[R/bd_loglik_choosepar.R:1:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik_choosepar.R:1:21:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Use <-, not =, for assignment.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                    ^
```
[R/bd_loglik_choosepar.R:1:42:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Commas should always have a space after.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                                         ^
```
[R/bd_loglik_choosepar.R:1:52:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Commas should always have a space after.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                                                   ^
```
[R/bd_loglik_choosepar.R:1:62:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Commas should always have a space after.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                                                             ^
```
[R/bd_loglik_choosepar.R:1:72:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Commas should always have a space after.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                                                                       ^
```
[R/bd_loglik_choosepar.R:1:78:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Commas should always have a space after.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                                                                             ^
```
[R/bd_loglik_choosepar.R:1:83:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Commas should always have a space after.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                                                                                ^
```
[R/bd_loglik_choosepar.R:1:95:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L1) *style:* **Commas should always have a space after.**
```r
bd_loglik_choosepar = function(trparsopt,trparsfix,idparsopt,idparsfix,pars2,brts,missnumspec,methode)
                                                                                ^
```
[R/bd_loglik_choosepar.R:2:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L2) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/bd_loglik_choosepar.R:3:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L3) *style:* **Use <-, not =, for assignment.**
```r
   trpars1 = rep(0,4)
           ^
```
[R/bd_loglik_choosepar.R:3:20:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L3) *style:* **Commas should always have a space after.**
```r
   trpars1 = rep(0,4)
                   ^
```
[R/bd_loglik_choosepar.R:4:23:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L4) *style:* **Use <-, not =, for assignment.**
```r
   trpars1[idparsopt] = trparsopt
                      ^
```
[R/bd_loglik_choosepar.R:5:6:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L5) *style:* **Place a space before left parenthesis, except in a function call.**
```r
   if(length(idparsfix) != 0)
     ^
```
[R/bd_loglik_choosepar.R:6:4:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L6) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
   {
   ^
```
[R/bd_loglik_choosepar.R:7:26:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L7) *style:* **Use <-, not =, for assignment.**
```r
      trpars1[idparsfix] = trparsfix
                         ^
```
[R/bd_loglik_choosepar.R:9:6:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L9) *style:* **Place a space before left parenthesis, except in a function call.**
```r
   if(max(trpars1) > 1 | min(trpars1) < 0)
     ^
```
[R/bd_loglik_choosepar.R:10:4:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L10) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
   {
   ^
```
[R/bd_loglik_choosepar.R:11:14:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L11) *style:* **Use <-, not =, for assignment.**
```r
      loglik = -Inf
             ^
```
[R/bd_loglik_choosepar.R:13:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L13) *style:* **Use <-, not =, for assignment.**
```r
      pars1 = trpars1/(1 - trpars1)
            ^
```
[R/bd_loglik_choosepar.R:13:22:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L13) *style:* **Put spaces around all infix operators.**
```r
      pars1 = trpars1/(1 - trpars1)
                    ~^~
```
[R/bd_loglik_choosepar.R:13:23:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L13) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      pars1 = trpars1/(1 - trpars1)
                      ^
```
[R/bd_loglik_choosepar.R:14:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L14) *style:* **Lines should not be more than 80 characters.**
```r
      loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik_choosepar.R:14:14:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L14) *style:* **Use <-, not =, for assignment.**
```r
      loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
             ^
```
[R/bd_loglik_choosepar.R:14:16:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L14) *warning:* **no visible global function definition for ‘bd_loglik’**
```r
      loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
               ^~~~~~~~~
```
[R/bd_loglik_choosepar.R:14:40:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L14) *style:* **Commas should always have a space after.**
```r
      loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
                                       ^
```
[R/bd_loglik_choosepar.R:14:59:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L14) *style:* **Commas should always have a space after.**
```r
      loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
                                                          ^
```
[R/bd_loglik_choosepar.R:14:71:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L14) *style:* **Commas should always have a space after.**
```r
      loglik = bd_loglik(pars1 = pars1,pars2 = pars2[1:6],brts = brts,missnumspec = missnumspec, methode = methode)
                                                                      ^
```
[R/bd_loglik_choosepar.R:15:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L15) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(is.nan(loglik) || is.na(loglik))
        ^
```
[R/bd_loglik_choosepar.R:16:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L16) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/bd_loglik_choosepar.R:17:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
         cat("There are parameter values used which cause numerical problems.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik_choosepar.R:18:17:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik_choosepar.R#L18) *style:* **Use <-, not =, for assignment.**
