My opinion :
`$oCriteria->compare('group.group_order', '<= '.$oCurrentQuestion->group->group_order);`
to
`$oCriteria->compare('group_order', '<= '.$oCurrentQuestion->group->group_order);` can fix the issue.

Bu clear '<' as operator …

$this->addCondition($column.$op.self::PARAM_PREFIX.self::$paramCount,'<');
=>
`$this->condition='('.$this->condition.') '.'<'.' ('.$condition.')';`

is broken …


Nice!


- borrowBook function fires data base borrowBook procedure


Install `ptvsd` to ensure visual debugger.


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/addad74a-2a69-4c77-81a9-60b7251a5c22?env_id=ibm%3Ayp%3Aus-east "simple-toolchain-20200123220721519"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/413249ce-cb0f-4f10-8a9e-68065e405bc0 "openshift101") deployed [openshift101](https://github.com/svennam92/openshift101/releases/tag/deploy-ibm-yp-us-south-svennam-us.ibm.com-dev-20200128-130349 "deploy-ibm-yp-us-south-svennam-us.ibm.com-dev-20200128-130349") to [dev](https://console.bluemix.net/apps/2cc5bcbb-a80b-4b5b-8c7e-a844d6465de0?env_id=ibm:yp:us-south "ibm:yp:us-south:svennam@us.ibm.com:dev"), including this commit


Successfully deployed to following URLs:

* https://speedruns-qganv3k9c.now.sh
* https://speedrun.ca
* https://master.speedruns.ca
* https://speedruns.speedruns.now.sh
* https://speedruns-git-master.speedruns.now.sh


remove_objexx_gio__4 (lefticus) - Win64-Windows-10-VisualStudio-16: OK (2392 of 2618 tests passed, 339 test warnings)

Messages:\n
 * 565 tests had: EIO diffs.
 * 226 tests had: Table big diffs.
 * 200 tests had: Table small diffs.

Failures:\n

regression Test Summary
 * Passed: 447
 * Failed: 226

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-91.37%25-yellow.png)


Successfully deployed to following URLs:

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


By the way, if (Initialized) return; do you want to delete?


Move comment to above code


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stack.isEmpty()메소드 사용


We don't actually need the exclude_urls functionality if you use the Primary ID of the Profiles table as the linkedin username which is unique. I.e. linkedin.com/in/waltonwang, my username is waltonwang. so now we can ditch the profile_url field in our table too.


@Rocky640 Sorry I overlooked this when approving the test...

You need to update the bench for the `base` branch (`DynamicComplexity`) in the Fishtest test setup manually.  Fishtest only automatically parses your commit message for the `new` branch; the `base` defaults to the current master bench regardless of whether you change the base branch yourself.


> Is the cons after the rounding strategy really necessary?

What do you mean by "cons"? If you mean comma, while not *strictly* necessary, as a rule I've been avoiding concatenating `<calc-sum>` with anything else, since it's a relatively complex grammar.

> Can we change to-zero to truncate to match JS slightly better?

I considered that, but it's not actually truncating anything. I think it would cause more confusion than it would avoid.

> I think there is merit in adding nearest-even (as suggested by IEEE 754) and perhaps also nearest-odd.

The point of nearest-even is to help reduce bias in estimates. I don't think there's currently a call for that in CSS.

(That said, if we do want to dictate the behavior of ties, the plan is to let you combine `nearest` with another keyword, so the default behavior is `nearest up`, and we'd indeed add at least `nearest even` as a possibility at that point.


Successfully deployed to following URLs:

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[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


### :x: 1 / 9 Rules Failed

##### :bookmark_tabs: Use Angular’s commit message convention

      :point_right: You can review your rules settings at smart policy management :point_left:

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


This is going to break the Python build. `setup.py` reads `README.md`, see [here](https://github.com/v3io/frames/blob/development/clients/py/setup.py#L63)


Successfully deployed to following URLs:

* https://next-starter-kit-8xz6qne65.now.sh
* https://next-starter-kit-acd.now.sh
* https://next-starter-kit.alexacd02.now.sh
* https://next-starter-kit-git-master.alexacd02.now.sh


Now LCD display is broken (very small).
Not sure it is due to this commit.


