<details>

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

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

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

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

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

```
docker-worker:capability:disableSeccomp
```

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

```
{
  "AllOf": [
    "docker-worker:cache:docker-worker-garbage-*",
    "docker-worker:capability:privileged",
    "docker-worker:capability:disableSeccomp",
    "docker-worker:capability:device:loopbackAudio",
    "docker-worker:capability:device:loopbackVideo",
    "secrets:get:project/taskcluster/testing/docker-worker/ci-creds",
    "secrets:get:project/taskcluster/testing/docker-worker/pulse-creds",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:proj-taskcluster/ci",
                "queue:create-task:very-high:proj-taskcluster/ci",
                "queue:create-task:high:proj-taskcluster/ci",
                "queue:create-task:medium:proj-taskcluster/ci",
                "queue:create-task:low:proj-taskcluster/ci",
                "queue:create-task:very-low:proj-taskcluster/ci",
                "queue:create-task:lowest:proj-taskcluster/ci"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:proj-taskcluster/ci",
            {
              "AllOf": [
                "queue:define-task:proj-taskcluster/ci",
                "queue:task-group-id:taskcluster-github/H0au6raKQHu2ix4fn92rVA",
                "queue:schedule-task:taskcluster-github/H0au6raKQHu2ix4fn92rVA/H0au6raKQHu2ix4fn92rVA"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2020-01-06T07:35:43.679Z

</details>


диаграммы у нас нет, но я бы не хранил эти три переменные вместе - они же никак не связаны?


When I installed the plugin using "cordova plugin add cordova-plugin-amazon-login --variable IOS_API_KEY =" XXX ", after compiling with xcode, I got this error:
  'LoginWithAmazon / LoginWithAmazon.h' file not found


깃허브 스레기같습니다


`Word32` means that blocks can be at most 4 GB. That should be enough :slightly_smiling_face:


Deployment failed with the following error:

~~~
Function Runtimes must have a valid version, for example `now-php@1.0.0`.
~~~


Successfully deployed to following URLs:

* https://portfolio-zachgw-h5z4rhpig.now.sh
* https://portfolio-zachgw-five-chi.now.sh
* https://www.zachgw.com
* https://zachgw.com
* https://portfolio-zachgw.zachgw.now.sh
* https://portfolio-zachgw-git-master.zachgw.now.sh


本は投稿したユーザーでなければ編集、削除出来ないようにしました。


일단 코드는 깔끔하게 짜여지는데, exeption을 enum class로 짬처리했다는 말을 들었는데 ㅋㅋㅋㅋ물론 크래시가 날 일은 없겠지만 ㅋㅋㅋㅋㅋㅋ 웃겼다.

그리고 대형 프로젝트의 경우에는 다른 예시 처럼 else -> throw exeption("블라블라") 형태로 처리해서 다른 개발자가 빠르게 알게하는 방법도 나쁘지 않을 것같다. 아니면 emptyView를 만든다음에 바로 GONE처리 해도 될 듯.


Why is that removed ? I thought 5.4.7 makes problems and not 5.4.6 ?


その本を投稿したユーザー以外はその本を編集出来ないようにしました。


Successfully deployed to following URLs:

* https://portfolio-zachgw-rg7rbshz4.now.sh
* https://portfolio-zachgw-five-chi.now.sh
* https://www.zachgw.com
* https://zachgw.com
* https://portfolio-zachgw.zachgw.now.sh
* https://portfolio-zachgw-git-master.zachgw.now.sh


I actually meant to invert this condition with an early condition, but will approve either way.


Create the theme of Assignment2


Fert
![Screenshot_20200105-033222](https://user-images.githubusercontent.com/59594537/71872405-9b259c00-311c-11ea-8599-de19956fe9c5.png)


Fastfood in r


Puzzle `207-39280bde` disappeared from [`src/ProjectNeon/Assets/Features/Battle/Cards/SelectCardTargets.cs`](https://github.com/EnigmaDragons/ProjectNeon/blob/master/src/ProjectNeon/Assets/Features/Battle/Cards/SelectCardTargets.cs), that's why I closed #211. Please, remember that the puzzle was not necessarily removed in this particular commit. Maybe it happened earlier, but we discovered this fact only now.


테스트


after give role, should shuffle it again, thats what i call randomize


Successfully deployed to following URLs:

* https://f1-ambd9kq0x.now.sh
* https://f1-orpin-alpha.now.sh
* https://f1.ay8s.now.sh
* https://f1-git-master.ay8s.now.sh


Thanks tons!
It works after a fresh installation!


This should return 'yes' or 'no', it's the 'toilet status' of Wheelmap classic. 'yes' means there is a wheelchair accessible toilet, 'no' means there isn't. contrary to the general wheelchair accessibility there is no 'limited' here.


How this allocation is freed?


7451_Documentation_2019b (jmarrec) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (674 of 675 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 674
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.4%25-green.png)


I'll revert that one. Just tried to get core-js to work.


ㅇㅇ


configuration


And change all `px` to `rem`.


Nice one fam


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/7600](https://github.com/JuliaRegistries/General/pull/7600)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.3.1 -m "<description of version>" 309750ff1dd63868f7527a34181e68b06c92cdef
git push origin v0.3.1
```


