[R/default_param_doc.R:120:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L120) *style:* **Variable or function name should be snake_case.**
```r
  L,
  ^
```
[R/default_param_doc.R:143:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L143) *style:* **Variable or function name should be snake_case.**
```r
  D0,
  ^~
```
[R/default_param_doc.R:144:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L144) *style:* **Variable or function name should be snake_case.**
```r
  D_0,
  ^~~
```
[R/default_param_doc.R:145:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L145) *style:* **Variable or function name should be snake_case.**
```r
  D0s,
  ^~~
```
[R/default_param_doc.R:146:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L146) *style:* **Variable or function name should be snake_case.**
```r
  D_0s,
  ^~~~
```
[R/default_param_doc.R:147:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L147) *style:* **Variable or function name should be snake_case.**
```r
  E0,
  ^~
```
[R/default_param_doc.R:148:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L148) *style:* **Variable or function name should be snake_case.**
```r
  E_0,
  ^~~
```
[R/default_param_doc.R:157:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/default_param_doc.R#L157) *style:* **Variable or function name should be snake_case.**
```r
  LOG,
  ^~~
```
[R/sls_conditionings.R:24:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_conditionings.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  A <- abs(t_d - t_c); B <- abs(t_p - t_d)
  ^
```
[R/sls_conditionings.R:24:24:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_conditionings.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  A <- abs(t_d - t_c); B <- abs(t_p - t_d)
                       ^
```
[R/sls_conditionings.R:30:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_conditionings.R#L30) *style:* **Variable or function name should be snake_case.**
```r
  PS   <- 1 - sls::pn(
  ^~
```
[R/sls_conditionings.R:50:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_conditionings.R#L50) *style:* **Variable or function name should be snake_case.**
```r
  P1   <- sum(aux1) #branch 2 survives till the present
  ^~
```
[R/sls_conditionings.R:52:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_conditionings.R#L52) *style:* **Variable or function name should be snake_case.**
```r
  P2   <- sum(aux2) #both branches 1 and 2 survive till the present
  ^~
```
[R/sls_convolutions.R:7:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L7) *style:* **Variable or function name should be snake_case.**
```r
phase.factor <- function(n_max, n, k) {
^~~~~~~~~~~~
```
[R/sls_convolutions.R:17:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L17) *style:* **Variable or function name should be snake_case.**
```r
DFT <- function(vec) {
^~~
```
[R/sls_convolutions.R:24:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  O <- outer(
  ^
```
[R/sls_convolutions.R:38:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L38) *style:* **Variable or function name should be snake_case.**
```r
IDFT <- function(vec) {
^~~~
```
[R/sls_convolutions.R:45:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  O <- outer(
  ^
```
[R/sls_convolutions.R:68:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L68) *style:* **Variable or function name should be snake_case.**
```r
  N <- length(times)
  ^
```
[R/sls_convolutions.R:69:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L69) *style:* **Variable or function name should be snake_case.**
```r
  X <- vector("list", N)
  ^
```
[R/sls_convolutions.R:97:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L97) *style:* **Variable or function name should be snake_case.**
```r
  N  <- length(times)
  ^
```
[R/sls_convolutions.R:105:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L105) *style:* **Variable or function name should be snake_case.**
```r
  LAMBDAS <- matrix(ls, nrow = dim(ns)[1], ncol = dim(ns)[2], byrow = T)
  ^~~~~~~
```
[R/sls_convolutions.R:107:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L107) *style:* **Variable or function name should be snake_case.**
```r
  MUS     <- matrix(ms, nrow = dim(ns)[1], ncol = dim(ns)[2], byrow = T)
  ^~~
```
[R/sls_convolutions.R:109:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L109) *style:* **Variable or function name should be snake_case.**
```r
  TIMES   <- matrix(times, nrow = dim(ns)[1], ncol = dim(ns)[2], byrow = T)
  ^~~~~
```
[R/sls_convolutions.R:140:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L140) *style:* **Variable or function name should be snake_case.**
```r
  N <- length(times)
  ^
```
[R/sls_convolutions.R:141:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_convolutions.R#L141) *style:* **Variable or function name should be snake_case.**
```r
  X <- vector("list", N)
  ^
```
[R/sls_likelihoods_bisse.R:12:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L12) *style:* **Variable or function name should be snake_case.**
```r
Dt <- function(pars, t_0, t_f, E_0, D_0) {
^~
```
[R/sls_likelihoods_bisse.R:12:32:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L12) *style:* **Variable or function name should be snake_case.**
