[R/cla_secsse_loglik.R:1:37:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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:12:26:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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:13:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L13) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:14:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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:14:17:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L15) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:16:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L16) *warning:* **local variable ‘nb_node’ assigned but may not be used**
```r
  nb_node <- phy$Nnode
  ^~~~~~~
```
[R/cla_secsse_loglik.R:16:10:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L18) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:19:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L19) *warning:* **local variable ‘hmax’ assigned but may not be used**
```r
  hmax <- NULL
  ^~~~
```
[R/cla_secsse_loglik.R:19:20:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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:20:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L20) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
  ly <- ncol(states)
  ^~
```
[R/cla_secsse_loglik.R:20:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L20) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:23:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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:24:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L24) *warning:* **no visible global function definition for ‘check_input’**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
      ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:27:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
  forTime,
  ^~~~~~~
```
[R/cla_secsse_loglik.R:33:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L33) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
){
^~
```
[R/cla_secsse_loglik.R:37:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:43:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L43) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
    ly <- ncol(states)
    ^~
```
[R/cla_secsse_loglik.R:43:20:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L43) *style:* **Put spaces around all infix operators.**
```r
  d <- ncol(states)/2
                  ~^~
```
[R/cla_secsse_loglik.R:44:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L44) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:45:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L45) *style:* **Commented code should be removed.**
```r
  #ances <- ances[1] #########################  REMOVE!!!!!!!!!!!!
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:46:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L46) *style:* **Commented code should be removed.**
```r
  #desIndex <- 1
   ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:47:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L47) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:49:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  desRows <- which(phy$edge[, 1] == focal)
  ^~~~~~~
```
[R/cla_secsse_loglik.R:50:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L50) *style:* **Variable and function name style should be snake_case.**
```r
  desNodes <- phy$edge[desRows, 2]
  ^~~~~~~~
```
[R/cla_secsse_loglik.R:51:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L51) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:52:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L52) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:53:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L53) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:55:6:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L55) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(desIndex in 1:2){
     ^
```
[R/cla_secsse_loglik.R:55:22:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L55) *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:56:36:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L56) *style:* **Commas should always have a space after.**
```r
    y <- states[desNodes[desIndex],]
                                   ^
```
[R/cla_secsse_loglik.R:57:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L57) *style:* **Variable and function name style should be snake_case.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
    ^~~~~~~~
```
[R/cla_secsse_loglik.R:57:40:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L57) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                       ^
```
[R/cla_secsse_loglik.R:57:66:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L57) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                                                 ^
```
[R/cla_secsse_loglik.R:58:9:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L58) *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:59:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L59) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:59:9:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L59) *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:60:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L60) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(use_fortran == FALSE){
      ^
```
[R/cla_secsse_loglik.R:60:28:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L60) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(use_fortran == FALSE){
                           ^~
```
[R/cla_secsse_loglik.R:61:8:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L61) *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:62:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L62) *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:62:40:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L62) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                       ^
```
[R/cla_secsse_loglik.R:62:69:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L62) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                                                    ^
```
[R/cla_secsse_loglik.R:63:40:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L63) *style:* **Commas should always have a space after.**
```r
                           hmax = NULL,method = methode)
                                       ^
```
[R/cla_secsse_loglik.R:65:8:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L65) *style:* **Variable and function name style should be snake_case.**
```r
       nodeMN <- ode_FORTRAN(y = y, func = func,
       ^~~~~~
```
[R/cla_secsse_loglik.R:66:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L66) *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:66:43:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L66) *style:* **Commas should always have a space after.**
```r
                              times = c(0,timeInte), parms = parameter, rtol = reltol, atol = abstol,
                                          ^
```
[R/cla_secsse_loglik.R:69:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 1){
      ^
```
[R/cla_secsse_loglik.R:69:21:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L69) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(desIndex == 1){
                    ^~
```
[R/cla_secsse_loglik.R:70:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L70) *style:* **Variable and function name style should be snake_case.**
```r
      nodeN <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:72:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L72) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 2){
      ^
```
[R/cla_secsse_loglik.R:72:21:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L72) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
    if(desIndex == 2){
                    ^~
```
[R/cla_secsse_loglik.R:73:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L73) *style:* **Variable and function name style should be snake_case.**
```r
      nodeM <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:73:9:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L73) *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:73:22:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L73) *style:* **Trailing whitespace is superfluous.**
```r
      nodeM <- nodeMN
                     ^
```
[R/cla_secsse_loglik.R:75:6:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L75) *style:* **Commented code should be removed.**
```r
