<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/mozilla-mobile/fenix:pull-request",
  "queue:route:checks",
  "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:

```
{
  "AnyOf": [
    {
      "AnyOf": [
        "queue:create-task:highest:aws-provisioner-v1/mobile-1-decision",
        "queue:create-task:very-high:aws-provisioner-v1/mobile-1-decision",
        "queue:create-task:high:aws-provisioner-v1/mobile-1-decision",
        "queue:create-task:medium:aws-provisioner-v1/mobile-1-decision",
        "queue:create-task:low:aws-provisioner-v1/mobile-1-decision",
        "queue:create-task:very-low:aws-provisioner-v1/mobile-1-decision",
        "queue:create-task:lowest:aws-provisioner-v1/mobile-1-decision"
      ]
    },
    {
      "AnyOf": [
        "queue:create-task:aws-provisioner-v1/mobile-1-decision",
        {
          "AllOf": [
            "queue:define-task:aws-provisioner-v1/mobile-1-decision",
            "queue:task-group-id:mobile-level-1/Gvl1OV81R1aIU8BGD4cJCg",
            "queue:schedule-task:mobile-level-1/Gvl1OV81R1aIU8BGD4cJCg/Gvl1OV81R1aIU8BGD4cJCg"
          ]
        }
      ]
    }
  ]
}
```

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

```
{
  "AllOf": [
    "assume:repo:github.com/mozilla-mobile/fenix:pull-request",
    "queue:route:checks",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:mobile-level-1",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/mobile-1-decision",
                "queue:create-task:very-high:aws-provisioner-v1/mobile-1-decision",
                "queue:create-task:high:aws-provisioner-v1/mobile-1-decision",
                "queue:create-task:medium:aws-provisioner-v1/mobile-1-decision",
                "queue:create-task:low:aws-provisioner-v1/mobile-1-decision",
                "queue:create-task:very-low:aws-provisioner-v1/mobile-1-decision",
                "queue:create-task:lowest:aws-provisioner-v1/mobile-1-decision"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/mobile-1-decision",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/mobile-1-decision",
                "queue:task-group-id:mobile-level-1/Gvl1OV81R1aIU8BGD4cJCg",
                "queue:schedule-task:mobile-level-1/Gvl1OV81R1aIU8BGD4cJCg/Gvl1OV81R1aIU8BGD4cJCg"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-11-20T16:00:41.269Z

</details>


Oh, is this the only place where the Lexer stuff is used? If this is the case then I would say: go for it :-)


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


Maybe change comment too?


Same here


Successfully deployed to following URLs:

* https://alexburgos-94r8v9zht.now.sh
* https://www.burgos.co
* https://burgos.co
* https://alexburgos.alexburgos.now.sh
* https://alexburgos-git-master.alexburgos.now.sh


Non c'est pas un doublon, la fonction recalcule le montant à ajouter au solde. J'aurai aimé me contenter faire la différence, mais il me semble qu'on perd cette information car tout provient de l'api Lydia et on ne reçoit que le montant payé (qui inclut donc la commission) :/


I propose this interface:

```
interface ContextInterface
{
    public function toArray(): array;
}
```


clarified process


This ? : is pretty useless, I guess you can do it in the xml too


Sinon oui, y'a parfois des écarts et quand y'en a, y'a un centime de plus qui s'ajoute au solde ! 🥇


[R/cla_secsse_loglik.R:1:37:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L1) *style:* **Commas should always have a space after.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                    ^
```
[R/cla_secsse_loglik.R:1:39:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L1) *style:* **Commas should always have a space after.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                      ^
```
[R/cla_secsse_loglik.R:1:48:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L1) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                               ^~
```
[R/cla_secsse_loglik.R:3:10:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L3) *style:* **Put spaces around all infix operators.**
```r
  d <- ly/2
        ~^~
```
[R/cla_secsse_loglik.R:4:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  Es <- y[1:d]
  ^~
```
[R/cla_secsse_loglik.R:5:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  Ds <- y[(d+1):ly]
  ^~
```
[R/cla_secsse_loglik.R:5:13:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L5) *style:* **Put spaces around all infix operators.**
```r
  Ds <- y[(d+1):ly]
           ~^~
```
[R/cla_secsse_loglik.R:8:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L8) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:10:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L10) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:11:26:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L11) *style:* **Commas should always have a space after.**
```r
  all_states <- cbind(Ds,Es)
                         ^
```
[R/cla_secsse_loglik.R:12:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L12) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:12:26:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                         ^
```
[R/cla_secsse_loglik.R:12:29:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                            ^
```
[R/cla_secsse_loglik.R:12:41:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                                        ^
```
[R/cla_secsse_loglik.R:14:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  cross_D_E <- a%*%b
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:14:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L14) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:14:17:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L14) *style:* **Put spaces around all infix operators.**
```r
  cross_D_E <- a%*%b
               ~^~~~
```
[R/cla_secsse_loglik.R:15:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L15) *warning:* **local variable ‘nb_node’ assigned but may not be used**
```r
  nb_node <- phy$Nnode
  ^~~~~~~
```
[R/cla_secsse_loglik.R:16:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:16:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
  ^~
```
[R/cla_secsse_loglik.R:16:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:16:10:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
         ^
```
[R/cla_secsse_loglik.R:16:34:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                 ^
```
[R/cla_secsse_loglik.R:16:62:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                             ^
```
[R/cla_secsse_loglik.R:16:73:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Put spaces around all infix operators.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                        ^~
```
[R/cla_secsse_loglik.R:16:74:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                         ^
```
[R/cla_secsse_loglik.R:16:75:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                          ^
```
[R/cla_secsse_loglik.R:16:84:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:118:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:122:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:133:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:17:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
  ^~
```
[R/cla_secsse_loglik.R:17:10:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
         ^
```
[R/cla_secsse_loglik.R:17:34:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                 ^
```
[R/cla_secsse_loglik.R:17:62:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                             ^
```
[R/cla_secsse_loglik.R:17:76:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                           ^
```
[R/cla_secsse_loglik.R:17:85:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:125:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:129:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:131:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Put spaces around all infix operators.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ~^~~~
```
[R/cla_secsse_loglik.R:17:141:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:18:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L18) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:18:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L18) *warning:* **local variable ‘hmax’ assigned but may not be used**
```r
  hmax <- NULL
  ^~~~
```
[R/cla_secsse_loglik.R:18:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L18) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:19:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L19) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
  ly <- ncol(states)
  ^~
```
[R/cla_secsse_loglik.R:19:20:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L19) *style:* **Commas should always have a space after.**
```r
  return(list(c(dE,dD)))
                   ^
```
[R/cla_secsse_loglik.R:22:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L22) *warning:* **no visible global function definition for ‘check_input’**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
      ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:23:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
cla_calThruNodes <- function(
^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:27:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
  forTime,
  ^~~~~~~
```
[R/cla_secsse_loglik.R:32:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L32) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
){
^~
```
[R/cla_secsse_loglik.R:36:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:41:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L41) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
    ly <- ncol(states)
    ^~
```
[R/cla_secsse_loglik.R:42:20:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L42) *style:* **Put spaces around all infix operators.**
```r
  d <- ncol(states)/2
                  ~^~
```
[R/cla_secsse_loglik.R:43:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:44:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L44) *style:* **Commented code should be removed.**
```r