```r
Dt <- function(pars, t_0, t_f, E_0, D_0) {
                               ^~~
```
[R/sls_likelihoods_bisse.R:12:37:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L12) *style:* **Variable or function name should be snake_case.**
```r
Dt <- function(pars, t_0, t_f, E_0, D_0) {
                                    ^~~
```
[R/sls_likelihoods_bisse.R:15:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L15) *style:* **Variable or function name should be snake_case.**
```r
  TT <- t_f - t_0
  ^~
```
[R/sls_likelihoods_bisse.R:16:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L16) *style:* **Variable or function name should be snake_case.**
```r
  LL <- exp(
  ^~
```
[R/sls_likelihoods_bisse.R:19:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  FF <- lambda * (1 - E_0) - LL * (mu - E_0 * lambda)
  ^~
```
[R/sls_likelihoods_bisse.R:20:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  DD <- (LL * D_0 * (lambda - mu) ^ 2) / FF ^ 2
  ^~
```
[R/sls_likelihoods_bisse.R:35:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L35) *style:* **Variable or function name should be snake_case.**
```r
Et <- function(pars, t_0, t_f, E_0, D_0) {
^~
```
[R/sls_likelihoods_bisse.R:35:32:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L35) *style:* **Variable or function name should be snake_case.**
```r
Et <- function(pars, t_0, t_f, E_0, D_0) {
                               ^~~
```
[R/sls_likelihoods_bisse.R:35:37:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L35) *style:* **Variable or function name should be snake_case.**
```r
Et <- function(pars, t_0, t_f, E_0, D_0) {
                                    ^~~
```
[R/sls_likelihoods_bisse.R:38:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L38) *style:* **Variable or function name should be snake_case.**
```r
  TT <- t_f - t_0
  ^~
```
[R/sls_likelihoods_bisse.R:39:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L39) *style:* **Variable or function name should be snake_case.**
```r
  LL <- exp(
  ^~
```
[R/sls_likelihoods_bisse.R:42:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L42) *style:* **Variable or function name should be snake_case.**
```r
  FF <- lambda * (1 - E_0) - LL * (mu - E_0 * lambda)
  ^~
```
[R/sls_likelihoods_bisse.R:43:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L43) *style:* **Variable or function name should be snake_case.**
```r
  EE <- 1 - (1 - E_0) * (lambda - mu) / FF
  ^~
```
[R/sls_likelihoods_bisse.R:63:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L63) *style:* **Variable or function name should be snake_case.**
```r
  D_0s = NULL,
  ^~~~
```
[R/sls_likelihoods_bisse.R:74:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L74) *style:* **Variable or function name should be snake_case.**
```r
  BRTS <- sort(c(brts, t_p, t_ds), decreasing = TRUE)
  ^~~~
```
[R/sls_likelihoods_bisse.R:80:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L80) *style:* **Variable or function name should be snake_case.**
```r
      D_0 <- rep(1, tips)
      ^~~
```
[R/sls_likelihoods_bisse.R:81:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L81) *style:* **Variable or function name should be snake_case.**
```r
      E_0 <- 0
      ^~~
```
[R/sls_likelihoods_bisse.R:83:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L83) *style:* **Variable or function name should be snake_case.**
```r
      D_0 <- DD
      ^~~
```
[R/sls_likelihoods_bisse.R:84:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L84) *style:* **Variable or function name should be snake_case.**
```r
      E_0 <- EE
      ^~~
```
[R/sls_likelihoods_bisse.R:88:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L88) *style:* **Variable or function name should be snake_case.**
```r
    DD   <- rep(NA, l_d)
    ^~
```
[R/sls_likelihoods_bisse.R:93:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L93) *style:* **Variable or function name should be snake_case.**
```r
    EE    <- Et(pars = pars, t_0 = t_0, t_f = t_f, E_0 = E_0, D_0 = D_0)
    ^~
```
[R/sls_likelihoods_bisse.R:98:9:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L98) *style:* **Variable or function name should be snake_case.**
```r
        DS0 <- D_0s
        ^~~
```
[R/sls_likelihoods_bisse.R:100:9:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L100) *style:* **Variable or function name should be snake_case.**
```r
        DS0 <- D_0s[which[t_ds == t_f]]
        ^~~
```
[R/sls_likelihoods_bisse.R:102:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L102) *style:* **Variable or function name should be snake_case.**
```r
      DD <- c(DD, DS0)
      ^~
```
[R/sls_likelihoods_bisse.R:105:9:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L105) *style:* **Variable or function name should be snake_case.**
```r
        DD <- c(
        ^~
```
[R/sls_likelihoods_bisse.R:113:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L113) *style:* **Variable or function name should be snake_case.**
```r
  DDf <- prod(DD)
  ^~~
```
[R/sls_likelihoods_bisse.R:128:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L128) *style:* **Variable or function name should be snake_case.**