```r
         loglik = -Inf
                ^
```
[R/bd_loglik.R:41:80:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L41) *style:* **Trailing whitespace is superfluous.**
```r
#' \cr \cr \code{pars2[4]} sets whether the parameters and likelihood should be
                                                                               ^
```
[R/bd_loglik.R:59:68:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L59) *style:* **Trailing whitespace is superfluous.**
```r
#' bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10,
                                                                   ^
```
[R/bd_loglik.R:66:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
  # - pars1[3] = la1 = parameter in exponential decay of speciation rate, OR K in
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:66:82:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L66) *style:* **Trailing whitespace is superfluous.**
```r
  # - pars1[3] = la1 = parameter in exponential decay of speciation rate, OR K in
                                                                                ^
```
[R/bd_loglik.R:70:62:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L70) *style:* **Trailing whitespace is superfluous.**
```r
  # - pars1[5] = T0 = age at which lambda is lambda0 (default
                                                             ^
```
[R/bd_loglik.R:76:73:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L76) *style:* **Trailing whitespace is superfluous.**
```r
  # . tdmodel == 2: stepwise decline following diversity-dependence when
                                                                        ^
```
[R/bd_loglik.R:77:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L77) *style:* **Commented code should be removed.**
```r
  #   extinction = 0
      ^~~~~~~~~~~~~~
```
[R/bd_loglik.R:78:80:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L78) *style:* **Trailing whitespace is superfluous.**
```r
  # . tdmodel == 3: decline in speciation rate following deterministic logistic
                                                                               ^
```
[R/bd_loglik.R:80:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L80) *style:* **Lines should not be more than 80 characters.**
```r
  # . tdmodel == 4...8: change in speciation/extinction rate following ddmodel =
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:80:81:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L80) *style:* **Trailing whitespace is superfluous.**
```r
  # . tdmodel == 4...8: change in speciation/extinction rate following ddmodel =
                                                                                ^
```
[R/bd_loglik.R:82:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
  # - pars2[2] = cond = conditioning on age (0), non-extinction of the clade and
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:82:81:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L82) *style:* **Trailing whitespace is superfluous.**
```r
  # - pars2[2] = cond = conditioning on age (0), non-extinction of the clade and
                                                                                ^
```
[R/bd_loglik.R:86:79:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
  # - pars2[5] = likelihood is for a tree with crown age (2) or stem age (1) -
                                                                              ^
```
[R/bd_loglik.R:89:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L89) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:105:74:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L105) *style:* **Trailing whitespace is superfluous.**
```r
      rtt <- mu0 / mu1 * (exp(-mu1 * t1) - exp(-mu1 * tau)) - la0 / la1 *
                                                                         ^
```
[R/bd_loglik.R:110:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L110) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:111:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L111) *style:* **Variable or function name should be snake_case.**
```r
  PtTint <- function(x, t1, pars){
  ^~~~~~
```
[R/bd_loglik.R:112:5:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L112) *style:* **Variable or function name should be snake_case.**
```r
    PtTint <- pars[2] * exp(-pars[4] * x) * exp(rhotaut(x, t1, pars))
    ^~~~~~
```
[R/bd_loglik.R:115:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L115) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:117:54:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L117) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    ff <- 1 / pars[3] + (1 / 2 - 1 / pars[3]) * exp(-(pars[1] - pars[2]) * t1)
                                                     ^
```
[R/bd_loglik.R:120:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L120) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:125:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L125) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:126:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L126) *style:* **Variable or function name should be snake_case.**
```r
  intPtTint2 <- function(t1, T, pars){
  ^~~~~~~~~~
```
[R/bd_loglik.R:127:5:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L127) *style:* **Variable or function name should be snake_case.**
```r
    intPtTint2 <- pars[2] / ff(t1,pars) *
    ^~~~~~~~~~
```
[R/bd_loglik.R:127:35:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L127) *style:* **Commas should always have a space after.**
```r
    intPtTint2 <- pars[2] / ff(t1,pars) *
                                  ^
```
[R/bd_loglik.R:127:42:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L127) *style:* **Trailing whitespace is superfluous.**
```r
    intPtTint2 <- pars[2] / ff(t1,pars) *
                                         ^
```
[R/bd_loglik.R:128:8:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L128) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      ( (T - t1) / pars[3] + (ff(t1, pars) - ff(T, pars)) /
       ^
```
[R/bd_loglik.R:128:60:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L128) *style:* **Trailing whitespace is superfluous.**
```r
      ( (T - t1) / pars[3] + (ff(t1, pars) - ff(T, pars)) /
                                                           ^
```
[R/bd_loglik.R:129:30:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L129) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
          (pars[1] - pars[2]) )
