[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/get_norm_brts.R:22:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:47:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L47) *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:70:27:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L70) *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:77:25:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L77) *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:102:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L102) *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:107:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L107) *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:108:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L108) *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:175:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L175) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:176:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L176) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:177:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L177) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:178:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L178) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:180:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L180) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:181:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L181) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:182:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L182) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L183) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:222:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L222) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:223:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L223) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:224:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L224) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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_brts.R:40:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_brts.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    regexp = "branching times must be negative, for example -3 time units since the present"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:66:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_brts.R#L66) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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:95:16:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_extinct.R#L95) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:96:16:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


Successfully deployed to following URLs:

* https://expensetracker-484fexr7l.now.sh
* https://expensetracker.now.sh
* https://expensetracker.cerivitos.now.sh
* https://expensetracker-git-master.cerivitos.now.sh


Looping over width of matrix


Successfully deployed to following URLs:

* https://react-tabs-qcvffpfgj.now.sh
* https://react-tabs.now.sh
* https://react-tabs.alpugachev96.now.sh
* https://react-tabs-git-master.alpugachev96.now.sh


Hczncddg hydekrb


⁰⁰0


Uhfntjm tx7


Супер активная площадка для общения. Я так и думал. что здесь тихо сам с собою можно вести беседу. Люди. Ау.


Nice catch, I was using the param before "demux" is appended.


Successfully deployed to following URLs:

* https://underreacted-jeulhphu7.now.sh
* https://underreacted.now.sh
* https://underreacted.io
* https://www.underreacted.io
* https://underreacted.christianjuth.now.sh
* https://underreacted-git-master.christianjuth.now.sh


TeamCity MAS / MAS [Build 1.1.0.760](https://teamcity.nice.org.uk/viewLog.html?buildId=65150&buildTypeId=Mas_Mas) outcome was **FAILURE**
Summary: Artifacts size 0 B is 100% different from 3.7 MB in build #1.1.0.719-MAS-150-WeeklyEmailN (new); exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:09


Deployment failed with the following error:

~~~
ENOENT: no such file or directory, stat '/tmp/vgq25RQtXbUFB0PbYjnTjAde/repo/packages/cli/example/app-shell/node_modules'
~~~


Successfully deployed to following URLs:

* https://formik-docs-qqlkk1zi8.now.sh
* https://formik-docs.now.sh
* https://formik-docs.jared.now.sh
* https://formik-docs-git-master.jared.now.sh


# 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)|


TeamCity MAS / MAS [Build 1.1.0.761-MAS-150-WeeklyEmailN](https://teamcity.nice.org.uk/viewLog.html?buildId=65151&buildTypeId=Mas_Mas) outcome was **SUCCESS**
Summary: Tests passed: 43 Build time: 00:01:24


Is this correct @mfuntowicz?


@AdhamAbozaeid Is there any need to use this update with SDIO interface implementations?