```r
  E_0 = 0,
  ^~~
```
[R/sls_likelihoods_bisse.R:129:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L129) *style:* **Variable or function name should be snake_case.**
```r
  D_0 = 1,
  ^~~
```
[R/sls_likelihoods_bisse.R:130:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L130) *style:* **Variable or function name should be snake_case.**
```r
  LOG = TRUE,
  ^~~
```
[R/sls_likelihoods_bisse.R:134:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L134) *style:* **Variable or function name should be snake_case.**
```r
  BRTS <- c(rep(brts[1], n_0 - 1), brts)
  ^~~~
```
[R/sls_likelihoods_bisse.R:135:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L135) *style:* **Variable or function name should be snake_case.**
```r
  DD <- prod(Dt(pars = pars, t_f = BRTS, t_0 = t_0, E_0 = E_0, D_0 = D_0))
  ^~
```
[R/sls_likelihoods_bisse.R:136:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_bisse.R#L136) *style:* **Variable or function name should be snake_case.**
```r
  DD <- DD * lambda ^ (length(brts[-1]) * lambdaterms)
  ^~
```
[R/sls_likelihoods_div.R:7:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L7) *style:* **Variable or function name should be snake_case.**
```r
loglik_slsP <- function(
^~~~~~~~~~~
```
[R/sls_likelihoods_div.R:40:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L40) *style:* **Variable or function name should be snake_case.**
```r
  BRTSM <- rbind(
  ^~~~~
```
[R/sls_likelihoods_div.R:44:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L44) *style:* **Variable or function name should be snake_case.**
```r
  TD <- c(t_d, -1); dim(TD) <- c(2, 1)
  ^~
```
[R/sls_likelihoods_div.R:45:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  EVENTSM <- (M <- cbind(BRTSM, TD))[, order(-M[1, ])]
  ^~~~~~~
```
[R/sls_likelihoods_div.R:45:15:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  EVENTSM <- (M <- cbind(BRTSM, TD))[, order(-M[1, ])]
              ^
```
[R/sls_likelihoods_div.R:60:28:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L60) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (length(ts_m_pre_shift ) == 0) {
                           ^
```
[R/sls_likelihoods_div.R:104:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L104) *style:* **Variable or function name should be snake_case.**
```r
  Pc <- sls::pc_1shift(
  ^~
```
[R/sls_likelihoods_div.R:124:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L124) *style:* **Variable or function name should be snake_case.**
```r
loglik_slsQ <- function(
^~~~~~~~~~~
```
[R/sls_likelihoods_div.R:164:10:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L164) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  while ( (clade <- clade + 1) <= n_clades) {
         ^
```
[R/sls_likelihoods_div.R:168:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L168) *style:* **Variable or function name should be snake_case.**
```r
    K      <- ks[clade]
    ^
```
[R/sls_likelihoods_div.R:226:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L226) *style:* **Variable or function name should be snake_case.**
```r
    P  <- vm * q_t[t, (missnumspec[clade] + 1)]
    ^
```
[R/sls_likelihoods_div.R:239:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_div.R#L239) *style:* **Variable or function name should be snake_case.**
```r
  Pc <- sls::pc_1shift(
  ^~
```
[R/sls_likelihoods_nee.R:7:17:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nee.R#L7) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
pt  <- function (lambda, mu, t) {
                ^
```
[R/sls_likelihoods_nee.R:9:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nee.R#L9) *style:* **Variable or function name should be snake_case.**
```r
  Lambda <- exp(
  ^~~~~~
```
[R/sls_likelihoods_nee.R:26:17:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nee.R#L26) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
ut  <- function (lambda, mu, t) {
                ^
```
[R/sls_likelihoods_nee.R:28:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nee.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  Lambda <- exp(
  ^~~~~~
```
[R/sls_likelihoods_nodiv.R:7:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L7) *style:* **Variable or function name should be snake_case.**
```r
loglik_slsP_nodiv <- function(
^~~~~~~~~~~~~~~~~
```
[R/sls_likelihoods_nodiv.R:29:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L29) *style:* **Variable or function name should be snake_case.**
```r
  BRTSM <- rbind(
  ^~~~~
```
[R/sls_likelihoods_nodiv.R:33:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  TD <- c(t_d, -1); dim(TD) <- c(2, 1)
  ^~
```
[R/sls_likelihoods_nodiv.R:45:28:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (length(ts_m_pre_shift ) == 0) {
                           ^
```
[R/sls_likelihoods_nodiv.R:108:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L108) *style:* **Variable or function name should be snake_case.**
```r
loglik_slsQ_nodiv <- function(
^~~~~~~~~~~~~~~~~
```
[R/sls_likelihoods_nodiv.R:143:10:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L143) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  while ( (clade <- clade + 1) <= n_clades ) {
         ^
```
[R/sls_likelihoods_nodiv.R:143:43:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L143) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  while ( (clade <- clade + 1) <= n_clades ) {
                                          ^
```
[R/sls_likelihoods_nodiv.R:147:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L147) *style:* **Variable or function name should be snake_case.**
```r
    K      <- ks[clade]
    ^
```
[R/sls_likelihoods_nodiv.R:205:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L205) *style:* **Variable or function name should be snake_case.**
```r
    P  <- vm * q_t[t, (missnumspec[clade] + 1)]
    ^
```
[R/sls_likelihoods_nodiv.R:238:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L238) *style:* **Variable or function name should be snake_case.**
```r
loglik_DDD <- function(
^~~~~~~~~~
```
[R/sls_likelihoods_nodiv.R:339:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L339) *style:* **Variable or function name should be snake_case.**
```r
  LOG = TRUE,
  ^~~
```
[R/sls_likelihoods_nodiv.R:346:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L346) *style:* **Variable or function name should be snake_case.**
```r
  DD1 <- sls::loglik_bisse2(
  ^~~
```
[R/sls_likelihoods_nodiv.R:360:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L360) *style:* **Variable or function name should be snake_case.**
```r
  DD2 <- sls::loglik_bisse2(
  ^~~
```
[R/sls_likelihoods_nodiv.R:369:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_likelihoods_nodiv.R#L369) *style:* **Variable or function name should be snake_case.**
```r
  DD <- DD1 * DD2 * lambda ^ (length(brts[-1]) * lambdaterms)
  ^~
```
[R/sls_loglik_choosepar.R:35:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_loglik_choosepar.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  Npars <- length(namepars)
  ^~~~~
```
[R/sls_loglik_choosepar.R:58:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_loglik_choosepar.R#L58) *style:* **Variable or function name should be snake_case.**
```r
  first_S_branch <- ifelse(length(brts_s) != 0, max(abs(brts_s)), 0)
  ^~~~~~~~~~~~~~
```
[R/sls_ML_cluster.R:56:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_ML_cluster.R#L56) *style:* **Variable or function name should be snake_case.**
```r
  NM <- (soc - 1) + length(brts_m)
  ^~
```
[R/sls_ML_cluster.R:57:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_ML_cluster.R#L57) *style:* **Variable or function name should be snake_case.**
```r
  NS <- 1 + length(brts_s)
  ^~
```
[R/sls_ML_cluster.R:91:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_ML_cluster.R#L91) *style:* **Variable or function name should be snake_case.**
```r
    MLE_1 <- unlist(
    ^~~~~
```
[R/sls_ML_cluster.R:166:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_ML_cluster.R#L166) *style:* **Variable or function name should be snake_case.**
```r
  NM <- (soc - 1) + length(brts_m)
  ^~
```
[R/sls_ML_cluster.R:167:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_ML_cluster.R#L167) *style:* **Variable or function name should be snake_case.**
```r
  NS <- 1 + length(brts_s)
  ^~
```
[R/sls_ML_cluster.R:197:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_ML_cluster.R#L197) *style:* **Variable or function name should be snake_case.**
```r
  MLE_1 <- unlist(
  ^~~~~
```
[R/sls_ML_cluster.R:230:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_ML_cluster.R#L230) *style:* **Variable or function name should be snake_case.**
```r
  MLE_2 <- unlist(
  ^~~~~
```
[R/sls_sim_utils.R:9:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L9) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_pars <- function(
^~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:46:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L46) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sls_sim.initialize_data_new_clade <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:46:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L46) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.initialize_data_new_clade <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:72:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L72) *style:* **Variable or function name should be snake_case.**
```r
  Nmax <- n_0
  ^~~~
```
[R/sls_sim_utils.R:76:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L76) *style:* **Variable or function name should be snake_case.**
```r
    Lmother <- l_1[[motherclade]]
    ^~~~~~~
```
[R/sls_sim_utils.R:83:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L83) *style:* **Variable or function name should be snake_case.**
```r
    L <- matrix(0, nrow = l_matrix_size, 5)
    ^
```
[R/sls_sim_utils.R:123:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L123) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.sample_deltas <- function(
^~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:132:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L132) *style:* **Variable or function name should be snake_case.**
```r
  PARS   <- pars[[clade]]
  ^~~~
```
[R/sls_sim_utils.R:136:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L136) *style:* **Variable or function name should be snake_case.**
```r
  N <- length(pool)
  ^
```
[R/sls_sim_utils.R:160:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L160) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.decide_event <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:170:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L170) *style:* **Variable or function name should be snake_case.**
```r
  L <- l_1[[clade]]
  ^
```
[R/sls_sim_utils.R:187:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L187) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( (t - delta_t) < 0 ) {
      ^
```
[R/sls_sim_utils.R:187:25:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L187) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( (t - delta_t) < 0 ) {
                        ^
```
[R/sls_sim_utils.R:210:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L210) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.use_event <- function(
^~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:220:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L220) *style:* **Variable or function name should be snake_case.**
```r
  L <- data$l_1[[clade]]
  ^
```
[R/sls_sim_utils.R:222:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L222) *style:* **Variable or function name should be snake_case.**
```r
  N <- length(pool)
  ^
```
[R/sls_sim_utils.R:223:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L223) *style:* **Variable or function name should be snake_case.**
```r
  Nmax <- data$Nmax[[clade]]
  ^~~~
```
[R/sls_sim_utils.R:244:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L244) *style:* **Variable or function name should be snake_case.**
```r
    L <- data$l_1[[clade]]
    ^
```
[R/sls_sim_utils.R:246:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    N <- length(pool)
    ^
```
[R/sls_sim_utils.R:253:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L253) *style:* **Variable or function name should be snake_case.**
```r
    Nmax <- Nmax + 1
    ^~~~
```
[R/sls_sim_utils.R:279:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L279) *style:* **Variable or function name should be snake_case.**
```r
    L2 <- sls_sim.cut_l_matrix(L)
    ^~
```
[R/sls_sim_utils.R:280:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L280) *style:* **Variable or function name should be snake_case.**
```r
    L <- L2
    ^
```
[R/sls_sim_utils.R:314:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L314) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.check_survival <- function(
^~~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:315:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L315) *style:* **Variable or function name should be snake_case.**
```r
  L,
  ^
```
[R/sls_sim_utils.R:332:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L332) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.conditioning <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:347:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L347) *style:* **Variable or function name should be snake_case.**
```r
    L <- l_1[[clade]]
    ^
```
[R/sls_sim_utils.R:363:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L363) *style:* **Variable or function name should be snake_case.**
```r
      L_left  <- L[coords_left, ]; dim(L_left)  <- c(sum(coords_left), 5)
      ^~~~~~
```
[R/sls_sim_utils.R:364:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L364) *style:* **Variable or function name should be snake_case.**
```r
      L_right <- L[coords_right, ]; dim(L_right) <- c(sum(coords_right), 5)
      ^~~~~~~
```
[R/sls_sim_utils.R:374:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L374) *style:* **Variable or function name should be snake_case.**
```r
      L_left_cs  <- L_left[coords_left_cs, ]
      ^~~~~~~~~
```
[R/sls_sim_utils.R:379:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L379) *style:* **Variable or function name should be snake_case.**
```r
      L_right_cs <- L_right[coords_right_cs, ]
      ^~~~~~~~~~
```
[R/sls_sim_utils.R:402:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L402) *style:* **Variable or function name should be snake_case.**
```r
      L <- l_1[[clade]]
      ^
```
[R/sls_sim_utils.R:430:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L430) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_brts <- function(
^~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:446:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L446) *style:* **Variable or function name should be snake_case.**
```r
      L <- sls_sim.cut_l_matrix(
      ^
```
[R/sls_sim_utils.R:484:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L484) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.read_l_1 <- function(
^~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:492:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L492) *style:* **Variable or function name should be snake_case.**
```r
    L <- l_1[[i]]
    ^
```
[R/sls_sim_utils.R:504:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L504) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_standard_l_2 <- function(
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:539:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L539) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_shifts_info <- function(
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:556:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L556) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_t_0 <- function(
^~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:570:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L570) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_n_0 <- function(
^~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:584:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L584) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_motherclade <- function(
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:598:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L598) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.get_pool <- function(
^~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:599:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L599) *style:* **Variable or function name should be snake_case.**
```r
  L
  ^
```
[R/sls_sim_utils.R:612:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L612) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.cut_l_matrix <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:613:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L613) *style:* **Variable or function name should be snake_case.**
```r
  L
  ^
```
[R/sls_sim_utils.R:619:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L619) *style:* **Variable or function name should be snake_case.**
```r
    Nmax <- max(abs(L[, 3]))
    ^~~~
```
[R/sls_sim_utils.R:620:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L620) *style:* **Variable or function name should be snake_case.**
```r
    L2 <- L[1:Nmax, ]
    ^~
```
[R/sls_sim_utils.R:621:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L621) *style:* **Variable or function name should be snake_case.**
```r
    cols_L <- ncol(L)
    ^~~~~~
```
[R/sls_sim_utils.R:623:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L623) *style:* **Variable or function name should be snake_case.**
```r
    Nmax <- max(abs(L[3]))
    ^~~~
```
[R/sls_sim_utils.R:624:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L624) *style:* **Variable or function name should be snake_case.**
```r
    L2 <- L
    ^~
```
[R/sls_sim_utils.R:625:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L625) *style:* **Variable or function name should be snake_case.**
```r
    cols_L <- length(L)
    ^~~~~~
```
[R/sls_sim_utils.R:637:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L637) *style:* **Variable or function name should be snake_case.**
```r
sls_sim.adapt_l_matrix_size <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sls_sim_utils.R:641:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L641) *style:* **Variable or function name should be snake_case.**
```r
  Nmax <- data$Nmax[[clade]]
  ^~~~
```
[R/sls_sim_utils.R:642:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L642) *style:* **Variable or function name should be snake_case.**
```r
  L <- data$l_1[[clade]]
  ^
```
[R/sls_sim_utils.R:644:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L644) *style:* **Variable or function name should be snake_case.**
```r
    append_L <- matrix(0, nrow = nrow(L), ncol = ncol(L))
    ^~~~~~~~
```
[R/sls_sim_utils.R:646:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_sim_utils.R#L646) *style:* **Variable or function name should be snake_case.**
```r
    L2 <- rbind(L, append_L)
    ^~
```
[R/sls_utils.R:7:1:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_utils.R#L7) *style:* **Variable or function name should be snake_case.**
```r
P_transition_matrix <- function(
^~~~~~~~~~~~~~~~~~~
```
[R/sls_utils.R:13:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/R/sls_utils.R#L13) *style:* **Variable or function name should be snake_case.**
```r
  M <- matrix(0, nrow = matrix_size, ncol = matrix_size)
  ^
```
[tests/testthat/test-conditionings.R:14:39:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    p_ns_cs * (1 - (p_0_sp) ^ (ns - 1) )
                                      ^
```
[tests/testthat/test-conditionings.R:43:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L43) *style:* **Variable or function name should be snake_case.**
```r
  Pc1 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:50:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L50) *style:* **Variable or function name should be snake_case.**
```r
  Pc3 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:67:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L67) *style:* **Variable or function name should be snake_case.**
```r
  Pc1 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:74:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L74) *style:* **Variable or function name should be snake_case.**
```r
  Pc3 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:91:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L91) *style:* **Variable or function name should be snake_case.**
```r
  Pc1 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:98:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L98) *style:* **Variable or function name should be snake_case.**
```r
  Pc3 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:118:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L118) *style:* **Variable or function name should be snake_case.**
```r
  Pc1 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:125:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L125) *style:* **Variable or function name should be snake_case.**
```r
  Pc3 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:142:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L142) *style:* **Variable or function name should be snake_case.**
```r
  Pc1 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:149:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L149) *style:* **Variable or function name should be snake_case.**
```r
  Pc3 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:166:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L166) *style:* **Variable or function name should be snake_case.**
```r
  Pc1 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:173:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L173) *style:* **Variable or function name should be snake_case.**
```r
  Pc3 <- sls::pc_1shift(
  ^~~
```
[tests/testthat/test-conditionings.R:185:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L185) *style:* **Variable or function name should be snake_case.**
```r
  diff_Pc_vs_DDD <- function(
  ^~~~~~~~~~~~~~
```
[tests/testthat/test-conditionings.R:219:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L219) *style:* **Variable or function name should be snake_case.**
```r
      DDDloglik0 <- DDD::dd_KI_loglik(
      ^~~~~~~~~~
```
[tests/testthat/test-conditionings.R:227:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L227) *style:* **Variable or function name should be snake_case.**
```r
      DDDloglik1 <- DDD::dd_KI_loglik(
      ^~~~~~~~~~
```
[tests/testthat/test-conditionings.R:235:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L235) *style:* **Variable or function name should be snake_case.**
```r
      Pc <- sls::pc_1shift(
      ^~
```
[tests/testthat/test-conditionings.R:243:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-conditionings.R#L243) *style:* **Variable or function name should be snake_case.**
```r
      DDD_Pc <- (DDDloglik0 - DDDloglik1)
      ^~~~~~
```
[tests/testthat/test-loglik-BISSE.R:3:11:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-BISSE.R#L3) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
test_that( "test bisse and DDD logliks equivalence", {
          ^
```
[tests/testthat/test-loglik-BISSE.R:22:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-BISSE.R#L22) *style:* **Variable or function name should be snake_case.**
```r
    Delta_ddd   <- ddd1 - ddd2
    ^~~~~~~~~
```
[tests/testthat/test-loglik-BISSE.R:23:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-BISSE.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    Deltabisse <- bisse1 - bisse2
    ^~~~~~~~~~
```
[tests/testthat/test-loglik-BISSE.R:56:11:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-BISSE.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
test_that( "test bisse alternative functions", {
          ^
```
[tests/testthat/test-loglik-division.R:3:11:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L3) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
test_that( "all the likelihoods with division yield the same result", {
          ^
```
[tests/testthat/test-loglik-division.R:24:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L24) *style:* **Variable or function name should be snake_case.**
```r
    res1.1 <- fun1(
    ^~~~~~
```
[tests/testthat/test-loglik-division.R:33:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L33) *style:* **Variable or function name should be snake_case.**
```r
    res2.1 <- fun2(
    ^~~~~~
```
[tests/testthat/test-loglik-division.R:42:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L42) *style:* **Variable or function name should be snake_case.**
```r
    res1.2 <- res2.2 <- 0
    ^~~~~~
```
[tests/testthat/test-loglik-division.R:42:15:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L42) *style:* **Variable or function name should be snake_case.**
```r
    res1.2 <- res2.2 <- 0
              ^~~~~~
```
[tests/testthat/test-loglik-division.R:46:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L46) *style:* **Variable or function name should be snake_case.**
```r
      res1.2 <- fun1(
      ^~~~~~
```
[tests/testthat/test-loglik-division.R:55:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L55) *style:* **Variable or function name should be snake_case.**
```r
      res2.2 <- fun2(
      ^~~~~~
```
[tests/testthat/test-loglik-division.R:65:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L65) *style:* **Variable or function name should be snake_case.**
```r
    Delta1 <- res1.1 - res1.2; Delta1
    ^~~~~~
```
