@sebasgross
Missing space


@mfontanini I would hold off on this PR until the other PR is merged. There are overlaps. The changes to the pkg_config file are the only ones needed. @ych, can you change the PR to only include the cppkafka.pc.in?


@sebasgross
Using `var`


Not really. We can make a new release in 1-2 weeks if no major issues show up.


Successfully aliased the URL <https://gelfand-gatsby-project-61ysvlss8.now.sh> to the following aliases.

* https://gelfand-gatsby-project.leoraw.now.sh
* https://gelfand-gatsby-project-git-master.leoraw.now.sh


@sebasgross
Missing spaces


@JuliaRegistrator register

Release notes:

improve the way `extrabits` works


Registration pull request created: [JuliaRegistries/General/1775](https://github.com/JuliaRegistries/General/pull/1775)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.6.1 -m "<description of version>" 0a952f2480f60818307aa4f599e6895cd7d218fb
git push origin v0.6.1
```


Code was not recognized as API Description file. Not updating.


Successfully aliased the URL <https://polscodingnotes-kxhw29yiz.now.sh> to the following aliases.

* https://pols-coding-notes.polcius.now.sh
* https://pols-coding-notes-git-master.polcius.now.sh


Fixes moved to https://github.com/Financial-Times/n-content-body/pull/107


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2825113)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/master/a073c81c457b9b8e1814481e69ac8fd0135f9b48/2825113/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>5 tests failed, 108 tests passed.</summary>

## Failed tests

 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/Debug: TimedOut (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7fccc4604ad0): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
 * [xUnit] Mono BCL tests group 4/iOS Unified 64-bits - device/Debug: HarnessException (Harness exception for '[xUnit] Mono BCL tests group 4': System.IO.IOException: Sharing violation on path /Users/xamarinqa/agent/_work/7/s/jenkins-results/tests/[xUnit] Mono BCL tests group 4/473/test-ios-20190704_023028.log
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share, System.Int32 bufferSize, System.Boolean anonymous, System.IO.FileOptions options) [0x00259] in /Users/builder/jenkins/workspace/build-package-osx-mono/2019-02/external/bockbuild/builds/mono-x64/mcs/class/corlib/System.IO/FileStream.cs:274
  at System.IO.FileStream..ctor (System.String path, System.IO.FileMode mode, System.IO.FileAccess access, System.IO.FileShare share, System.Int32 bufferSize, System.IO.FileOptions options) [0x00000] in /Users/builder/jenkins/workspace/build-package-osx-mono/2019-02/external/bockbuild/builds/mono-x64/mcs/class/corlib/System.IO/FileStream.cs:106
  at (wrapper remoting-invoke-with-check) System.IO.FileStream..ctor(string,System.IO.FileMode,System.IO.FileAccess,System.IO.FileShare,int,System.IO.FileOptions)
  at System.IO.StreamReader..ctor (System.String path, System.Text.Encoding encoding, System.Boolean detectEncodingFromByteOrderMarks, System.Int32 bufferSize) [0x00055] in /Users/builder/jenkins/workspace/build-package-osx-mono/2019-02/external/bockbuild/builds/mono-x64/external/corefx/src/Common/src/CoreLib/System/IO/StreamReader.cs:182
  at System.IO.StreamReader..ctor (System.String path, System.Boolean detectEncodingFromByteOrderMarks) [0x00000] in /Users/builder/jenkins/workspace/build-package-osx-mono/2019-02/external/bockbuild/builds/mono-x64/external/corefx/src/Common/src/CoreLib/System/IO/StreamReader.cs:157
  at System.IO.StreamReader..ctor (System.String path) [0x00000] in /Users/builder/jenkins/workspace/build-package-osx-mono/2019-02/external/bockbuild/builds/mono-x64/external/corefx/src/Common/src/CoreLib/System/IO/StreamReader.cs:152
  at (wrapper remoting-invoke-with-check) System.IO.StreamReader..ctor(string)
  at xharness.AppRunner.ParseResult (xharness.Log listener_log, System.Boolean timed_out, System.Boolean crashed) [0x00347] in /Users/xamarinqa/agent/_work/7/s/tests/xharness/AppRunner.cs:526
  at xharness.AppRunner.TestsSucceeded (xharness.Log listener_log, System.Boolean timed_out, System.Boolean crashed) [0x00001] in /Users/xamarinqa/agent/_work/7/s/tests/xharness/AppRunner.cs:547
  at xharness.AppRunner.RunAsync () [0x01909] in /Users/xamarinqa/agent/_work/7/s/tests/xharness/AppRunner.cs:893
  at xharness.RunDeviceTask.RunTestAsync () [0x0067e] in /Users/xamarinqa/agent/_work/7/s/tests/xharness/Jenkins.cs:3755
  at xharness.RunDeviceTask.RunTestAsync () [0x00c29] in /Users/xamarinqa/agent/_work/7/s/tests/xharness/Jenkins.cs:3805
  at xharness.RunTestTask.ExecuteAsync () [0x00191] in /Users/xamarinqa/agent/_work/7/s/tests/xharness/Jenkins.cs:3534
  at xharness.TestTask.RunInternalAsync () [0x00226] in /Users/xamarinqa/agent/_work/7/s/tests/xharness/Jenkins.cs:2619 )
 * [NUnit] Mono BCL tests group 1/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): TimedOut (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7ffea8c7d4f0): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Failed (HE0041: Error while processing device notifications from fff50:32:37:a1:c8:31fff (0x7f8438743ec0): Failed to communicate with the device. Please ensure the cable is properly connected, and try rebooting the device (error: 0xe8000065 kAMDMuxConnectError))
 * mscorlib/iOS Unified 64-bits - device/Release: TimedOut
</details>


> "Sorry, this diff is taking too long to generate."

Fair enough.


![](https://github.trello.services/images/mini-trello-icon.png) [High Priority: (DAC-FORMS-03) - Fix incorrect field types for first/last names](https://trello.com/c/tv2lbFHB/625-high-priority-dac-forms-03-fix-incorrect-field-types-for-first-last-names)


In the last time the upcoming Neural net engines like Leela Zero shows the benefit from complex evaluations with sufficient calculation power. I experiment now with a simple neural net for ordering quiet moves.

The network has as input the board (for each square there are 13 input neurons for empty and the 12 pieces from each color, expect for rank 1 and 8 where the pawns excluded) which gives 800 input neurons. I use no hidden layer, so the input layer is directly connected to the output layer. Each pair (Piece x Square) represents a move and has one output neuron (so illegal moves included but there not used anyway and make the net only bigger, perhaps later i optimize this). For the activation function at the output layer i use the sigmoid function. The net was trained on repeated iteration over my big bench.

Because this new ordering is a heavy speed penalty (par example if we use this only at each node with depth >= 7 the speed is roughly halfed) i test this first only for the rootNode and only if the depth >= 13 (speed penalty 1-2%).


The file, "platform/barefoot/python-saithrift.mk", is deleted.
but in platform/barefoot/rules.mk
...
include $(PLATFORM_PATH)/python-saithrift.mk

Is this an error?


<details>

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

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and is missing the following scopes:

