<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Taskcluster-GitHub attempted to create a task for this event with the following scopes:

```
[
  "assume:repo:github.com/walac/docker-worker:branch:master",
  "queue:route:statuses",
  "queue:scheduler-id:taskcluster-github"
]
```

The expansion of these scopes is not sufficient to create the task, leading to the following:

Client ID static/taskcluster/github does not have sufficient scopes and is missing the following scopes:

```
{
  "AllOf": [
    "docker-worker:cache:docker-worker-garbage-*",
    "docker-worker:capability:privileged",
    "docker-worker:capability:device:loopbackAudio",
    "docker-worker:capability:device:loopbackVideo",
    "secrets:get:project/taskcluster/testing/docker-worker/ci-creds",
    "secrets:get:project/taskcluster/testing/docker-worker/pulse-creds",
    {
      "AnyOf": [
        {
          "AnyOf": [
            "queue:create-task:highest:proj-taskcluster/ci",
            "queue:create-task:very-high:proj-taskcluster/ci",
            "queue:create-task:high:proj-taskcluster/ci",
            "queue:create-task:medium:proj-taskcluster/ci",
            "queue:create-task:low:proj-taskcluster/ci",
            "queue:create-task:very-low:proj-taskcluster/ci",
            "queue:create-task:lowest:proj-taskcluster/ci"
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:proj-taskcluster/ci",
            {
              "AllOf": [
                "queue:define-task:proj-taskcluster/ci",
                "queue:task-group-id:taskcluster-github/AdNGfvFAQQSaVYIeOjplJg",
                "queue:schedule-task:taskcluster-github/AdNGfvFAQQSaVYIeOjplJg/AdNGfvFAQQSaVYIeOjplJg"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

This request requires the client to satisfy the following scope expression:

```
{
  "AllOf": [
    "docker-worker:cache:docker-worker-garbage-*",
    "docker-worker:capability:privileged",
    "docker-worker:capability:device:loopbackAudio",
    "docker-worker:capability:device:loopbackVideo",
    "secrets:get:project/taskcluster/testing/docker-worker/ci-creds",
    "secrets:get:project/taskcluster/testing/docker-worker/pulse-creds",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:proj-taskcluster/ci",
                "queue:create-task:very-high:proj-taskcluster/ci",
                "queue:create-task:high:proj-taskcluster/ci",
                "queue:create-task:medium:proj-taskcluster/ci",
                "queue:create-task:low:proj-taskcluster/ci",
                "queue:create-task:very-low:proj-taskcluster/ci",
                "queue:create-task:lowest:proj-taskcluster/ci"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:proj-taskcluster/ci",
            {
              "AllOf": [
                "queue:define-task:proj-taskcluster/ci",
                "queue:task-group-id:taskcluster-github/AdNGfvFAQQSaVYIeOjplJg",
                "queue:schedule-task:taskcluster-github/AdNGfvFAQQSaVYIeOjplJg/AdNGfvFAQQSaVYIeOjplJg"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2020-01-14T14:42:04.537Z

</details>


A consulta tá ok. Dá uma olhada nas correções que sugeri.


Regarding color order: the next release will include every possible order for you to pick. No idea why LPD would not work correctly.


TugasBiodata


Successfully deployed to following URLs:

* https://interface-q1ppwv0pg.now.sh
* https://interface.avantgarde-finance.now.sh
* https://interface-git-master.avantgarde-finance.now.sh


Successfully deployed to following URLs:

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


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-with-alias-5891r51eu.now.sh
* https://z-github-e2e-tests-dev-alias-v2-with-alias.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias-git-master.zeit-github-test-dev1.now.sh


There is https://github.com/openwrt/openwrt/pull/2385, I haven't followed it closely, but it looks like there are still some issues.


I am comfortable with your suggestion (I think I inherited the use of the object term from some Vanilla code...)


Successfully deployed to following URLs:

* https://jinvengithubio-dqnsho4cs.now.sh
* https://jinwen.now.sh
* https://jinvengithubio.jinwen.now.sh
* https://jinvengithubio-git-master.jinwen.now.sh


Successfully deployed to following URLs:

* https://csb-qzyoe-fqzij4860.now.sh
* https://meb-labels.now.sh
* https://dev-meb-labels.now.sh
* https://csb-qzyoe.linwu.now.sh
* https://csb-qzyoe-git-relase.linwu.now.sh


Is still showing on the "Home" website.


