[R/assertions.R:210:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/assertions.R#L214) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/cohorts.R:47:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L243) *style:* **Lines should not be more than 100 characters.**
```r
  set(newPixelCohortData, which(is.na(newPixelCohortData$oldSumB)), "oldSumB", 0)   ## faster than [:=]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:248:26:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L248) *style:* **Variable or function name should be lowerCamelCase.**
```r
    newPixelCohortData[, B := NULL]
                         ^
```
[R/cohorts.R:252:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L252) *style:* **Lines should not be more than 100 characters.**
```r
  set(newPixelCohortData, NULL, "B", asInteger(pmin(newPixelCohortData$maxANPP, newPixelCohortData$B)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:258:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L258) *style:* **Lines should not be more than 100 characters.**
```r
    if (isTRUE(NROW(unique(newPixelCohortData, by = uniqueCohortDefinition)) != NROW(newPixelCohortData)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:263:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L263) *style:* **Commented code should be removed.**
```r
  # cohortData[, sumB := sum(B, na.rm = TRUE), by = "pixelGroup"]  ## recalculate sumB
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:265:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L265) *style:* **Commented code should be removed.**
```r
  #   set(cohortData, NULL, "sumB", asInteger(cohortData[["sumB"]]))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:295:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L295) *style:* **Lines should not be more than 100 characters.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:295:67:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L295) *style:* **Commas should always have a space after.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
                                                                  ^
```
[R/cohorts.R:295:70:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L295) *style:* **Commented code should be removed.**
```r
  pgsStillInCDGoneFromPGM <- cohortData[whPgsStillInCDGoneFromPGM,] #setdiff(unique(cohortData$pixelGroup), unique(pgmVals$pixelGroup))
                                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:296:4:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L296) *style:* **Commented code should be removed.**
```r
  #pgsStillInPGMGoneFromCD <- setdiff(unique(pgmVals$pixelGroup), unique(cohortData$pixelGroup))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:298:64:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L693) *style:* **Commented code should be removed.**
```r
    #describeCohortData(cohortData)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:702:16:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L702) *style:* **Variable or function name should be lowerCamelCase.**
```r
  cohortData[, V1 := NULL]
               ^~
```
[R/cohorts.R:707:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L707) *style:* **Commented code should be removed.**
```r
  # cohortData[speciesCode == "Popu_sp", cover := asInteger(cover / 2)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:709:14:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L709) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  cohortData[ , cover := {
             ^
```
[R/cohorts.R:709:15:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L709) *style:* **Commas should never have a space before.**
```r
  cohortData[ , cover := {
             ~^
```
[R/cohorts.R:721:14:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L721) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
             ^
```
[R/cohorts.R:721:15:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L721) *style:* **Commas should never have a space before.**
```r
  cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
             ~^
```
[R/cohorts.R:721:17:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L721) *style:* **Variable or function name should be lowerCamelCase.**
```r
  cohortData[ , B := mean(totalBiomass) * cover / 100, by = "pixelIndex"]
                ^
```
[R/cohorts.R:723:14:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L723) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
             ^
```
[R/cohorts.R:723:15:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L723) *style:* **Commas should never have a space before.**
```r
  cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
             ~^
```
[R/cohorts.R:723:17:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L723) *style:* **Variable or function name should be lowerCamelCase.**
```r
  cohortData[ , B := ceiling(B / pixelGroupBiomassClass) * pixelGroupBiomassClass]
                ^
```
[R/cohorts.R:725:14:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L725) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  cohortData[ , totalBiomass := asInteger(totalBiomass)]
             ^
```
[R/cohorts.R:725:15:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L725) *style:* **Commas should never have a space before.**
```r
  cohortData[ , totalBiomass := asInteger(totalBiomass)]
             ~^
```
[R/cohorts.R:831:36:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L831) *style:* **Variable or function name should be lowerCamelCase.**
```r
  cohortData[cover > 0 & age == 0, B := 0L]
                                   ^
```