   # print(nodeMN)
     ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:78:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:78:31:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L78) *style:* **Commas should always have a space after.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:79:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:79:31:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L79) *style:* **Commas should always have a space after.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:80:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L80) *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:80:43:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L80) *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:81:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L81) *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:81:43:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L81) *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:82:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L82) *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:83:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L83) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:84:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L84) *warning:* **no visible global function definition for ‘check_input’**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
      ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:84:52:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L84) *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:85:26:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L85) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                         ^
```
[R/cla_secsse_loglik.R:85:29:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L85) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                            ^
```
[R/cla_secsse_loglik.R:85:30:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L85) *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:85:41:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L85) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                                        ^
```
[R/cla_secsse_loglik.R:87:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  cross_M_N <- a%*%b
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:87:17:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L87) *style:* **Put spaces around all infix operators.**
```r
  cross_M_N <- a%*%b
               ~^~~~
```
[R/cla_secsse_loglik.R:88:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L88) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:89:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L89) *style:* **Commented code should be removed.**
```r
  # mergeBranch <- NULL
    ^~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:90:18:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L90) *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:91:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L91) *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:91:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L91) *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:92:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L92) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- c(mergeBranch,combProb)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:93:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L93) *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:93:54:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L93) *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:93:58:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L93) *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:93:69:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L93) *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:95:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L95) *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:95:38:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L95) *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:95:47:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L95) *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:96:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L96) *style:* **Commented code should be removed.**
```r
  #sumD <- sum(mergeBranch)
   ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:97:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L97) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- mergeBranch/sumD
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:98:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L98) *style:* **Commented code should be removed.**
```r
  #loglik <- loglik + log(sumD)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:99:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L99) *style:* **Commented code should be removed.**
```r
  #cat(mergeBranch,"\n")
   ^~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:101:26:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L101) *style:* **Commas should always have a space after.**
```r
  newstate <- c(newstate,mergeBranch)
                         ^
```
[R/cla_secsse_loglik.R:102:16:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L102) *style:* **Commas should always have a space after.**
```r
  states[focal,] <- newstate
               ^
```
[R/cla_secsse_loglik.R:103:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L103) *style:* **Commented code should be removed.**
```r
  #print(parameter); print(loglik)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:104:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L104) *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:104:31:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L104) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                              ^
```
[R/cla_secsse_loglik.R:104:47:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L104) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                              ^
```
[R/cla_secsse_loglik.R:104:73:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L104) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                                                        ^
```
[R/cla_secsse_loglik.R:111:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L111) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:111:30:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L111) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
                             ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:114:26:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L114) *style:* **Variable and function name style should be snake_case.**
```r
                         forTime,
                         ^~~~~~~
```
[R/cla_secsse_loglik.R:115:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L115) *warning:* **local variable ‘nodeN’ assigned but may not be used**
```r
      nodeN <- calcul$nodeN
      ^~~~~
```
[R/cla_secsse_loglik.R:120:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L120) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
){
^~
```
[R/cla_secsse_loglik.R:121:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L121) *style:* **Commented code should be removed.**
```r
  #cl <- makeCluster(2)
   ^~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:122:4:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L122) *style:* **Commented code should be removed.**
```r
  #registerDoParallel(cl)
   ^~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:123:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L124) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:125:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L125) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:129:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L129) *style:* **Variable and function name style should be snake_case.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:129:33:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L129) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
                                ^
```
[R/cla_secsse_loglik.R:143:47:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L143) *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:143:48:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L143) *style:* **Trailing whitespace is superfluous.**
```r
                                   )) %dopar% {
                                               ^
```
[R/cla_secsse_loglik.R:144:38:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L144) *style:* **Variable and function name style should be snake_case.**
