[R/default_params_doc.R:176:3:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/default_params_doc.R#L176) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:188:3:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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:36:3:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_choosepar.R#L36) *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:43:5:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_choosepar.R#L43) *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:45:23:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_choosepar.R#L45) *style:* **Put spaces around all infix operators.**
```r
      pars1 <- trpars1/(1 - trpars1)
                     ~^~
```
[R/mbd_loglik_choosepar.R:45:24:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_choosepar.R#L45) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      pars1 <- trpars1/(1 - trpars1)
                       ^
```
[R/mbd_loglik_choosepar.R:47:5:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_choosepar.R#L47) *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:63:3:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_choosepar.R#L63) *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:64:1:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_choosepar.R#L64) *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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L24) *style:* **Commented code should be removed.**
```r
# if (.Platform$OS.type=="windows"){matrix_builder = hyperA:::hyperA}
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:25:1:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
# if (.Platform$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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/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,
  ^~~~~
```
[R/mbd_loglik_utils.R:345:1:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L345) *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:345:5:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L345) *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:348:54:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L348) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  missingspecies_min <- max((tips_interval[1] - 2), 0 )
                                                     ^
```
[R/mbd_loglik_utils.R:350:1:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L350) *style:* **Lines should not be more than 80 characters.**
```r
  tips_components <- 1 + c(missingspecies_min, missingspecies_max) # +1 is because of the zero-th component
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:351:3:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L351) *style:* **Variable or function name should be snake_case.**
```r
  Pc <- sum(total_product[tips_components[1]:tips_components[2]])
  ^~
```
[R/mbd_loglik_utils.R:352:5:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L352) *style:* **Commented code should be removed.**
```r
  # Pc <- sum(total_product)
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:363:1:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L363) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:363:1:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L363) *style:* **Variable or function name should be snake_case.**
```r
calculate_conditional_probability0PB <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_loglik_utils.R:369:13:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L369) *style:* **Only use double-quotes.**
```r
  methode = 'expo',
            ^~~~~~
```
[R/mbd_loglik_utils.R:375:1:](https://github.com/Giappo/mbd/blob/eae9c085ad5d8d442b5efbe7cd50d1b1910c118c/R/mbd_loglik_utils.R#L375) *style:* **Lines should not be more than 80 characters.**
```r
  if (mu != 0){cat('mu is supposed to be equal zero to use this function'); return(Pc <- NA)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Copy of this build can be found at https://www.mewbuilds.com/build/c1747414e27c44f1bd330ea9071aa6408d8a6bda/index.html


`#!/bin/sh

rm -rf /tmp/{foo,bar}

cd /tmp
mkdir foo bar
echo 1 > foo/1
echo 2 > foo/2

find foo -mindepth 1 -maxdepth 1 -print0 | xargs -0 -I{} ln -s {} ./bar/

[ "1" == $(cat bar/1) ] && echo first worked || echo first failed

rm bar/{1,2}

cd bar

find ../foo -mindepth 1 -maxdepth 1 -exec ln -s -t . {} +

cd ..

[ "1" == $(cat bar/1) ] && echo second worked || echo second failed
`

when I run this:

`❯ sh test.sh
cat: bar/1: No such file or directory
test.sh: line 12: [: 1: unary operator expected
first failed
second worked
`


though perhaps this works fine in the tarball?


Indeed, with `-march=native` the compiler generates binary only optimized for that particular CPU architecture.

If a single binary file is desired, the workaround is to determine the lowest common denominator of march and set it so. Using `-march=x86-64` is a work around; However, it will only enable `-msse` and `-msse2` and will not enable `-msse3` or `-mssse3` by default. A more specific architecture would be helpful in this case.

Using specific binary for a given architecture is also an option.

Lastly, it is possible to generate both the SSE2/SSE3 and the non-SSE code at compile time and let VSEARCH to choose which to use at runtime.


One thing I noticed, is everything is in bold and I wasn't  sure if that is intended or not.
You are very thorough with the first step, it is very clear that everything needs to be clean. Good job.
Questions: What vehicles use this carburetor?
                  How long does one typically last?