                             ^
```
[R/bd_loglik.R:132:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L132) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:148:16:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L148) *style:* **Use <-, not =, for assignment.**
```r
      pars2[6] = Inf
               ^
```
[R/bd_loglik.R:150:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L150) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bd_loglik.R:153:73:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L153) *style:* **Trailing whitespace is superfluous.**
```r
        "Stem age and conditioning on extant taxa only have not yet been
                                                                        ^
```
[R/bd_loglik.R:158:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L158) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    } else {
           ^
```
[R/bd_loglik.R:158:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L158) *style:* **Trailing whitespace is superfluous.**
```r
    } else {
            ^~~~~~~~
```
[R/bd_loglik.R:164:10:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L164) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(i in 2:length(brts2)) {
         ^
```
[R/bd_loglik.R:172:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L172) *style:* **Variable or function name should be snake_case.**
```r
      TT <- brts[1]
      ^~
```
[R/bd_loglik.R:174:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L174) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:175:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L175) *style:* **Variable or function name should be snake_case.**
```r
      S <- length(brts)
      ^
```
[R/bd_loglik.R:176:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L176) *style:* **Variable or function name should be snake_case.**
```r
      N <- S + m
      ^
```
[R/bd_loglik.R:178:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L178) *style:* **Variable or function name should be snake_case.**
```r
      PtT <- rep(0, S)
      ^~~
```
[R/bd_loglik.R:180:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L180) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:181:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L181) *warning:* **local variable ‘abstol’ assigned but may not be used**
```r
      abstol <- 1e-16
      ^~~~~~
```
[R/bd_loglik.R:182:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L182) *warning:* **local variable ‘reltol’ assigned but may not be used**
```r
      reltol <- 1e-10
      ^~~~~~
```
[R/bd_loglik.R:183:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L183) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:184:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L184) *style:* **Variable or function name should be snake_case.**
```r
      T0 <- TT
      ^~
```
[R/bd_loglik.R:189:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L189) *style:* **Variable or function name should be snake_case.**
```r
        K <- pars1[3]
        ^
```
[R/bd_loglik.R:192:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L192) *style:* **Variable or function name should be snake_case.**
```r
          T0 <- pars1[5]
          ^~
```
[R/bd_loglik.R:193:10:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L193) *style:* **Trailing whitespace is superfluous.**
```r
        }
         ^
```
[R/bd_loglik.R:196:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L196) *style:* **Variable or function name should be snake_case.**
```r
        K <- Inf
        ^
```
[R/bd_loglik.R:198:31:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L198) *style:* **Commas should always have a space after.**
```r
        pars1 <- c(pars1, c(0,0))
                              ^
```
[R/bd_loglik.R:200:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L200) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:201:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L201) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(tdmodel == 1){
        ^
```
[R/bd_loglik.R:205:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L205) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:207:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L207) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:208:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L208) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(tdmodel == 0 | (tdmodel == 1 & la1 == 0 & mu1 == 0))
        ^
```
[R/bd_loglik.R:209:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L209) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/bd_loglik.R:210:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(abs(la0 - mu0) < 1E-10){
          ^
```
[R/bd_loglik.R:212:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L212) *style:* **Variable or function name should be snake_case.**
```r
          PtT <- 1 / (1 + lamu * (TT - t))
          ^~~
```
[R/bd_loglik.R:215:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L215) *style:* **Variable or function name should be snake_case.**
```r
          PtT <- (la0 - mu0) / (la0 - mu0 * exp(-(la0 - mu0) * (TT - t)))
          ^~~
```
[R/bd_loglik.R:215:50:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L215) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          PtT <- (la0 - mu0) / (la0 - mu0 * exp(-(la0 - mu0) * (TT - t)))
                                                 ^
```
[R/bd_loglik.R:216:29:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L216) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      ux <- la0 * (1 - exp(-(la0 - mu0) * (TT - t))) /
                            ^
```
[R/bd_loglik.R:217:27:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L217) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        (la0 - mu0 * exp(-(la0 - mu0) * (TT - t)))
                          ^
```
[R/bd_loglik.R:221:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L221) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(i in 1:S){
           ^
```
[R/bd_loglik.R:223:46:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L223) *style:* **Trailing whitespace is superfluous.**
```r
            PtTint, lower = t[i], upper = TT,
                                             ^
```
[R/bd_loglik.R:225:20:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L225) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          )$value)^(-1)
                   ^
```
[R/bd_loglik.R:233:22:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L233) *style:* **Commas should always have a space after.**
```r
