Nice hack! :+1:


E.g., I have a big Steam library. I changes only occasionally but when it does, it adds 50-100 GB of mostly unique data to the system (except the trend to put lots of small identical blocks inside of game data files, probably very common game assets show up again and again in various parts of the data files, and there is simply no one bothering to store them just once in the game data).


@CCMSAFG - If this is supposed to be number five, it is supposed to print a table of °C and their °F equivalents. However, it looks like it's the code for number one.


afe-refactor (jasondegraw) - i386-Windows-7-VisualStudio-14: OK (3037 of 3037 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)


@CCMSAFG - Please put the exercise number here.


не пойму, почему выдаёт ошибку при проверке пулла?


Now cannot deploy because all the allocated instances are in use.
You can either [upgrade](https://zeit.co/teams/projectfalcon/settings/plan) your plan or [down scale](https://zeit.co/docs/getting-started/scaling) existing [deployments](https://zeit.co/teams/projectfalcon/deployments).


ok


[Here is a regex for URLs](https://gist.github.com/gruber/8891611), if you need some inspiration


this is a commit comment


LGTM


![](https://github.trello.services/images/mini-trello-icon.png) [Implementação da classe funcionário](https://trello.com/c/TQqvHYkF/6-implementa%C3%A7%C3%A3o-da-classe-funcion%C3%A1rio)


![](https://github.trello.services/images/mini-trello-icon.png) [Implementação da classe produto](https://trello.com/c/bbkvEOAB/12-implementa%C3%A7%C3%A3o-da-classe-produto)


![](https://github.trello.services/images/mini-trello-icon.png) [Implementação da classe produtos vendidos](https://trello.com/c/8lz3HZef/13-implementa%C3%A7%C3%A3o-da-classe-produtos-vendidos)


![](https://github.trello.services/images/mini-trello-icon.png) [Implementação da classe vendas](https://trello.com/c/DmaYY41G/14-implementa%C3%A7%C3%A3o-da-classe-vendas)


*Consider* waiting 1 second after a "write" operation in GitHub's REST API to avoid abuse exceptions: https://developer.github.com/v3/guides/best-practices-for-integrators/#dealing-with-abuse-rate-limits


I found that one already, thanks. :) Probably going to take a different approach and avoid having (any more) monolithic regexes.


> So maybe invalidate_layout should be called from the set_value member function of each widget that changes size when its value changes?

No, i think this would make some dialogs, in particular the multiplayer lobby, which already suffers a lot from slowness even worse.

invalidate_layout has multipel disadvantages:
1) It's slow
2) It makes the dialog look realy bad if its size changes often, like for example when it happens whenever you click on a button. (invalidate layout will not only increase size, but also decrease size so calling on a invalidate_layout might cause it's size to change even when it is not neeced at all)

So most dialog are designed to allocate the correct size when the dialog layout is first created (layouted), meaning avoiding calling set_label while the dialog is shown and instead use a 'stacked_widget' or a 'multipage' widget that uses the maximum posible size for any of its child widgets then instead of setting the label you would have one 'page' with the first text, one page with the second text and then during the dialog switch just switch the pages instead of setting the label.

While this sounds good in theory there are unfortunteley some cases where calculating all sizes befor the widget is shown is not possible, and thus calling set_label cannot be avoided. For example:

1) the loadgame dialog, not only there are probably a lot of saves, some players have multiple hundred saved games so calculating their informaltion-panel-sizes alone woudl take a lot of time, also the game would probably need to open all of those savefiles to calculate that infromation which is also slow.

In cases like the savegame dialog it would clearly be best to somehow fix the size of left-side-panel and when a new game is selecrted to only relayout the size of that panel instead of of the whole dialog, In the case of the multiplayer create dialog (which also suffers froma  sinilar problem )

2) The multiplayer lobby, look for exampel at the 'turn_number' label, i would totally not be suprised if it'd be cut off when it exeeds 100 while the lobby is open, also it clearly wouldn't make sense to have like a 999-page multipage widget for every possible number.

In cases like that it'd be best if label had preallocaed the maximum possible size (assuming for example lesss than 1000 turns) and allocating these in advance.

3) Adding items on a listbox or a similar widget can cause an invalidate_layout when it casues the listbox to have a scrollbar, this isn't too bad because it can happen only at most once (per listbox) while the dialog is shown, but it you know in advance that many item will be added later to the list that the scrollbar is amost certainly needed , it doens make sense to set the scrollbar mode to always when the dialog is shown.


finished


Integrantes:
Gianina Garcia 5478136
Miguel Mendoza 5028491


Successfully aliased the URL <https://hyperlist-evzohdnfye.now.sh> to the following alias.

* https://hyperlist.now.sh


OK, good to know it, I didn't noticed it ^^ would you mind elaborate on why so?


OK, good to know it. Would you mind elaborate on why so?


Aw, just saw the issue. Sorry for the noise.


Sullivan - revised 2nd castle level - now going to basement


Similar results if emits are moved to StakeForCharityDialog::on_comboBox_currentIndexChanged(int) Which would be less than ideal anyway, because we do not want to replace the EGC logo on the overview unless they have actually enabled staking for a charity, not just when browsing charities. A function containing just the emit was tried also. Same results. In the wallet model was a thought, but then would signal Qt->daemon->Qt again. Will revisit when time permits.


Successfully aliased the URL <https://ianmitchell-shkkemgcnc.now.sh> to the following aliases.

* https://ianmitchell.io
* https://www.ianmitchell.io


I caught that I have the name inverted here. oops. The logic is correct in this method still, I just forgot to flip the inversion on the value.

I will fix in next build, but this isn't broken, just named incorrectly for what the value holds.