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/8545](https://github.com/JuliaRegistries/General/pull/8545)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.3.1 -m "<description of version>" 312bdce199f28db53e733e6995cf340a30f4cb58
git push origin v0.3.1
```


![Difference between blocks](https://raw.githubusercontent.com/cybersiddhu/mca_sparky_invaders/3504e86ef5cb33329a7ccb0a433b2b4d1ffa684f/.makecode/blocksdiff.png)


Successfully deployed to following URLs:

* https://pozole-50debtmim.now.sh
* https://pozole.now.sh
* https://pozole.puregarlic.now.sh
* https://pozole-git-master.puregarlic.now.sh


Jupiter notebook for manipulation with a list


I'm wondering if our versions of the tokenizers/models should _always_ have a padding token @thomwolf @LysandreJik


cf. 5004d5af42c61c91d5df07aa139d37599ceb6215


This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/great-reply-granted-date-is-actually-the-date-of-the-post/139802/3


Successfully deployed to following URLs:

* https://danestves-mplbgp3lz.now.sh
* https://danestves.com
* https://danestves.danestves.now.sh
* https://danestves-git-master.danestves.now.sh


Fashion is what am into it


Successfully deployed to following URLs:

* https://chhengwoon-ceu6c58jz.now.sh
* https://chhengwoon.now.sh
* https://chhengwoon.jeffchheng.now.sh
* https://chhengwoon-git-master.jeffchheng.now.sh


yes


Successfully deployed to following URLs:

* https://pozole-bh3t493tt.now.sh
* https://pozole.now.sh
* https://pozole.puregarlic.now.sh
* https://pozole-git-master.puregarlic.now.sh


Successfully deployed to following URLs:

* https://uiuchack4impactorg-d5c3kxgmd.now.sh
* https://uiuchack4impactorg.hack4impact1.now.sh
* https://uiuchack4impactorg-git-master.hack4impact1.now.sh


Successfully deployed to following URLs:

* https://itsuportegithubio-pw71zprml.now.sh
* https://itsuportegithubio.itsuporte.now.sh
* https://itsuportegithubio-git-master.itsuporte.now.sh


Successfully deployed to following URLs:

* https://jobsite-6ju3v7uom.now.sh
* https://jobsite.now.sh
* https://jobsite.dylandamsma.now.sh
* https://jobsite-git-master.dylandamsma.now.sh


[R/create_next_gen_traits.R:22:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L22) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:23:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L23) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_offspring_pop)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:24:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L24) *warning:* **no visible global function definition for ‘testarg_not_this’**
```r
  testarg_not_this(nb_offspring_pop, Inf)
  ^~~~~~~~~~~~~~~~
```
[R/create_next_gen_traits.R:25:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L25) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(nb_offspring_pop, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/create_next_gen_traits.R:26:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L26) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(prob_mutation)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:27:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L27) *warning:* **no visible global function definition for ‘testarg_prop’**
```r
  testarg_prop(prob_mutation)
  ^~~~~~~~~~~~
```
[R/create_next_gen_traits.R:28:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L28) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(mutation_sd)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:29:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L29) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(mutation_sd)
  ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:48:5:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L48) *warning:* **no visible global function definition for ‘testarg_num’**
```r
    testarg_num(next_gen_traits)
    ^~~~~~~~~~~
```
[R/create_next_gen_traits.R:49:5:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/create_next_gen_traits.R#L49) *warning:* **no visible global function definition for ‘testarg_length’**
```r
    testarg_length(next_gen_traits, sum(nb_offspring_pop))
    ^~~~~~~~~~~~~~
```
[R/draw_nb_offspring.R:12:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/draw_nb_offspring.R#L12) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(fitness)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:13:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/draw_nb_offspring.R#L13) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(fitness)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:20:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/draw_nb_offspring.R#L20) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_offspring)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:21:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/draw_nb_offspring.R#L21) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(nb_offspring)
  ^~~~~~~~~~~
```
[R/draw_nb_offspring.R:22:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/draw_nb_offspring.R#L22) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(nb_offspring, length(fitness))
  ^~~~~~~~~~~~~~
```
[R/get_carr_cap.R:17:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L17) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_ind)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:18:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L18) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:19:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L19) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:20:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L20) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt) # is a nb of ind
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:21:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L21) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:22:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L22) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width) # is a variance
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:46:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L46) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap) # catch NAs, NaNs and NULL
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:47:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L47) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap)