Your organization is great! I would just clarify who your audience is, for example: using the CofO dairy as an example to ensure that beginning dairy farmers in SW MO will be successful.  I know your's isn't complete, but it looks good as of now. Also one of the requirements was a FAQ section at the end for readers for just a few questions.


@lomlonde - Like you've done for`getSalePrice` and`isOdd`, all of these function can have parameters passed in so that you don't have to redefine variables within the function! (Whatever you put between the parentheses will be assigned to the variable name in the function parameter definition)


Hehe, was Du alles rausfindest :-) Jetzt hast Du einen (meinen) früheren commit kommentiert.

Das ist sowas wie ein implizites Issue für jeden einzelnen commit. Ich hatte das gar nicht
erwähnt, denn man nutzt es normalerweise für "Code-Reviews" (für Entwickler, um Änderungen
am Code zu diskutieren).
Genauso wie bei normalen Issues sind die Inhalte NICHT im eigentlichen repo. Und, wie Du selbst
gesehen hast, ist es wieder ein .png. Also das gleiche wie bei #4

Macht nix; zeigt mir, dass Du's wirklich versuchst. Danke.


@BugDiver no worries!


Is it clear who it is written for?
 Its pretty clear that the paper is written for those who want to raise show chickens.

Could it be clearer?
Maybe put something in the intro about who its for.

If it is clear, does the text serve that audience at all points?
I don't know a whole lot about show chicken but from reading this paper it sounds like you just raise a bunch of chickens normally and pick the pretty ones at the end. If that's how it is then yes but if there are any other procedures specific to raising show chickens I think they should be included.

•Is the process chosen sufficiently complex to sustain the project, or is it too simple?
Sufficiently complex

•Could you follow the instructions at all points?
Yes

Is there anything you don't understand, or could not follow?
I understood everything

•Does the document include all required elements, or a plan to add them?
Yes it does.


![](https://github.trello.services/images/mini-trello-icon.png) [GameDeck](https://trello.com/c/mpCgfKsu/3-gamedeck)


@IwanKaramazow I've reverted my last commit (the one that uses parcel and the underneath hole of doom) and now nothing works 🤣 OMG...


- Describe the audience for the text.
-- this text appears to be geared toward an audience that is familiar with leading worship services. Maybe members of the church band.

  > Is it clear who it is written for?
-- it does not clearly say who this article is geared towards. this is mainly assumed.

  > Could it be clearer?
--I think that providing a short sentence about our intended audience would be helpful so as not to overwhelm a novice that would come across this text.

  > If it is clear, does the text serve that audience at all points?

- Is the process chosen sufficiently complex to sustain the project, or is it too simple?
-- I think that this process can be complex enough  for this project. However, it appears that the text explains more about how to transition between specific songs, than how to go about choosing songs that will flow together throughout the worship service. I would keep the idea more general, but discuss more about choosing the songs.

- Could you follow the instructions at all points?
-- the instructions so far were clear enough. however, the bulleted lists sis not correlate to the example given at the bottom. I would like to see more references between the two sections

  > Is there anything you don't understand, or could not follow?
-- I was able to follow the document fairy well.

- Does the document include all required elements, or a plan to add them?
-- the text needs to provide some FAQs, but otherwise it looks like everything is there.


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

You are not getting this at all.
Greg's Intent, thus spoken by himself at the top:

> "The Code of Conflict is not achieving its implicit goal of fostering
civility and the spirit of 'be excellent to each other'.  Explicit
guidelines have demonstrated success in other projects and other areas
of the kernel."

What part of that matches Coraline's activism?  How did Sarah's twitter post abuse this CoC?  This isn't about fighting the status quo, this is about "if you continue to be a douchebag, go do it somewhere else."  So we can both agree the intent is probably correct.

You so easily dismiss his intent as irrelevant, but it is important.  Even a baseball bat can be used to play either baseball, or break into somebody's car -- and words are just tools as well.  Also let's be honest shall we?  Some of the CoC text is so vanilla, I doubt half of it is even original from Coraline.  Seems like the same boilerplate stuff we have all been reading for decades.  Greg just probably found the most HR sounding thing he could find that was community driven and went with it.  Yeah, in retrospect a better source could have been chosen, but so what.  It would have sounded about the same at the end of the day.  This is for fostering civility and reaping all of the benefits that come from that, not about anything other.