`name` could be used here. `givenName` has the exact same implementation as `name`. You could use that.


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

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

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

### Deployments updated

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

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


test test hello


Successfully deployed to following URLs:

* https://incidentmanager-59u1h1cd3.now.sh
* https://incidentmanager.now.sh
* https://incidentmanager.manuelwecker.now.sh
* https://incidentmanager-git-master.manuelwecker.now.sh


Well I guess it's possible t put a `pause` in there, but its effect range from doing nothing on many processors to waiting for about as long as the entire loop takes right now on others. I can't really test this properly (and give that we're almost never spinning in the first place I'd argue it's not particularly important anyway).


why did you change that?


Thanks bro!


Successfully deployed to following URLs:

* https://okansblog-bbaz6v1gc.now.sh
* https://okansblog.now.sh
* https://okansblog.okandvn.now.sh
* https://okansblog-git-master.okandvn.now.sh


commit


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


You are pushing commits at a very fast pace (across the whole organization).
Due to that, we cannot deploy the commit 0cededa29b9b90001d9c9aebd768d825a417b265.

You can try again later or [upgrade](https://zeit.co/account/plan) your plan.


Successfully deployed to following URLs:

* https://slowj-6r4t33ev6.now.sh
* https://slowj.now.sh
* https://slowj.joaorfclopes.now.sh
* https://slowj-git-master.joaorfclopes.now.sh


;-) right ...  I will change it for the 2.2.8


Successfully deployed to following URLs:

* https://okansblog-l4drotbze.now.sh
* https://okansblog.now.sh
* https://okansblog.okandvn.now.sh
* https://okansblog-git-master.okandvn.now.sh


Successfully deployed to following URLs:

* https://dotcom-d5dnqpzjg.now.sh
* https://smokeyfro.com
* https://dotcom.smokeyfro.now.sh
* https://dotcom-git-master.smokeyfro.now.sh


Successfully deployed to following URLs:

* https://slowj-q75jnarsz.now.sh
* https://slowj.now.sh
* https://slowj.joaorfclopes.now.sh
* https://slowj-git-master.joaorfclopes.now.sh


Successfully deployed to following URLs:

* https://websitenext-nbbuimv8e.now.sh
* https://websitenext.now.sh
* https://websitenext.ots-next.now.sh
* https://websitenext-git-master.ots-next.now.sh


I dont even know what that means. What software stack? The implementation? Does the web author have to do something? It is very hand wavy...

Web devs also have to treat input like external JSON (as david baron pointed out) - explaining something along those lines that when reading data which might be from unknown sources (if not depending on signatures to avoid those) then you need to treat the data as untrusted and bla blah blah


Successfully deployed to following URLs:

* https://homepage-qd1qlvcly.now.sh
* https://homepage-loose-bat.now.sh
* https://open.mp
* https://www.open.mp
* https://homepage.openmultiplayer.now.sh
* https://homepage-git-master.openmultiplayer.now.sh


Successfully deployed to following URLs:

* https://statsiege-client-8ws7h7wpm.now.sh
* https://statsiege-client.now.sh
* https://www.statsiege.live
* https://statsiege.live
* https://statsiege-client.cjrl98.now.sh
* https://statsiege-client-git-master.cjrl98.now.sh


macOS build available: [multipass-1.1.0-dev.524+gfe308379.mac-Darwin.pkg](https://transfer.sh/VqLlH/multipass-1.1.0-dev.524+gfe308379.mac-Darwin.pkg)


I would put this check on line 18 to make it more efficient.


