[R/assertions.R:210:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/assertions.R#L210) *style:* **Lines should not be more than 100 characters.**
```r
      stop("2 or more species share the same label under the 'EN_generic_short' or 'Leading' columns of sim$sppEquiv.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/assertions.R:214:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/assertions.R#L214) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/cohorts.R:47:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L47) *style:* **Lines should not be more than 100 characters.**
```r
#' @param treedFirePixelTableSinceLastDisp A data.table with at least 2 columns, \code{pixelIndex} and \code{pixelGroup}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:71:48:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L71) *style:* **Variable and function names should not be longer than 30 characters.**
```r
                             speciesEcoregion, treedFirePixelTableSinceLastDisp = NULL,
                                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:92:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L92) *style:* **Lines should not be more than 100 characters.**
```r
      message(crayon::green("  Regenerating only open pixels (e.g., likely resprouting & serotiny only)"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:93:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L93) *style:* **Lines should not be more than 100 characters.**
```r
    columnsForPG <- c("ecoregionGroup", "speciesCode", "age") # no Biomass because they all have zero
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:94:31:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L94) *style:* **Commas should always have a space after.**
```r
    cd <- newPixelCohortData[,c("pixelIndex", columnsForPG), with = FALSE]
                              ^
```
[R/cohorts.R:122:30:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    allCohortData <- cohorts[ , .(ecoregionGroup = ecoregionGroup[1],
                             ^
```
[R/cohorts.R:122:31:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L122) *style:* **Commas should never have a space before.**
```r
    allCohortData <- cohorts[ , .(ecoregionGroup = ecoregionGroup[1],
                             ~^
```
[R/cohorts.R:145:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L145) *style:* **Commented code should be removed.**
```r
  # newPixelCohortData[, sumB := sum(B, na.rm = TRUE), by = pixelGroup]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:221:3:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L221) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current <- speciesEcoregionLatestYear(speciesEcoregion, time)
  ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:222:3:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L222) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current <- setkey(specieseco_current[, .(speciesCode, maxANPP, maxB, ecoregionGroup)],
  ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:227:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L227) *style:* **Lines should not be more than 100 characters.**
```r
  #missingNewPixelCohortData <- newPixelCohortData[!specieseco_current, on = uniqueSpeciesEcoregionDefinition]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:227:4:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L227) *style:* **Commented code should be removed.**
```r
  #missingNewPixelCohortData <- newPixelCohortData[!specieseco_current, on = uniqueSpeciesEcoregionDefinition]
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:228:3:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L228) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current <- specieseco_current[!is.na(maxB)]
  ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:229:24:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L229) *style:* **Variable or function name should be lowerCamelCase.**
```r
  specieseco_current[, maxB_eco := max(maxB), by = ecoregionGroup]
                       ^~~~~~~~
```
[R/cohorts.R:230:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L230) *style:* **Lines should not be more than 100 characters.**
```r
  newPixelCohortData <- specieseco_current[newPixelCohortData, on = uniqueSpeciesEcoregionDefinition]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:236:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L236) *style:* **Commented code should be removed.**
```r
  # set(newPixelCohortData, NULL, "sumB", 0L)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:243:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L243) *style:* **Lines should not be more than 100 characters.**
```r
  set(newPixelCohortData, which(is.na(newPixelCohortData$oldSumB)), "oldSumB", 0)   ## faster than [:=]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:248:26:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L248) *style:* **Variable or function name should be lowerCamelCase.**
```r
    newPixelCohortData[, B := NULL]
                         ^
```
[R/cohorts.R:252:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L252) *style:* **Lines should not be more than 100 characters.**
```r
  set(newPixelCohortData, NULL, "B", asInteger(pmin(newPixelCohortData$maxANPP, newPixelCohortData$B)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:258:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L258) *style:* **Lines should not be more than 100 characters.**
```r
    if (isTRUE(NROW(unique(newPixelCohortData, by = uniqueCohortDefinition)) != NROW(newPixelCohortData)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:263:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L263) *style:* **Commented code should be removed.**
```r
  # cohortData[, sumB := sum(B, na.rm = TRUE), by = "pixelGroup"]  ## recalculate sumB
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:265:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L265) *style:* **Commented code should be removed.**
```r
  #   set(cohortData, NULL, "sumB", asInteger(cohortData[["sumB"]]))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:295:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L295) *style:* **Lines should not be more than 100 characters.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:295:67:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L295) *style:* **Commas should always have a space after.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
                                                                  ^
```
[R/cohorts.R:295:70:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L295) *style:* **Commented code should be removed.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
