[R/default_params_doc.R:57:1:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/default_params_doc.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
#' @param missnumspec The number of species that are in the clade but missing in the phylogeny_
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:175:3:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/default_params_doc.R#L175) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:176:3:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/default_params_doc.R#L176) *style:* **Variable or function name should be snake_case.**
```r
  N0,
  ^~
```
[R/default_params_doc.R:187:3:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/default_params_doc.R#L187) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/mbd_loglik_choosepar.R:23:1:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:29:26:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L29) *style:* **Commas should always have a space after.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                         ^
```
[R/mbd_loglik_choosepar.R:29:31:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L29) *style:* **Commas should always have a space after.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                              ^
```
[R/mbd_loglik_choosepar.R:29:36:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L29) *style:* **Commas should always have a space after.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                                   ^
```
[R/mbd_loglik_choosepar.R:29:42:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  namepars <- c("lambda","mu","nu","q"); Npars <- length(namepars);
                                         ^~~~~
```
[R/mbd_loglik_choosepar.R:30:52:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L31) *style:* **Use <-, not =, for assignment.**
```r
  trpars1 = rep(0, Npars)
          ^
```
[R/mbd_loglik_choosepar.R:34:3:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( min(trpars1[1:Npars]) < 0 ){loglik <- -Inf}else
      ^
```
[R/mbd_loglik_choosepar.R:37:33:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( min(trpars1[1:Npars]) < 0 ){loglik <- -Inf}else
                                ^
```
[R/mbd_loglik_choosepar.R:37:35:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:Npars]) < 0 ){loglik <- -Inf}else
                                  ^
```
[R/mbd_loglik_choosepar.R:37:50:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:Npars]) < 0 ){loglik <- -Inf}else
                                                 ^
```
[R/mbd_loglik_choosepar.R:38:3:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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:42:13:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L42) *style:* **Use <-, not =, for assignment.**
```r
      pars1 = trpars1/(1 - trpars1)
            ^
```
[R/mbd_loglik_choosepar.R:42:22:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L42) *style:* **Put spaces around all infix operators.**
```r
      pars1 = trpars1/(1 - trpars1)
                    ~^~
```
[R/mbd_loglik_choosepar.R:42:23:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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_choosepar.R:61:75:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L61) *style:* **Commas should always have a space after.**
```r
    cat("There are parameter values used which cause numerical problems:",trpars1,"\n")
                                                                          ^
```
[R/mbd_loglik_choosepar.R:61:83:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_choosepar.R#L61) *style:* **Commas should always have a space after.**
```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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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:16:11:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L16) *style:* **Commas should always have a space after.**
```r
    A[s+2,dst] <- A[s,src] + A[s+1,src]
          ^
```
[R/mbd_loglik_utils.R:16:23:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L16) *style:* **Commas should always have a space after.**
```r
    A[s+2,dst] <- A[s,src] + A[s+1,src]
                      ^
```
[R/mbd_loglik_utils.R:16:33:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:16:36:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L16) *style:* **Commas should always have a space after.**
```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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:9:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L18) *style:* **Commas should always have a space after.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
        ^
```
[R/mbd_loglik_utils.R:18:21:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L18) *style:* **Commas should always have a space after.**
```r
    A[s,src] <- A[s,src] * q^(m-n)*(1-q)^(2*n-m)
                    ^
```
[R/mbd_loglik_utils.R:18:30:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:32:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:35:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:36:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:38:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:42:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:44:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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:18:46:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L24) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="windows"){matrix_builder = hyperA:::hyperA}
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:1:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
# if (.Platform$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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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:95:64:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```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:95:76:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```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:95:84:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```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:95:90:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L95) *style:* **Commas should always have a space after.**
```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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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:107:35:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                  ^
```
[R/mbd_loglik_utils.R:107:38:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                     ^
```
[R/mbd_loglik_utils.R:107:40:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                       ^
```
[R/mbd_loglik_utils.R:107:42:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                         ^
```
[R/mbd_loglik_utils.R:107:44:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```r
create_B.no_mbd = function(lambda,nu,q,k,b,max_number_of_species,minimum_multiple_births){
                                           ^
```
[R/mbd_loglik_utils.R:107:66:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L107) *style:* **Commas should always have a space after.**
```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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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:109:80:](https://github.com/Giappo/mbd/blob/414258254ca2d2add4ee750443cdd1f8f114d974/R/mbd_loglik_utils.R#L109) *style:* **Commas should always have a space after.**
```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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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/414258254ca2d2add4ee750443cdd1f8f114d974/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,
  ^~
```


Тут аналогично go_forward


Conceptually looks OK. Please build pages similarly as in:
```
com.facebook.presto.operator.BenchmarkHashAndStreamingAggregationOperators.Context#setup
```
That is produce multiple pages, each with some amount of groups and partitions


Вернуть текущую станцию как результат


Generally it would be good, if we are able to merge also small changes and bugfixes into master. For this automatic testing should work and some manual tests should be performed. I.e.:
* check whether windows installer installs and program can be opened
* check whether new version of snap installs and program is working
* check whether new functionalities result in crashes in more sophisticated scenarios (this could also be automated)


Successfully aliased the URL <https://docs-pqueoyziqz.zeit.sh> to the following alias.

* https://docs.zeit.sh


👍👍👍 Thanks guys!


# webRTC : HTML5 视频 直播 技术

https://github.com/xgqfrms/xgqfrms/issues/46


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dibuat oleh junifar


As long as you are convinced the "randomness" of native-jitter and native-jitter+AES are practically equivalent then the added entropy rate AES provides is useful by default for jitter.


Хорошие строки вывода


Is anyone honestly going to ever read these commits? Is anyone going to transform education at scale? The work you've done here is a crystal ball into what learning looks like in the 22nd century.


The double think is amazing.
It's okay when the SJW does it, but when anyone else does it it's rape, murder, torture, and racism all packaged into one dehumanizing box.