[R/calc_rel_contr_node_time.R:61:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_rel_contr_node_time.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:61:48:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_rel_contr_node_time.R#L61) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
                                               ^
```
[R/calc_rel_contr_node_time.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_rel_contr_node_time.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (2 * num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:75:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_rel_contr_node_time.R#L75) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calc_expected_hidden_nodes_per_branch <- function(bl, lambda, mu) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:125:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_rel_contr_node_time.R#L125) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:64:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_summary_statistics.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
    # this is rather inefficient off course, RPANDA can do all pairwise comparisons?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_summary_statistics.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:93:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_summary_statistics.R#L65) *style:* **Commas should always have a space after.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
                                                                                ^
```
[R/calc_summary_statistics.R:79:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/calc_summary_statistics.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
                                 "mean_branch_length", "nLTT", "jsd", "topo_dist")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_hidden.R:7:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/count_hidden.R#L7) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
reduce_tree <- function(tree) {
^
```
[R/create_equal_alignment.R:4:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/create_equal_alignment.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param node_model model used to generate substitutions on the nodes (linked or unlinked)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:14:23:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/create_equal_alignment.R#L14) *warning:* **no visible global function definition for ‘count_hidden’**
```r
  num_hidden_nodes <- count_hidden(input_tree)
                      ^~~~~~~~~~~~
```
[R/infer_phylogeny.R:8:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/infer_phylogeny.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sub_rate substitution rate used to generate the original alignment (if available), default is 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:32:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/infer_phylogeny.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
          clock_rate_param = beautier::create_clock_rate_param(value = sub_rate),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:66:15:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/infer_phylogeny.R#L66) *warning:* **no visible binding for global variable ‘beast2_options_output_state_filename’**
```r
  file.remove(beast2_options_output_state_filename)
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:69:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:70:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L70) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:79:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:80:6:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L80) *style:* **Commented code should be removed.**
```r
   # P <- nodeSub::slow_matrix(eig_q2, node_time, rate2)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:92:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:93:6:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L93) *style:* **Commented code should be removed.**
```r
    #P <- nodeSub::slow_matrix(eig_q1, tl[i], rate1)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:105:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L105) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_dual_independent.R:114:42:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:117:34:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_independent.R#L117) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L112) *style:* **Variable and function name style should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:132:19:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:135:21:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L135) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:171:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L171) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:172:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L172) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:191:6:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L191) *style:* **Commented code should be removed.**
```r
   # total_node_subs <- total_node_subs + node_subs_1 + node_subs_2
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_linked.R:196:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L196) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:210:9:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(check_to_extinct_tip(offspring[i])) {
        ^
```
[R/sim_dual_linked.R:220:42:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_linked.R#L220) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_linked.R:13:24:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_linked.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_linked.R:33:19:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_linked.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_linked.R:36:21:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_linked.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_linked.R:88:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_linked.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_linked.R:108:42:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_linked.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_normal.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_normal.R#L43) *style:* **Variable and function name style should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_normal.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_normal.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_unlinked_tree.R:10:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(class(phy) != "phylo") {
    ^
```
[R/sim_unlinked_tree.R:34:51:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L34) *style:* **Put spaces around all infix operators.**
```r
      to_add <- c(start_node, end_node, t0, t1, t0-t1)
                                                 ~^~
```
[R/sim_unlinked_tree.R:40:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L40) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:50:35:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                  ^
```
[R/sim_unlinked_tree.R:50:39:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                      ^
```
[R/sim_unlinked_tree.R:52:36:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                        lambda, mu) )