Yes.


Is it clear who it is written

Fairly clear. Audience seems to be people who are not familiar with cameras other than the camera on their phone

Could it be clearer?
It will definitely be clearer with more expansion of text

If it is clear, does the text serve that audience at all points?
Is what you have supposed to be the introduction? If so, it might be helpful to introduce your topic more. At the moment you kind of just jump in.

Is the process chosen sufficiently complex to sustain the project, or is it too simple?
Yes, even those who are familiar with cameras can benefit. I knew a cloudy day was best for pictures but did not know why!

Could you follow the instructions at all points?
Kind of just jumped into the topic but clear other than that

Is there anything you don't understand, or could not follow?
No

Does the document include all required elements, or a plan to add them?
Does not yet include all required elements.


@lomlonde - Careful that you don't get to sloppy with syntax. I'd recommend always using brackets around if statement blocks, even if it's just one line, because it's much easier to read! Also: semicolons!!!


Describe the audience for the text.
- The audience was clearly state as level 1-4 H students

Is it clear who it is written for?
-Yes

Could it be clearer?
-You might elaborate a little more in the introduction about the subject so that the reader may know a little more background information about show chickens.

If it is clear, does the text serve that audience at all points?
- I think the purpose of the text was clear and you accomplished your purpose well.

Is the process chosen sufficiently complex to sustain the project, or is it too simple?
-Yes. I think the subject matter is perfect to sustain the project and illustrates how to raise show chickens clearly.

Could you follow the instructions at all points?
-I was able to clearly follow the instructions and was able to understand how to choose the right show chickens

Is there anything you don't understand, or could not follow?
- The only thing that might would make it even better is to add a link to a website that has all of the breeds with the perfect traits listed out for each breed.

Does the document include all required elements, or a plan to add them?
-Yes


`"phpunit/phpunit": "~6.5.5",` requires PHP 7.0, `php: ^7.0`, but the require statement specifies `"php": ">=5.4.0",`


Можем узнать тип поезда по классу. От type в конструкторе можно избавиться.


People who want to train a horse


Yes


탭해라,,,PHP표준이다,,,,


This Javadoc is incomplete, feel free to remove the parameters and return this is not a public method.


Is it clear who it is written for?

 From my understanding this is written for other Dietians

Could it be clearer?

It would be easier to understand who the audience is if it was stated in the summary or introduction, but I was able to find the audience without it being stated.

If it is clear, does the text serve that audience at all points?

Yes the text seems fit for the audience as long as they have some background information about this particular subject.

•	Is the process chosen sufficiently complex to sustain the project, or is it too simple?

This process seems complex enough. Experience or a background in this field would be needed to understand this document.

•	Could you follow the instructions at all points?

I could follow the steps but they need to be more detailed. I think you have a good outline fore what your steps should look like. You just need to add more detail.

Is there anything you don't understand, or could not follow?

•	Does the document include all required elements, or a plan to add them?

This document does not have all required elements. This is a good start to the assignment it just needs more detail.


I tuned it for my server "Lilly in the valley". That server is quiet low performant :)
The turning images had been a cpu performance issue, so I switched them off.
After all I did not find them very useful.


Looking forward to see less random routes picked by hunter pets (and NPCs as well).
Thank you to @xvwyh and TC for solving that issue by committing these changes.


I don't think this one is needed.


Note sure what this implies.

Could you create a issue and describe what the problem is and how to reproduce?


The steps within the steps could be a little bit clearer


Yes it is the appropriate amount of complexity


Whoops... This is a little fossil of a previous attempt. Will push a commit which removes this.


@191410
Is it clear who it is written for?
 "Yes, it states clearly in the beginning who it is intended for."

Could it be clearer?
"Not really; the article does a really good job with explaining the audience."

It it is clear, does the text serve that audience in all points?
 "Yes, it carries the same expectations throughout the piece that anyone reading this will probably have previous knowledge of the poultry industry."

Is the process chosen sufficiently complex to sustain the project, or is it too simple?
 "I think that there is enough information here; its not too much to be overwhelming, but it explains the process well."