[R/cohorts.R:837:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L837) *style:* **Commented code should be removed.**
```r
  # cohortData[ , coverProp := (cover/100 * (NROW(cohortData) - 1) + 0.5) / NROW(cohortData)]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:849:22:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L849) *style:* **Variable or function name should be lowerCamelCase.**
```r
subsetDT <- function(DT, by, doSubset = TRUE) {
                     ^~
```
[R/cohorts.R:854:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L854) *style:* **Lines should not be more than 100 characters.**
```r
              "using maximum of ", sam, " samples per combination of ecoregionGroup and speciesCode. ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cohorts.R:859:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/cohorts.R#L859) *style:* **Variable or function name should be lowerCamelCase.**
```r
      DT <- DT[a$lineNum]
      ^~
```
[R/ecoregionProducer.R:37:4:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L22) *style:* **Variable or function name should be lowerCamelCase.**
```r
defineFlammable <- function(LandCoverClassifiedMap = NULL,
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:128:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L128) *style:* **Variable or function name should be lowerCamelCase.**
```r
    MixedRas <- speciesStack[[1]]
    ^~~~~~~~
```
[R/maps.R:132:18:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L132) *style:* **Variable or function name should be lowerCamelCase.**
```r
    speciesStack$Mixed <- MixedRas
                 ^~~~~
```
[R/maps.R:191:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L191) *style:* **Lines should not be more than 100 characters.**
```r
    # 1. Find length of each pixelGroup -- don't include pixelGroups in "by" that have only 1 cohort: N = 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:195:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L195) *style:* **Lines should not be more than 100 characters.**
```r
    pixelGroupData1 <- cohortData1[, .(pixelGroup, B, speciesCode)][pixelGroupData1, on = "pixelGroup"]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:198:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L198) *style:* **Lines should not be more than 100 characters.**
```r
    pixelGroupData1 <- pixelGroupData1[, .(speciesGroupB = sum(B, na.rm = TRUE), totalB = totalB[1]), by = pgdAndSc]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:199:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L199) *style:* **Lines should not be more than 100 characters.**
```r
    set(pixelGroupData1, NULL, "speciesProportion", pixelGroupData1$speciesGroupB / pixelGroupData1$totalB)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:214:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L214) *style:* **Commented code should be removed.**
```r
    # setorderv(cohortData, "pixelGroup")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:217:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L217) *style:* **Variable or function name should be lowerCamelCase.**
```r
    N <- rep.int(pixelGroupData2$N, pixelGroupData2$N)
    ^
```
[R/maps.R:226:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L226) *style:* **Variable or function name should be lowerCamelCase.**
```r
    GT1 <- (b > 1)
    ^~~
```
[R/maps.R:229:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L229) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData2[[1]] <- cohortData2[GT1, .(speciesProportion = sum(B, na.rm = TRUE) / totalB[1]),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:233:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L233) *style:* **Lines should not be more than 100 characters.**
```r
      set(cohortData2, which(!GT1), "speciesProportion", cohortData2$B[!GT1] / cohortData2$totalB[!GT1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:234:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L234) *style:* **Lines should not be more than 100 characters.**
```r
      pixelGroupData2[[NROW(pixelGroupData2) + 1]] <- cohortData2[!GT1, c("pixelGroup", "speciesCode",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:245:28:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L245) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (isTRUE(doAssertion)) { # slower -- older, but simpler Eliot June 5, 2019
                           ^
```
[R/maps.R:274:14:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L274) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (FALSE) { # old algorithm
             ^
```
[R/maps.R:292:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L292) *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:307:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L307) *style:* **Commented code should be removed.**
```r
  # a2 <- Sys.time()
    ^~~~~~~~~~~~~~~~
```
[R/maps.R:311:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L311) *style:* **Commented code should be removed.**
```r
  # pixelGroupData2[mixed == TRUE, leading := "Mixed"]
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:312:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L312) *style:* **Commented code should be removed.**
```r
  # b2 <- Sys.time()
    ^~~~~~~~~~~~~~~~
```
[R/maps.R:466:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L466) *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:473:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L473) *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:476:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L476) *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:483:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L483) *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:501:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L501) *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:503:77:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L503) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  noDataLayers <- sapply(speciesLayers, function(x) if (maxValue(x) < thresh ) FALSE else TRUE)