  ^~~~~~~~~~~
```
[R/get_carr_cap.R:48:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_carr_cap.R#L48) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(carr_cap, length(trait_ind))
  ^~~~~~~~~~~~~~
```
[R/get_comp_coeff.R:22:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L22) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_ind)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:23:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L23) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(trait_ind, 1) # not vectorized!
  ^~~~~~~~~~~~~~
```
[R/get_comp_coeff.R:24:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L24) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:25:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L25) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:26:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L26) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width) # is a variance
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:37:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L37) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(coeffs, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/get_comp_coeff.R:49:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L49) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(coeffs)
  ^~~~~~~~~~~
```
[R/get_comp_coeff.R:50:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_comp_coeff.R#L50) *warning:* **no visible global function definition for ‘testarg_prop’**
```r
  testarg_prop(coeffs)
  ^~~~~~~~~~~~
```
[R/get_fitness.R:30:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L30) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/get_fitness.R:31:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L31) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(growth_rate)
  ^~~~~~~~~~~
```
[R/get_fitness.R:32:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L32) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(growth_rate)
  ^~~~~~~~~~~
```
[R/get_fitness.R:33:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L33) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:34:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L34) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:35:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L35) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/get_fitness.R:36:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L36) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/get_fitness.R:37:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L37) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/get_fitness.R:38:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L38) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:39:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L39) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width)
  ^~~~~~~~~~~
```
[R/get_fitness.R:61:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L61) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(fitness)
  ^~~~~~~~~~~
```
[R/get_fitness.R:62:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_fitness.R#L62) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(fitness, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/get_n_eff.R:12:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_n_eff.R#L12) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:13:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_n_eff.R#L13) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:14:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_n_eff.R#L14) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width) # is a variance
  ^~~~~~~~~~~
```
[R/get_n_eff.R:29:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_n_eff.R#L29) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(n_eff)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:30:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_n_eff.R#L30) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(n_eff)
  ^~~~~~~~~~~
```
[R/get_n_eff.R:31:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/get_n_eff.R#L31) *warning:* **no visible global function definition for ‘testarg_length’**
```r
  testarg_length(n_eff, length(traits_pop))
  ^~~~~~~~~~~~~~
```
[R/plot_generation_traits.R:14:23:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_generation_traits.R#L14) *style:* **Put spaces around all infix operators.**
```r
plot_generation_traits<- function(path_to_file,
                     ~^
```
[R/plot_generation_traits.R:17:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_generation_traits.R#L17) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(path_to_file)
  ^~~~~~~~~~~~
```
[R/plot_generation_traits.R:18:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_generation_traits.R#L18) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(generation)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:19:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_generation_traits.R#L19) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(generation)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:20:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_generation_traits.R#L20) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(binwidth)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:21:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_generation_traits.R#L21) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(binwidth)
  ^~~~~~~~~~~
```
[R/plot_generation_traits.R:36:20:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_generation_traits.R#L36) *warning:* **no visible global function definition for ‘%>%’**
```r
  gen_data <- data %>% dplyr::filter(data$t == generation)
                   ^~~
```
[R/plot_population_size.R:13:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_size.R#L13) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(path_to_file)
  ^~~~~~~~~~~~
```
[R/plot_population_size.R:23:5:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_size.R#L23) *style:* **Commented code should be removed.**
```r
