[R/default_params_doc.R:176:3:](https://github.com/Giappo/mbd/blob/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/R/default_params_doc.R#L176) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:177:3:](https://github.com/Giappo/mbd/blob/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/R/default_params_doc.R#L177) *style:* **Variable or function name should be snake_case.**
```r
  N0,
  ^~
```
[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/R/mbd_loglik_utils.R#L24) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="windows"){matrix_builder = hyperA:::hyperA}
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:1:](https://github.com/Giappo/mbd/blob/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/R/mbd_loglik_utils.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
# if (.Platform$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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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/93d3f5a75f51a76d2f53141cde7c6ae79bc0d90e/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,
  ^~~~~
```


Fixed bug failing to RESTORE FILELIST for versions > 2014


Successfully aliased the URL <https://distance-learning-lp-wancnzpmbs.now.sh> to the following alias.

* https://lp.onlineschool.ru


I would suggest:
```
// if this feature type mapping uses an external index and indexing is enable
// then create a specific iterator
```

That ``@TODO`` was some forgotten code ?


O Controlador `cadastroCliente.php` espera receber dados de um formulário (vide o `$_REQUEST` que ele acessa).

Não se pode criar um _link_ direto que nem esse daqui, senão faltarão os dados no `$_REQUEST` e o controlador falhará. É necessário criar um formulário HTML e colocar este controlador como destino dos dados:
```html
<form action="cadastroCliente.php">
    ...
</form>
```


Something like this. 😄

```js
return (tx ? knex.transaction(tx) : knex).from('...')
```


no, do not do that. putting the QList on the stack is not a problem.


This breaks "npm install" under Debian Stretch:
`
> sqlite3@4.0.2 install /home/z/opentrade/node_modules/sqlite3
> node-pre-gyp install --fallback-to-build

node-pre-gyp WARN Using request for node-pre-gyp https download
node-pre-gyp ERR! install error
node-pre-gyp ERR! stack TypeError: Cannot read property 'version' of null
node-pre-gyp ERR! stack     at Object.module.exports.evaluate (/home/z/opentrade/node_modules/node-pre-gyp/lib/util/versioning.js:288:32)
node-pre-gyp ERR! stack     at install (/home/z/opentrade/node_modules/node-pre-gyp/lib/install.js:204:31)
node-pre-gyp ERR! stack     at Object.self.commands.(anonymous function) [as install] (/home/z/opentrade/node_modules/node-pre-gyp/lib/node-pre-gyp.js:52:37)
node-pre-gyp ERR! stack     at run (/home/z/opentrade/node_modules/node-pre-gyp/bin/node-pre-gyp:82:30)
node-pre-gyp ERR! stack     at Object.<anonymous> (/home/z/opentrade/node_modules/node-pre-gyp/bin/node-pre-gyp:134:1)
node-pre-gyp ERR! stack     at Module._compile (module.js:569:30)
node-pre-gyp ERR! stack     at Object.Module._extensions..js (module.js:580:10)
node-pre-gyp ERR! stack     at Module.load (module.js:503:32)
node-pre-gyp ERR! stack     at tryModuleLoad (module.js:466:12)
node-pre-gyp ERR! stack     at Function.Module._load (module.js:458:3)
node-pre-gyp ERR! System Linux 4.9.0-8-amd64
node-pre-gyp ERR! command "/home/z/.nvm/versions/node/v8.0.0/bin/node" "/home/z/opentrade/node_modules/.bin/node-pre-gyp" "install" "--fallback-to-build"
node-pre-gyp ERR! cwd /home/z/opentrade/node_modules/sqlite3
node-pre-gyp ERR! node -v v8.0.0
node-pre-gyp ERR! node-pre-gyp -v vhttps://registry.npmjs.org/node-pre-gyp/-/node-pre-gyp-0.10.3.tgz
node-pre-gyp ERR! not ok
Cannot read property 'version' of null
npm WARN OpenTrade@0.1.0 No license field.

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! sqlite3@4.0.2 install: `node-pre-gyp install --fallback-to-build`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the sqlite3@4.0.2 install script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/z/.npm/_logs/2018-09-25T15_54_59_923Z-debug.log
`


is this syntax explained somewhere?


洗的路，洗的路


Add a `testrpc.WaitForTestAgent(t, a.RPC, "dc1")`


Due November 23, for distribution to devs the folloing week.


- Image works fine
- NOTE: MarkDown syntax doesn't seem to work within the alt tag for an image :(


Humm.. ??
https://gbatemp.net/threads/citra-unofficial-chinese-builds-discussion.431974/page-446#post-8301614


Humm.. ReplySleepQuery ??
https://gbatemp.net/threads/citra-unofficial-chinese-builds-discussion.431974/page-446#post-8301614


Is the script loaded? What does /script say?


解构时加默认值


Stop trolling. You can obviously see that the checksum did not change, and the removal of a ROM is obviously less serious than adding one unless you're being deliberately obtuse.


Added a jupyter notebook with some analysis I performed on the MTA turnstile data


... 让你不要特殊化


True! I am still trying to sort that #7 out :) with little success.