                                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:296:4:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L296) *style:* **Commented code should be removed.**
```r
  #pgsStillInPGMGoneFromCD <- setdiff(unique(pgmVals$pixelGroup), unique(cohortData$pixelGroup))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:298:64:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L298) *style:* **Commas should always have a space after.**
```r
  pgsStillInPGMGoneFromCD <- pgmVals[whPgsStillInPGMGoneFromCD,]
                                                               ^
```
[R/cohorts.R:349:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L349) *style:* **Lines should not be more than 100 characters.**
```r
  # concatenate within rows -- e.g., ecoregionCode_speciesCode_age_biomass or 647_11_Abie_sp_100_2000
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:353:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L353) *style:* **Lines should not be more than 100 characters.**
```r
  pcd[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"), by = "pixelIndex"]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:353:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L353) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  pcd[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"), by = "pixelIndex"]
      ^
```
[R/cohorts.R:353:8:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L353) *style:* **Commas should never have a space before.**
```r
  pcd[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"), by = "pixelIndex"]
      ~^
```
[R/cohorts.R:354:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L354) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  pcd[ , c("pixelGroup") := as.integer(maxPixelGroup) + as.integer(factor(uniqueComboByPixelIndex))]
      ^
```
[R/cohorts.R:354:8:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L354) *style:* **Commas should never have a space before.**
```r
  pcd[ , c("pixelGroup") := as.integer(maxPixelGroup) + as.integer(factor(uniqueComboByPixelIndex))]
      ~^
```
[R/cohorts.R:356:38:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L356) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (getOption("LandR.assertions")) { # old algorithm
                                     ^
```
[R/cohorts.R:360:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L360) *style:* **Lines should not be more than 100 characters.**
```r
    pcd[, pixelGroup2 := mapvalues(pixelGroup, from = unique(pixelGroup), to = as.character(seq_along(unique(pixelGroup))))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:366:12:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L366) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[ , c(columns2) := lapply(.SD, function(x) {
           ^
```
[R/cohorts.R:366:13:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L366) *style:* **Commas should never have a space before.**
```r
    pcdOld[ , c(columns2) := lapply(.SD, function(x) {
           ~^
```
[R/cohorts.R:370:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L370) *style:* **Lines should not be more than 100 characters.**
```r
    # concatenate within rows -- e.g., ecoregionCode_speciesCode_age_biomass or 647_11_Abie_sp_100_2000
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:371:52:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L371) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[, uniqueComboByRow := as.integer(factor( do.call(paste, as.list(.SD)))),
                                                   ^
```
[R/cohorts.R:375:12:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L375) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"),
           ^
```
[R/cohorts.R:375:13:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L375) *style:* **Commas should never have a space before.**
```r
    pcdOld[ , c("uniqueComboByPixelIndex") := paste(uniqueComboByRow, collapse = "__"),
           ~^
```
[R/cohorts.R:377:12:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L377) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pcdOld[ , c("pixelGroup") := as.integer(maxPixelGroup) +
           ^
```
[R/cohorts.R:377:13:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L377) *style:* **Commas should never have a space before.**
```r
    pcdOld[ , c("pixelGroup") := as.integer(maxPixelGroup) +
           ~^
```
[R/cohorts.R:382:25:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L382) *style:* **Put spaces around all infix operators.**
```r
    pcdOld[, pixelGroup2:=mapvalues(pixelGroup, from = unique(pixelGroup),
                       ~^~~
```
[R/cohorts.R:427:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L427) *style:* **Variable and function names should not be longer than 30 characters.**
```r
uniqueSpeciesEcoregionDefinition <- c("speciesCode", "ecoregionGroup")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:440:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L440) *style:* **Lines should not be more than 100 characters.**
```r
  message(magenta("Pixels with non-NA cover:, ", cohortData[!is.na(cover), length(unique(pixelIndex))]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:448:86:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L448) *style:* **Put spaces around all infix operators.**
```r
    pixelsZero <- NROW(cohortData[, all(get(val) == 0), by = "pixelIndex"][get("V1") ==TRUE])
                                                                                ^~~
```
[R/cohorts.R:449:40:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L449) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," == 0): ", format(pixelsZero, big.mark = ",")))
                                       ^
```
[R/cohorts.R:449:44:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L449) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," == 0): ", format(pixelsZero, big.mark = ",")))
                                           ^
```
[R/cohorts.R:450:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L450) *style:* **Lines should not be more than 100 characters.**
```r
    pixelsBiomassNonZero <- NROW(cohortData[, any(get(val) > 0), by = "pixelIndex"][get("V1") ==TRUE])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:450:95:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L450) *style:* **Put spaces around all infix operators.**
```r
    pixelsBiomassNonZero <- NROW(cohortData[, any(get(val) > 0), by = "pixelIndex"][get("V1") ==TRUE])
                                                                                ^~~
```
[R/cohorts.R:451:40:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L451) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," > 0): ", format(pixelsBiomassNonZero, big.mark = ",")))
