You are any casting strings instead of the values retrieved from the parameter map via the strings.  Remember that the param_map has prototype

std::map<std::string, boost::any>

To retrieve a value from the map, use the look up string.  For example, on line 177, you retrieve the value

param_map[S_RHO_1]

with the key S_RHO_1.  The value retrieved is of type boost::any, which you then must cast to a double.  Line 177 should thus read

boost::any_cast<double>( param_map[S_RHO_1] ) /


Начиная с C# версии 6 вместо String.Format рекомендуется использовать интерполяцию строк. Пожалуйста, посмотрите, что это такое и исправьте.


@chelmuth: please add to staging


What is beacon? What is "better debugging"? Why do we need it?


Gives error-
Traceback (most recent call last):
  File "C:\Users\bajpai\Documents\GitHub\LinkCheck\ark.py", line 21, in <module>
    FileName = sys.argv[1]
IndexError: list index out of range


We should rename this SiteToSiteProvenanceTaskReportingTask for consistency.


Then, I will back it :)


Any reason why this was changed from error to debug?


It would be better use more precise variables. I know the specification therefore I know what could be the x, y, z variables. It can be more descriptive if you use the eg. "height", "width" and "lenght" instead the letters.


@nokecskes nice :+1:


Great. That should do it. The command does require the directory to be supplied though (I think it should virtually always be /usr/share/glib-2.0/schemas/).


应该封装一个 `genFileByType(type)` 之类的方法来避免这些冗余代码


The completer is triggered when entering "(".
You can select an entry with up/down keys and insert it with return-key.
You can make it go away by pressing escape.


I am just using the default values descibed here:
https://github.com/KhronosGroup/glTF/blob/2.0/specification/2.0/schema/material.pbrMetallicRoughness.schema.json
So
[ 1.0, 1.0, 1.0, 1.0 ] for baseColorFactor
1.0 for metallicFactor
1.0 for roughnessFactor
[ 0.0, 0.0, 0.0 ] for emissiveFactor

As no occlusionTexture is present, the occlusion strength is not used.

So
"materials" : [
{
"name" : "Cube",
"pbrMetallicRoughness" : {}
}
],

results in the above image, which is also somehow a grey.


Are tests hadnwritten? Please test generated ones
other cases: LGTM


Add a TODO that Q8W8U8V8 might be applicable here too


Thanks will be fixed in different ticket https://djgusa.atlassian.net/browse/DIO-624


Let's say you want to at a flat layer at 1.2 km depth and Vp of 2.8 km/s :

```
layers = ((wbz,wbz,wbz,wbz),
         (0.35,0.35,0.35,0.35),
         (0.95,0.95,0.65,0.65),
         **(1.20,1.20,1.20,1.20),**
         (1.90,1.90,1.90,1.90))
velocities = (1.500,
               1.800,
               2.000,
               2.500,
               **2.800,**
               4.500)
```
You will remove the ** ** from the code above. I used it just to highlight the important changes.


/(?!^)([A-Z])/g


Let's say you want to add a flat layer at 1.2 km depth and Vp of 2.8 km/s :

```
layers = ((wbz,wbz,wbz,wbz),
         (0.35,0.35,0.35,0.35),
         (0.95,0.95,0.65,0.65),
         **(1.20,1.20,1.20,1.20),**
         (1.90,1.90,1.90,1.90))
velocities = (1.500,
               1.800,
               2.000,
               2.500,
               **2.800,**
               4.500)
```
You will remove the ** ** from the code above. I used it just to highlight the important changes.


可以通过传递 `options.styleType` 到一个 `genFileByType(options.styleType)` 来避免太多判断，这样扩展性也更好


It's unnecessary convert numbers to float. It also convert the integer numbers (eg. 10 -> 10.0).


@chelmuth: please consider for staging


don't you know, to write in a new line


@ehaberev это код жалобы, комментарий неправильный написал. Про идентификатор ведомства понял, допишу.


I do not really believe in the idea of distributing support ideas to pieces, but it needed to be checked


@ljharb why did we gain lodash as a dependency? ;)


@nokecskes there is no need to actually store the tiles in double arraylist, you're totally fine with a simple one


`try-catch` 直接抛出错误，那和不 `try` 没什么区别


@nokecskes you're doing something with the fields of the Hero class, that should happen in the Hero
(in an ideal world every field is private)


this does not fix the issue reported by the customer. What is this code doing?


我看了你写的一些东西，感觉特别好，尤其是对于我这个菜鸟新接触tensorflow。
我试着运行了你的XOR_gate代码，里面出现了一些问题。
1.第一个是权重初始化中，运行会报错，我试着将其修改为initial = tf.truncated_normal(shape, stddev=0.1)/tf.sqrt(np.array(shape[1],dtype='float32'))，才能运行通过
2.然后运行到所有变量的初始化，由于原先的initialize_all_variables被弃用，所以我根据提示修改为tf.global_variables_initializer().run()
3.最后得到的结果并不是和您的结果一致，我不知道是什么原因，怀疑是初始化方法的问题。
![qq 20170412200546](https://cloud.githubusercontent.com/assets/26303061/24956708/740044d8-1fbb-11e7-8814-0112567e9d27.png)
4.然后就是我想用tensorflow实现LSTM，并融入我自己的想法，想法还不够成熟。希望您能在百忙之中给予指点。非常感谢。


same here :)


While the audio plays, the output is some sort of error-
```
[03105ed4] core input error: ES_OUT_SET_(GROUP_)PCR  is called too late (pts_delay increased to 300 ms)
[03105ed4] core input error: ES_OUT_RESET_PCR called
[0312f4bc] mpgatofixed32 audio converter error: libmad error: bad main_data_begin pointer
```
Any idea what's wrong, also, I didn't know that the FileName had to be specified while running the script. Should I add how to use instructions within the readme.md or a separate file?
Thanks so much!