1. event minimum properties? Whatever goes in the "properties_core". You decide what you want to go into a typical invite for say an academic meeting event?
2. why not! If `sfg` exists then so should `ical`s :)
3. `"List columns" could resolve the 'NA` issue but add unwanted complexity`, indeed.

Great package!


This feature will be helpful to somehow overcome the grafana issue https://github.com/grafana/grafana/issues/6592


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

* https://cloudcmd.now.sh


Successfully aliased the URL <https://just-another-todo-app-pgqwefmhdv.now.sh> to the following alias.

* https://just-another-todo-app.now.sh


Thanks for that. I have added it to the setup dependencies now -- I hope that works too


Great! Still new to those backticks but sounds like they do the job.


WTF...


actually, i think this is supposed to be `${this.providers.aws} since you're accessing a property on the instance and not an input.


Oh, this isn't actually related to max. number of cursors, both just happen
to be hardcoded to 10000, so I assumed they depended on the same constant (
src/vs/editor/common/controller/cursor.ts
<https://github.com/Microsoft/vscode/blob/4e4e6f9b44dd9e6a53d1f08565c52b8ea9f61a5e/src/vs/editor/common/controller/cursor.ts>
was
actually changed 5 months back). Either way, I think it would be nicer if
both could be changed as settings, I've actually hacked the number in local
versions of vscode, but thats definitely not the 'pretty' way to do it.

On Tue, Sep 25, 2018 at 12:15 PM Rob Lourens <notifications@github.com>
wrote:

> This is an increase from 2048 to 10000 and it's from 18 months ago
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/Microsoft/vscode/commit/4c6c3ec3255ca9c38a93f83a7658675ab54586fb#commitcomment-30639716>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AJjYyNgnKT7JjmF3rns_kvhMizRcdabhks5uekh-gaJpZM4WpKy0>
> .
>

--
~Pedro R.
Master's Student, Software Developer, Technologist.


Get out and leave my wife the fuck alone


No me di cuenta de anotarlo en el commit propiamente dicho, pero este es el commit 666
Muahahahaha!


Pessoal, eu estou com a impressão que vocês estão duplicando esse código CSS (ou parte dele) em diversos arquivos diferentes.

Lembrem-se que duplicação de código é algo que deve ser **evitado**.

Nesse caso de CSS, vocês podem colocar as regras de estilo que sejam comuns em um arquivo separado (ex.: `estilo.css`) e referenciar ele em todas as páginas HTML que usam essas regras através do marcador [**`<link>`**](https://developer.mozilla.org/pt-BR/docs/Web/HTML/Element/link):

```html
<link href="estilo.css" rel="stylesheet">
```

Vocês podem ler mais sobre duplicação de código e os problemas que ela gera em: http://blog.evaldojunior.com.br/desenvolvimento/melhores%20pr%C3%A1ticas/2014/01/23/os-problemas-do-codigo-duplicado.html


@ddiezrod Can you check your computer clock?, you are alwys commiting in the future
![imagen](https://user-images.githubusercontent.com/19991680/46027614-93d8ab80-c0ee-11e8-8b66-b90f200f48b2.png)


> that sounds like a different (but truly related) story. maybe we should continue discussing that on a new issue. this is something of a broader interest.

Agreed.

> the docs (here: https://jedi.readthedocs.io/en/latest/docs/api.html#jedi.find_virtualenvs) summarizes this pretty good what happens in the code.
>
> by "which python is used for the jedi" I really mean, that this python will be executed to obtain all the paths needed to be gathered for the analysis, and also as the evaluator subprocess. see the code linked in the docs.

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?

>about that, I'd rather see that decoupled. consider the python would run in another container, and the stdio would be redirected. the virtualenv would be then configured independently, but we need to restart the ls.

decoupled from what?  I don't understand.

>@simark do we have an issue for this?

An issue for what?> that sounds like a different (but truly related) story. maybe we should continue discussing that on a new issue. this is something of a broader interest.

Agreed.

> the docs (here: https://jedi.readthedocs.io/en/latest/docs/api.html#jedi.find_virtualenvs) summarizes this pretty good what happens in the code.
>
> by "which python is used for the jedi" I really mean, that this python will be executed to obtain all the paths needed to be gathered for the analysis, and also as the evaluator subprocess. see the code linked in the docs.

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?

>about that, I'd rather see that decoupled. consider the python would run in another container, and the stdio would be redirected. the virtualenv would be then configured independently, but we need to restart the ls.

decoupled from what?  I don't understand.

>@simark do we have an issue for this?

An issue for what?


