[R/default_params_doc.R:176:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/default_params_doc.R#L176) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/default_params_doc.R#L188) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_choosepar.R:23:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
  #This function provides a likelihood for a subset of parameters. This is built to work inside mbd_minusLL_vs_single_parameter or any optimizer like simplex, optim or subplex
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_choosepar.R:30:52:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L30) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (length(trparsopt) == 4 && missing(trparsfix)){trparsfix <- NULL}
                                                   ^
```
[R/mbd_loglik_choosepar.R:30:70:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L30) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (length(trparsopt) == 4 && missing(trparsfix)){trparsfix <- NULL}
                                                                     ^
```
[R/mbd_loglik_choosepar.R:31:11:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L31) *style:* **Use <-, not =, for assignment.**
```r
  trpars1 = rep(0, n_pars)
          ^
```
[R/mbd_loglik_choosepar.R:34:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L34) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_choosepar.R:37:7:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( min(trpars1[1:n_pars]) < 0 ){loglik <- -Inf}else
      ^
```
[R/mbd_loglik_choosepar.R:37:34:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( min(trpars1[1:n_pars]) < 0 ){loglik <- -Inf}else
                                 ^
```
[R/mbd_loglik_choosepar.R:37:36:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L37) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if ( min(trpars1[1:n_pars]) < 0 ){loglik <- -Inf}else
                                   ^
```
[R/mbd_loglik_choosepar.R:37:51:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if ( min(trpars1[1:n_pars]) < 0 ){loglik <- -Inf}else
                                                  ^
```
[R/mbd_loglik_choosepar.R:38:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L38) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_choosepar.R:40:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L40) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_loglik_choosepar.R:42:23:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L42) *style:* **Put spaces around all infix operators.**
```r
      pars1 <- trpars1/(1 - trpars1)
                     ~^~
```
[R/mbd_loglik_choosepar.R:42:24:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L42) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      pars1 <- trpars1/(1 - trpars1)
                       ^
```
[R/mbd_loglik_choosepar.R:44:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L44) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_loglik_choosepar.R:60:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L60) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_choosepar.R:61:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_choosepar.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
    cat("There are parameter values used which cause numerical problems:", trpars1, "\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:5:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:5:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L5) *style:* **Variable or function name should be snake_case.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
^~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:5:27:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L5) *style:* **Variable or function name should be snake_case.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
                          ^
```
[R/mbd_loglik_utils.R:5:36:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L5) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
hyperA_HannoX <- function(N, k, q) {# HG function: fast O(N), updated after Moulis meeting
                                   ^
```
[R/mbd_loglik_utils.R:7:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
  #it produces the structure q^(m-n)*(1-q)^(k+2*n-m)*sum_j 2^j choose(k, j)*choose(n, m-n-j)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:9:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  A1 <- (1-q)^(k) * choose(k, j) * (2)^j
  ^~
```
[R/mbd_loglik_utils.R:9:11:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L9) *style:* **Put spaces around all infix operators.**
```r
  A1 <- (1-q)^(k) * choose(k, j) * (2)^j
         ~^~
```
[R/mbd_loglik_utils.R:9:15:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  A1 <- (1-q)^(k) * choose(k, j) * (2)^j
              ^
```
[R/mbd_loglik_utils.R:10:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L10) *style:* **Variable or function name should be snake_case.**
```r
  N <- N + 1
  ^
```
[R/mbd_loglik_utils.R:11:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
  ^
```
[R/mbd_loglik_utils.R:11:24:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                      ~^~
```
[R/mbd_loglik_utils.R:11:26:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                        ~^~
```
[R/mbd_loglik_utils.R:11:34:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                                ~^~
```
[R/mbd_loglik_utils.R:11:36:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L11) *style:* **Put spaces around all infix operators.**
```r
  A <- diag(A1[1], nrow=N+2, ncol=N+2)
                                  ~^~
```
[R/mbd_loglik_utils.R:12:9:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L12) *style:* **Put spaces around all infix operators.**
```r
  A[1:(k+1),1] <- A1
       ~^~
```
[R/mbd_loglik_utils.R:12:13:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L12) *style:* **Commas should always have a space after.**
```r
  A[1:(k+1),1] <- A1
            ^
```
[R/mbd_loglik_utils.R:15:20:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L15) *style:* **Commas should always have a space after.**
```r
    s <- src:min(N,2*src+k-1)
                   ^
```
[R/mbd_loglik_utils.R:15:21:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L15) *style:* **Put spaces around all infix operators.**
```r
    s <- src:min(N,2*src+k-1)
                   ~^~
```
[R/mbd_loglik_utils.R:15:25:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L15) *style:* **Put spaces around all infix operators.**
```r
    s <- src:min(N,2*src+k-1)
                       ~^~
```
[R/mbd_loglik_utils.R:15:27:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L15) *style:* **Put spaces around all infix operators.**
```r
    s <- src:min(N,2*src+k-1)
                         ~^~
```
[R/mbd_loglik_utils.R:16:8:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L16) *style:* **Put spaces around all infix operators.**
```r
    A[s+2, dst] <- A[s, src] + A[s+1, src]
      ~^~
```
[R/mbd_loglik_utils.R:16:35:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L16) *style:* **Put spaces around all infix operators.**
```r
    A[s+2, dst] <- A[s, src] + A[s+1, src]
                                 ~^~
```
[R/mbd_loglik_utils.R:17:11:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L17) *style:* **Put spaces around all infix operators.**
```r
    m <- s-1; n <- src-1;
         ~^~
```
[R/mbd_loglik_utils.R:17:23:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L17) *style:* **Put spaces around all infix operators.**
```r
    m <- s-1; n <- src-1;
                     ~^~
```
[R/mbd_loglik_utils.R:18:32:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                               ^
```
[R/mbd_loglik_utils.R:18:34:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                                ~^~
```
[R/mbd_loglik_utils.R:18:37:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                                   ~^~
```
[R/mbd_loglik_utils.R:18:38:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                                     ^
```
[R/mbd_loglik_utils.R:18:40:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                                      ~^~
```
[R/mbd_loglik_utils.R:18:44:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                                           ^