                                   ^
```
[R/sim_unlinked_tree.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:77:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L77) *style:* **functions should have cyclomatic complexity of less than 15, this has 43.**
```r
sim_unlinked_tree <- function(phy,
^
```
[R/sim_unlinked_tree.R:78:31:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
                              Q1 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:79:31:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
                              Q2 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:104:10:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L104) *style:* **Only use double-quotes.**
```r
    stop('lambda and mu have to be provided')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:113:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L113) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:114:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L114) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:117:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L117) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked_tree.R:118:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L118) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked_tree.R:131:51:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L131) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  hidden_nodes <- add_hidden_nodes(phy, lambda, mu )
                                                  ^
```
[R/sim_unlinked_tree.R:146:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:146:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
  ^~~
```
[R/sim_unlinked_tree.R:146:61:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L146) *style:* **Commented code should be removed.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
                                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:151:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L151) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:152:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:181:9:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L181) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( obs_hidden_nodes[i] > 0) {
        ^
```
[R/sim_unlinked_tree.R:186:10:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L186) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(j in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:188:14:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L188) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        while(focal_t + dt >= total_bl) {
             ^
```
[R/sim_unlinked_tree.R:198:8:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L198) *style:* **Commented code should be removed.**
```r
      #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:199:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L199) *style:* **Variable and function name style should be snake_case.**
```r
      P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
      ^~~
```
[R/sim_unlinked_tree.R:214:10:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L214) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(h in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:227:10:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L227) *style:* **Commented code should be removed.**
```r
        #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:228:9:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L228) *style:* **Variable and function name style should be snake_case.**
```r
        P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
        ^~~
```
[R/sim_unlinked_tree.R:247:8:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L247) *style:* **Commented code should be removed.**
```r
      #P <- get_p_matrix(tl[i], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:248:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L248) *style:* **Variable and function name style should be snake_case.**
```r
      P <-  nodeSub::slow_matrix(eig_q1, tl[i], rate1)
      ^
```
[R/sim_unlinked_tree.R:263:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L263) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_unlinked_tree.R:270:42:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L270) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked_tree.R:273:34:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L273) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_unlinked_tree.R:282:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:301:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L301) *style:* **functions should have cyclomatic complexity of less than 15, this has 19.**
```r
create_equal_alignment_tree <- function(input_tree,
^
```
[R/sim_unlinked_tree.R:303:41:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L303) *style:* **Variable and function name style should be snake_case.**
```r
                                        Q1 = NULL,
                                        ^~
```
[R/sim_unlinked_tree.R:304:41:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L304) *style:* **Variable and function name style should be snake_case.**
```r
                                        Q2 = NULL,
                                        ^~
```
[R/sim_unlinked_tree.R:318:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L318) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(focal_alignment)) {
    ^
```
[R/sim_unlinked_tree.R:320:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L320) *style:* **Lines should not be more than 80 characters.**
```r
    focal_alignment <- nodeSub::sim_normal(input_tree, l = l, Q = Q1, bf = bf, rootseq = rootseq, rate = rate1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:325:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L325) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(fraction) && is.null(node_time)) {
    ^
```
[R/sim_unlinked_tree.R:328:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L328) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(node_time)) {
    ^
```
[R/sim_unlinked_tree.R:329:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L329) *style:* **Lines should not be more than 80 characters.**
```r
    node_time <- nodeSub::calc_required_node_time(input_tree, s = fraction, model = model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:331:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L331) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(fraction)) {
    ^
```
[R/sim_unlinked_tree.R:332:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L332) *style:* **Lines should not be more than 80 characters.**
```r
    fraction <- nodeSub::calc_fraction(input_tree, node_time = node_time, model = model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:342:7:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L342) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(reconstruct_hidden_nodes) {
      ^
```
[R/sim_unlinked_tree.R:343:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L343) *style:* **Lines should not be more than 80 characters.**
```r
      if(model == "unlinked") proposed_alignment <- nodeSub::sim_unlinked_tree(input_tree,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:343:9:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L343) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "unlinked") proposed_alignment <- nodeSub::sim_unlinked_tree(input_tree,
