1
        ^
```
[R/lmm-locfdr.R:430:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L430) *style:* **Use <-, not =, for assignment.**
```r
    else b = 4.3 * exp(-0.26 * log(N, 10))
           ^
```
[R/lmm-locfdr.R:431:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L431) *style:* **Use <-, not =, for assignment.**
```r
    xlim = c(median(z), b * diff(quantile(z)[c(2, 4)])/(2 *
         ^
```
[R/lmm-locfdr.R:434:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L434) *style:* **Use <-, not =, for assignment.**
```r
  aorig = xlim[1] - xlim[2]
        ^
```
[R/lmm-locfdr.R:435:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L435) *style:* **Use <-, not =, for assignment.**
```r
  borig = xlim[1] + xlim[2]
        ^
```
[R/lmm-locfdr.R:436:6:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L436) *style:* **Use <-, not =, for assignment.**
```r
  z0 = z[which(z >= aorig & z <= borig)]
     ^
```
[R/lmm-locfdr.R:437:6:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L437) *style:* **Use <-, not =, for assignment.**
```r
  N0 = length(z0)
     ^
```
[R/lmm-locfdr.R:438:5:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L438) *style:* **Use <-, not =, for assignment.**
```r
  Y = c(mean(z0), mean(z0^2))
    ^
```
[R/lmm-locfdr.R:439:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L439) *style:* **Use <-, not =, for assignment.**
```r
  that = N0/N
       ^
```
[R/lmm-locfdr.R:441:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L441) *style:* **Use <-, not =, for assignment.**
```r
    bet = c(d/s^2, -1/(2 * s^2))
        ^
```
[R/lmm-locfdr.R:442:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L442) *style:* **Use <-, not =, for assignment.**
```r
    aa = (aorig - d)/s
       ^
```
[R/lmm-locfdr.R:443:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L443) *style:* **Use <-, not =, for assignment.**
```r
    bb = (borig - d)/s
       ^
```
[R/lmm-locfdr.R:444:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L444) *style:* **Use <-, not =, for assignment.**
```r
    H0 = pnorm(bb) - pnorm(aa)
       ^
```
[R/lmm-locfdr.R:445:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L445) *style:* **Use <-, not =, for assignment.**
```r
    fa = dnorm(aa)
       ^
```
[R/lmm-locfdr.R:446:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L446) *style:* **Use <-, not =, for assignment.**
```r
    fb = dnorm(bb)
       ^
```
[R/lmm-locfdr.R:447:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L447) *style:* **Use <-, not =, for assignment.**
```r
    H1 = fa - fb
       ^
```
[R/lmm-locfdr.R:448:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L448) *style:* **Use <-, not =, for assignment.**
```r
    H2 = H0 + aa * fa - bb * fb
       ^
```
[R/lmm-locfdr.R:449:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L449) *style:* **Use <-, not =, for assignment.**
```r
    H3 = (2 + aa^2) * fa - (2 + bb^2) * fb
       ^
```
[R/lmm-locfdr.R:450:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L450) *style:* **Use <-, not =, for assignment.**
```r
    H4 = 3 * H0 + (3 * aa + aa^3) * fa - (3 * bb + bb^3) *
       ^
```
[R/lmm-locfdr.R:452:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L452) *style:* **Use <-, not =, for assignment.**
```r
    H = c(H0, H1, H2, H3, H4)
      ^
```
[R/lmm-locfdr.R:453:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L453) *style:* **Use <-, not =, for assignment.**
```r
    r = d/s
      ^
```
[R/lmm-locfdr.R:454:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L454) *style:* **Use <-, not =, for assignment.**
```r
    I = matrix(rep(0, 25), 5)
      ^
```
[R/lmm-locfdr.R:455:40:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L455) *style:* **Use <-, not =, for assignment.**
```r
    for (i in 0:4) I[i + 1, 0:(i + 1)] = choose(i, 0:i)
                                       ^
```
[R/lmm-locfdr.R:456:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L456) *style:* **Use <-, not =, for assignment.**
```r
    u1 = s^(0:4)
       ^
```
[R/lmm-locfdr.R:457:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L457) *style:* **Use <-, not =, for assignment.**
```r
    II = pmax(row(I) - col(I), 0)