  #ances <- ances[1] #########################  REMOVE!!!!!!!!!!!!
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:45:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L45) *style:* **Commented code should be removed.**
```r
  #desIndex <- 1
   ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:46:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L46) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:48:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L48) *style:* **Variable and function name style should be snake_case.**
```r
  desRows <- which(phy$edge[, 1] == focal)
  ^~~~~~~
```
[R/cla_secsse_loglik.R:49:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  desNodes <- phy$edge[desRows, 2]
  ^~~~~~~~
```
[R/cla_secsse_loglik.R:50:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:51:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L51) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:52:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L52) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:54:6:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(desIndex in 1:2){
     ^
```
[R/cla_secsse_loglik.R:54:22:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L54) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  for(desIndex in 1:2){
                     ^~
```
[R/cla_secsse_loglik.R:55:36:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L55) *style:* **Commas should always have a space after.**
```r
    y <- states[desNodes[desIndex],]
                                   ^
```
[R/cla_secsse_loglik.R:56:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L56) *style:* **Variable and function name style should be snake_case.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
    ^~~~~~~~
```
[R/cla_secsse_loglik.R:56:40:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L56) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                       ^
```
[R/cla_secsse_loglik.R:56:66:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L56) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                                                 ^
```
[R/cla_secsse_loglik.R:57:9:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L57) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:58:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L58) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:58:9:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L58) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:59:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L59) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(use_fortran == FALSE){
      ^
```
[R/cla_secsse_loglik.R:59:28:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L59) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(use_fortran == FALSE){
                           ^~
```
[R/cla_secsse_loglik.R:60:8:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L60) *style:* **Variable and function name style should be snake_case.**
```r
       nodeMN <- deSolve::ode(y = y, func = cla_secsse_loglik_rhs,
       ^~~~~~
```
[R/cla_secsse_loglik.R:61:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:61:40:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L61) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                       ^
```
[R/cla_secsse_loglik.R:61:69:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L61) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                                                    ^
```
[R/cla_secsse_loglik.R:62:40:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L62) *style:* **Commas should always have a space after.**
```r
                           hmax = NULL,method = methode)
                                       ^
```
[R/cla_secsse_loglik.R:64:8:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
       nodeMN <- ode_FORTRAN(y = y, func = "cla_secsse_runmod",
       ^~~~~~
```
[R/cla_secsse_loglik.R:65:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
                              times = c(0,timeInte), parms = parameter, rtol = reltol, atol = abstol,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:65:43:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L65) *style:* **Commas should always have a space after.**
```r
                              times = c(0,timeInte), parms = parameter, rtol = reltol, atol = abstol,
                                          ^
```
[R/cla_secsse_loglik.R:68:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 1){
      ^
```
[R/cla_secsse_loglik.R:68:21:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L68) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(desIndex == 1){
                    ^~
```
[R/cla_secsse_loglik.R:69:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L69) *style:* **Variable and function name style should be snake_case.**
```r
      nodeN <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:71:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 2){
      ^
```
[R/cla_secsse_loglik.R:71:21:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L71) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(desIndex == 2){
                    ^~
```
[R/cla_secsse_loglik.R:72:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L72) *style:* **Variable and function name style should be snake_case.**
```r
      nodeM <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:72:9:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L72) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:72:22:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L72) *style:* **Trailing whitespace is superfluous.**
```r
      nodeM <- nodeMN
                     ^
```
[R/cla_secsse_loglik.R:74:6:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L74) *style:* **Commented code should be removed.**
```r
   # print(nodeMN)
     ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:77:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L77) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:77:31:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L77) *style:* **Commas should always have a space after.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:78:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:78:31:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L78) *style:* **Commas should always have a space after.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:79:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:79:43:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L79) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
                                          ^
```
[R/cla_secsse_loglik.R:80:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L80) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:80:43:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L80) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
                                          ^
```
[R/cla_secsse_loglik.R:81:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L81) *style:* **Commented code should be removed.**
```r