        ^
```
[R/sim_unlinked_tree.R:351:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L351) *style:* **Lines should not be more than 80 characters.**
```r
      if(model == "linked") stop("hidden nodes in linked model not implemented yet")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:351:9:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L351) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "linked") stop("hidden nodes in linked model not implemented yet")
        ^
```
[R/sim_unlinked_tree.R:353:9:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L353) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "unlinked") {
        ^
```
[R/sim_unlinked_tree.R:361:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L361) *style:* **Lines should not be more than 80 characters.**
```r
                                                            node_time = node_time)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:363:9:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L363) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "linked") {
        ^
```
[R/sim_unlinked_tree.R:367:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L367) *style:* **Lines should not be more than 80 characters.**
```r
                                                       node_mut_rate_double = focal_rate ^ 2,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:382:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked_tree.R#L382) *style:* **Lines should not be more than 80 characters.**
```r
  proposed_alignment <- propose_alignments(buffer = c(), focal_rate = adjusted_rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/sim_unlinked.R:14:26:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                         Q1 = NULL,
                         ^~
```
[R/sim_unlinked.R:15:26:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                         Q2 = NULL,
                         ^~
```
[R/sim_unlinked.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_unlinked.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_unlinked.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/sim_unlinked.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/util.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/util.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/util.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```
[R/util.R:116:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/R/util.R#L116) *style:* **Variable and function name style should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-dual_independent.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-dual_parent.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-dual-linked.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-relative_node_time.R:22:1:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-relative_node_time.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
  obs_fraction <- ali$total_node_substitutions / (ali$total_node_substitutions + ali$total_branch_substitutions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-sim_normal.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-substitution.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-substitution.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-substitution.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-substitution.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-substitution.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-substitution.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/5f3bff9c52aac5cf39668a5130ef4fd930b86ae1/tests/testthat/test-substitution.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


Successfully deployed to following URLs:

* https://nuro-sh-a23wzv8l3.now.sh
* https://nuro.sh
* https://www.nuro.sh
* https://blog.nuro.sh
* https://nuro-sh.nuro.now.sh
* https://nuro-sh-git-master.nuro.now.sh


This requires grammatical correction and clarification


Successfully deployed to following URLs:

* https://kendraio-app-3sprnxf8f.now.sh
* https://dev.app.kendra.io
* https://kendraio-app.kendraio.now.sh
* https://kendraio-app-git-develop.kendraio.now.sh


df


But isn't a _flat model_ something different than a _model_? - Encoding a type information in a version definition doesn't  seem right to me?


Shouldn't we catch by const ref here?


You have to keep in mind that you are describing the area of another system here -> Spark.

There is still a lot of space here, so plugins and other things can also be outsourced there. We could probably even reactivate PIP, although it only works in sd. However, there remains an area that can of course also be completely destroyed with the access.
Therefore the naming is not wrong.

Don't get me wrong ...
I have been using this area for my picons for a long time and think it's good.
Only the name tells you directly what you are doing.


Let's rename everything related to log level to `verbosity level` to avoid confusion with logging


Without understanding the code I cannot comment


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/www/cms/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Downloading https://github.com/Medium/phantomjs/releases/download/v2.1.1/phantomjs-2.1.1-linux-x86_64.tar.bz2
Saving to /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Receiving...

Received 22866K total.
Extracting tar contents (via spawned process)
Removing /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1576598938483/phantomjs-2.1.1-linux-x86_64 -> /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/www/cms/node_modules/core-js
> node scripts/postinstall || echo "ignore"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
> https://opencollective.com/core-js
> https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

added 134 packages from 190 contributors and audited 183 packages in 7.407s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/www/cms
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com 0
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-staging-cms-1188006.us-gov-west-1.elb.amazonaws.com/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Tue, 17 Dec 2019 16:09:02 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Tue, 17 Dec 2019 16:09:07 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** ip-10-247-34-171
- **In:** 01:55


Successfully deployed to following URLs:

* https://nuro-sh-ic8d2m5fo.now.sh
* https://nuro.sh
* https://www.nuro.sh
* https://blog.nuro.sh
* https://nuro-sh.nuro.now.sh
* https://nuro-sh-git-master.nuro.now.sh


People still use it? Why though? This was only intended for iOS 4 and iOS 5.


Successfully deployed to following URLs:

* https://myproxxy-e73jwfhuz.now.sh


you care too much about the prefs listed as "changed" in about:support :)
what they could (and ideally should) do is add a check that prevents prefs from being listed there if the user-set pref value matches FFs default value.

> reducing the number of changes for end users helps

it's not really "a change" if the value we set matches FFs default ;) But yeah, I get your point; I just don't think it matters all that much.
And they can already see that we're only enforcing a value thanks to our DEFAULT tags, so if they're reading through the user.js, they can just more or less skip over those prefs.