```
[R/mbd_loglik_utils.R:18:46:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                                            ~^~
```
[R/mbd_loglik_utils.R:18:48:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L18) *style:* **Put spaces around all infix operators.**
```r
    A[s, src] <- A[s, src] * q^(m-n)*(1-q)^(2*n-m)
                                              ~^~
```
[R/mbd_loglik_utils.R:20:7:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L20) *style:* **Commas should always have a space after.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
      ^
```
[R/mbd_loglik_utils.R:20:10:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L20) *style:* **Use <-, not =, for assignment.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
         ^
```
[R/mbd_loglik_utils.R:20:16:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L20) *style:* **Commas should always have a space after.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
               ^
```
[R/mbd_loglik_utils.R:20:23:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L20) *style:* **Put spaces around all infix operators.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
                     ~^~
```
[R/mbd_loglik_utils.R:20:27:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L20) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
                          ^
```
[R/mbd_loglik_utils.R:20:29:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L20) *style:* **Put spaces around all infix operators.**
```r
  A[N,N] = A[N,N] * (1-q)^(N-1);
                           ~^~
```
[R/mbd_loglik_utils.R:21:9:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L21) *style:* **Commas should always have a space after.**
```r
  A[1:N,1:N]
        ^
```
[R/mbd_loglik_utils.R:24:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L24) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="windows"){matrix_builder = hyperA:::hyperA}
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
# if (.Platform$OS.type=="unix")   {matrix_builder = hyperA_HannoX} #this is set to work with home directory of the cluster
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L25) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="unix")   {matrix_builder = hyperA_HannoX} #this is set to work with home directory of the cluster
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:31:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L31) *style:* **Lines should not be more than 80 characters.**
```r
create_A0 <- function(max_number_of_species, lambda, mu, q, k, matrix_builder = hyperA_HannoX){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:31:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L31) *style:* **Variable or function name should be snake_case.**
```r
create_A0 <- function(max_number_of_species, lambda, mu, q, k, matrix_builder = hyperA_HannoX){
^~~~~~~~~
```
[R/mbd_loglik_utils.R:32:8:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L32) *style:* **Use <-, not =, for assignment.**
```r
  nvec = 0:max_number_of_species
       ^
```
[R/mbd_loglik_utils.R:33:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  M = lambda * matrix_builder(N = max_number_of_species, k = k, q = q)
  ^
```
[R/mbd_loglik_utils.R:33:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L33) *style:* **Use <-, not =, for assignment.**
```r
  M = lambda * matrix_builder(N = max_number_of_species, k = k, q = q)
    ^
```
[R/mbd_loglik_utils.R:35:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
  # diag(M) = (-lambda)*c( (1-(1-q)^(k+( nvec[1:max_number_of_species] ) )),0 ) - mu*(nvec+k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:35:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L35) *style:* **Commented code should be removed.**
```r
  # diag(M) = (-lambda)*c( (1-(1-q)^(k+( nvec[1:max_number_of_species] ) )),0 ) - mu*(nvec+k)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:36:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:36:11:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L36) *style:* **Use <-, not =, for assignment.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
          ^
```
[R/mbd_loglik_utils.R:36:26:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
                         ^
```
[R/mbd_loglik_utils.R:36:39:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L36) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
                                      ^
```
[R/mbd_loglik_utils.R:36:49:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  diag(M) = (-lambda) * ( 1 - (1 - q)^(k + nvec) ) - mu * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
                                                ^
```
[R/mbd_loglik_utils.R:38:27:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L38) *style:* **Use <-, not =, for assignment.**
```r
  M[row(M) == col(M) - 1] = mu * nvec[2:(max_number_of_species + 1)]
                          ^
```
[R/mbd_loglik_utils.R:46:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
create_B0 <- function(max_number_of_species, q, k, b, matrix_builder = hyperA_HannoX){#lambda * choose(k, b) * q^b  is going to be added in logB in the main script
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:46:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L46) *style:* **Variable or function name should be snake_case.**
```r
create_B0 <- function(max_number_of_species, q, k, b, matrix_builder = hyperA_HannoX){#lambda * choose(k, b) * q^b  is going to be added in logB in the main script
^~~~~~~~~
```
[R/mbd_loglik_utils.R:46:86:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L46) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
create_B0 <- function(max_number_of_species, q, k, b, matrix_builder = hyperA_HannoX){#lambda * choose(k, b) * q^b  is going to be added in logB in the main script
                                                                                ^
```
[R/mbd_loglik_utils.R:48:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L48) *style:* **Variable or function name should be snake_case.**
```r
  B <- matrix_builder(N = max_number_of_species, k = k2, q = q)
  ^
```
[R/mbd_loglik_utils.R:57:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L57) *style:* **Variable or function name should be snake_case.**
```r
create_A <- function(lambda, mu, nu, q, k, max_number_of_species){
^~~~~~~~
```
[R/mbd_loglik_utils.R:59:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L59) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species,
  ^
```
[R/mbd_loglik_utils.R:61:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:61:97:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L61) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:61:99:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L61) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:63:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
  # M[row(M) == col(M)] = M[row(M) == col(M)] - c(lambda*(nvec[-length(nvec)]+k),0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:63:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L63) *style:* **Commented code should be removed.**
```r
  # M[row(M) == col(M)] = M[row(M) == col(M)] - c(lambda*(nvec[-length(nvec)]+k),0)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:64:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M)] <- M[row(M) == col(M)] - lambda * (nvec + k) #new version to avoid the dumpster problem at the end of the matrix
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:74:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L74) *style:* **Variable or function name should be snake_case.**
```r
create_B <- function(lambda, nu, q, k, b, max_number_of_species){
^~~~~~~~
```
[R/mbd_loglik_utils.R:75:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L75) *style:* **Lines should not be more than 80 characters.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:75:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L75) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
  ^
```
[R/mbd_loglik_utils.R:75:8:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L75) *warning:* **no visible global function definition for ‘create_B0’**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
       ^~~~~~~~~
```
