[R/ABC_SMC.R:11:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
# @param    current                 vector       Current parameter combination for which we are determining the weight
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:12:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                   scalar       standard deviation of the perturbation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:13:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function  function     Function to calculate the prior probability of a set of parameters
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:36:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
# @brief apply the ABC routine used in our Methods in Ecology and Evolution Paper
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:43:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
# @param    statistics                    vector      A vector containing functions that take a tree as an argument and return a single scalar value (the statistic).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:44:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
# @param    simulation_function           vector      A function that implements the diversification model and returns an object of class phylo
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:45:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
# @param    init_epsilon_values           vector      A vector containing the initial threshold values for the summary statistics from the vector statistics.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:46:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_generating_function     function    Function to generate parameters from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:47:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
# @param    prior_density_function        function    Function to calculate the prior probability of a set of parameters (should match prior_generating_function in shape)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:48:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
# @param    number_of_particles           scalar      Number of particles to be used per iteration of the ABC-SMC algorithm.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:49:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                         scalar      Standard deviation of the perturbance distribution (perturbance distribution is a gaussian with mean 0).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:50:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
# @param    stop_rate                     scalar      If the acceptance rate drops below \code{stopRate}, stop the ABC-SMC algorithm  and assume convergence.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:51:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
# @return                                 matrix      A matrix with n columns, where n is the number of parameters you are trying to estimate.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:75:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
#'   from the prior distribution of these parameters (e.g. a function returning lambda and mu in case of the birth-death model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:276:13:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L276) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( (number_accepted / tried) < stop_rate) {
            ^
```
[R/ABC_SMC.R:301:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L301) *style:* **Lines should not be more than 80 characters.**
```r
# @brief Estimate the likelihood of a given tree, provided a likelihood function, using a Monte Carlo Markov Chain
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:308:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L308) *style:* **Lines should not be more than 80 characters.**
```r
# @param    likelihood_function   function    Function that calculates the likelihood of our diversification model, given the tree.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:309:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#                                             function should be of the format function(parameters, phy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:310:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L310) *style:* **Lines should not be more than 80 characters.**
```r
# @param    parameters            vector      Initial parameters to start the chain.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:311:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L311) *style:* **Lines should not be more than 80 characters.**
```r
# @param    logtransforms         scalar      Whether to perform jumps on logtransformed parameters (TRUE) or not (FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:313:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L313) *style:* **Lines should not be more than 80 characters.**
```r
# @param    burnin                scalar      Length of the burnin, default is 30% of iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:315:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L315) *style:* **Lines should not be more than 80 characters.**
```r
# @param    sigma                 scalar      Standard deviation of the jumping distribution, which is N(0, sigma).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:316:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/ABC_SMC.R#L316) *style:* **Lines should not be more than 80 characters.**
```r
# @return                         mcmc        An MCMC object, as used by the package "coda".
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:183:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/nLTTDiff.R#L183) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculates the exact difference between the lineage through time curves of tree1 & tree2 (normalized in time and for the number of lineages)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:257:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/nLTTDiff.R#L257) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:258:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/nLTTDiff.R#L258) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:324:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/nLTTDiff.R#L324) *style:* **Lines should not be more than 80 characters.**
```r
# @param    distance_method        string     Method to calculate the difference, either absolute, or squared
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:325:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/nLTTDiff.R#L325) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:326:1:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/nLTTDiff.R#L326) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_nLTT.R:36:23:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/plot_nLTT.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
nltt_plot <- function( phy, xlab = "Normalized Time",
                      ^
```
[R/plot_nLTT.R:51:28:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                           ^
```
[R/plot_nLTT.R:51:33:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/plot_nLTT.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs( min( xy[, 1])) #make sure time runs from 0..T
                                ^
```
[R/plot_nLTT.R:52:28:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/plot_nLTT.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] / max( xy[, 1])      #normalize time
                           ^
```
[R/plot_nLTT.R:94:32:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/R/plot_nLTT.R#L94) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  xy[, 1] <- xy[, 1] + abs(min( xy[, 1])) #make sure time runs from 0..T
                               ^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-abc_smc_nltt.R#L30) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-abc_smc_nltt.R:35:3:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable or function name should be snake_case.**
```r
  ML <- stats::optimize(f = tofit, interval = c(0, 1))
  ^~
```
[tests/testthat/test-abc_smc_nltt.R:55:3:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable or function name should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-get_average_nltt.R#L10) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_average_nltt.R:41:5:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-get_average_nltt.R#L41) *style:* **Commented code should be removed.**
```r
  # suppressWarnings(RNGversion("3.5.0"))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-mcmc_nltt.R:14:3:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable or function name should be snake_case.**
```r
  ML <- optim(par = c(1, 0.001), fn = tofit)
  ^~
```
[tests/testthat/test-mcmc_nltt.R:58:3:](https://github.com/richelbilderbeek/nLTT/blob/7c4e44641a08fd86dc89bc31db1c260e4591c63d/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable or function name should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```


Deployment failed with the following error:

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


I don't like "encountered confusion", because I think it's the same typo ~10 times in a row :)


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-1084-mtcv.pantheonsite.io/)

Created multidev environment [ci-1084](https://dashboard.pantheon.io/sites/ad79477c-5d06-4234-b6b8-582ebeee0e5c#ci-1084) for mtcv.


Cool, but if I were you I'd finish working through Pierce before coming back to this. Pierce is just so much better.


The correct code is to call LP_EnterLP2 from hal_sleep as before and to call LP_EnterLP1 from hal_deepsleep. Problem is LP1 disables all clocks except for an enabled RTC 32kHz clock and this state will prevent DAPLink drag and drop from working.


TeamCity Architecture Team / Java Platform / otj-logging / otj-logging [Build 246](https://teamcity.otenv.com/viewLog.html?buildId=11019700&buildTypeId=ArchitectureTeam_JavaPlatform_OtjLogging_OtjLogging) is now running


