[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)
               ^
```


This all depends on how we handle changing the state but if this edge case does happen, we know it is because the leader has not played yet and needs to choose a card. If we go this path, we might want to use the suggestion Michael made where we mark the winner from the last state with a placeholder 31-34 until after they have made their decision, at which point we assign their past card properly and set the card they chose.


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Неправильная формула
> Год високосный, если он делится на четыре без остатка, но если он делится на 100 без остатка, это не високосный год. Однако, если он делится без остатка на 400, это високосный год.


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I love hearing I'm right, thanks @stevenharman!


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 0153502e1f990ffd3c12542ec982be0bd8834b9c.

You can try again later or [upgrade](https://zeit.co/teams/tribalteam/settings/plan) your plan.


You could just use 'cors' module it's easier and more efficient.


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RASPUNDE LA TELEFON PROSTULE


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Sorry, I was testing on an old version, it works as expected.


TeamCity MAS / MAS [Build 1.1.0.718](https://teamcity.nice.org.uk/viewLog.html?buildId=64953&buildTypeId=Mas_Mas) outcome was **FAILURE**
Summary: Artifacts size 0 B is 100% different from 3.7 MB in build #1.1.0.713-MAS-150-WeeklyEmailN (new); exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:13


#3 Something here about how this meets an ethical objective.


@ambergupta954 Bro please change this to proper class name.


@ambergupta954 Please don’t call the class names like section and container


based on [Image Classification using Python and Scikit-learn by Gogul09](https://gogul.dev/software/image-classification-python)


#3 Testing if a chunk of code can have a comment that references an issue.


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Yes and you can't do it both


Yes, thanks! This has already been fixed here 4b9887b406badb4985121f639f77793644ebd5d0.


7711_WaterThermalTanks_Crash (jmarrec) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

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


#3 What about a comment here?


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7711_WaterThermalTanks_Crash (jmarrec) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (11 of 11 tests passed, 0 test warnings)

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thanks :)


[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)
               ^
```


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You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 0153502e1f990ffd3c12542ec982be0bd8834b9c.

You can try again later or [upgrade](https://zeit.co/teams/tribalteam/settings/plan) your plan.


Copy of this build can be found at
https://www.mewbuilds.com/build/c4deee2ade96c9676540b2046730ec9a8191a56b/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmcsrNyyt3v1v8MvPFXcKHcVHb68pe6RkoMMFcqwxXfS7t
                       Virus Total analysis
                       https://www.virustotal.com/file/4df5357f7b0e487ad3bae7b45956d282875298cdbc859d175721ac8e98915dd2/analysis/1580155800/


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was this caused by the windows 10 update ?


