[R/DAISIE_area_params.R:18:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_area_params.R#L18) *style:* **functions should have cyclomatic complexity of less than 15, this has 31.**
```r
are_area_pars <- function(area_pars) {
^
```
[R/DAISIE_area_params.R:70:49:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_area_params.R#L70) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
                             sea_level_frequency){
                                                ^~
```
[R/DAISIE_check_format.R:6:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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:104:7:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_check_format.R#L104) *style:* **Commented code should be removed.**
```r
    # if (!"branching_times" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:105:7:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_check_format.R#L105) *style:* **Commented code should be removed.**
```r
    # if (!"stac" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:106:7:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_check_format.R#L106) *style:* **Commented code should be removed.**
```r
    # if (!"missing_species" %in% names(simulation_outputs)) return(FALSE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_check_format.R:120:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_check_format.R#L120) *style:* **functions should have cyclomatic complexity of less than 15, this has 75.**
```r
are_DAISIE_create_sim_pars <- function(pars) {
^
```
[R/DAISIE_check_format.R:120:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_check_format.R#L120) *style:* **Variable and function name style should be snake_case.**
```r
are_DAISIE_create_sim_pars <- function(pars) {
^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_island.R:18:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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:27:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_create_sim_params.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_create_sim_pars <- function(time = 10,
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_create_sim_params.R:28:31:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_create_sim_params.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
                              M = 1000,
                              ^
```
[R/DAISIE_data.R:8:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_ExpEIN.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:6:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_ExpEIN.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:7:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_ExpEIN.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:27:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_ExpEIN.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:28:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_ExpEIN.R#L31) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^~
```
[R/DAISIE_ExpEIN.R:37:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_ExpEIN.R#L37) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/DAISIE_ExpEIN.R:39:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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.R:13:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_CS.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 38.**
```r
DAISIE_format_CS <- function(island_replicates,
^
```
[R/DAISIE_format_CS.R:13:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_CS.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_format_CS <- function(island_replicates,
^~~~~~~~~~~~~~~~
```
[R/DAISIE_format_CS.R:15:30:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_CS.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                             M,
                             ^
```
[R/DAISIE_format_CS.R:57:51:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_CS.R#L57) *style:* **Commas should always have a space after.**
```r
      second_line_stts <- lapply(stt_list, "[", 2,)
                                                  ^
```
[R/DAISIE_format_CS.R:79:7:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_CS.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
      nI <- unlist(nI_list)
      ^~
```
[R/DAISIE_format_CS.R:80:7:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_CS.R#L80) *style:* **Variable and function name style should be snake_case.**
```r
      nA <- unlist(nA_list)
      ^~
```
[R/DAISIE_format_CS.R:81:7:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_CS.R#L81) *style:* **Variable and function name style should be snake_case.**
```r
      nC <- unlist(nC_list)
      ^~
```
[R/DAISIE_format_GW.R:17:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L54) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
        for (j in 1:length(full_list[[i]]$taxon_list)) {
                  ^
```
[R/DAISIE_format_GW.R:55:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L55) *style:* **Lines should not be more than 80 characters.**
```r
          init_nonend_spec_list[[i]] <- full_list[[i]]$taxon_list[[1]]$init_nonend_spec
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:56:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
          init_end_spec_list[[i]] <- full_list[[i]]$taxon_list[[1]]$init_end_spec
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:57:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
          carrying_capacity_list[[i]] <- full_list[[i]]$taxon_list[[1]]$carrying_capacity
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:71:14:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L71) *style:* **Commas should always have a space after.**
```r
    stt_all[,"Time"] <- rev(seq(from = 0,
             ^
```
[R/DAISIE_format_GW.R:76:11:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L76) *warning:* **local variable ‘row_index’ assigned but may not be used**
```r
          row_index <- max(which(stt_list[[x]][, "Time"] >= the_age))
          ^~~~~~~~~
```
[R/DAISIE_format_GW.R:93:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
          store_richness_time_slice[x, ] <- stt_list[[x]][max(which(stt_list[[x]][, "Time"] >= the_age)), 2:4]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:113:25:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L113) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
              for (j in 1:length(full_list[[i]]$taxon_list)) {
                        ^
```
[R/DAISIE_format_GW.R:114:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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]]$taxon_list)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_format_GW.R:114:66:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_GW.R#L114) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
                taxon_sublist_name <- paste0("taxon_sublist_", c(1:length(full_list[[i]]$taxon_list)))
                                                                 ^
```
[R/DAISIE_format_GW.R:116:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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:28:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_format_IW <- function(island_replicates,
^~~~~~~~~~~~~~~~
```
[R/DAISIE_format_IW.R:30:30:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
                             M,
                             ^
```
[R/DAISIE_format_IW.R:36:15:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L36) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
  for (rep in 1:length(island_replicates)) {
              ^
```
[R/DAISIE_format_IW.R:44:17:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L44) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (i in 1:length(the_island$taxon_list)) {
                ^
```
[R/DAISIE_format_IW.R:86:17:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L86) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (y in 1:length(the_island$taxon_list)) {
                ^
```
[R/DAISIE_format_IW.R:106:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L106) *style:* **Variable and function name style should be snake_case.**
```r
Add_brt_table <- function(island) {
^~~~~~~~~~~~~
```
[R/DAISIE_format_IW.R:117:15:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L117) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
    for (i in 1:length(island)) {
              ^
```
[R/DAISIE_format_IW.R:139:17:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L139) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (i in 1:length(island_no_stac1or5)) {
                ^
```
[R/DAISIE_format_IW.R:143:7:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L143) *style:* **Variable and function name style should be snake_case.**
```r
      brts_IWK <- matrix(ncol = 4, nrow = length(brts))
      ^~~~~~~~
```
[R/DAISIE_format_IW.R:145:17:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L145) *warning:* **Avoid 1:length(...) expressions, use seq_len.**
```r
      for (i in 1:length(btimes)) {
                ^
```
[R/DAISIE_format_IW.R:161:17:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_format_IW.R#L161) *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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_IC.R#L125) *style:* **Variable and function name style should be snake_case.**
```r
  WIC <- -2 * MLE_obs$loglik - 2 * mean(LL - MLE)
  ^~~
```
[R/DAISIE_IC.R:126:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_IC.R#L126) *style:* **Variable and function name style should be snake_case.**
```r
  AICb <- -2 * MLE_obs$loglik - 4 * mean(LL - MLE_obs)
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:11:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L13) *warning:* **local variable ‘ext_pars’ assigned but may not be used**
```r
  ext_pars <- pars1[6:7]
  ^~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:15:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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:18:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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:43:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L43) *style:* **Commented code should be removed.**
```r
#parsvec[1:4] = area_pars
 ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:44:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L44) *style:* **Commented code should be removed.**
```r
#parsvec[5] = lac0
 ^~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:45:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L45) *style:* **Commented code should be removed.**
```r
#parsvec[6:7] = mupars
 ^~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:46:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L46) *style:* **Commented code should be removed.**
```r
#parsvec[8] = K0
 ^~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:47:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L47) *style:* **Commented code should be removed.**
```r
#parsvec[9] = gam0
 ^~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:48:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L48) *style:* **Commented code should be removed.**
```r
#parsvec[10] = laa0
 ^~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:49:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L49) *style:* **Commented code should be removed.**
```r
#parsvec[11] = island_ontogeny
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:50:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L50) *style:* **Commented code should be removed.**
```r
#parsvec[12] = kk
 ^~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:51:2:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L51) *style:* **Commented code should be removed.**
```r
#parsvec[13] = ddep
 ^~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:53:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L53) *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:55:24:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L55) *style:* **Put spaces around all infix operators.**
```r
  lx <- (length(x) - 1)/2
                      ~^~
```
[R/DAISIE_loglik_CS_time.R:62:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L62) *style:* **Variable and function name style should be snake_case.**
```r
  K0 <- parsvec[8]
  ^~
```
[R/DAISIE_loglik_CS_time.R:120:40:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L120) *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:126:6:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L126) *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:128:11:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L128) *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:133:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L133) *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:135:20:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L135) *style:* **Put spaces around all infix operators.**
```r
  lx <- (length(x))/3
                  ~^~
```
[R/DAISIE_loglik_CS_time.R:143:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L143) *style:* **Variable and function name style should be snake_case.**
```r
  K0 <- parsvec[8]
  ^~
```
[R/DAISIE_loglik_CS_time.R:213:6:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L213) *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:215:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L215) *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:223:6:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L223) *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:227:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L227) *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:228:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L228) *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:232:6:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L232) *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:233:6:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L233) *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:238:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L238) *style:* **Commented code should be removed.**
```r
  # pars1[1:4] = area_pars
    ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:239:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L239) *style:* **Commented code should be removed.**
```r
  # pars1[5] = lac0
    ^~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:240:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L240) *style:* **Commented code should be removed.**
```r
  # pars1[6:7] = mupars
    ^~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:241:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L241) *style:* **Commented code should be removed.**
```r
  # pars1[8] = K0
    ^~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:242:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L242) *style:* **Commented code should be removed.**
```r
  # pars1[9] = gam0
    ^~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:243:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L243) *style:* **Commented code should be removed.**
```r
  # pars1[10] = laa0
    ^~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:244:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L244) *style:* **Commented code should be removed.**
```r
  # pars1[11] = island_ontogeny
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:245:5:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L245) *style:* **Commented code should be removed.**
```r
  # pars1[12] = t
    ^~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:250:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L250) *style:* **Variable and function name style should be snake_case.**
```r
  K0 <- pars1[8]
  ^~
```
[R/DAISIE_loglik_CS_time.R:262:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L262) *style:* **Variable and function name style should be snake_case.**
```r
  lacA <- lac0
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:263:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L263) *style:* **Variable and function name style should be snake_case.**
```r
  gamA <- gam0
  ^~~~
```
[R/DAISIE_loglik_CS_time.R:264:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L264) *style:* **Variable and function name style should be snake_case.**
```r
  KA <- area * K0
  ^~
```
[R/DAISIE_loglik_CS_time.R:266:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L266) *style:* **Variable and function name style should be snake_case.**
```r
  K <- KA
  ^
```
[R/DAISIE_loglik_CS_time.R:267:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L267) *style:* **Variable and function name style should be snake_case.**
```r
  lacgamK <- c(lacgam, K)
  ^~~~~~~
```
[R/DAISIE_loglik_CS_time.R:271:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L271) *style:* **Variable and function name style should be snake_case.**
```r
DAISIE_integrate_time <- function(initprobs,
^~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:279:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L279) *style:* **Lines should not be more than 80 characters.**
```r
  do_fun_1 <- grepl(pattern = "lx <- \\(length\\(x\\) - 1\\)/2", x = function_as_text)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS_time.R:280:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS_time.R#L280) *style:* **Lines should not be more than 80 characters.**
```r
  do_fun_2 <- grepl(pattern = "lx <- \\(length\\(x\\)\\)/3", x = function_as_text)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DAISIE_loglik_CS.R:1:1:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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/9425880415fd2599867b00c3e85fb572a417892c/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:24:43:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L24) *style:* **Put spaces around all infix operators.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
                                         ~^~
```
[R/DAISIE_loglik_CS.R:25:11:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L25) *style:* **Use <-, not =, for assignment.**
```r
    muvec = mu * rep(1,lnn)
          ^
```
[R/DAISIE_loglik_CS.R:25:24:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L25) *style:* **Commas should always have a space after.**
```r
    muvec = mu * rep(1,lnn)
                       ^
```
[R/DAISIE_loglik_CS.R:26:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L26) *style:* **Use <-, not =, for assignment.**
```r
    gamvec = gam * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:26:26:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L26) *style:* **Commas should always have a space after.**
```r
    gamvec = gam * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:27:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L27) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  } else if(ddep == 2)
           ^
```
[R/DAISIE_loglik_CS.R:28:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L28) *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:29:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L29) *style:* **Use <-, not =, for assignment.**
```r
    laavec = laa * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:29:26:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L29) *style:* **Commas should always have a space after.**
```r
    laavec = laa * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:30:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L30) *style:* **Use <-, not =, for assignment.**
```r
    lacvec = pmax(rep(0,lnn),lac * exp(-nn/K))
           ^
```
[R/DAISIE_loglik_CS.R:30:25:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L30) *style:* **Commas should always have a space after.**
```r
    lacvec = pmax(rep(0,lnn),lac * exp(-nn/K))
                        ^
```
[R/DAISIE_loglik_CS.R:30:30:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L30) *style:* **Commas should always have a space after.**
```r
    lacvec = pmax(rep(0,lnn),lac * exp(-nn/K))
                             ^
```
[R/DAISIE_loglik_CS.R:30:43:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L30) *style:* **Put spaces around all infix operators.**
```r
    lacvec = pmax(rep(0,lnn),lac * exp(-nn/K))
                                         ~^~
```
[R/DAISIE_loglik_CS.R:31:11:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L31) *style:* **Use <-, not =, for assignment.**
```r
    muvec = mu * rep(1,lnn)
          ^
```
[R/DAISIE_loglik_CS.R:31:24:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L31) *style:* **Commas should always have a space after.**
```r
    muvec = mu * rep(1,lnn)
                       ^
```
[R/DAISIE_loglik_CS.R:32:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L32) *style:* **Use <-, not =, for assignment.**
```r
    gamvec = gam * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:32:26:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L32) *style:* **Commas should always have a space after.**
```r
    gamvec = gam * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:33:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L33) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  } else if(ddep == 11)
           ^
```
[R/DAISIE_loglik_CS.R:34:3:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L34) *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:35:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L35) *style:* **Use <-, not =, for assignment.**
```r
    laavec = laa * rep(1,lnn)
           ^
```
[R/DAISIE_loglik_CS.R:35:26:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L35) *style:* **Commas should always have a space after.**
```r
    laavec = laa * rep(1,lnn)
                         ^
```
[R/DAISIE_loglik_CS.R:36:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L36) *style:* **Use <-, not =, for assignment.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
           ^
```
[R/DAISIE_loglik_CS.R:36:25:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L36) *style:* **Commas should always have a space after.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
                        ^
```
[R/DAISIE_loglik_CS.R:36:30:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L36) *style:* **Commas should always have a space after.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
                             ^
```
[R/DAISIE_loglik_CS.R:36:43:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L36) *style:* **Put spaces around all infix operators.**
```r
    lacvec = pmax(rep(0,lnn),lac * (1 - nn/K))
                                         ~^~
```
[R/DAISIE_loglik_CS.R:37:11:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L37) *style:* **Use <-, not =, for assignment.**
```r
    muvec = mu * rep(1,lnn)
          ^
```
[R/DAISIE_loglik_CS.R:37:24:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L37) *style:* **Commas should always have a space after.**
```r
    muvec = mu * rep(1,lnn)
                       ^
```
[R/DAISIE_loglik_CS.R:38:12:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L38) *style:* **Use <-, not =, for assignment.**
```r
    gamvec = pmax(rep(0,lnn),gam * (1 - nn/K))
           ^
```
[R/DAISIE_loglik_CS.R:38:25:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L38) *style:* **Commas should always have a space after.**
```r
    gamvec = pmax(rep(0,lnn),gam * (1 - nn/K))
                        ^
```
[R/DAISIE_loglik_CS.R:38:30:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L38) *style:* **Commas should always have a space after.**
```r
    gamvec = pmax(rep(0,lnn),gam * (1 - nn/K))
                             ^
```
[R/DAISIE_loglik_CS.R:38:43:](https://github.com/rsetienne/DAISIE/blob/9425880415fd2599867b00c3e85fb572a417892c/R/DAISIE_loglik_CS.R#L38) *style:* **Put spaces around all infix operators.**
```r
    gamvec = pmax(rep(0,lnn),gam * (1 - nn/K))
                                         ~^~
```


@danielnaber So dictionary version was moved from dependency to dependencyManagement section (by @FredKruse) in https://github.com/languagetool-org/languagetool/commit/fceff8b63d3585d082a15b0f192fe787fae8af97#diff-b7c5791fa6d481d34162cae172c77ccd
Shall I remove dependencyManagement section altogether and just have version sepcified in dependency section?


Wow you can really dance


What if you use a Unix Terminal inside Windows? There you can use Unix commands. One good example is [Cygwin](http://www.cygwin.com/). Actually I'm just waiting to have the fix in place inside this [issue](https://github.com/gatsbyjs/gatsby/issues/17335#issuecomment-529187007), then there won't be a need for this "hack".


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


This was supposed to be for #4


Successfully deployed to following URLs:

* https://javascript30-rl1rawp8b.now.sh
* https://javascript30-henna-xi.now.sh
* https://javascript30.jkkim98.now.sh
* https://javascript30-git-master.jkkim98.now.sh


<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/rail/shipit:branch:skip_phases",
  "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:releng-t/linux",
        "queue:create-task:very-high:releng-t/linux",
        "queue:create-task:high:releng-t/linux",
        "queue:create-task:medium:releng-t/linux",
        "queue:create-task:low:releng-t/linux",
        "queue:create-task:very-low:releng-t/linux",
        "queue:create-task:lowest:releng-t/linux"
      ]
    },
    {
      "AnyOf": [
        "queue:create-task:releng-t/linux",
        {
          "AllOf": [
            "queue:define-task:releng-t/linux",
            "queue:task-group-id:taskcluster-github/UAl2aX6VT3GEKUES98Bzxw",
            "queue:schedule-task:taskcluster-github/UAl2aX6VT3GEKUES98Bzxw/H892Iyo9SGiL-UwaGI_GsA"
          ]
        }
      ]
    }
  ]
}
```

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:releng-t/linux",
                "queue:create-task:very-high:releng-t/linux",
                "queue:create-task:high:releng-t/linux",
                "queue:create-task:medium:releng-t/linux",
                "queue:create-task:low:releng-t/linux",
                "queue:create-task:very-low:releng-t/linux",
                "queue:create-task:lowest:releng-t/linux"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:releng-t/linux",
            {
              "AllOf": [
                "queue:define-task:releng-t/linux",
                "queue:task-group-id:taskcluster-github/UAl2aX6VT3GEKUES98Bzxw",
                "queue:schedule-task:taskcluster-github/UAl2aX6VT3GEKUES98Bzxw/H892Iyo9SGiL-UwaGI_GsA"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-11-20T16:29:12.449Z

</details>


Successfully deployed to following URLs:

* https://weather-app-fu26fokh8.now.sh
* https://weather-app-perfect-dusky-dolphin.now.sh
* https://weather-app.ilyalesik.now.sh
* https://weather-app-git-master.ilyalesik.now.sh


Wow, dude, so good!


# 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)|


For reference: `urllib.requests.open` has a tendency to disconnect/fail to connect when run on Travis. Running the tests (or regular genomepy) locally does not. So this part does not alter the behavior of the program.


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


use this


Adresses


+1 to rename to `newFormLoadingIndicator`


@agrawalshriya You stole my PR :D


Successfully deployed to following URLs:

* https://heron-xjxpphdey.now.sh
* https://heron-three-topaz.now.sh
* https://heronstory.now.sh
* https://heron.heyrishi.now.sh
* https://heron-git-master.heyrishi.now.sh


What type of error/exception appears here? It would be good if we could catch the specific type of exception that appears here instead of a wild card.


TeamCity Identity and Access Management / identity-hostedpages [Build 1010](https://teamcity.nice.org.uk/viewLog.html?buildId=61942&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) is now running


Deployment failed with the following error:

~~~
The domain used as an alias zeit-iv.com is not verified yet. Please verify it.
~~~


Successfully deployed to following URLs:

* https://chameleon-bp7uaejz5.now.sh
* https://chameleon-dead-plane.now.sh
* https://chameleon.ebury.now.sh
* https://chameleon-git-master.ebury.now.sh


ahi la lleva


TeamCity Identity and Access Management / identity-hostedpages [Build 1011](https://teamcity.nice.org.uk/viewLog.html?buildId=61943&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) is now running


can we go home


Successfully deployed to following URLs:

* https://heron-crsrlab77.now.sh
* https://heron-three-topaz.now.sh
* https://heronstory.now.sh
* https://heron.heyrishi.now.sh
* https://heron-git-master.heyrishi.now.sh


does this mean i have to remove getPointerElementType() too


Successfully deployed to following URLs:

* https://pwavcoin-cj676v4io.now.sh
* https://pwavcoin.now.sh
* https://vcointransfers.com
* https://pwavcoin.erickoficial69.now.sh
* https://pwavcoin-git-master.erickoficial69.now.sh


@helioseven I'd take a PR to improve the comment 👍


Successfully deployed to following URLs:

* https://ui-dokhda3uw.now.sh
* https://ui.manifold.now.sh
* https://ui-git-master.manifold.now.sh


TeamCity Identity and Access Management / identity-hostedpages [Build 1010-IDAM-304-Migration](https://teamcity.nice.org.uk/viewLog.html?buildId=61942&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) outcome was **UNKNOWN**
Summary: Canceled (Tests passed: 62) Build time: 00:01:51


Successfully deployed to following URLs:

* https://heron-bnsluj5q3.now.sh
* https://heron-three-topaz.now.sh
* https://heronstory.now.sh
* https://heron.heyrishi.now.sh
* https://heron-git-master.heyrishi.now.sh


#3 완료


TeamCity Identity and Access Management / identity-hostedpages [Build 1011-IDAM-304-Migration](https://teamcity.nice.org.uk/viewLog.html?buildId=61943&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) outcome was **SUCCESS**
Summary: Tests passed: 62 Build time: 00:01:58


Successfully deployed to following URLs:

* https://tietorakenteet-ja-algoritmit-s19-material-e9qagjuiq.now.sh
* https://tira-s19.mooc.fi
* https://tietorakenteet-ja-algoritmit-s19-material.mooc.now.sh
* https://tietorakenteet-ja-algoritmit-s19-material-git-master.mooc.now.sh


Так, ну как ни странно, и строчка с версией тоже лишняя) Эта версия задана в spring-boot-starter-parent)


Successfully deployed to following URLs:

* https://ripe-components-vue-lavdwrnda.now.sh
* https://ripe-components-vue.platforme.now.sh
* https://ripe-components-vue-git-master.platforme.now.sh


Successfully deployed to following URLs:

* https://heron-73x9drs61.now.sh
* https://heron-three-topaz.now.sh
* https://heronstory.now.sh
* https://heron.heyrishi.now.sh
* https://heron-git-master.heyrishi.now.sh


Successfully deployed to following URLs:

* https://mubank-copy-i6bmzif2s.now.sh
* https://mubank-copy.fer2ap.now.sh
* https://mubank-copy-git-master.fer2ap.now.sh


Successfully deployed to following URLs:

* https://read-and-watch-g12yqg2qm.now.sh
* https://read-and-watch.com
* https://read-and-watch.psy667.now.sh
* https://read-and-watch-git-master.psy667.now.sh


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/2051) complete for merge to master.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/branch/master/index.html).

19 tests passed, 0 tests failed and 0 tests skipped in 13247 seconds

Tests produced 361 warnings. 361 were for lower-than-expected alignment scores


Ah sorry, I was not aware of that commit. @FredKruse do you remember the reason to use `dependencyManagement`?


> Will this work if i have R version 3.5.2?

Sorry, I didn't test R version 3.5.2. But if you follow this conda installation guide, conda will maintain a R version of 3.6.1, which works for me.

Best regards
Wallace


Successfully deployed to following URLs:

* https://badgennet-3cetplhqh.now.sh
* https://badgen.net
* https://flat.badgen.net
* https://badgennet.badgen.now.sh
* https://badgennet-git-master.badgen.now.sh


Any chance you still have a local checkout of the upstream of this repo, or a memory of whether you made and/or merged this PR?

I'm trying to recover some lost history for pygae/galgebra, which ends at pygae/galgebra@fab9012af52b2c9cee378ea0f923394dd3383d0b (newer than this commit)


aa


@amio, now it's always flat :laughing:


Successfully deployed to following URLs:

* https://confluenza-oefhv5uy1.now.sh
* https://confluenza.online
* https://confluenza.confluenza-online.now.sh
* https://confluenza-git-master.confluenza-online.now.sh


Yay! :tada:


Imagine you're using a CLI at 2am and you just hear LOADING WITH SPOTIFY URI


Successfully deployed to following URLs:

* https://front-end-eoef6xuvr.now.sh
* https://use-my-tools.now.sh
* https://front-end.use-my-tools.now.sh
* https://front-end-git-master.use-my-tools.now.sh


@JuliaRegistrator register

Release notes:

Updated documentation


Error while trying to register: "Tag with name `0.1.1` already exists and points to a different commit"


Successfully deployed to following URLs:

* https://pwavcoin-lpk98a4jw.now.sh
* https://pwavcoin.now.sh
* https://vcointransfers.com
* https://pwavcoin.erickoficial69.now.sh
* https://pwavcoin-git-master.erickoficial69.now.sh


Successfully deployed to following URLs:

* https://front-end-izyzeitir.now.sh
* https://front-end-omega-puce.now.sh
* https://front-end.hackernewstrolls.now.sh
* https://front-end-git-master.hackernewstrolls.now.sh


Ha or not actually, look like IMAGE_TAG is badly populated
```
docker build -t $BACKEND_IMAGE_NAME:$IMAGE_TAG -f Dockerfile .
invalid argument "index.docker.io/scpomedialab/hyphe_backend:([[" for "-t, --tag" flag: invalid reference format
See 'docker build --help'.
ERROR: Job failed: exit code 125
```


Successfully deployed to following URLs:

* https://cotmot-548v132wx.now.sh
* https://comot.vn
* https://cotmot.tranhiepqna.now.sh
* https://cotmot-git-master.tranhiepqna.now.sh


Registration pull request updated: [JuliaRegistries/General/5630](https://github.com/JuliaRegistries/General/pull/5630)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.1 -m "<description of version>" cce878fc4c0c927ed64122595296c3786b855604
git push origin v0.1.1
```


Successfully deployed to following URLs:

* https://vela-store-ar63ja80t.now.sh
* https://velabikes.com.br
* https://vela-store.velabikes1.now.sh
* https://vela-store-git-master.velabikes1.now.sh


### Demographic history

This repository contains all scripts for the manuscript titled " " (Sarabia et al., in preparation)


tu chyba inna nazwa klasy powinna być


Successfully deployed to following URLs:

* https://switcheolytics-api-tqyilqjydt.now.sh
* https://api.switcheolytics.tech


i tutaj opis też


remove  index.html


Should be fixed with PR #238


Successfully deployed to following URLs:

* https://front-end-aqt6cqt41.now.sh
* https://front-end-omega-puce.now.sh
* https://front-end.hackernewstrolls.now.sh
* https://front-end-git-master.hackernewstrolls.now.sh


Deployment failed with the following error:

~~~
Unexpected error. Please try again later. ()
~~~


you said you removed dups and then tried to reimport and dups did not show.
hazarding a guess, unless you have dt set to re-read existing xmp files, it would have no way to know that you had dups as you have removed them from the library and now except for the xmp files which you don't re-read, dt has no way to know they even exist.


Successfully deployed to following URLs:

* https://casamia-1wh8qlah8.now.sh
* https://casamia.chensiyu.now.sh
* https://casamia-git-master.chensiyu.now.sh


TeamCity Identity and Access Management / identity-hostedpages [Build 1012](https://teamcity.nice.org.uk/viewLog.html?buildId=61944&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) is now running


This was for testing only...
the real website will be added in abit after this test is done


WHY WONT IT WORK REEEEEEEEEEEE


Once done, feel free to add your own name to the credits


TeamCity Identity and Access Management / identity-hostedpages [Build 1012-IDAM-304-Migration](https://teamcity.nice.org.uk/viewLog.html?buildId=61944&buildTypeId=IdentityandAccessManagement_IdentityHostedpages) outcome was **SUCCESS**
Summary: Tests passed: 62 Build time: 00:01:57


I accidentally remove this one


Doh! I hate these two phase events... :P


@styfle 🤔 It looks like builders are replaced by "runtimes" https://zeit.co/docs/runtimes

Are we deprecating all builders? Is [`@now/next`](https://github.com/zeit/now/tree/master/packages/now-next) still recommended? I couldn't find any docs for builders now.


Successfully deployed to following URLs:

* https://bequia-forum-otbfh9z29.now.sh
* https://bequiaforum.com
* https://bequia-forum.ryancarville.now.sh
* https://bequia-forum-git-master.ryancarville.now.sh


We're having some weird troubles with this workaround right now and will possibly fix or roll it back in several days.


Successfully deployed to following URLs:

* https://gatsby-mdx-c80vc8n8i.now.sh
* https://gatsby-mdx-five-rosy.now.sh
* https://gatsby-mdx.efrenpastor.now.sh
* https://gatsby-mdx-git-master.efrenpastor.now.sh


Successfully deployed to following URLs:

* https://mcs-new-version-1cj4nd81n.now.sh
* https://mcs-new-version.m-c-s.now.sh
* https://mcs-new-version-git-master.m-c-s.now.sh


 Andela first challenge for preparing the bootcam

 Andela first challenge for preparing the **bootcamp** 👍


the application file that i have made is big for this. so i am going to mail both of them my work. Thanks


Are you sure the value here should be this instead of icons.populationIcon? (Seeing below the code of the function you moved here).


should be `sck-delay`


Don't you want to prove something like `Inj𝕌-inj : ∀ {X Y : Pi/.𝕌} → (Inj𝕌 X) ↔ (Inj𝕌 Y) → X ⟷ Y` here too, ie, Pi with fractionals is conservative over Pi without fractionals? (It is hard to prove without the free model)


Successfully deployed to following URLs:

* https://where-to-eat-obaqkwm5f.now.sh
* https://where-to-eat-glib-owl.now.sh
* https://where-to-eat.kollarovaa.now.sh
* https://where-to-eat-git-master.kollarovaa.now.sh


@tunnckoCore WAT? I need to submit everything through PR from now on 🙏


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


the negatives in this comment confuse me. "since we do not want the script not the reference"


this program includes C++


### Lipsum really

So we really were not able to find better filler text?


Successfully deployed to following URLs:

* https://front-end-ep8qtyub5.now.sh
* https://front-end-two-jet.now.sh
* https://front-end.pintereach-harms.now.sh
* https://front-end-git-master.pintereach-harms.now.sh


Great one! I was going to lay out some concerns of the copy plugin but you removed it here :)


Scripts to develop methodologies in digital carbon soil mapping


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* https://baseweb-37333e5te.now.sh
* https://baseweb.uber-ui-platform.now.sh
* https://baseweb-git-master.uber-ui-platform.now.sh


## Overview
There is too much wrong. If I would submit my changes I could just rewrite everything which would be (overall) faster.

## The guide
Overall it would be better to start from the ground and open source it, instead of publishing it on Google Docs he should use another platform like GitHub, GitLab etc, so that everyone can see and submit changes based on evidence and not based on years old and outdated "findings" - because that's what it is, it's a collection of outdated findings (with here and there some "comments" that it doesn't work on Windows build X ) and that's already pretty much it. I appricate his work and who helped him but some stuff is simply wrong, outdated and should not be followed.

## Credits
He mentioned some people (at the beginning) who apparently helped him to improve his guide, but he does not link to any source or their specific channels, there are some (I was counting 4) back links given but those aren't the links where he got the information from, because those links refering to other all-in-one tweak guides. What he does is he links to his GDrive and that's bad. Tools can have gotten taken-down for a reason or got an update in the meantime and I suggest that someone should download the tool from the official page instead.