```r
                                     ancesSub <- take_ancesSub[[ii]]
                                     ^~~~~~~~
```
[R/cla_secsse_loglik.R:145:41:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L145) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                                     for(i in 1:length(ancesSub)){
                                        ^
```
[R/cla_secsse_loglik.R:145:47:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L145) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
                                     for(i in 1:length(ancesSub)){
                                              ^
```
[R/cla_secsse_loglik.R:145:65:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L145) *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:146:49:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L146) *style:* **Trailing whitespace is superfluous.**
```r
                                       calcul <-
                                                ^
```
[R/cla_secsse_loglik.R:152:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L152) *style:* **Lines should not be more than 80 characters.**
```r
                                                          use_fortran = use_fortran,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:164:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L164) *style:* **Lines should not be more than 80 characters.**
```r
#' Logikelihood calculation for the cla_SecSSE model given a set of parameters and data
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:166:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L166) *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:167:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L167) *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:168:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L168) *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:169:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L169) *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:170:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L170) *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:172:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L172) *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:173:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L173) *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:174:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L174) *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:176:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L176) *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:177:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L177) *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:178:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L178) *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:179:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L179) *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:180:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L180) *style:* **Lines should not be more than 80 characters.**
```r
#' @param is_complete_tree whether or not a tree with all its extinct species is provided
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:181:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L181) *style:* **Lines should not be more than 80 characters.**
```r
#' @param func function to be used in solving the ODE system. Currently only for testing purposes.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:182:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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:185:35:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L185) *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:207:52:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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/b13b6ab0747aac9b1e16f148e2352e02341e1931/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:245:38:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L245) *style:* **Only use double-quotes.**
```r
                              func = 'cla_secsse_runmod'){
                                     ^~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:245:57:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L245) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
                              func = 'cla_secsse_runmod'){
                                                        ^~
```
[R/cla_secsse_loglik.R:249:3:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L249) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:250:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L250) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:251:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L251) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(run_parallel == TRUE){
    ^
```
[R/cla_secsse_loglik.R:251:26:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L251) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
  if(run_parallel == TRUE){
                         ^~
```
[R/cla_secsse_loglik.R:251:27:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L251) *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:251:28:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L251) *style:* **Trailing whitespace is superfluous.**
```r
  if(run_parallel == TRUE){
                           ^
```
[R/cla_secsse_loglik.R:252:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L252) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.null(setting_calculation)){
      ^
```
[R/cla_secsse_loglik.R:252:36:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L252) *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:253:26:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L253) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                         ^
```
[R/cla_secsse_loglik.R:253:30:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L253) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                             ^
```
[R/cla_secsse_loglik.R:253:48:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L253) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                                               ^
```
[R/cla_secsse_loglik.R:254:29:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L254) *style:* **Trailing whitespace is superfluous.**
```r
      setting_calculation <-
                            ^
```
[R/cla_secsse_loglik.R:255:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L255) *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:257:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L257) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:259:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L259) *style:* **Variable and function name style should be snake_case.**
```r
    forTime <- setting_calculation$forTime
    ^~~~~~~
```
[R/cla_secsse_loglik.R:260:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L260) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub1 <- setting_calculation$ancesSub1
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:261:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L261) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub2 <- setting_calculation$ancesSub2
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:262:5:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L262) *style:* **Variable and function name style should be snake_case.**
```r
    ancesRest <- setting_calculation$ancesRest
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:263:1:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L263) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:264:7:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L264) *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:264:59:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L264) *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:264:75:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L264) *style:* **Trailing whitespace is superfluous.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                                          ^
```
[R/cla_secsse_loglik.R:265:28:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L265) *style:* **Trailing whitespace is superfluous.**
```r
      d <- ncol(states) / 2
                           ^
```
[R/cla_secsse_loglik.R:266:29:](https://github.com/rsetienne/secsse/blob/b13b6ab0747aac9b1e16f148e2352e02341e1931/R/cla_secsse_loglik.R#L266) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                            ^
```


