[R/default_param_doc.R:125:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/default_param_doc.R#L125) *style:* **Variable or function name should be snake_case.**
```r
  L,
  ^
```
[R/default_param_doc.R:148:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/default_param_doc.R#L148) *style:* **Variable or function name should be snake_case.**
```r
  D0,
  ^~
```
[R/default_param_doc.R:149:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/default_param_doc.R#L149) *style:* **Variable or function name should be snake_case.**
```r
  D_0,
  ^~~
```
[R/default_param_doc.R:151:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/default_param_doc.R#L151) *style:* **Variable or function name should be snake_case.**
```r
  D0s,
  ^~~
```
[R/default_param_doc.R:152:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/default_param_doc.R#L152) *style:* **Variable or function name should be snake_case.**
```r
  D_0s,
  ^~~~
```
[R/default_param_doc.R:154:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/default_param_doc.R#L154) *style:* **Variable or function name should be snake_case.**
```r
  E0,
  ^~
```
[R/default_param_doc.R:155:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/default_param_doc.R#L155) *style:* **Variable or function name should be snake_case.**
```r
  E_0,
  ^~~
```
[R/sls_conditionings.R:24:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_convolutions.R#L141) *style:* **Variable or function name should be snake_case.**
```r
  X <- vector("list", N)
  ^
```
[R/sls_likelihoods_bisse.R:20:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_likelihoods_bisse.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  DD <- (exp_factor * d_0 * (lambda - mu) ^ 2) / denominator ^ 2
  ^~
```
[R/sls_likelihoods_bisse.R:74:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:98:9:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:134:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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_div.R:40:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:164:10:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_likelihoods_nee.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  Lambda <- exp(
  ^~~~~~
```
[R/sls_likelihoods_nodiv.R:29:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:143:10:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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_loglik_choosepar.R:35:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:76:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_sim_utils.R#L220) *style:* **Variable or function name should be snake_case.**
```r
  L <- data$l_1[[clade]]
  ^
```
[R/sls_sim_utils.R:222:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_sim_utils.R#L222) *style:* **Variable or function name should be snake_case.**
```r
  N <- length(pool)
  ^
```
[R/sls_sim_utils.R:244:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_sim_utils.R#L244) *style:* **Variable or function name should be snake_case.**
```r
    L <- data$l_1[[clade]]
    ^
```
[R/sls_sim_utils.R:246:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_sim_utils.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    N <- length(pool)
    ^
```
[R/sls_sim_utils.R:279:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_sim_utils.R#L613) *style:* **Variable or function name should be snake_case.**
```r
  L
  ^
```
[R/sls_sim_utils.R:620:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/R/sls_sim_utils.R#L620) *style:* **Variable or function name should be snake_case.**
```r
    L2 <- L[1:n_max, ]
    ^~
```
[R/sls_sim_utils.R:621:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:624:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:642:3:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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:22:5:](https://github.com/Giappo/sls/blob/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/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/7be9826a7ffd9e54a042c19dbb8e1f85563edd6e/tests/testthat/test-loglik-BISSE.R#L23) *style:* **Variable or function name should be snake_case.**
```r
    Deltabisse <- bisse1 - bisse2
    ^~~~~~~~~~
```


![](https://github.trello.services/images/mini-trello-icon.png) [(2) Implementar a visualização do conteúdo dos tweets selecionados [2]](https://trello.com/c/gkkN7cUw/17-2-implementar-a-visualiza%C3%A7%C3%A3o-do-conte%C3%BAdo-dos-tweets-selecionados-2)


https://www.khanacademy.org/math/geometry
this will help you catch up or already be ahead on it


![](https://github.trello.services/images/mini-trello-icon.png) [Filtrar informação do facebook, twitter, mail](https://trello.com/c/RLP7UxY5/37-filtrar-informa%C3%A7%C3%A3o-do-facebook-twitter-mail)


okay?


idk what I'm doing okay bye!--


Seems that's the practice?


why is this necessary given the above?


[R/AllClasses.R:66:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:71:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:76:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L76) *style:* **Commented code should be removed.**
```r
        #         y = colnames(rowData(data))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/AllClasses.R:79:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:167:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:177:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:50:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:57:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:109:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/plotDEGPCA-methods.R:85:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/R/plotDEGPCA-methods.R#L85) *style:* **Trailing whitespace is superfluous.**
```r
    f = "plotPCA",
                  ^
```
[tests/testthat/test_DESeqResultsTables.R:16:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L16) *style:* **Commented code should be removed.**
```r
#             dir = "resultsTables"
              ^~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:18:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L18) *style:* **Commented code should be removed.**
```r
#         type = "output"
          ^~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:21:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L21) *style:* **Commented code should be removed.**
```r
#         head(28L)
          ^~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:103:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L103) *style:* **Commented code should be removed.**
```r
#             rdsToken = "token.rds"
              ^~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:105:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L105) *style:* **Commented code should be removed.**
```r
#         expect_true("dropboxFiles" %in% names(resTbl))
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:110:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L110) *style:* **Commented code should be removed.**
```r
#                 grepl("^https://www.dropbox.com/s/", file[["url"]])
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:112:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L112) *style:* **Commented code should be removed.**
```r
#             FUN.VALUE = logical(1L)
              ^~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:115:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L115) *style:* **Commented code should be removed.**
```r
#         output <- capture.output(.markdownResultsTables(resTbl))
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_DESeqResultsTables.R:123:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_DESeqResultsTables.R#L123) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test_markdown.R:5:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_markdown.R#L5) *style:* **Variable or function name should be lowerCamelCase.**
```r
res_small <- as(deseq, "DESeqResults")
^~~~~~~~~
```
[tests/testthat/test_markdown.R:6:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/dd1a1e26dcc410cdde41131a6c1b68f99c34e12d/tests/testthat/test_markdown.R#L6) *style:* **Variable or function name should be lowerCamelCase.**
```r
res_tables <- DESeqResultsTables(res_small)
^~~~~~~~~~
```