Calcule ton score avec un ratio alpha/beta au lieu d'une moyenne, voire meme theta/beta
Il y a pas mal d'articles qui disent que le ratio de puissance entre les bande theta et beta corrèle avec le niveau d'attention, de concentration ou de meditation. C'est donc pile poil ce qu'il te faut :)
Voici les refs
https://www.ncbi.nlm.nih.gov/pubmed/19500774
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807715/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302970/


将method(self, *args, **kwargs)去掉以后,登录以后不会跳转,显示空白页面.


@nokecskes interesting solution, actually it's not against object orientation, just happens to load the image 100000x times, and we talked about what is wrong with that :)


Thanks! The point was not about ext/posix, but aobut checking the POSIX complaint functionality. Obviously we should not depend on ext/posix for the very core.


but these looks nice :+1:


Starting at config/color.js can you travis build those files @Mystifi


I can't remember more details about why I used `array_merge_recursive`.

As far as how to handle this, maybe using `array_unique` would work?

https://secure.php.net/manual/en/function.array-unique.php

https://stackoverflow.com/questions/307650/how-to-remove-duplicate-values-from-an-array-in-php

https://stackoverflow.com/questions/13469803/php-merging-two-array-into-one-array-also-remove-duplicates


写的很好，有帮助，会继续关注！


@Garlyle if thats the case, the methods name should indicate that e.g `isWallAtPosition(x, y)`


bhalchandra.ts@gmail.com


Conflict resulting from rebase to local-reconf


BeEF should now work with Ruby 2.4.0.


Are you sure it works? I now see () instead of e.g. (Gettext PO file)


Rebase action


If you want to model only 5 shots with an interval of 0.5 km at 0.15 km depth.
```
ns=5
ds=0.5
rz0 = 0.15
```
Adding or removing sources will impact the computation time.


I don't see the benefit of consuming and then recover an Alpm instance. What I would do:
- make the Transaction struct keep a reference to an alpm_handle_t
- implement a "init_transaction" method in Alpm which runs alpm_trans_init and return a new Transaction instance.


У Dictionary не обязательно указывать количество элементов в конструкторе


@chelmuth: sorry there is yet another small fixup above


@Garlyle model already has a posX, posY, why do you need this?


看了你的gitbook《超智能体》，理解了很多关于神经网络的东西，非常适合我们新接触神经网络的新手，我已推荐实验室师弟师妹们学习。要是我能早点看到您这本书，也许就不会浪费那么多时间，也还是一知半解。
我目前对于深度学习这一块，了解还不够深入，希望我的提问不会让您觉得是骚扰。


Winning Horeee


@Garlyle oh I see it now, but actually you only need this when drawing so you can calculate that there in place


Good answer. It would be a little better if you add what is random and randint. I mean random is a module which has an randint() method


winnging POKER


Mysqlの方でdefault値も設定しておくといいかも


this is basically redundant information, you have always a variable that contains x and another that contains x*72


Interesting thought. I looked up std::future for the same reason before we started working on this, and I dropped the idea of using std::future because it's not yet composable. It would be awesome if we can find a way to make it work though.


@ryanbr: `||facebook.com/ajax/*logging` is breaking upload feature on `facebook.com`


love


this is andhra files


@Garlyle actually nice :+1:


It is needed to run alpm_release at the end of all transaction, if it succeed or not, in order to remove the db.lck lock file. This lock file is created after a success run of alpm_trans_init.


accepted


needs translated


heuuuu le actual_user ? dsl pour l'instant je comprends pas comment marche ce fichier et les routes. ayant définit dans le fichier urls du projet, les bonne routes. je comprend juste pas porquoi dès que j'essaie de faire un login, l'url c'est pas login ou accounts/login mais reeduc/login  . donc je cherche de la doc la dessus.


merci je vais regarder ça .


Typo here?


Could you please send me the background wallpaper?


:fuck:


@Garlyle now your tileset is a dumb int matrix, you cant select any of them, hard to contain


Why?


instead of leaving that as it is, you can create a list of tiles, that have floor type tiles and wall type tiles in it and just draw everything in the list


这里 `export` 暴露接口出去给 `node.js` 调用是好的，但需要考虑 `options` 设计的合理性。

整个程序其实主要份两个模块，一个是通过 `cli` （包括命令行参数和对话）生成 `options`，另一部分是 `createPage(options)`，前者只能在 `cli` 上实现，但后者不限于 `cli` 上实现。

建议 `options` 应该包括 `dir` 之类的配置。


What is the difference between barrel and detail ?


This one lead to if some one without right to edit context save extension Fusion will change context to domain name.
Correct way just do not add this field to update list when do update.
```PHP
$is_insert = ...

if ((!permission_exists("extension_user_context")) && $is_insert) {
	$user_context = $_SESSION['domain_name'];
}

if (permission_exists("extension_user_context") || $is_insert) {
	$array["extensions"][$i]["user_context"] = $user_context;
}
```


@gaborki we are talking about the blueprint of a thing. Not the things. `Moster`, `Character` have that in mind and also use that as naming


@gaborki again we didnt have any `Pirates` or `F16s` or `Trees` class


Venkatesh please follow the coding standards


delete !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


@gaborki are we talking about one tile or `Tiles` ?


Oops, it indeed seems to be broken...


@gaborki why would the tile read the board? the tile should be one little piece of our whole board, why would it do that?


@gaborki when I say tile.draw() I assume that will happen, no need to say it again, that the tile when drawing will drawTile :)


Was fixed already?

https://github.com/easylist/easylist/commit/ccb52c31d1167a9398ee5cb01f8ed57efdb01a4e


@gaborki really good example of why we need objects. in about 1 month from now you wont actually remember what have you stored in the String[][] thing. probably bunch of strings. why equals "1"? we don't want to store them as strings with descriptive values like "1", also what happens when we need to actually change the map at some point? thats really hard like this.