                                       ^
```
[R/cohorts.R:451:44:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L451) *style:* **Commas should always have a space after.**
```r
    message(magenta("Pixels with all(",val," > 0): ", format(pixelsBiomassNonZero, big.mark = ",")))
                                           ^
```
[R/cohorts.R:452:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L452) *style:* **Lines should not be more than 100 characters.**
```r
    out <- list(pixelsNA = pixelsNA, pixelsZero = pixelsZero, pixelsBiomassNonZero = pixelsBiomassNonZero)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:518:32:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L518) *style:* **Variable or function name should be lowerCamelCase.**
```r
                               availableERC_by_Sp, theUnwantedPixels,
                               ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:530:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L530) *style:* **Variable or function name should be lowerCamelCase.**
```r
      availableERC_by_Sp <- as.data.table(availableERC_by_Sp)
      ^~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:554:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L554) *style:* **Commented code should be removed.**
```r
  #   numChar <- max(nchar(availableERC_by_Sp$initialEcoregionCode), na.rm = TRUE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:556:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L556) *style:* **Lines should not be more than 100 characters.**
```r
  #                      initialEcoregionCode := paste0("1_", paddedFloatToChar(as.integer(initialEcoregionCode), numChar))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:560:16:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L560) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (FALSE) { # This is old section... can be deleted soon (April 10, 2019, Eliot)
               ^
```
[R/cohorts.R:575:8:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L575) *style:* **Commented code should be removed.**
```r
    #  stop("values of 34 and 35 on pixelCohortData and sim$LCC2005 don't match")
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:604:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L604) *style:* **Lines should not be more than 100 characters.**
```r
    out <- out[initialPixels != pixels] # rm pixels which are same as initialPixels --> these are known wrong
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:607:42:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L607) *style:* **Put spaces around all infix operators.**
```r
    out[lcc %in% c(classesToReplace), lcc:=NA]
                                        ~^~~
```
[R/cohorts.R:610:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L610) *style:* **Lines should not be more than 100 characters.**
```r
                               on = c("pixelIndex" = "initialPixels"), nomatch = NA] # join the availableERC_by_Sp which has initialEcoregionCode
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:614:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L614) *style:* **Lines should not be more than 100 characters.**
```r
                               paddedFloatToChar(as.integer(lcc), padL = numCharLCCCodes, padR = 0))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:618:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L618) *style:* **Lines should not be more than 100 characters.**
```r
    out7 <- out5[availableERG2, on = c("speciesCode", "possERC" = "initialEcoregionCode"), nomatch = NA]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:668:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L668) *style:* **Commented code should be removed.**
```r
    # setnames(out3, c("initialPixels", "initialEcoregionCode"), c("pixelIndex", "ecoregionGroup"))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:670:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L670) *style:* **Commented code should be removed.**
```r
    # out3 <- unique(out3, by = c("pixelIndex", "ecoregionGroup"))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:693:6:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L693) *style:* **Commented code should be removed.**
```r
    #describeCohortData(cohortData)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:709:18:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L709) *style:* **Variable or function name should be lowerCamelCase.**
```r
    cohortData[, V1 := NULL]
                 ^~
```
[R/cohorts.R:711:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L711) *style:* **Commented code should be removed.**
```r
  # cohortData[cover == 0, `:=`(age = 0L, logAge = -Inf, B = 0)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:717:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L717) *style:* **Commented code should be removed.**
```r
  # cohortData[speciesCode == "Popu_sp", cover := asInteger(cover / 2)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:719:14:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L719) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  cohortData[ , cover := {
             ^
```
[R/cohorts.R:719:15:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L719) *style:* **Commas should never have a space before.**
```r
  cohortData[ , cover := {
             ~^
```
[R/cohorts.R:732:16:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L732) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
               ^
```
[R/cohorts.R:732:17:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L732) *style:* **Commas should never have a space before.**
```r
    cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
               ~^
```
[R/cohorts.R:732:19:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L732) *style:* **Variable or function name should be lowerCamelCase.**
```r
    cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
                  ^
```
[R/cohorts.R:734:16:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L734) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
               ^
```
[R/cohorts.R:734:17:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L734) *style:* **Commas should never have a space before.**
```r
    cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
               ~^
```
[R/cohorts.R:734:19:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L734) *style:* **Variable or function name should be lowerCamelCase.**
```r
    cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
                  ^
```
[R/cohorts.R:736:16:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L736) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    cohortData[ , totalBiomass := asInteger(totalBiomass)]
               ^
```