Aliasing failed with the following error:

~~~
Error! We couldn't verify the domain hyperlist.online.
~~~


afe-refactor (jasondegraw) - Win64-Windows-7-VisualStudio-14: OK (3037 of 3037 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)


@trungams if I see a commit message like this again, i'm gonna cry.


Unhandled Failure


this is a commit comment


Addresses backup scheduling with automator


best commit


labels for navbar ??? or what ?


hola


wow


Blocks server indefinitely if GUI client is not launched.


So, what are we supposed to set it to? 127.0.0.1:5601?


As you can see in https://github.com/rust-lang/rust/pull/51100/files#diff-124df07081a1185b5a4d40cdcf0cf4ffR230, sometimes we have to resort to these kinds of hacks :-/


The style throughout the compiler goes against padding to a margin like this (despite my own opinions in the matter) try to follow the style of the surrounding code to minimize the possibility of confusion in readers.


This makes the `universal-access` icon button toggle the "media hidden" widget on and off. Was this intentional? The commit message seems unrelated.


How are the addresses to the register nodes, lines 36, 43, and 44 generated?


These libraries uses for Android only


Aliasing failed with the following error:

~~~
Error! The certificate provider could not resolve the DNS queries for hyperlist.online.
~~~


I don't see the output for this file, but I gather from [your comment in the issue](https://github.com/rust-lang/rust/issues/54505#issuecomment-425648705) that these are suggesting using parenthesis even though they are not needed. That is indeed unfortunate. An alternative would be to get the `expr`'s span and see if it "looks" like a literal range (one way would be to look at the end of the span and seeing if it is a `}` char. It's definitely a hack, but it is crazy enough to work :)


samplerIndex is supposed to be Integer and as [0..7] are perfectly representable as float, this should be save. But what about the fall through case?


during a post or put,there is no role_id


transported from my shendusuipian repo


Now cannot deploy because all the allocated instances are in use.
You can either [upgrade](https://zeit.co/account/plan) your plan or [down scale](https://zeit.co/docs/getting-started/scaling) existing [deployments](https://zeit.co/dashboard/deployments).


Going forward, we will not be using participantId as the primary key, instead, we will be using participantCode.


Sorry I was frustrated :'( It was weird though, the output of yapf when I ran on my laptop and in the travis test were different


test


this is a commit comment


Es para resolver el punto 6: "Dado un depósito, obtener el conjunto formado por el vagón más pesado de cada formación; se espera un conjunto de vagones."

Lo que entiendo de este punto es que de alguna manera el deposito sepa, por cada una de las formaciones que posee, su vagón más pesado, teniendo como resultado un conjunto de vagones (lo que entiendo por conjunto, a una colección de vagones).

Lo que espero que haga el método "vagonMasPesadoXformacion", es que por cada formación guarde su vagón más pesado.

Lo pude resolver manteniendo el forEach, reemplazando en el bloque el "=" por el comportamiento ".add". Con esto guardo de cada formación, su vagón más pesado en la colección  "vagonesMasPesadosXformacion", que por ser una property, el deposito puede devolver un mensaje mostrando su contenido. Con esto, si es que no entendí mal, creo estar cumpliendo con el punto.

En un principio pensaba usar un método para devolver el conjunto de vagones que pide, pero no se si se puede, por eso es que creo la colección "vagonesMasPesadosXformacion". De no estar cumpliendo con el punto o de estar haciéndolo con una mala idea, me fijo de modificarlo.

Gracias


Successfully aliased the URL <https://hyperlist-djsvyxuoek.now.sh> to the following alias.

* https://hyperlist.online


@leiradel You would want to push this to your repo too.


No worries, you're not the first person here to do that. :wink:

Just adding a follow up commit to fix it is fine. :smile:


@leiradel Some fundamental issues I hope you can address -

https://hastebin.com/yorubizadu.coffeescript

C89 doesn't support unnamed structs/unions.


Un método si devuelve un conjunto, lo pude probar y funciona!!
Si lo vimos no lo recordaba. Eso, sumado a un map dentro del método para la colección de formaciones, y evito recordar el conjunto de vagones en una variable. Me parece que esta forma de resolverlo es más acorde.

Saludos


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

I updated the Github team because of this commit.

- @arnekr, @frodepedersen were added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

- @dbast was added to this feedstock maintenance team.

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/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


Successfully aliased the URL <https://homepage-kgxlqcezfn.now.sh> to the following aliases.

* https://andrewsosa-homepage.now.sh
* https://www.andrewsosa.com
* https://andrewsosa.com


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

I updated the Github team because of this commit.

- @dbast was added to this feedstock maintenance team.

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/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


Thanks!


Bhami added comment at main()


unified


почему такой странный синтаксис для массивов используешь?


давай ассоциативным сделаем


![](https://github.trello.services/images/mini-trello-icon.png) [【程式】旅程規劃 / 新增行程 點擊向右手邊展開編輯介面、該旅程 / 新增行程 改變樣式 (for UI)](https://trello.com/c/VnmHIqa9/71-%E3%80%90%E7%A8%8B%E5%BC%8F%E3%80%91%E6%97%85%E7%A8%8B%E8%A6%8F%E5%8A%83-%E6%96%B0%E5%A2%9E%E8%A1%8C%E7%A8%8B-%E9%BB%9E%E6%93%8A%E5%90%91%E5%8F%B3%E6%89%8B%E9%82%8A%E5%B1%95%E9%96%8B%E7%B7%A8%E8%BC%AF%E4%BB%8B%E9%9D%A2%E3%80%81%E8%A9%B2%E6%97%85%E7%A8%8B-%E6%96%B0%E5%A2%9E%E8%A1%8C%E7%A8%8B-%E6%94%B9%E8%AE%8A%E6%A8%A3%E5%BC%8F-for-ui)


вот это как ключи пойдут к предыдущему


Should we not rename the IF nodes reset voltage to rest to make it consistent with other nodes? I know IF nodes do not have resting voltage technically, but it might prevent future bugs. @djsaunde @Hananel-Hazan


переименуй тут $key и $value


To something such as—

    /// Gets the current nickname in use. This may be the primary nickname set in the configuration;
    /// any of the alternative nicknames listed in the configuration; or a nickname set by the
    /// server, such as `Guest0123`. As a result, this is the preferred way to refer to the
    /// client's nickname.

