[R/cla_secsse_loglik.R:1:37:](https://github.com/rsetienne/secsse/blob/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/R/cla_secsse_loglik.R#L48) *style:* **Variable and function name style should be snake_case.**
```r
  desRows <- which(phy$edge[, 1] == focal)
  ^~~~~~~
```
[R/cla_secsse_loglik.R:49:3:](https://github.com/rsetienne/secsse/blob/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/R/cla_secsse_loglik.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  desNodes <- phy$edge[desRows, 2]
  ^~~~~~~~
```
[R/cla_secsse_loglik.R:50:1:](https://github.com/rsetienne/secsse/blob/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/R/cla_secsse_loglik.R#L257) *style:* **Variable and function name style should be snake_case.**
```r
    forTime <- setting_calculation$forTime
    ^~~~~~~
```
[R/cla_secsse_loglik.R:258:5:](https://github.com/rsetienne/secsse/blob/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/R/cla_secsse_loglik.R#L258) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub1 <- setting_calculation$ancesSub1
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:259:5:](https://github.com/rsetienne/secsse/blob/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/R/cla_secsse_loglik.R#L259) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub2 <- setting_calculation$ancesSub2
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:260:5:](https://github.com/rsetienne/secsse/blob/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/R/cla_secsse_loglik.R#L260) *style:* **Variable and function name style should be snake_case.**
```r
    ancesRest <- setting_calculation$ancesRest
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:261:1:](https://github.com/rsetienne/secsse/blob/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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/2d480ca6b0fdd0d9929f1611e3d44b3675050e55/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)]
                            ^
```


@JuliaRegistrator register


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Still needs work on viewed prop: where should we attached viewed prop? Thinking that maybe somewhere near setToggled (Redux command). Another question: how to anchor the pin to the x, y coord? Currently the styling moves the pin up and to the left


if this is the exact same method than unsupervised trainer, better just inherit from UnsupervisedTrainer and overload just the train-test split ? Again, let's avoid duplicate code


this is some debugging code and needs to be removed :)


This commit should solve #91


Now i'm really curious. I think i'll trap the return from pre_match and see what it is. This should not be an issue regardless if windows.  I'm on PHP 7.2.4


When receiving non-numerical first argument (or no arguments), `repeat` got stuck in an infinite cycle.


Deployment failed with the following error:

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


Hi Evariste
Peut tu donner quelques infos concernant le fonctionnement du pluto avec DVBsdr , je trouve ce programme super et j'ai déjà rajouté la cam usb avec jetson .
Merci pour tes précisions
73. F4fdw. Laurent


Falta mirar el constructor de Administrador


If this inference is the exact same than VAE, can we inherit from VAE ? I think just the prior part of the ELBO changes


Same gut-reflex here for `paste0()` but `paste()` on purpose to not depend on newer R.

Not sure a unit test is needed.  Next (bigger) todo item is converting all tests to tinytest.


OK


bug fix


👍 неплохо идешь


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the elbo should be log p(x \mid z) + log p(z) - log q(z \mid x). The last term is missing ? You can look at the VAE class to get it.


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/5640](https://github.com/JuliaRegistries/General/pull/5640)

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:
```
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git push origin v0.1.7
```


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Thus `reverse` won't mutate its input


Falta por terminar el menu con las demas funciones de Usuario y comprobar si el DNI ya existe en el sistema en modificarDatosPerosnales()


@mattjones315 here are some comments


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For me,
`D = one.load(eid[0], clobber=False, download_only=True)`
returns `D` as an empty `SessionDataInfo` dataclass if the data is already saved locally:
(`SessionDataInfo(dataset_type=[], dataset_id=[], local_path=[], eid=[], url=[], data=[])`)
 For you, what does `D` look like in this case? I was thinking it should be empty based on the `clobber=False` input argument.


TeamCity Bvcms / Build [Build 2833](https://builds.tpsdb.com/viewLog.html?buildId=9957&buildTypeId=Bvcms_Build) outcome was **FAILURE**
Summary: Compilation error: IntegrationTests\IntegrationTests.csproj Build time: 00:06:00


TeamCity Bvcms / Build [Build 2834](https://builds.tpsdb.com/viewLog.html?buildId=9960&buildTypeId=Bvcms_Build) is now running


int8_t можно без const - всё равно копия создастся


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It si first commit.


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

I updated the Github team because of this commit.

- @jhunkeler was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


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@JuliaRegistrator register()


Registration pull request updated: [JuliaRegistries/General/5640](https://github.com/JuliaRegistries/General/pull/5640)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.7 -m "<description of version>" d4288448e36835721b4b32917c65feadfb6fac27
git push origin v0.1.7
```


What
chat-spaceのテーブル作成の練習として、READMEにマークダウン方式でコードを記述しました。

Why
実装にさしあたっての練習として作成しています。


Show, obrigado @boidacarapreta .