[R/buildMetadata.R:5:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param isRasterToMatch Logical. Is this(these) layer(s) the \code{rasterToMatch} layers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:6:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#'        If \code{TRUE}, then this layer can be accessed by \code{rasterToMatch(map)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:12:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#'  If \code{TRUE} or a character vector, then this layer will be added to a leaflet map.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:13:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
#'  For \code{RasterLayer} object, this will trigger a call to \code{gdal2tiles}, making tiles.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:20:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
buildMetadata <- function(metadata, isStudyArea, isRasterToMatch, layerName, obj,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:20:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L20) *style:* **Variable or function name should be snake_case.**
```r
buildMetadata <- function(metadata, isStudyArea, isRasterToMatch, layerName, obj,
^~~~~~~~~~~~~
```
[R/buildMetadata.R:20:37:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L20) *style:* **Variable or function name should be snake_case.**
```r
buildMetadata <- function(metadata, isStudyArea, isRasterToMatch, layerName, obj,
                                    ^~~~~~~~~~~
```
[R/buildMetadata.R:20:50:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L20) *style:* **Variable or function name should be snake_case.**
```r
buildMetadata <- function(metadata, isStudyArea, isRasterToMatch, layerName, obj,
                                                 ^~~~~~~~~~~~~~~
```
[R/buildMetadata.R:20:67:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L20) *style:* **Variable or function name should be snake_case.**
```r
buildMetadata <- function(metadata, isStudyArea, isRasterToMatch, layerName, obj,
                                                                  ^~~~~~~~~
```
[R/buildMetadata.R:21:27:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L21) *style:* **Variable or function name should be snake_case.**
```r
                          columnNameForLabels, objHash, leaflet, envir, ...) {
                          ^~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:21:48:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L21) *style:* **Variable or function name should be snake_case.**
```r
                          columnNameForLabels, objHash, leaflet, envir, ...) {
                                               ^~~~~~~
```
[R/buildMetadata.R:22:8:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L22) *warning:* **no visible global function definition for ‘copy’, Did you mean 'coef'?**
```r
  b <- copy(.singleMetadataNAEntry)
       ^~~~
```
[R/buildMetadata.R:22:13:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L22) *warning:* **no visible binding for global variable ‘.singleMetadataNAEntry’**
```r
  b <- copy(.singleMetadataNAEntry)
            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:28:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L28) *style:* **Variable or function name should be snake_case.**
```r
    studyAreaNumber <- 1 + NROW(metadata[compareNA(studyArea, TRUE) |
    ^~~~~~~~~~~~~~~
```
[R/buildMetadata.R:29:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
                                               (is.numeric(studyArea) & studyArea > 0)])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:30:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L30) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
    set(b, NULL, "studyArea", studyAreaNumber)
    ^~~
```
[R/buildMetadata.R:31:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L31) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
    set(b, NULL, "area", area)
    ^~~
```
[R/buildMetadata.R:35:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L35) *style:* **Variable or function name should be snake_case.**
```r
    rasterToMatchNumber <- 1 + NROW(metadata[compareNA(rasterToMatch, TRUE) |
    ^~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:36:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
                                           (is.numeric(rasterToMatch) & rasterToMatch > 0)])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:37:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L37) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
    set(b, NULL, "rasterToMatch", rasterToMatchNumber)
    ^~~
```
[R/buildMetadata.R:43:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L43) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
  set(b, NULL, "layerName", layerName)
  ^~~
```
[R/buildMetadata.R:44:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L44) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
  set(b, NULL, "layerType", class(obj))
  ^~~
```
[R/buildMetadata.R:47:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L47) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
      set(b, NULL, "columnNameForLabels", columnNameForLabels)
      ^~~
```
[R/buildMetadata.R:50:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L50) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
  set(b, NULL, "objectHash", objHash)
  ^~~
```
[R/buildMetadata.R:53:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L53) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
    set(b, NULL, "leaflet", leaflet)
    ^~~
```
[R/buildMetadata.R:55:14:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L55) *warning:* **no visible global function definition for ‘.robustDigest’**
```r
      dig <- .robustDigest(obj)
             ^~~~~~~~~~~~~
```
[R/buildMetadata.R:56:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L56) *style:* **Variable or function name should be snake_case.**
```r
      tilePath <- ifelse(is.na(leaflet), asPath(NA_character_),
      ^~~~~~~~
```
[R/buildMetadata.R:58:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L58) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
      set(b, NULL, "leafletTiles", tilePath)
      ^~~
```
[R/buildMetadata.R:62:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L62) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
  set(b, NULL, "envir", list(list(envir)))
  ^~~
```
[R/buildMetadata.R:66:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    dots <- dots[!unlist(lapply(dots, is.null))] # remove NULL because that isn't added to data.table anyway
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:79:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L79) *style:* **Variable or function name should be snake_case.**
```r
  columnsToAdd <- dots
  ^~~~~~~~~~~~
```
[R/buildMetadata.R:84:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L84) *style:* **Lines should not be more than 80 characters.**
```r
        ## a data.table can't handle all types of objects. need to wrap in a list to stick it there
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:86:9:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L86) *style:* **Variable or function name should be snake_case.**
```r
        needToSet <- TRUE
        ^~~~~~~~~
```
[R/buildMetadata.R:89:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L89) *style:* **Lines should not be more than 80 characters.**
```r
          needToSet <- tryCatch(set(b, NULL, nta, cta), silent = TRUE, error = function(x) TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/buildMetadata.R:89:11:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L89) *style:* **Variable or function name should be snake_case.**
```r
          needToSet <- tryCatch(set(b, NULL, nta, cta), silent = TRUE, error = function(x) TRUE)
          ^~~~~~~~~
```
[R/buildMetadata.R:89:33:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/buildMetadata.R#L89) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
          needToSet <- tryCatch(set(b, NULL, nta, cta), silent = TRUE, error = function(x) TRUE)
                                ^~~
```
[R/GIS.R:7:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @return list containing: \code{sizeInHa}, the area; and \code{polyID}, the polygon ID.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/GIS.R:11:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L11) *style:* **Variable or function name should be snake_case.**
```r
areaAndPolyValue <- function(ras) {
^~~~~~~~~~~~~~~~
```
[R/GIS.R:12:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L12) *style:* **Variable or function name should be snake_case.**
```r
  polyIndivSpecies <- gdal_polygonizeR(ras) # 99 seconds with full ras
  ^~~~~~~~~~~~~~~~
```
[R/GIS.R:12:23:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L12) *warning:* **no visible global function definition for ‘gdal_polygonizeR’**
```r
  polyIndivSpecies <- gdal_polygonizeR(ras) # 99 seconds with full ras
                      ^~~~~~~~~~~~~~~~
```
[R/GIS.R:13:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  pArea <- as.numeric(sf::st_area(polyIndivSpecies) / 1e4)
  ^~~~~
```
[R/GIS.R:19:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L19) *style:* **Lines should not be more than 80 characters.**
```r
#' Based on \url{https://johnbaumgartner.wordpress.com/2012/07/26/getting-rasters-into-shape-from-r/}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/GIS.R:33:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L33) *style:* **Variable or function name should be snake_case.**
```r