I was going to file a PR just now, but, taking a closer look at the repository locally, it seems that this commit's changes were lost in commit 53fb890a7e69d4fa65bba4c07dd46e32e71d3022.


gross but ok.


arch is an lvalue whereas mrpt::serialization::archiveFrom(f) is an rvalue.

That's probably the difference.


зачем комменты оставляешь?


DeepCode analyzed this commit and found no issues.


(Relevant points in the diff include <https://github.com/aatxe/irc/commit/53fb890a7e69d4fa65bba4c07dd46e32e71d3022#diff-77939fc9650773355cff92fe8aef3e90L843> and <https://github.com/aatxe/irc/commit/53fb890a7e69d4fa65bba4c07dd46e32e71d3022#diff-77939fc9650773355cff92fe8aef3e90L358>.)


IBM Cloud [toolchain](https://console.ng.bluemix.net/devops/toolchains/f094bbc3-fc3f-402f-b769-7d23d4d5533c?env_id=ibm%3Ayp%3Aus-south "hive764"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/8e16040c-6017-478f-90c4-f224ad9a140e?env_id=ibm%3Ayp%3Aus-south "HIVE764") deployed [hive](https://github.com/WEITAO764/hive/releases/tag/deploy-ibm-yp-us-south-wtao-deakin.edu.au_1532874841224-dev-20181001-015629 "deploy-ibm-yp-us-south-wtao-deakin.edu.au_1532874841224-dev-20181001-015629") to [dev](https://console.bluemix.net/apps/247b1604-f5f3-41a1-b4ba-3af134758235?env_id=ibm:yp:us-south "ibm:yp:us-south:wtao@deakin.edu.au_1532874841224:dev"), including this commit


httpメソッドが必ずPOSTになっているがよいか


print文は削除


what happened to that diff? All those red numbers?


d


code need Careful. It cost me 2 hours to find this bug in Oct 1. It just a wrong funtion name finally


Hi @ElizabethGow,

Another problem: in Arabic_MS_8.xml there are four instances of author elements with key attributes that are "person_". You either need to find the VIAF number and fill that in (e.g. `key="person_1234567"`) or leave it blank if you can't find them in VIAF (e.g. `person=""`). As it is, they're broken links on [this page](https://www.fihrist.org.uk/catalog/manuscript_13708).

Andrew.


"Der mere funktionelitet i:
FindDate"

Der MANGLER mere funktionelitet i:
FindDate
fuck


Additional notes: Even though original fakespot is a page action chrome extension I didnt create a page action chrome extension(e.g event pages and stuff) as it seemed unnecessary for this exercise. Correct me if I am wrong.


Unfortunately some other dependency is still installing a version ^3.* .... in order to make dev work i had to disable the generation in the startup script, do `composer require zircote/swagger-php:2.*` and finally i could generate the API


El menu de la izquierda debería de funcionar como está en:

`src/ThemeBundle/Resources/views/Sidebar/left_menu.html.twig`

Es ahi donde se llama a diferentes menus (profile, course, session, skills, etc)
Tambien es ahi donde está el login.

Los menus son construidos por clases y funciones, por ejemplo:

```
{{ macro.panel(
        'Courses' | trans,
        mopa_bootstrap_menu('ChamiloCoreBundle:LeftMenuBuilder:courseMenu', {'automenu': 'navbar', 'stacked':false})
    ) }}
```

Ver la clase "LeftMenuBuilder" y función "courseMenu"

Actualmente en master no hay login! Lo que haces aqui es construir "a mano" cada link ...


@joaomoreno any reason you are only using this node.js version for Windows and not the others?


갸아아아악


Successfully aliased the URL <https://nanimokamo-uoibehndhx.now.sh> to the following alias.

* https://nanimokamo.com


This looks not quite right as it prints the password.


collections/the university of manchester/Persian_MS_3.xml

Hi @ElizabethGow,

On line 48 in Persian_MS_3.xml, you've used a Library of Congress identifier for a person. It was agreed back in July that VIAF should be used (which includes all of the person names in the Library of Congress Name Authority). So, in this case, it should be `key="person_74086465"`).

Andrew.


reviewing has done


@lizmat I'm pushed my roast changes now. Everything should be good now :)


`libraryDependencies ++= Seq("org.apache.spark" %% "spark-sql" % "1.2.0" % "provided").map(_.exclude("javax.servlet", "servlet-api"))`


fixed by https://github.com/odoo/odoo/commit/48b596d5332df4ebd2900fad46242aa201bc8bac

@alexkuhn  thanks for pointing us


Yes, thank you very much for the fix. However, there seems to be a regression in the published version.

The latest working revision for me is d0fb8ceaad57ecca371c7ed36c8ecd36e0e8fcce. It is broken again after a967e2be15a587fa56940798a166a0c265eecf54.


здравствуйте. мой телефон не видит робота.что не так?помогите


Hi @busterb , yes you can set the `kibiter_url` to:
- http://localhost:5601 (for `bitergia/kibiter:6.1.0-optimized` docker image)
- https://your-username:your-password@localhost:5601 (for `bitergia/kibiter:6.1.0-secured` image)


Script is using functions from Python Library for Automating Molecular Simulations (PLAMS).

It connects XYZ coordinate files of multiple molecules, resulting in new XYZ files of all possible combinations of given molecules.

Substitution is done on the first atom of coordinate list, which should be hydrogen atom. Hydrogen that is supposed to be substituted should be on the top of the coordinate list of both - core and ligand. There is a script for automating this process.
Program defines vector between hydrogen atom and one other atom that its connected to it (X atom), for core and ligand. Rotates ligand with aim to make H-X vectors parallel. Translates ligand to the position of H(core) and deletes redundant H atoms on both molecules.

Stores monosubstituted and disubstituted in specific folder. Molecules with problematic geometry are places in error folder.


Successfully aliased the URL <https://lingonsaft-hacktober-zftwjaywok.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


Needed to fix librepo build failure for raspberrypi3 and AArch64 ILP32.


@sunnyquiver can I just add a suggestion to look at https://chris.beams.io/posts/git-commit/ - the commit message
```
Fixes #23. This seems to fix this problem. Not much thought has
gone into this fix, please use with caution.
```
does not follow the recommended practices. I would suggest to use something like e.g. this:
```
Fix a bug computing Dimension and quotients of PathAlgebraModules

Not much thought has gone into this fix, please use with caution.
Closes #23.
```


[R/mbd_ml.R:205:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_ml.R#L205) *style:* **Variable or function name should be snake_case.**
```r
  ML <- as.numeric(unlist(out$fvalues))
  ^~
```
[R/mbd_pure_multiple_birth.R:42:72:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L42) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      ii <- i[stats::dpois(i, nu * time_intervals[t], log = FALSE) != 0 ]
                                                                       ^
```
[R/mbd_pure_multiple_birth.R:46:24:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L46) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:46:61:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L46) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:90:47:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L90) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    a_term <- rep(1, length(time_intervals)    ) #branches
                                              ^
```
[R/mbd_pure_multiple_birth.R:100:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
      # (1) nu contribution: (1-q)^(k * i) * (nu *(t_k-t_k-1))^i * exp(-nu *(t_k-t_k-1)) / i!
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:102:24:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                       ^
```
[R/mbd_pure_multiple_birth.R:102:61:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      a_term[t] <- sum( (1 - q) ^ (ii * k[t]) * poisson_term ) * # (1)
                                                            ^
```
[R/mbd_pure_multiple_birth.R:110:17:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L110) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        (1 - q)^(k[-length(k)] - births)                 # (1)
                ^
```
[R/mbd_pure_multiple_birth.R:161:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L161) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:", trpars1, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:185:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L185) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:187:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L187) *style:* **Lines should not be more than 80 characters.**
```r
  # - changeloglikifnoconv = if T the loglik will be set to -Inf if ML does not converge
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:188:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L188) *style:* **Lines should not be more than 80 characters.**
```r
  # - optimmethod = "simplex" (current default) or 'subplex' (default of previous versions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:193:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L193) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(namepars); #if you add more parameters to your model just change this
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:194:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L194) *style:* **Lines should not be more than 80 characters.**
```r
  failpars <- rep(-1, n_pars); names(failpars) <- namepars; #those are the parameters that you get if something goes sideways
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:237:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L237) *style:* **Lines should not be more than 80 characters.**
```r
      cat("The loglikelihood for the initial parameter values is", initloglik, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:240:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L240) *style:* **Lines should not be more than 80 characters.**
```r
        cat("The initial parameter values have a likelihood that is equal to 0 or below machine precision. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:244:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L244) *style:* **Lines should not be more than 80 characters.**
```r
                               fun = pmb_loglik_choosepar, trparsopt = trparsopt,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pure_multiple_birth.R:249:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_pure_multiple_birth.R#L249) *style:* **Lines should not be more than 80 characters.**
```r
          cat("Optimization has not converged. Try again with different initial values.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:92:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L92) *style:* **Variable or function name should be snake_case.**
```r
      L <- matrix(0, nrow = 1e6, 4)
      ^
```
[R/mbd_sim.R:101:11:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L101) *style:* **Variable or function name should be snake_case.**
```r
          deltaT <- stats::rexp(1, rate = total_rate)
          ^~~~~~
```
[R/mbd_sim.R:102:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
          outcome <- sample(c(-1, 1, 2), size = 1, prob = c(n_species * mu, n_species * lambda, nu))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:103:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
          delta_n <- -1 * (outcome == -1) + 1 * (outcome == 1) + (outcome == 2) * stats::rbinom(n = 1, size = n_species, prob = q)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:113:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L113) *style:* **Lines should not be more than 80 characters.**
```r
            L[new_interval, 1] <- t#-(delta_n:1)* 1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:134:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L134) *style:* **Variable or function name should be snake_case.**
```r
    L <- L[(1:total_count), ]
    ^
```
[R/mbd_sim.R:142:35:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L142) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    crown_species_dead <- (length( unique(sign(alive[, 3]))) != 2 ) * cond
                                  ^
```
[R/mbd_sim.R:142:66:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L142) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    crown_species_dead <- (length( unique(sign(alive[, 3]))) != 2 ) * cond
                                                                 ^
```
[R/mbd_sim.R:144:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L144) *style:* **Lines should not be more than 80 characters.**
```r
    births.reconstructed_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:144:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L144) *style:* **Variable or function name should be snake_case.**
```r
    births.reconstructed_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:145:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L145) *style:* **Lines should not be more than 80 characters.**
```r
    births.full_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = FALSE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:145:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L145) *style:* **Variable or function name should be snake_case.**
```r
    births.full_tree <- unlist(unname(sort(DDD::L2brts(L, dropextinct = FALSE), decreasing = TRUE)))
    ^~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L146) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L146) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:146:47:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L146) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.reconstructed_tree <- sum( duplicated(births.reconstructed_tree))
                                              ^
```
[R/mbd_sim.R:147:35:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L147) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multi_births_full_tree <- sum( duplicated(births.full_tree))
                                  ^
```
[R/mbd_sim.R:149:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L149) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:150:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L150) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check <- (multiple_births.reconstructed_tree >= minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:152:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L152) *style:* **Lines should not be more than 80 characters.**
```r
    keep_the_sim <- (!crown_species_dead) & (tips >= tips_interval[1] & tips <= tips_interval[2]) #should i keep this simulation?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:154:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
  time_points <- unlist(unname(sort(DDD::L2brts(L, dropextinct = TRUE), decreasing = TRUE)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:172:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L172) *style:* **Lines should not be more than 80 characters.**
```r
#' @description mbd_sim0 produces simulated trees including multiple speciations at the same time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:179:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L179) *style:* **Lines should not be more than 80 characters.**
```r
#' @return The function returns a list of L table, branching times and number of extinct species.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:182:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L182) *style:* **Lines should not be more than 80 characters.**
```r
#'   \item tes is a tree-object corresponding to the reconstructed phylogenetic tree;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:184:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L184) *style:* **Lines should not be more than 80 characters.**
```r
#'   \item extinct_species is the number of species gone extinct before the present time;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:188:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L188) *style:* **Lines should not be more than 80 characters.**
```r
#'      \item second is the label of the parent of the species; positive and negative values only indicate whether the species belongs to the left or right crown lineage;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:189:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L189) *style:* **Lines should not be more than 80 characters.**
```r
#'      \item third is the label of the daughter species itself; positive and negative values only indicate whether the species belongs to the left or right crown lineage;
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:190:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L190) *style:* **Lines should not be more than 80 characters.**
```r
#'      \item fourth is the time of extinction of the species. If this is equal to -1, then the species is still extant.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:195:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L195) *style:* **Lines should not be more than 80 characters.**
```r
#' out = mbd_sim0( pars=c(2.5, 0.1, 0.1), soc=2, age=10, cond=1, tips_interval=c(0,Inf))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:227:18:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L227) *style:* **Use <-, not =, for assignment.**
```r
      total_count=init_n_lineages
                 ^
```
[R/mbd_sim.R:227:18:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L227) *style:* **Put spaces around all infix operators.**
```r
      total_count=init_n_lineages
                ~^~
```
[R/mbd_sim.R:231:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L231) *style:* **Variable or function name should be snake_case.**
```r
      L <- matrix(0, nrow=1e6, 4)
      ^
```
[R/mbd_sim.R:231:26:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L231) *style:* **Put spaces around all infix operators.**
```r
      L <- matrix(0, nrow=1e6, 4)
                        ~^~
```
[R/mbd_sim.R:238:9:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L238) *style:* **Variable or function name should be snake_case.**
```r
        deltaT <- stats::rexp(1, rate = (lambda + n_species * mu))
        ^~~~~~
```
[R/mbd_sim.R:250:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L250) *style:* **Lines should not be more than 80 characters.**
```r
          L[new_interval, 1] <- t#-(delta_n:1)* 1e-5 add this if you need separate time points
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:252:50:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L252) *style:* **Put spaces around all infix operators.**
```r
          L[new_interval, 3] <- abs(new_interval)* sign(parents)
                                                ~^
```
[R/mbd_sim.R:254:44:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L254) *style:* **Put spaces around all infix operators.**
```r
          pool <- c(pool, abs(new_interval)* sign(parents))
                                          ~^
```
[R/mbd_sim.R:255:37:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L255) *style:* **Put spaces around all infix operators.**
```r
          total_count <- total_count+delta_n
                                   ~^~
```
[R/mbd_sim.R:259:51:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L259) *style:* **Put spaces around all infix operators.**
```r
            dead <- sample(pool, replace = F, size=1)
                                                 ~^~
```
[R/mbd_sim.R:264:28:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L264) *style:* **Put spaces around all infix operators.**
```r
          pool <- pool[pool!=dead]
                          ~^~~
```
[R/mbd_sim.R:268:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L268) *style:* **Variable or function name should be snake_case.**
```r
    L=L[(1:total_count), ]
    ^
```
[R/mbd_sim.R:268:6:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L268) *style:* **Use <-, not =, for assignment.**
```r
    L=L[(1:total_count), ]
     ^
```
[R/mbd_sim.R:268:6:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L268) *style:* **Put spaces around all infix operators.**
```r
    L=L[(1:total_count), ]
    ~^~
```
[R/mbd_sim.R:269:21:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L269) *style:* **Use <-, not =, for assignment.**
```r
    extinct_species = sum(L[, 4]!=-1)
                    ^
```
[R/mbd_sim.R:269:33:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L269) *style:* **Put spaces around all infix operators.**
```r
    extinct_species = sum(L[, 4]!=-1)
                               ~^~~
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L271) *style:* **Use <-, not =, for assignment.**
```r
    tips=length(L[, 4][L[, 4]==-1])
        ^
```
[R/mbd_sim.R:271:9:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[, 4][L[, 4]==-1])
       ~^~
```
[R/mbd_sim.R:271:30:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L271) *style:* **Put spaces around all infix operators.**
```r
    tips=length(L[, 4][L[, 4]==-1])
                            ~^~~
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L273) *style:* **Use <-, not =, for assignment.**
```r
    alive=L[L[, 4]==-1, ]
         ^
```
[R/mbd_sim.R:273:10:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[, 4]==-1, ]
        ~^~
```
[R/mbd_sim.R:273:19:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L273) *style:* **Put spaces around all infix operators.**
```r
    alive=L[L[, 4]==-1, ]
                 ~^~~
```
[R/mbd_sim.R:274:10:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L274) *style:* **Use <-, not =, for assignment.**
```r
    alive=matrix(alive, ncol=4)
         ^
```
[R/mbd_sim.R:274:10:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L274) *style:* **Put spaces around all infix operators.**
```r
    alive=matrix(alive, ncol=4)
        ~^~
```
[R/mbd_sim.R:274:29:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L274) *style:* **Put spaces around all infix operators.**
```r
    alive=matrix(alive, ncol=4)
                           ~^~
```
[R/mbd_sim.R:275:30:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L275) *style:* **Use <-, not =, for assignment.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                             ^
```
[R/mbd_sim.R:275:33:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                ^
```
[R/mbd_sim.R:275:41:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                        ^
```