  # xgrain <- max(data$t) / 100
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_population_size.R:30:1:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_size.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_hline(yintercept = 1000, linetype = "dashed", color = "grey60") +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:14:1:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_trait_evolution.R#L14) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_population_trait_evolution <- function(path_to_file,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:17:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_trait_evolution.R#L17) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(path_to_file)
  ^~~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:18:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_trait_evolution.R#L18) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(xgrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:19:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_trait_evolution.R#L19) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(xgrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:20:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_trait_evolution.R#L20) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(ygrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:21:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_trait_evolution.R#L21) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(ygrain)
  ^~~~~~~~~~~
```
[R/plot_population_trait_evolution.R:31:5:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/plot_population_trait_evolution.R#L31) *style:* **Commented code should be removed.**
```r
  # xgrain <- max(data$t) / 100
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/run_generation_step.R:14:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L14) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(traits_pop)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:15:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L15) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(growth_rate)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:16:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L16) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(growth_rate)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:17:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L17) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:18:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L18) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:19:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L19) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:20:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L20) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:21:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L21) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:22:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L22) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:23:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L23) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:24:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L24) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(prob_mutation)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:25:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L25) *warning:* **no visible global function definition for ‘testarg_prop’**
```r
  testarg_prop(prob_mutation)
  ^~~~~~~~~~~~
```
[R/run_generation_step.R:26:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L26) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(mutation_sd)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:27:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L27) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(mutation_sd)
  ^~~~~~~~~~~
```
[R/run_generation_step.R:39:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L39) *warning:* **no visible global function definition for ‘testarg_not_this’**
```r
  testarg_not_this(fitness_pop, Inf)
  ^~~~~~~~~~~~~~~~
```
[R/run_generation_step.R:42:23:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_generation_step.R#L42) *warning:* **no visible global function definition for ‘draw_nb_offspring’**
```r
  nb_offspring_pop <- draw_nb_offspring(fitness = fitness_pop)
                      ^~~~~~~~~~~~~~~~~
```
[R/run_simulation.R:41:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L41) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(init_pop)
  ^~~~~~~~~~~
```
[R/run_simulation.R:42:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L42) *warning:* **no visible global function definition for ‘testarg_char’**
```r
  testarg_char(output_path)
  ^~~~~~~~~~~~
```
[R/run_simulation.R:43:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L43) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(sampling_frequency)
  ^~~~~~~~~~~
```
[R/run_simulation.R:44:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L44) *warning:* **no visible global function definition for ‘testarg_int’**
```r
  testarg_int(sampling_frequency)
  ^~~~~~~~~~~
```
[R/run_simulation.R:45:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L45) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(seed)
  ^~~~~~~~~~~
```
[R/run_simulation.R:46:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L46) *warning:* **no visible global function definition for ‘testarg_int’**
```r
  testarg_int(seed)
  ^~~~~~~~~~~
```
[R/run_simulation.R:47:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L47) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_generations)
  ^~~~~~~~~~~
```
[R/run_simulation.R:48:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L48) *warning:* **no visible global function definition for ‘testarg_int’**
```r
  testarg_int(nb_generations)
  ^~~~~~~~~~~
```
[R/run_simulation.R:49:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L49) *warning:* **no visible global function definition for ‘testarg_not_this’**
```r
  testarg_not_this(nb_generations, c(0, Inf))
  ^~~~~~~~~~~~~~~~
```
[R/run_simulation.R:50:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L50) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(growth_rate)
  ^~~~~~~~~~~
```
[R/run_simulation.R:51:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L51) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(growth_rate)
  ^~~~~~~~~~~
```