       ^
```
[R/lmm-locfdr.R:458:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L458) *style:* **Use <-, not =, for assignment.**
```r
    II = r^II
       ^
```
[R/lmm-locfdr.R:459:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L459) *style:* **Use <-, not =, for assignment.**
```r
    I = u1 * (I * II)
      ^
```
[R/lmm-locfdr.R:460:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L460) *style:* **Use <-, not =, for assignment.**
```r
    E = as.vector(I %*% H)/H0
      ^
```
[R/lmm-locfdr.R:461:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L461) *style:* **Use <-, not =, for assignment.**
```r
    E1 = E[2]
       ^
```
[R/lmm-locfdr.R:462:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L462) *style:* **Use <-, not =, for assignment.**
```r
    E2 = E[3]
       ^
```
[R/lmm-locfdr.R:463:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L463) *style:* **Use <-, not =, for assignment.**
```r
    E3 = E[4]
       ^
```
[R/lmm-locfdr.R:464:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L464) *style:* **Use <-, not =, for assignment.**
```r
    E4 = E[5]
       ^
```
[R/lmm-locfdr.R:465:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L465) *style:* **Use <-, not =, for assignment.**
```r
    mu = c(E1, E2)
       ^
```
[R/lmm-locfdr.R:466:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L466) *style:* **Use <-, not =, for assignment.**
```r
    V = matrix(c(E2 - E1^2, E3 - E1 * E2, E3 - E1 * E2, E4 -
      ^
```
[R/lmm-locfdr.R:468:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L468) *style:* **Use <-, not =, for assignment.**
```r
    bett = bet + solve(V, Y - mu)/(1 + 1/j^2)
         ^
```
[R/lmm-locfdr.R:470:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L470) *style:* **Use <-, not =, for assignment.**
```r
      bett = bet + 0.1 * solve(V, Y - mu)/(1 + 1/j^2)
           ^
```
[R/lmm-locfdr.R:475:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L475) *style:* **Use <-, not =, for assignment.**
```r
    d = -bett[1]/(2 * bett[2])
      ^
```
[R/lmm-locfdr.R:476:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L476) *style:* **Use <-, not =, for assignment.**
```r
    s = 1/sqrt(-2 * bett[2])
      ^
```
[R/lmm-locfdr.R:481:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L481) *style:* **Use <-, not =, for assignment.**
```r
    mle = rep(NA, 6)
        ^
```
[R/lmm-locfdr.R:482:14:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L482) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = NA
             ^
```
[R/lmm-locfdr.R:483:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L483) *style:* **Use <-, not =, for assignment.**
```r
    Cor = matrix(NA, 3, 3)
        ^
```
[R/lmm-locfdr.R:486:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L486) *style:* **Use <-, not =, for assignment.**
```r
    mle = rep(NA, 6)
        ^
```
[R/lmm-locfdr.R:487:14:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L487) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = Cov.out = NA
             ^
```
[R/lmm-locfdr.R:487:24:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L487) *style:* **Use <-, not =, for assignment.**
```r
    Cov.lfdr = Cov.out = NA
                       ^
```
[R/lmm-locfdr.R:488:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L488) *style:* **Use <-, not =, for assignment.**
```r
    Cor = matrix(NA, 3, 3)
        ^
```
[R/lmm-locfdr.R:491:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L491) *style:* **Use <-, not =, for assignment.**
```r
    aa = (aorig - d)/s
       ^
```
[R/lmm-locfdr.R:492:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L492) *style:* **Use <-, not =, for assignment.**
```r
    bb = (borig - d)/s
       ^
```
[R/lmm-locfdr.R:493:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L493) *style:* **Use <-, not =, for assignment.**
```r
    H0 = pnorm(bb) - pnorm(aa)
       ^
```
[R/lmm-locfdr.R:494:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L494) *style:* **Use <-, not =, for assignment.**
```r
    p0 = that/H0
       ^
```
[R/lmm-locfdr.R:495:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L495) *style:* **Use <-, not =, for assignment.**