Successfully deployed to following URLs:

* https://iiwt-ljcqr07k3.now.sh
* https://iiwt.now.sh
* https://iiwt.bsba.now.sh
* https://iiwt-git-master.bsba.now.sh


Deployment failed with the following error:

~~~
Could not find a secret by name "klarna-username"
~~~


Successfully deployed to following URLs:

* https://hire-oleg-d88kmps0f.now.sh
* https://hire-oleg.now.sh
* https://hire-oleg.elmaester.now.sh
* https://hire-oleg-git-master.elmaester.now.sh


新增
coupon 頁面功能（新增｜刪除｜修改)
order 頁面功能 (單筆、多筆加入購物車）
order 頁面功能 (購物車清單）
order 頁面功能 (處理購物車刪除中...)


Successfully deployed to following URLs:

* https://ui-n1bqyfgi8.now.sh
* https://ui.roleypoly.com
* https://ui.roleypoly.now.sh
* https://ui-git-master.roleypoly.now.sh


I suggest using a test option directly (no subshell, faster, shorter, better semantics):
```sh
if [[ -s "${ERROR_CORES_FILE}" ]]
```
From `man [`:
> -s FILE: True if file exists and is not empty.

PS: thank you for maintaining these scripts and adding new features. It really makes life easier for MiSTer owners.


Successfully deployed to following URLs:

* https://kanazawa-jsgithubio-7lehnffxl.now.sh
* https://kanazawajs.now.sh
* https://kanazawa-jsgithubio.kanazawajs.now.sh
* https://kanazawa-jsgithubio-git-master.kanazawajs.now.sh


Please make use of fd899b3bbd2c7107f708ed46ba3798c48e2cfadd and do not add any new `UT_LIST_BASE_NODE_T`, but use `intrusive::list` instead.


Блок descritpion при этом visual-hidden ? Ты уверенна что тебе нужна оббертка в виде дива и еще скрываешь ее ?


Successfully deployed to following URLs:

* https://bruno-arizio-case-study-animations-9mkjjlsou.now.sh
* https://bruno-arizio-case-study-animations.now.sh
* https://bruno-arizio-case-study-animations.alexm.now.sh
* https://bruno-arizio-case-study-animations-git-master.alexm.now.sh


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit ddbb05c58aefa4870dee02df300e6fd45aebd7e9.

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


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 22eb71ddaab60dafaf0f359d09bfcca9e4099273.

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


Successfully deployed to following URLs:

* https://international-fhq92a298.now.sh
* https://international.robinandeer.now.sh
* https://international-git-master.robinandeer.now.sh


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 622540d2668edd0d91ad7d30ee4700ca0395f69c.

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


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit a665ea2aaeb1274733c40e63de3a2c81c532141e.

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


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit b8b803ac001167033566f2467c1243a320829495.

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


Instead of Panel, the label of the link should be probably `$page->category()->title()` or something, not sure what is your field structure.


thats correct


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 74d00139fe4acc670765a00c3e76460cd1e585fa.

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


Successfully deployed to following URLs:

* https://web-guide-l0jtp5pfv.now.sh
* https://web-guide.now.sh
* https://web-guide.yurikarkhachev.now.sh
* https://web-guide-git-master.yurikarkhachev.now.sh


перевести на эффекты NgRx


    :x: Test Failed: va/deploy/1-cache

drush $DRUSH_ALIAS cr

```
Command "@pr827.ci.cms.va.gov" is not defined.
```

- **On:** devshop.cms.va.gov
- **In:** 0.735s


First file


    :x: Test Failed: va/deploy/2-update

drush $DRUSH_ALIAS updatedb --yes

```
Command "@pr827.ci.cms.va.gov" is not defined.
```

- **On:** devshop.cms.va.gov
- **In:** 0.298s


    :x: Test Failed: va/deploy/3-config

drush $DRUSH_ALIAS cim --yes && drush $DRUSH_ALIAS cr

```
Command "@pr827.ci.cms.va.gov" is not defined.
```