        la <- pmax(0,la0 * (1 - (2:S) / K))
                     ^
```
[R/bd_loglik.R:234:33:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L234) *style:* **Commas should always have a space after.**
```r
        dx <- c(abs(diff(brts)),brts[S])[2:S]
                                ^
```
[R/bd_loglik.R:235:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L235) *style:* **Commented code should be removed.**
```r
        # mpfr(la, precBits = 500)
          ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:236:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L236) *style:* **Commented code should be removed.**
```r
        # mpfr(dx, precBits = 500)
          ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:238:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L238) *style:* **Variable or function name should be snake_case.**
```r
        PtT <- rep(1,S)
        ^~~
```
[R/bd_loglik.R:238:22:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L238) *style:* **Commas should always have a space after.**
```r
        PtT <- rep(1,S)
                     ^
```
[R/bd_loglik.R:239:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L239) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(i in 2:S){
           ^
```
[R/bd_loglik.R:244:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L244) *style:* **Variable or function name should be snake_case.**
```r
        PtT <- 1 / (1 + intPtTint2(t, TT, pars1))
        ^~~
```
[R/bd_loglik.R:247:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L247) *style:* **Variable or function name should be snake_case.**
```r
        Kprime <- la0 / (la0 - mu0) * K
        ^~~~~~
```
[R/bd_loglik.R:250:32:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L250) *style:* **Trailing whitespace is superfluous.**
```r
          ceiling(Kprime) < N |
                               ^
```
[R/bd_loglik.R:251:39:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L251) *style:* **Trailing whitespace is superfluous.**
```r
          K >= 0.9 * round(pars2[6]) |
                                      ^
```
[R/bd_loglik.R:252:18:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L252) *style:* **Trailing whitespace is superfluous.**
```r
          K < 1 |
                 ^
```
[R/bd_loglik.R:253:22:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L253) *style:* **Trailing whitespace is superfluous.**
```r
          la0 < mu0 |
                     ^
```
[R/bd_loglik.R:264:25:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L264) *style:* **Trailing whitespace is superfluous.**
```r
        latd[1] <- mu0 +
                        ^
```
[R/bd_loglik.R:266:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L266) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(k in 2:np){
           ^
```
[R/bd_loglik.R:270:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L270) *style:* **Lines should not be more than 80 characters.**
```r
          #y2 = deSolve::ode(variables, c(t1, t2), td_loglik_rhs, c(pars1[1:min(4, length(pars1))], tdmodel - 3, lx), rtol = 1e-10, atol = 1e-16, method = methode)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:270:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L270) *style:* **Commented code should be removed.**
```r
          #y2 = deSolve::ode(variables, c(t1, t2), td_loglik_rhs, c(pars1[1:min(4, length(pars1))], tdmodel - 3, lx), rtol = 1e-10, atol = 1e-16, method = methode)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:287:19:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L287) *style:* **Only use double-quotes.**
```r
              cat('NA or NaN issues encountered.\n')
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:292:15:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L292) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            if(verbose) cat('Probabilities smaller than 0 encountered\n')
              ^
```
[R/bd_loglik.R:292:29:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L292) *style:* **Only use double-quotes.**
```r
            if(verbose) cat('Probabilities smaller than 0 encountered\n')
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:294:35:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L294) *style:* **Commas should always have a space after.**
```r
            variables <- rep(-Inf,length(variables))
                                  ^
```
[R/bd_loglik.R:295:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L295) *style:* **Trailing whitespace is superfluous.**
```r
          }
           ^
```
[R/bd_loglik.R:296:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L296) *style:* **Commented code should be removed.**
```r
          #variables2 = y2[2, 2:(lx + k)]
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:298:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L298) *style:* **Trailing whitespace is superfluous.**
```r
          #{
            ^
```
[R/bd_loglik.R:299:15:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L299) *style:* **Commented code should be removed.**
```r
          #   print(variables2 - variables)
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:300:15:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L300) *style:* **Commented code should be removed.**
```r
          #   unequal <- which(variables != variables2)
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:301:14:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L301) *style:* **Commented code should be removed.**
```r
          #  if(length(unequal) > 0) stop('Stop here')
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:305:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L305) *style:* **Variable or function name should be snake_case.**
```r
          dEN_dt <- (la0 - mu0) * expn[k] - expn2 * (la0 - mu0) / K
          ^~~~~~
```
[R/bd_loglik.R:308:40:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L308) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if (sum(variables[1:lx]) < 0.99 ) {
                                       ^
```
[R/bd_loglik.R:309:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L309) *style:* **Commented code should be removed.**
```r
          #print(lx)
           ^~~~~~~~~
```
[R/bd_loglik.R:310:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L310) *style:* **Commented code should be removed.**
```r
          #print(sum(variables[1:lx]))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:311:15:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L311) *style:* **Only use double-quotes.**
```r
          cat('Leaking probabilities detected.')