There is also no copyright for the tools he hosts on Google Drive. Basically spoken there anren't any "real" credits given for this nor does he provides a link to the homepage he took it from. List only a few names is not enough and you don't know in which context those people are standing to him or this guide. You simply don't know if he got influenced by those people or not. Just because "my friend said" is not really a reference and only a claim than a prove. He did the same, in his video too "my friend xyz got 100 more fps". Yes, and does your friend tweaked the OS and why you mention it when he uses another OS?! You can't verify anything here, it's not helpful at all.

There is one mention, a guy who coded a little utility and that is the only exception he made. That however is more than okay. It was in the DWM (composition "killing" section).

## Self-advertising
He writes at the very beginning that this is "our guide "and not "his", if that were true why does he advertise "our" guide as his and why does he link to "his" channels (Youtube etc)?

## Wrong and outdated Infos - e.g. network "latency" section
The entire network latency topic is very critical and it's the reason why I did not (yet) fully integrated it in this GitHub guide.

One example; he mention that "ecncapability" should be disabled, while [others say it should be enabled](https://forums.elderscrollsonline.com/en/discussion/97277/enable-ctcp-and-ecn-in-windows-may-reduce-latency-in-some-online-applications). [Microsoft officially says that we should go with the defaults](http://www.microsoft.com/whdc/device/network/TCP_Chimney.mspx) (enabled). Whatever you do here, you only can fail because a) the articles are YEARS old b) Windows changed as well as online games c) depending on how the developer implemented the netcode it's good or bad (typically a developer tests his stuff against Windows defaults and not what some individuals "tweak").

Here are some (_not all_) official articles on the "net code" (_some are so old that are already been taken down_):
* http://blogs.technet.com/b/exchange/archive/2011/11/14/time-to-revisit-recommendations-around-windows-networking-enhancements-usually-called-microsoft-scalable-networking-pack.aspx
* http://msdn.microsoft.com/en-us/windows/hardware/gg463253
* http://download.microsoft.com/download/a/d/f/adf1347d-08dc-41a4-9084-623b1194d4b2/RSS_Server2008.docx
* http://download.microsoft.com/download/5/b/9/5b97017b-e28a-4bae-ba48-174cf47d23cd/net097_wh06.ppt
* http://blogs.technet.com/b/exchange/archive/2007/07/18/446400.aspx (one example which is down or under "rewrite status")
* http://blogs.technet.com/dmelanchthon/archive/2008/03/13/windows-server-2003-scalable-network-pack.aspx
* http://download.microsoft.com/download/8/E/D/8EDE21BC-0E3B-4E14-AAEA-9E2B03917A09/HSN_Deployment_Guide.doc
* https://blogs.technet.microsoft.com/onthewire/2014/01/21/tcp-offloadingchimney-rsswhat-is-it-and-should-i-disable-it/
* http://msdn.microsoft.com/en-us/windows/hardware/gg463253
* http://download.microsoft.com/download/a/d/f/adf1347d-08dc-41a4-9084-623b1194d4b2/RSS_Server2008.docx
* http://support.microsoft.com/kb/977977
* http://support.microsoft.com/kb/948496
* http://support.microsoft.com/kb/979614
* https://support.microsoft.com/en-us/help/4494445/tcp-receive-auto-tuning-level-feature-in-windows

NONE (!) of them are mentioned as reference in his guide and you see very fast that these are mostly for server SKUs. A lot of those "tweak toggles" are been added back in the old days eg. Vista etc. and if you check [Wikipedia](http://en.wikipedia.org/wiki/Explicit_Congestion_Notification) (which usually providing a better documentation on specific things than MS, you will notice they recommend enabling most of the stuff (again it's already Windows 10 default). It's impossible to verify the "better latency" claim without any specific details on what game it was tested on and if it was tested with an external network card or not (some professional cards including their own CPU on it). The entire circumstances are unclear and the user can't do anything except to blindly apply the mentioned tweaks without any background and "test" it, the problem is here that the user has other hardware and other circumstances.

## Changeing some toggles result in a "placebo effect"
MS even sometimes warns in their KB articles that this is application or game specific e.g. in case of  [Auto-Tuning](https://support.microsoft.com/en-us/help/4494445/tcp-receive-auto-tuning-level-feature-in-windows). I also highly doubt that you see any difference if your router/application/game doesn't support "feature" X which you enabled or disabled to "improve" something.

## My final conclusion
I do not claim to know everything, but that's the whole point in open source'ing a guide - others can see it and comment or fix (submit) their findings. However,  I do not mention stuff which are "critical" because as said, you can only fail. The Windows (10) net code is quite complex and changing the global defaults one one hand _could_ help but on the other hand it's placebo or doesn't work for your Browser or your apllications, and you typically use those apps more often and there is also the security and privacy factor.

There are a lot variables, I already wrote that lots of stuff is depending on e.g. Router/Firmware/Application/Game and how the net code got implemented within the game itself.

Battalion 1944 is one of the games which came to my mind with a good net code, they even [explained and reviewed the net code in detail](https://www.youtube.com/watch?v=mFzbJzl3zT8) and you can learn a lot of more from such ["in-depth" guides](https://www.youtube.com/watch?v=bAQH3saaVE0).  And of course, you have a reference and example which you can test against to check if that what was advertised as "tweak" really helps or not, otherwise it's just a claim with nothing behind.