[R/run_simulation.R:52:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L52) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(comp_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:53:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L53) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(comp_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:54:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L54) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(trait_opt)
  ^~~~~~~~~~~
```
[R/run_simulation.R:55:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L55) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_simulation.R:56:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L56) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_opt)
  ^~~~~~~~~~~
```
[R/run_simulation.R:57:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L57) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:58:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L58) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(carr_cap_width)
  ^~~~~~~~~~~
```
[R/run_simulation.R:59:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L59) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(prob_mutation)
  ^~~~~~~~~~~
```
[R/run_simulation.R:60:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L60) *warning:* **no visible global function definition for ‘testarg_prop’**
```r
  testarg_prop(prob_mutation)
  ^~~~~~~~~~~~
```
[R/run_simulation.R:61:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L61) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(mutation_sd)
  ^~~~~~~~~~~
```
[R/run_simulation.R:62:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/run_simulation.R#L62) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(mutation_sd)
  ^~~~~~~~~~~
```
[R/set_sampling_frequency.R:21:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/set_sampling_frequency.R#L21) *warning:* **no visible global function definition for ‘testarg_num’**
```r
  testarg_num(nb_generations)
  ^~~~~~~~~~~
```
[R/set_sampling_frequency.R:22:3:](https://github.com/TheoPannetier/comrad/blob/6d1314fe68e4341ba740c0013efcef3198bfadbd/R/set_sampling_frequency.R#L22) *warning:* **no visible global function definition for ‘testarg_pos’**
```r
  testarg_pos(nb_generations)
  ^~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://pblog-d7audinm0.now.sh
* https://pblog.now.sh
* https://pblog.argumentativeyouth.now.sh
* https://pblog-git-master.argumentativeyouth.now.sh


PascalCase


Successfully deployed to following URLs:

* https://ghost-og-6j7ei1fdu.now.sh
* https://ghost-og.now.sh
* https://ghost-og.m1guelpf.now.sh
* https://ghost-og-git-master.m1guelpf.now.sh


Successfully deployed to following URLs:

* https://sanblas-nrowhjxxb.now.sh
* https://sanbl.as
* https://www.sanbl.as
* https://sanblas.nathanielhill.now.sh
* https://sanblas-git-master.nathanielhill.now.sh


Successfully deployed to following URLs:

* https://pingpong-airforce-5joxmm297.now.sh
* https://www.pingpong.airforce
* https://pingpong.airforce
* https://pingpong-airforce.jonathan-wbn.now.sh
* https://pingpong-airforce-git-master.jonathan-wbn.now.sh


# 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)|


Thank you for noticing this.
It should be [fixed](https://github.com/macports/macports-ports/commit/30b61019f425be0550b70efa0a60b0f0d457091d#diff-32ee8876141e9bcf8fec046e619b40a7).


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

Messages:\n
 * 20 tests had: BND diffs.

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-54.39%25-red.png)


The intention would not be to narrow the API. After all, the constructor would still be directly accessible for special use cases. The main intention was to make the common use cases really simple, while not preventing any other use case. The whole BCM support is already on a slightly higher level with the enums for flags, slightly narrowing the API (which is not bad, BCM is a higher level protocol I'd say).

I'm generally a friend of compile-time guarantees and builders done this way remove some of the guarantees. And with this "confusion" around which ival to use with which opcode and what not, I actually see this problem coming up.


Successfully deployed to following URLs:

* https://bu-4zs2g6imf.now.sh
* https://bukinoshita.io
* https://bu.bukinoshita.now.sh
* https://bu-git-canary.bukinoshita.now.sh


Successfully deployed to following URLs:

* https://wanders-69bwiog0l.now.sh
* https://wanders.now.sh
* https://vadrouilles.co
* https://wanders.ys1.now.sh
* https://wanders-git-master.ys1.now.sh


Successfully deployed to following URLs:

* https://react-awesome-reveal-jjrf34y04.now.sh
* https://react-awesome-reveal.morello.dev
* https://react-awesome-reveal.dennismorello.now.sh
* https://react-awesome-reveal-git-master.dennismorello.now.sh


Такие условия лучше в одну строку записывать:
```
months[2] = 29 if ((year % 4 == 0) && (year % 100 != 0)) || (year % 400 == 0)
```


Successfully deployed to following URLs:

* https://pretty-json-1tmho4w7e.now.sh
* https://pretty-json.now.sh
* https://pretty-json.kikobeats.now.sh
* https://pretty-json-git-master.kikobeats.now.sh


This is in the documentation section of sample kamailio.cfg, line 82. The
configuration section itself seems correct.

On Mon, 27 Jan 2020 at 20:07, George Diamantopoulos <
notifications@github.com> wrote:

> Is there such a thing as route[JSONRPC]? Shouldn't this be
> event_route[xhttp:request] instead?
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/kamailio/kamailio/commit/9b97d01e90963851eaa698b2ab1e04fe43822b98?email_source=notifications&email_token=ABO7UZKE5LXUAJ53BOPRVSLQ74PFDA5CNFSM4KMFVID2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBDIWND#commitcomment-36985251>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ABO7UZI56Z6ZXPILSEHKERDQ74PFDANCNFSM4KMFVIDQ>
> .
> _______________________________________________
> Kamailio (SER) - Development Mailing List
> sr-dev@lists.kamailio.org
> https://lists.kamailio.org/cgi-bin/mailman/listinfo/sr-dev
>


Successfully deployed to following URLs:

* https://boabot-7qwb7cetq.now.sh
* https://boabot-hong.now.sh


Successfully deployed to following URLs:

* https://nateradebaughreact-datetime-p74d4i77x.now.sh
* https://nateradebaugh-datetime.now.sh
* https://react-datetime.now.sh
* https://react-datetime.naterad.com
* https://nateradebaugh-react-datetime.nateradebaugh.now.sh