Successfully deployed to following URLs:

* https://notyuri-nygeweuoz.now.sh
* https://notyuri.now.sh
* https://notyuri.yuriystar.now.sh
* https://notyuri-git-master.yuriystar.now.sh


@gavindsouza  unable to run bench update after this commit


[R/count_hidden.R:7:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/count_hidden.R#L7) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
reduce_tree <- function(tree) {
^
```
[R/create_equal_alignment.R:14:23:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/create_equal_alignment.R#L14) *warning:* **no visible global function definition for ‘count_hidden’**
```r
  num_hidden_nodes <- count_hidden(input_tree)
                      ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:14:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_dual_independent.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_parent.R:14:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_dual_parent.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_unlinked_tree.R:78:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_unlinked_tree.R#L78) *style:* **functions should have cyclomatic complexity of less than 15, this has 43.**
```r
sim_unlinked_tree <- function(phy,
^
```
[R/sim_unlinked_tree.R:300:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_unlinked_tree.R#L300) *style:* **functions should have cyclomatic complexity of less than 15, this has 19.**
```r
create_equal_alignment_tree <- function(input_tree,
^
```
[R/sim_unlinked.R:14:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/sim_unlinked.R#L14) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/cf1b09992b5beaae45dc8159fd732937f41a290b/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```


@jarun Done. Sorry for the delay, I was away for a while.


파이썬 고수시네요.....