[R/mbd_loglik_utils.R:76:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L76) *style:* **Lines should not be more than 80 characters.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k, b) * (q^b) * M
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:76:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L76) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k, b) * (q^b) * M
  ^
```
[R/mbd_loglik_utils.R:85:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L85) *style:* **Variable or function name should be snake_case.**
```r
create_A.no_mbd = function(
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:85:17:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L85) *style:* **Use <-, not =, for assignment.**
```r
create_A.no_mbd = function(
                ^
```
[R/mbd_loglik_utils.R:95:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L95) *style:* **Lines should not be more than 80 characters.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species, lambda = nu, mu = mu, q = q, k = k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:95:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L95) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_A0(max_number_of_species = max_number_of_species, lambda = nu, mu = mu, q = q, k = k)
  ^
```
[R/mbd_loglik_utils.R:95:8:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L95) *warning:* **no visible global function definition for ‘create_A0’**
```r
  M <- create_A0(max_number_of_species = max_number_of_species, lambda = nu, mu = mu, q = q, k = k)
       ^~~~~~~~~
```
[R/mbd_loglik_utils.R:96:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:96:97:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L96) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:96:99:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L96) *style:* **Put spaces around all infix operators.**
```r
  M[row(M) == col(M) + 1] <- M[row(M) == col(M) + 1] + lambda * (nvec[1:(max_number_of_species)]+2*k)
                                                                                ~^~
```
[R/mbd_loglik_utils.R:97:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L97) *style:* **Lines should not be more than 80 characters.**
```r
  M[row(M) == col(M)]     <- M[row(M) == col(M)] - c(lambda * (nvec[-length(nvec)] + k), 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:107:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
create_B.no_mbd = function(lambda, nu, q, k, b, max_number_of_species, minimum_multiple_births){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:107:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L107) *style:* **Variable or function name should be snake_case.**
```r
create_B.no_mbd = function(lambda, nu, q, k, b, max_number_of_species, minimum_multiple_births){
^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:107:17:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L107) *style:* **Use <-, not =, for assignment.**
```r
create_B.no_mbd = function(lambda, nu, q, k, b, max_number_of_species, minimum_multiple_births){
                ^
```
[R/mbd_loglik_utils.R:108:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L108) *style:* **Lines should not be more than 80 characters.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:108:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L108) *style:* **Variable or function name should be snake_case.**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
  ^
```
[R/mbd_loglik_utils.R:108:8:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L108) *warning:* **no visible global function definition for ‘create_B0’**
```r
  M <- create_B0(max_number_of_species = max_number_of_species, q = q, k = k, b = b)
       ^~~~~~~~~
```
[R/mbd_loglik_utils.R:109:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L109) *style:* **Lines should not be more than 80 characters.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k, b) * (q^b) * M
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:109:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L109) *style:* **Variable or function name should be snake_case.**
```r
  B <- lambda * k * diag(max_number_of_species + 1) * (b == 1) + nu * choose(k, b) * (q^b) * M
  ^
```
[R/mbd_loglik_utils.R:110:48:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L110) *style:* **Use <-, not =, for assignment.**
```r
  B[row(B) > col(B) + minimum_multiple_births] = 0
                                               ^
```
[R/mbd_loglik_utils.R:119:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L119) *style:* **Variable or function name should be snake_case.**
```r
A_operator <- function(Q, transition_matrix, time_interval, precision = 50L,
^~~~~~~~~~
```
[R/mbd_loglik_utils.R:119:24:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L119) *style:* **Variable or function name should be snake_case.**
```r
A_operator <- function(Q, transition_matrix, time_interval, precision = 50L,
                       ^
```
[R/mbd_loglik_utils.R:130:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L130) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_utils.R:132:7:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L132) *style:* **Commented code should be removed.**
```r
    # exp_matrix <- rsexpm:::sexpm(transition_matrix * time_interval)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:133:7:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L133) *style:* **Commented code should be removed.**
```r
    # result     <- exp_matrix %*% Q
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:137:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L137) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_utils.R:138:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L138) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
    ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:138:19:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L138) *style:* **Variable or function name should be snake_case.**
```r
    result.nan <- result.negative <- 1
                  ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:140:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L140) *style:* **Lines should not be more than 80 characters.**
```r
    while ((result.nan == 1| result.negative == 1) & repetition < max_repetitions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:140:28:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L140) *style:* **Put spaces around all infix operators.**
```r
    while ((result.nan == 1| result.negative == 1) & repetition < max_repetitions)
                          ~^
```
[R/mbd_loglik_utils.R:141:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L141) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/mbd_loglik_utils.R:142:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L142) *style:* **Lines should not be more than 80 characters.**
```r
      result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:144:7:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L144) *style:* **Variable or function name should be snake_case.**
```r
      result.nan <- (any(!is.numeric(result)) || any(is.nan(result)))
      ^~~~~~~~~~
```
[R/mbd_loglik_utils.R:146:7:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L146) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/mbd_loglik_utils.R:149:7:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L149) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/mbd_loglik_utils.R:150:9:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L150) *style:* **Variable or function name should be snake_case.**
```r
        result.negative <- (any(result < 0))
        ^~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:152:9:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L152) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        {
        ^
```
[R/mbd_loglik_utils.R:155:11:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L155) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          {
          ^
```
[R/mbd_loglik_utils.R:165:20:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L165) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (!bad_result) {bad_result <- (any(result < 0))}
                   ^
```
[R/mbd_loglik_utils.R:165:52:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L165) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  if (!bad_result) {bad_result <- (any(result < 0))}