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~~~
Configuring `regions` is not necessary for Static Files. Deploying Serverless Functions to multiple regions is restricted to paid plans. Upgrade here: https://zeit.co/account/billing.
~~~


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[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/terminus-build-tools-plugin/master/assets/images/visit-site-36.png)](https://pr-6-jilt-gh-pantheon-demo.pantheonsite.io/)

Created multidev environment [pr-6](https://dashboard.pantheon.io/sites/a86d4f47-aef7-466a-8822-2f79911c00c1#pr-6) for jilt-gh-pantheon-demo.


rotti was here
and yes, a grat course


International Journal of Science Annals, Vol. 2, No. 1-2, 2019
[1.pdf](https://github.com/IJSA/IJSA/files/4119125/1.pdf)
[3.pdf](https://github.com/IJSA/IJSA/files/4119126/3.pdf)
[4.pdf](https://github.com/IJSA/IJSA/files/4119127/4.pdf)
[5.pdf](https://github.com/IJSA/IJSA/files/4119128/5.pdf)
[6.pdf](https://github.com/IJSA/IJSA/files/4119129/6.pdf)
[7.pdf](https://github.com/IJSA/IJSA/files/4119130/7.pdf)


@JuliaRegistrator register


this needs 1.11 removed from the all target as well


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Schau dir mal CORS an


Only `Yes/No` is useful in flags, other flags are meaningless.
`create_message_window` - it is quite normal to used it with a single line. (can be redone using the delimiters '|' as you have)

the ability to set the color of the text... well, I do not know, but whether it is necessary?


On previous Chucker version everything works fine?
Just of curiosity - do you override `downloader` with your OkHttp client in Picasso?

Also, as far as I see, Picasso is quite tricky, according to latest opened issues:
<img width="507" alt="Screenshot 2020-01-28 at 14 01 31" src="https://user-images.githubusercontent.com/13467769/73262475-e5a7af00-41d6-11ea-9c45-051b9a3ee8d2.png">


Upgrading


`Float.MIN_VALUE` - содержит минимальную мантису, и получается **очень маленькое положительное число**

`Double.MIN_VALUE` - аналогичная ситуация

Нам же нужно вывести минимальные числа, например число **-1** будет меньше чем `Float.MIN_VALUE`


what is this


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Those change would be unnecessary if your `IM_ASSERT` macro was written sandwidched by a `do { } while (0)` statement as it is custom to create multi-staements macros which will work in a single-line statement context.


Yes 5.7.1. I forgot which last stable was!


The "view embedded content" button wasn't showing up at the right [breakpoint](https://material-ui.com/customization/breakpoints/) for me. Looking at it again, it was actually right originally (the `.down('lg')` check hides the button for screens <1920px). It wasn't showing up for me because my screen was smaller than I thought :man_facepalming: I reverted the change in the latest commit (8a0e064b667634ee42aa3aef95e8033438a70037).


Or rather misspellings - mostly not typos


It would be very nice if we could have badge for last stable and last beta release in readme?


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look good


We are.


Thank you for noticing this.
It should now be [fixed](https://github.com/macports/macports-ports/commit/6aab220fa22e8506cb6d1b4721ed2d01edb329c6).


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~~~
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An orphans cuddle in his master's arms...The nuns in Vietnam are doing their religious tasks. Their duty - to serve people as the greatest offerings to Buddha.


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Forgot to add the initial commit message - adding more information to the Contents section and fixing my github link.


NFP---Connect-split-DX-to-VRF-refrigerant-loop (rraustad) - 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-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.28%25-green.png)


2nd and 3rd lines are wrapped if they're too long; and it's done by engine so yay, less work for us :>
```pascal
r_message_box("Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1 Line1|Line2 Line2 Line2 Line2 Line2 Line2 Line2 Line2 Line2 Line2 Line2 Line2 Line2 Line2|Line3 Line3 Line3 Line3 Line3 Line3 Line3 Line3 Line3 Line3 Line3 Line3 Line3 Line3");
```
![yey](https://user-images.githubusercontent.com/1433300/73226879-dd695880-4171-11ea-89a9-03006aeba707.png)

> Also maybe it's possible to merge DialogOut and DialogOutEx as an universal one?

https://github.com/rotators/sfall/blob/13ad7450b730abd07788d9c61de5b847f5b88a83/sfall/Modules/Rotators.Script.cpp#L94-L142


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iiab-update-map is only needed if adm cons (and js-menu) is installed and otherwise it does nothing.


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


fixed in https://github.com/S-S-X/protector/commit/20f57dd497318f37beddacb5c7341a80ff069a26


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 246ce9b10971b15055c22882de817fd44720347a.

You can try again later or [upgrade](https://zeit.co/account/plan) your plan.


Well done!


{
  "object": {
    "id": "transfers",
    "object": "capability",
    "account": "acct_1F8VJnBRyMRKcdHD",
    "requested": true,
    "requested_at": 1566063875,
    "status": "active"
  },
  "previous_attributes": {
    "requested": false,
    "requested_at": null,
    "status": "unrequested"
  }


I have a feeling you actually had to make you tests conditional on the Ruby version. :-) Grep for `:ruby27` and you'll see what I mean.


Successfully deployed to following URLs:

* https://site3-4zsb3q3vu.now.sh
* https://danmo.co
* https://www.danmo.co
* https://site3.morrisondanr.now.sh
* https://site3-git-master.morrisondanr.now.sh


Successfully deployed to following URLs:

* https://gatsby-starter-forestry-61vqi7s9v.now.sh
* https://gatsby-starter-forestry.now.sh
* https://gatsby-starter-forestry.paulbremer.now.sh
* https://gatsby-starter-forestry-git-master.paulbremer.now.sh


Successfully deployed to following URLs:

* https://avilena-backend-qtbwws4is.now.sh
* https://avilena.now.sh
* https://avilena-backend.alzheimind-backend1.now.sh
* https://avilena-backend-git-master.alzheimind-backend1.now.sh


Klasa powinna zawierać zmienną typu `boolean` o nazwie np `isTaskExecuted`. Metody `isTaskExecuted()` oraz `executeTask()` powinny używać tej zmiennej


Successfully deployed to following URLs:

* https://awanisiusme-bznnn8dyq.now.sh
* https://awanisius.me
* https://awanisiusme.awanisius.now.sh
* https://awanisiusme-git-master.awanisius.now.sh


Ich glaube du hast nun in UBA an mehreren Stellen `uba` durch `bfs` ersetzt.


Should we turn this into a protected function then?


Successfully deployed to following URLs:

* https://about-inkohx-me-2ufr0izis.now.sh
* https://about-inkohx-me.now.sh
* https://about.inkohx.me
* https://about-inkohx-me.inkohx.now.sh
* https://about-inkohx-me-git-master.inkohx.now.sh


Successfully deployed to following URLs:

* https://ccc-bmli04l9g.now.sh
* https://ccc.zeit-github-test-dev1.now.sh
* https://ccc-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-with-alias-jybo6bcie.now.sh
* https://z-github-e2e-tests-dev-alias-v2-with-alias.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-without-alias-j1exzqufy.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-bqnnzgnqwj.now.sh
* https://z-github-e2e-tests-dev-only.now.sh


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