  # cat(rbind(nodeM[(d+1):length(nodeM)],nodeN[(d+1):length(nodeN)]),"\n")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:81:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L81) *warning:* **no visible global function definition for ‘check_input’**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
      ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:82:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L82) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:82:30:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L82) *warning:* **no visible global function definition for ‘build_initStates_time’**
```r
      setting_calculation <- build_initStates_time(phy,traits,num_concealed_states,sampling_fraction)
                             ^~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:83:52:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L83) *style:* **Commas should always have a space after.**
```r
  all_states <- cbind(nodeM[(d + 1):length(nodeM)],nodeN[(d + 1):length(nodeN)])
                                                   ^
```
[R/cla_secsse_loglik.R:84:26:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                         ^
```
[R/cla_secsse_loglik.R:84:29:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                            ^
```
[R/cla_secsse_loglik.R:84:41:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                                        ^
```
[R/cla_secsse_loglik.R:86:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
  cross_M_N <- a%*%b
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:86:17:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L86) *style:* **Put spaces around all infix operators.**
```r
  cross_M_N <- a%*%b
               ~^~~~
```
[R/cla_secsse_loglik.R:87:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L87) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:88:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L88) *style:* **Commented code should be removed.**
```r
  # mergeBranch <- NULL
    ^~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:89:18:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L89) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  #for(iii in 1:d){
                 ^~
```
[R/cla_secsse_loglik.R:90:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L90) *style:* **Lines should not be more than 80 characters.**
```r
  #combProb <- 0.5*sum(lapply(lambdas,"*",cross_M_N)[[1]]) ## multiplication of probabilities of both branches
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:90:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L90) *style:* **Commented code should be removed.**
```r
  #combProb <- 0.5*sum(lapply(lambdas,"*",cross_M_N)[[1]]) ## multiplication of probabilities of both branches
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:91:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L91) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- c(mergeBranch,combProb)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:92:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
  ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:92:54:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                     ^
```
[R/cla_secsse_loglik.R:92:58:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                         ^
```
[R/cla_secsse_loglik.R:92:69:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                                    ^
```
[R/cla_secsse_loglik.R:94:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L94) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:94:38:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L94) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
                                     ^
```
[R/cla_secsse_loglik.R:94:47:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
                                              ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:95:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L95) *style:* **Commented code should be removed.**
```r
  #sumD <- sum(mergeBranch)
   ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:96:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L96) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- mergeBranch/sumD
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:97:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L97) *style:* **Commented code should be removed.**
```r
  #loglik <- loglik + log(sumD)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:98:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L98) *style:* **Commented code should be removed.**
```r
  #cat(mergeBranch,"\n")
   ^~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:100:26:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L100) *style:* **Commas should always have a space after.**
```r
  newstate <- c(newstate,mergeBranch)
                         ^
```
[R/cla_secsse_loglik.R:101:16:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L101) *style:* **Commas should always have a space after.**
```r
  states[focal,] <- newstate
               ^
```
[R/cla_secsse_loglik.R:102:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L102) *style:* **Commented code should be removed.**
```r
  #print(parameter); print(loglik)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:103:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:103:31:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                              ^
```
[R/cla_secsse_loglik.R:103:47:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                              ^
```
[R/cla_secsse_loglik.R:103:73:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                                                        ^
```
[R/cla_secsse_loglik.R:104:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L104) *warning:* **local variable ‘nodeN’ assigned but may not be used**
```r
      nodeN <- calcul$nodeN
      ^~~~~
```
[R/cla_secsse_loglik.R:110:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L110) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:110:30:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L110) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
                             ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:113:26:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L113) *style:* **Variable and function name style should be snake_case.**
```r
                         forTime,
                         ^~~~~~~
```
[R/cla_secsse_loglik.R:118:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L118) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:119:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L119) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
){
^~
```
[R/cla_secsse_loglik.R:120:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L120) *style:* **Commented code should be removed.**
```r
  #cl <- makeCluster(2)
   ^~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:121:4:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L121) *style:* **Commented code should be removed.**
```r
  #registerDoParallel(cl)