gdal_polygonizeR <- function(x, outshape = NULL, gdalformat = "ESRI Shapefile",
^~~~~~~~~~~~~~~~
```
[R/GIS.R:48:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
  if (!file.exists(pypath)) stop("Can't find gdal_polygonize.py on your system.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/GIS.R:56:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L56) *style:* **Variable or function name should be snake_case.**
```r
    f.exists <- file.exists(paste(outshape, c("shp", "shx", "dbf"), sep = "."))
    ^~~~~~~~
```
[R/GIS.R:59:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L59) *style:* **Lines should not be more than 80 characters.**
```r
                   toString(paste(outshape, c("shp", "shx", "dbf"), sep = ".")[f.exists])),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/GIS.R:65:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L65) *warning:* **no visible global function definition for ‘writeRaster’**
```r
    writeRaster(x, rastpath, datatype = assessDataType(x))
    ^~~~~~~~~~~
```
[R/GIS.R:65:41:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L65) *warning:* **no visible global function definition for ‘assessDataType’**
```r
    writeRaster(x, rastpath, datatype = assessDataType(x))
                                        ^~~~~~~~~~~~~~
```
[R/GIS.R:73:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
    shp <- sf::read_sf(dsn = dirname(outshape), layer = basename(file_path_sans_ext(outshape)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/GIS.R:73:66:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L73) *warning:* **no visible global function definition for ‘file_path_sans_ext’**
```r
    shp <- sf::read_sf(dsn = dirname(outshape), layer = basename(file_path_sans_ext(outshape)))
                                                                 ^~~~~~~~~~~~~~~~~~
```
[R/GIS.R:74:22:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L74) *warning:* **no visible global function definition for ‘extent’, Did you mean 'extends'?**
```r
    sf::st_bbox(shp, extent(x))
                     ^~~~~~
```
[R/GIS.R:89:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L89) *style:* **Variable or function name should be snake_case.**
```r
.rasterToMemory <- function(x, ...) {
^~~~~~~~~~~~~~~
```
[R/GIS.R:90:8:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L90) *warning:* **no visible global function definition for ‘raster’, Did you mean 'paste'?**
```r
  r <- raster(x, ...)
       ^~~~~~
```
[R/GIS.R:108:24:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L108) *style:* **Variable or function name should be snake_case.**
```r
fasterize2 <- function(emptyRaster, polygonToFasterize, field) {
                       ^~~~~~~~~~~
```
[R/GIS.R:108:37:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L108) *style:* **Variable or function name should be snake_case.**
```r
fasterize2 <- function(emptyRaster, polygonToFasterize, field) {
                                    ^~~~~~~~~~~~~~~~~~
```
[R/GIS.R:109:10:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L109) *warning:* **no visible global function definition for ‘raster’, Did you mean 'paste'?**
```r
  ras <- raster(emptyRaster)
         ^~~~~~
```
[R/GIS.R:111:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L111) *style:* **Lines should not be more than 80 characters.**
```r
    polygonToFasterize <- Cache(cropInputs, polygonToFasterize, rasterToMatch = ras)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/GIS.R:111:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    polygonToFasterize <- Cache(cropInputs, polygonToFasterize, rasterToMatch = ras)
    ^~~~~~~~~~~~~~~~~~
```
[R/GIS.R:111:27:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L111) *warning:* **no visible global function definition for ‘Cache’**
```r
    polygonToFasterize <- Cache(cropInputs, polygonToFasterize, rasterToMatch = ras)
                          ^~~~~
```
[R/GIS.R:111:33:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L111) *warning:* **no visible binding for global variable ‘cropInputs’**
```r
    polygonToFasterize <- Cache(cropInputs, polygonToFasterize, rasterToMatch = ras)
                                ^~~~~~~~~~
```
[R/GIS.R:113:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L113) *style:* **Variable or function name should be snake_case.**
```r
  thePoly <- projectInputs(polygonToFasterize, targetCRS = crs(ras))
  ^~~~~~~
```
[R/GIS.R:113:14:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L113) *warning:* **no visible global function definition for ‘projectInputs’**
```r
  thePoly <- projectInputs(polygonToFasterize, targetCRS = crs(ras))
             ^~~~~~~~~~~~~
```
[R/GIS.R:113:60:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L113) *warning:* **no visible global function definition for ‘crs’, Did you mean 'cars'?**
```r
  thePoly <- projectInputs(polygonToFasterize, targetCRS = crs(ras))
                                                           ^~~
```
[R/GIS.R:114:11:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/GIS.R#L114) *style:* **Variable or function name should be snake_case.**
```r
  thePoly$polygonNum <- seq_along(thePoly)
          ^~~~~~~~~~
```
[R/makeTiles.R:1:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L1) *style:* **Variable or function name should be snake_case.**
```r
makeTiles <- function(tilePath, obj) {
^~~~~~~~~
```
[R/makeTiles.R:1:23:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L1) *style:* **Variable or function name should be snake_case.**
```r
makeTiles <- function(tilePath, obj) {
                      ^~~~~~~~
```
[R/makeTiles.R:2:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L2) *style:* **Variable or function name should be snake_case.**
```r
  dirNotExist <- !dir.exists(tilePath)
  ^~~~~~~~~~~
```
[R/makeTiles.R:4:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
  if (dirNotExist) { # assume that tilePath is unique for that obj, via .robustDigest
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeTiles.R:4:20:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L4) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (dirNotExist) { # assume that tilePath is unique for that obj, via .robustDigest
                   ^
```
[R/makeTiles.R:8:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
    objLflt <- try(projectRaster(obj, crs = CRS("+init=epsg:4326")), silent = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeTiles.R:8:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L8) *style:* **Variable or function name should be snake_case.**
```r
    objLflt <- try(projectRaster(obj, crs = CRS("+init=epsg:4326")), silent = TRUE)
    ^~~~~~~
```
[R/makeTiles.R:8:20:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L8) *warning:* **no visible global function definition for ‘projectRaster’**
```r
    objLflt <- try(projectRaster(obj, crs = CRS("+init=epsg:4326")), silent = TRUE)
                   ^~~~~~~~~~~~~
```
[R/makeTiles.R:8:45:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L8) *warning:* **no visible global function definition for ‘CRS’, Did you mean 'C'?**
```r
    objLflt <- try(projectRaster(obj, crs = CRS("+init=epsg:4326")), silent = TRUE)
                                            ^~~
```
[R/makeTiles.R:9:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L9) *style:* **Variable or function name should be snake_case.**
```r
    tmpFile <- tempfile(fileext = ".tif")
    ^~~~~~~
```
[R/makeTiles.R:10:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L10) *style:* **Variable or function name should be snake_case.**
```r
    objLflt <- try(writeRaster(objLflt, tmpFile), silent = TRUE)
    ^~~~~~~
```
[R/makeTiles.R:10:20:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L10) *warning:* **no visible global function definition for ‘writeRaster’**
```r
    objLflt <- try(writeRaster(objLflt, tmpFile), silent = TRUE)
                   ^~~~~~~~~~~
```
[R/makeTiles.R:12:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L12) *style:* **Variable or function name should be snake_case.**
```r
    toDo <- TRUE
    ^~~~
```
[R/makeTiles.R:13:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L13) *style:* **Variable or function name should be snake_case.**
```r
    tryNum <- 1
    ^~~~~~
```
[R/makeTiles.R:16:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
      out <- try(tiler::tile(tmpFile, tilePath, zoom = "1-10", crs = CRS("+init=epsg:4326"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/makeTiles.R:18:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L18) *style:* **Variable or function name should be snake_case.**
```r
      toDo <- is(out, "try-error")
      ^~~~
```
[R/makeTiles.R:22:9:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L22) *style:* **Variable or function name should be snake_case.**
```r
        toDo <- TRUE
        ^~~~
```
[R/makeTiles.R:25:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/makeTiles.R#L25) *style:* **Variable or function name should be snake_case.**
```r
      tryNum <- tryNum + 1
      ^~~~~~
```
[R/map-analysis.R:17:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
#'   \code{analysisGroup2} column of the \code{map@@metadata} or a \code{functionName}.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:39:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L39) *style:* **Variable or function name should be snake_case.**
```r
mapAnalysis <- function(map, functionName = NULL, purgeAnalyses = NULL,
^~~~~~~~~~~
```
[R/map-analysis.R:39:30:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L39) *style:* **Variable or function name should be snake_case.**
```r