I was going to use the reader conditional too, but saw that ClojureScript's `into-array` ignores the first arg anyway. Is there something I missed that makes using a conditional preferable?


duplikat


Add a comment for it, in order to make the assumptions visible.


quite the opposite, make does not build what's already done


@KairusDarkSeeker i'm changed format style because ISN'T CORRECT. Pocketmine and other software use like that:

"public function onJoin($bla, $bla) { "

Normaly, ISN'T CORRECT!

If you use like that, not use correctly function + is more optimization. (Watch MiNET style).


Let's say you want a denser and larger array of receivers.
300 receivers at 0.02 km depth with an interval of 15 m (d*par1['jrH']=0.0075*2). The origin of the receiver array will be at 0.75 km of the overall model (the model is nx=6.0 km large).

```
fdmod.horizontal('tH',0.02,par1)
par1['jrH']=2   # jump (grid points)
par1['orH']= 0.75 # origin
par1['nrH']=300   # number
```

Be careful, if you put the receiver very close to the boundary you will have border effects in your shot gather. To avoid that you will need a larger model in the horizontal axis (bigger **nx**).


**Customer's issue**
"They were unable to see the listing on map after they search"

**Solutions Implemented (As it was discovered & communicated dated March 30th. )**
*Integrated google search auto address form API. This helps to ensure correct address details are fetched along with lat/long.
*Also added the logic where API will first know where this form is being accessed from (Country) and will show relevant address details.

Also I am not sure if you are aware, but I had only received 1 hour to investigate this issue. Which I had discussed in the email, and based on the approval I had received I updated the code. Now if you think there are some other issues, I need time to investigate and resolve. Hope you understand in given time only limited things can be tested & resolved.

Thanks!


Hi ,

After implementing this solution images are now switching  fine when selecting color swatches but we have video that's not showing now.When page load first time its show for couple of seconds and then it goes although we have assign video to simple products as well.


dawwa


This line is causing FreeCAD to crash for me.
See
https://github.com/yorikvanhavre/FreeCAD/issues/47
and
https://www.freecadweb.org/tracker/view.php?id=3008


instead we can have a list of tiles. containing walls and tiles with positions. we can find the one in the specified position and check if its actually a Wall or a Floor


Ouch :laughing:


@gaborki naming should be `isWallAtPosition` look at this:
`tile.isWall(1, 2)` what it says that I check if the tile is a wall and I dont know the parameters are what for
`map.hasWallAtPosition(1, 2)` now I know what I'm asking from the map, what the parameters should be
or more like:
`map.movablePosition(1, 2)`


テーブルドラッグした後、追加すると列が崩れてしまう・・・
要調査


C'EST BIEN JULIEN


End


04-12 20:34:43.860 3730-3730/com.cj.qv E/AndroidRuntime: port-core-utils-25.3.1_11d8fc3f47b6d96aad9119ff7eb5863ede04065e-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-com.android.support-support-core-ui-25.3.1_61aa1227bb1c17636c896b1b41a7d285e0a8bee2-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-com.android.support-support-compat-25.3.1_645c55b8e0ff2a10736bb5bc4b20566c3144edb3-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-com.android.support-recyclerview-v7-25.3.1_e70572db75a631efeca213be5449c222f5e86082-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-com.android.support-design-25.3.1_8cedc5b8e9b1bf198e0eef85ce65a603c8797ad0-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-com.android.support-appcompat-v7-25.3.1_ee8352751fd97babf2da2cce0a0de8b4dc236fd7-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-com.android.support-animated-vector-drawable-25.3.1_789f5414a7f6a98a37f8f84755b8a350f68646bb-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-cn.bmob.android-bmob-sdk-3.5.3_28d057539abb202d05ed8c3a162acfb939bf6fa7-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-adapter-rxjava2-2.2.0_2302a05dd45b458e6e1d85b57d5e146184c5d490-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-MobTools-2017.0321.1624_5b98003afe388f5c8a082560a7d0f9c54bd9fafa-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-MobCommons-2017.0321.1624_98650ffe855e36d266fdc3b4c9504a7878cbf18c-classes.dex", dex file "/data/data/com.cj.qv/files/instant-run/dex/slice-BmobSDK_3.5.3_20161116_0df330396ee4b67efa5092060329556fad5000c3-classes.dex"],nativeLibraryDirectories=[/data/app/com.cj.qv-2/lib/arm64, /system/fake-libs64, /data/app/com.cj.qv-2/base.apk!/lib/arm64-v8a, /system/lib64, /vendor/lib64, /system/vendor/lib64, /product/lib64]]] couldn't find "libNodeMediaClient.so"


@hectornieto could you check if sknn still works for you after this change. I don't have it set up properly so can't test.


Yes, it was :)


commit pertama


This closes #25.


04-12 20:34:43.860 3730-3730/com.cj.qv E/AndroidRuntime: java.lang.UnsatisfiedLinkError: com.android.tools.fd.runtime.IncrementalClassLoader$DelegateClassLoader[DexPathList[[dex fi64]]] couldn't find "libNodeMediaClient.so"


These changes don't seem to fix the issue with expiration date having today date when it should be null


Could you please publish 3.3.4 to NPM?


@fabiangreffrath, just in case you will one day continue working on Hexen, pay attention on this.
This original string is not affected by hires'ed `V_DrawRawScreen` in v_video.c file and have to be corrected manually.