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:315:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L315) *style:* **Variable or function name should be snake_case.**
```r
        PtT <- 1 / (1 + sig)
        ^~~
```
[R/bd_loglik.R:318:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L318) *style:* **Variable or function name should be snake_case.**
```r
          PtT <- c(PtT[1], PtT)
          ^~~
```
[R/bd_loglik.R:322:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L322) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:324:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L324) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(tdmodel == 0) {
          ^
```
[R/bd_loglik.R:326:34:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L326) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        } else if (tdmodel == 1) {
                                 ^
```
[R/bd_loglik.R:326:35:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L326) *style:* **Trailing whitespace is superfluous.**
```r
        } else if (tdmodel == 1) {
                                  ^
```
[R/bd_loglik.R:330:18:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L330) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        } else if(tdmodel == 3) {
                 ^
```
[R/bd_loglik.R:332:18:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L332) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        } else if(tdmodel == 4) {
                 ^
```
[R/bd_loglik.R:336:64:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L336) *style:* **Trailing whitespace is superfluous.**
```r
          loglik <- loglik + sum(log(lavec[soc:length(lavec)]))
                                                               ^
```
[R/bd_loglik.R:339:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L339) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:341:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L341) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(cond == 1) {
        ^
```
[R/bd_loglik.R:342:14:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L342) *style:* **Use <-, not =, for assignment.**
```r
        logp = soc * log(PtT[1])
             ^
```
[R/bd_loglik.R:344:9:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L344) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(cond == 2 | cond == 3) {
        ^
```
[R/bd_loglik.R:345:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L345) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(tdmodel == 2) {
          ^
```
[R/bd_loglik.R:347:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L347) *style:* **Variable or function name should be snake_case.**
```r
          K2 <- K
          ^~
```
[R/bd_loglik.R:348:39:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L348) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          if (floor(K) == ceiling(K)) {
                                      ^
```
[R/bd_loglik.R:348:40:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L348) *style:* **Trailing whitespace is superfluous.**
```r
          if (floor(K) == ceiling(K)) {
                                       ^
```
[R/bd_loglik.R:349:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L349) *style:* **Variable or function name should be snake_case.**
```r
            K2 <- K + eps
            ^~
```
[R/bd_loglik.R:350:52:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L350) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          } else if (floor(K + eps) == ceiling(K)) {
                                                   ^
```
[R/bd_loglik.R:350:53:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L350) *style:* **Trailing whitespace is superfluous.**
```r
          } else if (floor(K + eps) == ceiling(K)) {
                                                    ^
```
[R/bd_loglik.R:351:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L351) *style:* **Variable or function name should be snake_case.**
```r
            K2 <- K - eps
            ^~
```
[R/bd_loglik.R:353:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L353) *style:* **Variable or function name should be snake_case.**
```r
            K2 <- K + eps
            ^~
```
[R/bd_loglik.R:363:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L363) *style:* **Commented code should be removed.**
```r
          #pB = max(50,round(3/la0))
           ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:364:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L364) *style:* **Commented code should be removed.**
```r
          #s = mpfr(s, precBits = pB)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:364:38:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L364) *style:* **Trailing whitespace is superfluous.**
```r
          #s = mpfr(s, precBits = pB)
                                     ^~~~~~
```
[R/bd_loglik.R:365:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L365) *style:* **Commented code should be removed.**
```r
          #sgnsdiff = mpfr(sgnsdiff, precBits = pB)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:366:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L366) *style:* **Commented code should be removed.**
```r
          #logsdiff = mpfr(logsdiff, precBits = pB)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:367:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L367) *style:* **Commented code should be removed.**
```r
          #sgnsdiff2 = mpfr(sgnsdiff2, precBits = pB)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:368:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L368) *style:* **Commented code should be removed.**
```r
          #logsdiff2 = mpfr(logsdiff2, precBits = pB)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:369:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L369) *style:* **Commented code should be removed.**