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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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Are the ```Build-Depends: postgresql-server-dev-9.4 | postgresql-server-dev-9.5 ``` in
https://github.com/giggls/mapnik-german-l10n/blob/master/debian/control
still necessary?


Registration pull request created: [JuliaRegistries/General/5641](https://github.com/JuliaRegistries/General/pull/5641)

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 v0.7.1 -m "<description of version>" bee6caff9dc9bd76b4642b74824a311a570055a6
git push origin v0.7.1
```


You are pushing commits at a very fast pace (accross the whole organization).
Due to that, we cannot deploy the commit c90b57de4d0c68acb4ebf4e8357e3330fe25693b.

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


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во 1 не уверен, что это писал я, т.к. не шарб почему после мок методов вообще идут какие-то параметры (да я не любитель писать тесты и не шарю за gtest)
во 2-х там в методе Set константный указатель на данные передается. У тебя был `const int value`, и я поставил `const int * value`, а здесь видимо не поменял
Окей, исправлю


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Código de Yerlyn


You are pushing commits at a very fast pace (accross the whole organization).
Due to that, we cannot deploy the commit d2855264a500d2147be51e80766304560ff51d44.

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This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/suppress-category-from-latest-topics-gone/133894/6


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p = ProxySpace.push(s.boot)

MIDIIn.connectAll;
MIDIClient.init;
MIDIClient.destinations;

m.noteOn(0, 60, 64);
m.noteOff(0, 60, 64);

m = MIDIOut.new(0);
m.latency = 0;

//ich schicke Midi nach Logic
//des Codes Prinzip habe ich hier gesehen (https://www.youtube.com/watch?v=ih2uqOaqb4c)
(r = Routine({
	[35, 40, 45, 50, 45, 40, 45, 50, 25].do{|i|
		m.noteOn(9, i);
		0.25.wait;
	};
}).play;
)

//dann schreibe ich eine Melodie in Logic (ich benutze SuperCollider MIDI als background Sound + Charles Bukowski voice = Computerlove.wav)

//dann benutze ich diese Melodie als ein Teil von Code

b = Buffer.read(s,/*__________audio Computerlove.wav*/ );

b.play //test

(
var r;
r = Routine{
	inf.do({var x;

x = "abcdefghijklmnopqrstuvwxyz";
	{x.find("love").isNil}.while({
		x=x.scramble;
		x.postln;
		0.001.wait;
	});
		1105920.do({PlayBuf.ar(2, b, 1)}.play);
		2211840.wait;
})}.play;
)


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169840232_Issue7547 (Unknown) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


a


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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):
~~~


169840232_Issue7547 (Unknown) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (11 of 11 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


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süper 👍


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/efc15c98-b512-4f54-879c-70f8dd541c04?env_id=ibm%3Ayp%3Aus-south "kube-toolchain-20191107190907850"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/78160c83-6edd-4cef-86bc-228872c4d65e "hello-containers-20191107190907850") deployed [CustFeedBackReact](https://github.com/jayadevanmp/CustFeedBackReact/releases/tag/deploy-mycluster-20191120-192801 "deploy-mycluster-20191120-192801") to [mycluster](https://console.bluemix.net/kubernetes/clusters/bn1a6egd0d8l8bb2t810/overview "There was a problem retrieving the space name"), including this commit


