[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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:126:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/ABC_SMC.R:320:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/nltt_diff_exact_notnorm.R:25:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
nltt_diff_exact_notnorm <- function(
^
```
[R/nltt_diff_exact_notnorm.R:47:27:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L47) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_notnorm.R:54:25:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L54) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_notnorm.R:116:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L116) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:117:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L117) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:118:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L118) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:119:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L119) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:121:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L121) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:122:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L122) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:123:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L123) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:124:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L124) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L186) *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:274:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L274) *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:275:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L344) *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:345:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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
                               ^
```
[R/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style 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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style 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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:29:16:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-nltt_diff_exact_notnorm.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:30:16:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-nltt_diff_exact_notnorm.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


КомментарииПодЗадачи.os

предполагаем, что в структуре шаблона его маска идет после третьей запятой


Thanks for this hint!
I’ve added some index option conflict detection in f4057d8d050989c0c7a36d0188f5e2ba0caf48f2.
Note that it’s limited because not all index options are supported yet. PRs are welcome to improve it ;)


Successfully deployed to following URLs:

* https://paste-fcxiokh5p.now.sh
* https://paste.twilio.design
* https://paste.twilio-dsys.now.sh
* https://paste-git-master.twilio-dsys.now.sh


Try to get in the habit of having your commit messages explain what the **commit** _does_, not what **you** _did_.


Successfully deployed to following URLs:

* https://dotwatcher-upload-2ssq95itr.now.sh
* https://dotwatcher-upload-sparkling-fur-seal.now.sh
* https://upload.dotwatcher.cc
* https://dotwatcher-upload.dotwatchers1.now.sh
* https://dotwatcher-upload-git-master.dotwatchers1.now.sh


It's not guaranteed to be non-null, if that's what you mean; `pcap_findalldevs()` and `pcap_findalldevs_ex()` can return success and set `alldevs` to NULL - if no errors occur, but there are no adapters on which libpcap can capture, that'll happen.


Successfully deployed to following URLs:

* https://falahansblogapp-i1k85z6ke.now.sh
* https://falahansblogapp.phirmware.now.sh
* https://falahansblogapp-git-master.phirmware.now.sh


Puzzle `3-1c90eb18` discovered in   [`src/App.js`](  https://github.com/p-siriphanthong/chim-shop-chai/blob/master/src/App.js)   and submitted as #3. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


let's try `"//*[@id='wfm-pmd_deals_section']/div[6]//li[.//div[contains(@class, 'brand-name')]]"` ?


Modifiquei o titulo do arquivo Registro de  alunos


great job. for Q1, you can do it with better way, i believe you can do it.
you can use only on if condition and the use as may as you want of else if and at the end use else.


More importantly, from what I just tested, the way this requirement check is structured, it causes a site running a lower version of WP to "lock up," which would make deactivating the plugin very difficult for non-technical users and those who don't have direct filesystem or database access.


Successfully deployed to following URLs:

* https://ui-hvmek0uio.now.sh
* https://ui-adorable-bornean-orang-utan.now.sh
* https://ui.bshell.now.sh
* https://ui-git-master.bshell.now.sh


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
audited 183 packages in 1.538s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/aegir/projects/cms/pr679
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov 0
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr679.ci.cms.va.gov/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Fri, 01 Nov 2019 17:24:32 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Fri, 01 Nov 2019 17:24:35 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** devshop.cms.va.gov
- **In:** 01:19


Probably don't want to move the BUILD_DATE arg before the expensive build step (below).  If the date arg changes, the subsequent steps will miss the Docker layer cache.  Nightly relies heavily on the caching to keep build time short.


Not working on `https://www.eurogamer.net/articles/2019-10-29-the-outer-worlds-reputation-factions-6050` I hover and the number never appears.


Successfully deployed to following URLs:

* https://41waller-kjoldlo8b.now.sh
* https://41waller.com
* https://*.41waller.com
* https://41waller.ahrjarrett.now.sh
* https://41waller-git-master.ahrjarrett.now.sh


Successfully deployed to following URLs:

* https://dotwatcher-upload-2urngav9o.now.sh
* https://dotwatcher-upload-sparkling-fur-seal.now.sh
* https://upload.dotwatcher.cc
* https://dotwatcher-upload.dotwatchers1.now.sh
* https://dotwatcher-upload-git-master.dotwatchers1.now.sh


Awesome trick, I did not know you could do that ^^


Great job, thanks for fixing the old ones as well.
I added a locator in the comment, it should help.


How dare you!