```
queue:create-task:highest:aws-provisioner-v1/mobile-1-decision
```

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

```
{
  "AllOf": [
    "assume:repo:github.com/MihaiTabara/android-components:branch:dummy",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/mobile-1-decision"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-07-04T10:46:08.197Z

</details>


I suggest using a table instead of too many else-if strucs :)


why converting _sathosies to string and then bellow converting it back to int (Int64.parseInt)?
I suggest:
```
setState(() {
      _amount = _bitcoinEquivalent * 100000000
    });
```

This way you save only the numeric amount in the state and use the formatting function only when needed e.g in the build function or when calling the callback `_onConvert`.


Could you upload new assets to github with TFLite model compatible with DeepSpeech 0.5.1? It works only with that new model.


Successfully aliased the URL <https://uechidev-7etphwh9h.now.sh> to the following aliases.

* https://uechi.dev
* https://uechidev.uechi.now.sh
* https://uechidev-git-master.uechi.now.sh


@sebasgross
Using `var`


@sebasgross
Using `var` and missing space


Successfully aliased the URL <https://uechidev-msaj4ncjs.now.sh> to the following aliases.

* https://uechi.dev
* https://uechidev.uechi.now.sh
* https://uechidev-git-master.uechi.now.sh


Successfully aliased the URL <https://xstate-redux-react-lrh9yrfi5.now.sh> to the following aliases.

* https://xstate-redux-react.danhtran94.now.sh
* https://xstate-redux-react-git-master.danhtran94.now.sh


Кажется, это попало сюда случайно, хотя само изменение выглядит осмысленным, можно оставить так :)


@sebasgross
Commented out code


@sebasgross
Useless `console.log`


# 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)|


Code was not recognized as API Description file. Not updating.


Successfully aliased the URL <https://blog-bw3b4dn53.now.sh> to the following aliases.

* https://linghao.io
* https://blog.linghao.now.sh
* https://blog-git-master.linghao.now.sh


Btw. it works for Postgres - there it's converted from the `QVariantList` - probably we have to solve it in the OGR provider. But the whole decoding part is done in the widget as well at the moment.


Right


skill update


Successfully aliased the URL <https://freddieridellcom-9azngt3kq.now.sh> to the following aliases.

* https://freddieridell.com
* https://www.freddieridell.com
* https://freddieridellcom.freddieridell.now.sh
* https://freddieridellcom-git-master.freddieridell.now.sh


can u explain the the changes


嗯 这个分页只能用于连续的数字类型的字段 最好是有索引的


Jupyter notebook


This is smth new and cool :)
I honestly think that net will be most useful in pawn evaluation.
If you need any help with net training I have semiidle 1080 on my laptop - mail me if needed :D


Yes, this look great!


Please add a space before the backslash. Thanks.


✅ Device tests passed on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=2825115)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/master/a073c81c457b9b8e1814481e69ac8fd0135f9b48/2825115/device-tests/jenkins-results/tests/index.html) ✅

# Test results

# All 113 tests passed


@sebasgross
Missing spaces


demo=spring-cloud


спрятала пароль от почтового ящика cool.efekta@yandex.ru


Проверено.


remove this method.


Is it really sane here to use a hardcoded gcc?


blyat ne ta huinya


<details>

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

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and is missing the following scopes:

```
queue:create-task:highest:aws-provisioner-v1/mobile-1-decision
```

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

```
{
  "AllOf": [
    "assume:repo:github.com/MihaiTabara/android-components:branch:dummy",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/mobile-1-decision"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-07-04T11:06:59.831Z

</details>


Successfully aliased the URL <https://portfolio-1otb17nm9.now.sh> to the following aliases.

* https://akhilaariyachandra.com
* https://portfolio.heshan-1010.now.sh
* https://portfolio-git-master.heshan-1010.now.sh


Intégrer fonction renvoi de message


@hawkeye116477 pierwszy na PC a drugi na Mobile.

Jednak WP dalej ma i zakamuflowane paski cookies.


looks good to me.


добавила в файл .gitignore файл .env (для того что бы не индексировать его)


Il est intéressant de créer renvoyer message quand celui ci n'est jamais parti


courtesy of J. David Moreno Hernández [https://stackoverflow.com/a/53162439](url)


тестировалась рассылка письма на несколько почтовых ящиков


width: calc(100% - 100px);


please add a space before that backslash. thanks


Should these really be updated to use em's?
It's OK within the theme/css etc, but the config doesn't make the same sense to update.

A different body font-size throws everything off and means the values are not as they used to be.
This only works if the body font-size remains at 16px.


Successfully aliased the URL <https://mysmanalytics-atgzxg8xe.now.sh> to the following aliases.

* https://mysmanalytics.smanalytics.now.sh
* https://mysmanalytics-git-master.smanalytics.now.sh


удалила закомментированный код


why/when did this change?
Maybe you could add a "Fixes: " line with a reference to the commit?


国旗画像のURLは取得してきたテンプレートの `国旗画像` って項目にあったはず。URLべた書きじゃなくてプログラム書いて取ってこよう :+1:

APIエンドポイントは今回の場合 `http://ja.wikipedia.org/w/api.php` でいいと思います
あとは https://www.mediawiki.org/wiki/API:Imageinfo を参考に


задание к уроку 3. Рассылаем имейлы


Incorrect order import of modules
Have a consistent order when requiring modules.
1. core modules come first
2. public modules from npm / node_modules folder come second
3. Your own modules come at the end


@sebasgross
Missing spacea


All up and run. Thank you.


@sebasgross
Missing semicolon


@sebasgross
Commented out code


@sebasgross
Missing space


Thanks!


no test? :)


Successfully aliased the URL <https://gelfand-gatsby-project-d1xqemjmm.now.sh> to the following aliases.

* https://gelfand-gatsby-project.leoraw.now.sh
* https://gelfand-gatsby-project-git-master.leoraw.now.sh


Названия переменных user и user1 во-первых не соответсвуют Java Code Convention, а во-вторых противоречат логике наименований, так как спикер из secondSide (т.е. второй) почему-то содержит в названии единицу.
Спикеров-оппонентов можно назвать first- и secondOpponent.


I would say that as long as you don't break any existing test and you write new test cases for this, go ahead.


Typo


The code looks good!
I suggest you create README file with sort instructions on how to start the application?


Successfully aliased the URL <https://bible-strong-website-4z23jj11i.now.sh> to the following aliases.

* https://bible-strong.app
* https://bible-strong-website.bulby97.now.sh
* https://bible-strong-website-git-master.bulby97.now.sh


Why do we move this around in do_compile?
IMHO following alternatives would be better:
   a) move it in an do_unpack_append or
   b) leave the source where it is and just symlink it to the correct directory or
   c) adapt the build script/recipe to handle the directory correctly.

Where c (without moving/linking/copying) would be the preferred one...


This variable is still used but no longer declared, resulting in a compile-time error.


20.py の処理と同じはずなので、https://docs.python.org/ja/3/tutorial/modules.html で紹介されているように module を import すると良いと思います :+1:


@greg0ire can this please be tagged?


難しい正規表現ですが、理解大丈夫ですか？


#2

temporary fix to travis CI, removing nunit from build. As there are no tests for now.


ok


😬 Hi @mypplication Pauland, thank you once again for the PR. I'll add this fix and commit to master directly, just so we don't have the big diff due to the auto formatting.
As soon as the code is pushed I'll create a new release (`2.4.1`) and let you know when it's published via Slack.


@sebasgross
Missing spaces


@sebasgross
Useless `console.log`


1-05.py と全く同じなので import できたらいいですね: https://docs.python.org/ja/3/tutorial/modules.html


![](https://github.trello.services/images/mini-trello-icon.png) [Medium Priority: (DAC-COLOUR-01) - Improve colour contrast of Start New Application button](https://trello.com/c/hJ9xSRIQ/629-medium-priority-dac-colour-01-improve-colour-contrast-of-start-new-application-button)


![](https://github.trello.services/images/mini-trello-icon.png) [Medium Priority: (DAC-COLOUR-02) - Improve colour contrast of "not yet completed" text](https://trello.com/c/4TmtI4qZ/630-medium-priority-dac-colour-02-improve-colour-contrast-of-not-yet-completed-text)


@JuliaRegistrator register


There is no need to edit all language files separate.
Only edit and add English language file. Rest of translations will be done via Crowdin.


Registration pull request created: [JuliaRegistries/General/1776](https://github.com/JuliaRegistries/General/pull/1776)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.2 -m "<description of version>" 2dfae219086fc41c95d67a5c719c2c3945014b17
git push origin v0.1.2
```


word


Very interesting!
Two things though that I can see
1. sizeof(input) (on VLA arrays) is not standard C++, and not widely supported
2. changing order of ranks of the net array to have the index be last would enable vectorization and have better cache locality


Add a space before 500px


You can rename this file to index.html.erb and not require this line


You only add this to the debug, not the actual command.

Why not use something like:

```
cmd = [SQUEEZE_LITE, '-o', 'bluealsa:HCI=%s,DEV=%s,PROFILE=a2dp' % ( hci,dev), '-n', name, '-m', dev , '-f', /dev/null']
debug(str(cmd))
players[key ] Popen(cmd, stdout=DEVNULL, stderr=DEVNULL, shell=False)
```


tfvars


![](https://github.trello.services/images/mini-trello-icon.png) [Medium Priority: (DAC-KEYBOARD-01) - No focus highlighting on search input](https://trello.com/c/AZZq5q8a/631-medium-priority-dac-keyboard-01-no-focus-highlighting-on-search-input)


@sebasgross
Incorrect order import of modules
Have a consistent order when requiring modules.
1. core modules come first
2. public modules from npm / node_modules folder come second
3. Your own modules come at the end


can you write a comment about the check you are changing?


xxxxx


2.基本權限


從反規避法律角度保護用戶的合法權益。


根據第6d條收費


Lets refactor to just one line `index == 0 && 'carousel-item active' || 'carousel-item'`


めちゃくちゃ細かくて申し訳ないんだけど、「および」ってAND（`intersection`）な気がする。XかYのどちらかで良いなら「または」（`union`）かな？
日本語苦手なので間違ってたらおしえてください 🙏


Initial


a）放棄保修或限制責任不同於
    本許可證第15和16條的條款; 要么


8.終止


@JuliaRegistrator register


format使えたらいいですね。あと関数名もうちょっと頑張ってみよう


Registration pull request updated: [JuliaRegistries/General/1776](https://github.com/JuliaRegistries/General/pull/1776)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.2 -m "<description of version>" e64efff68a095f026d602d1afb1937027c49ee2c
git push origin v0.1.2
```


承保工作，您表明您接受本許可證


@ebuchman do we have the plan to deco this from cosmos-sdk? If this is removed, would it cause previously saved local keys cannot be loaded?


銷售，或導入本程序或其任何部分


[A MEIA IDADE NO MERCADO DE TRABALHO - Formato SBC.pdf](https://github.com/gustavopinto/tesl/files/3359072/A.MEIA.IDADE.NO.MERCADO.DE.TRABALHO.-.Formato.SBC.pdf)


@krakjoe, it seems this commit broke [bug64433.phpt](https://github.com/php/php-src/blob/PHP-7.4/ext/standard/tests/streams/bug64433.phpt) on Windows. Test now always [fails](https://ci.appveyor.com/project/php/php-src/builds/25723730/job/n48cm3ojc2sfbin3#L5648) after [10 min](https://ci.appveyor.com/project/php/php-src/builds/25723730/job/n48cm3ojc2sfbin3#L5723)! Problem seems to be the 305 response code. Any idea?


有關這方面的更多信息，以及如何應用和遵循GNU AGPL，請參閱
<https://www.gnu.org/licenses/>。


Add space before closing ruby tag


move "MariaDB key definition" one tab.


これ `len()` しなくても `word_split` をそのまま for 文にかけられないかな？　そうするとわざわざ `word = word_split[i]` する必要がなくなる


![](https://github.trello.services/images/mini-trello-icon.png) [Low Priority: (DAC-FORMS-01) - Change number inputs to type=tel](https://trello.com/c/mREeDd7w/636-low-priority-dac-forms-01-change-number-inputs-to-typetel)


you can write bool too_big_key_part_length(). you don't need extra line


@sebasgross
Commented out code


@sebasgross
Missing spaces


> More files to "collect", e.g. also `.deps`.

good point. let's add `scripts/` later.


GNU 通用公共許可證 (GPL)
GNU 次通用公共許可證 (LGPL)
GNU 自由文檔許可證 (FDL)
非官方的翻譯工作
逐字的複製與分發
自由軟體許可證列表
何為 Copyl


@sebasgross
Missing semicolons


@sebasgross
Useless `console.log`


Что ето за "А"?))))


アップロードミスのため削除


This commit implements right-justification at a timestamp assigned to a `<dynam>` element in the Humdrum-to-MEI converter.  The commit also implements coloring of dynamics (similar to `<dir>`, using the `color` layout parameter).

Example:

<img width="959" alt="Screen Shot 2019-07-04 at 1 30 51 PM" src="https://user-images.githubusercontent.com/3487289/60663546-d25e7c00-9e5f-11e9-9b5c-013f182c2f4e.png">

Humdrum data:

```
**kern		**dynam		**kern		**dynam
*M4/4		*		*M4/4		*
=1		=1		=1		=1
!!LO:TX:a:t=dynamics left aligned to timestamp
!!LO:TX:b:t=dynamics right aligned to timestamp
1F		.		1F		.
=2		=2		=2		=2
!		!LO:DY:rj	!		!LO:DY:color=chartreuse
1G-		fff		1G-		fff
=3		=3		=3		=3
!LO:DY:rj:color=hotpink	!	!		!
1A-z		.		1A-z		.
=5		=5		=5		=5
1c		.		1c		.
==		==		==		==
*-		*-		*-		*-
```

MEI conversion:

```bash
verovio file.krn -atmei
```

```xml
<?xml version="1.0" encoding="UTF-8"?>
<?xml-model href="http://music-encoding.org/schema/4.0.0/mei-all.rng" type="application/xml" schematypens="http://relaxng.org/ns/structure/1.0"?>
<?xml-model href="http://music-encoding.org/schema/4.0.0/mei-all.rng" type="application/xml" schematypens="http://purl.oclc.org/dsdl/schematron"?>
<mei xmlns="http://www.music-encoding.org/ns/mei" meiversion="4.0.0">
 <meiHead>
  <fileDesc>
   <titleStmt>
    <title />
   </titleStmt>
   <pubStmt />
  </fileDesc>
  <encodingDesc>
   <appInfo>
    <application isodate="2019-07-04T13:33:13" version="2.2.0-dev-9eb4d78">
     <name>Verovio</name>
     <p>Transcoded from Humdrum</p>
    </application>
   </appInfo>
  </encodingDesc>
  <workList>
   <work>
    <title />
   </work>
  </workList>
 </meiHead>
 <music>
  <body>
   <mdiv xml:id="mdiv-0000000527028095">
    <score xml:id="score-0000001538632437">
     <scoreDef xml:id="scoredef-0000001901679428" midi.bpm="400">
      <staffGrp xml:id="staffgrp-0000001445474164" symbol="brace" bar.thru="true">
       <staffDef xml:id="staffdef-0000001134536184" clef.shape="G" clef.line="2" meter.count="4" meter.unit="4" n="1" lines="5" />
       <staffDef xml:id="staffdef-0000000768214203" clef.shape="G" clef.line="2" meter.count="4" meter.unit="4" n="2" lines="5" />
      </staffGrp>
     </scoreDef>
     <section xml:id="section-L1F1">
      <measure xml:id="measure-L1" n="0">
       <staff xml:id="staff-0000000766236772" n="1">
        <layer xml:id="layer-L1F3N1" n="1">
         <note xml:id="note-L6F3" dur="1" oct="3" pname="f" accid.ges="n" />
        </layer>
       </staff>
       <staff xml:id="staff-0000001829479592" n="2">
        <layer xml:id="layer-L1F1N1" n="1">
         <note xml:id="note-L6F1" dur="1" oct="3" pname="f" accid.ges="n" />
        </layer>
       </staff>
       <dir xml:id="dir-L6F3" place="above" staff="1" tstamp="1.000000">
        <rend xml:id="rend-0000000283000724" fontstyle="normal">dynamics left aligned to timestamp</rend>
       </dir>
       <dir xml:id="dir-L6F1" place="below" staff="2" tstamp="1.000000">
        <rend xml:id="rend-0000000552548552" fontstyle="normal">dynamics right aligned to timestamp</rend>
       </dir>
      </measure>
      <measure xml:id="measure-L7" n="2">
       <staff xml:id="staff-L7F3N1" n="1">
        <layer xml:id="layer-L7F3N1" n="1">
         <note xml:id="note-L9F3" dur="1" oct="3" pname="g" accid="f" />
        </layer>
       </staff>
       <staff xml:id="staff-L7F1N1" n="2">
        <layer xml:id="layer-L7F1N1" n="1">
         <note xml:id="note-L9F1" dur="1" oct="3" pname="g" accid="f" />
        </layer>
       </staff>
       <dynam xml:id="dynam-L9F4" staff="1" tstamp="1.000000" vgrp="100">
        <rend xml:id="rend-0000000746405364" color="chartreuse" fontsize="large" fontweight="bold">fff </rend>
       </dynam>
       <dynam xml:id="dynam-L9F2" staff="2" tstamp="1.000000" vgrp="100">
        <rend xml:id="rend-0000000370144791" halign="right" fontsize="large" fontweight="bold">fff </rend>
       </dynam>
      </measure>
      <measure xml:id="measure-L10" n="3">
       <staff xml:id="staff-L10F3N1" n="1">
        <layer xml:id="layer-L10F3N1" n="1">
         <note xml:id="note-L12F3" dur="1" oct="3" pname="a" accid="f" />
        </layer>
       </staff>
       <staff xml:id="staff-L10F1N1" n="2">
        <layer xml:id="layer-L10F1N1" n="1">
         <note xml:id="note-L12F1" dur="1" oct="3" pname="a" accid="f" />
        </layer>
       </staff>
       <dynam xml:id="dynam-L12F3" staff="1" tstamp="1.000000">sf</dynam>
       <dynam xml:id="dynam-L12F1" staff="2" tstamp="1.000000">
        <rend xml:id="rend-0000000174330405" halign="right" color="hotpink" fontsize="large" fontweight="bold">sf </rend>
       </dynam>
      </measure>
      <measure xml:id="measure-L13" right="end" n="5">
       <staff xml:id="staff-L13F3N1" n="1">
        <layer xml:id="layer-L13F3N1" n="1">
         <note xml:id="note-L14F3" dur="1" oct="4" pname="c" accid.ges="n" />
        </layer>
       </staff>
       <staff xml:id="staff-L13F1N1" n="2">
        <layer xml:id="layer-L13F1N1" n="1">
         <note xml:id="note-L14F1" dur="1" oct="4" pname="c" accid.ges="n" />
        </layer>
       </staff>
      </measure>
     </section>
    </score>
   </mdiv>
  </body>
 </music>
</mei>
```

The conversion is implemented by mapping the layout parameter `rj` to `rend@halign="right"`.  An extra space is needed at the moment after the dynamic text to force it to be right-justified.  Currently right-justified dynamics are displayed as text, but simulating graphical symbols by making the font bold and large.  This is related to issue  https://github.com/rism-ch/verovio/issues/1117 .


![](https://github.trello.services/images/mini-trello-icon.png) [Low Priority: (DAC-LAYOUT-01) - Improve link style for low-vision users (eg. underline/borders on Back link)](https://trello.com/c/w4cw5MSj/637-low-priority-dac-layout-01-improve-link-style-for-low-vision-users-eg-underline-borders-on-back-link)


Проверено.


Set a Mac Wifi name via Bash, good for Kaseya/Jamf


Я бы назвал `clean` или `clear` (не помню какой лучше подходит). Ты очищаешь карту.


Successfully aliased the URL <https://texttv-3-app-2e58uo2xu.now.sh> to the following aliases.

* https://app.texttv.nu
* https://texttv-3-app.bonny.now.sh
* https://texttv-3-app-git-texttv2019.bonny.now.sh


Successfully aliased the URL <https://news-client-eg58gowhm.now.sh> to the following aliases.

* https://news-client.andrewtomanek.now.sh
* https://news-client-git-master.andrewtomanek.now.sh


**Please tell me how to contact you**


15 fautes ca reste raisonnable


Withdraw to all token


Successfully aliased the URL <https://next-3zezpztmi.now.sh> to the following aliases.

* https://next.oacore.now.sh
* https://next-git-content.oacore.now.sh


I add some more


Successfully aliased the URL <https://skyscraperai-landingpage-np5klrkdl.now.sh> to the following aliases.

* https://skyscraper.ai
* https://www.skyscraper.ai
* https://skyscraperai-landing-page.kazazes.now.sh
* https://skyscraperai-landing-page-git-master.kazazes.now.sh


Thanks @oliverfoster I have commented here: https://github.com/adaptlearning/adapt_framework/commit/d751f357804990e6eed24f66a36fa56842421835#commitcomment-34184695 to query changing the config sizes.


See Issue #3


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

* https://www.connordav.is


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/1777](https://github.com/JuliaRegistries/General/pull/1777)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.25.3 -m "<description of version>" 64e035c53c886869d987a2f68a4134534b771c19
git push origin v0.25.3
```


[``](url)


![](https://github.trello.services/images/mini-trello-icon.png) [Low Priority: (DAC-FORMS-07) - Move "Your Idea" character length text above the fields](https://trello.com/c/flfqRYrR/634-low-priority-dac-forms-07-move-your-idea-character-length-text-above-the-fields)


Ok @Ian1971 it would be very useful for me...I need to update 22 projects inside a solution...

Do you know when release the new version?

Thanks.


Just testing deifferent versions


cc @sonata-project/release-managers


# 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)|


<details>

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

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and is missing the following scopes:

```
queue:create-task:highest:aws-provisioner-v1/mobile-1-decision
```

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

```
{
  "AllOf": [
    "assume:repo:github.com/MihaiTabara/android-components:branch:dummy",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/mobile-1-decision"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-07-04T11:52:23.670Z

</details>


Successfully aliased the URL <https://skyscraperai-landingpage-qlinok2nu.now.sh> to the following aliases.

* https://skyscraper.ai
* https://www.skyscraper.ai
* https://skyscraperai-landing-page.kazazes.now.sh
* https://skyscraperai-landing-page-git-master.kazazes.now.sh


@techAPJ sure, I can add the test. Any particular scenario? (failed trying to get any particular attribute?)


I don't as I am not the owner of the package just a random guy. You could
however grab the code and build it instead?

On Thu, 4 Jul 2019, 12:49 Nicolas Pablo Fernandez Theillet, <
notifications@github.com> wrote:

> Ok @Ian1971 <https://github.com/Ian1971> it would be very useful for
> me...I need to update 22 projects inside a solution...
>
> Do you know when release the new version?
>
> Thanks.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/Ian1971/TargetFrameworkMigrator/commit/85e37a725288d4b57a3ec11489163d46152be8c9?email_source=notifications&email_token=AACN2SOMFMX6DQVHNBUY4ILP5XPWNA5CNFSM4H5W6ND2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBATH76#commitcomment-34185214>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AACN2SOCTMJSVPNRYD5LXQDP5XPWNANCNFSM4H5W6NDQ>
> .
>


I have no idea... Actually if I force the DEPENDENCY ecj-initial-native and then I use it, I get the error:

```
| mkdir classes
| /workdir/build/tmp/work/dbfp4-poky-linux/jamvm/2.0.0-devel+gitAUTOINC+6cef41d859-r0/recipe-sysroot-native/usr/bin/ecj-initial -bootclasspath /workdir/build/tmp/work/dbfp4-poky-linux/jamvm/2.0.0-devel+gitAUTOINC+6cef41d859-r0/recipe-sysroot-native/usr/share/classpath/glibj.zip -d classes ../../../../../git/src/classlib/gnuclasspath/lib/jamvm/java/lang/JarLauncher.java ../../../../../git/src/classlib/gnuclasspath/lib/jamvm/java/lang/VMClassLoaderData.java ../../../../../git/src/classlib/gnuclasspath/lib/jamvm/ThreadInfoHelper.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/VMRuntime.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/VMClass.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/VMClassLoader.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/VMString.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/VMThread.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/VMThrowable.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/reflect/VMConstructor.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/reflect/VMField.java ../../../../../git/src/classlib/gnuclasspath/lib/java/lang/reflect/VMMethod.java ../../../../../git/src/classlib/gnuclasspath/lib/java/security/VMAccessController.java ../../../../../git/src/classlib/gnuclasspath/lib/gnu/classpath/VMSystemProperties.java ../../../../../git/src/classlib/gnuclasspath/lib/sun/reflect/annotation/AnnotationInvocationHandler.java ../../../../../git/src/classlib/gnuclasspath/lib/gnu/classpath/VMStackWalker.java
| LOG: [0x00007fe3c01f8400] java/lang/NoClassDefFoundError: java/lang/Object
| Aborted (core dumped)

```


I have workaround it, but using javac when not class-native.


Successfully aliased the URL <https://next-ic8ejl5j7.now.sh> to the following aliases.

* https://next.oacore.now.sh
* https://next-git-content.oacore.now.sh


Is this still correct? TODO?


we can avoid this local variable. we can use rec_max_size  += (field_max_size < 256 ? 1 : 2); directly


@Sopel97
Thanks for the hints. I'am not an expert with neural nets that just my first real experiments. I will have a closer look if i have time (to explore the general idea is in the moment more interresting than speed optimization (but i forget them not)).


Successfully aliased the URL <https://texttv-3-app-g8hk8k9yy.now.sh> to the following aliases.

* https://app.texttv.nu
* https://texttv-3-app.bonny.now.sh
* https://texttv-3-app-git-texttv2019.bonny.now.sh


@glwagner, these changes in `problem.jl` broke the code.. I'm revering back and you can revise later.


deleted folder


ok


mantap


the above doesn't quite correspond with the actual data structure, it has objects with keys by geographic names


@sebasgross
Commented out code


Could you actually also add a test where kibana is not enabled, now that you added the kill switch handler?


Obsoletp


при этом переменная count осталась неизменной и то что массив пустой осталось только информацией на экране :)
Мне кажется эта строчка немного избыточной, то что выполняется в блоке else ниже верно даже если массив после удаления стал пустым.
Тут на твоё усмотрение.


[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after an infinite number of generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:11:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L11) *style:* **Variable or function name should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L12) *style:* **Variable or function name should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  K <- H_0 * C * 2 * N * R / (2 * N * C + R)
  ^
```
[R/calc_K.R:19:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L19) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calc_K.R#L27) *style:* **Variable or function name should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the error in the estimate of the onset of hybridisation, following Equations 3 & 4 in the Supplementary information of Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param relative Boolean flag, if TRUE: return the relative error, if FALSE: return error in generations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:15:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L15) *style:* **Variable or function name should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L17) *style:* **Variable or function name should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L18) *style:* **Variable or function name should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_error.R:30:7:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
      ^
```
[R/calculate_error.R:30:25:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
                        ^
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Function that calculates the maximum time after hybridization after which the number of junctions can still be reliably used to estimate the onset of hybridization. This is following equation 15 in Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:12:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L12) *style:* **Variable or function name should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_MAT.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_time.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the number of junctions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 14 in Janzen et al. 2018
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' estimate_time(J = J, N = 100, R = 1000, H_0 = 0.5, C = 1)  # should be 200 again
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:13:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L13) *style:* **Variable or function name should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L16) *style:* **Variable or function name should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/calculate_time.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/estimate_time_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 1 in Janzen et al. unpublished
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:8:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:12:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200, marker_distribution = markers)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L18) *style:* **Variable or function name should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L19) *style:* **Variable or function name should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:108:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L108) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_phased.R:135:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:135:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L135) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:138:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L138) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:142:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:143:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L143) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:147:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:148:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L148) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:149:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L149) *style:* **Lines should not be more than 80 characters.**
```r
#' @param optim_pop_size If TRUE, population size is also optimized. Starting point of the optimizaton will then be on the given population size, and half the maximum time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:184:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L184) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:191:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_phased.R#L191) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L2) *style:* **Variable or function name should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                       ^
```
[R/estimate_time_unphased.R:12:43:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                                          ^
```
[R/estimate_time_unphased.R:18:22:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- p * q * ( p * q * P[3] +
                     ^
```
[R/estimate_time_unphased.R:35:24:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                       ^
```
[R/estimate_time_unphased.R:88:19:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L88) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_unphased.R:115:23:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:115:32:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L115) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:118:12:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L118) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:175:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L175) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:182:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/estimate_time_unphased.R#L182) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, in a backcrossing mating scheme.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:4:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:10:43:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_backcross.R#L10) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected number of junctions between two markers separated by a given amount of recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distance between two markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:12:36:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L12) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_di <- function(N = Inf,
                                   ^
```
[R/number_of_junctions_di.R:13:36:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_di.R#L13) *style:* **Variable or function name should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected total number of junctions in a chromosome, given the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distribution of markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L20) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions_markers <- function(N = Inf,
                                        ^
```
[R/number_of_junctions_markers.R:21:41:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L21) *style:* **Variable or function name should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions_markers.R#L32) *warning:* **no visible global function definition for ‘number_of_junctions_di’**
```r
    expected_junctions <- number_of_junctions_di(N, H_0, t, di)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after t generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:13:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L13) *style:* **Variable or function name should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L14) *style:* **Variable or function name should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L15) *style:* **Variable or function name should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/number_of_junctions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param calc_func function to calculate the time, should accept two arguments: upper, lower and should return a stats::optimize object with two properties: $minimum and $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:38:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/phased_log_likelihood.R:45:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/phased_log_likelihood.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:12:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_backcrossing.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with regularly distributed markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:5:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:17:27:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
sim_fin_chrom <- function (pop_size = 100,
                          ^
```
[R/sim_fin_chrom.R:22:28:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_fin_chrom.R#L22) *style:* **Variable or function name should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with an infinite number of recombination sites.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param markers The number of genetic markers superimposed on the chromosome. If markers is set to -1, no markers are superimposed (faster simulation)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_inf_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:6:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:11:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/sim_phased_unphased.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the unphased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:34:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/unphased_log_likelihood.R:41:58:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/util.R:22:10:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( get_states_vector(local_anc))
         ^
```
[R/util.R:22:11:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L22) *warning:* **no visible global function definition for ‘get_states_vector’**
```r
  return( get_states_vector(local_anc))
          ^~~~~~~~~~~~~~~~~
```
[R/util.R:56:42:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    (local_anc_matrix[, 1 ] == local_anc_matrix[, 2]))
                                         ^
```
[R/util.R:108:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:108:37:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L108) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state <- function(P, p, focal_state) {
                                    ^
```
[R/util.R:116:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 3) cond_prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:122:49:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (focal_state == 4) cond_prob <- (p ^ 2) * ( P[1] + P[4] + P[7]) +
                                                ^
```
[R/util.R:146:1:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/util.R:146:44:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L146) *style:* **Variable or function name should be snake_case.**
```r
get_expectation_O_state_phased <- function(P, p, focal_state) {
                                           ^
```
[R/util.R:151:18:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/R/util.R#L151) *warning:* **no visible global function definition for ‘get_expectation_O_state’**
```r
    cond_prob <- get_expectation_O_state(P, p, focal_state)
                 ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-equations.R#L18) *style:* **Variable or function name should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L17) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L60) *style:* **Variable or function name should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-marker_dist.R#L61) *style:* **Variable or function name should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L4) *style:* **Variable or function name should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L5) *style:* **Variable or function name should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/0f6e260da45978fc0050cef055790f7c11fb7b96/tests/testthat/test-sims.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```


Thank you for contributing jskeus documentation

Please check latest documents before merging

PDF version of Japanese jmanual: jmanual.pdf
HTML version of Japanese manual: jmanual.html
Sphinx (ReST) version of Japanese manual: jmanual.rst


@sebasgross
Incorrect order import of modules
Have a consistent order when requiring modules.
1. core modules come first
2. public modules from npm / node_modules folder come second
3. Your own modules come at the end


<details>

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

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and is missing the following scopes:

```
queue:create-task:highest:aws-provisioner-v1/mobile-1-decision
```

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

```
{
  "AllOf": [
    "assume:repo:github.com/MihaiTabara/android-components:branch:dummy",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/mobile-1-decision"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-07-04T12:00:51.511Z

</details>


But... sadly it's still not perfect. It is mostly better than without polling because at least I always have the state updated but there are times when I can't send any command. it can last like 20 seconds. I wait and then I can once more send commands with success.

When I cannot send command, the log is filled with this error:
```
2019-07-04 13:58:23 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:23 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:23 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:23 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:23 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:23 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:24 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:25 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:25 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:25 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:25 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:25 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
2019-07-04 13:58:26 ERROR (ZiGate-Decode data) [zigate] Command 0x0100 failed Failed (ZigBee event codes) 15 : b''
```


Olá, mais alguém com o app não está funcionando hoje? O meu não entrou... Alguém tem um link para baixá-lo novamente? Ou alguma atualização? Obrigada.


please undo this commit and only commit the first one


hah, idk. prolly too much copying and not enough thinking on my part.

On Wed, Jul 3, 2019 at 1:58 PM Niko <notifications@github.com> wrote:

> curious, why are you deferring a log statement rather than putting it
> after the next line?
>
> —
> You are receiving this because you authored the thread.
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This should be self.refs rather than self.refs.keys(); if the value of the ref changes you'd also want to refresh the commit time.


I think you forgot to run "npm build". I'm getting the following error now:

`While trying to resolve module `@benawad/expo-mixpanel-analytics` from file `/Users/holgersindbaek/CloudDrive/HolgerSindbaek/HabitTracker/Programming/HabitTracker/utils/track.js`, the package `/Users/holgersindbaek/CloudDrive/HolgerSindbaek/HabitTracker/Programming/HabitTracker/node_modules/@benawad/expo-mixpanel-analytics/package.json` was successfully found. However, this package itself specifies a `main` module field that could not be resolved (`/Users/holgersindbaek/CloudDrive/HolgerSindbaek/HabitTracker/Programming/HabitTracker/node_modules/@benawad/expo-mixpanel-analytics/src/dist/index.js`. Indeed, none of these files exist:

  * `/Users/holgersindbaek/CloudDrive/HolgerSindbaek/HabitTracker/Programming/HabitTracker/node_modules/@benawad/expo-mixpanel-analytics/src/dist/index.js(.native||.ios.js|.native.js|.js|.ios.json|.native.json|.json|.ios.ts|.native.ts|.ts|.ios.tsx|.native.tsx|.tsx)`
  * `/Users/holgersindbaek/CloudDrive/HolgerSindbaek/HabitTracker/Programming/HabitTracker/node_modules/@benawad/expo-mixpanel-analytics/src/dist/index.js/index(.native||.ios.js|.native.js|.js|.ios.json|.native.json|.json|.ios.ts|.native.ts|.ts|.ios.tsx|.native.tsx|.tsx)`
Failed building JavaScript bundle.`


{
    "Width": 1024,
    "Height": 768,
    "Origin": {
        "x": 0,
        "y": 0,
        "z": 0
    },
    "Spheres": [
        {
            "Radius": 2,
            "Center": {
                "x": -3,
                "y": 0,
                "z": -16
            },
            "Material": {
                "RefIndex": 1,
                "DiffColor": {
                    "x": 125,
                    "y": 100,
                    "z": 15
                },
                "SpecExp": 150,
                "Albedo": [
                    0.6,
                    0.3,
                    0,
                    0
                ]
            }
        },
        {
            "Radius": 2,
            "Center": {
                "x": 2,
                "y": -1.5,
                "z": -12
            },
            "Material": {
                "RefIndex": 1.5,
                "DiffColor": {
                    "x": 148,
                    "y": 125,
                    "z": 136
                },
                "SpecExp": 10,
                "Albedo": [
                    0.9,
                    0.1,
                    0,
                    0
                ]
            }
        },
        {
            "Radius": 3,
            "Center": {
                "x": 1.5,
                "y": -.5,
                "z": -18
            },
            "Material": {
                "RefIndex": 1,
                "DiffColor": {
                    "x": 148,
                    "y": 125,
                    "z": 136
                },
                "SpecExp": 1425,
                "Albedo": [
                    0,
                    10,
                    0.8,
                    0
                ]
            }
        },
        {
            "Radius": 4,
            "Center": {
                "x": -3,
                "y": 5,
                "z": -18
            },
            "Material": {
                "RefIndex": 1,
                "DiffColor": {
                    "x": 148,
                    "y": 125,
                    "z": 136
                },
                "SpecExp": 125,
                "Albedo": [
                    0,
                    0.5,
                    0.1,
                    0.8
                ]
            }
        }
    ],
    "CheckerBoard": [
        {
            "Color1": {
                "x": 1,
                "y": 1,
                "z": 1
            },
            "Color2": {
                "x": 255,
                "y": 255,
                "z": 255
            }
        }
    ],
    "PathBack": "https://img3.akspic.ru/image/104835-prirodnyj_zapovednik-peyzash-polevoj_cvetok-priroda-pejzazhi_gor-2048x1152.jpg",
    "Lights": [
        {
            "intensity": 1,
            "position": {
                "x": -20,
                "y": 20,
                "z": 20
            }
        },
        {
            "intensity": 1.8,
            "position": {
                "x": 30,
                "y": 50,
                "z": -25
            }
        }
    ]
}

http://localhost:44375/api/Render/RenderImage


Исправленный  update_related_data_marts.py в коммите:
https://github.com/infolabs/django-edw/commit/73283999095861974cd70f4b5dc58bf88d1529ee


@sebasgross
Missing spaces.
Should be used single quotes instead of double


@bpar476, this change causes issues if you have similarly named stacks. E.g. our taskcat builds are creating stacks  `tCaT-tag-jira-524afe87` but this is then trimmed to `tcat-db`, which causes issues in case you are deploying multiple builds or even different products. These are the constraints:

* Must contain from 1 to 63 letters, numbers, or hyphens.
* First character must be a letter.
* Can't end with a hyphen or contain two consecutive hyphens.

Taskcat generates 23-30 characters for the name of the root stack. I would say we shouldn't trim this to the prefix as some customers might use for example just `eu-stack-something-nothing` and we would try to reuse `eu-db` for all Atlassian stacks with Postgres. What was the motivation to change this?


@sebasgross
Using `let` instead `const`
`data` doesn't change so should be used `let`


Sorry for missing that you published this… That's worth a 🌟