Created multidev environment [dgreat#pr-373](https://dashboard.pantheon.io/sites/41cad7fe-472d-43a9-a470-d391b9622376#pr-373).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-373-dgreat.pantheonsite.io/)


- You can now pin the Overlay Text Chat widget
- New keybind: `Activate Overlay Chat`
##
- New action types: `OVERLAY_SET_TEXT_WIDGET_OPACITY`, `OVERLAY_ACTIVATE_REGION`, `OVERLAY_DEACTIVATE_ALL_REGIONS`, `OVERLAY_SET_PREVIEW_IN_GAME_MODE`, `OVERLAY_ACTIVATE_REGION_TEXT_WIDGET`
- Action types removed: `PREMIUM_CODE_ACTIVATION_MODAL_OPEN`, `PREMIUM_CODE_ACTIVATION_MODAL_CLOSE`
- New constants:
```js
t.OverlayActiveRegions = {
    TEXT_WIDGET: null
},
t.AnalyticsOverlayUnlockTypes = {
    FULL_OVERLAY: "full_overlay",
    PINNED_TEXT_WIDGET: "pinned_text_widget"
}
```
- New icon: `Opacity`

## New strings
- `KEYBIND_ACTIVATE_OVERLAY_CHAT: "Activate Overlay Chat"`
- `OVERLAY_CHAT_HOTKEY: "Press !!{keybind}!! to chat"`
- `OVERLAY_TEXT_WIDGET_SETTINGS: "Text Widget In-Game Settings"`
- `FORM_LABEL_OVERLAY_CHAT_OPACITY: "Opacity"`
- `PREMIUM_CODE_REDEMPTION_CONFIRMATION_BLURB: "Thanks to a random string of digits, you now have enhanced chat perks for {numMonths, plural, one {1 month} other {{numMonths} months}}!"`
- `PREMIUM_CODE_REDEMPTION_CONFIRMATION_BUTTON: "Ooh, Sweet!"`


Indentation normal kod olsa bile hatalı + bu golfing problemi, bundan çok daha kısa bir şekilde yazılabilir bu problem.


Nachtrag Quellen
Image für heartEmptySprite -> https://pixabay.com/de/favorit-herz-nicht-ausgew%C3%A4hlte-wei%C3%9F-154756/
Image für heartFullSprite ->https://pixabay.com/de/herz-rot-einfache-symbol-157534/


# 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)|


Indentationlar problemli (Tab kullanmayın lütfen eger dil zorlamiyorsa, bknz: go)

Algoritmik acidan gelistirilebilir.


Did you make this?


It`s work?


This is bas solution


Bad


@danieldietsch Are you fine with this modification?


Remove this string


**NOTE:** Commit message is erroneous and was accidentally based on changes made to desktopStartup.ahk. What this commit actually involved was improved maintainability by abbreviating the lengthy "CommitAnyFile" sub-string that appeared in many of the functions and variable names within the file.


Текст меню можно вынести в константы. Если заменить эту строку на `print MAIN_MENU`, метод станет читабельнее


Here you can write just `return` instead of `if` (your choice)


这里为什么通过 mMonthViewClassPath 判断是否指定了自定义 WeekBar? 我在使用时没有指定这三种自定义视图时会崩溃，是不是和这个有关？


use without player + dot

only call method, like addSongs();


Guu


@hammacktony correct if I am wrong. Your migration file does contain category?


Great work @weaselp !


Hi,

Thank you very much for your interest in our work. Let me clarify your questions.

Q1. Data[0][i] represents i-th batch in the data, Data[0][i][j] represents the j-th feature value, Data[0][i][j][k] represents k-th element (visit) of your time sequence and finally Data[0][i][j][k][l] represents l-th data point (patient) in your batch. Before I feed it to the network, I take the transpose then input becomes a tensor of size: number of samples X sequence length X feature dimensionality. Therefore, you can directly save your data in this form and feed it to the network.

Q2. Time data follows the same structure as data. The only difference time data does not feature dimensionality, it is just a scalar. Therefore, the input of the network should be number of samples X sequence length. If we look at the i-th batch, Time[0][I], before taking the transpose, then it is sequence length X number of samples.

Assignments have the cluster assignments for this synthetic experiment since we want to show the clusters after representation learning. Assignments[0][i] has the cluster labels for each sample in the i-th batch. Note that we do not necessarily know the assignments in real data. You also may not need mini-batch training for the synthetic example since the scale is small but I tried to give an example when you have larger scale data.

Hope this helps. Please let me know if you have further questions.

Regards,
İnci

On Sep 25, 2018, at 4:59 AM, linciheng <notifications@github.com<mailto:notifications@github.com>> wrote:

Hi! Excellent job! Thanks for your code and essay.
I have spent lots of time to study your source code and the related article. But, I really dont understand the means of input data.
Q1:What the means of each demension in input data(Clustering_Data_1D.mat.tar.gz)?
In your source code, 'Data[0][i]' represents patients? 'Data[0][i][j]' represents visit sequence? And the last demension represents features?
Q2:The same queation in Time data.
I also mention that the 'Assignments' data seems to correspond to the columns of 'Data'?

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oo_plant_load_profile (drewyh) - i386-Windows-7-VisualStudio-14: OK (3033 of 3033 tests passed, 0 test warnings)

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


the page of demo and document are both 404


Should be !!!, not just one


Yo


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


Are you sure semantic is not changed here? Before it, you did not access `KotlinTopLevelFunctionFqnNameIndex`.