* https://nateradebaugh-react-datetime-git-master.nateradebaugh.now.sh


Successfully deployed to following URLs:

* https://okay-jxsw9as0y.now.sh
* https://okay-beta-lake.now.sh
* https://okscrapbooker.design
* https://okay.iammatthias.now.sh
* https://okay-git-master.iammatthias.now.sh


TeamCity Bvcms / Build [Build 3460](https://builds.tpsdb.com/viewLog.html?buildId=11690&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 225 Build time: 00:27:14


@Acentelles Error is still left in the code?


170926542_Issue7681 (mitchute) - Win64-Windows-10-VisualStudio-16: OK (2617 of 2617 tests passed, 0 test warnings)

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


Successfully deployed to following URLs:

* https://interface-6utqom6yl.now.sh
* https://melon.avantgarde.finance
* https://interface.avantgarde-finance.now.sh
* https://interface-git-master.avantgarde-finance.now.sh


Successfully deployed to following URLs:

* https://nateradebaughreact-datetime-69yaafags.now.sh
* https://nateradebaugh-datetime.now.sh
* https://react-datetime.now.sh
* https://react-datetime.naterad.com
* https://nateradebaugh-react-datetime.nateradebaugh.now.sh
* https://nateradebaugh-react-datetime-git-master.nateradebaugh.now.sh


Successfully deployed to following URLs:

* https://ember-pdf-gifiiv3g6.now.sh
* https://ember-pdf.now.sh
* https://ember-pdf.emberhub.now.sh
* https://ember-pdf-git-master.emberhub.now.sh


Removing this from OSS


170926542_Issue7681 (mitchute) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (677 of 678 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 677
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.35%25-green.png)


No need to elif after a return


Bunch of line-too-long changes


170926542_Issue7681 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1270 of 1270 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.71%25-green.png)


Successfully deployed to following URLs:

* https://blogstate-5xxw8puwk.now.sh
* https://blogstate.roshnet.now.sh
* https://blogstate-git-master.roshnet.now.sh


Protected access... but I just ignored these because it was easier and its just a test.


@nathanhleung


Successfully deployed to following URLs:

* https://blogstate-a9m65ykae.now.sh
* https://blogstate.roshnet.now.sh
* https://blogstate-git-master.roshnet.now.sh


Successfully deployed to following URLs:

* https://ose-c6ousrk51.now.sh
* https://ose.now.sh
* https://ose.phenomen.now.sh
* https://ose-git-master.phenomen.now.sh


Successfully deployed to following URLs:

* https://contentful-xpm7w9eau.now.sh
* https://contentful-eight.now.sh
* https://contentful.one-aalam.now.sh
* https://contentful-git-master.one-aalam.now.sh


Successfully deployed to following URLs:

* https://biblidev-8kqlfvsdg.now.sh
* https://biblidev.fr
* https://biblidev.icez.now.sh
* https://biblidev-git-master.icez.now.sh


Successfully deployed to following URLs:

* https://the-localhost-blog-jga9g73c8.now.sh
* https://the-localhost-blog.now.sh
* https://thelocalhost.blog
* https://www.thelocalhost.blog
* https://the-localhost-blog.spences10.now.sh
* https://the-localhost-blog-git-master.spences10.now.sh


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/get_n_lineages.R#L17) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    return(1:length(phylogeny$tip.label))
           ^
```
[R/get_norm_brts.R:22:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:47:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L47) *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:70:27:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L70) *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:77:25:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L77) *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:102:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L102) *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:107:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L107) *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:108:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L108) *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:175:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L175) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:176:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L176) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:177:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L177) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:178:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L178) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:180:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L180) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:181:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L181) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:182:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L182) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:5:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L183) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:222:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L222) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:223:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L223) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:224:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/R/nltt_diff_exact_extinct.R#L224) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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_brts.R:40:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_brts.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    regexp = "branching times must be negative, for example -3 time units since the present"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-nltt_diff_exact_brts.R:66:1:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_brts.R#L66) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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/13da68d1b53eb143403d1a1d35fdf2d54881daa9/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:95:16:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_extinct.R#L95) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:96:16:](https://github.com/Neves-P/nLTT/blob/13da68d1b53eb143403d1a1d35fdf2d54881daa9/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