mapAnalysis <- function(map, functionName = NULL, purgeAnalyses = NULL,
                             ^~~~~~~~~~~~
```
[R/map-analysis.R:39:51:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L39) *style:* **Variable or function name should be snake_case.**
```r
mapAnalysis <- function(map, functionName = NULL, purgeAnalyses = NULL,
                                                  ^~~~~~~~~~~~~
```
[R/map-analysis.R:40:25:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L40) *style:* **Variable or function name should be snake_case.**
```r
                        useParallel = getOption("map.useParallel"), ...) {
                        ^~~~~~~~~~~
```
[R/map-analysis.R:42:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L42) *warning:* **local variable ‘dots’ assigned but may not be used**
```r
  dots <- list(...)
  ^~~~
```
[R/map-analysis.R:54:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L54) *style:* **Variable or function name should be snake_case.**
```r
  AGs <- sort(unique(colnames(m)[startsWith(colnames(m), "analysisGroup")]))
  ^~~
```
[R/map-analysis.R:56:31:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L56) *style:* **Variable or function name should be snake_case.**
```r
  ags <- lapply(AGs, function(AG) sort(na.omit(unique(m[[AG]]))))
                              ^~
```
[R/map-analysis.R:58:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L58) *style:* **Variable or function name should be snake_case.**
```r
  combosCompleted <- lapply(functionName, function(fn)
  ^~~~~~~~~~~~~~~
```
[R/map-analysis.R:60:4:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L60) *style:* **Commented code should be removed.**
```r
  #combosCompleted <- map@analysesData[[functionName]]$.Completed
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:71:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L71) *style:* **Variable or function name should be snake_case.**
```r
  combosAll <- expandAnalysisGroups(ags)
  ^~~~~~~~~
```
[R/map-analysis.R:71:16:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L71) *warning:* **no visible global function definition for ‘expandAnalysisGroups’**
```r
  combosAll <- expandAnalysisGroups(ags)
               ^~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:74:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
  # This is only for the first one to do, as it is just finding the columns required
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:76:42:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L76) *style:* **Variable or function name should be snake_case.**
```r
  args1 <- lapply(functionName, function(funName) {
                                         ^~~~~~~
```
[R/map-analysis.R:79:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L79) *style:* **Variable or function name should be snake_case.**
```r
    keepArgs <- unlist(lapply(args, function(arg) length(arg) > 0))
    ^~~~~~~~
```
[R/map-analysis.R:83:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L83) *style:* **Variable or function name should be snake_case.**
```r
  AGsByFunName <- lapply(functionName, function(funName) {
  ^~~~~~~~~~~~
```
[R/map-analysis.R:83:49:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L83) *style:* **Variable or function name should be snake_case.**
```r
  AGsByFunName <- lapply(functionName, function(funName) {
                                                ^~~~~~~
```
[R/map-analysis.R:88:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L88) *style:* **Variable or function name should be snake_case.**
```r
  combosAll <- Map(agsByFunName = AGsByFunName,
  ^~~~~~~~~
```
[R/map-analysis.R:90:29:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L90) *style:* **Variable or function name should be snake_case.**
```r
                   function(agsByFunName, ags) {
                            ^~~~~~~~~~~~
```
[R/map-analysis.R:91:22:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L91) *warning:* **no visible global function definition for ‘expandAnalysisGroups’**
```r
                     expandAnalysisGroups(ags[agsByFunName])
                     ^~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:94:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L94) *style:* **Variable or function name should be snake_case.**
```r
  combosToDo <- Map(cc = combosCompleted, ca = combosAll, function(cc, ca) {
  ^~~~~~~~~~
```
[R/map-analysis.R:96:32:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L96) *style:* **Commas should always have a space after.**
```r
      setDT(ca[!ca$all %in% cc,])
                               ^
```
[R/map-analysis.R:101:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L101) *style:* **Variable or function name should be snake_case.**
```r
  combosToDo <- Map(ctd = combosToDo, fn = functionName,
  ^~~~~~~~~~
```
[R/map-analysis.R:102:45:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L102) *style:* **Variable or function name should be snake_case.**
```r
                    function(ctd, fn) ctd[, functionName := fn])
                                            ^~~~~~~~~~~~
```
[R/map-analysis.R:103:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L103) *style:* **Variable or function name should be snake_case.**
```r
  combosToDoDT <- rbindlist(combosToDo)
  ^~~~~~~~~~~~
```
[R/map-analysis.R:103:19:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L103) *warning:* **no visible global function definition for ‘rbindlist’**
```r
  combosToDoDT <- rbindlist(combosToDo)
                  ^~~~~~~~~
```
[R/map-analysis.R:105:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L105) *style:* **Lines should not be more than 80 characters.**
```r
  combosToDo <- combosToDo[!unlist(lapply(combosToDo, function(ctd) NROW(ctd) == 0))]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:105:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L105) *style:* **Variable or function name should be snake_case.**
```r
  combosToDo <- combosToDo[!unlist(lapply(combosToDo, function(ctd) NROW(ctd) == 0))]
  ^~~~~~~~~~
```
[R/map-analysis.R:108:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L108) *style:* **Variable or function name should be snake_case.**
```r
    funNames <- unique(combosToDoDT$functionName)
    ^~~~~~~~
```
[R/map-analysis.R:111:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    otherFormalsInFunction <- lapply(funNames, function(funName) {
    ^~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:111:57:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    otherFormalsInFunction <- lapply(funNames, function(funName) {
                                                        ^~~~~~~
```
[R/map-analysis.R:112:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L112) *style:* **Variable or function name should be snake_case.**
```r
      otherFormalsInFunction <- formalArgs(funName)[formalArgs(funName) %in%
      ^~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:125:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L125) *style:* **Commented code should be removed.**
```r
    # browser()
      ^~~~~~~~~
```
[R/map-analysis.R:126:11:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L126) *warning:* **no visible global function definition for ‘makeOptimalCluster’**
```r
    cl <- makeOptimalCluster(useParallel, maxNumClusters = NROW(combosToDoDT))
          ^~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:127:17:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L127) *warning:* **no visible global function definition for ‘stopCluster’**
```r
    on.exit(try(stopCluster(cl), silent = TRUE))
                ^~~~~~~~~~~
```
[R/map-analysis.R:129:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L129) *style:* **Variable or function name should be snake_case.**
```r
    combosToDoList <- split(combosToDoDT, combosToDoDT$all)
    ^~~~~~~~~~~~~~
```
[R/map-analysis.R:132:20:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L132) *style:* **Variable or function name should be snake_case.**
```r
                   funName <- combo$functionName
                   ^~~~~~~
```
[R/map-analysis.R:134:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L134) *style:* **Lines should not be more than 80 characters.**
```r
                                                   combo = combo, AGs = AGs, funName = funName)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:137:20:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L137) *style:* **Variable or function name should be snake_case.**
```r
                   fnOut <- do.call(Cache,
                   ^~~~~
```
[R/map-analysis.R:140:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L140) *style:* **Lines should not be more than 80 characters.**
```r
                                                         otherFormalsInFunction[[funName]])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:145:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L145) *style:* **Variable or function name should be snake_case.**
```r
      fromFunName <- combosToDoDT$functionName == funName
      ^~~~~~~~~~~
```
[R/map-analysis.R:147:35:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L147) *style:* **Variable or function name should be snake_case.**
```r
      map@analysesData[[funName]]$.Completed <- names(out3[fromFunName])
                                  ^~~~~~~~~~
```
[R/map-analysis.R:150:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L150) *style:* **Lines should not be more than 80 characters.**
```r
    message("  ", paste(functionName, collapse = ", "), " already run on all layers")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:168:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L168) *style:* **Variable or function name should be snake_case.**