[R/mbd_sim.R:275:67:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                                                 ~^~~
```
[R/mbd_sim.R:275:70:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L275) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                                                     ^
```
[R/mbd_sim.R:275:72:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L275) *style:* **Put spaces around all infix operators.**
```r
    conditioning_on_survival = ( length( unique(sign(alive[, 3])))!=2 )* cond
                                                                      ~^
```
[R/mbd_sim.R:278:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L278) *style:* **Lines should not be more than 80 characters.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:278:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L278) *style:* **Variable or function name should be snake_case.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:278:30:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L278) *style:* **Use <-, not =, for assignment.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
                             ^
```
[R/mbd_sim.R:278:30:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L278) *style:* **Put spaces around all infix operators.**
```r
    births.reconstructed_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
                            ~^~
```
[R/mbd_sim.R:279:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:279:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L279) *style:* **Variable or function name should be snake_case.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
    ^~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L279) *style:* **Use <-, not =, for assignment.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
                    ^
```
[R/mbd_sim.R:279:21:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L279) *style:* **Put spaces around all infix operators.**
```r
    births.full_tree=unlist(unname(sort(DDD::L2brts(L, dropextinct = F), decreasing = T)))
                   ~^~
```
[R/mbd_sim.R:280:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L280) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L280) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L280) *style:* **Variable or function name should be snake_case.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:280:40:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L280) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
                                       ^
```
[R/mbd_sim.R:280:46:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L280) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multiple_births.reconstructed_tree = sum( duplicated(births.reconstructed_tree))
                                             ^
```
[R/mbd_sim.R:281:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L281) *warning:* **local variable ‘multi_births_full_tree’ assigned but may not be used**
```r
    multi_births_full_tree = sum( duplicated(births.full_tree))
    ^~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:281:28:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L281) *style:* **Use <-, not =, for assignment.**
```r
    multi_births_full_tree = sum( duplicated(births.full_tree))
                           ^
```
[R/mbd_sim.R:281:34:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L281) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    multi_births_full_tree = sum( duplicated(births.full_tree))
                                 ^
```
[R/mbd_sim.R:283:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L283) *style:* **Commented code should be removed.**
```r
    # multiple_births_check = (multi_births_full_tree>=minimum_multiple_births)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:284:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L284) *style:* **Lines should not be more than 80 characters.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:284:27:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L284) *style:* **Use <-, not =, for assignment.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
                          ^
```
[R/mbd_sim.R:284:64:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L284) *style:* **Put spaces around all infix operators.**
```r
    multiple_births_check = (multiple_births.reconstructed_tree>=minimum_multiple_births)
                                                              ~^~~
```
[R/mbd_sim.R:286:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L286) *style:* **Lines should not be more than 80 characters.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L286) *style:* **Use <-, not =, for assignment.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
             ^
```
[R/mbd_sim.R:286:14:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L286) *style:* **Put spaces around all infix operators.**
```r
  time_points=unlist(unname(sort(DDD::L2brts(L, dropextinct = T), decreasing = T)))
            ~^~
```
[R/mbd_sim.R:287:8:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L287) *style:* **Use <-, not =, for assignment.**
```r
  brts = -sort(abs(as.numeric(time_points)), decreasing = TRUE)
       ^
```
[R/mbd_sim.R:288:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L288) *style:* **Use <-, not =, for assignment.**
```r
  tes = DDD::L2phylo(L, dropextinct = T)
      ^
```
[R/mbd_sim.R:289:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L289) *style:* **Use <-, not =, for assignment.**
```r
  tas = DDD::L2phylo(L, dropextinct = F)
      ^
```
[R/mbd_sim.R:290:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L290) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tas)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:291:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L291) *style:* **Commented code should be removed.**
```r
  #   graphics::plot(tes)
      ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:304:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L304) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Creates a full simulated dataset of trees under the multiple birth death process
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:305:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L305) *style:* **Lines should not be more than 80 characters.**
```r
#' @description mbd_sim_dataset produces a full dataset of max_sims simulated trees including multiple speciations at the same time. This second version takes into account the possibility both of allopatric and sympatric speciation.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:307:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L307) *style:* **Lines should not be more than 80 characters.**
```r
#' @param edge the program automatically detects the (estimated) average number of tips. "edge" defines the width of the spread around the mean.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:308:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L308) *style:* **Lines should not be more than 80 characters.**
```r
#' @return The function returns a list of brts vectors, one for each of the max_sims simulations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:309:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L309) *style:* **Lines should not be more than 80 characters.**
```r
#' It also saves those in a file called "sim_data" and saves all the settings in a "general_settings" file.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:314:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L314) *style:* **Lines should not be more than 80 characters.**
```r
#' # out <- mbd_sim_dataset( pars=c(0.4, 0.1, 0.2, 0.15), soc=2, age=10, cond=1, edge=Inf )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:328:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L328) *style:* **Lines should not be more than 80 characters.**
```r
  #"edge" gives the extent of fluctuations around the mean that i want to consider
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:338:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L338) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_sim.R:349:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L349) *style:* **Lines should not be more than 80 characters.**
```r
    tips_interval <- c(min_tips, max_tips) #c(10, 45) #setting the upper limit over 50 may be a problem #min and max number of tips for simulated trees
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:349:45:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L349) *style:* **Commented code should be removed.**
```r
    tips_interval <- c(min_tips, max_tips) #c(10, 45) #setting the upper limit over 50 may be a problem #min and max number of tips for simulated trees