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3285813)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/master/bc6735374b1bb31d58e228304ea89815c57004a1/3285813/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>7 tests failed, 106 tests passed.</summary>

## Failed tests

 * monotouch-test/iOS Unified 64-bits - device/Debug (dynamic registrar): Failed
 * link all/iOS Unified 64-bits - device/Release: TimedOut
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): TimedOut
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): TimedOut
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/Release: TimedOut
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): TimedOut
 * [xUnit] Mono BCL tests group 3/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): TimedOut
</details>


you have 90Hz on OP6?


第一句是否可以改为“爱好者们很快发现HTM，L文档格式所支持的内容具有较大局限性”


if a single recipient rejects a transfer, then the whole balance will remain in the to the contract


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I was testing it lol

On Mon, 2 Dec 2019 at 11:47, che19117522 <notifications@github.com> wrote:

> //need to make myself a branch? also jack stop editing in master??
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
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> or unsubscribe
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> .
>


why would that be useful?

Also, this isn't to best place to have this discussion. Please send an email to the mailing list, open an issue or a pull request. Thank you.


@kruthinarayan can you please close the meta tag properly.


Yes, I just copy pasted from poitto.


[R/check_pff_pir_params.R:9:3:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/R/check_pff_pir_params.R#L9) *warning:* **no visible global function definition for ‘check_pff_twinning_params’**
```r
  check_pff_twinning_params(pir_params$twinning_params) # nolint peregrine function
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:10:3:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/R/check_pff_pir_params.R#L10) *warning:* **no visible global function definition for ‘check_pff_alignment_params’**
```r
  check_pff_alignment_params(pir_params$alignment_params) # nolint peregrine function
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_pff_pir_params.R:11:3:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/R/check_pff_pir_params.R#L11) *warning:* **no visible global function definition for ‘check_pff_experiments’**
```r
  check_pff_experiments(pir_params$experiments) # nolint peregrine function
  ^~~~~~~~~~~~~~~~~~~~~
```
[R/create_pff_pir_params.R:28:21:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/R/create_pff_pir_params.R#L28) *warning:* **no visible global function definition for ‘to_pff_pir_params’**
```r
  pff_pir_params <- to_pff_pir_params(pir_params)
                    ^~~~~~~~~~~~~~~~~
```
[R/get_pff_tempfile.R:6:18:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/R/get_pff_tempfile.R#L6) *warning:* **no visible global function definition for ‘is_pff’**
```r
  testit::assert(is_pff(pff_tmpdir)) # nolint peregrine function
                 ^~~~~~
```
[tests/testthat/test-check_pff_experiment.R:23:1:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/tests/testthat/test-check_pff_experiment.R#L23) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-to_pff_experiments.R:29:1:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/tests/testthat/test-to_pff_experiments.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
  experiments[[2]]$inference_model$site_model <- beautier::create_gtr_site_model()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-to_pff_experiments.R:43:1:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/tests/testthat/test-to_pff_experiments.R#L43) *style:* **Lines should not be more than 80 characters.**
```r
  experiments[[2]]$inference_model$site_model <- beautier::create_gtr_site_model()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-to_pff_experiments.R:44:1:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/tests/testthat/test-to_pff_experiments.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
  experiments[[3]]$inference_model$site_model <- beautier::create_tn93_site_model()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-to_pff_experiments.R:59:1:](https://github.com/richelbilderbeek/peregrine/blob/0415968172dabf2ccd91db0844f99434ef0bddf6/tests/testthat/test-to_pff_experiments.R#L59) *style:* **Lines should not be more than 80 characters.**
```r
  experiments[[2]]$inference_model$site_model <- beautier::create_gtr_site_model()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


@ms2sato  find_byにしたらエラーが解消しました。findとfind_byの違いについて[https://udemy.benesse.co.jp/development/web/rails-find.html](url)

確かにおっしゃる通り文章で解説できなければ、理解しているとは言い難いですね。読んでみます！


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Definitely. Let's keep it this way for now and implement my suggestion and specific handling of just-completed if the need arises.


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

I updated the Github team because of this commit.