                                                   ^
```
[R/mbd_loglik_utils.R:168:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L168) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/mbd_loglik_utils.R:171:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L171) *style:* **Lines should not be more than 80 characters.**
```r
    R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol = a_abstol, rtol = a_reltol)[2,-1], timeout = 1001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:171:78:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L171) *warning:* **no visible binding for global variable ‘mbd_loglik_rhs’**
```r
    R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol = a_abstol, rtol = a_reltol)[2,-1], timeout = 1001)
                                                                             ^~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:171:150:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L171) *style:* **Commas should always have a space after.**
```r
    R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol = a_abstol, rtol = a_reltol)[2,-1], timeout = 1001)
                                                                                ^
```
[R/mbd_loglik_utils.R:181:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L181) *style:* **Lines should not be more than 80 characters.**
```r
#' A_operator_old <- function(Q, transition_matrix, time_interval, precision = 50L,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:192:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L192) *style:* **Lines should not be more than 80 characters.**
```r
#'     result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:193:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L193) *style:* **Lines should not be more than 80 characters.**
```r
#'     while ( ( any(!is.numeric(result)) || any(is.nan(result)) ) && precision < precision_limit )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:196:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
#'       result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = T)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:202:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L202) *style:* **Lines should not be more than 80 characters.**
```r
#'         result <- try(expoRkit::expv(v = Q, x = transition_matrix, t = time_interval, m = precision), silent = T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:209:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
#'     # result<-deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol=a_abstol, rtol=a_reltol)[2,-1]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:210:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L210) *style:* **Lines should not be more than 80 characters.**
```r
#'     R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol=a_abstol, rtol=a_reltol)[2,-1], timeout = 1000)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:213:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L213) *style:* **Lines should not be more than 80 characters.**
```r
#'   if (any(!is.numeric(result)) || any(is.nan(result))) #sometimes expoRkit gives weird negative values. In this case perform standard lsoda integration.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:217:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L217) *style:* **Lines should not be more than 80 characters.**
```r
#'     # result<-deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol=a_abstol, rtol=a_reltol)[2,-1]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:218:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L218) *style:* **Lines should not be more than 80 characters.**
```r
#'     R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol=a_abstol, rtol=a_reltol)[2,-1], timeout = 1000)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:220:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
#'   else if (any(result < 0)) #sometimes expoRkit gives weird negative values. In this case perform standard lsoda integration.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:224:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L224) *style:* **Lines should not be more than 80 characters.**
```r
#'     # result=deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol=a_abstol, rtol=a_reltol)[2,-1]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:225:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L225) *style:* **Lines should not be more than 80 characters.**
```r
#'     R.utils::withTimeout(result <- deSolve::ode(y = Q, times = times, func = mbd_loglik_rhs, parms = ode_matrix, atol=a_abstol, rtol=a_reltol)[2,-1], timeout = 1000)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:228:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L228) *style:* **Lines should not be more than 80 characters.**
```r
#'   # if ( ( any(!is.numeric(result)) || any(is.nan(result)) ) && methode!="sexpm"){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:229:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L229) *style:* **Lines should not be more than 80 characters.**
```r
#'   #     # to run this you actually need sexpm to be installed which, on the cluster, might not be the case.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:245:21:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L245) *style:* **Use <-, not =, for assignment.**
```r
    starting_vector = x
                    ^
```
[R/mbd_loglik_utils.R:246:23:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L246) *style:* **Use <-, not =, for assignment.**
```r
    transition_matrix = pars
                      ^
```
[R/mbd_loglik_utils.R:247:9:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L247) *style:* **Use <-, not =, for assignment.**
```r
    dx  = rep(0, length(starting_vector))
        ^
```
[R/mbd_loglik_utils.R:248:9:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L248) *style:* **Use <-, not =, for assignment.**
```r
    dx  = drop(transition_matrix %*% starting_vector)
        ^
```
[R/mbd_loglik_utils.R:249:9:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L249) *style:* **Use <-, not =, for assignment.**
```r
    out = (dx)
        ^
```
[R/mbd_loglik_utils.R:250:16:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L250) *style:* **Use <-, not =, for assignment.**
```r
    names(out) = names(x)
               ^
```
[R/mbd_loglik_utils.R:260:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L260) *style:* **Lines should not be more than 80 characters.**
```r
determine_k_limit <- function(pars, brts, lx, soc, methode, abstol = 1e-16, reltol = 1e-10) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:261:22:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L261) *warning:* **local variable ‘mu’ assigned but may not be used**
```r
  lambda <- pars[1]; mu <- pars[2]; nu <- pars[3]; q <- pars[4]
                     ^~
```
[R/mbd_loglik_utils.R:263:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L263) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx))
  ^~
```
[R/mbd_loglik_utils.R:265:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L265) *style:* **Variable or function name should be snake_case.**
```r
  T0 <- create_A(lambda = lambda, mu = 0, nu = nu, q = q, k = soc,
  ^~
```
[R/mbd_loglik_utils.R:266:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L266) *style:* **Lines should not be more than 80 characters.**
```r
                       max_number_of_species = lx); #dim(TM); max(is.na(TM)); max(is.infinite(TM))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:266:54:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L266) *style:* **Commented code should be removed.**
```r
                       max_number_of_species = lx); #dim(TM); max(is.na(TM)); max(is.infinite(TM))
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:267:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L267) *style:* **Variable or function name should be snake_case.**
```r
  Pm <- A_operator(Q = Qi, transition_matrix = T0, time_interval = total_time,
  ^~
```
[R/mbd_loglik_utils.R:268:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L268) *style:* **Lines should not be more than 80 characters.**
```r