The "best" (subjectively spoken) is if the game studio/developer address problems so that you do not have to "tweak" anything. The whole point should be that you use Windows (10) out of the box and play your games, if that doesn't work you should in (_my opinion_) contact the developer and only if he refuses or can't/won't fix it only then you should apply or think about a "tweak" (unless the tweak is "universal").


@amio Yes `builds` are deprecated. You can remove the property completely.

https://zeit.co/blog/zero-config


Successfully deployed to following URLs:

* https://front-end-8dx7g9rt1.now.sh
* https://front-end-ten-liart.now.sh
* https://airbnboptimal.now.sh
* https://front-end.airbnboptimal.now.sh
* https://front-end-git-master.airbnboptimal.now.sh


Successfully deployed to following URLs:

* https://mcs-new-version-pgiu2sb2o.now.sh
* https://mcs-new-version.m-c-s.now.sh
* https://mcs-new-version-git-master.m-c-s.now.sh


comment....


That's not the direction I need.


@masc4ii lets just include raw2mlv executable in mlv app instead of needing to install it


Successfully deployed to following URLs:

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* https://statickit.com
* https://statickit-site.unstacked.now.sh
* https://statickit-site-git-master.unstacked.now.sh


@victorMagalhaesPacheco, acho que precisa tirar o Space daqui, não?


Nope set to look for new XMP files….so I don’t think that is it…..to me it just seems like import is only one xmp per image…

From: ptilopteri <notifications@github.com>
Sent: November 20, 2019 11:48 AM
To: darktable-org/darktable <darktable@noreply.github.com>
Cc: Prior,Todd <priort@mcmaster.ca>; Comment <comment@noreply.github.com>
Subject: Re: [darktable-org/darktable] database: backup db for each new release. (e15db65)

you said you removed dups and then tried to reimport and dups did not show.
hazarding a guess, unless you have dt set to re-read existing xmp files, it would have no way to know that you had dups as you have removed them from the library and now except for the xmp files which you don't re-read, dt has no way to know they even exist.

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The following doc(s) have been deployed to the [segmentena](https://segmentena-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/caching-advanced-topics](https://segmentena-static-docs.pantheonsite.io/docs/caching-advanced-topics)
- [/docs/composer](https://segmentena-static-docs.pantheonsite.io/docs/composer)
- [/docs/custom-upstream](https://segmentena-static-docs.pantheonsite.io/docs/custom-upstream)
- [/docs/domains](https://segmentena-static-docs.pantheonsite.io/docs/domains)
- [/docs/drupal-8-cache](https://segmentena-static-docs.pantheonsite.io/docs/drupal-8-cache)
- [/docs/drupal-cache](https://segmentena-static-docs.pantheonsite.io/docs/drupal-cache)


@brammool , it looks like runtime/syntax/2html.vim was missed in this update.


Successfully deployed to following URLs:

* https://ripe-components-vue-6zm2qc430.now.sh
* https://ripe-components-vue.platforme.now.sh
* https://ripe-components-vue-git-master.platforme.now.sh


History continues before this commit at de36eb2e133b4de32ec5e5c303a491300842f2c0. You can get to this automatically by running `git fetch origin 'refs/replace/*:refs/replace/*'`


Is it possible that this would return without children? Do we need a check to confirm that a child is present before we call getChild


ADC Code


Yeah, the singleton set thingsis great.
 - ChainRules two of them `DNE` (throws errors if it makes it to the gradient desent stage) and `Zero` (hard zero) in that category
 - Zygote calls all these things `nothing`, going to change that with more ChainRules integration.
 - I need to write a bunch of stuff down, and normalize terminology, its mostly scattered through issues and no where has it all written down.


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* https://front-end.airbnboptimal.now.sh
* https://front-end-git-master.airbnboptimal.now.sh


TeamCity Bvcms / Build [Build 2829](https://builds.tpsdb.com/viewLog.html?buildId=9953&buildTypeId=Bvcms_Build) is now running


Successfully deployed to following URLs:

* https://mcs-new-version-fby6v0rm3.now.sh
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Successfully deployed to following URLs:

* https://confluenza-j68c11peo.now.sh
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Successfully deployed to following URLs:

* https://commercetools-docs-kit-btm9x6iav.now.sh
* https://commercetools-docs-kit.now.sh
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* https://commercetools-docs-kit-git-master.commercetools.now.sh


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-117-reits-across-america-d8.pantheonsite.io/)

Created multidev environment [pr-117](https://dashboard.pantheon.io/sites/afa5510e-3253-42b8-b3a4-35622f7e9eae#pr-117) for reits-across-america-d8.


TeamCity Bvcms / Build [Build 2829](https://builds.tpsdb.com/viewLog.html?buildId=9953&buildTypeId=Bvcms_Build) outcome was **UNKNOWN**
Summary: Canceled (The build was triggered in the branch refs/pull/717/merge which does not correspond to any branch monitored by the build VCS roots (the branch is either closed or excluded / not matched by any branch specification). Because of that default ... Build time: 00:00:58


Hey, do you remember how we got this 262_144? It seems I changed this, but can't remember how this magic number came up.


Надо передать пустой массив `[]` как вторым аргументом. Тогда `useEffect` сработает только один раз.

```diff
  React.useEffect(
    () => { props.loadUsers(); console.log('init 2 ok'); },
+   []
  )
```