- @bwinkel 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)


修改了readme.md


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Sun 公司的 HotJava 浏览器是世界上第一款通过将Java 代码内嵌入 HTML 页面之内，从而展现出 Java 语言某些有趣特性的浏览器。


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Just curious, why isn't this merged? I was spending an hour trying to find out why async component load doesn't work for child components😥


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什么是放心的假定？……中国人好像不这么说话吧……应该是“用户可以确保他们的机器不会受到内容的损害”


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@shuma1020
これ、collection が2つありますが、一つにまとまりますよ。


TeamCity Identity and Access Management / identity-hostedpages [Build 1045](https://teamcity.nice.org.uk/viewLog.html?buildId=62470&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) is now running


Yeah, I've updated to 5.4.9, and it's working fine!
Sorry for not updating here..


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Hello, thank you for the code, it is useful to me, but I can't find the function mexTrainDL, can you help me？


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横に衝突されたりカーブしまくるとまれにずっとｘ軸方向へいくことがある


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TeamCity Identity and Access Management / identity-hostedpages [Build 1045-IDAM-121-Auth0UserId](https://teamcity.nice.org.uk/viewLog.html?buildId=62470&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) outcome was **SUCCESS**
Summary: Tests passed: 62 Build time: 00:01:51


co ta funkcja robi?


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[工作進度.xlsx](https://github.com/AARONHWL/Nanshan/files/3911318/default.xlsx)


我用navicat premium运行SQL文件的时候报错，我想问一下， 此项目sql的编码格式是怎么设计的，utf-8好像不对啊


TeamCity Identity and Access Management / identity-hostedpages [Build 1046](https://teamcity.nice.org.uk/viewLog.html?buildId=62472&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) is now running


rename finalMana to manaCost


`$entityManager->flush();` nebūtina dėti į `foreach`. Verta suvokti, kad `persist` funkcija įdeda visus būsimus pakeitimus į atmintį. O tada `flush` komanda apskaičiuoja geriausia būdą tą pakeitimą išsaugoti.

T.y. geriau padaryti daug `$entityManager->persist(` ir viską pabaigus padaryti vieną `$entityManager->flush`. (Daroma prielaida, kad visi iki tol buvę pakeitimai turėtų būti atlikti kartu, t.y. vienoje transakcijoje)

Plačiau:
 * https://stackoverflow.com/questions/30343951/difference-between-persistandflush-and-persist-flush
 * https://www.doctrine-project.org/api/orm/latest/Doctrine/ORM/EntityManager.html


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It depends on how we want to kill the contract. in my opinion, if a bug found in the contract we should move the funds as soon as possible in a safe way and as less as possible txs. Other possible way could be for example to kill all contracts' function expects one function that would allow users to withdraws their available funds


@shuma1020 find find_by where first あたりはいつも見るやつなので、ちゃんと理解しておくと早いです！


- NamelessCoder\GizzleGitPlugins\GizzlePlugins\ClonePlugin:000000005568f21b0000000002eec668:
  - 0: Executing Git clone command: /usr/bin/git clone --depth 1 --single-branch --branch '4.0.2' 'https://github.com/nitsan-technologies/nitsan_maintenance.git' /tmp/34e949a4f614c33925000342f68972f32933ee07/nitsan_maintenance
  - NamelessCoder\TYPO3RepositoryGizzle\GizzlePlugins\ExtensionRepositoryReleasePlugin:000000005568f2050000000002eec668:
    - resultCode: 10504
    - resultMessages:
      - 0: Please note that it might take a while (up to an hour) until your extension and the documentation appear on TYPO3.org.
      - version: 4.0.2


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As well as `pure` functions?


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[R/mbd_main_utils.R:13:3:](https://github.com/Giappo/mbd/blob/5e5837f442bdb4dba925ed8f660eec51326e0a32/R/mbd_main_utils.R#L13) *warning:* **local variable ‘pkg_name’ assigned but may not be used**
```r
  pkg_name <- get_pkg_name() # nolint internal function
  ^~~~~~~~
```
[R/mbd_main_utils.R:13:15:](https://github.com/Giappo/mbd/blob/5e5837f442bdb4dba925ed8f660eec51326e0a32/R/mbd_main_utils.R#L13) *warning:* **no visible global function definition for ‘get_pkg_name’**
```r
  pkg_name <- get_pkg_name() # nolint internal function
              ^~~~~~~~~~~~
```


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js的一个for循环

输入：

a=[11,22,33,44]
for(var item in a){
      console.log(item);
}

输出：

0
1
2
3

输入：

a=[11,22,33,44]
for(var item in a){
      console.log(a[item]);
}

输出：

11
22
33
44


+1. will do
thx


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:+1: Kad naudojate `Service`.