- **On:** devshop.cms.va.gov
- **In:** 0.302s


    :x: Test Failed: va/tests/phpunit

phpunit --exclude-group disabled tests/phpunit --colors=always

```
PHPUnit 6.5.14 by Sebastian Bergmann and contributors.

Testing tests/phpunit
....................F......                                       27 / 27 (100%)

Time: 15.93 seconds, Memory: 124.00MB

There was 1 failure:

1) tests\phpunit\SecurityRolesPermissions::testSecurityRolesPermissions with data set #2 ('content_admin', array('access administration pages', 'access files overview', 'access image_browser entity b... pages', 'access media overview', 'access media_browser entity b... pages', 'access toolbar', 'access user profiles', 'access vamc_operating_statuse... pages', 'administer menu', 'administer nodes', 'administer taxonomy', 'break content lock', 'bypass node access', 'bypass workbench access', 'clone block entity', 'clone block_content entity', 'clone field_config entity', 'clone file entity', 'clone media entity', 'clone menu entity', 'clone node entity', 'clone paragraph entity', 'create alert block content', 'create document media', 'create image media', 'create media', 'create promo block content', 'create url aliases', 'create video media', 'delete any alert block content', 'delete any document media', 'delete any image media', 'delete any media', 'delete any promo block content', 'delete any video media', 'delete media', 'delete own document media', 'delete own image media', 'delete own video media', 'edit any document media', 'edit any image media', 'edit any video media', 'edit own document media', 'edit own image media', 'edit own video media', 'export tablefield', 'import tablefield', 'link to any page', 'manipulate all entityqueues', 'manipulate entityqueues', 'notify of path changes', 'rebuild tablefield', 'update any alert block content', 'update any media', 'update any promo block content', 'update media', 'use editorial transition archive', 'use editorial transition arch...lished', 'use editorial transition crea..._draft', 'use editorial transition publish', 'use editorial transition review', 'use editorial transition stag...ishing', 'use moderation sidebar', 'use text format rich_text', 'use workbench access', 'va gov deploy content build', 'view all media revisions', 'view any unpublished content', 'view latest version', 'view sections in toolbar', 'view the administration theme', 'view unpublished paragraphs', 'view workbench access information'))
The permissions for the content_admin do not match the expected permissions:
 'access administration pages',
 'access files overview',
 'access image_browser entity browser pages',
 'access media overview',
 'access media_browser entity browser pages',
 'access toolbar',
 'access user profiles',
 'access vamc_operating_statuses entity browser pages',
 'administer menu',
 'administer nodes',
 'administer taxonomy',
 'break content lock',
 'bypass node access',
 'bypass workbench access',
 'clone block entity',
 'clone node entity',
 'create alert block content',
 'create document media',
 'create image media',
 'create media',
 'create promo block content',
 'create url aliases',
 'create video media',
 'delete any alert block content',
 'delete any document media',
 'delete any image media',
 'delete any media',
 'delete any promo block content',
 'delete any video media',
 'delete media',
 'delete own document media',
 'delete own image media',
 'delete own video media',
 'edit any document media',
 'edit any image media',
 'edit any video media',
 'edit own document media',
 'edit own image media',
 'edit own video media',
 'export tablefield',
 'import tablefield',
 'link to any page',
 'manipulate all entityqueues',
 'manipulate entityqueues',
 'notify of path changes',
 'rebuild tablefield',
 'update any alert block content',
 'update any media',
 'update any promo block content',
 'update media',
 'use editorial transition archive',
 'use editorial transition archived_published',
 'use editorial transition create_new_draft',
 'use editorial transition publish',
 'use editorial transition review',
 'use editorial transition stage_for_publishing',
 'use moderation sidebar',
 'use text format rich_text',
 'use workbench access',
 'va gov deploy content build',
 'view all media revisions',
 'view any unpublished content',
 'view latest version',
 'view sections in toolbar',
 'view the administration theme',
 'view unpublished paragraphs',
 'view workbench access information'

Failed asserting that false is true.

/var/aegir/projects/cms/pr827/docroot/core/tests/Drupal/KernelTests/AssertLegacyTrait.php:31
/var/aegir/projects/cms/pr827/tests/phpunit/SecurityRolesPermissionsTest.php:36

FAILURES!
Tests: 27, Assertions: 66, Failures: 1.

Operation took 0.083 seconds compared to the benchmark of 2 seconds.

Operation took 0.058 seconds compared to the benchmark of 2 seconds.

Operation took 0.146 seconds compared to the benchmark of 5 seconds.

Operation took 0.028 seconds compared to the benchmark of 5 seconds for type page.

Operation took 0.041 seconds compared to the benchmark of 5 seconds for type landing_page.

Operation took 0.533 seconds compared to the benchmark of 2 seconds.
```