                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:356:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L356) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_sim.R:359:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L359) *style:* **Lines should not be more than 80 characters.**
```r
                                tips_interval = tips_interval, minimum_multiple_births = minimum_multiple_births)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:366:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L366) *style:* **Lines should not be more than 80 characters.**
```r
  max_k <- (init_n_lineages - 1) + (is.list(sim_data)) * max(sapply(sim_data, length)) + (1 - is.list(sim_data)) * length(sim_data)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:368:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L368) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_sim.R:381:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L381) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_sim.R:386:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L386) *style:* **Lines should not be more than 80 characters.**
```r
  # simpath=paste("sims /", sim_pars[1], "-", sim_pars[2], "-", sim_pars[3], "-", sim_pars[4], "/", sep = '')
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:386:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L386) *style:* **Commented code should be removed.**
```r
  # simpath=paste("sims /", sim_pars[1], "-", sim_pars[2], "-", sim_pars[3], "-", sim_pars[4], "/", sep = '')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:392:34:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L392) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (file.exists(sim_data_name)){suppressWarnings( file.remove(sim_data_name))}
                                 ^
```
[R/mbd_sim.R:392:52:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L392) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(sim_data_name)){suppressWarnings( file.remove(sim_data_name))}
                                                   ^
```
[R/mbd_sim.R:392:80:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L392) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (file.exists(sim_data_name)){suppressWarnings( file.remove(sim_data_name))}
                                                                               ^
```
[R/mbd_sim.R:394:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L394) *style:* **Lines should not be more than 80 characters.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:394:42:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L394) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
                                         ^
```
[R/mbd_sim.R:394:60:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L394) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
                                                           ^
```
[R/mbd_sim.R:394:96:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L394) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (file.exists(general_settings_name)){suppressWarnings( file.remove(general_settings_name))}
                                                                                ^
```
[R/mbd_sim.R:395:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L395) *style:* **Lines should not be more than 80 characters.**
```r
  save(sim_pars, soc, age, cond, max_sims, tips_interval, max_k, max_b, ext_species, additional_species, tips, minimum_multiple_births, file=general_settings_name)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:395:141:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L395) *style:* **Put spaces around all infix operators.**
```r
  save(sim_pars, soc, age, cond, max_sims, tips_interval, max_k, max_b, ext_species, additional_species, tips, minimum_multiple_births, file=general_settings_name)
                                                                                ~^~
```
[R/mbd_sim.R:396:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L396) *style:* **Lines should not be more than 80 characters.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:396:35:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L396) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                  ^
```
[R/mbd_sim.R:396:53:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L396) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                                    ^
```
[R/mbd_sim.R:396:82:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_sim.R#L396) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (file.exists(sim_trees_name)){suppressWarnings( file.remove(sim_trees_name))}
                                                                                ^
```
[R/mbd_utils.R:20:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:20:31:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L20) *style:* **Commented code should be removed.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:21:26:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                         ^
```
[R/mbd_utils.R:21:41:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Use <-, not =, for assignment.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                        ^
```
[R/mbd_utils.R:21:41:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Put spaces around all infix operators.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                       ~^~
```
[R/mbd_utils.R:21:50:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                 ^
```
[R/mbd_utils.R:21:55:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                      ^
```
[R/mbd_utils.R:21:70:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Use <-, not =, for assignment.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                                     ^
```
[R/mbd_utils.R:21:70:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Put spaces around all infix operators.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                                    ~^~
```
[R/mbd_utils.R:21:80:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (missing(idparsopt)){estimated_pars=1:n_pars}else{estimated_pars=idparsopt}
                                                                               ^
```
[R/mbd_utils.R:24:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:24:43:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L24) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                          ^
```
[R/mbd_utils.R:24:69:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L24) *style:* **Use <-, not =, for assignment.**
```r
  truevalues_color <- "red"; points_color = "azure4"; medians_color = "blue3"#"chartreuse3";
                                                                    ^
```
[R/mbd_utils.R:25:55:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L25) *style:* **Use <-, not =, for assignment.**
```r
  medians_color_name <- "blue"; truevalues_color_name = "red";
                                                      ^
```
[R/mbd_utils.R:31:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L31) *style:* **Lines should not be more than 80 characters.**
```r
  medians_string <- paste0( "MLE Medians (", medians_color_name, ") = (", paste(signif(medians, 2), sep = "''", collapse = ", "), ")")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:31:28:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  medians_string <- paste0( "MLE Medians (", medians_color_name, ") = (", paste(signif(medians, 2), sep = "''", collapse = ", "), ")")
                           ^
```
[R/mbd_utils.R:32:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
  truevalues_string <- paste0( "True Values (", truevalues_color_name, ") = (", paste(signif(sim_pars, 2), sep = "''", collapse = ", "), ")")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:32:31:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L32) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  truevalues_string <- paste0( "True Values (", truevalues_color_name, ") = (", paste(signif(sim_pars, 2), sep = "''", collapse = ", "), ")")
                              ^
```
[R/mbd_utils.R:45:29:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L45) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for (i in estimated_pars) { for (j in estimated_pars) {
                            ^
```
[R/mbd_utils.R:46:5:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L46) *style:* **Variable or function name should be snake_case.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
    ^~~~~~~~~~
```