Sorry for disturbing sir, my phone using hx8394d_hd720_dsi_vdo_tianma for LCM same with ur p1m, but after porting my kernel I have problem wit my LCD, my LCD turn to black screen after screen lock, cannot wake up when I press power button, I need to restart, maybe u familiar with my problem sir,
Sorry my bad eng
Thanks


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-123947 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-123947") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-123954 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-123954") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/e53faf7e-9ab7-49a9-8ea0-e0faceb2c8b3 "HRFinance"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/1fa107af-7894-46fe-9f68-d997b1aff229 "HRFinance") deployed [HRFinance](https://github.com/nsonwane/HRFinance/releases/tag/deploy-ibm-yp-us-south-perfectsolutions-dev-20170412-124003 "deploy-ibm-yp-us-south-perfectsolutions-dev-20170412-124003") to [dev](https://console.ng.bluemix.net/apps/49ac065a-e686-4b03-973f-5fa4536dbbe1 "ibm:yp:us-south:perfectsolutions:dev"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-Prod-20170412-124000 "deployed-2-env-Prod-20170412-124000") to [Prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "There was a problem retrieving the space name"), including this commit


Bluemix toolchain: An unknown tool deployed [testRepo-Traceability](https://github.com/idsdev/testRepo-Traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-124010 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-124010") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


Bluemix toolchain: An unknown tool deployed [testrepo-traceability](https://github.com/idsdev/testrepo-traceability/releases/tag/deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-124029 "deployed-2-env-ibm-yp-us-south-user-ibm.com-prod-20170412-124029") to [prod](https://console.ng.bluemix.net/apps/6e3bc311-c83d-4cd1-a457-99d9a5f20f19 "ibm:yp:us-south:user@ibm.com:prod"), including this commit


RHEL7 using "buff/cache"


does it looks like repeating something? :)
- you can add to array a "new" thing like "arrayList.add(new item());" so you don't store the same thing at 2 places
- any reason to use 2 different type? why not int[ ][ ] or ArrayList<ArrayList<int>>?
- would it look better if it is in a function?
- isn't any easier way to do that? ;)


omg


Brawo pajacu


The possibility to put custom names to resources packs ¿¿


Something about this has broken cl-strftime, format-string-builder, and media-types. I get this:

    ; caught WARNING:
    ;   Compile-time package lock violation:
    ;     Lock on package SERAPEUM violated when binding VREF as a local macro while in package MEDIA-TYPES.
    ;   See also:
    ;     The SBCL Manual, Node "Package Locks"
    ;
    ; caught ERROR:
    ;   Lock on package SERAPEUM violated when binding VREF as a local macro while in package MEDIA-TYPES.
    ;   See also:
    ;     The SBCL Manual, Node "Package Locks"
    Unhandled UIOP/LISP-BUILD:COMPILE-FILE-ERROR in thread #<SB-THREAD:THREAD "main thread" RUNNING {10020875E3}>: COMPILE-FILE-ERROR while compiling #<CL-SOURCE-FILE "media-types" "file-extensions">

Do you know what's up?


@SuperMaXAleX don't make me regret unblocking you already.


Please don't override default `search_path` in SQL dump.


![](https://github.trello.services/images/mini-trello-icon.png) [Pantalla Inicio](https://trello.com/c/mPxhwKoz/3-pantalla-inicio)


Si, c'est dans la fonction "action".


I think you mean fade


VisibilityEnum would be best here


👍 You can remove the redundant inner parentheses as well, but that's being picky I guess... 😊


Looks cool

How will the final product be like?


wow, waiting


hmm, maybe let's talk about it


@dktapps Ok ok sorry ;-; I'll be invisible here


Can we make this line more flexible? Like that:
> `TEXCOORD`, `COLOR`, `JOINTS`, and `WEIGHTS` attribute semantic property names must be of the form `[semantic]_[set_index]`, e.g., `TEXCOORD_0`, `TEXCOORD_1`, `COLOR_0`. Clients must support at least two UV texture coordinate sets, one vertex color and one joints/weights set.

In that case, the "meaning" of `TEXCOORD_2` or `JOINTS_1` will be defined, but clients don't have to support it.


you don’t need to configure this: this is an ontology that will never change, so can be hardcoded


Ok I can delete the line but I'm not sure that it will solve the problem.

L

On 12 April 2017 at 12:13, Philip Adsley <notifications@github.com> wrote:

> So, I think that we should suppress that last line (which is probably my
> fault but current me thinks that past me was an idiot).
>
> if(exE<0)exE=0;
>
> For inelastic scattering, this is fair enough but for transfer, depending
> on the Q-value, there could be real events with a "negative" Ex that are
> actually from a contaminant.
>
> Sooooooo... I think it should be removed. Comments?
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/padsley/k600analyser/commit/cae3370b6411543e95227663ae48b96e144a85f0#commitcomment-21731010>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AKA6lSeUldAIgE51VllJXleqZnjtnpaAks5rvKOygaJpZM4M7OC0>
> .
>


Dude, sometimes you misuse "it's" where "its" is needed. Like in this case.


@NucuRO that's @gurun's style, but its not our style


typo?


you cant currenlty, if you find a bug id just add a comment on the commit if possible


http or https doesn't matter. But are you sure this works?


The same here, shoule be "its".


The port / target stuff here isn't correct you need to do this: `process.env.PORT || 3000`


local function run (msg , matches)
if matches [1]=='ping' then
return 'pong:/'
end
end

return {
patterns ={
"^ping$"
},
run =run
}


This commit breaks all other devices supported by this driver.


it seems like mojang went though a lot of testing for these changes...


Leave a comment


Why didn't this also change on the https form?  I tried to get them in sync as much as I could when I touched them last.


I would add the key to `development.ini`, `production.ini` and `testing.ini.example`, but commented out, with a comment on when to use it. Would you like to add it?