> If you want me to make it active again

yes, please do, thanks 💋


Assume that these work exactly like log levels, which means it is enough to register verbosity level `INFO` to automatically keep `WARN` and `ERR` as well. Essentially stack model.


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/www/cms/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Downloading https://github.com/Medium/phantomjs/releases/download/v2.1.1/phantomjs-2.1.1-linux-x86_64.tar.bz2
Saving to /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Receiving...

Received 22866K total.
Extracting tar contents (via spawned process)
Removing /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1576599014180/phantomjs-2.1.1-linux-x86_64 -> /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/www/cms/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/www/cms/node_modules/core-js
> node scripts/postinstall || echo "ignore"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
> https://opencollective.com/core-js
> https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

added 134 packages from 190 contributors and audited 183 packages in 18.876s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/www/cms
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com 0
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://internal-dsva-vagov-dev-cms-812329399.us-gov-west-1.elb.amazonaws.com/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Tue, 17 Dec 2019 16:10:18 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Tue, 17 Dec 2019 16:10:22 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** ip-10-247-96-123
- **In:** 01:54


afin que le "sans notification" soit affiché par défaut


Successfully deployed to following URLs:

* https://nosql-server-pgi4a8qbu.now.sh
* https://nosql-server.now.sh
* https://nosql-server.gayankuruppu.now.sh
* https://nosql-server-git-master.gayankuruppu.now.sh


No non-null data in prod


Uploaded test apks for
 - [**armv7**](https://download.opengis.ch/qfield/ci-builds/qfield-dev--105cd145ba8f17930116eab6e39c7e06ce88fc87-armv7.apk)
 - [arm64_v8a](https://download.opengis.ch/qfield/ci-builds/qfield-dev--105cd145ba8f17930116eab6e39c7e06ce88fc87-arm64_v8a.apk)
 - [x86](https://download.opengis.ch/qfield/ci-builds/qfield-dev--105cd145ba8f17930116eab6e39c7e06ce88fc87-x86.apk)
 - [x86_64](https://download.opengis.ch/qfield/ci-builds/qfield-dev--105cd145ba8f17930116eab6e39c7e06ce88fc87-x86_64.apk)


j'ai supprimé ça juste après


[Circle has built](https://circleci.com/gh/cypress-io/cypress/217612) the `linux x64` version of the Test Runner.

You can install this pre-release platform-specific build using instructions at [https://on.cypress.io/installing-cypress#Install-pre-release-version](https://on.cypress.io/installing-cypress#Install-pre-release-version).

You will need to use custom `CYPRESS_INSTALL_BINARY` url and install Cypress using an url instead of the version.

    export CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.1/linux-x64/circle-develop-343c0f459c5c2fa2ff26f4cbcc14561860317da8-217607/cypress.zip
    npm install https://cdn.cypress.io/beta/npm/3.8.1/circle-develop-343c0f459c5c2fa2ff26f4cbcc14561860317da8-217567/cypress.tgz


@VadiqueMe You have been asked repeatedly to engage with the repository in the manner everyone else does, still you refuse.

We are here to answer questions, and have done so repeatedly. Not just here on GitHub either, spanning multiple communities, platforms and assorted questions. Where your questions were answered, only for us to be berated because **you** did not _like_ the answer. Forgetting that while we do engage with you, there is no requirement for us to simply accept being harassed, attacked nor abused. **No one has that obligation.** You have even harassed services people (volunteers who just run external things) across three platforms in your quest for answers.

You dislike something, have your own personal ideals on what things should be, that is clear. What you seem to be missing is that your entire fight here is you complaining about a bug being fixed, which was **causing issues for services in the real time using real user funds.** I am sorry you dislike that we fixed an issue, given the real time impact on users; it needed to be sorted out.

This is not the place to have the discussion, so once more I ask that you bring the suggestions up, and present your ideals in a way that is more transparent, able to be engaged with and has concept proofs behind it. Failing this further understand that spamming the repository, having consensus impacting conversations cloistered off on the whims of a singular are not real things I am comfortable with nor are they things that should be supported I feel.


Successfully deployed to following URLs:

* https://design-b4x6jhnvl.now.sh
* https://design.oacore.now.sh
* https://design-git-dev.oacore.now.sh