Jis dažniau naudojamas, kai tas pats kodas kviečiamas bent keliose vietose.
Ir didesnėse sistemoje geriau priklausyti nuo `interface`, o ne nuo klasės.

Vis dėlto – tai geriau nei naudoti daug `private` funkcijų controller'yje


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

I updated the Github team because of this commit.

- @albansouche, @aslakbergersen were added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

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)


Very well. I'll get it done by the end of the day.


All looks good. I'll write that Bioconductor submission is pending. Will get to resubmission tomorrow.


Hey, why did you need this fix? I just tried it, and was able to drag smoothly


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This code can be more efficiently implemented using https://tour.golang.org/methods/16.
Please check this later. @KimKyungup


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'highest priority (highest number)' is slightly redundant but I think it makes it clearer than assuming people will think that is the case. So I think it's the best unambiguous option.


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个人博客


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![](https://github.trello.services/images/mini-trello-icon.png) [(2) Functionality for viewing previously created rules (java class "GUI_Rule_Frame_Viewing" use) [?]](https://trello.com/c/xiSKNauj/117-2-functionality-for-viewing-previously-created-rules-java-class-guiruleframeviewing-use)


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Stay leader on CompanionManager. It's impossible give it via constructor. If you want a net-leader, give it into manager.


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Summary: Will fail Build time: 00:01:51


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uh


Check if "dtb" symbolic ink is present, if not create it and try again ...


- NamelessCoder\GizzleGitPlugins\GizzlePlugins\ClonePlugin:0000000040fc58ce000000006745a9c0:
  - 0: Executing Git clone command: /usr/bin/git clone --depth 1 --single-branch --branch '4.0.2' 'https://github.com/nitsan-technologies/ns_news_comments.git' /tmp/ea76f6317a922e9f39c642bc797159c7e8c68ecd/ns_news_comments
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    - resultCode: 10504
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      - version: 4.0.2


Will be NetEvents only on manager? Or you can need it in AI or other instances or services? If yes, create NetEvents service on NpcAdventures mod like CompanionManager and drivers. They are services and NetEvents can be service too.


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@JuliaRegistrator register()


Hi,
In the last test.
I'll let you know after the update today.


Registration pull request created: [JuliaRegistries/General/6132](https://github.com/JuliaRegistries/General/pull/6132)