                                                                            ^
```
[R/maps.R:506:76:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L506) *style:* **Commas should always have a space after.**
```r
    message("removing ", sum(!noDataLayers), " species because they had <",thresh,
                                                                           ^
```
[R/maps.R:508:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L508) *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:530:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L530) *style:* **Commented code should be removed.**
```r
  # layerData <- Cache(sapply, X = speciesLayers, function(x) sum(x[] > 0, na.rm = TRUE))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:532:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L532) *style:* **Commented code should be removed.**
```r
  # ## remove layers that had < thresh pixels with biomass
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:533:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L533) *style:* **Commented code should be removed.**
```r
  # belowThresh <- layerData < thresh
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:535:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L535) *style:* **Commented code should be removed.**
```r
  #   message(names(belowThresh)[belowThresh], " was removed because it had no data")
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:536:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L536) *style:* **Commented code should be removed.**
```r
  #   speciesLayers[belowThresh] <- NULL
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:635:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L635) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRastName <- basename(tempfile(fileext = ".tif"))
      ^~~~~~~~~~
```
[R/maps.R:637:9:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L637) *style:* **Variable or function name should be lowerCamelCase.**
```r
        LQCurName <- basename(tempfile(fileext = ".tif"))
        ^~~~~~~~~
```
[R/maps.R:644:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L644) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRastInHQcrs <- projectExtent(lowQualityStack, crs = crs(highQualityStack))
      ^~~~~~~~~~~~~
```
[R/maps.R:657:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L657) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- raster(LQRastName)
      ^~~~~~
```
[R/maps.R:675:9:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L675) *style:* **Variable or function name should be lowerCamelCase.**
```r
        HQRast <- raster(tmpHQName)
        ^~~~~~
```
[R/maps.R:680:9:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L680) *style:* **Variable or function name should be lowerCamelCase.**
```r
        HQRast <- highQualityStack[[SPP]]
        ^~~~~~
```
[R/maps.R:683:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L683) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- lowQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:684:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L684) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:691:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L691) *style:* **Variable or function name should be lowerCamelCase.**
```r
    NAs <- is.na(HQRast[])
    ^~~
```
[R/maps.R:695:5:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L695) *style:* **Variable or function name should be lowerCamelCase.**
```r
    HQRast <- writeRaster(HQRast, datatype = "INT1U",
    ^~~~~~
```
[R/maps.R:705:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L705) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:709:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L709) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LQRast <- lowQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:713:7:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L713) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- highQualityStack[[SPP]]
      ^~~~~~
```
[R/maps.R:745:4:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/maps.R#L745) *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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/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/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/overlayLCCs.R#L96) *style:* **Variable or function name should be lowerCamelCase.**
```r
        dt[, NNcondition := eval(parse(text = NNcondition))]
             ^~~~~~~~~~~
```
[R/overlayLCCs.R:101:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/overlayLCCs.R#L101) *style:* **Lines should not be more than 100 characters.**
```r
          ## It's possible that there are no pixels with classesToReplace that fulfill the NNcondition
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:105:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/overlayLCCs.R#L105) *style:* **Lines should not be more than 100 characters.**
```r
                                  availableERC_by_Sp = na.omit(dt)[, c("initialEcoregionCode", "pixelIndex")])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:128:13:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/overlayLCCs.R#L128) *style:* **Only use double-quotes.**
```r
