[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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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remove_objexx_gio__3 (lefticus) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (11 of 11 tests passed, 0 test warnings)

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


**Hello!**


Doesn't matter if it's deprecated or not. If you're overriding a method, you annotate it with @Override


updated cname


Sure, what do you mean by "breaks my dev environment"? What command is giving the output you pasted?


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_I'm Vika_


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

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---|---|---
[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)

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|Deployment project |
----|
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Ну что за хрень, Илья?! Почему качается только readme?


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I see your token)


merge this


:smile:


@OlafvdSpek can you explain why you want backend validation on INTs ??


遗忘神殿，死核entwatch


I'd prefer overrides to have the current syntax `\override TupletBracket.stencil = ##f`


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SubcoolReheatMode (energy-plus) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (683 of 685 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 683
 * Failed: 1
 * Timeout: 1

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why ?


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Thank you :+1:


Hi @yaronkoren! Did you forget a negation?

When I make an edit via action=formedit, then this cookie does not get set due to the code you added here.


@JuliaRegistrator register


eir_hp_plr_error (mitchute) - x86_64-MacOS-10.13-clang: Tests Failed (0 of 0 tests passed, 0 test warnings)

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You could extract this to a widget so it reads nicely. Its was had to spot the `SizedBox` below


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- Add SECRAT_KEY to .env file
- Add func get_vk_group to get all groups by api method
- Add get_upload_url to get url to upload image to server
- Add func upload_image_to_group to upload image to serve
- Add func upload_image_to_group to upload image
- Add func save_image_to_group to save image in group album


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Looks good to me. Please create the pull request and we can merge it in the
call on Monday.

On Sun, Jan 26, 2020 at 6:19 AM MitsiCash <notifications@github.com> wrote:

> It makes sense to move the dependencies up. See my proposed gist
> https://gist.github.com/MitsiCash/46886afa3fa2d3dcaafee86d4f8cf363
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/MitsiCash/deliberation-ruleml/commit/14e1a2bfeec888bc4aaad8ab67a9249613b5a3de?email_source=notifications&email_token=AAJQYVIGRYCQDCTEVVGYLYTQ7VWUNA5CNFSM4KLI5W4KYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBDIF46#commitcomment-36968350>,
> or unsubscribe
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> .
>


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I feel it would read nicely if `PlayerState.getInstance()` was `Provided` from the widget calling this `ListPage` as an actual instance. It would become clearer that you don't need a singleton for this.


Thanks for the explanation, no worries about the implementation - as long as I know how to do it, I can do it :)

Speaking of that: We have added a lot of new features regarding actors and possibilites. Could you somehow give me a small overview of all the new things so I can add them to the DOC at the webpage? No need to style things, I just need to know where to put it and what is actually possible since our last update. I think it's a good thing to have all the features at one spot in case I forget them or in case we (or other modders) will continue with addons for Blade of Agony.


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
audited 183 packages in 1.501s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/aegir/projects/cms/pr744
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov 1
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr744.ci.cms.va.gov/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 6 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Fri, 24 Jan 2020 17:52:47 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Fri, 24 Jan 2020 17:52:52 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** devshop.cms.va.gov
- **In:** 02:10


Registration pull request created: [JuliaRegistries/General/8378](https://github.com/JuliaRegistries/General/pull/8378)

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 v0.1.0 -m "<description of version>" 2c4568b11c8a8392119284e6ceddca6ebd5488b5
git push origin v0.1.0
```


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[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


Commit messages are not proper
Good that OR condition is used in while loop


revert


так ок. Но зачем ты снова в return переменным присваиваешь заново значения если строкой выше ты уже присвоил эти значения?


Leave a comment
everyone Leave my phone


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~~~


aachal


This breaks the "Fade recordings" function


Fix in https://github.com/redaxo/redaxo/pull/3212


SubcoolReheatMode (energy-plus) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1276 of 1276 tests passed, 0 test warnings)

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Don't set here. It is set in the AudioStopRequestedHandler which is called when you use StopRecordingCommand.Execute()


Get out for watching me


Dòng 102, 108, 109, 111, 112


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test comment


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Thanks a bigger list. You the man


Awesome, we need to implement more spies :)


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* https://turing-hw-2-git-master.filipobsivac.now.sh


![Difference between blocks](https://raw.githubusercontent.com/daniel-stewart/maze-game/876412c95dd27090a7510bb6afac7e3015dbc0a4/.makecode/blocksdiff.png)


BTW it's prettier formatting on save making some file changes.


![](https://github.trello.services/images/mini-trello-icon.png) [#2.17 Select doctors for operation](https://trello.com/c/2WtaLmxk/340-217-select-doctors-for-operation)


That's awesome. Thank you for your hard work and help

On Sat, Jan 25, 2020, 5:40 AM rusty-snake <notifications@github.com> wrote:

> Add a profile for clipgrab
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Successfully deployed to following URLs:

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Successfully deployed to following URLs:

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なるほど、そのほうがわかりやすくていいね！反映します。


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not actually finished yet, nevermind.


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* https://dnh-backend-git-master.david63.now.sh


That makes sense.


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/8448](https://github.com/JuliaRegistries/General/pull/8448)

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:
```
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git push origin v0.1.1
```


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Deployment failed with the following error:

~~~
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~~~
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~~~


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[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/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/9719eff87cca4777815e20910a23df215952d77c/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


This commit message is missing a crucial piece of information, even if it could be gleaned by looking deeper at the changes made: The commit pertains to the nRF24L01+ driver.


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