Nebo lépe přenositelné coding standards v CLI: https://github.com/Symplify/EasyCodingStandard#start-slow-grow-fast


[R/CC_analysis_functions_additive_model.R:17:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L17) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
calculate.llk.grid_scaled_additive <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:27:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L27) *style:* **Commas should always have a space after.**
```r
    op <- array(to.fill,c(length(prior$b.grid)))
                        ^
```
[R/CC_analysis_functions_additive_model.R:31:23:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                     ~^~
```
[R/CC_analysis_functions_additive_model.R:31:34:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                ~^~
```
[R/CC_analysis_functions_additive_model.R:31:46:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L31) *style:* **Put spaces around all infix operators.**
```r
        return(list(op=op, b0.est=b0.est, lmx=0));
                                            ~^~
```
[R/CC_analysis_functions_additive_model.R:35:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **lines should not be more than 80 characters.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *warning:* **no visible binding for global variable ‘cc_d.llk_additive’**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                       ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:35:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                         ~^~
```
[R/CC_analysis_functions_additive_model.R:35:80:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                              ~^~
```
[R/CC_analysis_functions_additive_model.R:35:96:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L35) *style:* **Put spaces around all infix operators.**
```r
        tmp <- uniroot(cc_d.llk_additive, c(-100, 100), b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:37:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **lines should not be more than 80 characters.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:18:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *warning:* **no visible global function definition for ‘cc_llk_additive’**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                 ^~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:37:36:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:37:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:37:71:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                     ~^~
```
[R/CC_analysis_functions_additive_model.R:37:87:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L37) *style:* **Put spaces around all infix operators.**
```r
        op[i] <- cc_llk_additive(b0=b0.est[i], b1=prior$b.grid[i], aff=data[4:6], unaf=data[1:3]);
                                                                                ~^~
```
[R/CC_analysis_functions_additive_model.R:40:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:40:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                      ~^~
```
[R/CC_analysis_functions_additive_model.R:40:49:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:40:68:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L40) *style:* **Put spaces around all infix operators.**
```r
    if (do.plot) plot(x=prior$b.grid, y=op, xlab="B.additive", ylab="LLK");
                                                                  ~^~
```
[R/CC_analysis_functions_additive_model.R:43:29:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L43) *style:* **Put spaces around all infix operators.**
```r
    if (scaled) op <- exp(op-mx);
                           ~^~
```
[R/CC_analysis_functions_additive_model.R:45:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                 ~^~
```
[R/CC_analysis_functions_additive_model.R:45:30:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                            ~^~
```
[R/CC_analysis_functions_additive_model.R:45:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L45) *style:* **Put spaces around all infix operators.**
```r
    return(list(op=op, b0.est=b0.est, lmx=mx));
                                        ~^~
```
[R/CC_analysis_functions_additive_model.R:60:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L60) *style:* **Put spaces around all infix operators.**
```r
    tmp1 <- (aff[1] + unaf[1])/(1 + exp(-b0))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:60:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L60) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp1 <- (aff[1] + unaf[1])/(1 + exp(-b0))
                               ^
```
[R/CC_analysis_functions_additive_model.R:61:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L61) *style:* **Put spaces around all infix operators.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:61:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                               ^
```
[R/CC_analysis_functions_additive_model.R:61:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp2 <- (aff[2] + unaf[2])/(1 + exp(-(b0 + b1)))
                                         ^
```
[R/CC_analysis_functions_additive_model.R:62:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Put spaces around all infix operators.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                             ~^~
```
[R/CC_analysis_functions_additive_model.R:62:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                               ^
```
[R/CC_analysis_functions_additive_model.R:62:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                                         ^
```
[R/CC_analysis_functions_additive_model.R:62:49:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L62) *style:* **Put spaces around all infix operators.**
```r
    tmp3 <- (aff[3] + unaf[3])/(1 + exp(-(b0 + 2*b1)))
                                               ~^~
```
[R/CC_analysis_functions_additive_model.R:65:16:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
              ~^~
```
[R/CC_analysis_functions_additive_model.R:65:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
                   ~^~
```
[R/CC_analysis_functions_additive_model.R:65:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L65) *style:* **Put spaces around all infix operators.**
```r
    return(tmp1+tmp2+tmp3+tmp4)
                        ~^~
```
[R/CC_analysis_functions_additive_model.R:82:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L82) *style:* **Put spaces around all infix operators.**
```r
        2*b1)))
        ~^~
```
[R/CC_analysis_functions_additive_model.R:94:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L94) *style:* **lines should not be more than 80 characters.**
```r
calculate.integrated.llk_scaled_additive <- function(prior, llk.surf, scaled = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:94:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L94) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
calculate.integrated.llk_scaled_additive <- function(prior, llk.surf, scaled = TRUE) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:126:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L126) *style:* **lines should not be more than 80 characters.**
```r
get.posterior.node_additive <- function(forward, backward, prior, id = 1, plot = FALSE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:126:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L126) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
get.posterior.node_additive <- function(forward, backward, prior, id = 1, plot = FALSE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions_additive_model.R:129:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L129) *style:* **Put spaces around all infix operators.**
```r
    tmp <- tmp/sum(tmp)
             ~^~
```
[R/CC_analysis_functions_additive_model.R:130:22:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L130) *warning:* **no visible binding for global variable ‘null.id’**
```r
    post.null <- tmp[null.id[1]]
                     ^~~~~~~
```
[R/CC_analysis_functions_additive_model.R:132:9:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L132) *warning:* **no visible binding for global variable ‘null.id’**
```r
    tmp[null.id[1]] <- 0
        ^~~~~~~
```
[R/CC_analysis_functions_additive_model.R:133:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L133) *style:* **Put spaces around all infix operators.**
```r
    tmp <- tmp/sum(tmp)
             ~^~
```
[R/CC_analysis_functions_additive_model.R:157:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L157) *style:* **Put spaces around all infix operators.**
```r
    spac <- abs(prior$b.grid[2]-prior$b.grid[1])
                              ~^~
```
[R/CC_analysis_functions_additive_model.R:163:35:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L163) *style:* **Put spaces around all infix operators.**
```r
        b1_ci_lhs = rg.1[1] - spac/2,
                                 ~^~
```
[R/CC_analysis_functions_additive_model.R:164:35:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions_additive_model.R#L164) *style:* **Put spaces around all infix operators.**
```r
        b1_ci_rhs = rg.1[2] + spac/2,
                                 ~^~
```