Is this line needed? It's a bit confusing seeing as the module itself is licensed under the MIT license.


Successfully deployed to following URLs:

* https://5thdapp-iwuje46vb.now.sh
* https://5thdapp.now.sh
* https://5thdapp.dapp5th.now.sh
* https://5thdapp-git-master.dapp5th.now.sh


Successfully deployed to following URLs:

* https://next-starter-kit-owb2s4rly.now.sh
* https://next-starter-kit-acd.now.sh
* https://next-starter-kit.alexacd02.now.sh
* https://next-starter-kit-git-master.alexacd02.now.sh


Successfully deployed to following URLs:

* https://smart-reads-ps2ctq5hh.now.sh
* https://smart-reads.now.sh
* https://smart-reads.emmazarate.now.sh
* https://smart-reads-git-master.emmazarate.now.sh


Successfully deployed to following URLs:

* https://roman-numerals-app-f9ihwnbrp.now.sh
* https://roman-numerals-app.now.sh
* https://roman-numerals-app.shalanazim.now.sh
* https://roman-numerals-app-git-master.shalanazim.now.sh


@dshuman52
This (2336-42) doesn't look right?
This is the same as **`if (sc.chNext == 0) { sc.ch = ' ' }`** (the value of `sc.ch` doesn't matter)


Successfully deployed to following URLs:

* https://game-backend-iivzfo0lc.now.sh
* https://game-backend.now.sh
* https://game-backend.pokatilov0802.now.sh
* https://game-backend-git-master.pokatilov0802.now.sh


Successfully deployed to following URLs:

* https://hmgundudev-n73uoy1lq.now.sh
* https://hmgundu.dev
* https://hmgundudev.hiranmayagundu.now.sh
* https://hmgundudev-git-master.hiranmayagundu.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):
~~~


Registration pull request created: [JuliaRegistries/General/8532](https://github.com/JuliaRegistries/General/pull/8532)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.3.2 -m "<description of version>" 91a17c9caa900e55a035cd939ee8ac5748cc62ef
git push origin v0.3.2
```


Nope, I just forgot to add the brightness multipliers, as seen in the diff.


Das muss dann später auf prod angepasst werden


Copy of this build can be found at
https://www.mewbuilds.com/build/0bef27545014ffb091610b831a32ad3228774af3/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmP4PQJqQQ7BtJjAiNprNgoa49HEtxFBsf9XY4jAw429wm
                       Virus Total analysis
                       https://www.virustotal.com/file/b3816c1d7d22ab050d518ead518ea8836921a59efae2ced45821a68bca80296a/analysis/1580155967/


Successfully deployed to following URLs:

* https://resume-nouo7a4zt.now.sh
* https://resume-pi.now.sh
* https://resume.grifstuf.com
* https://resume.gpolonus.now.sh
* https://resume-git-master.gpolonus.now.sh


Successfully deployed to following URLs:

* https://tembo-site-1m0ur3dsv.now.sh
* https://tembo-site.now.sh
* https://tembo.ai
* https://www.tembo.ai
* https://tembo-site.tembo.now.sh
* https://tembo-site-git-master.tembo.now.sh


We are aware of that, bug is still not fixed.


Added JMP ESP and Buffer space of NOP (16 bytes) for padding.


@AlexMSchakel Im Done!


@avanigoyal-trc  lines 21 through 23 have been changed


[Circle has built](https://circleci.com/gh/cypress-io/cypress/236962) the `linux x64` 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.

    export CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.4/linux-x64/circle-develop-ae81d5d71341fa887482eb66f8b0f7b66be9a30c-236959/cypress.zip
    npm install https://cdn.cypress.io/beta/npm/3.8.4/circle-develop-ae81d5d71341fa887482eb66f8b0f7b66be9a30c-236912/cypress.tgz


maybe this should point to a separate markdown? Mainly I'm somewhat concerned about the main readme now advising users to load `scala:advanced_usage/scala.bzl`.