Could you follow the instructions at all points, it there anything you don't understand or couldn't follow?
"on the first read through, it took me a minute to figure out what you meant by partitions. also, step six seems a little vague. I think I understand what it is meaning, but i think pictures for those would help allot."

does the document include all required elements, or a plan to add them?
There needs to be an FAQ section at the end, and other than that, i think all the required sections are there."


Describe the audience for the text.
Is it clear who it is written for?
Could it be clearer?
If it is clear, does the text serve that audience at all points?
Is the process chosen sufficiently complex to sustain the project, or is it too simple?
Could you follow the instructions at all points?
Is there anything you don't understand, or could not follow?
Does the document include all required elements, or a plan to add them?

It is clear that the audience is for hunters that are just getting into bird dog hunting. Despite you outright stating who the audience was it was obvious who the audience was. I feel that the document was clear all the way through.

The process seems complex enough for this assignment.

I was able to follow the instructions at all points. The use of jargon I found acceptable for the target audience. There was not anything that I did not understand.

The document includes all of the required elements. Great job.


Yes. Very easy to understand


ah! the missing piece is the `find` is always absolute, observe:

```
8c85901a2682:nixpkgs a602204$ mkdir foo bar
8c85901a2682:nixpkgs a602204$ echo 1 > foo/1
8c85901a2682:nixpkgs a602204$ echo 2 > foo/2
8c85901a2682:nixpkgs a602204$
8c85901a2682:nixpkgs a602204$ find foo -mindepth 1 -maxdepth 1
foo/1
foo/2
8c85901a2682:nixpkgs a602204$ find $(pwd)/foo -mindepth 1 -maxdepth 1
/Users/a602204/projects/nixpkgs/foo/1
/Users/a602204/projects/nixpkgs/foo/2
```


No


created #4


I definitely learned something through this instructional! I didn't know anything about processing a calf, or that calves even needed to be processed, but now I feel like I know a bit more about it. Before I get into answering your specific questions, I'm just going to answer the ones from the repository.
1. Audience: I was a bit unclear who the intended audience was, and knowing that will help Dr. Miller decide if the jargon you used were well defined enough. I was sort of able to make sense of the jargon with the definitions you provided, but would the intended audience have a better understanding of the jargon?

2. The Process: I think the process you have chosen is definitely technical enough to support the assignment! As I said above, I have no knowledge of any of this. I think you did a good job at explaining why someone would need these instructions and outlining the process. I had no trouble following the process.

I think that your paper is fairly clear for someone who doesn't know animals, but I think some pictures of the processes could help add clarity. I'm not sure if you are able to get pictures of what tagging, weighing, etc would look like, but that would be very helpful! As far as readability, you may consider adding some headers before each step for easy navigation. It reads like an  informational paper right now, but I would rather have this information written out in an instructional format. I think the content of the paper is good, but there are a few grammatical errors and clunky language that I noticed throughout the paper, so you may want to have someone look over it with you or do some editing yourself.

Overall, this paper is very interesting! It was short enough to hold my attention, but I felt like I knew how to do the process by the end. Nice job! :)


Was it clear?
Altogether, the document was very well written and understandable. However, some of it felt relatively brief, so adding some additional information could be helpful. A good example of this is your paragraph about a business plan. Perhaps you could incorporate example of business plans from farms that were ran very effectively.

Who was it written for?
It clearly seems to be written for a beginner to the farm industry who is interested in learning more about the field.

Understandably, the document is incomplete. Although, I would try to elaborate on the questions you asked. If you decide to keep them, I would be sure to include some form of an answer to each so that the audience is not left wondering. Also, for the one's that are largely opinionated, you could include some possible approaches.

The url under marketing and advertising does not seem to be working.

Altogether, this document was very understandable and easy to follow even for someone new to the information.