      dt2[, ':='(initialEcoregionCode = newLCC, ecoregionCode = newLCC)]
            ^~~~
```
[R/overlayLCCs.R:128:17:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/overlayLCCs.R#L128) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      dt2[, ':='(initialEcoregionCode = newLCC, ecoregionCode = newLCC)]
                ^
```
[R/overlayLCCs.R:131:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/overlayLCCs.R#L131) *style:* **Lines should not be more than 100 characters.**
```r
      dt1 <- dt2[initialEcoregionCode %in% classesToReplace, c("initialEcoregionCode", "pixelIndex")]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/overlayLCCs.R:138:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/overlayLCCs.R#L138) *style:* **Lines should not be more than 100 characters.**
```r
                                availableERC_by_Sp = na.omit(dt2)[, c("initialEcoregionCode", "pixelIndex")])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputObjects.R:3:83:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/prepInputObjects.R#L3) *style:* **Trailing whitespace is superfluous.**
```r
                           "lcc", "longevity", "maxB", "maxANPP", "postfireregen",
                                                                                ^
```
[R/prepInputObjects.R:10:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/prepInputObjects.R#L10) *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/prepInputObjects.R:11:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/prepInputObjects.R#L11) *style:* **Lines should not be more than 100 characters.**
```r
#' @param sppColorVect A named vector of colors to use for plotting. The names must conform with \code{names(speciesLayers)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputObjects.R:39:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/prepInputObjects.R#L39) *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/prepInputObjects.R:60:55:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/prepInputObjects.R#L60) *style:* **Variable or function name should be lowerCamelCase.**
```r
                           biomassMap, rasterToMatch, LCC2005, pixelGroupAgeClass) {
                                                      ^~~~~~~
```
[R/prepInputObjects.R:71:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/prepInputObjects.R#L71) *style:* **Lines should not be more than 100 characters.**
```r
                                                                       ecoregionFiles$ecoregionMap[],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/prepInputObjects.R:87:1:](https://github.com/PredictiveEcology/LandR/blob/e12bcf06b21e6df3cc30424042dc2abbe5dba4e9/R/prepInputObjects.R#L87) *style:* **Lines should not be more than 100 characters.**
```r
            "\n  Check if sim$rasterToMatch shoudn't also only have data where there is cover data,",


Successfully aliased the URL <https://khromedev-hy1ou2uz6.now.sh> to the following aliases:

* https://khrome.dev
* https://khromedev.khrome83.now.sh
* https://khromedev-git-master.khrome83.now.sh


`getting_started.rst:59` also mentions that the examples can be downloaded from <https://github.com/RSGInc/populationSim_resources/raw/master/example_setup/PopulationSimExampleSetUps.7z>. Do we need to package this new example into that?


PWM_RATE_ONOESHOT -> PWM_RATE_ONESHOT


Successfully aliased the URL <https://accessabar-4xxfgrdi6.now.sh> to the following aliases:

* https://accessabar.handsfree.now.sh
* https://accessabar-git-master.handsfree.now.sh


Yeah! `0` will be a good default value. It can cause an error when `compression_type` = `ZLIB`/`GZIP`, so it can remind users to explicitly specify the value.

```C++
struct CompressionParams {
  CompressionType compression_type = CompressionType::UNCOMPRESSED;
  int32 input_buffer_size = 0;
  int32 output_buffer_size = 0;
};
```


this is probably from https://github.com/bminor/newlib/commit/c53c2915a72063009c38b3046b772821e8cf8149


Successfully aliased the URL <https://revisionist-j3jp1wv3m.now.sh> to the following aliases:

* https://revisionist.miles.dev
* https://revisionist.lededje.now.sh
* https://revisionist-git-master.lededje.now.sh


Every single user's "getMessages" call was triggering "getMessagesResponse" callback to All connected users


Successfully aliased the URL <https://oasis500-client-4nhuziazv.now.sh> to the following aliases:

* https://oasis500-client.jafaralbadarneh.now.sh
* https://oasis500-client-git-master.jafaralbadarneh.now.sh


ZEIT Now cannot deploy this project to production due to following domain related issues:

 * `cspringer.co`(for alias `cspringer.co`) is not found inside your account. [Add it](https://zeit.co/dashboard/domains?action=add&domain=cspringer.co).


excuse me，I would like to know how to submit an assignment, and how to confirm my name with my homework？


Successfully aliased the URL <https://jobify-jcwnmf85y.now.sh> to the following aliases:

* https://jobify.luizholanda1408.now.sh
* https://jobify-git-master.luizholanda1408.now.sh


Deferred is not Promise/A compliant. Might look for something else, or use async/await which is native to recent versions of JS.


Deployment failed with the following error:

~~~
The chosen alias "back-end.now.sh" is already in use by another account.
~~~


EPG settings are in the EPG menu on PLI dev now. Plugins will also go in there. Just like how tuning plugins go in the tuners and scanning menu.

This is an OEA plugin. As far as I am aware, all OEA images have the EPG menu. If you want to put the fallback for any images that don't have the EPG menu, please feel free to submit a pull request. IMO it should go in the plugins menu.