~~~
The domain wbhlndebuo.com is not verfied and cannot be used as an alias.
~~~

([Learn more](http://localhost:3000/zeit-github-test-dev/github-e2e-test-dev-domain-issues/fkaj1r9xe) or [visit](https://github-e2e-test-dev-domain-issues-fkaj1r9xe.now.sh) the non-aliased deployment)


# 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)|


7648_VRF_HREIRFTHeat_uses_Cap (jmarrec) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2658 of 2658 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://underreacted-dky46f1cp.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


Successfully deployed to following URLs:

* https://de-gifs-client-59lropx3j.now.sh
* https://de-gifs-client.now.sh
* https://gif.daneden.me
* https://de-gifs-client.daneden.now.sh
* https://de-gifs-client-git-master.daneden.now.sh


Could also be imported: `import java.nio.charset.StandardCharsets;`


Successfully deployed to following URLs:

* https://client-qllyi4xf3.now.sh
* https://client-ten-pearl.now.sh
* https://client.dloft9.now.sh
* https://client-git-master.dloft9.now.sh


Successfully deployed to following URLs:

* https://jobsite-qz4akfszc.now.sh
* https://jobsite.now.sh
* https://jobsite.dylandamsma.now.sh
* https://jobsite-git-master.dylandamsma.now.sh


[AppVeyor has built](https://ci.appveyor.com/project/cypress-io/cypress/builds/30385843/job/997atc0rq0sgl628) the `win32 ia32` version of the Test Runner.

You can install this pre-release platform-specific build using instructions at [https://on.cypress.io/installing-cypress#Install-pre-release-version](https://on.cypress.io/installing-cypress#Install-pre-release-version).

You will need to use custom `CYPRESS_INSTALL_BINARY` url and install Cypress using an url instead of the version.

    Instructions are included below, depending on the shell you are using.

    In Command Prompt (`cmd.exe`):

      set CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.4/win32-ia32/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.zip
      npm install https://cdn.cypress.io/beta/npm/3.8.4/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.tgz

    In PowerShell:

      $env:CYPRESS_INSTALL_BINARY = https://cdn.cypress.io/beta/binary/3.8.4/win32-ia32/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.zip
      npm install https://cdn.cypress.io/beta/npm/3.8.4/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.tgz

    In Git Bash:

      export CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.4/win32-ia32/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.zip
      npm install https://cdn.cypress.io/beta/npm/3.8.4/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.tgz

    If the above commands do not work for you, you can also try using `cross-env`:

      npm i -g cross-env
      cross-env CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.4/win32-ia32/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.zip npm install https://cdn.cypress.io/beta/npm/3.8.4/appveyor-fix-win-install-message-cd955db8d07e14e9ba090563f9cd007c7c949b41-30385843/cypress.tgz


Is there such a thing as route[JSONRPC]? Shouldn't this be event_route[xhttp:request] instead?


@MrSunshyne


自动构建 [auto-dragalia-1ab5e1d2.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/941/artifacts/0/home/circleci/project/artifacts/auto-dragalia-1ab5e1d2.zip)


Successfully deployed to following URLs:

* https://nextjs-fd7wfcx6u.now.sh
* https://nextjs.hhoomph.now.sh
* https://nextjs-git-master.hhoomph.now.sh


poner un //TODO remover


matplotlib를 통해 Gray 컬러 이미지 출력시 배경 색깔이 노란색으로 뜨는 문제 해결
ref : https://github.com/opencv/opencv/issues/10587


Successfully deployed to following URLs:

* https://tejaskumarcom-cclry3fpy.now.sh
* https://tejaskumar.com
* https://www.tejaskumar.com
* https://xn--pn8hl7g.ws
* https://tejaskumarcom.tejask.now.sh
* https://tejaskumarcom-git-master.tejask.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):
~~~


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-with-alias-cbz5kmas8.now.sh
* https://z-github-e2e-tests-dev-alias-v2-with-alias.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://ccc-3w8zj97mq.now.sh
* https://ccc.zeit-github-test-dev1.now.sh
* https://ccc-git-master.zeit-github-test-dev1.now.sh


done :) thank you


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-jhmvalpoza.now.sh
* https://z-github-e2e-tests-dev-only.now.sh


![](https://github.trello.services/images/mini-trello-icon.png) [Promo web prototype](https://trello.com/c/uD80WX80/7-promo-web-prototype)


Successfully deployed to following URLs:

* https://fe-foundation-p2qp0bxky.now.sh
* https://fe-foundation.now.sh
* https://fe.rualc.com
* https://fe-foundation.seognil.now.sh
* https://fe-foundation-git-master.seognil.now.sh


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

~~~
The domain v2k7mgfa9y.com is not verfied and cannot be used as an alias.
~~~

([Learn more](http://localhost:3000/zeit-github-test-dev/github-e2e-test-dev-domain-issues/jezg9dg2b) or [visit](https://github-e2e-test-dev-domain-issues-jezg9dg2b.now.sh) the non-aliased deployment)


Successfully deployed to following URLs:

* https://baseholdit-8q9bka47z.now.sh
* https://basehold.it
* https://baseholdit.daneden.now.sh
* https://baseholdit-git-master.daneden.now.sh


![](https://github.trello.services/images/mini-trello-icon.png) [creating the HTML and CSS of the travel agency page](https://trello.com/c/28XFvyta/7-creating-the-html-and-css-of-the-travel-agency-page)