   ^~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:122:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L122) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:123:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L123) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:124:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L124) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:128:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L128) *style:* **Variable and function name style should be snake_case.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:128:33:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L128) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
                                ^
```
[R/cla_secsse_loglik.R:145:47:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L145) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
                                   )) %dopar% {
                                              ^
```
[R/cla_secsse_loglik.R:145:48:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
                                   )) %dopar% {
                                               ^
```
[R/cla_secsse_loglik.R:146:38:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
                                     ancesSub <- take_ancesSub[[ii]]
                                     ^~~~~~~~
```
[R/cla_secsse_loglik.R:147:41:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L147) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                                     for(i in 1:length(ancesSub)){
                                        ^
```
[R/cla_secsse_loglik.R:147:47:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L147) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
                                     for(i in 1:length(ancesSub)){
                                              ^
```
[R/cla_secsse_loglik.R:147:65:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L147) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
                                     for(i in 1:length(ancesSub)){
                                                                ^~
```
[R/cla_secsse_loglik.R:148:49:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L148) *style:* **Trailing whitespace is superfluous.**
```r
                                       calcul <-
                                                ^
```
[R/cla_secsse_loglik.R:154:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
                                                          use_fortran = use_fortran,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:165:28:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
#' Logikelihood calculation
                           ^
```
[R/cla_secsse_loglik.R:168:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L168) *style:* **Lines should not be more than 80 characters.**
```r
#' @param parameter list where the first is a table where lambdas across different modes of speciation are shown, the second mus and the third transition rates.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:169:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L169) *style:* **Lines should not be more than 80 characters.**
```r
#' @param phy phylogenetic tree of class phylo, ultrametric, fully-resolved, rooted and with branch lengths.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:170:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L170) *style:* **Lines should not be more than 80 characters.**
```r
#' @param traits vector with trait states, order of states must be the same as tree tips, for help, see vignette.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:171:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L171) *style:* **Lines should not be more than 80 characters.**
```r
#' @param num_concealed_states number of concealed states, generally equivalent to number of examined states.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:172:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L172) *style:* **Lines should not be more than 80 characters.**
```r
#' @param use_fortran Should the Fortran code for numerical integration be called? Default is TRUE.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:174:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L174) *style:* **Lines should not be more than 80 characters.**
```r
#' @param cond condition on the existence of a node root: "maddison_cond","proper_cond"(default). For details, see vignette.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:174:35:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L174) *warning:* **no visible global function definition for ‘penalty’**
```r
  LL <- log(wholeLike) + loglik - penalty(pars = parameter,loglik_penalty = loglik_penalty)
                                  ^~~~~~~
```
[R/cla_secsse_loglik.R:175:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L175) *style:* **Lines should not be more than 80 characters.**
```r
#' @param root_state_weight the method to weigh the states:"maddison_weights","proper_weights"(default) or "equal_weights". It can also be specified the root state:the vector c(1,0,0) indicates state 1 was the root state.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:176:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L176) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sampling_fraction vector that states the sampling proportion per trait state. It must have as many elements as trait states.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:178:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L178) *style:* **Lines should not be more than 80 characters.**
```r
#' @param setting_calculation argument used internally to speed up calculation. It should be leave blank (default : setting_calculation = NULL)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:179:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L179) *style:* **Lines should not be more than 80 characters.**
```r
#' @param setting_parallel argument used internally to set a parallel calculation. It should be left blank (default : setting_parallel = NULL)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:180:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L180) *style:* **Lines should not be more than 80 characters.**
```r
#' @param see_ancestral_states should the ancestral states be shown? Deafault FALSE
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:181:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L181) *style:* **Lines should not be more than 80 characters.**
```r
#' @param loglik_penalty the size of the penalty for all parameters; default is 0 (no penalty)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:182:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L182) *style:* **Lines should not be more than 80 characters.**
```r
#' @note To run in parallel it is needed to load the following libraries when windows: apTreeshape, doparallel and foreach. When unix, it requires: apTreeshape, doparallel, foreach and doMC