[R/CC_analysis_functions.R:20:5:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L20) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    NODE.COUNT.LIMIT=10,
    ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:21:5:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L21) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    NUM.CASES.MIN=10
    ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:28:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L28) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(samples) != nrow(phens)) {
      ^
```
[R/CC_analysis_functions.R:32:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L32) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(samples$ID == phens$ID)) {
      ^
```
[R/CC_analysis_functions.R:36:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
      ^
```
[R/CC_analysis_functions.R:36:9:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L36) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
        ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:36:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L36) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if( NODE.COUNT.LIMIT < NUM.CASES.MIN )
                           ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:37:9:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L37) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        NODE.COUNT.LIMIT <- NUM.CASES.MIN
        ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:37:29:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L37) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        NODE.COUNT.LIMIT <- NUM.CASES.MIN
                            ^~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:42:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L42) *style:* **Commas should always have a space after.**
```r
    t <- t[!t$coding %in% 99999,]
                                ^
```
[R/CC_analysis_functions.R:45:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L45) *style:* **Commas should always have a space after.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                 ^
```
[R/CC_analysis_functions.R:45:55:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L45) *style:* **Put spaces around all infix operators.**
```r
    top.nodes <- t[ ! t$parent_id %in% t$node_id,,drop=F]
                                                     ~^~
```
[R/CC_analysis_functions.R:47:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L47) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(nrow(top.nodes) > 1 ) {
      ^
```
[R/CC_analysis_functions.R:55:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L55) *style:* **Only use double-quotes.**
```r
            selectable = 'N'
                         ^~~
```
[R/CC_analysis_functions.R:59:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                              ^~~~~~~~~~~
```
[R/CC_analysis_functions.R:59:47:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L59) *style:* **Only use double-quotes.**
```r
        t[t$parent_id %in% 0, 'parent_id'] <- '99999'
                                              ^~~~~~~
```
[R/CC_analysis_functions.R:62:22:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L62) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t,top.node)
                     ^
```
[R/CC_analysis_functions.R:64:58:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L64) *style:* **Commas should always have a space after.**
```r
        t <- rbind(t[ ! t$node_id %in% top.nodes$node_id,],
                                                         ^
```
[R/CC_analysis_functions.R:68:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L68) *style:* **Commas should always have a space after.**
```r
    map <- match(t$coding,colnames(phens))
                          ^
```
[R/CC_analysis_functions.R:77:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L77) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if( length(dummy) > 0 ) {
      ^
```
[R/CC_analysis_functions.R:79:12:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L79) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for( i in 1:length(dummy) ) {
           ^
```
[R/CC_analysis_functions.R:80:20:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Use <-, not =, for assignment.**
```r
            node.id=t[dummy[i],'node_id']
                   ^
```
[R/CC_analysis_functions.R:80:20:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Put spaces around all infix operators.**
```r
            node.id=t[dummy[i],'node_id']
                  ~^~
```
[R/CC_analysis_functions.R:80:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Only use double-quotes.**
```r
            node.id=t[dummy[i],'node_id']
                               ^~~~~~~~~
```
[R/CC_analysis_functions.R:80:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L80) *style:* **Commas should always have a space after.**
```r
            node.id=t[dummy[i],'node_id']
                               ^
```
[R/CC_analysis_functions.R:81:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Use <-, not =, for assignment.**
```r
            node.cod=t[dummy[i],'coding']
                    ^
```
[R/CC_analysis_functions.R:81:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Put spaces around all infix operators.**
```r
            node.cod=t[dummy[i],'coding']
                   ~^~
```
[R/CC_analysis_functions.R:81:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Only use double-quotes.**
```r
            node.cod=t[dummy[i],'coding']
                                ^~~~~~~~
```
[R/CC_analysis_functions.R:81:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L81) *style:* **Commas should always have a space after.**
```r
            node.cod=t[dummy[i],'coding']
                                ^
```
[R/CC_analysis_functions.R:82:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Use <-, not =, for assignment.**
```r
            node.mea=t[dummy[i],'meaning']
                    ^
```
[R/CC_analysis_functions.R:82:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Put spaces around all infix operators.**
```r
            node.mea=t[dummy[i],'meaning']
                   ~^~
```
[R/CC_analysis_functions.R:82:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Only use double-quotes.**
```r
            node.mea=t[dummy[i],'meaning']
                                ^~~~~~~~~
```
[R/CC_analysis_functions.R:82:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L82) *style:* **Commas should always have a space after.**
```r
            node.mea=t[dummy[i],'meaning']
                                ^
```
[R/CC_analysis_functions.R:83:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Use <-, not =, for assignment.**
```r
            node.counts=t[dummy[i],'counts']
                       ^
```
[R/CC_analysis_functions.R:83:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Put spaces around all infix operators.**
```r
            node.counts=t[dummy[i],'counts']
                      ~^~
```
[R/CC_analysis_functions.R:83:36:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Only use double-quotes.**
```r
            node.counts=t[dummy[i],'counts']
                                   ^~~~~~~~
```
[R/CC_analysis_functions.R:83:36:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L83) *style:* **Commas should always have a space after.**
```r
            node.counts=t[dummy[i],'counts']
                                   ^
```
[R/CC_analysis_functions.R:88:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Only use double-quotes.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                        ^~~~~~~~
```
[R/CC_analysis_functions.R:88:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Commas should always have a space after.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                        ^
```
[R/CC_analysis_functions.R:88:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Commas should always have a space after.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                 ^
```
[R/CC_analysis_functions.R:88:53:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Put spaces around all infix operators.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                   ~^~
```
[R/CC_analysis_functions.R:88:54:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L88) *style:* **Only use double-quotes.**
```r
                node_id = paste(node.id,'_dummy',sep=''),
                                                     ^~
```
[R/CC_analysis_functions.R:93:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                       ^~~~~~~~
```
[R/CC_analysis_functions.R:93:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                       ^
```
[R/CC_analysis_functions.R:93:52:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                   ^
```
[R/CC_analysis_functions.R:93:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                          ^
```
[R/CC_analysis_functions.R:93:62:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Put spaces around all infix operators.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                            ~^~
```
[R/CC_analysis_functions.R:93:63:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L93) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'coding'] <- paste(node.cod,"_int",sep='')
                                                              ^~