```r
mapAddAnalysis <- function(map, functionName,
^~~~~~~~~~~~~~
```
[R/map-analysis.R:168:33:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L168) *style:* **Variable or function name should be snake_case.**
```r
mapAddAnalysis <- function(map, functionName,
                                ^~~~~~~~~~~~
```
[R/map-analysis.R:169:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L169) *style:* **Lines should not be more than 80 characters.**
```r
                           useParallel = getOption("map.useParallel", FALSE), ...) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:169:28:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L169) *style:* **Variable or function name should be snake_case.**
```r
                           useParallel = getOption("map.useParallel", FALSE), ...) {
                           ^~~~~~~~~~~
```
[R/map-analysis.R:171:8:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L171) *warning:* **no visible global function definition for ‘data.table’**
```r
  b <- data.table(functionName = functionName, t(dots))
       ^~~~~~~~~~
```
[R/map-analysis.R:172:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L172) *style:* **Variable or function name should be snake_case.**
```r
  prevEntry <- map@analyses$functionName == functionName
  ^~~~~~~~~
```
[R/map-analysis.R:173:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L173) *style:* **Variable or function name should be snake_case.**
```r
  purgeAnalyses <- NULL # Set default as NULL
  ^~~~~~~~~~~~~
```
[R/map-analysis.R:174:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L174) *style:* **Variable or function name should be snake_case.**
```r
  newDigest <- fastdigest::fastdigest(
  ^~~~~~~~~
```
[R/map-analysis.R:178:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L178) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
  set(b, NULL, "argHash", newDigest)
  ^~~
```
[R/map-analysis.R:179:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L179) *style:* **Variable or function name should be snake_case.**
```r
  doRbindlist <- TRUE
  ^~~~~~~~~~~
```
[R/map-analysis.R:182:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L182) *style:* **Lines should not be more than 80 characters.**
```r
      message("An analysis called ", functionName, " already added to map obj; ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:184:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L184) *style:* **Variable or function name should be snake_case.**
```r
      purgeAnalyses <- functionName
      ^~~~~~~~~~~~~
```
[R/map-analysis.R:187:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L187) *style:* **Variable or function name should be snake_case.**
```r
      doRbindlist <- FALSE
      ^~~~~~~~~~~
```
[R/map-analysis.R:188:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L188) *style:* **Lines should not be more than 80 characters.**
```r
      message("An analysis called ", functionName, " with identical function and ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:194:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L194) *style:* **Lines should not be more than 80 characters.**
```r
    map@analyses <- rbindlist(list(map@analyses, b), fill = TRUE, use.names = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:196:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
  map <- runMapAnalyses(map = map, purgeAnalyses = purgeAnalyses, useParallel = useParallel)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:196:10:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L196) *warning:* **no visible global function definition for ‘runMapAnalyses’**
```r
  map <- runMapAnalyses(map = map, purgeAnalyses = purgeAnalyses, useParallel = useParallel)
         ^~~~~~~~~~~~~~
```
[R/map-analysis.R:210:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
#'   \code{analysisGroups} i.e., \code{"analysisGroup1"} or \code{"analysisGroup2"}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:223:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L223) *style:* **Lines should not be more than 80 characters.**
```r
mapAddPostHocAnalysis <- function(map, functionName, postHocAnalysisGroups = NULL,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:223:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L223) *style:* **Variable or function name should be snake_case.**
```r
mapAddPostHocAnalysis <- function(map, functionName, postHocAnalysisGroups = NULL,
^~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:223:40:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L223) *style:* **Variable or function name should be snake_case.**
```r
mapAddPostHocAnalysis <- function(map, functionName, postHocAnalysisGroups = NULL,
                                       ^~~~~~~~~~~~
```
[R/map-analysis.R:223:54:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L223) *style:* **Variable or function name should be snake_case.**
```r
mapAddPostHocAnalysis <- function(map, functionName, postHocAnalysisGroups = NULL,
                                                     ^~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:224:35:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L224) *style:* **Variable or function name should be snake_case.**
```r
                                  postHocAnalyses = "all",
                                  ^~~~~~~~~~~~~~~
```
[R/map-analysis.R:225:35:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L225) *style:* **Variable or function name should be snake_case.**
```r
                                  useParallel = getOption("map.useParallel"),
                                  ^~~~~~~~~~~
```
[R/map-analysis.R:230:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L230) *style:* **Lines should not be more than 80 characters.**
```r
    stop("postHocAnalysisGroups cannot be NULL. It should be one of the column names ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:232:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L232) *style:* **Lines should not be more than 80 characters.**
```r
  b <- data.table(functionName = functionName, postHocAnalysisGroups = postHocAnalysisGroups,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:235:10:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L235) *warning:* **no visible global function definition for ‘data.table’**
```r
    b <- data.table(b, t(dots))
         ^~~~~~~~~~
```
[R/map-analysis.R:237:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L237) *style:* **Variable or function name should be snake_case.**
```r
  prevEntry <- map@analyses$functionName == functionName
  ^~~~~~~~~
```
[R/map-analysis.R:238:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L238) *style:* **Variable or function name should be snake_case.**
```r
  purgeAnalyses <- NULL # Set default as NULL
  ^~~~~~~~~~~~~
```
[R/map-analysis.R:239:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L239) *style:* **Variable or function name should be snake_case.**
```r
  newDigest <- fastdigest::fastdigest(
  ^~~~~~~~~
```
[R/map-analysis.R:243:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L243) *warning:* **no visible global function definition for ‘set’, Did you mean 'det'?**
```r
  set(b, NULL, "argHash", newDigest)
  ^~~
```
[R/map-analysis.R:244:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L244) *style:* **Variable or function name should be snake_case.**
```r
  doRbindlist <- TRUE
  ^~~~~~~~~~~
```
[R/map-analysis.R:247:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L247) *style:* **Lines should not be more than 80 characters.**
```r
      message("An analysis called ", functionName, " already added to map obj; ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:249:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L249) *style:* **Variable or function name should be snake_case.**
```r
      purgeAnalyses <- functionName
      ^~~~~~~~~~~~~
```
[R/map-analysis.R:252:7:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L252) *style:* **Variable or function name should be snake_case.**
```r
      doRbindlist <- FALSE
      ^~~~~~~~~~~
```
[R/map-analysis.R:253:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L253) *style:* **Lines should not be more than 80 characters.**
```r
      message("An analysis called, ", functionName, " with identical function and ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:259:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L259) *style:* **Lines should not be more than 80 characters.**
```r
    map@analyses <- rbindlist(list(map@analyses, b), fill = TRUE, use.names = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:261:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L261) *style:* **Lines should not be more than 80 characters.**
```r
  map <- runMapAnalyses(map = map, purgeAnalyses = purgeAnalyses, useParallel = useParallel)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:261:10:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L261) *warning:* **no visible global function definition for ‘runMapAnalyses’**
```r
  map <- runMapAnalyses(map = map, purgeAnalyses = purgeAnalyses, useParallel = useParallel)
         ^~~~~~~~~~~~~~
```
[R/map-analysis.R:266:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L266) *style:* **Variable or function name should be snake_case.**
```r
runMapAnalyses <- function(map, purgeAnalyses = NULL,
^~~~~~~~~~~~~~
```
[R/map-analysis.R:266:33:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L266) *style:* **Variable or function name should be snake_case.**