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 v1.3.1 -m "<description of version>" 9619bcde00d059dcc357ee674875b3a21939a76a
git push origin v1.3.1
```


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package mercan;
import java.io.*;

class cevir
{
        public void cevcev(String girdi)
        {
                int toplam = 0;
                int ilkdeger = 0;
                int i;
                String roma = "IVXLC";
                for (int h = 0; h < girdi.length(); h++)
                {
                        if (girdi.charAt(h) == roma.charAt(1))
                        {
                                toplam += 5;
                        }

                        if (girdi.charAt(h) == roma.charAt(2))
                        {
                                toplam += 10;
                        }

                        if (girdi.charAt(h) == roma.charAt(3))
                        {
                                toplam += 50;
                        }
                        if (girdi.charAt(h) == roma.charAt(4))
                        {
                                toplam += 100;
                        }
                }
                for (i = 0; i < girdi.length(); i++)
                {
                        if (girdi.charAt(i) == roma.charAt(1) || girdi.charAt(i) == roma.charAt(2) || girdi.charAt(i) == roma.charAt(3) || girdi.charAt(i) == roma.charAt(4))
                        {
                                ilkdeger = i;
                                break;
                        }
                }
                if (ilkdeger != 0)
                {
                        for (int h = 0; h < ilkdeger; h++)
                        {
                                toplam = toplam - 1;
                        }
                }
                else
                {
                        for (int u = 0; u < girdi.length(); u++)
                        {
                                if (girdi.charAt(u) == roma.charAt(0))
                                {
                                        toplam += 1;
                                }
                        }
                }

                System.out.println(toplam);
        }
}

public class Lol
{

        public static void main(String args[]) throws IOException
        {

                String giris;

                BufferedReader b = new BufferedReader(new InputStreamReader(System.in));

                System.out.println("Roma rakamini giriniz:  ");

                giris = b.readLine();

                cevir c = new cevir();

                c.cevcev(giris);

        }

}


Maybe name `Net` for this namespace will be better.


that's not black/white symmetric... is that intentional?


Was supposed to be but Visual Studio completely bugged out and was refusing to make a directory called Net, "because it already exists". Even after `rm -rf` -ing it from my workdir and restarting VS :)


@jokehl I also believe this commit broke the support for relative path.

BTW, @SmilingXinyi Why do we suddenly support protocol here?  Can `//domain.com/path-to-your-file` meets your requirement?


Everything will be moved to constants, don't worry.


ummm..


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True. All the more so that you also emit in the constructor.


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Enums is better tahn constants in this usecase.


Yes, or when Alice informs them off-chain. But then again, from the point of view of the shop, it is only "yeah maybe" until Bob gives a valid password.


Checkmarx scan results 02 Dec 2019 15:09 UTC +02:00

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 Open Viewer
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Commit ID	Owner

1e71c4b085217e0cab2013734fb62a6c80309419	@web-flow


Yep, thanks.
I've fixed them up.


Separate processor classes into single files.


Same thing


js的第二个for循环

输入：

a={'k1':'v1','k2':'v2'}
  for(var item in a){
console.log(item);
}

输出：

k1
k2

输入：

a={'k1':'v1','k2':'v2'}
for(var item in a){
console.log(a[item]);
}

输出：

v1
v2


That is indeed what the code above implements. But I thought your comment was about what you wanted to achieve in your next iteration. And I see that your "version10" did case 3.


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@JuliaRegistrator register


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Registration pull request created: [JuliaRegistries/General/6133](https://github.com/JuliaRegistries/General/pull/6133)

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 v4.0.5 -m "<description of version>" 77e22893997ed971f4fdeabff101ce1d777eaa2b
git push origin v4.0.5
```
Also, note the warning: Version 4.0.5 skips over 4.0.4
This can be safely ignored. However, if you want to fix this you can do so. Call register() again after making the fix. This will update the Pull request.


here


Yes, we have no perfect answer here.


Yep


Use `string` instead.


Please, write `GitHub Actions` explicitly because I alway think about `Google Analytics`


Usesless methos. `Name` is public, can be set directly.


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Can be `Farmer` instance serialized?


ignore upp


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no, but it's not meant to be. It's meant to be loaded within `on message received` with the sender (owner) of the message and passed further. I guess it *could* be thrown as an arg to the `Process` if it comes to it


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      - 0: Please note that it might take a while (up to an hour) until your extension and the documentation appear on TYPO3.org.
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btw: It's a field. Fialts starts with lowercase. You can use property instead and keep thois name with Upprcase first letter.


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Why this constructor?


Deployment failed with the following error:

~~~
An internal error occurred with ZEIT Now.
~~~


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Same thing as on line #158


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Main constructor when creating a class?


I gave it a brief look but ExecStartPost didn't have a condition. Can be a separate service but I didn't want to spread this logic elsewhere.


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This part seems to be wrong for me:
> BleachBit version 2.2 required Python 2.7 and GTK version 2. It did *not* support Python 2.5, Python 2.7, Python 3, or GTK 3.

...it require Python 2.7 but it did *not* support Python 2.7 ???

Also I guess that wget should also get used with https, not http...


new


I never used this property. I used ever property Name. Do this same thing like name? Any difference? Why you think this porperty is better to use?


In the next iteration, `selfdestruct()` will be removed and we only transfer the whole funds to the contract owner.


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:white_check_mark: All Rules (8 / 8) Passed

      :crown: Good job! this pull request is aligned with your organization's best practices!

      :point_right: You can review your rules settings at smart policy management :point_left:

:point_right: click here to view a full list of the events :point_left: