[R/DAISIE_area_params.R:16:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_area_params.R#L16) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
are_area_params <- function(area_params) {
^
```
[R/DAISIE_check_format.R:6:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_check_format.R#L6) *style:* **functions should have cyclomatic complexity of less than 15, this has 35.**
```r
are_rates <- function(x) {
^
```
[R/DAISIE_check_format.R:79:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_check_format.R#L79) *style:* **Commented code should be removed.**
```r
    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:80:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_check_format.R#L80) *style:* **Commented code should be removed.**
```r
    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:81:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_check_format.R#L81) *style:* **Commented code should be removed.**
```r
    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:95:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_check_format.R#L95) *style:* **functions should have cyclomatic complexity of less than 15, this has 84.**
```r
are_DAISIE_create_sim_params <- function(params) {
^
```
[R/DAISIE_check_format.R:95:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_check_format.R#L95) *style:* **Variable and function name style should be snake_case.**
```r
are_DAISIE_create_sim_params <- function(params) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:142:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_check_format.R#L142) *style:* **Commented code should be removed.**
```r
  #testit::assert(params$stored_data) #Pedro to write test
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:18:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_create_island.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_create_island <- function(stt_table,
^~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_sim_params.R:30:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_create_sim_params.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_create_sim_params <- function(time = 10,
^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_sim_params.R:31:31:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_create_sim_params.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                              M = 1000,
                              ^
```
[R/DAISIE_create_sim_params.R:44:31:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_create_sim_params.R#L44) *style:* **Variable and function name style should be snake_case.**
```r
                              Apars = NULL,
                              ^~~~~
```
[R/DAISIE_create_sim_params.R:45:31:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_create_sim_params.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
                              Epars = NULL,
                              ^~~~~
```
[R/DAISIE_data.R:8:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' #' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:48:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Colonization and branching times of 8 terrestrial avifaunal clades in list
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:53:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:93:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
#' @title Colonization and branching times of 8 terrestrial avifaunal clades in table
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:97:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L97) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A table containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:104:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L104) *style:* **Lines should not be more than 80 characters.**
```r
#' * Non_endemic: for cases where both island and non-island populations of the species have been sampled) \cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:105:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L105) *style:* **Lines should not be more than 80 characters.**
```r
#' * Non_endemic_MaxAge: for cases where island population of the species has not
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:125:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L125) *style:* **Lines should not be more than 80 characters.**
```r
#' @title 1000 islands in RAW format simulated with the ML parameters of the CR model
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:128:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L128) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:159:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
#' @title 1000 islands in DAISIE format simulated with the ML parameters of the CR
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:162:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L162) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:198:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L198) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Each simulated dataset is an element of the list, which can be called using
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:248:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L248) *style:* **Lines should not be more than 80 characters.**
```r
#' @description A list containing the colonization and branching times of the terrestrial
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:257:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L257) *style:* **Lines should not be more than 80 characters.**
```r
#' The following elements of the list each contains information on a single colonist lineage
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:271:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L271) *style:* **Lines should not be more than 80 characters.**
```r
#' #' \code{$missing_species} - number of island species that were not sampled for
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:287:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L287) *style:* **Lines should not be more than 80 characters.**
```r
#' format, accepted by DAISIE_ML, DAISIE_SR_ML, DAISIE_loglik_all and DAISIE_SR_loglik_all
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_data.R:322:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_data.R#L322) *style:* **Lines should not be more than 80 characters.**
```r
#' @seealso \code{\link{DAISIE_dataprep}}, \code{\link{DAISIE_ML}}, \code{\link{DAISIE_SR_ML}}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:91:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L91) *style:* **Lines should not be more than 80 characters.**
```r
#' ### Create Galapagos data object where all taxa have the same macroevolutionary process
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:101:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L101) *style:* **Lines should not be more than 80 characters.**
```r
#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:116:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L116) *style:* **Lines should not be more than 80 characters.**
```r