                         precision = 250L, methode = methode, a_abstol = abstol, a_reltol = reltol)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:269:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L269) *style:* **Commented code should be removed.**
```r
  # graphics::plot((Pm/sum(Pm)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:270:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L270) *style:* **Lines should not be more than 80 characters.**
```r
  k_limit <- soc + max(mvec[(mvec %in% which((cumsum(Pm/sum(Pm))) <= 0.95))]); k_limit
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:270:56:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L270) *style:* **Put spaces around all infix operators.**
```r
  k_limit <- soc + max(mvec[(mvec %in% which((cumsum(Pm/sum(Pm))) <= 0.95))]); k_limit
                                                      ~^~
```
[R/mbd_loglik_utils.R:279:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L279) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:285:13:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L285) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:293:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L293) *style:* **Variable or function name should be snake_case.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
  ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:293:31:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L293) *style:* **Put spaces around all infix operators.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                             ~^~
```
[R/mbd_loglik_utils.R:293:32:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L293) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                               ^
```
[R/mbd_loglik_utils.R:294:25:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L294) *style:* **Put spaces around all infix operators.**
```r
  one_over_qm_binom <- 1/choose((m + soc), soc); length(one_over_qm_binom)
                       ~^~
```
[R/mbd_loglik_utils.R:295:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L295) *style:* **Commented code should be removed.**
```r
  # Qi <- c(1, rep(0, lx)); length(Qi)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:296:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L296) *style:* **Lines should not be more than 80 characters.**
```r
  Qi <- rep(0, lx + 1);  Qi[3] <- 1 #starting with k = 0 and m = 2 missing species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:296:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L296) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- rep(0, lx + 1);  Qi[3] <- 1 #starting with k = 0 and m = 2 missing species
  ^~
```
[R/mbd_loglik_utils.R:297:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L297) *warning:* **local variable ‘k’ assigned but may not be used**
```r
  k <- 0 #assuming 0 species
  ^
```
[R/mbd_loglik_utils.R:299:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L299) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_A(lambda = lambda, mu = mu, nu = nu, q = q, k = 0,
  ^~
```
[R/mbd_loglik_utils.R:300:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L300) *style:* **Lines should not be more than 80 characters.**
```r
                       max_number_of_species = lx); #dim(TM); max(is.na(TM)); max(is.infinite(TM))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:300:54:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L300) *style:* **Commented code should be removed.**
```r
                       max_number_of_species = lx); #dim(TM); max(is.na(TM)); max(is.infinite(TM))
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:302:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L302) *style:* **Lines should not be more than 80 characters.**
```r
  A2_v1 <- A_operator(Q = Qi, transition_matrix = TM, time_interval = total_time,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:302:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L302) *style:* **Variable or function name should be snake_case.**
```r
  A2_v1 <- A_operator(Q = Qi, transition_matrix = TM, time_interval = total_time,
  ^~~~~
```
[R/mbd_loglik_utils.R:303:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L303) *style:* **Lines should not be more than 80 characters.**
```r
                            precision = 250L, methode = methode, a_abstol = abstol, a_reltol = reltol); A2_v1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:305:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L305) *style:* **Lines should not be more than 80 characters.**
```r
  # A2_v1 <- try(expoRkit::expv(v = Qi, x = TM, t = total_time, m = 50L), silent = T)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:305:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L305) *style:* **Commented code should be removed.**
```r
  # A2_v1 <- try(expoRkit::expv(v = Qi, x = TM, t = total_time, m = 50L), silent = T)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:308:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L308) *style:* **Lines should not be more than 80 characters.**
```r
  tips_components <- 1 + 0:1 #these are the components I want to exclude (the one corresponding to 0 and 1 tips)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:309:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L309) *style:* **Variable or function name should be snake_case.**
```r
  Pc <- 1 - sum(total_product[tips_components]); Pc
  ^~
```
[R/mbd_loglik_utils.R:310:5:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L310) *style:* **Commented code should be removed.**
```r
  # Pc <- sum(total_product)
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:321:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L321) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:327:13:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L327) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:335:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L335) *style:* **Variable or function name should be snake_case.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
  ^~~~~~~~~~~
```
[R/mbd_loglik_utils.R:335:31:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L335) *style:* **Put spaces around all infix operators.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                             ~^~
```
[R/mbd_loglik_utils.R:335:32:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L335) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  one_over_Cm <- (3 * (m + 1))/(m + 3); length(one_over_Cm)
                               ^
```
[R/mbd_loglik_utils.R:336:25:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L336) *style:* **Put spaces around all infix operators.**
```r
  one_over_qm_binom <- 1/choose((m + soc), soc); length(one_over_qm_binom)
                       ~^~
```
[R/mbd_loglik_utils.R:337:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L337) *style:* **Variable or function name should be snake_case.**
```r
  Qi <- c(1, rep(0, lx)); length(Qi)
  ^~
```
[R/mbd_loglik_utils.R:339:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L339) *style:* **Variable or function name should be snake_case.**
```r
  TM <- create_A(lambda = lambda, mu = mu, nu = nu, q = q, k = soc,
  ^~
```
[R/mbd_loglik_utils.R:340:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L340) *style:* **Lines should not be more than 80 characters.**
```r
                       max_number_of_species = lx); #dim(TM); max(is.na(TM)); max(is.infinite(TM))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:340:54:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L340) *style:* **Commented code should be removed.**
```r
                       max_number_of_species = lx); #dim(TM); max(is.na(TM)); max(is.infinite(TM))
                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:342:1:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L342) *style:* **Lines should not be more than 80 characters.**
```r
  A2_v1 <- A_operator(Q = Qi, transition_matrix = TM, time_interval = total_time,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:342:3:](https://github.com/Giappo/mbd/blob/a905886076b092efa273540715f0b05125c99a97/R/mbd_loglik_utils.R#L342) *style:* **Variable or function name should be snake_case.**
```r
  A2_v1 <- A_operator(Q = Qi, transition_matrix = TM, time_interval = total_time,
  ^~~~~
```