[R/cohorts.R:736:17:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L736) *style:* **Commas should never have a space before.**
```r
    cohortData[ , totalBiomass := asInteger(totalBiomass)]
               ~^
```
[R/cohorts.R:843:36:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L843) *style:* **Variable or function name should be lowerCamelCase.**
```r
  cohortData[cover > 0 & age == 0, B := 0L]
                                   ^
```
[R/cohorts.R:849:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L849) *style:* **Commented code should be removed.**
```r
  # cohortData[ , coverProp := (cover/100 * (NROW(cohortData) - 1) + 0.5) / NROW(cohortData)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:861:22:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L861) *style:* **Variable or function name should be lowerCamelCase.**
```r
subsetDT <- function(DT, by, doSubset = TRUE) {
                     ^~
```
[R/cohorts.R:866:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L866) *style:* **Lines should not be more than 100 characters.**
```r
              "using maximum of ", sam, " samples per combination of ecoregionGroup and speciesCode. ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:871:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/cohorts.R#L871) *style:* **Variable or function name should be lowerCamelCase.**
```r
      DT <- DT[a$lineNum]
      ^~
```
[R/ecoregionProducer.R:37:4:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/ecoregionProducer.R#L37) *style:* **Commented code should be removed.**
```r
  #ecoregionMapInStudy <- raster::intersect(ecoregionMapFull, fixErrors(aggregate(studyArea)))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:54:3:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/ecoregionProducer.R#L54) *style:* **Variable or function name should be lowerCamelCase.**
```r
  NAs <- rtmNAs | rstEcoregionNAs
  ^~~
```
[R/ecoregionProducer.R:71:4:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/ecoregionProducer.R#L71) *style:* **Commented code should be removed.**
```r
  #ecoregionFactorValues <- na.omit(unique(rstEcoregion[]))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:73:4:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/ecoregionProducer.R#L73) *style:* **Commented code should be removed.**
```r
  #ecoregionTable <- raster::levels(rstEcoregion)[[1]]
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:81:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/ecoregionProducer.R#L81) *style:* **Lines should not be more than 100 characters.**
```r
    # rstEcoregion[] <- plyr::mapvalues(rstEcoregion[], from = ecoregionTable$ecoregion, to = ecoregionTable$mapcode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:81:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/ecoregionProducer.R#L81) *style:* **Commented code should be removed.**
```r
    # rstEcoregion[] <- plyr::mapvalues(rstEcoregion[], from = ecoregionTable$ecoregion, to = ecoregionTable$mapcode)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ecoregionProducer.R:96:37:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/ecoregionProducer.R#L96) *style:* **Commas should always have a space after.**
```r
  ecoregionTable <- ecoregionTable[,.(active = "yes", mapcode, ecoregion)]
                                    ^
```
[R/LANDIS-II-tables.R:76:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L76) *style:* **Lines should not be more than 100 characters.**
```r
    sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:84:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L84) *style:* **Lines should not be more than 100 characters.**
```r
  speciesTable <- speciesTable[species %in% equivalentName(sppNameVector, sppEquiv, "LANDIS_traits", multi = TRUE) &
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:101:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L101) *style:* **Lines should not be more than 100 characters.**
```r
#' (\url{https://raw.githubusercontent.com/dcyr/LANDIS-II_IA_generalUseFiles/master/speciesTraits.csv}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:105:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L105) *style:* **Lines should not be more than 100 characters.**
```r
#' @param species a \code{data.table} that has species traits such as longevity, shade tolerance, etc.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:122:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L122) *style:* **Lines should not be more than 100 characters.**
```r
    sppEquiv <- data.table(utils::data("sppEquivalencies_CA", package = "LandR", envir = environment()))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:144:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L144) *style:* **Lines should not be more than 100 characters.**
```r
  speciesTableShort[species == "PSEU.MEN", longevity := 525] ## only in MC area, corresponding to var. glauca
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:153:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L153) *style:* **Lines should not be more than 100 characters.**
```r
  speciesTableShort <- speciesTableShort[species %in% equivalentName(sppNameVector, sppEquiv, "LANDIS_traits", multi = TRUE)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:170:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L170) *style:* **Lines should not be more than 100 characters.**
```r
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession_test.txt"}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:190:17:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L190) *style:* **Commented code should be removed.**
```r
  maxcol <- 13 #max(count.fields(file.path(dPath, "species.txt"), sep = ""))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:211:13:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L211) *style:* **Only use double-quotes.**
```r
  species[, ':='(seeddistance_eff = gsub(",", "", seeddistance_eff),
            ^~~~
```
[R/LANDIS-II-tables.R:211:17:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  species[, ':='(seeddistance_eff = gsub(",", "", seeddistance_eff),
                ^
```
[R/LANDIS-II-tables.R:224:18:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L224) *style:* **Only use double-quotes.**
```r
  speciesAddon[, ':='(leaflongevity = as.numeric(leaflongevity),
                 ^~~~
```
[R/LANDIS-II-tables.R:224:22:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L224) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesAddon[, ':='(leaflongevity = as.numeric(leaflongevity),
                     ^
```
[R/LANDIS-II-tables.R:236:13:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L236) *style:* **Only use double-quotes.**
```r
  species[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