[R/mbd_utils.R:46:16:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L46) *style:* **Use <-, not =, for assignment.**
```r
    good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
               ^
```
[R/mbd_utils.R:47:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:47:33:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L47) *style:* **Variable or function name should be snake_case.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                ^~~~~~~~~~~~
```
[R/mbd_utils.R:47:72:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L47) *style:* **Variable or function name should be snake_case.**
```r
    ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                                                       ^~~~~~~~~~~~
```
[R/mbd_utils.R:64:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
      graphics::points(x = sim_pars[j], y = sim_pars[i], col = truevalues_color, pch = 10, cex = 1.5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:65:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
      graphics::points(x = medians[j], y = medians[i], col = medians_color, pch = 10, cex = 1.5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:68:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:68:27:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L68) *style:* **Variable or function name should be snake_case.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                          ^~~~~~~~~~
```
[R/mbd_utils.R:68:37:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L68) *style:* **Put spaces around all infix operators.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                   ~^~~
```
[R/mbd_utils.R:68:39:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                      ^
```
[R/mbd_utils.R:68:115:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L68) *style:* **Only use double-quotes.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                                                                ^~
```
[R/mbd_utils.R:68:127:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L68) *style:* **Put spaces around all infix operators.**
```r
  graphics::title(main = (titolo.pdf<-(paste("\n\n", titolo, "\n", medians_string, "\n", truevalues_string, sep = ''))), outer=T)
                                                                                ~^~
```
[R/mbd_utils.R:79:31:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L79) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    for (i in estimated_pars) { for (j in estimated_pars) {
                              ^
```
[R/mbd_utils.R:80:7:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L80) *style:* **Variable or function name should be snake_case.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
      ^~~~~~~~~~
```
[R/mbd_utils.R:80:18:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L80) *style:* **Use <-, not =, for assignment.**
```r
      good.lines = results[, i] < axislimits[i] & results[, j] < axislimits[j]
                 ^
```
[R/mbd_utils.R:81:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L81) *style:* **Lines should not be more than 80 characters.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:81:35:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L81) *style:* **Variable or function name should be snake_case.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                  ^~~~~~~~~~~~
```
[R/mbd_utils.R:81:74:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L81) *style:* **Variable or function name should be snake_case.**
```r
      ifelse(any(good.lines) > 0, good.results <- results[good.lines, ], good.results <- results)
                                                                         ^~~~~~~~~~~~
```
[R/mbd_utils.R:84:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L84) *style:* **Lines should not be more than 80 characters.**
```r
        graphics::hist((good.results[, i]), main = NULL, xlab = paste(par_names[i]), breaks = 15)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:125:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L125) *style:* **Lines should not be more than 80 characters.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, stats::quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:125:31:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L125) *style:* **Commented code should be removed.**
```r
  n_pars <- length(sim_pars);#pars_interval=list(c(0, stats::quantile(results[, 1],.95)), c(0, quantile(results[, 2],.95)), c(0, quantile(results[, 3],.95)))
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:128:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L128) *style:* **Lines should not be more than 80 characters.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:128:27:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L128) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                          ^
```
[R/mbd_utils.R:128:104:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L128) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  for (idpar in 1:n_pars) { percentiles[[idpar]] <- stats::quantile(results[, idpar], quantiles_choice)}
                                                                                ^
```
[R/mbd_utils.R:134:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L134) *warning:* **local variable ‘out’ assigned but may not be used**
```r
  out <- percentiles
  ^~~
```
[R/mbd_utils.R:141:19:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L141) *style:* **Use <-, not =, for assignment.**
```r
heatmap2dataframe = function(
                  ^
```
[R/mbd_utils.R:147:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L147) *style:* **Variable or function name should be snake_case.**
```r
  heatmap.name="HeatMap"
  ^~~~~~~~~~~~
```
[R/mbd_utils.R:150:46:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L150) *style:* **Commas should always have a space after.**
```r
  df <- data.frame(expand.grid(x = x, y = y),HeatMap = matrix_2)
                                             ^
```
[R/mbd_utils.R:157:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L157) *style:* **Lines should not be more than 80 characters.**
```r
#' Converts branching times to "time intervals between branching times" and "birth at nodes" vectors
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:167:1:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L167) *style:* **Lines should not be more than 80 characters.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:167:54:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L167) *style:* **Commas should always have a space after.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:167:54:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L167) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  time_intervals <- c((diff(unique_branching_times)),(abs(utils::tail(unique_branching_times, 1))))
                                                     ^
```
[R/mbd_utils.R:169:29:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L169) *style:* **Put spaces around all infix operators.**
```r
  out <- list(time_intervals=time_intervals, births=births)
                           ~^~
```
[R/mbd_utils.R:169:52:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L169) *style:* **Put spaces around all infix operators.**
```r
  out <- list(time_intervals=time_intervals, births=births)
                                                  ~^~
```
[R/mbd_utils.R:189:3:](https://github.com/Giappo/mbd/blob/23b4f0fa4118829d41e80f1ba0cbc416776e5752/R/mbd_utils.R#L189) *style:* **Variable or function name should be snake_case.**
```r
  create_mbd_P_matrix <- function(
  ^~~~~~~~~~~~~~~~~~~
```


Нужно ли удалять индекс после каждого теста или только в конце Suite


`.shellescape` should only decide if the string needs to be wrapped in `"` or not.
Your code should probably work as it is, but often people use `'` to wrap command line params which does not work on Windows.


LGTM! 👍


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Successfully aliased the URL <https://lingonsaft-hacktober-pwrokiuffh.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


Now could not deploy this pull request since it contains the following references to invalid secrets in the `env` sections of the `now.json` file:

* `oaktoken` (in env: `TOKEN)`
* `mongourl` (in env: `MONGO_URL)`

Add those secrets or remove them from the `env` maps in the `now.json` file.


Хватит только в конце, они вроде не должны никак пересекаться


HI,
this is balaji


Successfully aliased the URL <https://lingonsaft-hacktober-dzsqdwhram.now.sh> to the following alias.

* https://hacktoberfest.lingonsaft.com


stimmt, brauchts nicht mehr