```r
runMapAnalyses <- function(map, purgeAnalyses = NULL,
                                ^~~~~~~~~~~~~
```
[R/map-analysis.R:267:28:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L267) *style:* **Variable or function name should be snake_case.**
```r
                           useParallel = getOption("map.useParallel")) {
                           ^~~~~~~~~~~
```
[R/map-analysis.R:268:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L268) *style:* **Variable or function name should be snake_case.**
```r
  isPostHoc <- if (is.null(map@analyses$postHoc)) {
  ^~~~~~~~~
```
[R/map-analysis.R:271:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L271) *warning:* **no visible global function definition for ‘compareNA’**
```r
    compareNA(map@analyses$postHoc, TRUE)
    ^~~~~~~~~
```
[R/map-analysis.R:276:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L276) *style:* **Variable or function name should be snake_case.**
```r
    funName <- map@analyses$functionName[!isPostHoc]
    ^~~~~~~
```
[R/map-analysis.R:277:12:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L277) *warning:* **no visible global function definition for ‘mapAnalysis’**
```r
    map <- mapAnalysis(map, funName, purgeAnalyses = purgeAnalyses)
           ^~~~~~~~~~~
```
[R/map-analysis.R:287:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L287) *style:* **Lines should not be more than 80 characters.**
```r
           forms <- forms[!forms %in% c("map", "functionName", "analysisGroups")]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:298:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L298) *style:* **Lines should not be more than 80 characters.**
```r
                                                            analysisGroups = x$postHocAnalysisGroups),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:299:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L299) *style:* **Lines should not be more than 80 characters.**
```r
                                                       unlist(as.list(x[ , forms, with = FALSE]))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:299:73:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L299) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                                       unlist(as.list(x[ , forms, with = FALSE]))))
                                                                        ^
```
[R/map-analysis.R:299:74:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L299) *style:* **Commas should never have a space before.**
```r
                                                       unlist(as.list(x[ , forms, with = FALSE]))))
                                                                        ~^
```
[R/map-analysis.R:313:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L313) *style:* **Variable or function name should be snake_case.**
```r
getFormalsFromMetadata <- function(metadata, combo, AGs, funName) {
^~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:313:53:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L313) *style:* **Variable or function name should be snake_case.**
```r
getFormalsFromMetadata <- function(metadata, combo, AGs, funName) {
                                                    ^~~
```
[R/map-analysis.R:313:58:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L313) *style:* **Variable or function name should be snake_case.**
```r
getFormalsFromMetadata <- function(metadata, combo, AGs, funName) {
                                                         ^~~~~~~
```
[R/map-analysis.R:314:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L314) *style:* **Lines should not be more than 80 characters.**
```r
  formalsInFunction <- formalArgs(funName)[formalArgs(funName) %in% colnames(metadata)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:314:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L314) *style:* **Variable or function name should be snake_case.**
```r
  formalsInFunction <- formalArgs(funName)[formalArgs(funName) %in% colnames(metadata)]
  ^~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:316:32:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L316) *style:* **Variable or function name should be snake_case.**
```r
  args <- lapply(AGs, function(AG) {
                               ^~
```
[R/map-analysis.R:330:4:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L330) *style:* **Commented code should be removed.**
```r
  #args <- unlist(unname(args), recursive = FALSE)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:335:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L335) *style:* **Variable or function name should be snake_case.**
```r
expandAnalysisGroups <- function(ags) {
^~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:336:3:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L336) *style:* **Variable or function name should be snake_case.**
```r
  combosAll <- NULL
  ^~~~~~~~~
```
[R/map-analysis.R:338:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L338) *style:* **Lines should not be more than 80 characters.**
```r
    combosAll <- do.call(expand.grid, args = append(list(stringsAsFactors = FALSE),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-analysis.R:338:5:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-analysis.R#L338) *style:* **Variable or function name should be snake_case.**
```r
    combosAll <- do.call(expand.grid, args = append(list(stringsAsFactors = FALSE),
    ^~~~~~~~~
```
[R/map-class.R:6:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @slot metadata  \code{data.table} with columns describing metadata of map objects in
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:9:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @slot .xData Named environment of map-type objects (e.g., \code{sf}, \code{Raster*},
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:10:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#'            \code{Spatial*}. Each entry may also be simply an environment, which
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:11:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#'            indicates where to find the object, i.e., via \code{get(layerName, envir = environment)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:15:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' @slot paths File paths. A named list of paths. The default is a list of length 2,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:18:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
#' @slot analyses    A \code{data.table} or \code{data.frame} of the types of analyses to perform.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:20:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
#' @slot analysesData A \code{data.table} or \code{data.frame} of the results of the analyses.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:41:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
  #             c(layerName = "character", layerType = "character", columnNameForLabels = "character",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:42:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
  #               leaflet = "character", studyArea = "numeric", rasterToMatch = "logical"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:47:20:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L47) *style:* **Variable or function name should be snake_case.**
```r
          function(.Object, ...) {
                   ^~~~~~~
```
[R/map-class.R:48:13:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L48) *style:* **Variable or function name should be snake_case.**
```r
            .Object <- callNextMethod()
            ^~~~~~~
```
[R/map-class.R:49:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
            .Object@metadata <- data.table(layerName = character(), layerType = character(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:52:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
                                           studyArea = numeric(), rasterToMatch = logical())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map-class.R:54:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map-class.R#L54) *style:* **Lines should not be more than 80 characters.**
```r
            .Object@analyses <- data.table::data.table(functionName = character())#, quotedFn = character())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map.R:2:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
  utils::globalVariables(c(".", ":=", ".I", ".N", ".SD", "envir", "layerName", "objectHash"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map.R:17:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
#' @param layerName Required. A label for this map layer. This can be the same as
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map.R:26:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map.R#L26) *style:* **Lines should not be more than 80 characters.**
```r
#'  If \code{TRUE} or a character vector, then this layer will be added to a leaflet map.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map.R:27:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
#'  For \code{RasterLayer} object, this will trigger a call to \code{gdal2tiles}, making tiles.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/map.R:69:1:](https://github.com/PredictiveEcology/map/blob/461e434e85b62146701c6a32b07cf4256ab0e522/R/map.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
#'                layerName = "Smaller Study Area") # adds a second studyArea within 1st
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