            ^~~~
```
[R/LANDIS-II-tables.R:236:17:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L236) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  species[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
                ^
```
[R/LANDIS-II-tables.R:240:13:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L240) *style:* **Only use double-quotes.**
```r
  species[, ':='(species1 = NULL, species2 = NULL)]
            ^~~~
```
[R/LANDIS-II-tables.R:240:17:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L240) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  species[, ':='(species1 = NULL, species2 = NULL)]
                ^
```
[R/LANDIS-II-tables.R:268:39:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L268) *style:* **Commas should always have a space after.**
```r
  mainInput <- mainInput[col1 != ">>",]
                                      ^
```
[R/LANDIS-II-tables.R:278:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L278) *style:* **Lines should not be more than 100 characters.**
```r
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/ecoregion.txt"}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:295:16:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L295) *style:* **Commented code should be removed.**
```r
  maxcol <- 5 #max(count.fields(file.path(dPath, "ecoregions.txt"), sep = ""))
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:311:47:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L311) *style:* **Commas should always have a space after.**
```r
  ecoregion <- ecoregion[col1 != "LandisData",]
                                              ^
```
[R/LANDIS-II-tables.R:312:39:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L312) *style:* **Commas should always have a space after.**
```r
  ecoregion <- ecoregion[col1 != ">>",]
                                      ^
```
[R/LANDIS-II-tables.R:324:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L324) *style:* **Lines should not be more than 100 characters.**
```r
#' \url{https://github.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession-dynamic-inputs_test.txt"}).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/LANDIS-II-tables.R:356:61:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L356) *style:* **Commas should always have a space after.**
```r
  speciesEcoregion <- speciesEcoregion[col1 != "LandisData",]
                                                            ^
```
[R/LANDIS-II-tables.R:357:53:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L357) *style:* **Commas should always have a space after.**
```r
  speciesEcoregion <- speciesEcoregion[col1 != ">>",]
                                                    ^
```
[R/LANDIS-II-tables.R:368:22:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L368) *style:* **Only use double-quotes.**
```r
  speciesEcoregion[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
                     ^~~~
```
[R/LANDIS-II-tables.R:368:26:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L368) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesEcoregion[, ':='(species = paste0(toupper(substring(species1, 1, 1)),
                         ^
```
[R/LANDIS-II-tables.R:371:22:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L371) *style:* **Only use double-quotes.**
```r
  speciesEcoregion[, ':='(species1 = NULL, species2 = NULL)]
                     ^~~~
```
[R/LANDIS-II-tables.R:371:26:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/LANDIS-II-tables.R#L371) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesEcoregion[, ':='(species1 = NULL, species2 = NULL)]
                         ^
```
[R/maps.R:22:29:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L22) *style:* **Variable or function name should be lowerCamelCase.**
```r
defineFlammable <- function(LandCoverClassifiedMap = NULL,
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:177:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L177) *style:* **Variable and function names should not be longer than 30 characters.**
```r
vegTypeMapGenerator.RasterStack <- function(x, ...) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:177:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L177) *style:* **Variable or function name should be lowerCamelCase.**
```r
vegTypeMapGenerator.RasterStack <- function(x, ...) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:188:14:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L188) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (FALSE) { # This is the old version -- Eliot & Alex July 11, 2019
             ^
```
[R/maps.R:198:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L198) *style:* **Lines should not be more than 100 characters.**
```r
      whMixed <- which(sum(speciesStack < (100 * vegLeadingProportion))[] == numLayers(speciesStack))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:199:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L199) *style:* **Variable or function name should be lowerCamelCase.**
```r
      MixedRas <- speciesStack[[1]]
      ^~~~~~~~
```
[R/maps.R:203:20:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L203) *style:* **Variable or function name should be lowerCamelCase.**
```r
      speciesStack$Mixed <- MixedRas
                   ^~~~~
```
[R/maps.R:232:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L232) *style:* **Variable or function name should be lowerCamelCase.**
```r
vegTypeMapGenerator.data.table <- function(x, pixelGroupMap, vegLeadingProportion = 0.8,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:279:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L279) *style:* **Lines should not be more than 100 characters.**
```r
    # 1. Find length of each pixelGroup -- don't include pixelGroups in "by" that have only 1 cohort: N = 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:289:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L289) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData1[N != 1, (totalOfLeadingBasedOn) := sum(cover, na.rm = TRUE), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:290:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L290) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData1 <- pixelGroupData1[, list(sum(cover, na.rm = TRUE), totalcover[1]), by = pgdAndSc]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:292:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L292) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData1[N != 1, (totalOfLeadingBasedOn) := sum(B, na.rm = TRUE), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:295:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L295) *style:* **Lines should not be more than 100 characters.**
```r