```r
          #logsdiff3 = mpfr(logsdiff3, precBits = pB)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:371:26:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L371) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
          for (i in 1:N) {
                         ^
```
[R/bd_loglik.R:371:27:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L371) *style:* **Trailing whitespace is superfluous.**
```r
          for (i in 1:N) {
                          ^
```
[R/bd_loglik.R:372:45:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L372) *style:* **Commas should always have a space after.**
```r
            sgnsdiff[i] <- prod(sign(s[-c(1,i)] - s[i]))
                                            ^
```
[R/bd_loglik.R:373:47:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L373) *style:* **Commas should always have a space after.**
```r
            logsdiff[i] <- sum(log(abs(s[-c(1,i)] - s[i])))
                                              ^
```
[R/bd_loglik.R:376:50:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L376) *style:* **Put spaces around all infix operators.**
```r
            logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
                                                ~^~
```
[R/bd_loglik.R:376:58:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L376) *style:* **Commas should always have a space after.**
```r
            logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
                                                         ^
```
[R/bd_loglik.R:376:60:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L376) *style:* **Commas should always have a space after.**
```r
            logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
                                                           ^
```
[R/bd_loglik.R:376:68:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L376) *style:* **Trailing whitespace is superfluous.**
```r
            logsdiff3[i] <- -sum(log(abs(1 - s[i]/s[-c(1,i,N)]))) -
                                                                   ^
```
[R/bd_loglik.R:381:77:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L381) *style:* **Trailing whitespace is superfluous.**
```r
            #         logp <- sum(log(s[2:(N-1)])) + log(sum(sgnsdiff[2:N] *
                                                                            ^
```
[R/bd_loglik.R:383:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L383) *style:* **Lines should not be more than 80 characters.**
```r
            #         logp <- log(sum(sgnsdiff[2:N] * exp(sum(log(s[2:(N-1)])) -
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:383:81:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L383) *style:* **Trailing whitespace is superfluous.**
```r
            #         logp <- log(sum(sgnsdiff[2:N] * exp(sum(log(s[2:(N-1)])) -
                                                                                ^
```
[R/bd_loglik.R:387:35:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L387) *style:* **Put spaces around all infix operators.**
```r
            logp <- sum(log(s[1:(N-1)])) +
                                 ~^~
```
[R/bd_loglik.R:387:43:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L387) *style:* **Trailing whitespace is superfluous.**
```r
            logp <- sum(log(s[1:(N-1)])) +
                                          ^
```
[R/bd_loglik.R:392:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L392) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(cond == 2) {
            ^
```
[R/bd_loglik.R:393:70:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L393) *style:* **Trailing whitespace is superfluous.**
```r
            logp <- (soc == 2) * log(S + m - 1) + soc * log(PtT[1]) +
                                                                     ^
```
[R/bd_loglik.R:396:57:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L396) *style:* **Trailing whitespace is superfluous.**
```r
            logp <- log(PtT[1]) - log(S + missnumspec) -
                                                        ^
```
[R/bd_loglik.R:401:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L401) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:403:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L403) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:405:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L405) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(tdmodel == 2) {
          ^
```
[R/bd_loglik.R:407:60:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L407) *style:* **Trailing whitespace is superfluous.**
```r
            "Missing species in diversity-dependence models
                                                           ^
```
[R/bd_loglik.R:412:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L412) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(cond == 3) {
          ^
```
[R/bd_loglik.R:413:27:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L413) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          x <- (1 - ux[1]^((0:m)+1)) / (1 - ux[1])
                          ^
```
[R/bd_loglik.R:413:33:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L413) *style:* **Put spaces around all infix operators.**
```r
          x <- (1 - ux[1]^((0:m)+1)) / (1 - ux[1])
                               ~^~
```
[R/bd_loglik.R:415:36:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L415) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          x <- (1:(m + 1)) * ux[1]^(0:m)
                                   ^
```
[R/bd_loglik.R:417:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L417) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(j in 2:S) {
           ^
```
[R/bd_loglik.R:418:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L418) *style:* **Lines should not be more than 80 characters.**