#' # for the Darwin's finches. One process applies to type 1 species (all species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:118:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L118) *style:* **Lines should not be more than 80 characters.**
```r
#' # (Darwin's finches). Set fraction of potential colonists of type 2 to be 0.163.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:131:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L131) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
DAISIE_dataprep <- function(datatable,
^
```
[R/DAISIE_dataprep.R:131:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L131) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_dataprep <- function(datatable,
^~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:133:28:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L133) *style:* **Variable and function name style should be snake_case.**
```r
                           M,
                           ^
```
[R/DAISIE_dataprep.R:141:13:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L141) *style:* **Variable and function name style should be snake_case.**
```r
  datatable$Missing_species <- as.numeric(as.character
            ^~~~~~~~~~~~~~~
```
[R/DAISIE_dataprep.R:152:40:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L152) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      not_present_type1 <- DDD::roundn( (M / number_colonisations) *
                                       ^
```
[R/DAISIE_dataprep.R:155:40:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L155) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      not_present_type2 <- DDD::roundn( (M / number_colonisations) *
                                       ^
```
[R/DAISIE_dataprep.R:168:13:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L168) *warning:* **Avoid 1:nrow(...) expressions, use seq_len.**
```r
  for (i in 1:nrow(datatable)) {
            ^
```
[R/DAISIE_dataprep.R:198:37:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_dataprep.R#L198) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
      if (max(the_brts) > island_age){
                                    ^~
```
[R/DAISIE_ExpEIN.R:2:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:6:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:7:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:27:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:28:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
#' ### Compute the expected values at t = 4, for a mainland pool size of 1000 potential
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_ExpEIN.R:29:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
#' # colonists and a vector of 5 parameters (cladogenesis, extinction, clade-level carrying
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_ExpEIN.R:31:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_ExpEIN.R:37:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L37) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:39:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L39) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_ExpEIN <- function(t, pars, M, initEI = c(0, 0)) {
^~~~~~~~~~~~~
```
[R/DAISIE_ExpEIN.R:39:36:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L39) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_ExpEIN <- function(t, pars, M, initEI = c(0, 0)) {
                                   ^
```
[R/DAISIE_ExpEIN.R:39:39:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L39) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_ExpEIN <- function(t, pars, M, initEI = c(0, 0)) {
                                      ^~~~~~
```
[R/DAISIE_ExpEIN.R:46:8:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L46) *style:* **Variable and function name style should be snake_case.**
```r
       M2 <- M - DDD::roundn(pars1[11] * M)
       ^~
```
[R/DAISIE_ExpEIN.R:48:8:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L48) *style:* **Variable and function name style should be snake_case.**
```r
       M2 <- M
       ^~
```
[R/DAISIE_ExpEIN.R:50:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L50) *style:* **Variable and function name style should be snake_case.**
```r
   A <- mu - lac
   ^
```
[R/DAISIE_ExpEIN.R:51:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L51) *style:* **Variable and function name style should be snake_case.**
```r
   B <- lac + mu + ga + laa
   ^
```
[R/DAISIE_ExpEIN.R:52:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L52) *style:* **Variable and function name style should be snake_case.**
```r
   C <- laa + 2 * lac + ga
   ^
```
[R/DAISIE_ExpEIN.R:53:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L53) *style:* **Variable and function name style should be snake_case.**
```r
   DD <- laa + 2 * lac
   ^~
```
[R/DAISIE_ExpEIN.R:54:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L54) *style:* **Variable and function name style should be snake_case.**
```r
   E0 <- initEI[1]
   ^~
```
[R/DAISIE_ExpEIN.R:55:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
   I0 <- initEI[2]
   ^~
```
[R/DAISIE_ExpEIN.R:57:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L57) *style:* **Variable and function name style should be snake_case.**
```r
      Imm <- ga * M2 / B
      ^~~
```
[R/DAISIE_ExpEIN.R:58:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
      End <- DD / A * Imm
      ^~~
```
[R/DAISIE_ExpEIN.R:60:8:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L60) *style:* **Commented code should be removed.**
```r
      #Imm = M2 * ga / B * (1 - exp(-B * t))
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_ExpEIN.R:63:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L63) *style:* **Variable and function name style should be snake_case.**
```r
      Imm <- M2 * ga / B - (M2 * ga / B - I0) * exp(-B * t)
      ^~~
```
[R/DAISIE_ExpEIN.R:64:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
      End <- DD / C * (M2 * ga / A - M2 * ga / B +
      ^~~
```
[R/DAISIE_ExpEIN.R:68:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L68) *style:* **Variable and function name style should be snake_case.**
```r
   All <- End + Imm
   ^~~
```
[R/DAISIE_ExpEIN.R:69:4:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_ExpEIN.R#L69) *style:* **Variable and function name style should be snake_case.**
```r
   expEIN <- list(End, Imm, All)
   ^~~~~~
```
[R/DAISIE_extract_stt_median.R:5:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_extract_stt_median.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_extract_stt_median <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_extract_stt_median.R:5:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_extract_stt_median.R#L5) *warning:* **local variable ‘time’ assigned but may not be used**
```r
  time <- max(island_replicates[[1]][[1]]$stt_all[, 1])
  ^~~~
```
[R/DAISIE_format_CS_full_stt.R:13:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 35.**
```r
DAISIE_format_CS_full_stt <- function(island_replicates,
^
```
[R/DAISIE_format_CS_full_stt.R:13:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_format_CS_full_stt <- function(island_replicates,
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:15:39:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                      M,
                                      ^
```
[R/DAISIE_format_CS_full_stt.R:199:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L199) *style:* **Commented code should be removed.**
```r
# pars_equas <- c(2.550687345, 2.683454548, Inf, 0.00933207, 1.010073119)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:204:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L204) *style:* **Commented code should be removed.**
```r
#   replicates = 2
    ^~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:206:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L206) *style:* **Commented code should be removed.**
```r
# stt_list <- island_replicates_equal[[1:1000]]
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:207:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L207) *style:* **Commented code should be removed.**
```r
# unlist(stt_list[1])
  ^~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:208:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L208) *style:* **Commented code should be removed.**
```r
# which(stt_list)
  ^~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:210:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L210) *style:* **Commented code should be removed.**
```r
# small_stts <- lapply(stt_list, nrow) == 2
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:211:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L211) *style:* **Commented code should be removed.**
```r
# second_line_stts <- lapply(stt_list, "[", 2,)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:212:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L212) *style:* **Commented code should be removed.**
```r
# zeros_second_line <- sapply(second_line_stts, sum) == 0
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:214:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L214) *style:* **Commented code should be removed.**
```r
# comparisson <- zeros_second_line == small_stts
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:215:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L215) *style:* **Commented code should be removed.**
```r
# testit::assert(all(comparisson))
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:217:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L217) *style:* **Commented code should be removed.**
```r
# filled_stt_lists <- stt_list[!zeros_second_line]
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:219:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L219) *style:* **Commented code should be removed.**
```r
# filled_stt_lists[[1]][, 1]
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:220:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L220) *style:* **Commented code should be removed.**
```r
# filled_stt_lists[[1]][, 1]
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:221:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L221) *style:* **Commented code should be removed.**
```r
# times <- sapply(filled_stt_lists, "[", ,1)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:223:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L223) *style:* **Commented code should be removed.**
```r
# times_without_last <- lapply(times, head, -1)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:224:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L224) *style:* **Commented code should be removed.**
```r
# times_without_last_first <- sapply(times_without_last, "[", -1)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS_full_stt.R:226:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS_full_stt.R#L226) *style:* **Commented code should be removed.**
```r
# sort(unlist(times_without_last_first))
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS.R:15:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS.R#L15) *style:* **functions should have cyclomatic complexity of less than 15, this has 40.**
```r
DAISIE_format_CS <- function(island_replicates,
^
```
[R/DAISIE_format_CS.R:15:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_format_CS <- function(island_replicates,
^~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS.R:17:29:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_CS.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                            M,
                            ^
```
[R/DAISIE_format_GW.R:17:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 39.**
```r
DAISIE_format_GW <- function(island_replicates,
^
```
[R/DAISIE_format_GW.R:17:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_format_GW <- function(island_replicates,
^~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:19:29:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                            M,
                            ^
```
[R/DAISIE_format_GW.R:27:15:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L27) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  for (rep in 1:length(island_replicates)) {
              ^
```
[R/DAISIE_format_GW.R:31:15:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L31) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    for (i in 1:length(full_list)) {
              ^
```
[R/DAISIE_format_GW.R:35:19:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L35) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
        for (j in 1:length(full_list[[i]]$taxon_list)) {
                  ^
```
[R/DAISIE_format_GW.R:48:15:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L48) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    for (i in 1:length(full_list)) {
              ^
```
[R/DAISIE_format_GW.R:54:19:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L54) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
        for (j in 1:length(full_list[[i]]$taxon_list)) {
                  ^
```
[R/DAISIE_format_GW.R:55:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L55) *style:* **Lines should not be more than 80 characters.**
```r
          init_nonend_spec_list[[i]] <- full_list[[i]]$taxon_list[[1]]$init_nonend_spec
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:56:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
          init_end_spec_list[[i]] <- full_list[[i]]$taxon_list[[1]]$init_end_spec
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:57:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
          carrying_capacity_list[[i]] <- full_list[[i]]$taxon_list[[1]]$carrying_capacity
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:71:14:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L71) *style:* **Commas should always have a space after.**
```r
    stt_all[,"Time"] <- rev(seq(from = 0,
             ^
```
[R/DAISIE_format_GW.R:76:11:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L76) *warning:* **local variable ‘row_index’ assigned but may not be used**
```r
          row_index <- max(which(stt_list[[x]][, "Time"] >= the_age))
          ^~~~~~~~~
```
[R/DAISIE_format_GW.R:93:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
          store_richness_time_slice[x, ] <- stt_list[[x]][max(which(stt_list[[x]][, "Time"] >= the_age)), 2:4]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:113:25:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L113) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
              for (j in 1:length(full_list[[i]]$taxon_list)) {
                        ^
```
[R/DAISIE_format_GW.R:114:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
                taxon_sublist_name <- paste0("taxon_sublist_", c(1:length(full_list[[i]]$taxon_list)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:114:66:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L114) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
                taxon_sublist_name <- paste0("taxon_sublist_", c(1:length(full_list[[i]]$taxon_list)))
                                                                 ^
```
[R/DAISIE_format_GW.R:116:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L116) *style:* **Lines should not be more than 80 characters.**
```r
                island_list <- append(island_list, list(get(taxon_sublist_name[[j]])))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:128:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L128) *style:* **Lines should not be more than 80 characters.**
```r
                                 not_present = M, #check what not_present should be
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:136:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_GW.R#L136) *style:* **Lines should not be more than 80 characters.**
```r
                                 all_carrying_capacities = carrying_capacity_vec)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_IW.R:30:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_format_IW <- function(island_replicates,
^~~~~~~~~~~~~~~~
```
[R/DAISIE_format_IW.R:32:30:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L32) *style:* **Variable and function name style should be snake_case.**
```r
                             M,
                             ^
```
[R/DAISIE_format_IW.R:38:15:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L38) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  for (rep in 1:length(island_replicates)) {
              ^
```
[R/DAISIE_format_IW.R:46:17:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L46) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (i in 1:length(the_island$taxon_list)) {
                ^
```
[R/DAISIE_format_IW.R:88:17:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L88) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (y in 1:length(the_island$taxon_list)) {
                ^
```
[R/DAISIE_format_IW.R:108:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L108) *style:* **Variable and function name style should be snake_case.**
```r
Add_brt_table <- function(island) {
^~~~~~~~~~~~~
```
[R/DAISIE_format_IW.R:119:15:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L119) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    for (i in 1:length(island)) {
              ^
```
[R/DAISIE_format_IW.R:141:17:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L141) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (i in 1:length(island_no_stac1or5)) {
                ^
```
[R/DAISIE_format_IW.R:145:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L145) *style:* **Variable and function name style should be snake_case.**
```r
      brts_IWK <- matrix(ncol = 4, nrow = length(brts))
      ^~~~~~~~
```
[R/DAISIE_format_IW.R:147:17:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L147) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (i in 1:length(btimes)) {
                ^
```
[R/DAISIE_format_IW.R:163:17:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_format_IW.R#L163) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (i in 1:length(stac1_5s)) {
                ^
```
[R/DAISIE_get_brts_mya.R:12:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_get_brts_mya.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_get_brts_mya <- function(data_table) {
^~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_IC.R:61:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_IC.R#L61) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_IC <- function(datalist,
^~~~~~~~~
```
[R/DAISIE_IC.R:70:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_IC.R#L70) *style:* **Variable and function name style should be snake_case.**
```r
  MLE_obs <- DAISIE_ML(
  ^~~~~~~
```
[R/DAISIE_IC.R:97:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_IC.R#L97) *style:* **Variable and function name style should be snake_case.**
```r
  MLE <- rep(0, endmc)
  ^~~
```
[R/DAISIE_IC.R:98:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_IC.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  LL <- rep(0, endmc)
  ^~
```
[R/DAISIE_IC.R:125:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_IC.R#L125) *style:* **Variable and function name style should be snake_case.**
```r
  WIC <- -2 * MLE_obs$loglik - 2 * mean(LL - MLE)
  ^~~
```
[R/DAISIE_IC.R:126:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_IC.R#L126) *style:* **Variable and function name style should be snake_case.**
```r
  AICb <- -2 * MLE_obs$loglik - 4 * mean(LL - MLE_obs)
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:6:79:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#'   \item{[2]: value from 0 to 1 indicating where in the island's history the
                                                                              ^
```
[R/DAISIE_loglik_CS_time.R:9:14:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L9) *warning:* **no visible global function definition for ‘create_area_params’**
```r
    Apars <- create_area_params(Apars[1], Apars[2], Apars[3], Apars[4])
             ^~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:11:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' @param island_ontogeny a string describing the type of island ontogeny. Can be \code{NULL},
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:11:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L11) *warning:* **local variable ‘gam0’ assigned but may not be used**
```r
  gam0 <- parsvec[9]
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:12:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L12) *warning:* **local variable ‘laa0’ assigned but may not be used**
```r
  laa0 <- parsvec[10]
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:13:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L13) *warning:* **local variable ‘Epars’ assigned but may not be used**
```r
  Epars <- pars1[6:7]
  ^~~~~
```
[R/DAISIE_loglik_CS_time.R:15:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L15) *warning:* **local variable ‘ddep’ assigned but may not be used**
```r
  ddep <- parsvec[13]
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:16:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L16) *warning:* **local variable ‘ddep’ assigned but may not be used**
```r
  ddep <- parsvec[13]
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:16:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L16) *warning:* **local variable ‘laa0’ assigned but may not be used**
```r
  laa0 <- pars1[10]
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:16:78:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L16) *style:* **Trailing whitespace is superfluous.**
```r
#' @references Valente, Luis M., Rampal S. Etienne, and Albert B. Phillimore.