    setnames(pixelGroupData1, old = c("V1", "V2"), new = c(speciesOfLeadingBasedOn, totalOfLeadingBasedOn))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:314:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L314) *style:* **Commented code should be removed.**
```r
    # setorderv(x, pixelGroupColName)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:317:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L317) *style:* **Variable or function name should be lowerCamelCase.**
```r
    N <- rep.int(pixelGroupData2$N, pixelGroupData2$N)
    ^
```
[R/maps.R:321:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L321) *style:* **Lines should not be more than 100 characters.**
```r
        totalBNot1 <- cohortData2[!wh1, list(N = .N, totalcover = sum(cover, na.rm = TRUE)), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:323:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L323) *style:* **Lines should not be more than 100 characters.**
```r
        totalBNot1 <- cohortData2[!wh1, list(N = .N, totalB = sum(B, na.rm = TRUE)), by = pixelGroupColName]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:330:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L330) *style:* **Variable or function name should be lowerCamelCase.**
```r
      GT1 <- (b > 1)
      ^~~
```
[R/maps.R:335:10:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L335) *style:* **Commented code should be removed.**
```r
        #pixelGroupData2List[[2]] <- cohortData2[!GT1]
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:336:10:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L336) *style:* **Commented code should be removed.**
```r
        #pixelGroupData2 <- rbindlist(pixelGroupData2List)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:338:11:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L338) *style:* **Commented code should be removed.**
```r
        # cols <- c(pixelGroupColName, "speciesCode", "speciesProportion")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:339:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L339) *style:* **Lines should not be more than 100 characters.**
```r
        set(cohortData2, NULL, "speciesProportion", cohortData2[[leadingBasedOn]] / cohortData2[[totalOfLeadingBasedOn]])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:340:11:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L340) *style:* **Commented code should be removed.**
```r
        # pixelGroupData2[[NROW(pixelGroupData2) + 1]] <- cohortData2[!GT1, ..cols]
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:398:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L398) *style:* **Lines should not be more than 100 characters.**
```r
    ## 2. sort on pixelGroup and speciesProportion, reverse so that 1st row of each pixelGroup is the largest
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:412:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L412) *style:* **Commented code should be removed.**
```r
    # a2 <- Sys.time()
      ^~~~~~~~~~~~~~~~
```
[R/maps.R:413:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L413) *style:* **Lines should not be more than 100 characters.**
```r
    # pixelGroupData2 <- pixelGroupData[, list(mixed = all(speciesProportion < vegLeadingProportion),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:416:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L416) *style:* **Commented code should be removed.**
```r
    # pixelGroupData2[mixed == TRUE, leading := "Mixed"]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:417:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L417) *style:* **Commented code should be removed.**
```r
    # b2 <- Sys.time()
      ^~~~~~~~~~~~~~~~
```
[R/maps.R:439:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L439) *style:* **Lines should not be more than 100 characters.**
```r
    pixelGroupData3 <- pixelGroupData3[, .SD[1], by = pixelGroupColName] ## sp. w/ highest prop. per pixelGroup
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:447:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L447) *style:* **Lines should not be more than 100 characters.**
```r
  if ("pixelIndex" %in% colnames(pixelGroupData3)) { #(!any(duplicated(pixelGroupData3[[pixelGroupColName]]))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:447:52:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L447) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if ("pixelIndex" %in% colnames(pixelGroupData3)) { #(!any(duplicated(pixelGroupData3[[pixelGroupColName]]))) {
                                                   ^
```
[R/maps.R:492:14:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L492) *style:* **Variable or function name should be lowerCamelCase.**
```r
    pgTest[, Type := equivalentName(speciesCode, sppEquiv, "Type")]
             ^~~~
```
[R/maps.R:630:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L630) *style:* **Lines should not be more than 100 characters.**
```r
  ## select which archives/targetFiles to extract -- because there was "multi" above, need unique here
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:637:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L637) *style:* **Lines should not be more than 100 characters.**
```r
                    archive2 = file.path(dPath, paste0("NFI_MODIS250m_kNN_Species_", kNNnames, "_v0.zip")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:640:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L640) *style:* **Lines should not be more than 100 characters.**
```r
  if (!all(reproducible::basename2(file_path_sans_ext(names(archives))) == file_path_sans_ext(targetFiles)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:647:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L647) *style:* **Lines should not be more than 100 characters.**
```r
    message("This looks like a lot of species; did you mean to pass only a subset of this to sppEquiv?",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:665:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L665) *style:* **Lines should not be more than 100 characters.**
```r
                         prepInputs, quick = TRUE) # don't need to digest all the "targetFile" and "archives"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:667:79:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L667) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  noDataLayers <- sapply(speciesLayers, function(xx) if (maxValue(xx) < thresh ) FALSE else TRUE)
                                                                              ^
```
[R/maps.R:670:76:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L670) *style:* **Commas should always have a space after.**
```r
    message("removing ", sum(!noDataLayers), " species because they had <",thresh,