```r
    J = s^2 * matrix(c(1, 0, 2 * d, s), 2)
      ^
```
[R/lmm-locfdr.R:496:8:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L496) *style:* **Use <-, not =, for assignment.**
```r
    JV = J %*% solve(V)
       ^
```
[R/lmm-locfdr.R:497:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L497) *style:* **Use <-, not =, for assignment.**
```r
    JVJ = JV %*% t(J)
        ^
```
[R/lmm-locfdr.R:498:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L498) *style:* **Use <-, not =, for assignment.**
```r
    mat2 = cbind(0, JVJ/N0)
         ^
```
[R/lmm-locfdr.R:499:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L499) *style:* **Use <-, not =, for assignment.**
```r
    mat1 = c((p0 * H0 * (1 - p0 * H0))/N, 0, 0)
         ^
```
[R/lmm-locfdr.R:500:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L500) *style:* **Use <-, not =, for assignment.**
```r
    mat = rbind(mat1, mat2)
        ^
```
[R/lmm-locfdr.R:501:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L501) *style:* **Use <-, not =, for assignment.**
```r
    h = c(H1/H0, (H2 - H0)/H0)
      ^
```
[R/lmm-locfdr.R:502:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L502) *style:* **Use <-, not =, for assignment.**
```r
    matt = c(1/H0, -(p0/s) * t(h))
         ^
```
[R/lmm-locfdr.R:503:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L503) *style:* **Use <-, not =, for assignment.**
```r
    matt = rbind(matt, cbind(0, diag(2)))
         ^
```
[R/lmm-locfdr.R:504:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L504) *style:* **Use <-, not =, for assignment.**
```r
    C = matt %*% (mat %*% t(matt))
      ^
```
[R/lmm-locfdr.R:505:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L505) *style:* **Use <-, not =, for assignment.**
```r
    mle = c(p0, d, s, diag(C)^0.5)
        ^
```
[R/lmm-locfdr.R:507:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L507) *style:* **Use <-, not =, for assignment.**
```r
      sd = mle[4:6]
         ^
```
[R/lmm-locfdr.R:508:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L508) *style:* **Use <-, not =, for assignment.**
```r
      Co = C/outer(sd, sd)
         ^
```
[R/lmm-locfdr.R:509:20:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L509) *style:* **Use <-, not =, for assignment.**
```r
      dimnames(Co) = list(c("p0", "d", "s"), c("p0", "d",
                   ^
```
[R/lmm-locfdr.R:511:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L511) *style:* **Use <-, not =, for assignment.**
```r
      Cor = Co[c(2, 3, 1), c(2, 3, 1)]
          ^
```
[R/lmm-locfdr.R:514:10:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L514) *style:* **Use <-, not =, for assignment.**
```r
      i0 = which(Cov.in$x > aa & Cov.in$x < bb)
         ^
```
[R/lmm-locfdr.R:515:15:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L515) *style:* **Use <-, not =, for assignment.**
```r
      Cov.out = loccov(N, N0, p0, d, s, Cov.in$x, Cov.in$X,
              ^
```
[R/lmm-locfdr.R:519:14:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L519) *style:* **Use <-, not =, for assignment.**
```r
  names(mle) = c("p0", "del0", "sig0", "sd.p0", "sd.del0",
             ^
```
[R/lmm-locfdr.R:521:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L521) *style:* **Use <-, not =, for assignment.**
```r
  mle = mle[c(2, 3, 1, 5, 6, 4)]
      ^
```
[R/lmm-locfdr.R:522:7:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L522) *style:* **Use <-, not =, for assignment.**
```r
  out = list(mle = mle)
      ^
```
[R/lmm-locfdr.R:524:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L524) *style:* **Use <-, not =, for assignment.**
```r
    Cor = list(Cor = Cor)
        ^
```
[R/lmm-locfdr.R:525:9:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L525) *style:* **Use <-, not =, for assignment.**
```r
    out = c(out, Cor)
        ^
```
[R/lmm-locfdr.R:529:12:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L529) *style:* **Use <-, not =, for assignment.**
```r
      pds. = list(pds. = Cov.out)
           ^
```
[R/lmm-locfdr.R:530:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L530) *style:* **Use <-, not =, for assignment.**
```r
      out = c(out, pds.)