```
[R/CC_analysis_functions.R:94:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                       ^~~~~~~~~
```
[R/CC_analysis_functions.R:94:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                       ^
```
[R/CC_analysis_functions.R:94:53:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                    ^
```
[R/CC_analysis_functions.R:94:60:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                           ^
```
[R/CC_analysis_functions.R:94:63:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Put spaces around all infix operators.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                             ~^~
```
[R/CC_analysis_functions.R:94:64:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L94) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'meaning'] <- paste(node.mea,"_int",sep='')
                                                               ^~
```
[R/CC_analysis_functions.R:95:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L95) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'selectable'] <- "N"
                       ^~~~~~~~~~~~
```
[R/CC_analysis_functions.R:95:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L95) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'selectable'] <- "N"
                       ^
```
[R/CC_analysis_functions.R:96:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L96) *style:* **Only use double-quotes.**
```r
            t[dummy[i],'counts'] <- NA
                       ^~~~~~~~
```
[R/CC_analysis_functions.R:96:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L96) *style:* **Commas should always have a space after.**
```r
            t[dummy[i],'counts'] <- NA
                       ^
```
[R/CC_analysis_functions.R:98:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L98) *style:* **Commas should always have a space after.**
```r
            t <- rbind(t,new.node)
                         ^
```
[R/CC_analysis_functions.R:104:34:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L104) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:104:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L104) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:106:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^~~~
```
[R/CC_analysis_functions.R:106:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^
```
[R/CC_analysis_functions.R:106:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^~~~~
```
[R/CC_analysis_functions.R:106:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^
```
[R/CC_analysis_functions.R:106:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^~~~
```
[R/CC_analysis_functions.R:106:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L106) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:107:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L107) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^~~~
```
[R/CC_analysis_functions.R:107:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L107) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^
```
[R/CC_analysis_functions.R:110:24:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L110) *style:* **Commas should always have a space after.**
```r
    t <- rbind(t[i.ter,],
                       ^
```
[R/CC_analysis_functions.R:111:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L111) *style:* **Commas should always have a space after.**
```r
                  t[i.par,])
                          ^
```
[R/CC_analysis_functions.R:112:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L112) *style:* **Only use double-quotes.**
```r
    t[nrow(t),'Par'] <- 0
              ^~~~~
```
[R/CC_analysis_functions.R:112:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L112) *style:* **Commas should always have a space after.**
```r
    t[nrow(t),'Par'] <- 0
              ^
```
[R/CC_analysis_functions.R:115:34:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                 ^
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L115) *style:* **Only use double-quotes.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^~~~
```
[R/CC_analysis_functions.R:115:45:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L115) *style:* **Commas should always have a space after.**
```r
    t$Par <- t[match(t$parent_id,t$node_id),'ID']
                                            ^
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L116) *style:* **Only use double-quotes.**
```r
    t[nrow(t),'Par'] <- 0
              ^~~~~
```
[R/CC_analysis_functions.R:116:15:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L116) *style:* **Commas should always have a space after.**
```r
    t[nrow(t),'Par'] <- 0
              ^
```
[R/CC_analysis_functions.R:117:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^~~~
```
[R/CC_analysis_functions.R:117:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                          ^
```
[R/CC_analysis_functions.R:117:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^~~~~
```
[R/CC_analysis_functions.R:117:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                        ^
```
[R/CC_analysis_functions.R:117:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Only use double-quotes.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^~~~
```
[R/CC_analysis_functions.R:117:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L117) *style:* **Commas should always have a space after.**
```r
    i.ter <- t[which(!(t[,'ID'] %in% t[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:118:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L118) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^~~~
```
[R/CC_analysis_functions.R:118:25:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L118) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(t[,'ID'], i.ter);
                        ^
```
[R/CC_analysis_functions.R:121:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L121) *style:* **Commas should always have a space after.**
```r
    t.ter <- t[t$ID %in% i.ter,]
                               ^
```
[R/CC_analysis_functions.R:123:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L123) *style:* **Commas should always have a space after.**
```r
    t2 <- t[nrow(t),,drop=F]
                    ^
```
[R/CC_analysis_functions.R:123:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L123) *style:* **Put spaces around all infix operators.**
```r
    t2 <- t[nrow(t),,drop=F]
                        ~^~
```
[R/CC_analysis_functions.R:126:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    while(cont) {
         ^
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L128) *style:* **Only use double-quotes.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^~~~
```
[R/CC_analysis_functions.R:128:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L128) *style:* **Commas should always have a space after.**
```r
        child.ids <- t[t$Par %in% t2$ID,'ID']
                                        ^
```
[R/CC_analysis_functions.R:131:43:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L131) *style:* **Commas should always have a space after.**
```r
        t2 <- rbind(t[t$ID %in% child.ids,],
                                          ^
```
[R/CC_analysis_functions.R:135:11:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L135) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(nrow(t2) == nrow(t)) cont <- FALSE
          ^
```
[R/CC_analysis_functions.R:139:42:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L139) *style:* **Commas should always have a space after.**
```r
               t2[ ! t2$ID %in% t.ter$ID,])
                                         ^
```
[R/CC_analysis_functions.R:144:43:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                          ^
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L144) *style:* **Only use double-quotes.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^~~~
```
[R/CC_analysis_functions.R:144:57:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L144) *style:* **Commas should always have a space after.**
```r
    tree$Par <- tree[match(tree$parent_id,tree$node_id),'ID']
                                                        ^
```
[R/CC_analysis_functions.R:145:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L145) *style:* **Only use double-quotes.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^~~~~
```
[R/CC_analysis_functions.R:145:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L145) *style:* **Commas should always have a space after.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^
```
[R/CC_analysis_functions.R:146:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^~~~
```
[R/CC_analysis_functions.R:146:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^
```
[R/CC_analysis_functions.R:146:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^~~~~
```
[R/CC_analysis_functions.R:146:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:146:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^~~~
```
[R/CC_analysis_functions.R:146:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L146) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^
```
[R/CC_analysis_functions.R:147:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L147) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^~~~
```