**Describe the audience for the text.**
Somebody who has not processed a hog before and is wanting a step by step guide.
**Is it clear who it is written for?**
Yes!
**Could it be clearer?**
I think the instructions are very good. Since I do not really know anything about processing a hog, visual aids would be very beneficial. Other than that, it was worded clearly. The only thing that maybe you could try would be numbering things out so it is not as much a paragraph but rather smaller points of reference that can be easy to check back on as someone begins processing.. but that also is more of a personal preference and probably isn't necessary.
**If it is clear, does the text serve that audience at all points?**
I would say so, there wasn't anything that I found that left me confused. However, I wasn't actually out processing a hog so there may be more questions if I was out doing that.
**Is the process chosen sufficiently complex to sustain the project, or is it too simple?**
I definitely think this was complex enough, with the different tools that have to be used and the style and approach of making cuts, is not something that is simple in which anyone could do properly without guidance. Step by step was good.
**Could you follow the instructions at all points?**
Yes, again I wasn't actually doing it, but in my head I could somewhat envision everything.
**Is there anything you don't understand, or could not follow?**
No, I think it did a great job and left me with WAY more knowledge on processing a hog than what I had before.
**Does the document include all required elements, or a plan to add them?**
I would just add some images to give more clarity.

GOOD JOB
@CDIlbeck56


Audience: potential hog farmers or hog farmers starting out
Each point is explained precisely, I think I could probably do any of these tasks if necessary after reading this document. It provides useful information that is applicable to success in hog farming.

After you castrate, is the incision small enough to leave open or do you need to do stitches or bandage it in any way?
What is the chance of infection in docking tails or castrating?
How does the ear notch system work exactly? I gather that the ear is divided into four quadrants, each quadrant has a value of 1, 3, 9, and 27, and each quadrant can have up to two notches, but how do you know which notch to put where and how to calculate it correctly so you know exactly which litter and pig id it is? Could you provide a visual and/or an example?
My assumption is that the piglets are normally squirmy so once you catch one to do one of the above tasks, is it difficult to hold on to the pig with one hand while its hanging upside down by its rear legs? Is there a helpful technique that you recommend to ensure the safety of the pig and the handler or to keep the pig still? Is this a two person process?


This Javadoc is art.


•Describe the audience for the text.
I can definitely tell that the audience is someone, about our age, who has not made a blog before but want to know how. Your thesis was clear and easily noted.  I felt you did answer the who, what, and how.

Is it clear who it is written for?
yes

Could it be clearer?
I thought you were clear, I do believe I could use your instructions to make my own blog.

If it is clear, does the text serve that audience at all points?
yes

•Is the process chosen sufficiently complex to sustain the project, or is it too simple?
This could be a hard process but I like how you made it simple. I think your content is adequate and good.

•Could you follow the instructions at all points?
yes

Is there anything you don't understand, or could not follow?
If I had to make a blog, I now could.

•Does the document include all required elements, or a plan to add them?
yes

Questions I would ask would be like, where do I post my blog? How long is a good blog? I know you said it could be short or long, but how long would standard blog be. I think your steps are great. I like the illustrations, pictures, and headings!  That did make it easier to follow!


Is this reordering of the imports really needed?


Is line 1031 supposed to skip the first two arguments?


Can we define attributes in general as `private`?


![](https://github.trello.services/images/mini-trello-icon.png) [Build Out :Home page desktop design](https://trello.com/c/m4GPqhyl/1-build-out-home-page-desktop-design)


Navigation Property to navigate to other object with current object as well


Can we extract such literals into constants?


Commit message is wrong - it is not about AmazonLinux 1, still this ami is for AmazonLinux 2.


foriegn key to navigate to the other object with loading it.


lol


ah, so the difference is that ${contents} is an absolute path? got it


Missing copyright header.


Aliasing failed with the following error:

~~~
Error! The alias nextjsorg.now.sh is a deployment URL or it's in use by a different team.
~~~


forgot to remove


The lockfile is generated by vba-blocks to ensure reproducible builds. Each dependency is represented as `name version source`, which you can see matches the "test" package below


uh...


test comment


I'm having issue with proper translation with `wrapper_mask_color:Modal wrapper`. Can you give me bit more detailed explanation where this part goes?


the if condition is `feedforward ` but here the mechanism appended is `attention_mechs.append(MultiplicativeImageAttention`. Is it a mistake?


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

* https://spotted-city.com


Working my way to an official v0.1.0 release of vba-blocks where I'll explain everything


Can dbdt be moved up to NeuralNetwork from Layer? Since the bias gradient for each layer is equal to the error on the layer below, updating dbdt can be handled on the NeuralNetwork level rather than the layer level. This would also make the gradients (dWdt, dMdt, dbdt) consistent.