@JuliaRegistrator register()


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


array1s-experiment (jasondegraw) - 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)


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/2499) complete for branch overlay-algorithms.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/commit/7d37b61292921ce55af0db07491118e835ec036c/index.html).

16 tests passed, 0 tests failed and 0 tests skipped in 9834 seconds

Tests produced 382 warnings. 382 were for lower-than-expected alignment scores


Successfully deployed to following URLs:

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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-2-voso.pantheonsite.io/)

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~~~
The `version` property inside your now.json file must be a number.
~~~


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Created multidev environment [pr-36](https://dashboard.pantheon.io/sites/40c6fd46-0ec3-4987-b917-9489fc102ca5#pr-36) for ivycat-build-tools-test.


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1) Remove tag please
2) Why do you need to kang if it's pushes in my source


On building project files for visual studio:

Running C:/UE_4.24/Engine/Binaries/DotNET/UnrealBuildTool.exe  -projectfiles -project="K:/BuildingEscapeClone/BuildingEscape/BuildingEscape.uproject" -game -rocket -progress -log="K:\BuildingEscapeClone\BuildingEscape/Saved/Logs/UnrealVersionSelector-2020.01.27-19.00.04.log"
Discovering modules, targets and source code for project...
While compiling K:\BuildingEscapeClone\BuildingEscape\Intermediate\Build\BuildRules\BuildingEscapeModuleRules.dll:
k:\BuildingEscapeClone\BuildingEscape\Source\BuildingEscape\BuildingEscape.Build.cs(7,45) : error CS1502: The best overloaded method match for 'UnrealBuildTool.ModuleRules.ModuleRules(UnrealBuildTool.ReadOnlyTargetRules)' has some invalid arguments
k:\BuildingEscapeClone\BuildingEscape\Source\BuildingEscape\BuildingEscape.Build.cs(7,50) : error CS1503: Argument 1: cannot convert from 'UnrealBuildTool.TargetInfo' to 'UnrealBuildTool.ReadOnlyTargetRules'
ERROR: Unable to compile source files.

***
The Build.cs file:

// Fill out your copyright notice in the Description page of Project Settings.

using UnrealBuildTool;

public class BuildingEscape : ModuleRules
{
	public BuildingEscape(TargetInfo Target) : base(Target)
	{
		PublicDependencyModuleNames.AddRange(new string[] { "Core", "CoreUObject", "Engine", "InputCore" });
		PrivateDependencyModuleNames.AddRange(new string[] {  });

		// Uncomment if you are using Slate UI
		// PrivateDependencyModuleNames.AddRange(new string[] { "Slate", "SlateCore" });

		// Uncomment if you are using online features
		// PrivateDependencyModuleNames.Add("OnlineSubsystem");
		// if ((Target.Platform == UnrealTargetPlatform.Win32) || (Target.Platform == UnrealTargetPlatform.Win64))
		// {
		//		if (UEBuildConfiguration.bCompileSteamOSS == true)
		//		{
		//			DynamicallyLoadedModuleNames.Add("OnlineSubsystemSteam");
		//		}
		// }
	}
}


[Dan Ungureanu posted](https://review.discourse.org/t/fix-hide-notification-content-for-encrypted-posts/5788/5):

This was followed-up in [4d44916](https://github.com/discourse/discourse-encrypt/commit/4d44916393fe2ca65c422f5f785a6d973bc7c5de#diff-b61ae67bc6a57a3decb8d15b832077f4R186-R191).


Successfully deployed to following URLs:

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


Successfully deployed to following URLs:

* https://ccc-h2k8mjs0y.now.sh
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Successfully deployed to following URLs:

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


Good catch ;)


Successfully deployed to following URLs:

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


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

~~~
The domain ykgvlkk8ez.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/ipk8hk7mz) or [visit](https://github-e2e-test-dev-domain-issues-ipk8hk7mz.now.sh) the non-aliased deployment)


Successfully deployed to following URLs:

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Successfully deployed to following URLs:

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* https://www.pkgreview.dev
* https://pkgreviewdev.iqubex-technologies.now.sh
* https://pkgreviewdev-git-master.iqubex-technologies.now.sh


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @hubertjaworskineptune was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


Where is that index created?


Если сделать список поездов (`@@all`) хэшем с ключом в виде номера, то поиск будет просто выбором по номеру. Это будет оптимальней, так как хэш "заточен" на такую операцию


Good work Neha. This seems to be fine


Diesabled => Disabled


So why did you hack my phone


Successfully deployed to following URLs:

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* https://www.le3.io
* https://le3io.deslee.now.sh
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@JuliaRegistrator register


Registration pull request created: [JuliaRegistries/General/8494](https://github.com/JuliaRegistries/General/pull/8494)

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 v0.1.5 -m "<description of version>" 0823b8c7f366ca023e26caceb0e8b78da745ca93
git push origin v0.1.5
```


Successfully deployed to following URLs:

* https://scribe-hhvwosvjk.now.sh
* https://scribe-nine-theta.now.sh
* https://scribe.francescolanciana.now.sh
* https://scribe-git-master.francescolanciana.now.sh


after all of this i tried to log in ... but it did not worked .. the login button was not responding !
i opened the console and its says : index.html:43 Uncaught TypeError: firebase.auth is not a function
    at index.html:43


Successfully deployed to following URLs:

* https://ag-blog-kybh6gf4j.now.sh
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* https://blog.aaronguostudio.com
* https://ag-blog.aaronguo1.now.sh
* https://ag-blog-git-master.aaronguo1.now.sh


I thought if something is a link but unclickable it means OctoLinker broke somehow. Maybe we do miss a style if it's different on the default GH theme.


Successfully deployed to following URLs:

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Нужно использовать soft tab (2 пробела), в настройках редактора это должно быть


Красная стрелка указывает на отсутствие пустой строки в конце файла, поищи в интернете зачем она нужна. И многие редакторы настраиваются так, чтобы исправлять это автоматически


Successfully deployed to following URLs:

* https://midi-web-2idpgz44b.now.sh
* https://midi-web.now.sh
* https://midi.hearing.cloud
* https://midi-web.michalstrzelczyk.now.sh
* https://midi-web-git-master.michalstrzelczyk.now.sh


//this is tip!


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/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/6cc27fe7801a5c14890936711d3b5f0ee18c162b/tests/testthat/test-nltt_diff_exact_extinct.R#L96) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```


Successfully deployed to following URLs:

* https://birdapp-6dbgxtxz2.now.sh
* https://birdapp.now.sh
* https://birdapp.velveteer.now.sh
* https://birdapp-git-master.velveteer.now.sh


여러개의 pos & neg 이미지를 생성할 경우 triplet.py의 query 열에 중복된 이미지 경로들이 존재하기 때문에
해당 중복된 값들을 제거하고 pandas 데이터 프레임 인덱스 값들을 0번부터 다시 매김


@JuliaRegistrator `register()`


Registration pull request updated: [JuliaRegistries/General/8490](https://github.com/JuliaRegistries/General/pull/8490)

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 v0.4.0 -m "<description of version>" 14c403a58ba0bec12e9893a3acf0b28dfc8ffa3a
git push origin v0.4.0
```


Successfully deployed to following URLs:

* https://guac-web-lx2enjl63.now.sh
* https://guac.live
* https://www.guac.live
* https://guac-web.guaclive.now.sh
* https://guac-web-git-master.guaclive.now.sh


In the first part of the tutorial I didn't have everything on the same server.
Cognito was on one server and DynamoDB on another or something similar and it caused me some small issues.
Recommend everything on the same server for anyone learning.