`lastToken=el;` should be out of `if` scope


Dear Poggit user,

This is an automatic message from Poggit-CI. Poggit-CI was triggered by this commit, but failed to create builds due to the following error:

```
Error parsing .poggit.yml: .poggit.yml should contain a YAML mapping
```

As a result, no builds could be created from this commit. More details might be available for repo admins at [the webhook delivery response log](https://github.com/Droll-PmmP/FFA/settings/hooks) — see the webhook starting with `https://poggit.pmmp.io/webhooks.gh.repo` and look for the delivery with ID `f3940cca-fccc-11e9-8d2b-112a6eb0477f`.

Shall you need any assistance, you may contact us on [on Discord](https://discord.gg/NgHf9jt), or more publicly, [on GitHub](https://github.com/poggit/support/issues). Commenting on this commit directly will **not** notify any Poggit staff.

Regards,
Poggit Bot (@poggit-bot)
The official Poggit automation account


ReadMe


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/www/cms/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Downloading https://github.com/Medium/phantomjs/releases/download/v2.1.1/phantomjs-2.1.1-linux-x86_64.tar.bz2
Saving to /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Receiving...

Received 22866K total.
Extracting tar contents (via spawned process)
Removing /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1572629187868/phantomjs-2.1.1-linux-x86_64 -> /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/www/cms/node_modules/core-js
> node scripts/postinstall || echo "ignore"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
> https://opencollective.com/core-js
> https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

added 134 packages from 190 contributors and audited 183 packages in 7.61s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/www/cms
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com 0
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Fri, 01 Nov 2019 17:26:32 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Fri, 01 Nov 2019 17:26:37 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** ip-10-247-34-165
- **In:** 02:07


bro Will You share This course with me
I also want to learn Core data
please


Done.


my email Id prati1907@gmail.com


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/www/cms/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Downloading https://github.com/Medium/phantomjs/releases/download/v2.1.1/phantomjs-2.1.1-linux-x86_64.tar.bz2
Saving to /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Receiving...

Received 22866K total.
Extracting tar contents (via spawned process)
Removing /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1572629235194/phantomjs-2.1.1-linux-x86_64 -> /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/www/cms/node_modules/core-js
> node scripts/postinstall || echo "ignore"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
> https://opencollective.com/core-js
> https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

added 134 packages from 190 contributors and audited 183 packages in 7.948s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/www/cms
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com 0
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Fri, 01 Nov 2019 17:27:19 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Fri, 01 Nov 2019 17:27:24 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** ip-10-247-96-210
- **In:** 01:59


The main project is to create an app that manages to associate 100 cryptocurrencies among the most quoted and known in the world. Through an algorithm it would be possible to know their value instantly, and therefore the exchange value would be immediately accessible. The crypto with the payment of a fee would be converted into fiat currency and through a payment system with QRCODE. With MASTERCARD channels. Obviously, the merchant would receive his currency quickly and instantaneously using the convectional or banking method.

Obviously the same app would also have its currency just the AZM Crypto, the initial value of this Token would be 1 $ with an available quantity of 50 Ml of coins. Upon payment of the Fee, 30% of the commission paid would be to consume the remaining value of the currency, creating its shortage and therefore the increasing value of the currency.

70% of the fee would go to the WALLET of the DAO that created the Token itself, the AZM token and still under development and would be supported on the ethereum blockchain. It is also foreseen the dissemination and the realization of a community that marries the same project and the currency by purchasing MINING packages connected to the Ethereum and BTC blockchain. At the start of D.A.O and ICO the value of each Token would be $ 1. In the time necessary for the creation of the definitive platform and the app connected to the platform we could start with the sale of the currency (AZM Crypto) by taking advantage of the companies of MINING in this way we would create an initial shortage of the crypto and we would have the possibility to pay the fees of the prof. off-work you have miners who would marry the project. The packages would be to be viewed and evaluated, but would start from a base accessible to all with a minimum cost of $ 50 to an initial maximum of $ 5000.

At the start of the new app the fees of the fees due to the D.A.O with the project participants could be divided into the following formula

example

30% coin shortage
25% to the participant who would be associated with the causal customer owner of the app and a crypto or AZM Crypto
45% of the fee to the D.A.O.

All would benefit from this and disclosure could also be made in the form of Marketing following agreements with mining companies or mining and machinery rental companies

the blockchain chosen for the use of the crypto would always be connected to Ethereum


Okay, seems count will not happen if `$generichide` is present.


Dear Poggit user,

This is an automatic message from Poggit-CI. Poggit-CI was triggered by this commit, but failed to create builds due to the following error:

```
Error parsing .poggit.yml: .poggit.yml should contain a YAML mapping
```

As a result, no builds could be created from this commit. More details might be available for repo admins at [the webhook delivery response log](https://github.com/Droll-PmmP/FFA/settings/hooks) — see the webhook starting with `https://poggit.pmmp.io/webhooks.gh.repo` and look for the delivery with ID `4411338a-fccd-11e9-8b42-9d614f45793b`.

Shall you need any assistance, you may contact us on [on Discord](https://discord.gg/NgHf9jt), or more publicly, [on GitHub](https://github.com/poggit/support/issues). Commenting on this commit directly will **not** notify any Poggit staff.

Regards,
Poggit Bot (@poggit-bot)
The official Poggit automation account


<html>
<h1> Esta es mi primera página con GitHub Pages </h1>
<p>¡Gracias GitHub!</p>
</html>


Successfully deployed to following URLs:

* https://ui-cixd7m4gx.now.sh
* https://ui-adorable-bornean-orang-utan.now.sh
* https://ui.bshell.now.sh
* https://ui-git-master.bshell.now.sh


merci coach


Successfully deployed to following URLs:

* https://codepici-blog-mf1oogllb.now.sh
* https://codepici-blog-gentle-lion.now.sh
* https://codepici-blog.juandelgado06.now.sh
* https://codepici-blog-git-master.juandelgado06.now.sh


Successfully deployed to following URLs:

* https://sapic-mgkejysuy.now.sh
* https://sapic-technical-african-clawed-frog.now.sh
* https://sapic.sapic.now.sh
* https://sapic-git-master.sapic.now.sh


editing this file


Finals are always CAPS_CASE


[It seems](https://issues.apache.org/jira/projects/MGPG?selectedItem=com.atlassian.jira.jira-projects-plugin:release-page) the next version planned is 1.7.


Why is build date set as an external parameter anyway? shouldn't it be calculated inside this docker image? We also talked and think we should calc the git rev inside as well instead of passing it in


## Joker
Este es mi villano favorito


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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:126:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/ABC_SMC.R:320:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/nltt_diff_exact_notnorm.R:25:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
nltt_diff_exact_notnorm <- function(
^
```
[R/nltt_diff_exact_notnorm.R:47:27:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L47) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_notnorm.R:54:25:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L54) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_notnorm.R:116:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L116) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:117:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L117) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:118:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L118) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:119:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L119) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:121:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L121) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:122:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L122) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:123:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L123) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:124:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltt_diff_exact_notnorm.R#L124) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L186) *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:274:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L274) *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:275:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L344) *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:345:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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
                               ^
```
[R/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style 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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style 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/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:29:16:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-nltt_diff_exact_notnorm.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:30:16:](https://github.com/Neves-P/nLTT/blob/f09f21f207201ba75f1f03e805043782b932bed2/tests/testthat/test-nltt_diff_exact_notnorm.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


I added `@@*$generichide,domain=eurogamer.net` and this works as expected: when no element are hidden, there is no badge, the `...` is removed.


# Notas

Entiendo por qué agregaste a Deadshot, lo necesitaremos


@diver libre office seems to depend on mdds 1.4. could you check whether mdds 1.4 can be kept available? Alternatively libre office has to be patched to support mdds 1.5


> when no element are hidden, there is no badge, the ... is removed.

https://i.gyazo.com/e7916949190a5f39aa1c40653b2914b7.png

Lots of site specific elements hidden and yet it happens.


FYI - Everything in my test branch has been merged into typed-screeps/master. Check it out. Test branch deleted.


Successfully deployed to following URLs:

* https://dotwatcher-upload-ped43jy3j.now.sh
* https://dotwatcher-upload-sparkling-fur-seal.now.sh
* https://upload.dotwatcher.cc
* https://dotwatcher-upload.dotwatchers1.now.sh
* https://dotwatcher-upload-git-master.dotwatchers1.now.sh


Successfully deployed to following URLs:

* https://sevesosite-gzowgjhjp.now.sh
* https://www.seveso.site
* https://sevesosite.efattal.now.sh
* https://sevesosite-git-master.efattal.now.sh


Successfully deployed to following URLs:

* https://baseweb-a8iytbac4.now.sh
* https://baseweb.uber-ui-platform.now.sh
* https://baseweb-git-master.uber-ui-platform.now.sh


Successfully deployed to following URLs:

* https://vue-functional-calendar-d7gndq8b3.now.sh
* https://vue-functional-calendar.now.sh
* https://vue-functional-calendar.manukminasyan.now.sh
* https://vue-functional-calendar-git-master.manukminasyan.now.sh


The changes to Uniqueness & BUG were bug fixes by lksudoku to the original SE code that I committed to Master without an option to disable like the chaining fix which was debatabale. I tested on a variety of puzzles and they resulted in all test cases having no change or reduction in rating as demonstrated.

This issue has been highlighted as well in previous discussion on the players forum


数据收集工作


Je ne sais pas si je dois d'abord faire la pull request avant de changer cela en "true". C'est pour cela que je l'ai laissé en "false".


What does the `CONFIG` option do? I am reading https://cmake.org/cmake/help/v3.12/command/find_package.html#command:find_package but I can't understand its purpose...


Successfully deployed to following URLs:

* https://aleatorios-7ay5bt644.now.sh
* https://aleatorios.tk
* https://aleatorios.now.sh
* https://aleatorios.fernandopinedo.now.sh
* https://aleatorios-git-master.fernandopinedo.now.sh


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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:126:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/ABC_SMC.R#L126) *style:* **functions should have cyclomatic complexity of less than 15, this has 42.**
```r
abc_smc_nltt <- function(tree,
^
```
[R/ABC_SMC.R:276:13:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/ABC_SMC.R:320:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/ABC_SMC.R#L320) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
mcmc_nltt <- function(phy, likelihood_function,
^
```
[R/get_average_nltt_matrix.R:14:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/get_average_nltt_matrix.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
get_average_nltt_matrix <- function(
^
```
[R/get_n_lineages.R:17:12:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/nltt_diff_exact_notnorm.R:25:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
nltt_diff_exact_notnorm <- function(
^
```
[R/nltt_diff_exact_notnorm.R:47:27:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L47) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_notnorm.R:54:25:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L54) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_notnorm.R:116:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L116) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:117:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L117) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:118:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L118) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:119:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L119) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:121:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L121) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:122:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L122) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:123:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L123) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_notnorm.R:124:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltt_diff_exact_notnorm.R#L124) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nLTTDiff.R:66:25:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L66) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nLTTDiff.R:186:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L186) *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:274:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L274) *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:275:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:283:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L283) *style:* **Lines should not be more than 80 characters.**
```r
#' @usage nLTTstat(tree1, tree2, distance_method = "abs", ignore_stem = TRUE, log_transform = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:344:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L344) *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:345:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L345) *style:* **Lines should not be more than 80 characters.**
```r
# @param    ignore_stem            logical    Should the phylogeny its stem be ignored?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nLTTDiff.R:346:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nLTTDiff.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
# @return                          scalar     normalized Lineage-Through-Time difference between tree1 & tree2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltts_plot.R:19:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/nltts_plot.R#L19) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
nltts_plot <- function(
^
```
[R/plot_nLTT.R:36:23:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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
                               ^
```
[R/stretch_nltt_matrix.R:22:1:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/R/stretch_nltt_matrix.R#L22) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
stretch_nltt_matrix <- function(
^
```
[tests/testthat/test-abc_smc_nltt.R:30:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-abc_smc_nltt.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-abc_smc_nltt.R:49:3:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-abc_smc_nltt.R#L49) *style:* **Variable and function name style 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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-abc_smc_nltt.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  A <- abc_smc_nltt(
  ^
```
[tests/testthat/test-get_average_nltt.R:10:5:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-mcmc_nltt.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-mcmc_nltt.R:31:3:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-mcmc_nltt.R#L31) *style:* **Variable and function name style 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/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-mcmc_nltt.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  LL_BD <- function(params, phy) {
  ^~~~~
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:29:16:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-nltt_diff_exact_notnorm.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_notnorm.R:30:16:](https://github.com/Neves-P/nLTT/blob/4230ca872dc5a253169cdb8a2af90a9fb4fabed6/tests/testthat/test-nltt_diff_exact_notnorm.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


Successfully deployed to following URLs:

* https://sevesosite-ffkcwigt3.now.sh
* https://www.seveso.site
* https://sevesosite.efattal.now.sh
* https://sevesosite-git-master.efattal.now.sh


Ok I get an scriptlet error in the console, it's trying to use an empty selector, as a result of `generichide`.


"In the **Logic App Designer**" is the correct version.


Successfully deployed to following URLs:

* https://flashcard-web-gfkmfwe99.now.sh
* https://flashcard-web.now.sh
* https://flashcard-web.ngocdh236.now.sh
* https://flashcard-web-git-master.ngocdh236.now.sh


TeamCity Bvcms / Build [Build 2561](https://builds.tpsdb.com/viewLog.html?buildId=9574&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 151 Build time: 00:29:29


TeamCity Bvcms / Build [Build 2562](https://builds.tpsdb.com/viewLog.html?buildId=9575&buildTypeId=Bvcms_Build) is now running


yes saved 300 gas by assigning to a local var. $0.00081 per transaction.