          ^
```
[R/lmm-locfdr.R:533:13:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L533) *style:* **Use <-, not =, for assignment.**
```r
      Ilfdr = list(Ilfdr = Cov.out)
            ^
```
[R/lmm-locfdr.R:534:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L534) *style:* **Use <-, not =, for assignment.**
```r
      out = c(out, Ilfdr)
          ^
```
[R/lmm-locfdr.R:537:16:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L537) *style:* **Use <-, not =, for assignment.**
```r
      Cov.lfdr = list(Cov.lfdr = Cov.out)
               ^
```
[R/lmm-locfdr.R:538:11:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L538) *style:* **Use <-, not =, for assignment.**
```r
      out = c(out, Cov.lfdr)
          ^
```
[R/lmm-locfdr.R:549:5:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L549) *style:* **Use <-, not =, for assignment.**
```r
  d = ests[1]
    ^
```
[R/lmm-locfdr.R:550:5:](https://github.com/dirmeier/knockout/blob/e7ee6bb56b5035d41e7ec1e2f18c971e239f1a40/R/lmm-locfdr.R#L550) *style:* **Use <-, not =, for assignment.**
```r
  s = ests[2]
    ^
```


I normally mark variables as `transient` that we don't serialize, but it is up to you. Just helps document the code a bit more.


Correct, that was the thought behind it.


> string лучше всегда по ссылке передавать?

Да, если только строка не меняется в другом потоке.
При передаче по значению выделяется память и всё содержимое строки копируется.
Это медленнее, чем дополнительное разыменование или копирование указателя и длины, если передавать не строку, а [string_view](http://en.cppreference.com/w/cpp/string/basic_string_view).

> У меня была мысль, что т.к. один и тот же ключ может встречаться несколько раз, а он должен быть уникальным, то мне нужно будет реализовывать проверку есть такой ключ или нет.

В `unordered_map` ключи не повторяются, для повторяющихся ключей есть отдельный [unordered_multimap](http://www.cplusplus.com/reference/unordered_map/unordered_multimap/).


You forgot remove HardwareInfo import.


This line should be removed. It is already being added in the next commit (ed74674550f0e1d25d32b0e78b84d6dcac0e4bfd)


This question is being added again in the next commit (ed74674550f0e1d25d32b0e78b84d6dcac0e4bfd).


Positive, it might look even cleaner.


TeamCity Platform Services :: Environment Manager 2 :: Package [Build 3.37.2-pre-9-g6c412cc](http://infra.teamcity.ci.ttldev/viewLog.html?buildId=55081&buildTypeId=PlatformServices_EnvironmentManager2_Package) outcome was **SUCCESS**
Summary: Running Build time: 00:00:38


Hej guys
Jeg har lige været inde at ændre navnet på rummene således at de hedder det samme i udskrift som i navn. Bare for at se hvordan det virker-


I think your code will not work as intended. func and type are only send with learn telegrams, normal data telegrams do not provide this info.


Maybe we can consolidate this code using `WriteCommand` as the captured arg instead?


Creating a personified audience is a good idea. Your outline and project description reflect a very specific purpose, and I this your approach makes a lot of sense. FocusWriter does not have much documentation as it stands, so I think it's reasonable that you could contribute this documentation to the developers if you wanted to. Dividing the documentation up into shorter pages is a good idea (discoverability). Great work so far: this is coming together nicely.


Older nugget clients don't support it


Would you please tell me the result?
Does it work or not?


OK~I did it.


D was here


Yes it is.
Having a different solution takes times and we should need to do it and test more.
See: https://github.com/zeit/next.js/issues/1436#issuecomment-287615991

So, we took this for 2.0 release. It's a much better than the current case :)


We use node 4.x.


remove readme


Same thing about consolidating code


##sdfdfdfdf#


I'm trying to fix this problem. But now I don't have a result 😊 I need
more time.

Il lun 20 mar 2017, 15:35 Y.Kentaro <notifications@github.com> ha scritto:

> Would you please tell me the result?
> Does it work or not?
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/ottimo/fluent-plugin-twitter/commit/a2e7df6240722eeea83ff9bd81648e86e22c9bf9#commitcomment-21398793>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAMFT84DnCAkkg-kHWC1_u2p55-FBrU5ks5rno7GgaJpZM4Mig5W>
> .