fixes #3


Right, yup.Still testing though :)


For #1399


Done 👍


[R/default_param_doc.R:125:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/default_param_doc.R#L125) *style:* **Variable or function name should be snake_case.**
```r
  L,
  ^
```
[R/default_param_doc.R:148:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/default_param_doc.R#L148) *style:* **Variable or function name should be snake_case.**
```r
  D0,
  ^~
```
[R/default_param_doc.R:149:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/default_param_doc.R#L149) *style:* **Variable or function name should be snake_case.**
```r
  D_0,
  ^~~
```
[R/default_param_doc.R:151:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/default_param_doc.R#L151) *style:* **Variable or function name should be snake_case.**
```r
  D0s,
  ^~~
```
[R/default_param_doc.R:152:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/default_param_doc.R#L152) *style:* **Variable or function name should be snake_case.**
```r
  D_0s,
  ^~~~
```
[R/default_param_doc.R:154:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/default_param_doc.R#L154) *style:* **Variable or function name should be snake_case.**
```r
  E0,
  ^~
```
[R/default_param_doc.R:155:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/default_param_doc.R#L155) *style:* **Variable or function name should be snake_case.**
```r
  E_0,
  ^~~
```
[R/sls_conditionings.R:24:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_convolutions.R#L141) *style:* **Variable or function name should be snake_case.**
```r
  X <- vector("list", N)
  ^
```
[R/sls_likelihoods_bisse.R:20:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_likelihoods_bisse.R#L20) *style:* **Variable or function name should be snake_case.**
```r
  DD <- (exp_factor * d_0 * (lambda - mu) ^ 2) / denominator ^ 2
  ^~
```
[R/sls_likelihoods_bisse.R:74:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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:98:9:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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:134:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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_div.R:40:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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:164:10:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_likelihoods_nee.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  Lambda <- exp(
  ^~~~~~
```
[R/sls_likelihoods_nodiv.R:29:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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:143:10:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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_loglik_choosepar.R:35:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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:76:5:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_sim_utils.R#L220) *style:* **Variable or function name should be snake_case.**
```r
  L <- data$l_1[[clade]]
  ^
```
[R/sls_sim_utils.R:222:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_sim_utils.R#L222) *style:* **Variable or function name should be snake_case.**
```r
  N <- length(pool)
  ^
```
[R/sls_sim_utils.R:244:5:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_sim_utils.R#L244) *style:* **Variable or function name should be snake_case.**
```r
    L <- data$l_1[[clade]]
    ^
```
[R/sls_sim_utils.R:246:5:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_sim_utils.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    N <- length(pool)
    ^
```
[R/sls_sim_utils.R:279:5:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_sim_utils.R#L613) *style:* **Variable or function name should be snake_case.**
```r
  L
  ^
```
[R/sls_sim_utils.R:620:5:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/R/sls_sim_utils.R#L620) *style:* **Variable or function name should be snake_case.**
```r
    L2 <- L[1:n_max, ]
    ^~
```
[R/sls_sim_utils.R:621:5:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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:624:5:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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:642:3:](https://github.com/Giappo/sls/blob/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/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/5024f4e50ef535751fbc0d20190474b133ba927b/tests/testthat/test-conditionings.R#L243) *style:* **Variable or function name should be snake_case.**
```r
      DDD_Pc <- (DDDloglik0 - DDDloglik1)
      ^~~~~~
```