                                                                           ^
```
[R/maps.R:672:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L672) *style:* **Lines should not be more than 100 characters.**
```r
            "\n  These species are retained (and could be further culled manually, if desired):\n  ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:694:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L694) *style:* **Commented code should be removed.**
```r
  # layerData <- Cache(sapply, X = speciesLayers, function(xx) sum(xx[] > 0, na.rm = TRUE))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:696:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L696) *style:* **Commented code should be removed.**
```r
  # ## remove layers that had < thresh pixels with biomass
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:697:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L697) *style:* **Commented code should be removed.**
```r
  # belowThresh <- layerData < thresh
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:699:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L699) *style:* **Commented code should be removed.**
```r
  #   message(names(belowThresh)[belowThresh], " was removed because it had no data")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:700:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L700) *style:* **Commented code should be removed.**
```r
  #   speciesLayers[belowThresh] <- NULL
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:799:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L799) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRastName <- basename(tempfile(fileext = ".tif"))
      ^~~~~~~~~~
```
[R/maps.R:801:9:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L801) *style:* **Variable or function name should be lowerCamelCase.**
```r
        LQCurName <- basename(tempfile(fileext = ".tif"))
        ^~~~~~~~~
```
[R/maps.R:808:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L808) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRastInHQcrs <- projectExtent(lowQualityStack, crs = crs(highQualityStack))
      ^~~~~~~~~~~~~
```
[R/maps.R:821:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L821) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- raster(LQRastName)
      ^~~~~~
```
[R/maps.R:839:9:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L839) *style:* **Variable or function name should be lowerCamelCase.**
```r
        HQRast <- raster(tmpHQName)
        ^~~~~~
```
[R/maps.R:844:9:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L844) *style:* **Variable or function name should be lowerCamelCase.**
```r
        HQRast <- highQualityStack[[SPP]]
        ^~~~~~
```
[R/maps.R:847:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L847) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- lowQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:848:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L848) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:855:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L855) *style:* **Variable or function name should be lowerCamelCase.**
```r
    NAs <- is.na(HQRast[])
    ^~~
```
[R/maps.R:859:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L859) *style:* **Variable or function name should be lowerCamelCase.**
```r
    HQRast <- writeRaster(HQRast, datatype = "INT1U",
    ^~~~~~
```
[R/maps.R:869:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L869) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:873:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L873) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- lowQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:877:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L877) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:909:4:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/maps.R#L909) *style:* **Commented code should be removed.**
```r
  #names(sppMerges) <- equivalentName(names(sppMerges), sppEquiv,  column = sppEquivCol)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/misc.R:23:1:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/misc.R#L23) *style:* **Lines should not be more than 100 characters.**
```r
#' Essentially a wrapper around \code{round}, rather than \code{truncate}, which is what \code{as.integer}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:47:25:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L47) *style:* **Variable or function name should be lowerCamelCase.**
```r
overlayLCCs <- function(LCCs, forestedList, outputLayer,
                        ^~~~
```
[R/overlayLCCs.R:48:25:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L48) *style:* **Variable or function name should be lowerCamelCase.**
```r
                        NAcondition, NNcondition, remapTable = NULL,
                        ^~~~~~~~~~~
```
[R/overlayLCCs.R:48:38:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L48) *style:* **Variable or function name should be lowerCamelCase.**
```r
                        NAcondition, NNcondition, remapTable = NULL,
                                     ^~~~~~~~~~~
```
[R/overlayLCCs.R:49:43:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L49) *style:* **Variable or function name should be lowerCamelCase.**
```r
                        classesToReplace, availableERC_by_Sp,
                                          ^~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:65:5:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L65) *style:* **Variable or function name should be lowerCamelCase.**
```r
    LCCs <- stack(LCCs)
    ^~~~
```
[R/overlayLCCs.R:81:7:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L81) *style:* **Variable or function name should be lowerCamelCase.**
```r
      availableERC_by_Sp <- data.table(initialEcoregionCode = LCCs[[outputLayer]][])
      ^~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:90:14:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L90) *style:* **Variable or function name should be lowerCamelCase.**
```r
        dt[, NAs := eval(parse(text = NAcondition)), with = TRUE]
             ^~~
```
[R/overlayLCCs.R:92:14:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L92) *style:* **Variable or function name should be lowerCamelCase.**
```r
        dt[, NAs := NULL]
             ^~~
```
[R/overlayLCCs.R:96:14:](https://github.com/PredictiveEcology/LandR/blob/284799636e1088f54b118805bb6017da79a89421/R/overlayLCCs.R#L96) *style:* **Variable or function name should be lowerCamelCase.**
```r
        dt[, NNcondition := eval(parse(text = NNcondition))]
             ^~~~~~~~~~~
```


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ReadMe


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re-added Deliver stage.