TeamCity Architecture Team / Java Platform / otj-logging / otj-logging [Build 246](https://teamcity.otenv.com/viewLog.html?buildId=11019700&buildTypeId=ArchitectureTeam_JavaPlatform_OtjLogging_OtjLogging) outcome was **SUCCESS**
Summary: Tests passed: 14 Build time: 00:01:24


How about using a `TinyPtrVector` here?


ok


New-Feature-CBVAV-Mods (rraustad) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1134 of 1134 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-42.59%25-green.png)


Successfully aliased the URL <https://react100sandiegotopspots-eqqwkexhp.now.sh> to the following aliases:

* https://react100sandiegotopspots.jhkim8268.now.sh
* https://react100sandiegotopspots-git-master.jhkim8268.now.sh


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* https://portfolio-redesign-2019-git-master.jayfallon1.now.sh


I think you need a case here that extracts the second child when `nameNode` is a `Demangle::Node::Kind::RelatedEntityDeclName`.


Hey @SimonRichardson do you have any intuition why the latter is preferred by the linter here? It feels like we're swapping out explicit for implicit.


Successfully aliased the URL <https://react100sandiegotopspots-5slszacc4.now.sh> to the following aliases:

* https://react100sandiegotopspots.jhkim8268.now.sh
* https://react100sandiegotopspots-git-master.jhkim8268.now.sh


I have an epic solution to the problem `refctd_dynamic_array`

make `dynamic_array<T,Alloc>` that is not constructible, and hopefully non copyable and nonmovable, and has a factory method
```cpp
template<class Alloc>
struct dynamic_array_base_members
{
   size_t item_count;
   Alloc allocator;
}

template<typename T, class Alloc=core::allocator<void>>
auto* create_dynamic_array(size_t length, Alloc&& allocator=Alloc())
{
   void* mem = allocator.allocate(sizeof(dynamic_array_base_members<Alloc>)+length*sizeof(T));
   return new(mem) dynamic_array<T,Alloc>(length,std::move(allocator));
}
void destroy_dynamic_array(dynamic_array<T,Alloc>* arr)
{
   size_t bytesize = sizeof(dynamic_array_base_members<Alloc>)+arr->length(()*sizeof(T);
   Alloc allocator(std::move(arr->allocator));
   arr->~dynamic_array<T,Alloc>();
   allocator.deallocate(arr,bytesize);
}
```

You can also do this by overriding new and delete class methods.

Then derive from `dynamic_array` a `refctd_dynamic_array` that inherits `IReferenceCounted` as well, then instead of copying the IAsset array+cache string and mallocing those arrays every time a copy ctor is invoked, you just pass around the refcounted dynamic array pointers!


AutoExecConfig(true, "stratroulette");


By moving this defunct array to only be appended to in the case where this cronjob actually should have a native cronjob pod, we can effectively cover the edge case where a cronjob is amended from a runtime >15 minutes to a runtime <15 minutes.


Copy of this build can be found at
https://builds.myetherwallet.com/build/97e05f4fbe65dc94c912476216e0716774266cc4/index.html
                       https://www.cloudflare-ipfs.com/ipfs/Qma2JYvpkaMeX81KBf6m93MFMQ6GjmhHx4k29zx8EPPJPD
                       Virus Total analysis
                       https://www.virustotal.com/file/8ca59417a95cd2959b5528ff207d328a8b076e1cfae4dcf79482f97db6198b14/analysis/1565298476/


> Is there any data on the difference this setting makes?

When I tested with old dbcache=100 in RC1 it was really slow and that was part of this twitter discussion: https://twitter.com/rootzoll/status/1158661244439748609?s=20
Now with the bigger values (from 100MB to 1GB) it crunched much faster and I was able to sync in under 2.5days. Prople with RP4 with 4GB and using that for dbcache reported even getting close to just 2days. And if the RAM is there .. why not use it.