[tests/testthat/test-loglik-division.R:66:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L66) *style:* **Variable or function name should be snake_case.**
```r
    Delta2 <- res2.1 - res2.2; Delta2
    ^~~~~~
```
[tests/testthat/test-loglik-division.R:72:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-division.R#L72) *style:* **Variable or function name should be snake_case.**
```r
  test.diff <- function(
  ^~~~~~~~~
```
[tests/testthat/test-loglik-nodivision.R:3:11:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L3) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
test_that( "all the likelihoods with no division yield the same result", {
          ^
```
[tests/testthat/test-loglik-nodivision.R:23:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    res1.1 <- fun1(
    ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:32:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L32) *style:* **Variable or function name should be snake_case.**
```r
    res2.1 <- fun2(
    ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:41:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L41) *style:* **Variable or function name should be snake_case.**
```r
    res1.2 <- res2.2 <- 0
    ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:41:15:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L41) *style:* **Variable or function name should be snake_case.**
```r
    res1.2 <- res2.2 <- 0
              ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:45:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L45) *style:* **Variable or function name should be snake_case.**
```r
      res1.2 <- fun1(pars_m = pars_m2,
      ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:53:7:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L53) *style:* **Variable or function name should be snake_case.**
```r
      res2.2 <- fun2(
      ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:63:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L63) *style:* **Variable or function name should be snake_case.**
```r
    Delta1 <- res1.1 - res1.2; Delta1
    ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:64:5:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L64) *style:* **Variable or function name should be snake_case.**
```r
    Delta2 <- res2.1 - res2.2; Delta2
    ^~~~~~
```
[tests/testthat/test-loglik-nodivision.R:70:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-loglik-nodivision.R#L70) *style:* **Variable or function name should be snake_case.**
```r
  test.diff <- function(
  ^~~~~~~~~
```
[tests/testthat/test-sims.R:11:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L11) *style:* **Variable or function name should be snake_case.**
```r
  Nsup <- n_species * 2
  ^~~~
```
[tests/testthat/test-sims.R:12:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L12) *style:* **Variable or function name should be snake_case.**
```r
  L <- matrix(0, ncol = 5, nrow = Nsup)
  ^
```
[tests/testthat/test-sims.R:31:8:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L31) *style:* **Variable or function name should be snake_case.**
```r
  data$Nmax <- length(
       ^~~~
```
[tests/testthat/test-sims.R:301:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L301) *style:* **Variable or function name should be snake_case.**
```r
  L0 <- data$l_1[[clade]]
  ^~
```
[tests/testthat/test-sims.R:308:6:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L308) *style:* **Variable or function name should be snake_case.**
```r
  ); L <- out$l_1[[clade]]
     ^
```
[tests/testthat/test-sims.R:336:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L336) *style:* **Variable or function name should be snake_case.**
```r
  L0 <- data$l_1[[clade]]
  ^~
```
[tests/testthat/test-sims.R:343:6:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L343) *style:* **Variable or function name should be snake_case.**
```r
  ); L <- out$l_1[[clade]]
     ^
```
[tests/testthat/test-sims.R:362:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L362) *style:* **Variable or function name should be snake_case.**
```r
  L0 <- data$l_1[[clade]]
  ^~
```
[tests/testthat/test-sims.R:369:6:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L369) *style:* **Variable or function name should be snake_case.**
```r
  ); L <- out$l_1[[clade]]
     ^
```
[tests/testthat/test-sims.R:388:3:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L388) *style:* **Variable or function name should be snake_case.**
```r
  L0 <- data$l_1[[clade]]
  ^~
```
[tests/testthat/test-sims.R:395:6:](https://github.com/Giappo/sls/blob/f1922240b553dc32a2cea020980cd17be6579f19/tests/testthat/test-sims.R#L395) *style:* **Variable or function name should be snake_case.**
```r
  ); L <- out$l_1[[clade]]
     ^
```


Created multidev environment [newupstream#ci-550](https://dashboard.pantheon.io/sites/8be50dbc-4463-43b5-bd18-d83046623820#ci-550).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-550-newupstream.pantheonsite.io/)


@dsainati1 Awesome! Is new lint rule coming?


Not easily. Submit it as a PR and I can test it.


siwtch case, i zamiana (GET, GET1) na (GET, GET_ALL)