_ sender: UIButton


Probably a typo in `<data>`?


Successfully deployed to following URLs:

* https://sergeyfilimonovcom-7a83114so.now.sh
* https://sergeyfilimonov.com
* https://sergeyfilimonovcom.sfilimonov.now.sh
* https://sergeyfilimonovcom-git-master.sfilimonov.now.sh


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


Deployment failed with the following error:

~~~
Could not find a secret by name "auth0_client_secret"
~~~


See here: https://en.wikipedia.org/wiki/Variadic_macro
Let's use something like `dbgprintf`


travis is lately not quite happy


Not used?


Thanks.
Looks pretty now.


Successfully deployed to following URLs:

* https://ember-pdf-mp5i6dbnf.now.sh
* https://ember-pdf.now.sh
* https://ember-pdf.emberhub.now.sh
* https://ember-pdf-git-master.emberhub.now.sh


@JuliaRegistrator register


Hi @jewertow thanks for this PR and the explanation! I decided to change this assertion to an easier version as under the hood nanoseconds are compared and it will be very hard to have the same values in this kind of test. However we will back to it if it will be a problem.


Registration pull request created: [JuliaRegistries/General/8515](https://github.com/JuliaRegistries/General/pull/8515)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.46.0 -m "<description of version>" 308df182dc0057157e7af8687681a21a968a3fa5
git push origin v0.46.0
```


So this change would mean we can't deprecate in advance. Any reason we can't accept true/date for deprecation, same as the RFC?


Ugh. Control over colors/flags still not available to modders. `create_message_window` not updated, which means it's still limited to 1 line - pointless to use in practice. Hell, why it's even separated function? Can we expect `dialog_box_top`, `dialog_box_right`, etc. next to support other flags (and all combinations of them)?


might be a good idea to indicate why a policy change is made?


all tests pass:
success: https://travis-ci.org/stellar/stellar-core/builds/642684120?utm_source=github_status&utm_medium=notification


array1s-experiment (jasondegraw) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (677 of 678 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 677
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.35%25-yellow.png)


Successfully deployed to following URLs:

* https://tessitura-books-cs3cmxk5k.now.sh
* https://tessitura-books.now.sh
* https://tessitura-books.devdavi.now.sh
* https://tessitura-books-git-master.devdavi.now.sh


npm i now


Successfully deployed to following URLs:

* https://workshop-cards-bn22a8nr9.now.sh
* https://workshop-cards.now.sh
* https://workshop-cards.hack-club.now.sh
* https://workshop-cards-git-master.hack-club.now.sh


Successfully deployed to following URLs:

* https://portal-g6sdb1c6w.now.sh
* https://antive.tech
* https://www.antive.tech
* https://portal.antive.now.sh
* https://portal-git-master.antive.now.sh


Failed to assign a domain to your deployment due to the following error:

~~~
The chosen alias "portfolio.now.sh" is already in use.
~~~

([Learn more](https://zeit.co/dannydi12/its-me-daniel/ji2kc4h9r) or [visit](https://its-me-daniel-ji2kc4h9r.now.sh) the non-aliased deployment)


Successfully deployed to following URLs:

* https://tessitura-books-popvq3wq8.now.sh
* https://tessitura-books.now.sh
* https://tessitura-books.devdavi.now.sh
* https://tessitura-books-git-master.devdavi.now.sh


Oops. I mixed up the submodule name with the class name.


fast-forwarding master to auto = 50ab8ee5


![Difference between blocks](https://raw.githubusercontent.com/cybersiddhu/mca_sparky_invaders/bdd9dca3e631d106b0f9f39cac8adc8cb74823ac/.makecode/blocksdiff.png)