Unification


add parameter into arguments of this method (like "List<String> songs")
and after that write cycle by your List


Done


@AntonioMeireles is there a special reason to increase the minimum required version to `2.1.5`?


variable names not very clear on what they are used for


 - Move current year == 0 code to top
- Change the window year average code to only have 1 division instead of 2
- Change the name of add_here to oldest_index


## What is it for ???

Please explain this line better


## Commit comment

Looking at how this commit was created.


Можно добавление вагона вынести в Train. В подклассах оставить проверку:
def can_attach_wagon?(wagon)
end


this test just reproduces your documentation, is it easy to just turn your documentation into a doctest?


Closes #21


I assume this is because media embed plugin was not released yet. You can try nightly docs: https://ckeditor5.github.io/docs/nightly/ckeditor5/latest/api/media-embed.html


dfdf


Successfully aliased the URL <https://micro-mongodb-aseclltygl.now.sh> to the following alias.

* https://mongo.wezeit.co


I like where this is going!

Do we still use this code path? If not, maybe we can merge this logic into `storage_access.js`?

If we do use this code path, we should decouple it from the storage access stuff (i.e. ideally this function does only one thing (starts up storage access logic) and we have a different function to do normal redirect stuff).


No worries :)

On Tue, 25 Sep 2018, 2:00 pm Aurélien Mino, <notifications@github.com>
wrote:

> Ok. I was not sure for support in Node and was wondering about the
> alignment with the 'es6' declaration in eslint. Sorry for this
> disturbance...
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/jhipster/generator-jhipster/commit/931614738e7583e7494c27aebf8f869b6a89861c#commitcomment-30636798>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/ABDlF06SnlGdayyeTegFUeLuuVcWs1Kxks5uehrdgaJpZM4W23sF>
> .
>


It has happened before, the author behind the contributor-covenant.org:
https://github.com/opal/opal/issues/941
These kind of policies have to be cut down before they take the hold, Linux community did fine for decades without this nonsense.


Thanks

> On 25 Sep 2018, at 17:56, Victor Toso <notifications@github.com> wrote:
>
> I just merged this one
> https://gitlab.freedesktop.org/spice/spice-gtk/commit/8f38461e31bec98e4d3e1bc503da07f33931d0b7
>
> Cheers,
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
>


Klaidingas formatas


> Dear @artulloss:
> I regret to inform you that the release you submitted, named "**VPNBlock**" (v1.3.1), for the project [VPNBlock](https://poggit.pmmp.io/ci/artulloss/VPNBlocker/VPNBlock) on 2018-09-25T00:50:29.000Z, has been rejected.