                                                                             ^
```
[R/DAISIE_loglik_CS_time.R:17:72:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L17) *style:* **Trailing whitespace is superfluous.**
```r
#' "The effects of island ontogeny on species diversity and phylogeny."
                                                                       ^
```
[R/DAISIE_loglik_CS_time.R:18:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L18) *style:* **Lines should not be more than 80 characters.**
```r
#' Proceedings of the Royal Society of London B: Biological Sciences 281.1784 (2014): 20133227.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:19:41:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
island_area_vector <- function(timeval, Apars, island_ontogeny) {
                                        ^~~~~
```
[R/DAISIE_loglik_CS_time.R:27:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
    Apars <- create_area_params(Apars[1], Apars[2], Apars[3], Apars[4])
    ^~~~~
```
[R/DAISIE_loglik_CS_time.R:39:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L39) *style:* **Commented code should be removed.**
```r
#parsvec[1:4] = Apars
 ^~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:40:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L40) *style:* **Commented code should be removed.**
```r
#parsvec[5] = lac0
 ^~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:41:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L41) *style:* **Commented code should be removed.**
```r
#parsvec[6:7] = mupars
 ^~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:42:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L42) *style:* **Commented code should be removed.**
```r
#parsvec[8] = K0
 ^~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:43:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L43) *style:* **Commented code should be removed.**
```r
#parsvec[9] = gam0
 ^~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:44:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L44) *style:* **Commented code should be removed.**
```r
#parsvec[10] = laa0
 ^~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:45:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L45) *style:* **Commented code should be removed.**
```r
#parsvec[11] = island_ontogeny
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:46:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L46) *style:* **Commented code should be removed.**
```r
#parsvec[12] = kk
 ^~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:47:2:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L47) *style:* **Commented code should be removed.**
```r
#parsvec[13] = ddep
 ^~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:49:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_loglik_rhs_time <- function(t, x, parsvec) {
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:55:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L55) *style:* **Variable and function name style should be snake_case.**
```r
  Apars <- parsvec[1:4]
  ^~~~~
```
[R/DAISIE_loglik_CS_time.R:57:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L57) *style:* **Variable and function name style should be snake_case.**
```r
  Epars <- parsvec[6:7]
  ^~~~~
```
[R/DAISIE_loglik_CS_time.R:58:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L58) *style:* **Variable and function name style should be snake_case.**
```r
  K0 <- parsvec[8]
  ^~
```
[R/DAISIE_loglik_CS_time.R:110:40:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L110) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    muvec[il2] * nn[in2] * xx1[ix2] + -(muvec[il3] + lacvec[il3]) *
                                       ^
```
[R/DAISIE_loglik_CS_time.R:116:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L116) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    -(muvec[il3 + 1] + lacvec[il3 + 1]) * nn[in3 + 1] * xx2[ix3] +
     ^
```
[R/DAISIE_loglik_CS_time.R:118:11:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L118) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dx3 <- -(laavec[il3[1]] + lacvec[il3[1]] + gamvec[il3[1]] +
          ^
```
[R/DAISIE_loglik_CS_time.R:123:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L123) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_loglik_rhs_time2 <- function(t, x, parsvec) {
^~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:130:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L130) *style:* **Variable and function name style should be snake_case.**
```r
  Apars <- parsvec[1:4]
  ^~~~~
```
[R/DAISIE_loglik_CS_time.R:132:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  Epars <- parsvec[6:7]
  ^~~~~
```
[R/DAISIE_loglik_CS_time.R:133:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L133) *style:* **Variable and function name style should be snake_case.**
```r
  K0 <- parsvec[8]
  ^~
```
[R/DAISIE_loglik_CS_time.R:200:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L200) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    -(muvec[il3] + lacvec[il3]) * nn[in3] * xx1[ix3] - gamvec[il3] * xx1[ix3]
     ^
```
[R/DAISIE_loglik_CS_time.R:202:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L202) *style:* **Lines should not be more than 80 characters.**
```r
  # immigration when there are n+k species: Q^k,n -> Q^M,k_n; n+k species present
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:210:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    -(muvec[il3 + 1] + lacvec[il3 + 1]) * nn[in3 + 1] * xx2[ix3] +
     ^
```
[R/DAISIE_loglik_CS_time.R:212:20:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L212) *style:* **Trailing whitespace is superfluous.**
```r
  # only when k = 1
                   ^~~~~~~
```
[R/DAISIE_loglik_CS_time.R:214:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L214) *style:* **Lines should not be more than 80 characters.**
```r
  # cladogenesis in one of the n-1 species: Q_M,n-1 -> Q_M,n; n+k-1 species present; rate once
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:215:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L215) *style:* **Lines should not be more than 80 characters.**
```r
  # extinction in one of the n+1 species: Q_M,n+1 -> Q_M,n; n+k+1 species present
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:219:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L219) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    -(lacvec[il3] + muvec[il3]) * nn[in3] * xx3[ix3] +
     ^
```
[R/DAISIE_loglik_CS_time.R:220:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L220) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    -(laavec[il3] + gamvec[il3]) * xx3[ix3]
     ^
```
[R/DAISIE_loglik_CS_time.R:225:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L225) *style:* **Commented code should be removed.**
```r
  # pars1[1:4] = Apars
    ^~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:226:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L226) *style:* **Commented code should be removed.**
```r
  # pars1[5] = lac0
    ^~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:227:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L227) *style:* **Commented code should be removed.**
```r
  # pars1[6:7] = mupars
    ^~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:228:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L228) *style:* **Commented code should be removed.**
```r
  # pars1[8] = K0
    ^~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:229:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L229) *style:* **Commented code should be removed.**
```r
  # pars1[9] = gam0
    ^~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:230:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L230) *style:* **Commented code should be removed.**
```r
  # pars1[10] = laa0
    ^~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:231:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L231) *style:* **Commented code should be removed.**
```r
  # pars1[11] = island_ontogeny
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:232:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L232) *style:* **Commented code should be removed.**
```r
  # pars1[12] = t
    ^~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:234:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L234) *style:* **Variable and function name style should be snake_case.**
```r
  Apars <- pars1[1:4]
  ^~~~~
```
[R/DAISIE_loglik_CS_time.R:236:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L236) *style:* **Variable and function name style should be snake_case.**
```r
  Epars <- pars1[6:7]
  ^~~~~
```
[R/DAISIE_loglik_CS_time.R:237:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L237) *style:* **Variable and function name style should be snake_case.**
```r
  K0 <- pars1[8]
  ^~
```
[R/DAISIE_loglik_CS_time.R:249:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L249) *style:* **Variable and function name style should be snake_case.**
```r
  lacA <- lac0
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:250:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L250) *style:* **Variable and function name style should be snake_case.**
```r
  gamA <- gam0
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:251:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L251) *style:* **Variable and function name style should be snake_case.**
```r
  KA <- area * K0
  ^~
```
[R/DAISIE_loglik_CS_time.R:253:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L253) *style:* **Variable and function name style should be snake_case.**
```r
  K <- KA
  ^
```
[R/DAISIE_loglik_CS_time.R:254:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L254) *style:* **Variable and function name style should be snake_case.**
```r
  lacgamK <- c(lacgam, K)
  ^~~~~~~
```
[R/DAISIE_loglik_CS_time.R:258:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS_time.R#L258) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_integrate_time <- function(initprobs,
^~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS.R:1:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L1) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_loglik_rhs_precomp <- function(pars,lx)
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS.R:1:44:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L1) *style:* **Commas should always have a space after.**
```r
DAISIE_loglik_rhs_precomp <- function(pars,lx)
                                           ^
```
[R/DAISIE_loglik_CS.R:2:1:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L2) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/DAISIE_loglik_CS.R:3:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L3) *style:* **Use <-, not =, for assignment.**
```r
  lac = pars[1]
      ^
```
[R/DAISIE_loglik_CS.R:4:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L4) *style:* **Use <-, not =, for assignment.**
```r
  mu = pars[2]
     ^
```
[R/DAISIE_loglik_CS.R:5:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  K = pars[3]
  ^
```
[R/DAISIE_loglik_CS.R:5:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L5) *style:* **Use <-, not =, for assignment.**
```r
  K = pars[3]
    ^
```
[R/DAISIE_loglik_CS.R:6:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L6) *style:* **Use <-, not =, for assignment.**
```r
  gam = pars[4]
      ^
```
[R/DAISIE_loglik_CS.R:7:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L7) *style:* **Use <-, not =, for assignment.**
```r
  laa = pars[5]
      ^
```
[R/DAISIE_loglik_CS.R:8:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L8) *style:* **Use <-, not =, for assignment.**
```r
  kk = pars[6]
     ^
```
[R/DAISIE_loglik_CS.R:8:16:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L8) *warning:* **no visible global function definition for ‘divdepvec_time’**
```r
    lacgamK <- divdepvec_time(lacgam, pars1, lx, k1, ddep, island_ontogeny)
               ^~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS.R:9:8:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L9) *style:* **Use <-, not =, for assignment.**
```r
  ddep = pars[7]
       ^
```
[R/DAISIE_loglik_CS.R:11:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L11) *style:* **Use <-, not =, for assignment.**
```r
  nn = -2:(lx+2*kk+1)
     ^
```
[R/DAISIE_loglik_CS.R:11:14:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L11) *style:* **Put spaces around all infix operators.**
```r
  nn = -2:(lx+2*kk+1)
            ~^~
```
[R/DAISIE_loglik_CS.R:11:16:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L11) *style:* **Put spaces around all infix operators.**
```r
  nn = -2:(lx+2*kk+1)
              ~^~
```
[R/DAISIE_loglik_CS.R:11:19:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L11) *style:* **Put spaces around all infix operators.**
```r
  nn = -2:(lx+2*kk+1)
                 ~^~
```
[R/DAISIE_loglik_CS.R:12:7:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L12) *style:* **Use <-, not =, for assignment.**
```r
  lnn = length(nn)
      ^
```
[R/DAISIE_loglik_CS.R:13:6:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L13) *style:* **Use <-, not =, for assignment.**
```r
  nn = pmax(rep(0,lnn),nn)
     ^
```
[R/DAISIE_loglik_CS.R:13:19:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L13) *style:* **Commas should always have a space after.**
```r
  nn = pmax(rep(0,lnn),nn)
                  ^
```
[R/DAISIE_loglik_CS.R:13:24:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L13) *style:* **Commas should always have a space after.**
```r
  nn = pmax(rep(0,lnn),nn)
                       ^
```
[R/DAISIE_loglik_CS.R:15:5:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L15) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(ddep == 0)
    ^
```
[R/DAISIE_loglik_CS.R:16:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L16) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/DAISIE_loglik_CS.R:17:12:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L17) *style:* **Use <-, not =, for assignment.**
```r
    laavec = laa * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:17:26:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L17) *style:* **Commas should always have a space after.**
```r
    laavec = laa * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:18:12:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L18) *style:* **Use <-, not =, for assignment.**
```r
    lacvec = lac * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:18:26:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L18) *style:* **Commas should always have a space after.**
```r
    lacvec = lac * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:19:11:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L19) *style:* **Use <-, not =, for assignment.**
```r
    muvec = mu * rep(1,lnn)
          ^
```
[R/DAISIE_loglik_CS.R:19:24:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L19) *style:* **Commas should always have a space after.**
```r
    muvec = mu * rep(1,lnn)
                       ^
```
[R/DAISIE_loglik_CS.R:20:12:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L20) *style:* **Use <-, not =, for assignment.**
```r
    gamvec = gam * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:20:26:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L20) *style:* **Commas should always have a space after.**
```r
    gamvec = gam * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:21:12:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L21) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  } else if(ddep == 1)
           ^
```
[R/DAISIE_loglik_CS.R:22:3:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L22) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/DAISIE_loglik_CS.R:23:12:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L23) *style:* **Use <-, not =, for assignment.**
```r