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:207:52:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L207) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(4,ncol=3,nrow=3,byrow=TRUE)
                                                   ^
```
[R/cla_secsse_loglik.R:211:67:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L211) *style:* **Trailing whitespace is superfluous.**
```r
#'prepare_full_lambdas(traits,num_concealed_states,idparlist[[1]])
                                                                  ^
```
[R/cla_secsse_loglik.R:212:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L212) *style:* **Lines should not be more than 80 characters.**
```r
#'# which is a list with 9 matrices, corresponding to the 9 states (0A,1A,2A,0B,etc)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:217:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L217) *style:* **Lines should not be more than 80 characters.**
```r
#'parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,lambd_and_modeSpe)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:217:88:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L217) *style:* **Trailing whitespace is superfluous.**
```r
#'parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,lambd_and_modeSpe)
                                                                                ^
```
[R/cla_secsse_loglik.R:219:55:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L219) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(0.07,ncol=3,nrow=3,byrow=TRUE)
                                                      ^
```
[R/cla_secsse_loglik.R:223:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L223) *style:* **Lines should not be more than 80 characters.**
```r
#'                  use_fortran = FALSE, methode = "ode45", cond = "maddison_cond",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:230:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L230) *style:* **functions should have cyclomatic complexity of less than 15, this has 26.**
```r
cla_secsse_loglik <- function(parameter,
^
```
[R/cla_secsse_loglik.R:243:49:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L243) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
                              loglik_penalty = 0){
                                                ^~
```
[R/cla_secsse_loglik.R:247:3:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L247) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:248:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L248) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:249:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L249) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(run_parallel == TRUE){
    ^
```
[R/cla_secsse_loglik.R:249:26:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L249) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(run_parallel == TRUE){
                         ^~
```
[R/cla_secsse_loglik.R:249:27:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L249) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(run_parallel == TRUE){
                          ^
```
[R/cla_secsse_loglik.R:249:28:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L249) *style:* **Trailing whitespace is superfluous.**
```r
  if(run_parallel == TRUE){
                           ^
```
[R/cla_secsse_loglik.R:250:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L250) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.null(setting_calculation)){
      ^
```
[R/cla_secsse_loglik.R:250:36:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L250) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(is.null(setting_calculation)){
                                   ^~
```
[R/cla_secsse_loglik.R:251:26:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                         ^
```
[R/cla_secsse_loglik.R:251:30:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                             ^
```
[R/cla_secsse_loglik.R:251:48:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                                               ^
```
[R/cla_secsse_loglik.R:252:29:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L252) *style:* **Trailing whitespace is superfluous.**
```r
      setting_calculation <-
                            ^
```
[R/cla_secsse_loglik.R:253:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L253) *style:* **Lines should not be more than 80 characters.**
```r
        build_initStates_time_bigtree(phy, traits, num_concealed_states, sampling_fraction)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:255:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L255) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:257:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L257) *style:* **Variable and function name style should be snake_case.**
```r
    forTime <- setting_calculation$forTime
    ^~~~~~~
```
[R/cla_secsse_loglik.R:258:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L258) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub1 <- setting_calculation$ancesSub1
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:259:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L259) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub2 <- setting_calculation$ancesSub2
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:260:5:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L260) *style:* **Variable and function name style should be snake_case.**
```r
    ancesRest <- setting_calculation$ancesRest
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:261:1:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L261) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:262:7:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L262) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
      ^
```
[R/cla_secsse_loglik.R:262:59:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L262) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                          ^~
```
[R/cla_secsse_loglik.R:262:75:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L262) *style:* **Trailing whitespace is superfluous.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                                          ^
```
[R/cla_secsse_loglik.R:263:28:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L263) *style:* **Trailing whitespace is superfluous.**
```r
      d <- ncol(states) / 2
                           ^
```
[R/cla_secsse_loglik.R:264:29:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L264) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                            ^
```
[R/cla_secsse_loglik.R:264:41:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L264) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                                        ^
```
[R/cla_secsse_loglik.R:264:41:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L264) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                                        ^
```
[R/cla_secsse_loglik.R:265:29:](https://github.com/rsetienne/secsse/blob/643dfe1c5d36ad78a00a20f0f2ee0af8f122a6b9/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                            ^
```