Plugin uses Windows directory separators and only works on Windows.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


It doesn't work, this is so sad


@daherb @heatherleaf This is commit no one thousand. We should celebrate. :D


No, it does not.


overall this looks good. I really like the description of the algorithm which is the description of this PR, and I don't see why not include it in the source code directly


that makes sense to me


Используй вместо select итерактор detect, он тебе и вернет первый попавший под условие объект


> Dear @AngelsFlyyin:
> I regret to inform you that the release you submitted, named "**PCFly**" (v3.0.0), for the project [PCFly](https://poggit.pmmp.io/ci/AngelsFlyyin/PCFly/PCFly) on 2018-09-19T14:34:56.000Z, has been rejected.

Special colors including red, yellow, gold, green, aqua, etc. are reserved for notices, warnings, errors and other important messages. You are not allowed to use them for meaningless messages like who wrote the plugin in onEnable/onDisable, as they distract the user from real errors/warnings. You may still write that message (although we discourage you to), but please keep it white.

See https://bit.ly/pmcolors for more info.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


> Dear @itzandrei100:
> I regret to inform you that the release you submitted, named "**Sell**" (v3.0.0), for the project [Sell](https://poggit.pmmp.io/ci/itzandrei100/Sell/Sell) on 2018-09-22T20:28:11.000Z, has been rejected.

Advertising servers in plugin description is disallowed.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


> Dear @itzandrei100:
> Regarding the release you submitted, named "**Sell**" (v3.0.0), for the project [Sell](https://poggit.pmmp.io/ci/itzandrei100/Sell/Sell) on 2018-09-22T20:28:11.000Z, there are some problems with the values in the submit form.

Advertising servers in plugin description is disallowed.

> Your release has been reset to draft. Please [edit the release](https://poggit.pmmp.io/edit/itzandrei100/Sell/Sell/2) to resolve these problems, then click "Submit" on the edit page to have the plugin reviewed again.
> Note: This comment is created here because this is the last commit when the released build was created.


This is Yunfan's Fibonacci function


will move javascript to static files, public folder, once done.


@JungTsungChiang - (as discussed in class) Make sure you're using the function parameters as variables so you can call the function with different variables! You're solution might look like:

`return "Hi, " + name + "!";`

Where `name` ends up being whatever you put between the parentheses when you call the function (e.g. `sayHello("Stan")` would return "Hi, Stan!" and `sayHello("Emily")` would return "Hi, Emily!")


###test edit


I think this change is responsible for some side effects I've started to observe a couple weeks ago. On a cluster of computers, all with Intel CPUs but from different generations, vsearch works correctly on the nodes equipped with the same architecture than the frontal node (on which the compilation was done). On older nodes, vsearch crashes with a core-dump and the OS message _illegal instruction_.

A workaround is to compile with:
```sh
CFLAGS="-march=x86-64" ./configure && make -j
```
or to target only cluster nodes with the same architecture than the frontal node.


Well, if that was not the case, you probably do not want to compute the address as `16 * coffset` :wink:


El Hornet's comeback HMMMM


Commito zinutes formatas yra:

evelinamon: Pakeitimai liepiamaja nuosaka

- Konkretus ivardinimas pakeitimo

Sakiniai pradedami didziaja raide, taskas pabaigoje sakinio nededamas


Is my paper clear for someone who doesn't know animals? Is the jargon used explained enough? I am not a good writer, does it look ok?


> Dear @AlexPads:
> I regret to inform you that the release you submitted, named "**ShopUI**" (v1.0.2), for the project [SimpleShopGUI](https://poggit.pmmp.io/ci/AlexPads/TinyPixelShopGUI/SimpleShopGUI) on 2018-09-25T00:37:32.000Z, has been rejected.

From API 3.2.0 onward, plugins must use the form API offered by PocketMine to use custom UI.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


My document is incomplete and needs added text and images to make sense


This paper is still in progress, I'm not sure what the best way to introduce this paper. I also still have a few tables to add.


*corporates
also more like Overcompensation Turret :P


@JungTsungChiang - Looks like you missed the `incrementCounter` function; take a look at it and let me know if you have any questions!


Latest build number is `5` and this change is for the build number `3`. The latest one is tested on Windows too and everything works as expected. Note that you must install it inside an env though to get the environment variables properly activated.


I'm not confusing Greg with anybody.

I'm simply stating, that the CoC is political. Gregs intentions don't matter, it may well be non-political, the CoC however is. And it will be abused, actually, Sarah Sharp already started doing so.


~or just do your job properly~ <3<3<3


> Dear @joshuasing:
> I regret to inform you that the release you submitted, named "**TempBanUI**" (v2.8), for the project [TempBanUI](https://poggit.pmmp.io/ci/joshuasing/TempBanUI/TempBanUI) on 2018-09-11T02:25:46.000Z, has been rejected.

We do not accept submissions for API 4.0.0, because it does not exist. It is still under development and is subject to change, so it is unreasonable to mark your plugin as supporting 4.0.0.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


Successfully aliased the URL <https://simple-now-app-kuiudokpre.zeit.sh> to the following aliases.

* https://simple-now-app.zeit.sh
* https://simple-now-app-2.now.sh
* https://simple-now-app-3.zeit.sh


Not that I know of :(


@JungTsungChiang - This is where you would pass in values to assign to the function parameter values. For example, calculateVolume is defined as:

`function calculateVolume(w, l, h){ ... }`

So here you would call:

`var result = calculateVolume(10, 5, 20)`

Which would assign 10 to w, 5 to l, and 20 to h.


smh


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

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

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

### Deployments updated

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

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


I have: created a branch, created a file and made a commit, and opened a pull request


better than the prequel


Может select_station назвать, чтобы в одном стиле было?