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[R/ggbarstats.R:68:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/ggbarstats.R#L68) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
ggbarstats <- function(data,
^
```
[R/ggbetweenstats.R:194:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/ggbetweenstats.R#L194) *style:* **functions should have cyclomatic complexity of less than 15, this has 33.**
```r
ggbetweenstats <- function(data,
^
```
[R/ggcoefstats.R:282:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/ggcoefstats.R#L282) *style:* **functions should have cyclomatic complexity of less than 15, this has 60.**
```r
ggcoefstats <- function(x,
^
```
[R/ggcorrmat.R:167:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/ggcorrmat.R#L167) *style:* **functions should have cyclomatic complexity of less than 15, this has 29.**
```r
ggcorrmat <- function(data,
^
```
[R/gghistostats.R:79:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/gghistostats.R#L79) *style:* **functions should have cyclomatic complexity of less than 15, this has 24.**
```r
gghistostats <- function(data,
^
```
[R/ggpiestats.R:109:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/ggpiestats.R#L109) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
ggpiestats <- function(data,
^
```
[R/ggscatterstats.R:96:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/ggscatterstats.R#L96) *style:* **functions should have cyclomatic complexity of less than 15, this has 34.**
```r
ggscatterstats <- function(data,
^
```
[R/ggwithinstats.R:61:1:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/ggwithinstats.R#L61) *style:* **functions should have cyclomatic complexity of less than 15, this has 31.**
```r
ggwithinstats <- function(data,
^
```
[R/helpers_gghistostats_graphics.R:13:5:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/R/helpers_gghistostats_graphics.R#L13) *warning:* **local variable ‘label.value’ assigned but may not be used**
```r
    label.value <- x_pos
    ^~~~~~~~~~~
```
[tests/testthat/test-ggbetweenstats.R:159:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggbetweenstats.R#L159) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb$data[[4]]), c(7L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggbetweenstats.R:161:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggbetweenstats.R#L161) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb$data[[6]]), c(4L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggbetweenstats.R:461:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggbetweenstats.R#L461) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb1$data[[3]]), c(2L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggbetweenstats.R:463:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggbetweenstats.R#L463) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb1$data[[5]]), c(2L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggbetweenstats.R:470:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggbetweenstats.R#L470) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb1$data[[3]]), c(2L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggbetweenstats.R:472:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggbetweenstats.R#L472) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb1$data[[5]]), c(2L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggcoefstats.R:71:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggcoefstats.R#L71) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb$data[[4]]), c(4L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggcoefstats.R:1213:11:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggcoefstats.R#L1213) *style:* **Commented code should be removed.**
```r
    #     "list(~italic(beta)==-0.15, ~italic(t)==-0.93, ~italic(p)== 0.352)"
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggscatterstats.R:63:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggscatterstats.R#L63) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb$data[[7]]), c(2L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggwithinstats.R:60:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggwithinstats.R#L60) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb1$data[[7]]), c(2L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggwithinstats.R:133:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggwithinstats.R#L133) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb1$data[[4]]), c(4L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-ggwithinstats.R:135:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-ggwithinstats.R#L135) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb1$data[[6]]), c(3L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-helpers_ggbetweenstats.R:47:6:](https://github.com/IndrajeetPatil/ggstatsplot/blob/5be96459560fde19c79024ae2e526dfa59f4fc8d/tests/testthat/test-helpers_ggbetweenstats.R#L47) *style:* **Commented code should be removed.**
```r
    #testthat::expect_equal(dim(pb_mean$data[[3]]), c(4L, 15L))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


I just noticed there is a comma too much, can you take care of this?


work version


That's ok, the trailing comma doesn't hurt


Métodos de clase.


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Pasar los parámetros como string.


Revisar.


@digitall Thanks for taking care of this. I figured I would miss something and was keeping my eye on the buildbots... but that's when they done imploded =)

I just implemented horz shake on DINGUX and GPH, but does LINUXMOTO even compile? The relevant lines call effectiveScreenHeight() which existed 10 years ago when they written but doesn't anymore... so I'm just backing slowly away from this one.


Something seems to be buggy here.
This commit breaks my setups with `preload_from_files` (e.g. shallow fusion).
We should also check the tests again.


ffff


which line?


shower = cleanup... creativity=zero 😶


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I think checking this the other way around may be faster, as the .fetch can be an expensive operation, right?


0.4 elo? lol
-37 in 122k games is nothing ;)


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I meant a duplicate moz rule only for these.


you could have just used `make lfosim` and it would do the same thing.


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Correct/Valid Json responses


thanks. updated with `map[<constraint_key>]tags` design, let me know what you think


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any reason you don't just do `element = await page.find('testing-props-shadow >>> div')`?  just curious


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Может @DeleteMapping для улучшения читаемости?


зря убрали, толковое разъяснение


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TeamCity Bvcms / Build [Build 2834](https://builds.tpsdb.com/viewLog.html?buildId=9960&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 163 Build time: 00:24:24


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TeamCity Bvcms / Build [Build 2835](https://builds.tpsdb.com/viewLog.html?buildId=9958&buildTypeId=Bvcms_Build) outcome was **UNKNOWN**
Summary: Canceled (Error while applying patch; cannot find commit 33db5894d3967d695b6014e9328721170b08aace in the https://bvcms-teamcity@github.com/bvcms/bvcms repository, possible reason: refs/pull/681/merge branch was updated and the commit selected for the... Build time: 00:00:07


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TeamCity Bvcms / Build [Build 2836](https://builds.tpsdb.com/viewLog.html?buildId=9959&buildTypeId=Bvcms_Build) outcome was **UNKNOWN**
Summary: Canceled (Error while applying patch; cannot find commit 91d539c7df297454be36dc130ff0ae0e81e09b0a in the https://bvcms-teamcity@github.com/bvcms/bvcms repository, possible reason: refs/pull/714/merge branch was updated and the commit selected for the... Build time: 00:00:06


Перенести скобки вверх


`count` on a `Set` shouldn't produce an error


an element needs to be visible to be clickable, right? Also `find` doesn't support the `{visible: true}` option, so shouldn't this be `await element.waitForSelector('[data-test="day"]:nth-child(3)', {visible: true})` or some util function?