@r15ch13 Invalid download url, here the valid url:

- 64bit
https://www.eclipse.org/downloads/download.php?r=1&file=/mat/1.8.1/rcp/MemoryAnalyzer-1.8.1.20180910-win32.win32.x86_64.zip
- 32bit
https://www.eclipse.org/downloads/download.php?r=1&file=/mat/1.8.1/rcp/MemoryAnalyzer-1.8.1.20180910-win32.win32.x86.zip


полностью поддерживаю
и даже если ты где-то будешь в дальнейшем использовать в такой форме - отступы нужны!


Файлам названия давать лучше в snake_case


Created multidev environment [dgreat#pr-368](https://dashboard.pantheon.io/sites/41cad7fe-472d-43a9-a470-d391b9622376#pr-368).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-368-dgreat.pantheonsite.io/)


Pessoal, a ideia é que os arquivos de código-fonte do sistema de vocês (`*.html`, `*.php`, `*.css`, `*.js` etc.) sejam guardados diretamente dentro do repositório Git de vocês (dentro de uma pasta `Codigo`, por exemplo), e não dentro de um arquivo `.zip`.


Created multidev environment [i-health-test#ci-2](https://dashboard.pantheon.io/sites/49a8c118-5716-4ac1-8f07-ca8ee74dc8f7#ci-2).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-2-i-health-test.pantheonsite.io/)


@Semigradsky can you release it? I have no access.


TeamCity Architecture Team :: Java Platform :: otj-kafka :: BuildTest [Build 218](https://teamcity.otenv.com/viewLog.html?buildId=9424099&buildTypeId=ArchitectureTeam_JavaPlatform_OtjKafka_BuildTest) is now running


TeamCity Architecture Team :: Java Platform :: otj-kafka :: BuildTest [Build 219](https://teamcity.otenv.com/viewLog.html?buildId=9424100&buildTypeId=ArchitectureTeam_JavaPlatform_OtjKafka_BuildTest) is now running


![](https://github.trello.services/images/mini-trello-icon.png) [Fix Push Notifications icon](https://trello.com/c/90aGnu0h/167-fix-push-notifications-icon)


add `set -eu`?


TeamCity Architecture Team :: Java Platform :: otj-kafka :: BuildTest [Build 219](https://teamcity.otenv.com/viewLog.html?buildId=9424100&buildTypeId=ArchitectureTeam_JavaPlatform_OtjKafka_BuildTest) outcome was **FAILURE**
Summary: Exit code 137 (new) Build time: 00:00:26


TeamCity Architecture Team :: Java Platform :: otj-kafka :: BuildTest [Build 218](https://teamcity.otenv.com/viewLog.html?buildId=9424099&buildTypeId=ArchitectureTeam_JavaPlatform_OtjKafka_BuildTest) outcome was **SUCCESS**
Summary: Tests passed: 9 Build time: 00:00:56


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

What does this mean? I made a UI for the plugin because FormAPI and the one
offered by PocketMine don't always work and I have never been able to get
them to work on any of my 10+ servers all running different plugins and
versions of PocketMine and "Custom UI?"

On Tue, Sep 25, 2018 at 12:49 PM SOFe <notifications@github.com> wrote:

> Dear @AlexPads <https://github.com/AlexPads>:
> I regret to inform you that the release you submitted, named "*ShopUI*"
> (v1.0.2), for the project SimpleShopGUI
> <https://poggit.pmmp.io/ci/AlexPads/TinyPixelShopGUI/SimpleShopGUI> on
> 2018-09-25T00:37:32.000Z, has been rejected.
>
> From API 3.2.0 onward, plugins must use the form API offered by PocketMine
> to use custom UI.
>
> Please resolve the issues listed above and submit the updated plugin again.
> Note: This comment is created here because this is the last commit when
> the released build was created.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/AlexPads/TinyPixelShopGUI/commit/8f8fbe3c32951002bf06da3e4047a76f8827c5ae#commitcomment-30641303>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AjtnuDixDctLwpAu_hdnWmOlbops7Hhwks5uel6VgaJpZM4W5CjX>
> .
>


откуда тут puts?
все puts должны быть в Interface


replacing `$tarsum` by using `$tarsum` is a big confusing. It would be better to have tarsum on the PATH to make the script self-contained