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[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:77:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L77) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:78:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L78) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


cc @mfuntowicz @VictorSanh


[Robin Ward posted](https://review.discourse.org/t/refactor-restoring-of-backups-and-migration-of-uploads-to-s3/8269/4):

This is a huge improvement. Thanks :clap:


EIR_AWHP (Myoldmopar) - Win64-Windows-10-VisualStudio-16: Tests Failed (740 of 2612 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 1
 * Failed: 673

regression Test Summary
 * Passed: 670
 * Failed: 2

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-28.33%25-red.png)


y


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* https://website-git-master.dankestkush.now.sh


Removal of barrelstrength\sproutfields\fields\Phone::getCountries() isn't noted in release notes, which caused some problems for us.


When would both SidecarsReady and ContainersWaiting be true ?


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[Copy of facebook-jonathanbeacham9277 (4).zip](https://github.com/desktop/desktop/files/4066032/Copy.of.facebook-jonathanbeacham9277.4.zip)


Successfully deployed to following URLs:

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idx usually means the index to the slice.
Probably rename the variable.


:point_right: click here to view a full list of the events :point_left:


Yes, I'm aware of this function, but I didn't want to change all the existing functionality at once. There's still room for improvement and with all the specs it's a lot easier to change things. I'll put it on my list of things to change.


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.env file committed in error :(
SendGrid API key no longer active on SendGrid account


added


You probably don't need this any more.


Deployment failed with the following error:

~~~
Could not find a secret by name "react_app_api_url"
~~~


.env file committed in error.
Sendgrid API key now deactivated.


We'd have to invent some assembly syntax, which we could, but I just stuck to what's in the spec.


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- imprimer les écritures extraites,
- éditer/modifier/une écriture
- Clôturer, lettrer ou délettrer une écriture...


You can perform hard delete by uncommenting 100th  line VesselService


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* https://james-grantham-git-master.jamesrgrantham.now.sh


Une fois avoir sélectionné l'exercice d'import, le journal et les informations de format de votre fichier CSV,

Note MD : peut-être préciser la structure que doit avoir le fichier CSV (champs)


I have removed it, thanks!


vous serez ammené à associer les champs des écritures aux colonnes de votre document (la première ligne de votre document doit décrire la nature de chaque colonne).


@penguindark first of all let me apologize for the harsh jump in - I should have had first read your PR description.

To put it short I absolutely agree with all your goals and I'm glad there is even the todo/improvement list.

I'd though still advocate for claiming a full POSIX ERE compatibility in the documentation. I'm fully aware of the issue `Regex doesn't have a real standard` as there is really no one-rule-them-all standard, but **there are** several well defined and widely used standards - you mentioned some of them and I'm convinced POSIX ERE is the most proliferated one. It seems though POSIX EREs are more or less supported already, but I didn't test it properly and didn't analyze your code.

POSIX EREs support things like `^[[]+[]]{1}([^]]{,5}|([^[])){9999,}$` (I didn't spot in your tests e.g. the set complement nor matching of `[` or `]` characters which are exceptions in POSIX ERE rules as at least `]` must be the first character in the set). POSIX EREs also define some classes to be matched either like `[:class:]+` or nested in a set `[a-z[:class:]]` and stuff with `[..]` etc. POSIX EREs are also always greedy (there is no lookahead/lookbehind, but because it essentially just reverses the greediness for the specified subregex, it doesn't conflict with POSIX ERE semantics and can be implemented alongside pretty much as you implemented `\w` etc.). Lastly POSIX EREs support non-English languages (e.g. collation digraphs/trigraphs/... in certain languages must be treated as one character or e.g. `[[=e=]]` matches set of characters of the class of `e` characters which means for Czech `eéě`, for French `eéèê`, but for English just `e`), but if this won't be supported, it's fine, but has to be documented next to the words, that this regex engine supports POSIX EREs :wink:. See [POSIX ERE grammar](https://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html#tag_09_04 ) in the newest POSIX standard (it's actually quite short and readable, so no worries :wink:).

With backtracking I meant primarily NFA approach, but I'm totally fine with either approach after seeing all your goals :wink:.

Thanks a lot for your contribution and keep the good work!


[core] fix(EditableText): allow setting value to null in controlled mode (#3924)

Previews: documentation | landing | table


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:77:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L77) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:78:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L78) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


WARNING: [Autofill] Missing `autofillHints` attribute
 Specify an `autofillHints` attribute when targeting SDK version 26 or higher or explicitly specify that the view is not important for autofill. Your app can help an autofill service classify the data correctly by providing the meaning of each view that could be autofillable, such as views representing usernames, passwords, credit card fields, email addresses, etc.

The hints can have any value, but it is recommended to use predefined values like 'username' for a username or 'creditCardNumber' for a credit card number. For a list of all predefined autofill hint constants, see the `AUTOFILL_HINT_` constants in the `View` reference at https://developer.android.com/reference/android/view/View.html.

You can mark a view unimportant for autofill by specifying an `importantForAutofill` attribute on that view or a parent view. See https://developer.android.com/reference/android/view/View.html#setImportantForAutofill(int).


Successfully deployed to following URLs:

* https://booktracker-ehdinrxch.now.sh
* https://booktracker.now.sh
* https://booktracker.vassbence.dev
* https://booktracker.vassbence.now.sh
* https://booktracker-git-master.vassbence.now.sh


"宝宝",


```julia
julia> Bool(2)
ERROR: InexactError: Bool(2)
Stacktrace:
 [1] Bool(::Int64) at ./float.jl:73
 [2] top-level scope at REPL[19]:1
```


Successfully deployed to following URLs:

* https://beam-invoice-n36hca5fa.now.sh
* https://beam-invoice.now.sh
* https://beam-invoice.clementdlc.now.sh
* https://beam-invoice-git-master.clementdlc.now.sh


Successfully deployed to following URLs:

* https://firstmeanseverythingcom-iao0oxkrt.now.sh
* https://firstmeanseverything.com
* https://firstmeanseverythingcom.firstmeanseverything.now.sh
* https://firstmeanseverythingcom-git-master.firstmeanseverything.now.sh


[inst/tests/testthat/test_combinatie_voorwaarden.R:5:1:](https://github.com/inbo/LSVI/blob/5ab4cb15230b0052b97487a2ac4661d90a8d19c2/inst/tests/testthat/test_combinatie_voorwaarden.R#L5) *style:* **Variable and function name style should be camelCase, CamelCase or snake_case.**
```r
Data_habitat <-
^~~~~~~~~~~~
```
[inst/tests/testthat/test_combinatie_voorwaarden.R:7:1:](https://github.com/inbo/LSVI/blob/5ab4cb15230b0052b97487a2ac4661d90a8d19c2/inst/tests/testthat/test_combinatie_voorwaarden.R#L7) *style:* **Variable and function name style should be camelCase, CamelCase or snake_case.**
```r
Data_voorwaarden <-
^~~~~~~~~~~~~~~~
```


Deployment failed with the following error:

~~~
Could not find a secret by name "gatsby_lrqst_url"
~~~


ya veo ... (y por qué femenino :))


Tweeted:

- https://twitter.com/SnakesThree/status/1216704127792766976


Successfully deployed to following URLs:

* https://crawl-7jddxs6up.now.sh
* https://crawl.now.sh
* https://crawl.benarthurstuart.now.sh
* https://crawl-git-master.benarthurstuart.now.sh


This `&&` implies that {columns} has to succeed. I wouldn't say so. I'd rather put a semicolon there.


EIR_AWHP (mitchute) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: Build Failed

Failures:\n

integration Test Summary
 * Passed: 1
 * Failed: 675

regression Test Summary
 * Passed: 689
 * Failed: 2

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-28.65%25-red.png)


краще використовувати background-image в с css
```background-image: ### image-set(url('img/1.jpg') 1x, url('img/1x2.jpg) 2x);``` etc для srcset


en case de que quede abierto o sea liquidacion se deberia llamar este bloque tambien?


<!DOCTYPE html>

    <meta charset="utf-8" />
    <link rel="stylesheet" href="style.css" />

    <title>Assignment 1: GitHub practice</title>

About me

 My name is Chatlada Panya. My Student ID is 622115006. My friends calls me Liew. I'm 19 years old now and currently study in
                First year at Faculty of Bachelor of Science Program in Software Engineering (International Program). The reasons I choose to study
                software engineering is The ability of a programmer to make a machine work as per his desire just by writing a few commands. It was that 'absolute power' and the 'simplicity' of the process which got me hooked. The software engineer title was offered by the company who hired me. I really wouldnot have mind if they called it anything else and Problem solving keeps me motivated. Thinking of multiple solutions to various problems keeps me interested


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Successfully deployed to following URLs:

* https://quotes-ae9sh0nn0.now.sh
* https://quotes-tau-ochre.now.sh
* https://quotes.qdeck.uk
* https://quotes.quarterdeck.now.sh
* https://quotes-git-master.quarterdeck.now.sh


I don't think this CS-specific change could have affected that 3m test. More likely, it's a bug in the the tested `read-bytes-evt` function or maybe a problem with the test.


$this->columnsSql = implode (", ",$file->fgetcsv(","));
} // end of loadColumns method

public function loadValuse($fileCsvPath): string
{
        $file = new \SplFileObject($fileCsvPath);
        $file->setFlags(\SplFileObject::READ_CSV);


Memindahkan file style.css ke repo public


Successfully deployed to following URLs:

* https://diecknet-blog-mkl82uvr6.now.sh
* https://diecknet.de
* https://diecknet-blog.diecknet.now.sh
* https://diecknet-blog-git-master.diecknet.now.sh


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/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_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L29) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:30:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:77:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L77) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:78:16:](https://github.com/Neves-P/nLTT/blob/839a7da6e6f00a4bcf38dd506daec880ac8f22cc/tests/testthat/test-nltt_diff_exact_extinct.R#L78) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


Successfully deployed to following URLs:

* https://danestves-5drk30b99.now.sh
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* https://danestves-git-master.danestves.now.sh


Successfully deployed to following URLs:

* https://blowltd-challenge-8fqludmyc.now.sh
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It's more optimal, your suggestion generates an intermediate string.


Successfully deployed to following URLs:

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Issue7187 (dareumnam) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1258 of 1259 tests passed, 0 test warnings)

Failures:\n

EnergyPlusFixture Test Summary
 * Passed: 819
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.92%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.59%25-green.png)


Successfully deployed to following URLs:

* https://statickit-site-6oak2oikb.now.sh
* https://statickit.com
* https://statickit-site.unstacked.now.sh
* https://statickit-site-git-master.unstacked.now.sh


Please cache this in a local var and use it below


Successfully deployed to following URLs:

* https://blowltd-challenge-afph91nxy.now.sh
* https://blowltd-challenge.now.sh
* https://blowltd-challenge.ricardojrm.now.sh
* https://blowltd-challenge-git-master.ricardojrm.now.sh


Successfully deployed to following URLs:

* https://testagaintracker-qge7qg8xy.now.sh
* https://testagaintracker.now.sh
* https://testagaintracker.blackaswan22.now.sh
* https://testagaintracker-git-master.blackaswan22.now.sh


Successfully deployed to following URLs:

* https://testagaintracker-ndx930m5m.now.sh
* https://testagaintracker.now.sh
* https://testagaintracker.blackaswan22.now.sh
* https://testagaintracker-git-master.blackaswan22.now.sh


Might be nice to verify that it hasn't been sent before you send your KEYCODE_ENTER.


too many spaces


❌ [Build was (probably) aborted](https://jenkins.internalx.com/job/macios/job/master/1096/display/redirect)

🔥 [Jenkins job](https://jenkins.internalx.com/job/macios/job/master/1096/display/redirect) (on internal Jenkins) failed in stage(s) 'Running XM tests on '10.15', Running XM tests on '10.15'' 🔥

✅ [Build succeeded](https://jenkins.internalx.com/job/macios/job/master/1096//console)
✅ Packages:
* [xamarin.ios-13.15.1.62.pkg (Not notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/package/xamarin.ios-13.15.1.62.pkg)
* [xamarin.mac-6.15.1.62.pkg (Not notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/package/xamarin.mac-6.15.1.62.pkg)
* [xamarin.ios-13.15.1.62.pkg (Notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/package/notarized/xamarin.ios-13.15.1.62.pkg)
* [xamarin.mac-6.15.1.62.pkg (Notarized)](https://bosstoragemirror.blob.core.windows.net/wrench/jenkins/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/package/notarized/xamarin.mac-6.15.1.62.pkg)

✅ [API Diff (from stable)](http://xamarin-storage/jenkins/xamarin-macios/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/jenkins-results/api-diff/index.html)
✅ [API Diff (from PR only)](http://xamarin-storage/jenkins/xamarin-macios/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/jenkins-results/apicomparison/api-diff.html) (no change)
✅ [Generator Diff](http://xamarin-storage/jenkins/xamarin-macios/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/jenkins-results/generator-diff/index.html) (no change)
🔥 [Xamarin.Mac tests on 10.15 failed: Xamarin.Mac tests on macOS 10.15 failed (apitest)](https://jenkins.internalx.com/job/macios/job/master/1096/display/redirect) 🔥
🔥 [Test run failed](http://xamarin-storage/jenkins/xamarin-macios/master/d84a4f23ff8fe7547da4338a0f751aefde18ce4c/1096/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>1 tests failed, 177 tests passed.</summary>

## Failed tests

 * monotouch-test/watchOS 32-bits - simulator/Debug: Crashed
</details>


#this was from notepad, looks like I will need to modify the file once I get onto my own computer


Successfully deployed to following URLs:

* https://mak-5rrrra2hp.now.sh
* https://mak-umber-two.now.sh
* https://mak.nursultansharsheev.now.sh
* https://mak-git-master.nursultansharsheev.now.sh


Successfully deployed to following URLs:

* https://haywire-kf4wwomqn.now.sh
* https://haywire.now.sh
* https://haywire.dagwoodsandwich56.now.sh
* https://haywire-git-master.dagwoodsandwich56.now.sh


Successfully deployed to following URLs:

* https://cielmusic-frontend-rdaei6f22.now.sh
* https://cielmusic.now.sh
* https://cielmusic-frontend.splitz.now.sh
* https://cielmusic-frontend-git-master.splitz.now.sh


自动构建 [auto-dragalia-200d2cba.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/841/artifacts/0/home/circleci/project/artifacts/auto-dragalia-200d2cba.zip)


Successfully deployed to following URLs:

* https://excalidraw-mwj6lih6c.now.sh
* https://excalidraw.now.sh
* https://excalidraw.vjeux.now.sh
* https://excalidraw-git-master.vjeux.now.sh


自动构建 [auto-dragalia-a852c92b.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/843/artifacts/0/home/circleci/project/artifacts/auto-dragalia-a852c92b.zip)


Deploy preview for _website_ ready!

Built with commit 3c9f7df5094ea1f05a167fafc4f79a2018f11a93

https://zeit-now-deployment-i0x1kdoew.now.sh


Successfully deployed to following URLs:

* https://haywire-htyn3cg1g.now.sh
* https://haywire.now.sh
* https://haywire.dagwoodsandwich56.now.sh
* https://haywire-git-master.dagwoodsandwich56.now.sh


Remove which one? The bike one?

Em qua, 15 de jan de 2020 09:32, Pierre Kancir <notifications@github.com>
escreveu:

> I would remove that one . Last year, there were a lot of submission
> without content on this subject .
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/ArduPilot/ardupilot_wiki/commit/eea5f92515d108b7601773dbdfa2fca5694a4fbd?email_source=notifications&email_token=AA4X5PUJAEDLVPCUJNXVH23Q53657A5CNFSM4KHBK4WKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBDDKOV#commitcomment-36809173>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AA4X5PTMWLK7L6B5TN6D5KTQ53657ANCNFSM4KHBK4WA>
> .
>


> Who play cards like Gson?
> Who break hearts like Gson?
> Who's much more than the sum of their parts like Gson?


Successfully deployed to following URLs:

* https://merchant-center-application-kit-o7c2ifiwf.now.sh
* https://mc-custom-applications.now.sh
* https://merchant-center-application-kit.commercetools.now.sh
* https://merchant-center-application-kit-git-master.commercetools.now.sh


Deploy preview for _website_ ready!

Built with commit d82794df150157d8f444616646c6c121f4de4dfb

https://zeit-now-deployment-pjogxa58y.now.sh


> Breaks some photos, e.g. https://s4.reutersmedia.net/resources/r/?m=02&d=20200110&t=2&i=1474699281&w=780&fh=&fw=&ll=&pl=&sq=&r=2020-01-10T153504Z_13778_MRPRC219E9IA30G_RTRMADP_0_AUSTRALIA-BUSHFIRES on https://de.reuters.com/news/picture/photos-of-the-week-idUKRTS2XVJF

@thohh removed in 48ef3bf
Thanks for reporting!


For information, I tried to compile with this morning's version on a slackware 14.0.

I use :
```
cmake . -DCHANNEL_URBDRC_CLIENT=ON
make

```
I have :

> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:74:2: error: unknown type name 'libusb_hotplug_callback_handle'
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c: In function 'udevman_cancel_all_device_requests':
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:296:11: warning: unused variable 'udevman' [-Wunused-variable]
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c: In function 'udevman_free':
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:508:2: warning: implicit declaration of function 'libusb_hotplug_deregister_callback' [-Wimplicit-function-declaration]
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c: At top level:
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:526:29: error: unknown type name 'libusb_hotplug_event'
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c: In function 'libusb_freerdp_urbdrc_client_subsystem_entry':
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:800:2: warning: implicit declaration of function 'libusb_hotplug_register_callback' [-Wimplicit-function-declaration]
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:801:24: error: 'LIBUSB_HOTPLUG_EVENT_DEVICE_ARRIVED' undeclared (first use in this function)
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:801:24: note: each undeclared identifier is reported only once for each function it appears in
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:801:62: error: 'LIBUSB_HOTPLUG_EVENT_DEVICE_LEFT' undeclared (first use in this function)
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:802:9: error: 'LIBUSB_HOTPLUG_MATCH_ANY' undeclared (first use in this function)
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:803:32: error: 'hotplug_callback' undeclared (first use in this function)
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c: At top level:
> /root/FreeRDP-master/channels/urbdrc/client/libusb/libusb_udevman.c:294:13: warning: 'udevman_cancel_all_device_requests' defined but not used [-Wunused-function]
> make[2]: *** [channels/urbdrc/client/libusb/CMakeFiles/urbdrc-client-libusb.dir/libusb_udevman.c.o] Error 1
> make[1]: *** [channels/urbdrc/client/libusb/CMakeFiles/urbdrc-client-libusb.dir/all] Error 2