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SwimmingPool_Refactoring (dareumnam) - Win64-Windows-10-VisualStudio-16: OK (2581 of 2581 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


better replace to `art\intrface\PIP2.frm` or to FID `0x6000080`


Может добавить final? (Для всех **Controller** и **Service** классов


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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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Analogous to the clojure.core implementation.


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design addresses common tags in a package when reporting stats. once we add more metrics, there can be common tags to share.


FYI I'm building an Image for RPI4.


@JuliaRegistrator register


Registration pull request created: [JuliaRegistries/General/5643](https://github.com/JuliaRegistries/General/pull/5643)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.4 -m "<description of version>" 119358a6f50d4acdc0af69c1a3ec314da1a2ae86
git push origin v0.1.4
```


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I had to make my own graphic, because the vanilla .frm uses offsets and the game will crash.


Looks like tools/build/options/WITH_AMD needs to be removed?


Just a test comment!


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SwimmingPool_Refactoring (dareumnam) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (674 of 674 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.44%25-green.png)


Следует добавить проверку на наличие с помощью isPresent() (при всех использованиях **get** запросов)


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/2055) complete for branch gam-ids.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/commit/dd9113afb32dc8658fb744227ed6957b3f400f96/index.html).

5 tests passed, 12 tests failed and 0 tests skipped in 5122 seconds

Failed tests:

* test_map_mhc_primary (247 seconds)
* test_map_mhc_primary_genotype (244 seconds)
* test_map_mhc_snp1kg (388 seconds)
* test_map_mhc_snp1kg_genotype (363 seconds)
* test_full_brca2_cactus (37 seconds)
* test_full_brca2_primary (40 seconds)
* test_full_brca2_snp1kg (39 seconds)
* test_map_brca1_cactus (34 seconds)
* test_map_brca1_primary (34 seconds)
* test_map_brca1_snp1kg (37 seconds)
* test_map_brca1_snp1kg_genotype (37 seconds)
* test_map_brca1_snp1kg_mpmap (39 seconds)

Tests produced 326 warnings. 326 were for lower-than-expected alignment scores


Copy of this build can be found at
https://www.mewbuilds.com/build/5a33a089ac0b23c13beb42a3d095171c2b888ce0/index.html
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                       Virus Total analysis
                       https://www.virustotal.com/file/8ef350fbab47047b172cfeb0849aadb59c7b4e0587ce218ce0d3b932da628ee4/analysis/1574279082/


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/96575206-a4e3-460e-a999-a5afad396c34?env_id=ibm%3Ayp%3Aus-south "helm-toolchain-20191120171033193"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/2f4b2da5-89b9-45cc-9e03-8eeb84446ad5 "hello-helm-20191120171033193") deployed [CloudNativeBootCampNov19](https://github.com/khuramj/CloudNativeBootCampNov19/releases/tag/deploy-mycluster-20191120-194523 "deploy-mycluster-20191120-194523") to [mycluster](https://console.bluemix.net/kubernetes/clusters/bnaka36d0r592meli7bg/overview "There was a problem retrieving the space name"), including this commit


I'am sorry for being undisciplined. As soon as i met serious troubles in syntax/logics i forgot about making commits. I'll do my best next module.


this is basic c program


Thanks very much @dorbin!


`(pr-str (Date.))` prints out an `#inst` value (and `#inst` is a standard EDN tag), so there's no reason for it to not be parseable


Nice!
The Surface Works Great on TFT35 1.2 .  I didn't test the print function yet. Some German translate issue, but not critical; i think it depend on the length of german words (Some Words are longer in german and need too much space on Display)

See Ya


trajper.md

https://raw.githack.com/trajper/trajper.github.io/trajper-mdwiki-page/#!pages/vi/profiles/trajper.md


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Weird. preg_match returned true when I set to a var. But failed in conditional. So I typed in the statement(previous I had cut and pasted from git PR) and it now works. Still, why did it work when I added empty()? I even removed empty() in follow on testing with it still not working.
So bottom line, I don't know what happened but, ! works as you'd expect. Still empty() is a good practice in this case.
I don't know if I should say sorry or continue to scratch my head:)


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Задача «Производители-потребители»


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> Looks like tools/build/options/WITH_AMD needs to be removed?
Added locally


169840232_Issue7547 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: OK (2623 of 2623 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


extra comment, once watching!


hi


Deployment failed with the following error:

~~~
Unexpected error. Please try again later. ()
~~~


@JuliaRegistrator register


todo: add new value for speed of effects


Registration pull request created: [JuliaRegistries/General/5645](https://github.com/JuliaRegistries/General/pull/5645)

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 v2.2.0 -m "<description of version>" 30f644fddda278599ef51073902471be827177cf
git push origin v2.2.0
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