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Deployment failed with the following error:

~~~
The property `builds` is not allowed in now.json when using Now 2.0 – please remove it.
~~~


Yes, you're right. Already know what's wrong. Will fix this ASAP.


thanks


Added a show/hide raw data button


If this is going to be the case of the final release as well, then please raise an InvalidConfiguration exeption when these compiler versions are trying to get used


It shows travis changes under "Bug Fixes" because they used the `fix` type on the commit message
![image](https://user-images.githubusercontent.com/97994/69255282-2e127300-0b7d-11ea-9e7e-1f40f29509c9.png)

To me that doesn't really make sense unless the change is actually fixing something.

The point of the changelog is to list human readable changes to the application.

Changing travis or a test doesn't change the input or output of the application so there is no reason for users to care about that.

Essentially, the commit log is for all changes to the code and the change log is for all changes to the application.


Nice


We need to deprecate the argument in the respective constructors:
```
public function __constructor(/** ContextInterface **/ array $defaultContext = []) {
  if (!$defaultContext instanceof ContextInterface) {
       $defaultContext = new DefaultContext($defaultContext);
      trigger_error("blabla deprecated version x", E_DEPRECATED);
  }
}
```


I will, but I'm waiting for the final release to check in the actual documentation


la liste des opérateurs à la fin, c'est normal qu'il n'étaient pas en commentaire pour voir si la colorisation syntaxique marchait ou non


this is basic c program


Of course, now we need to figure out how to protect Hogwarts.....


These optional parameters aren't needed since you're using the default, right?


Its makes sense though its not how I ever used changelogs or see them being used unless its with these "standards" anyway, were not getting mileage out of this discussion, Its one opinion over another and defending each view is pointless.


WorldGuard seems a good idea but it doesn't have a per world option, it's purely region defined.


@amio You can't mix `functions` and `builds`. You can completely `remove` builds and make sure you `package.json` build script emits files to a `public` directory.


Checkmarx scan results 20 Nov 2019 18:14 UTC +02:00

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Included commits

Commit ID	Owner

1e71c4b085217e0cab2013734fb62a6c80309419	@web-flow


Pourquoi le fichier `.env.example` a-t-il été supprimé ?


Very small typo


`file_path` can be both a derived and a constant attribute right?


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great stuff, a few comments:
- drawer is missing "Replications (legacy)" and "Help" links as last 2 items (see #75 specs)
- clicking LEARN MORE https://curate-science-staging-2.appspot.com/app/home#for-authors within landing page for "Are you an author" doesn't work
- clicking "Landing" (https://curate-science-staging-2.appspot.com/app/home) for non-logged-in users doesn't work
- duplicate text in HIW "For Educators" section ("Curate replication metadata on its own article page and easily share it. Create collections of replications across different methods of testing an effect, and meta-analyze and track replication evidence (coming soon)."
- weird padding/clipping issue (on right-hand side) for smaller screen sizes (see screenshot below). perhaps related to pre-existing issue of missing viewport tag: `<meta name="viewport" content="width=device-width, initial-scale=.5">` (though unsure what initial-scale value should be)
![Untitled](https://user-images.githubusercontent.com/4512335/69256056-dbd64f80-0b86-11ea-8d01-06fee675c1dd.png)


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revert css


@gotcha. Yes, thanks. It's a very good idea and implementation. But I found it more complex.
And, in my use cases, it is preferred a notfound instead of a redirect, ... anyway probably this could be an option in redirectacquired


Этот класс отображает строку таблицы базы данных. А чтобы хранить внутри обьекты для этого нужно сделать другой класс?


Merging into master


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yes, the requested values (here: `source1`) will be added prior to the derivation


Was this intended to affect the behavior of -Wswitch-bool?  The following code did not trigger a warning with -Wswitch-bool prior to this commit, but now it does:

`typedef enum GizmoDeviceStateE
{
    GizmoDevice_ModeIdle,
    GizmoDevice_ModeJiggle
} GizmoDeviceStateE;

typedef struct GizmoStatus
{
   ...
   unsigned int      devState:1;
   ...
}
...
   switch (giz23status->devState)
   {
      case GizmoDevice_ModeIdle:
         ...
         break;
      case GizmoDevice_ModeJiggle:
         ...
         break;
      default:
         break;
   }
...
`

There are valid criticisms of the code presented here, of course-- but the main question is whether the change was intended to flag constructs like this for -Wswitch-bool as well as for -Wobjc-signed-char-bool false-positive.


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Это маленькая халтура :)


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Idk if needed but just in case.


@dougalm thanks very much for this detailed reply. It clarifies a lot of things for me and points me in the direction to review some more things I still don't quite understand.

>Note there's one dual space for the whole vector space, not one for each point.

I suspect this is critical to my misunderstanding, so I will go and review dual spaces.

I agree with @oxinabox that I'd love to see some justification for whether the separation of vectors and covectors is a practical concern here (reminds me a bit of Julia's longest issue thread, https://github.com/JuliaLang/julia/issues/4774. Maybe time for a Taking Function Transposes Seriously thread?).

I know @jrevels had some thoughts about the upper/lower indices in Ricci Calculus notation. And [Computing Higher Order Derivatives of Matrix and Tensor Expressions](http://www.matrixcalculus.org/matrixcalculus.pdf) from last NeurIPS suggests it might be practically important at least in higher derivatives (which as you know is interesting to me). Am I correct that these are related to the question of covector type?

@oxinabox I loved the `DateTime` example when you first described it on Julia slack, very glad you brought it out here. Also does the singleton set being the differential type for non-differentiables answer that discussion you were having before where you thought it could be nothing (? I actually don't remember where you landed)? Is that a contradiction?


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This is basic C Program.


That moment when you realize that freaking partition was enough to piss you off XD But still this journey was worth it. Once again thanks to you for keeping this device alive.  i literally had a rough time booting it. Surprisingly there are so many changes made in android 10. Can't wait for next year. Thanks to the community for all the support. This community is enough for keeping us motivated to develop this device.


I'd like to keep it here for now, because it is very likely that we want to throw away current design and start from scratch. Once this (or another) branch is ready for peer review or feedbacks, I think we can create a PR or a feature branch.


@TheSaimun change commit ..
'add officer_account table in admin'


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


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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)|


Successfully deployed to following URLs:

* https://portfolio-igk6uielh.now.sh
* https://portfolio-delta-rust.now.sh
* https://portfolio.nursultansharsheev.now.sh
* https://portfolio-git-master.nursultansharsheev.now.sh


Successfully deployed to following URLs:

* https://the-kana-jfilz71l6.now.sh
* https://the-kana.now.sh
* https://the-kana.com
* https://the-kana.dshlass.now.sh
* https://the-kana-git-master.dshlass.now.sh


Successfully deployed to following URLs:

* https://serverless-graphql-api-example-k27bp349l.now.sh
* https://serverless-graphql-api-example-five-gamma.now.sh
* https://serverless-graphql-api-example.heshan-1010.now.sh
* https://serverless-graphql-api-example-git-master.heshan-1010.now.sh


Uhh, i think we're going over doing the mark down version of the resume
tonight. Brad mentioned that on Monday.

On Wed, Nov 20, 2019, 9:51 AM Johnny Reina <notifications@github.com> wrote:

> What's up with the markdown version of this?
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
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> .
>


все это можно перенести в onCreateView


Successfully deployed to following URLs:

* https://carbon-website-pkqawc9yr.now.sh
* https://carbondesignsystem.now.sh
* https://carbon-website.carbon-design-system.now.sh
* https://carbon-website-git-master.carbon-design-system.now.sh


![](https://github.trello.services/images/mini-trello-icon.png) [Search Graph](https://trello.com/c/OS7tMowR/8-search-graph)


@simonetripodi  Just to note that this way of logging causes String based concatenation even if the log message is not output. That's why the placeholder based variant is better as it doesn't concatenate the strings if they are not actually logged. This is especially important for the case below...


Successfully deployed to following URLs:

* https://kpacholski-6c84zx3qi.now.sh
* https://kpacholski.pachol2001.now.sh
* https://kpacholski-git-master.pachol2001.now.sh


Successfully deployed to following URLs:

* https://portfolio-aefwv1qx2.now.sh
* https://portfolio-seven-tau.now.sh
* https://vikramsolanki.in
* https://portfolio.vikramsolanki25.now.sh
* https://portfolio-git-master.vikramsolanki25.now.sh