- **On:** devshop.cms.va.gov
- **In:** 15.986s


Hey,
I'm interested in contributing to this project. Could you please let me know the current status of this? and what are the pending tasks?


Висеть, подвешивать, повисать... при чём тут конь?


Isn't this the wrong fix? ModelicaExternalC so-file uses math, not Tables.c. So autoconf would need to be used to figure out which so-files should link the math library


Successfully deployed to following URLs:

* https://interface-hnpzo3wma.now.sh
* https://interface.avantgarde-finance.now.sh
* https://interface-git-master.avantgarde-finance.now.sh


method name `isBalanced` suggests that it **only** checks if genes is balanced (this while loop with empty body looks like code someone forgot to remove). If it was designed to fix the genes balance, I would call it `fixGeneBalance` and move while loop inside it.


Лучше так оставь, по смыслу правильней. Хотя перевод конечно именно "принять ванну"


develop (mitchute) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (1960 of 1960 tests passed, 0 test warnings)

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


hm. I thought the space was required, but it appears it is not so I removed that.


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

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

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

### Deployments updated

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

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


The same


Successfully deployed to following URLs:

* https://now-gk98leqbq.now.sh
* https://now-rho-two.now.sh
* https://api-frameworks.zeit.sh
* https://now.zeit.now.sh
* https://now-git-master.zeit.now.sh


Is it a business logic?


![](https://github.trello.services/images/mini-trello-icon.png) [Separate graphics dialogue manager and text dialogue manager](https://trello.com/c/3akhC7QB/77-separate-graphics-dialogue-manager-and-text-dialogue-manager)


Deployment failed with the following error:

~~~
The function for *.js can't be handled by any builder
~~~


Endre "kr. 5000" til "kr. 10000" er foreslått.


[R/ABC_SMC.R:11:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/get_norm_brts.R#L22) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:27:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
nltt_diff_exact_extinct <- function(
^
```
[R/nltt_diff_exact_extinct.R:50:27:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L50) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "since"){
                          ^~
```
[R/nltt_diff_exact_extinct.R:57:25:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L57) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if (time_unit == "ago"){
                        ^~
```
[R/nltt_diff_exact_extinct.R:82:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    species_number_n <- species_number / max(species_number)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:87:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
    event_times2_n <- 1 - event_times2 / min(event_times2) #normalize branching times
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:88:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    species_number2_n <- species_number2 / max(species_number2)  #normalize lineages
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:136:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L136) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:137:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L137) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:138:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L138) *style:* **Commented code should be removed.**
```r
  # testit::assert(event_times2[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:139:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L139) *style:* **Commented code should be removed.**
```r
  # testit::assert(species_number[1] >= 0.0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:141:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L141) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times >= 0.0 & event_times <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:142:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L142) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:143:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L143) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(event_times2 >= 0.0 & event_times2 <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:144:5:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L144) *style:* **Commented code should be removed.**
```r
  # testit::assert(all(species_number >= 0.0 & species_number <= 1.0))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/nltt_diff_exact_extinct.R:183:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L183) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:184:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L184) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nltt_diff_exact_extinct.R:185:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/R/nltt_diff_exact_extinct.R#L185) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/nLTTDiff.R:59:27:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/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:54:1:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_brts.R#L54) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:29:16:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/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/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_extinct.R#L30) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:77:16:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_extinct.R#L77) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages1 <- 1:length(event_times)
               ^
```
[tests/testthat/test-nltt_diff_exact_extinct.R:78:16:](https://github.com/Neves-P/nLTT/blob/4455dbd8f7adb503cf8f037304043259d7cb65f8/tests/testthat/test-nltt_diff_exact_extinct.R#L78) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  lineages2 <- 1:length(event_times2)
               ^
```