[R/default_params_doc.R:15:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' @param idparsopt The ids of the parameters that must be optimized. The ids are defined as follows:
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:95:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L95) *style:* **Lines should not be more than 80 characters.**
```r
#' @param cond Set 1 if you want to condition on stem or crown age and non-extinction of the phylogeny. Set 0 otherwise.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:98:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L98) *style:* **Lines should not be more than 80 characters.**
```r
#' @author Documentation by Giovanni Laudanno, use of this function by Richel J.C. Bilderbeek
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:103:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L103) *style:* **Variable or function name should be snake_case.**
```r
  A_abstol,
  ^~~~~~~~
```
[R/default_params_doc.R:104:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L104) *style:* **Variable or function name should be snake_case.**
```r
  A_reltol,
  ^~~~~~~~
```
[R/default_params_doc.R:117:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L117) *style:* **Variable or function name should be snake_case.**
```r
  interval.max,
  ^~~~~~~~~~~~
```
[R/default_params_doc.R:118:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L118) *style:* **Variable or function name should be snake_case.**
```r
  interval.min,
  ^~~~~~~~~~~~
```
[R/default_params_doc.R:133:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L133) *style:* **Variable or function name should be snake_case.**
```r
  mbd.lambda,
  ^~~~~~~~~~
```
[R/default_params_doc.R:139:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L139) *style:* **Variable or function name should be snake_case.**
```r
  N,
  ^
```
[R/default_params_doc.R:140:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L140) *style:* **Variable or function name should be snake_case.**
```r
  N0,
  ^~
```
[R/default_params_doc.R:141:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L141) *style:* **Variable or function name should be snake_case.**
```r
  Nsteps,
  ^~~~~~
```
[R/default_params_doc.R:142:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L142) *style:* **Variable or function name should be snake_case.**
```r
  Nsubs,
  ^~~~~
```
[R/default_params_doc.R:145:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L145) *style:* **Variable or function name should be snake_case.**
```r
  pars.transform,
  ^~~~~~~~~~~~~~
```
[R/default_params_doc.R:149:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L149) *style:* **Variable or function name should be snake_case.**
```r
  Q,
  ^
```
[R/default_params_doc.R:169:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L169) *style:* **Variable or function name should be snake_case.**
```r
  x.name,
  ^~~~~~
```
[R/default_params_doc.R:170:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L170) *style:* **Variable or function name should be snake_case.**
```r
  x.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:172:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L172) *style:* **Variable or function name should be snake_case.**
```r
  y.name,
  ^~~~~~
```
[R/default_params_doc.R:173:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L173) *style:* **Variable or function name should be snake_case.**
```r
  y.splits,
  ^~~~~~~~
```
[R/default_params_doc.R:175:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/default_params_doc.R#L175) *style:* **Variable or function name should be snake_case.**
```r
  z.name,
  ^~~~~~
```
[R/simulate_alignments.R:5:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L5) *style:* **Variable or function name should be snake_case.**
```r
P_t1_t2 <- function(lambda, mu, t1, t2) {
^~~~~~~
```
[R/simulate_alignments.R:6:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Variable or function name should be snake_case.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
  ^~~~~~~
```
[R/simulate_alignments.R:6:21:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                   ~^~
```
[R/simulate_alignments.R:6:29:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                           ~^~
```
[R/simulate_alignments.R:6:30:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                             ^
```
[R/simulate_alignments.R:6:38:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                    ~^~
```
[R/simulate_alignments.R:6:54:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                                     ^
```
[R/simulate_alignments.R:6:68:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Put spaces around all infix operators.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                                                   ^~
```
[R/simulate_alignments.R:6:69:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                                                    ^
```
[R/simulate_alignments.R:6:79:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L6) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  P_t1_t2 <- (1 - mu/lambda)/(1 - (mu/lambda) * exp(-(lambda - mu) *(t2 - t1)) )
                                                                              ^
```
[R/simulate_alignments.R:14:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
BD.Nct <- function(lambda, mu, t, N0 = 2, age) {
^~~~~~
```
[R/simulate_alignments.R:14:35:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
BD.Nct <- function(lambda, mu, t, N0 = 2, age) {
                                  ^~
```
[R/simulate_alignments.R:16:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
  #Nct <- N0 * Lt/(1 - ((mu * (Lt - 1))/(Lt * lambda - mu))^N0) #old version from etienne 2008
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:16:4:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L16) *style:* **Commented code should be removed.**
```r
  #Nct <- N0 * Lt/(1 - ((mu * (Lt - 1))/(Lt * lambda - mu))^N0) #old version from etienne 2008
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:18:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L18) *style:* **Variable or function name should be snake_case.**
```r
  TT  <- abs(age)
  ^~
```
[R/simulate_alignments.R:19:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  Lt  <- exp((lambda - mu) * tt)
  ^~
```
[R/simulate_alignments.R:20:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  Nct <- N0 * Lt * P_t1_t2(lambda = lambda, mu = mu, t1 = tt, t2 = TT) *
  ^~~
```
[R/simulate_alignments.R:21:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
    (P_t1_t2(lambda = lambda, mu = mu, t1 = 0, t2 = TT))^-1#new version from etienne & rosindell 2012, formula #15
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:30:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
BD.Nmutations <- function(lambda, mu, age, N0 = 2, sequence_length = 1000, mutation_rate = 1/age) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:30:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L30) *style:* **Variable or function name should be snake_case.**
```r
BD.Nmutations <- function(lambda, mu, age, N0 = 2, sequence_length = 1000, mutation_rate = 1/age) {
^~~~~~~~~~~~~
```
[R/simulate_alignments.R:30:44:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L30) *style:* **Variable or function name should be snake_case.**
```r
BD.Nmutations <- function(lambda, mu, age, N0 = 2, sequence_length = 1000, mutation_rate = 1/age) {
                                           ^~
```
[R/simulate_alignments.R:30:93:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L30) *style:* **Put spaces around all infix operators.**
```r
BD.Nmutations <- function(lambda, mu, age, N0 = 2, sequence_length = 1000, mutation_rate = 1/age) {
                                                                                ~^~
```
[R/simulate_alignments.R:33:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
  ft  <- function(t) {mbd::BD.Nct(t, lambda = lambda, mu = mu, N0 = N0, age = age)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:33:22:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L33) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  ft  <- function(t) {mbd::BD.Nct(t, lambda = lambda, mu = mu, N0 = N0, age = age)}
                     ^
```
[R/simulate_alignments.R:33:83:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L33) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  ft  <- function(t) {mbd::BD.Nct(t, lambda = lambda, mu = mu, N0 = N0, age = age)}
                                                                                ^
```
[R/simulate_alignments.R:34:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L34) *style:* **Lines should not be more than 80 characters.**
```r
  Nmutations <- mutation_rate * sequence_length * stats::integrate(f = ft, lower = 0, upper = age)[[1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:34:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  Nmutations <- mutation_rate * sequence_length * stats::integrate(f = ft, lower = 0, upper = age)[[1]]
  ^~~~~~~~~~
```
[R/simulate_alignments.R:42:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L42) *style:* **Variable or function name should be snake_case.**
```r
BD.infer.lambda.from.mutations <- function(Nsubs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:42:44:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L42) *style:* **Variable or function name should be snake_case.**
```r
BD.infer.lambda.from.mutations <- function(Nsubs,
                                           ^~~~~
```
[R/simulate_alignments.R:43:44:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L43) *style:* **Variable or function name should be snake_case.**
```r
                                           mbd.lambda,
                                           ^~~~~~~~~~
```
[R/simulate_alignments.R:46:44:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L46) *style:* **Variable or function name should be snake_case.**
```r
                                           N0 = 2,
                                           ^~
```
[R/simulate_alignments.R:48:61:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L48) *style:* **Put spaces around all infix operators.**
```r
                                           mutation_rate = 1/age,
                                                           ~^~
```
[R/simulate_alignments.R:49:44:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L49) *style:* **Variable or function name should be snake_case.**
```r
                                           Nsteps = 40) {
                                           ^~~~~~
```
[R/simulate_alignments.R:50:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
  lavec <- seq((min.lambda <- 0.5 * mbd.lambda), (max.lambda <- 6 * mbd.lambda), by = abs(max.lambda - min.lambda)/(Nsteps))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:50:17:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L50) *style:* **Variable or function name should be snake_case.**
```r
  lavec <- seq((min.lambda <- 0.5 * mbd.lambda), (max.lambda <- 6 * mbd.lambda), by = abs(max.lambda - min.lambda)/(Nsteps))
                ^~~~~~~~~~
```
[R/simulate_alignments.R:50:51:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L50) *style:* **Variable or function name should be snake_case.**
```r
  lavec <- seq((min.lambda <- 0.5 * mbd.lambda), (max.lambda <- 6 * mbd.lambda), by = abs(max.lambda - min.lambda)/(Nsteps))
                                                  ^~~~~~~~~~
```
[R/simulate_alignments.R:50:115:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L50) *style:* **Put spaces around all infix operators.**
```r
  lavec <- seq((min.lambda <- 0.5 * mbd.lambda), (max.lambda <- 6 * mbd.lambda), by = abs(max.lambda - min.lambda)/(Nsteps))
                                                                                ~^~
```
[R/simulate_alignments.R:50:116:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L50) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  lavec <- seq((min.lambda <- 0.5 * mbd.lambda), (max.lambda <- 6 * mbd.lambda), by = abs(max.lambda - min.lambda)/(Nsteps))
                                                                                ^
```
[R/simulate_alignments.R:51:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L51) *style:* **Variable or function name should be snake_case.**
```r
  NN <- rep(NA, length(lavec))
  ^~
```
[R/simulate_alignments.R:53:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L53) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/simulate_alignments.R:55:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L55) *style:* **Lines should not be more than 80 characters.**
```r
                           N0 = N0, sequence_length = sequence_length, mutation_rate = mutation_rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:58:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L58) *style:* **Variable or function name should be snake_case.**
```r
  fit.test <- stats::nls(
  ^~~~~~~~
```
[R/simulate_alignments.R:59:11:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L59) *style:* **Put spaces around all infix operators.**
```r
    NN ~ b*exp(m*lavec),
         ~^~
```
[R/simulate_alignments.R:59:17:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L59) *style:* **Put spaces around all infix operators.**
```r
    NN ~ b*exp(m*lavec),
               ~^~
```
[R/simulate_alignments.R:65:5:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L65) *style:* **Commented code should be removed.**
```r
  # graphics::plot(lavec, predict(fit.test), type = "l"); points(lavec, NN)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:66:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
  # graphics::plot(stats::coef(fit.test)[2] * exp(stats::coef(fit.test)[1] * lavec) ~ lavec , type = "l"); points(lavec, NN)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:66:5:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L66) *style:* **Commented code should be removed.**
```r
  # graphics::plot(stats::coef(fit.test)[2] * exp(stats::coef(fit.test)[1] * lavec) ~ lavec , type = "l"); points(lavec, NN)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:67:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L67) *style:* **Lines should not be more than 80 characters.**
```r
  best.lambda <- (log(Nsubs) - log(stats::coef(fit.test)[2]))/stats::coef(fit.test)[1]; #best.lambda
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:67:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L67) *style:* **Variable or function name should be snake_case.**
```r
  best.lambda <- (log(Nsubs) - log(stats::coef(fit.test)[2]))/stats::coef(fit.test)[1]; #best.lambda
  ^~~~~~~~~~~
```
[R/simulate_alignments.R:67:62:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L67) *style:* **Put spaces around all infix operators.**
```r
  best.lambda <- (log(Nsubs) - log(stats::coef(fit.test)[2]))/stats::coef(fit.test)[1]; #best.lambda
                                                            ~^~
```
[R/simulate_alignments.R:80:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L80) *style:* **Lines should not be more than 80 characters.**
```r
                                         mutation_rate = 1/max(abs(ape::branching.times(sim_phylo)))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:80:59:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L80) *style:* **Put spaces around all infix operators.**
```r
                                         mutation_rate = 1/max(abs(ape::branching.times(sim_phylo)))) {
                                                         ~^~
```
[R/simulate_alignments.R:85:25:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L85) *style:* **Put spaces around all infix operators.**
```r
  quality_ratio <- esses/(chain_length/sample_interval)
                       ~^~
```
[R/simulate_alignments.R:85:26:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L85) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  quality_ratio <- esses/(chain_length/sample_interval)
                         ^
```
[R/simulate_alignments.R:85:39:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L85) *style:* **Put spaces around all infix operators.**
```r
  quality_ratio <- esses/(chain_length/sample_interval)
                                     ~^~
```
[R/simulate_alignments.R:88:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L88) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/simulate_alignments.R:90:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L90) *style:* **Lines should not be more than 80 characters.**
```r
    pirouette.out <- pirouette::pir_run( #test1 is a posterior of 10001 trees generated from sim_tes[[1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:90:5:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L90) *style:* **Variable or function name should be snake_case.**
```r
    pirouette.out <- pirouette::pir_run( #test1 is a posterior of 10001 trees generated from sim_tes[[1]]
    ^~~~~~~~~~~~~
```
[R/simulate_alignments.R:90:41:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L90) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    pirouette.out <- pirouette::pir_run( #test1 is a posterior of 10001 trees generated from sim_tes[[1]]
                                        ^
```
[R/simulate_alignments.R:94:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L94) *style:* **Lines should not be more than 80 characters.**
```r
      mcmc = beautier::create_mcmc(chain_length = chain_length, store_every = sample_interval), #store_every = -1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:94:98:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L94) *style:* **Commented code should be removed.**
```r
      mcmc = beautier::create_mcmc(chain_length = chain_length, store_every = sample_interval), #store_every = -1
                                                                                ^~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:98:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L98) *style:* **Lines should not be more than 80 characters.**
```r
      mrca_distr = beautier::create_normal_distr(mean = beautier::create_mean_param(value = age), sigma = beautier::create_sigma_param(value = 0.001)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:106:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L106) *style:* **Lines should not be more than 80 characters.**
```r
    esses2 <- tracerer::calc_esses(pirouette.out$estimates, sample_interval = sample_interval) #effective sample size: has to be at least 200, try not to be over 1000 otherwise you're overkilling (try to stick to 1/5 rule of thumb)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:108:27:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L108) *style:* **Put spaces around all infix operators.**
```r
    quality_ratio <- esses/(nrow(pirouette.out$estimates))
                         ~^~
```
[R/simulate_alignments.R:108:28:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L108) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    quality_ratio <- esses/(nrow(pirouette.out$estimates))
                           ^
```
[R/simulate_alignments.R:110:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L110) *style:* **Lines should not be more than 80 characters.**
```r
    #this will apply at the next while run if you don't fulfill the quality condition
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:115:41:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L115) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if (repetitions >= max_repetitions) {break}
                                        ^
```
[R/simulate_alignments.R:115:47:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L115) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if (repetitions >= max_repetitions) {break}
                                              ^
```
[R/simulate_alignments.R:119:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L119) *style:* **Variable or function name should be snake_case.**
```r
  nLTT.diff <- rep(NA, length(pirouette.out$trees))
  ^~~~~~~~~
```
[R/simulate_alignments.R:121:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L121) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/simulate_alignments.R:124:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L124) *style:* **Variable or function name should be snake_case.**
```r
  mean.nLTT <- mean(nLTT.diff); mean.nLTT
  ^~~~~~~~~
```
[R/simulate_alignments.R:125:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L125) *style:* **Variable or function name should be snake_case.**
```r
  std.nLTT  <- sqrt(stats::var(nLTT.diff)); std.nLTT
  ^~~~~~~~
```
[R/simulate_alignments.R:147:20:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L147) *style:* **Put spaces around all infix operators.**
```r
  mutation_rate = 1/age
                  ~^~
```
[R/simulate_alignments.R:156:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L156) *style:* **Lines should not be more than 80 characters.**
```r
  dir_name <- paste0(dirname(getwd()),"//results//nLTT//"); suppressWarnings(dir.create(dir_name))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:156:39:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L156) *style:* **Commas should always have a space after.**
```r
  dir_name <- paste0(dirname(getwd()),"//results//nLTT//"); suppressWarnings(dir.create(dir_name))
                                      ^
```
[R/simulate_alignments.R:160:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L160) *style:* **Lines should not be more than 80 characters.**
```r
  j <- 1; while ((file_name <- paste0("nLTT", j)) %in% list.files(folder_name)) {j <- j + 1}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:160:81:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L160) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  j <- 1; while ((file_name <- paste0("nLTT", j)) %in% list.files(folder_name)) {j <- j + 1}
                                                                                ^
```
[R/simulate_alignments.R:160:92:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L160) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
  j <- 1; while ((file_name <- paste0("nLTT", j)) %in% list.files(folder_name)) {j <- j + 1}
                                                                                ^
```
[R/simulate_alignments.R:163:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
  mbd.estimates   <- mbd.trees <- mbd.alignment <- mbd.nLTT <- vector("list", max_sims)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:163:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L163) *style:* **Variable or function name should be snake_case.**
```r
  mbd.estimates   <- mbd.trees <- mbd.alignment <- mbd.nLTT <- vector("list", max_sims)
  ^~~~~~~~~~~~~
```
[R/simulate_alignments.R:163:22:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L163) *style:* **Variable or function name should be snake_case.**
```r
  mbd.estimates   <- mbd.trees <- mbd.alignment <- mbd.nLTT <- vector("list", max_sims)
                     ^~~~~~~~~
```
[R/simulate_alignments.R:163:35:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L163) *style:* **Variable or function name should be snake_case.**
```r
  mbd.estimates   <- mbd.trees <- mbd.alignment <- mbd.nLTT <- vector("list", max_sims)
                                  ^~~~~~~~~~~~~
```
[R/simulate_alignments.R:163:52:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L163) *style:* **Variable or function name should be snake_case.**
```r
  mbd.estimates   <- mbd.trees <- mbd.alignment <- mbd.nLTT <- vector("list", max_sims)
                                                   ^~~~~~~~
```
[R/simulate_alignments.R:164:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L164) *style:* **Lines should not be more than 80 characters.**
```r
  BD.simulations  <- BD.estimates  <- BD.trees  <- BD.alignment  <- BD.nLTT  <- vector("list", max_sims)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:164:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L164) *style:* **Variable or function name should be snake_case.**
```r
  BD.simulations  <- BD.estimates  <- BD.trees  <- BD.alignment  <- BD.nLTT  <- vector("list", max_sims)
  ^~~~~~~~~~~~~~
```
[R/simulate_alignments.R:164:22:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L164) *style:* **Variable or function name should be snake_case.**
```r
  BD.simulations  <- BD.estimates  <- BD.trees  <- BD.alignment  <- BD.nLTT  <- vector("list", max_sims)
                     ^~~~~~~~~~~~
```
[R/simulate_alignments.R:164:39:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L164) *style:* **Variable or function name should be snake_case.**
```r
  BD.simulations  <- BD.estimates  <- BD.trees  <- BD.alignment  <- BD.nLTT  <- vector("list", max_sims)
                                      ^~~~~~~~
```
[R/simulate_alignments.R:164:52:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L164) *style:* **Variable or function name should be snake_case.**
```r
  BD.simulations  <- BD.estimates  <- BD.trees  <- BD.alignment  <- BD.nLTT  <- vector("list", max_sims)
                                                   ^~~~~~~~~~~~
```
[R/simulate_alignments.R:164:69:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L164) *style:* **Variable or function name should be snake_case.**
```r
  BD.simulations  <- BD.estimates  <- BD.trees  <- BD.alignment  <- BD.nLTT  <- vector("list", max_sims)
                                                                    ^~~~~~~
```
[R/simulate_alignments.R:165:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L165) *style:* **Variable or function name should be snake_case.**
```r
  Nsubstitutions  <- rep(NA, (max_sims2 <- 100 * max_sims))
  ^~~~~~~~~~~~~~
```
[R/simulate_alignments.R:165:31:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L165) *warning:* **local variable ‘max_sims2’ assigned but may not be used**
```r
  Nsubstitutions  <- rep(NA, (max_sims2 <- 100 * max_sims))
                              ^~~~~~~~~
```
[R/simulate_alignments.R:167:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L167) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/simulate_alignments.R:168:5:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L168) *style:* **Variable or function name should be snake_case.**
```r
    mbd.simulation <- mbd::mbd_sim(pars = sim_pars,
    ^~~~~~~~~~~~~~
```
[R/simulate_alignments.R:178:5:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L178) *style:* **Variable or function name should be snake_case.**
```r
    mbd.out <- alignments_comparison_single(sim_phylo = mbd.simulation$tes,
    ^~~~~~~
```
[R/simulate_alignments.R:191:5:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L191) *style:* **Variable or function name should be snake_case.**
```r
    BD.lambda <- BD.infer.lambda.from.mutations(Nsubs = Nsubstitutions[s],
    ^~~~~~~~~
```
[R/simulate_alignments.R:196:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L196) *style:* **Lines should not be more than 80 characters.**
```r
                                                sequence_length = sequence_length,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:208:5:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L208) *style:* **Variable or function name should be snake_case.**
```r
    BD.out <- alignments_comparison_single(sim_phylo = BD.simulations[[s]]$tes,
    ^~~~~~
```
[R/simulate_alignments.R:220:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L220) *style:* **Variable or function name should be snake_case.**
```r
  mbd.nLTT.total <- unname(unlist(mbd.nLTT))
  ^~~~~~~~~~~~~~
```
[R/simulate_alignments.R:221:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L221) *style:* **Variable or function name should be snake_case.**
```r
  BD.nLTT.total  <- unname(unlist(BD.nLTT))
  ^~~~~~~~~~~~~
```
[R/simulate_alignments.R:225:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L225) *style:* **Variable or function name should be snake_case.**
```r
  mbd.mean <- mean(df.mbd.nLTT$mbd.nLTT)
  ^~~~~~~~
```
[R/simulate_alignments.R:226:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L226) *style:* **Variable or function name should be snake_case.**
```r
  mbd.std  <- sqrt(stats::var(df.mbd.nLTT$mbd.nLTT))
  ^~~~~~~
```
[R/simulate_alignments.R:227:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L227) *style:* **Variable or function name should be snake_case.**
```r
  BD.mean  <- mean(df.BD.nLTT$BD.nLTT)
  ^~~~~~~
```
[R/simulate_alignments.R:228:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L228) *style:* **Variable or function name should be snake_case.**
```r
  BD.std   <- sqrt(stats::var(df.BD.nLTT$BD.nLTT))
  ^~~~~~
```
[R/simulate_alignments.R:231:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L231) *style:* **Variable or function name should be snake_case.**
```r
  mbd.nLTT.plot <- ggplot2::ggplot(df.mbd.nLTT, ggplot2::aes(x = mbd.nLTT)) +
  ^~~~~~~~~~~~~
```
[R/simulate_alignments.R:232:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L232) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_histogram(ggplot2::aes(y = ..count..), colour = "darkblue", fill = "lightblue", bins = 40) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:233:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L233) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_vline(ggplot2::aes(xintercept = mean(mbd.nLTT)), color = "red", linetype = "dashed", size = 1) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:234:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L234) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::ggtitle(paste0("nLTT statistics for a mbd tree compared \nwith tree posterior generated from alignments and BD prior \nmean = ", signif(mbd.mean, digits = 2), ", std = ", signif(mbd.std, digits = 2))) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:238:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L238) *style:* **Variable or function name should be snake_case.**
```r
  BD.nLTT.plot <- ggplot2::ggplot(df.BD.nLTT, ggplot2::aes(x = BD.nLTT)) +
  ^~~~~~~~~~~~
```
[R/simulate_alignments.R:239:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L239) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_histogram(ggplot2::aes(y = ..count..), colour = "darkblue", fill = "lightblue", bins = 40) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:240:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L240) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::geom_vline(ggplot2::aes(xintercept = mean(BD.nLTT)), color = "red", linetype = "dashed", size = 1) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:241:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L241) *style:* **Lines should not be more than 80 characters.**
```r
    ggplot2::ggtitle(paste0("nLTT statistics for a BD tree compared \nwith tree posterior generated from alignments and BD prior \nmean = ", signif(BD.mean, digits = 2), ", std = ", signif(BD.std, digits = 2))) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:254:34:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L254) *style:* **Commas should always have a space after.**
```r
       file = paste0(folder_name,"//" ,file_name))
                                 ^
```
[R/simulate_alignments.R:254:39:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L254) *style:* **Commas should never have a space before.**
```r
       file = paste0(folder_name,"//" ,file_name))
                                     ~^
```
[R/simulate_alignments.R:254:40:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L254) *style:* **Commas should always have a space after.**
```r
       file = paste0(folder_name,"//" ,file_name))
                                       ^
```
[R/simulate_alignments.R:256:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L256) *style:* **Lines should not be more than 80 characters.**
```r
  grDevices::png(filename = paste0(folder_name, "//" ,file_name, "_mbd_plot.png"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:256:54:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L256) *style:* **Commas should never have a space before.**
```r
  grDevices::png(filename = paste0(folder_name, "//" ,file_name, "_mbd_plot.png"))
                                                    ~^
```
[R/simulate_alignments.R:256:55:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L256) *style:* **Commas should always have a space after.**
```r
  grDevices::png(filename = paste0(folder_name, "//" ,file_name, "_mbd_plot.png"))
                                                      ^
```
[R/simulate_alignments.R:260:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L260) *style:* **Lines should not be more than 80 characters.**
```r
  grDevices::png(filename = paste0(folder_name, "//" ,file_name, "_BD_plot.png"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:260:54:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L260) *style:* **Commas should never have a space before.**
```r
  grDevices::png(filename = paste0(folder_name, "//" ,file_name, "_BD_plot.png"))
                                                    ~^
```
[R/simulate_alignments.R:260:55:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L260) *style:* **Commas should always have a space after.**
```r
  grDevices::png(filename = paste0(folder_name, "//" ,file_name, "_BD_plot.png"))
                                                      ^
```
[R/simulate_alignments.R:268:1:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L268) *style:* **Lines should not be more than 80 characters.**
```r
#test <- mbd::alignments_comparison_multiple(sim_pars = (sim_pars <- c(0.2, 0.15, 2, 0.15)), max_sims = 100)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:268:2:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L268) *style:* **Commented code should be removed.**
```r
#test <- mbd::alignments_comparison_multiple(sim_pars = (sim_pars <- c(0.2, 0.15, 2, 0.15)), max_sims = 100)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:271:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L271) *style:* **Commented code should be removed.**
```r
# devtools::install_github("richelbilderbeek/tracerer", dependencies = TRUE)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:272:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L272) *style:* **Commented code should be removed.**
```r
# devtools::install_github("richelbilderbeek/beastier", dependencies = TRUE)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:273:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L273) *style:* **Commented code should be removed.**
```r
# devtools::install_github("richelbilderbeek/babette", dependencies = TRUE)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:274:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L274) *style:* **Commented code should be removed.**
```r
# devtools::install_github("richelbilderbeek/pirouette", dependencies = TRUE)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:275:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L275) *style:* **Commented code should be removed.**
```r
# devtools::install_github("richelbilderbeek/ribir", dependencies = TRUE)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:276:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L276) *style:* **Commented code should be removed.**
```r
# install.packages('xmlparsedata')
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:277:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L277) *style:* **Commented code should be removed.**
```r
# install.packages('lintr')
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:278:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L278) *style:* **Commented code should be removed.**
```r
# devtools::install_github("richelbilderbeek/raket", dependencies = TRUE)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:279:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L279) *style:* **Commented code should be removed.**
```r
# install.packages("nLTT")
  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/simulate_alignments.R:280:3:](https://github.com/richelbilderbeek/razzo/blob/6e2e1d246d7a9309987fa21a8200bca0356c26fb/R/simulate_alignments.R#L280) *style:* **Commented code should be removed.**
```r
# library("ape"); library("raket"); library("nLTT")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


yippie!


в таких случаях удобно использовать всегда связку размер шрифта + высота строки
и называть их как-нибудь
main-heading для заголовков
sub-heading для подзаголовков
text для основного текста на странице


явный возврат "нил" - это лишнее здесь
достаточно найти объект, а если он найден не будет, то метод и так вернет "нил"
```ruby
@route.stations[@current_station - 1] if @current_station > 0
```
такой вариант будет работать точно как твой
если индекс не больше ноля, то вернется "нил"
если больше ноля. то вернется объект
что нам и нужно


относись к этому как к класса
ты бы в хтмл не стал делать класс только для высоты строки


belle correction


@tbickford If webpack does include global after main, yes we should follow that order. Can you PR this ?


are you counting on some sort of polymorphism without virtual functions through the use of `this->` ?


@sweir27 Just came across this; if I understand this code correctly then this feels like it’s prone to race conditions, in that it changes a singleton at the start of a request, while Node may be processing multiple concurrent requests.

Additionally, I wonder if this is creating a huge stack as time progresses, as it appears that on each request the previously wrapped monkey-patch is wrapped again. Is that correct?


FWIW, this shouldn't be necessary when [this PR](https://github.com/civicrm/civicrm-wordpress/pull/134) is merged. The code in the PR's description should provide you with the means to implement the GDPR shortcode without modifying the CiviCRM WordPRess plugin itself.


тут неправильный подход
#0f1521 это @darkblue
а вот уже @color__bg: @darkblue
потому что если нужно будет поменять цвет, то он поменяется конкретно у этого фона


better call it `dumpDebug` if you're doing to dump loaders and writers


ну и дальше у тебя та же проблема
заводи переменные с цветами
и переиспользуй их в смысловых переменных


This looks like a workaround but as a regex, $ and / normally need escaped. The worry is that ths regex isnt strict enough. I would prefer it to be along the lines of /^vr_name\/route$/

so that a `foobar/wibble` doesnt get confused with a `bar/wibble`.