Successfully aliased the URL <https://veldu-rafbil-faft3kc94.now.sh> to the following aliases:

* https://veldurafbil.is
* https://veldu-rafbil.hugihlynsson.now.sh
* https://veldu-rafbil-git-master.hugihlynsson.now.sh


Successfully aliased the URL <https://revisionist-1j3ylq3km.now.sh> to the following aliases:

* https://revisionist.miles.dev
* https://revisionist.lededje.now.sh
* https://revisionist-git-master.lededje.now.sh


Now could not deploy this pull request since the `package.json` file does not contain valid JSON.

  Click here to see the contents of `package.json`

{
    "name": "my-dev-docz",
    "description": "my own documentation spot that might be useful to others",
    "version": "1.0.0",
    "main": "public/index.html",
    "scripts": {
        "test": "echo \"Error: no test specified\" && exit 1",
        "dev": "docz dev",
        "start": "npm run dev --port 5400",
        "build": "docz build",
        "now-build": "yarn build",
        "newpage": "./newpage",
        "live-start": "node run",
        "deploy": "node _updatedocs.js"
    },
    "repository": {
        "type": "git",
        "url": "git+https://github.com/CliffCrerar/dev-docz.git"
    },
    "keywords": [
        "docs"
    ],
    "author": "Cliff Crerar & others",
    "license": "MIT",
    "devDependencies": {
        "docz": "^1.2.0",
        "docz-theme-default": "^1.2.0"
    },
    "dependencies": {
        "docz-knobs": "^0.1.1",
        "docz-theme-umi": "^2.0.5",
        "dotenv": "^8.0.0",
        "gh-pages": "^2.0.1",
        "react": "^16.8.6",
        "react-dom": "^16.8.6",
        "request": "^2.88.0"
    }
}
w


Commented this out as can't usually return in the OpenMP target loop, per the XL compiler.


PLI have added a commit where you enter the option in  menus where only item is listed. Hope that makes sense.

If no EPG plugins, you will go straight into EPG settings. If there are plugins, you will see the EPG settings as well as EPG plugins


PR should be good when you are ready. Updated framework to 4.7, let me know if you want me to do anything else.


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* https://test1.w3bdesign.now.sh
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Successfully aliased the URL <https://veldu-rafbil-5yj78fcet.now.sh> to the following aliases:

* https://veldurafbil.is
* https://veldu-rafbil.hugihlynsson.now.sh
* https://veldu-rafbil-git-master.hugihlynsson.now.sh


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* https://veldurafbil.is
* https://veldu-rafbil.hugihlynsson.now.sh
* https://veldu-rafbil-git-master.hugihlynsson.now.sh


TeamCity Bvcms / Build [Build 1492](https://builds.tpsdb.com/viewLog.html?buildId=7236&buildTypeId=Bvcms_Build) is now running


Hi Marian,
I was doing your Quick Blog and I didn't have any errors so far - but in Quick Blog Day 3 I inserted the colours like in the tutorial, but the colours don't show up on my website and the Console said that the SCSS was not running; but the other files were; I don't know where to ask. (I'm not part of your team, just doing website tutorials.)


This is a comment on the code above.


for Services Unplanned Preventive Maintenances


fail


Yes it should be actually `<span></span>` indeed 👍 created https://github.com/matomo-org/matomo/pull/14649


css


Raj made was active on Github today, he's not dead


bien


ok


We all know that, even though we dare not admit


Cool. Thanks!


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* https://kana-trainer.jaredkent.now.sh
* https://kana-trainer-git-master.jaredkent.now.sh


Successfully aliased the URL <https://nextjs-nb6u6wrlz.now.sh> to the following aliases:

* https://nextjs.hlhr202.now.sh
* https://nextjs-git-master.hlhr202.now.sh


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-133-upzone.pantheonsite.io/)

Created multidev environment [ci-133](https://dashboard.pantheon.io/sites/34fd7546-af37-459b-8d53-377104708647#ci-133) for upzone.


OpenPLi have an "epg" menu in developer branch. In the other builds (7.0 and rc7.1) this plugin is locked by hash so this commit will not show.