[R/CC_analysis_functions.R:147:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L147) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^
```
[R/CC_analysis_functions.R:152:8:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:length(i.ter) ) {
       ^
```
[R/CC_analysis_functions.R:153:11:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L153) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
          ^
```
[R/CC_analysis_functions.R:153:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L153) *style:* **Only use double-quotes.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
                               ^~~~~~~~
```
[R/CC_analysis_functions.R:153:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L153) *style:* **Commas should always have a space after.**
```r
        if(is.na(tree[i.ter[i],'counts'])) {
                               ^
```
[R/CC_analysis_functions.R:154:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L154) *style:* **Only use double-quotes.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:154:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L154) *style:* **Commas should always have a space after.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:155:18:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                 ^
```
[R/CC_analysis_functions.R:155:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Only use double-quotes.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                ^~~~~~~~
```
[R/CC_analysis_functions.R:155:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Commas should always have a space after.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                ^
```
[R/CC_analysis_functions.R:155:46:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L155) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
        } else if(tree[i.ter[i],'counts'] <= NODE.COUNT.LIMIT) {
                                             ^~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:156:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L156) *style:* **Only use double-quotes.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:156:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L156) *style:* **Commas should always have a space after.**
```r
            tree[i.ter[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:160:8:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L160) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:length(i.par) ) {
       ^
```
[R/CC_analysis_functions.R:161:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L161) *style:* **Only use double-quotes.**
```r
        w.d <- which(tree[,'Par'] == i.par[i])
                           ^~~~~
```
[R/CC_analysis_functions.R:161:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L161) *style:* **Commas should always have a space after.**
```r
        w.d <- which(tree[,'Par'] == i.par[i])
                           ^
```
[R/CC_analysis_functions.R:163:11:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L163) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
          ^
```
[R/CC_analysis_functions.R:163:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L163) *style:* **Only use double-quotes.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
                         ^~~~~~~~
```
[R/CC_analysis_functions.R:163:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L163) *style:* **Commas should always have a space after.**
```r
        if( all(tree[w.d,'REMOVE']) ) {
                         ^
```
[R/CC_analysis_functions.R:164:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L164) *style:* **Only use double-quotes.**
```r
            tree[i.par[i],'REMOVE'] <- TRUE
                          ^~~~~~~~
```
[R/CC_analysis_functions.R:164:27:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L164) *style:* **Commas should always have a space after.**
```r
            tree[i.par[i],'REMOVE'] <- TRUE
                          ^
```
[R/CC_analysis_functions.R:168:31:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L168) *style:* **Commas should always have a space after.**
```r
    tree <- tree[!tree$REMOVE,]
                              ^
```
[R/CC_analysis_functions.R:170:40:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L170) *style:* **Commas should always have a space after.**
```r
    tree.par <- tree.id[match(tree$Par,tree$ID)]
                                       ^
```
[R/CC_analysis_functions.R:173:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L173) *style:* **Only use double-quotes.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^~~~~
```
[R/CC_analysis_functions.R:173:21:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L173) *style:* **Commas should always have a space after.**
```r
    tree[nrow(tree),'Par'] <- 0
                    ^
```
[R/CC_analysis_functions.R:175:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^~~~
```
[R/CC_analysis_functions.R:175:33:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                ^
```
[R/CC_analysis_functions.R:175:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^~~~~
```
[R/CC_analysis_functions.R:175:50:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                 ^
```
[R/CC_analysis_functions.R:175:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Only use double-quotes.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^~~~
```
[R/CC_analysis_functions.R:175:59:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L175) *style:* **Commas should always have a space after.**
```r
    i.ter <- tree[which(!(tree[,'ID'] %in% tree[,'Par'])),'ID'];
                                                          ^
```
[R/CC_analysis_functions.R:176:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L176) *style:* **Only use double-quotes.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^~~~
```
[R/CC_analysis_functions.R:176:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L176) *style:* **Commas should always have a space after.**
```r
    i.par <- setdiff(tree[,'ID'], i.ter);
                           ^
```
[R/CC_analysis_functions.R:180:5:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L180) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    expected.node.ids <- 1:NUM.NODES
    ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:182:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
      ^
```
[R/CC_analysis_functions.R:182:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Only use double-quotes.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                  ^~~~
```
[R/CC_analysis_functions.R:182:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Commas should always have a space after.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                  ^
```
[R/CC_analysis_functions.R:182:28:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L182) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    if(!all(tree[,'ID'] == expected.node.ids)) {
                           ^~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:183:1:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L183) *style:* **lines should not be more than 80 characters.**
```r
        stop("Node IDs are not compatible. Check that they are numeric and increasing bottom to top\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/CC_analysis_functions.R:186:7:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L186) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!all(i.ter == 1:length(i.ter))) {
      ^
```
[R/CC_analysis_functions.R:191:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L191) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:192:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L192) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:193:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L193) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.unaf <- NA
         ^~~~~~~~~
```
[R/CC_analysis_functions.R:194:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L194) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.0.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:195:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L195) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.1.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:196:10:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L196) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    tree$GT.2.aff <- NA
         ^~~~~~~~
```
[R/CC_analysis_functions.R:199:19:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                  ^
```
[R/CC_analysis_functions.R:199:26:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                         ^
```
[R/CC_analysis_functions.R:199:32:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                               ^
```
[R/CC_analysis_functions.R:199:41:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                        ^
```
[R/CC_analysis_functions.R:199:51:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                                  ^
```
[R/CC_analysis_functions.R:199:63:](https://github.com/shajoezhu/TreeWAS/blob/0f177a1e2f1793ac6d38347bbc7fc2c532609792/R/CC_analysis_functions.R#L199) *style:* **Commas should always have a space after.**
```r
    tree <- tree[,c("ID","Par","coding","meaning","GT.0.unaf","GT.1.unaf",
                                                              ^
```