> I have read the bigger problem is USB spinning HDD's and SSD's help the most.

Sure all those tests already run with SSD .. HDD is a big slow down. Giving a bigger dbcache in RAM is the next step giving further speedup so that we getting close to 2 day full sync that seem possible with RP4 - which is the golden goal to setup a RaspiBlitz over the weekend: but this time with dont trust, verify :)

> optimize for HDD

I dont think we can do much other then give more dbcache here (if available). Havent tested with HDD  yet. Also HDDs are on phase out for RaspiBlitz. 500 GB SSDs getting close to same price then 1TB HDDs now and with USB3 on RP4 we can finally utilize the speedup. In the new shopping lists I keep the HDD as part of the "minimal/cheap package" that also still will work with a RP3 - but for those minimal setup making a selfvalidation on the RaspberryPi itself is not recommended and thats why we still have the torrents available as fallbacks.


Successfully aliased the URL <https://reactrello-ctiekvm8e.now.sh> to the following aliases:

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so those cvars can have their own file to be edited at


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @mikehinchey, @jpharvey were added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

- @andrewseidl, @randyzwitch were added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


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You can directly `export default` here.


This was far easier than expected. View previous commit message to see other changes.


I know we consciously skipped doing this back then when this code was still in the `ButtonCard` to not unnecessarily bloat the `ButtonCard` code but now that it's an own component I think we should handle cancelling previous timeouts.


I guess you could now also simply use the `.transition-fade` defined in the global style in `App`.
`fadeout` is also not a good name anymore, as this transition is also used for fading in.


Maybe `QR_CODE_GRADIENT` would be a better name.
And it can be `readonly`.


An alternative to clicking a temporary anchor element could be to make the `.qr-code-download` an anchor itself and to update the href via a watcher (see the `QrCode` component for an example of how to define watchers as decorator).


Ok, but could be achieved in a nicer way by setting an appropriate padding on `.qr-code-download`.


You can simply specify `color: white` on `.qr-code-download`.


全角から半角への変換をやったり両方のパターンで空白に変換する前にUnicode Normalizationをやったほうがすっきりするかもしれない。NFKCで正規化すると、全角の半角やドル記号は全て半角になる。

```
In [1]: import unicodedata

In [2]: unicodedata.normalize('NFKC', u'\u2167')
Out[2]: 'VIII'

In [3]: print(u'\u2167')
Ⅷ
```


Das ganze fußte auf einer Diskussion in Slack: Beschriftungen sind gegenüber Icons eindeutig. PR fände ich ok.


Curious what the thinking was about not bundling the CSS together?


Successfully aliased the URL <https://gelfand-gatsby-project-6d5e96l12.now.sh> to the following aliases:

* https://gelfand-gatsby-project.leoraw.now.sh
* https://gelfand-gatsby-project-git-master.leoraw.now.sh


> Do you have a reason to believe there to be a field trip bug? Or is it just that your own script was doing some non-fieldtrip specific bookkeeping [...] that does not work any more?

Definitely the former. Jumping on thread #1184 as you managed to replicate the problem.


ah, I see.  okay, I'll revert.


Missed one!


Copy of this build can be found at
https://builds.myetherwallet.com/build/97e05f4fbe65dc94c912476216e0716774266cc4/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmRVgH8JWJrcf6Z7BmAXUm2r3Zy6mdnuygJogQ6CVzKuef
                       Virus Total analysis
                       https://www.virustotal.com/file/fa43056568d3626ea0b4d3d356f7eb616b80934d59d38b1623ce268510914114/analysis/1565299176/


There were the following issues with your Pull Request

  * Subject needs to conform to "%{type} #%{issue_number}: %{description}"
  * Subject must be equal or less than 50

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Yeah, too strong.  I meant for those documents using txns.


Deployment failed with the following error:

~~~
Free Docker deployment capacity exceeded in this region. Please consider upgrading to Now 2.0 (https://zeit.co/upgrade) for alternative ways to build your project or try again later.
~~~


Successfully aliased the URL <https://eusy-bckvd8pj2.now.sh> to the following aliases:

* https://eusy.briandombrowski.now.sh
* https://eusy-git-master.briandombrowski.now.sh


Deployment failed with the following error:

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


167702185_Issue6950 (Unknown) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

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


167702185_Issue6950 (Unknown) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (9 of 9 tests passed, 0 test warnings)

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


Is not neccesary


Nossa que merda, cade o código ? kkkkkkkkk


167702185_Issue6950 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2487 of 2500 tests passed, 0 test warnings)

Messages:\n
 * 10 tests had: EIO diffs.
 * 10 tests had: ESO big diffs.
 * 5 tests had: MTR small diffs.
 * 3 tests had: Table small diffs.
 * 3 tests had: MTR big diffs.
 * 7 tests had: Table big diffs.

Failures:\n

EnergyPlusFixture Test Summary
 * Passed: 778
 * Failed: 3

regression Test Summary
 * Passed: 673
 * Failed: 10

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.48%25-yellow.png)


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Created multidev environment [ci-1089](https://dashboard.pantheon.io/sites/ad79477c-5d06-4234-b6b8-582ebeee0e5c#ci-1089) for mtcv.


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

* https://antitesis.fobossalmeron.now.sh
* https://antitesis-git-master.fobossalmeron.now.sh


Thanks for the explanation!


:D


Copy of this build can be found at
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                       Virus Total analysis
                       https://www.virustotal.com/file/7c8d00e691547927b18bdfceac9b33de6acdcb9ea0868593006380b98e9a27a5/analysis/1565299580/


done.


Created multidev environment [eari-contenta#pr-4](https://dashboard.pantheon.io/sites/6207a978-eea6-466e-b84a-7fd8be31b6c6#pr-4).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-4-eari-contenta.pantheonsite.io/)


Updated


Understood. I have been looking at the midcourse corrections and abort documents a lot this week and this seems like a good opportunity to do some testing.


maybe it should be Action instead of action.


167702185_Issue6950 (Unknown) - x86_64-MacOS-10.13-clang: OK (2447 of 2460 tests passed, 0 test warnings)

Messages:\n
 * 10 tests had: EIO diffs.
 * 10 tests had: ESO big diffs.
 * 5 tests had: MTR small diffs.
 * 3 tests had: Table small diffs.
 * 3 tests had: MTR big diffs.
 * 7 tests had: Table big diffs.

Failures:\n

EnergyPlusFixture Test Summary
 * Passed: 778
 * Failed: 3

regression Test Summary
 * Passed: 653
 * Failed: 10

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.47%25-yellow.png)


why is this needed?