Вынести из цикла?


> An issue for what?

to move this discussion there ;-)


unificar


Note that the removal of this function removes the "random walk with restart" algorithm from the repository.


@leonstafford That's an affirmative. My plan is to complete my first pass, merge from master, and then complete a final pass for the PR.


Ver posible solución en el issue #135 para una nueva forma de detección de colisiones


> I don't understand fully, but from what I understand, it's fine if we set the VIRTUAL_ENV env var and then execute pyls with any Python executable. Is that right?

yes.


e


Created multidev environment [sfgov#ci-1562](https://dashboard.pantheon.io/sites/91d50373-c4cf-40e4-a646-cb73e16a140c#ci-1562).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-1562-sfgov.pantheonsite.io/)


Successfully aliased the URL <https://api-ovikhvkdhf.now.sh> to the following alias.

* https://api.thegospelfund.com


> Dear @chaosfreak93:
> I regret to inform you that the release you submitted, named "**Scoreboard**" (v0.1.7), for the project [Scoreboard](https://poggit.pmmp.io/ci/chaosfreak93/Scoreboard/Scoreboard) on 2018-09-18T10:19:11.000Z, has been rejected.

Special colors including red, yellow, gold, green, aqua, etc. are reserved for notices, warnings, errors and other important messages. You are not allowed to use them for meaningless messages like who wrote the plugin in onEnable/onDisable, as they distract the user from real errors/warnings. You may still write that message (although we discourage you to), but please keep it white.

See https://bit.ly/pmcolors for more info.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


Successfully aliased the URL <https://chartcomposer-bsdctwjbmo.now.sh> to the following alias.

* https://chartcomposer.com


> Dear @BaconOFBurger:
> I regret to inform you that the release you submitted, named "**NoVoid**" (v1.0.0), for the project [NoVoid-beginer](https://poggit.pmmp.io/ci/BaconOFBurger/NoVoid/NoVoid-beginer) on 2018-09-21T13:16:37.000Z, has been rejected.

The plugin namespace violates PQRS-1. The namespace must contain the plugin name. You are suggested to refactor the plugin namespace to `BaconOFBurger\NoVoid`.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


I over did this by accident – originally i thought it was just the uppercase in cuisine not matching the database field but it wasn't that.. (see further down!)


It was that in your form params, it wasn't allowing the cuisine to be submitted so all your reviews didn't have a cuisine!


day001 - bite_007_Parsing_dates_from_logs


Manage payments and billing.


I wanted scores to be between 0 and 10 and atm it was just 10 or more which felt a bit off so I added this change


@Alan-FGR is famous now


> Dear @WeekThor:
> I regret to inform you that the release you submitted, named "**GeoIP**" (v2.0), for the project [GeoIP](https://poggit.pmmp.io/ci/WeekThor/GeoIP/GeoIP) on 2018-09-24T15:06:49.000Z, has been rejected.

1. Special colors including red, yellow, gold, green, aqua, etc. are reserved for notices, warnings, errors and other important messages. You are not allowed to use them for meaningless messages like who wrote the plugin in onEnable/onDisable, as they distract the user from real errors/warnings. You may still write that message (although we discourage you to), but please keep it white. See https://bit.ly/pmcolors for more info.
2. The plugin must be available in English.
3. I suggest you to download the database from plugin code rather than telling the user to do so.

> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when the released build was created.


I was having trouble fixing this (but solved it with the migration in the next change) but this should work now


This just needed a <%= instead of <%+ to work


Shouldn't this be this?  I don't think it will do anything as is.  I like to also add an inline comment about the deprecation.
```
{% if copyToClipboard %}
{% set copy_to_clipboard = copyToClipboard %}
{% endif %}
```


> decoupled from what? I don't understand.

to decouple the setting of the VIRTUAL_ENV env var from the `PythonContribution`. though we definitely need a mechanism to restart the contribution/LS after changing the virtualenv. how this is to be triggered remains a bit unclear. though we might have a component to trigger restarts. let's think about that.


Dang. Somehow I missed that debug ‘echo’.
Thanks for removing it.


The following doc(s) have been deployed to the [debugloglo](https://debugloglo-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/logs](https://debugloglo-static-docs.pantheonsite.io/docs/logs)
- [/docs/wp-config-php](https://debugloglo-static-docs.pantheonsite.io/docs/wp-config-php)


@boberfly he's one of the 5 people on the internet, he must be famous


![](https://github.trello.services/images/mini-trello-icon.png) [Добавить ограничения на размер картинки в markdown](https://trello.com/c/1SBFdHav/121-%D0%B4%D0%BE%D0%B1%D0%B0%D0%B2%D0%B8%D1%82%D1%8C-%D0%BE%D0%B3%D1%80%D0%B0%D0%BD%D0%B8%D1%87%D0%B5%D0%BD%D0%B8%D1%8F-%D0%BD%D0%B0-%D1%80%D0%B0%D0%B7%D0%BC%D0%B5%D1%80-%D0%BA%D0%B0%D1%80%D1%82%D0%B8%D0%BD%D0%BA%D0%B8-%D0%B2-markdown)


this line makes broken symlinks, right?


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

I updated the Github team because of this commit.

- @m-rossi 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/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)