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missing comma


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Just need to correct the missing comma and it's good.


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之前會發生的原因是因為 :
框線太粗，畫下去之後，某些地方就那麼剛好，超過canvas的畫布大小，
就顯示不出來，看起來就像線凹進去了

![螢幕快照 2019-07-12 下午12 09 36](https://user-images.githubusercontent.com/12346882/61101911-50450780-a49e-11e9-9839-e32ff02b80d8.png)

現在加一個offset 讓圓相對應畫布大小  畫小一點點，就能簡單地修正這個問題


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Due to that, we cannot deploy the commit 551ee7dc5b2540a6af46ded1d7001d5357af74e8.

You can try again later or [upgrade](https://zeit.co/account/plan) your plan.


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167109939_Issue7365 (Nigusse) - Win64-Windows-10-VisualStudio-16: OK (2441 of 2441 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)


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remove excess spaces


Model-DOAS-to-Multiple-Air-Handling-Units (lgu1234) - x86_64-MacOS-10.13-clang: OK (2444 of 2444 tests passed, 0 test warnings)

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


if we are passing in dir_entry, shouldn't we be doing dir_entry.changePermission() instead of getDirectoryEntry(addr).changePermission?


dwad


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Model-DOAS-to-Multiple-Air-Handling-Units (lgu1234) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (666 of 668 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 666
 * Timeout: 2

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.7%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.37%25-yellow.png)


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You are pushing commits at a very fast pace (accross the whole organization).
Due to that, we cannot deploy the commit 042a50c1ea8a021c1d4b95397091ba0b908b683d.

You can try again later or [upgrade](https://zeit.co/account/plan) your plan.


same with lines 148-149 here, I think we can use dir_entry directly?


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same with line 133 here -- can use dir_entry directly?


Hey @jpalardy! Great library! I just installed on my vimrc and was blown away with the magic and wanted to say thanks for the work, it made me smile in front of my computer :smile:


Step 2 completed... (Cloned Armadillo Library)
Step3: Generate C++ extension module (clipDCD optimizer)
Warning: Extension name 'clipdcd' does not match fully qualified name 'ltsvm.optimizer.clipdcd' of 'clipdcd.pyx'
running build_ext
building 'clipdcd' extension
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -IC:\Users\cumt\Anaconda3\lib\site-packages\numpy\core\include -I./armadillo-code/include -IC:\Users\cumt\Anaconda3\include -IC:\Users\cumt\Anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\8.1\include\shared" "-IC:\Program Files (x86)\Windows Kits\8.1\include\um" "-IC:\Program Files (x86)\Windows Kits\8.1\include\winrt" /EHsc /Tpclipdcd.cpp /Fobuild\temp.win-amd64-3.6\Release\clipdcd.obj
clipdcd.cpp
c1xx: fatal error C1083: Cannot open source file: 'clipdcd.cpp': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\x86_amd64\\cl.exe' failed with exit status 2


GSHP_desuperheater (yzhou601) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1114 of 1114 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-42.37%25-green.png)


why


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BinaryTree Implementation


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TeamCity Architecture Team / Java Platform / otj-kafka / BuildTest [Build 449](https://teamcity.otenv.com/viewLog.html?buildId=10890918&buildTypeId=ArchitectureTeam_JavaPlatform_OtjKafka_BuildTest) is now running


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`-Winline` can also be removed - it just produces a lot of informal warnings which cannot (and should not) be fixed


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nit: describe a little bit about what the pipeline does