>
--
Matteo
http://about.me/ottimorosi


accidentally capitalized the argument name


@jensens Jenkins CI reporting about code analysis
See the full report here: http://jenkins.plone.org/job/package-plone.app.z3cform/51/violations
```
plone/app/z3cform/inline_validation.py:15:1: C901 'InlineValidationView.__call__' is too complex (15)
```
Follow [these instructions](https://github.com/plone/jenkins.plone.org/blob/master/docs/source/run-qa-on-package.rst) to reproduce it locally.


fluidity test


adv-ss-nv-docs (jasondegraw) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-UnitTestsCoverage-Debug: OK (1286 of 1286 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-37.45%25-green.png)


@SyedAsherAhmed why you did this ?


🐄 It's worth linking to Jupyter Notebook, Plotly, and nbconvert below, so someone who finds this repo somehow knows what it's for.


Bluemix [toolchain](https://dev-console.stage1.ng.bluemix.net/devops/toolchains/702021e9-bdf7-422a-bd71-9a53bb1688bf "tc-pre-traceability"): [Delivery Pipeline](https://dev-console.stage1.ng.bluemix.net/devops/pipelines/141ea314-9649-4329-9a2a-7ab3cf4cf408 "deploy pipeline") deployed [pre-traceability](https://github.com/jauninb/pre-traceability/releases/tag/deploy-ibm-ys1-us-south-jaunin.b-fr.ibm.com_other-test-20170320-144155 "deploy-ibm-ys1-us-south-jaunin.b-fr.ibm.com_other-test-20170320-144155") to [test](https://dev-console.stage1.ng.bluemix.net/apps/c44d2e93-4a72-4835-9719-d1d45f0f058b "ibm:ys1:us-south:jaunin.b@fr.ibm.com_other:test"), including this commit


Hi there, why is there a commit hash ? thanks.


K.


adv-ss-nv-docs (jasondegraw) - x86_64-MacOS-10.9-clang: OK (2480 of 2480 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


here


here is not working now. so you can mail to me. admin@rtrobot.org.
Please tell me what prompted the driver's error. tell me the error code.
mail to me. thanks


Today all tests has been passed...


I also suggest explaining how this differs from the standard exporter, and why someone would use it.


What encoding is here?


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability-jerome-lanneluc](https://github.com/idsdev/testRepo-Traceability-jerome-lanneluc/releases/tag/deployed-2-env-w3ibm-prod-us-south-user-ibm.com-prod-20170320-144452 "deployed-2-env-w3ibm-prod-us-south-user-ibm.com-prod-20170320-144452") to [prod](https://dev-console.stage1.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "w3ibm:prod:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability-jerome-lanneluc](https://github.com/idsdev/testRepo-Traceability-jerome-lanneluc/releases/tag/deployed-2-env-w3ibm-prod-us-south-user-ibm.com-prod-20170320-144515 "deployed-2-env-w3ibm-prod-us-south-user-ibm.com-prod-20170320-144515") to [prod](https://dev-console.stage1.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "w3ibm:prod:us-south:user@ibm.com:prod"), including this commit


hey Clark, I hope this make things easier but all these parts will just be in the package edu.jalc.automobile.parts


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability-jerome-lanneluc](https://github.com/idsdev/testRepo-Traceability-jerome-lanneluc/releases/tag/deployed-2-env-Prod-20170320-144521 "deployed-2-env-Prod-20170320-144521") to [Prod](https://dev-console.stage1.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "There was a problem retrieving the space name"), including this commit


$oCompanies should be $oCompany


Idem.


TeamCity Platform Services :: Environment Manager 2 :: Package [Build 3.37.2-pre-32-g48dcf0d](http://infra.teamcity.ci.ttldev/viewLog.html?buildId=55088&buildTypeId=PlatformServices_EnvironmentManager2_Package) outcome was **SUCCESS**
Summary: Running Build time: 00:00:55


🐄 This comment doesn't explain much. A better comment would be "Make `text/vnd.plotly.v1+html` content (which is trusted) available as `text/html`.


If you are using prefixes, please provide consistent prefixes. So $gOrders -> oOrders; $aOrders -> $aOrder.


Das "CardNumber"  muss raus.


Dr Xuan thanks for update the repo.  It is faster to pull large files from git.