    laavec = laa * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:23:26:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L23) *style:* **Commas should always have a space after.**
```r
    laavec = laa * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:24:12:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L24) *style:* **Use <-, not =, for assignment.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
           ^
```
[R/DAISIE_loglik_CS.R:24:25:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L24) *style:* **Commas should always have a space after.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
                        ^
```
[R/DAISIE_loglik_CS.R:24:30:](https://github.com/rsetienne/DAISIE/blob/49178a56da9610f819b9f6dd221aa5dcdc97f214/R/DAISIE_loglik_CS.R#L24) *style:* **Commas should always have a space after.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
                             ^
```


These libraries are used anymore


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Taskcluster-GitHub attempted to create a task for this event with the following scopes:

```
[
  "assume:repo:github.com/mozilla/code-review:pull-request",
  "queue:route:statuses",
  "queue:scheduler-id:taskcluster-github"
]
```

The expansion of these scopes is not sufficient to create the task, leading to the following:

Client ID static/taskcluster/github does not have sufficient scopes and is missing the following scopes:

```
{
  "AnyOf": [
    {
      "AnyOf": [
        "queue:create-task:highest:aws-provisioner-v1/github-worker",
        "queue:create-task:very-high:aws-provisioner-v1/github-worker",
        "queue:create-task:high:aws-provisioner-v1/github-worker",
        "queue:create-task:medium:aws-provisioner-v1/github-worker",
        "queue:create-task:low:aws-provisioner-v1/github-worker",
        "queue:create-task:very-low:aws-provisioner-v1/github-worker",
        "queue:create-task:lowest:aws-provisioner-v1/github-worker"
      ]
    },
    {
      "AnyOf": [
        "queue:create-task:aws-provisioner-v1/github-worker",
        {
          "AllOf": [
            "queue:define-task:aws-provisioner-v1/github-worker",
            "queue:task-group-id:taskcluster-github/cgaqNjDzQRyw0xbwCuj3kA",
            "queue:schedule-task:taskcluster-github/cgaqNjDzQRyw0xbwCuj3kA/Zyx63mtFQCGzC8MYBNctHQ"
          ]
        }
      ]
    }
  ]
}
```

This request requires the client to satisfy the following scope expression:

```
{
  "AllOf": [
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/github-worker",
                "queue:create-task:very-high:aws-provisioner-v1/github-worker",
                "queue:create-task:high:aws-provisioner-v1/github-worker",
                "queue:create-task:medium:aws-provisioner-v1/github-worker",
                "queue:create-task:low:aws-provisioner-v1/github-worker",
                "queue:create-task:very-low:aws-provisioner-v1/github-worker",
                "queue:create-task:lowest:aws-provisioner-v1/github-worker"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/cgaqNjDzQRyw0xbwCuj3kA",
                "queue:schedule-task:taskcluster-github/cgaqNjDzQRyw0xbwCuj3kA/Zyx63mtFQCGzC8MYBNctHQ"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-11-07T13:56:49.035Z

</details>


why have u removed update feature?


You forgot to change the description.


Why was this change made?


Successfully deployed to following URLs:

* https://commercetools-docs-kit-p3bwo8o94.now.sh
* https://commercetools-docs-kit.now.sh
* https://commercetools-docs-kit.commercetools.now.sh
* https://commercetools-docs-kit-git-master.commercetools.now.sh


请问运行的是那个文件


luca update


Successfully deployed to following URLs:

* https://nit-bssnv9hk3.now.sh
* https://nit.sketch-sh.now.sh
* https://nit-git-master.sketch-sh.now.sh


Successfully deployed to following URLs:

* https://serverlessrandombot-h0np27f1o.now.sh
* https://serverlessrandombot-psi-steel.now.sh
* https://serverlessrandombot.leoriether.now.sh
* https://serverlessrandombot-git-master.leoriether.now.sh


Sekunda pauzy dla docenienia tego sposobu generowania danych <3


Successfully deployed to following URLs:

* https://mm-test-31ot4z80p.now.sh
* https://mm-test-zeta-pink.now.sh
* https://mm-test.lkatartn.now.sh
* https://mm-test-git-master.lkatartn.now.sh


thx


Deployment failed with the following error:

~~~
invalid json response body at https://api.zeit.co/v10/now/deployments reason: Unexpected token A in JSON at position 0
~~~


The sensor_exclusion.jpg shows a different model, where there are also holes for the front camera's.


Because of: https://github.com/Nefelim4ag/Ananicy/issues/172


I forgot to add that you better change the argument of the other dump() function from char* to const char* because then in client code also a std::string's c_str() method can be used and I think newer compiler versions will raise a warning too when you use dump("Here is my text") if the argument is a non-const char*.

Thanks.


Successfully deployed to following URLs:

* https://abschaffenjetzt-i1iwb9ggw.now.sh
* https://abschaffen.jetzt
* https://*.abschaffen.jetzt
* https://abschaffen.now.sh
* https://abschaffenjetzt.nicolindemann.now.sh
* https://abschaffenjetzt-git-master.nicolindemann.now.sh