Crawl image using python


[R/calc_rel_contr_node_time.R:61:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_rel_contr_node_time.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:61:48:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_rel_contr_node_time.R#L61) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
                                               ^
```
[R/calc_rel_contr_node_time.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_rel_contr_node_time.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (2 * num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:75:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_rel_contr_node_time.R#L75) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calc_expected_hidden_nodes_per_branch <- function(bl, lambda, mu) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:125:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_rel_contr_node_time.R#L125) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:64:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_summary_statistics.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
    # this is rather inefficient off course, RPANDA can do all pairwise comparisons?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_summary_statistics.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:93:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_summary_statistics.R#L65) *style:* **Commas should always have a space after.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
                                                                                ^
```
[R/calc_summary_statistics.R:79:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/calc_summary_statistics.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
                                 "mean_branch_length", "nLTT", "jsd", "topo_dist")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_hidden.R:7:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/count_hidden.R#L7) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
reduce_tree <- function(tree) {
^
```
[R/create_equal_alignment.R:4:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/create_equal_alignment.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param node_model model used to generate substitutions on the nodes (linked or unlinked)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:14:23:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/create_equal_alignment.R#L14) *warning:* **no visible global function definition for ‘count_hidden’**
```r
  num_hidden_nodes <- count_hidden(input_tree)
                      ^~~~~~~~~~~~
```
[R/infer_phylogeny.R:8:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/infer_phylogeny.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sub_rate substitution rate used to generate the original alignment (if available), default is 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:32:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/infer_phylogeny.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
          clock_rate_param = beautier::create_clock_rate_param(value = sub_rate),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:69:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:70:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L70) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:79:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:80:6:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L80) *style:* **Commented code should be removed.**
```r
   # P <- nodeSub::slow_matrix(eig_q2, node_time, rate2)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:92:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:93:6:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L93) *style:* **Commented code should be removed.**
```r
    #P <- nodeSub::slow_matrix(eig_q1, tl[i], rate1)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:105:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L105) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_dual_independent.R:114:42:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:117:34:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_independent.R#L117) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L112) *style:* **Variable and function name style should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:132:19:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:135:21:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L135) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:171:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L171) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:172:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L172) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:191:6:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L191) *style:* **Commented code should be removed.**
```r
   # total_node_subs <- total_node_subs + node_subs_1 + node_subs_2
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_linked.R:196:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L196) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:210:9:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(check_to_extinct_tip(offspring[i])) {
        ^
```
[R/sim_dual_linked.R:220:42:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_linked.R#L220) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_linked.R:13:24:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_linked.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_linked.R:33:19:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_linked.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_linked.R:36:21:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_linked.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_linked.R:88:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_linked.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_linked.R:108:42:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_linked.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_normal.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_normal.R#L43) *style:* **Variable and function name style should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_normal.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_normal.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_unlinked_tree.R:10:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(class(phy) != "phylo") {
    ^
```
[R/sim_unlinked_tree.R:34:51:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L34) *style:* **Put spaces around all infix operators.**
```r
      to_add <- c(start_node, end_node, t0, t1, t0-t1)
                                                 ~^~
```
[R/sim_unlinked_tree.R:40:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L40) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:50:35:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                  ^
```
[R/sim_unlinked_tree.R:50:39:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                      ^
```
[R/sim_unlinked_tree.R:52:36:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                        lambda, mu) )
                                   ^
```
[R/sim_unlinked_tree.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:77:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L77) *style:* **functions should have cyclomatic complexity of less than 15, this has 43.**
```r
sim_unlinked_tree <- function(phy,
^
```
[R/sim_unlinked_tree.R:78:31:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
                              Q1 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:79:31:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
                              Q2 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:104:10:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L104) *style:* **Only use double-quotes.**
```r
    stop('lambda and mu have to be provided')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:113:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L113) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:114:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L114) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:117:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L117) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked_tree.R:118:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L118) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked_tree.R:131:51:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L131) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  hidden_nodes <- add_hidden_nodes(phy, lambda, mu )
                                                  ^
```
[R/sim_unlinked_tree.R:146:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:146:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
  ^~~
```
[R/sim_unlinked_tree.R:146:61:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L146) *style:* **Commented code should be removed.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
                                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:151:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L151) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:152:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:181:9:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L181) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( obs_hidden_nodes[i] > 0) {
        ^
```
[R/sim_unlinked_tree.R:186:10:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L186) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(j in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:188:14:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L188) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        while(focal_t + dt >= total_bl) {
             ^
```
[R/sim_unlinked_tree.R:198:8:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L198) *style:* **Commented code should be removed.**
```r
      #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:199:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L199) *style:* **Variable and function name style should be snake_case.**
```r
      P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
      ^~~
```
[R/sim_unlinked_tree.R:214:10:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L214) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(h in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:227:10:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L227) *style:* **Commented code should be removed.**
```r
        #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:228:9:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L228) *style:* **Variable and function name style should be snake_case.**
```r
        P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
        ^~~
```
[R/sim_unlinked_tree.R:247:8:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L247) *style:* **Commented code should be removed.**
```r
      #P <- get_p_matrix(tl[i], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:248:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L248) *style:* **Variable and function name style should be snake_case.**
```r
      P <-  nodeSub::slow_matrix(eig_q1, tl[i], rate1)
      ^
```
[R/sim_unlinked_tree.R:263:7:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L263) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_unlinked_tree.R:270:42:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L270) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked_tree.R:273:34:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L273) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_unlinked_tree.R:282:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:301:40:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L301) *style:* **Variable and function name style should be snake_case.**
```r
                                       Q1 = NULL,
                                       ^~
```
[R/sim_unlinked_tree.R:302:40:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L302) *style:* **Variable and function name style should be snake_case.**
```r
                                       Q2 = NULL,
                                       ^~
```
[R/sim_unlinked_tree.R:313:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L313) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(geiger::is.extinct(input_tree)) > 0) {
    ^
```
[R/sim_unlinked_tree.R:320:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L320) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(focal_alignment)) {
    ^
```
[R/sim_unlinked_tree.R:322:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L322) *style:* **Lines should not be more than 80 characters.**
```r
    focal_alignment <- nodeSub::sim_normal(input_tree, l = l, Q = Q1, bf = bf, rootseq = rootseq, rate = rate1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:336:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L336) *style:* **Lines should not be more than 80 characters.**
```r
    proposed_alignment <- nodeSub::sim_unlinked_tree(input_tree, Q1 = Q1, Q2 = Q2,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:337:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L337) *style:* **Lines should not be more than 80 characters.**
```r
                                                     rate1 = focal_rate, rate2 = focal_rate, l = l, bf = bf, rootseq = rootseq,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:338:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L338) *style:* **Lines should not be more than 80 characters.**
```r
                                                     node_time = node_time, lambda = lambda, mu = mu)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:347:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked_tree.R#L347) *style:* **Lines should not be more than 80 characters.**
```r
  proposed_alignment <- propose_alignments(buffer = c(), focal_rate = adjusted_rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/sim_unlinked.R:14:26:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                         Q1 = NULL,
                         ^~
```
[R/sim_unlinked.R:15:26:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                         Q2 = NULL,
                         ^~
```
[R/sim_unlinked.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_unlinked.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_unlinked.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/sim_unlinked.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/util.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/util.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/util.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```
[R/util.R:116:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/R/util.R#L116) *style:* **Variable and function name style should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-dual_independent.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-dual_parent.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-dual-linked.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-relative_node_time.R:22:1:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-relative_node_time.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
  obs_fraction <- ali$total_node_substitutions / (ali$total_node_substitutions + ali$total_branch_substitutions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-sim_normal.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-substitution.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-substitution.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-substitution.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-substitution.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-substitution.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-substitution.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/8dad26e6c7b340d175be9acfecba586aa584e011/tests/testthat/test-substitution.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


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