[R/collect_esses.R:11:3:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/collect_esses.R#L11) *warning:* **no visible global function definition for ‘check_project_folder_name’**
```r
  check_project_folder_name(project_folder_name)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_bd_tree.R:70:18:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/create_bd_tree.R#L70) *warning:* **no visible global function definition for ‘bd_phylo_2_l_table’**
```r
  bd_l_matrix <- bd_phylo_2_l_table(bd_tree)
                 ^~~~~~~~~~~~~~~~~~
```
[R/create_esses_file.R:15:21:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/create_esses_file.R#L15) *warning:* **no visible global function definition for ‘get_results_path’**
```r
  results_folder <- get_results_path(project_folder_name)
                    ^~~~~~~~~~~~~~~~
```
[R/create_fig_1_file.R:15:21:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/create_fig_1_file.R#L15) *warning:* **no visible global function definition for ‘get_results_path’**
```r
  results_folder <- get_results_path(project_folder_name)
                    ^~~~~~~~~~~~~~~~
```
[R/create_marg_liks_file.R:15:21:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/create_marg_liks_file.R#L15) *warning:* **no visible global function definition for ‘get_results_path’**
```r
  results_folder <- get_results_path(project_folder_name)
                    ^~~~~~~~~~~~~~~~
```
[R/create_nltt_stats_file.R:15:21:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/create_nltt_stats_file.R#L15) *warning:* **no visible global function definition for ‘get_results_path’**
```r
  results_folder <- get_results_path(project_folder_name)
                    ^~~~~~~~~~~~~~~~
```
[R/get_data_paths.R:11:3:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/get_data_paths.R#L11) *warning:* **no visible global function definition for ‘check_project_folder_name’**
```r
  check_project_folder_name(project_folder_name)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_results_paths.R:11:3:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/get_results_paths.R#L11) *warning:* **no visible global function definition for ‘check_project_folder_name’**
```r
  check_project_folder_name(project_folder_name)
  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/utils.R:65:10:](https://github.com/richelbilderbeek/razzo/blob/16ee8bee84d3596f7700863603be6fd1aefd2045/R/utils.R#L65) *warning:* **no visible global function definition for ‘convert_tree2brts’**
```r
  brt <- convert_tree2brts(phylo)
         ^~~~~~~~~~~~~~~~~
```


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


[Evan Saltzman CV 11-21-2018.pdf](https://github.com/easalt/easalt.github.io/files/2606205/Evan.Saltzman.CV.11-21-2018.pdf)


I'm glad you got this worked out. Sorry for the trouble, and please don't hesitate to report any issues that come up. I'm honored that you're doing Handmade Hero in Zig and I intend to unblock you if you run into trouble using Zig.

I'll be sure to let you know when the linking issue with xinput is resolved.