```r
          #x = convolve(x,rev((1:(m + 1)) * ux[j]^(0:m)),type = 'open')[1:(m + 1)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:418:12:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L418) *style:* **Commented code should be removed.**
```r
          #x = convolve(x,rev((1:(m + 1)) * ux[j]^(0:m)),type = 'open')[1:(m + 1)]
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:419:16:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L419) *warning:* **no visible global function definition for ‘conv’, Did you mean 'cond'?**
```r
          x <- conv(x, (1:(m + 1)) * ux[j]^(0:m))[1:(m+1)]
               ^~~~
```
[R/bd_loglik.R:419:44:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L419) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          x <- conv(x, (1:(m + 1)) * ux[j]^(0:m))[1:(m+1)]
                                           ^
```
[R/bd_loglik.R:419:55:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L419) *style:* **Put spaces around all infix operators.**
```r
          x <- conv(x, (1:(m + 1)) * ux[j]^(0:m))[1:(m+1)]
                                                     ~^~
```
[R/bd_loglik.R:421:59:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L421) *style:* **Trailing whitespace is superfluous.**
```r
        loglik <- loglik + lgamma(S + 1) + lgamma(m + 1) -
                                                          ^
```
[R/bd_loglik.R:423:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L423) *style:* **Lines should not be more than 80 characters.**
```r
        #loglik = loglik - log(S + m + 1) + log(S + 1) + log(S + m - 1) - log(S - 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:423:10:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L423) *style:* **Commented code should be removed.**
```r
        #loglik = loglik - log(S + m + 1) + log(S + 1) + log(S + m - 1) - log(S - 1)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:426:11:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L426) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(tdmodel == 0) {
          ^
```
[R/bd_loglik.R:427:25:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L427) *style:* **Only use double-quotes.**
```r
          s1 <- sprintf('Parameters: %f %f', pars1[1], pars1[2])
                        ^~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:430:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L430) *style:* **Only use double-quotes.**
```r
            'Parameters: %f %f %f %f', pars1[1], pars1[2], pars1[3], pars1[4]
            ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:433:25:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L433) *style:* **Only use double-quotes.**
```r
          s1 <- sprintf('Parameters: %f %f %f', pars1[1], pars1[2], pars1[3])
                        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:435:23:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_loglik.R#L435) *style:* **Only use double-quotes.**
```r
        s2 <- sprintf(', Loglikelihood: %f', loglik)
                      ^~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:3:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L3) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:8:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:14:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L14) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:40:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
#' tdmodel == 4 : decline in speciation rate such that the expected number of species matches with
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:48:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
#' cond == 3 : conditioning on the total number of extant taxa (including missing species)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:63:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
#' do as many cycles as needed to meet the tolerance set for the target function.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:67:19:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L67) *style:* **Trailing whitespace is superfluous.**
```r
#' loglik function
                  ^
```
[R/bd_ML.R:87:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:88:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
#' cat("Estimating parameters for a set of branching times brts with the default settings:")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:91:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:93:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L93) *style:* **Variable or function name should be snake_case.**
```r
bd_ML = function(brts,
^~~~~
```
[R/bd_ML.R:93:7:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L93) *style:* **Use <-, not =, for assignment.**
```r
bd_ML = function(brts,
      ^
```
[R/bd_ML.R:94:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L94) *style:* **Lines should not be more than 80 characters.**
```r
    initparsopt = c(0.1,0.05 * (tdmodel <= 1) + 10 * (length(brts) + missnumspec) * (tdmodel > 1)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:94:25:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L94) *style:* **Commas should always have a space after.**
```r
    initparsopt = c(0.1,0.05 * (tdmodel <= 1) + 10 * (length(brts) + missnumspec) * (tdmodel > 1)),
                        ^
```
[R/bd_ML.R:95:21:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L95) *style:* **Commas should always have a space after.**
```r
    idparsopt = c(1,2 + (tdmodel > 1)),
                    ^
```
[R/bd_ML.R:96:52:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L96) *style:* **Commas should always have a space after.**
```r
    idparsfix = (1:4)[-idparsopt], parsfix = rep(0,4)[idparsfix],
                                                   ^
```
[R/bd_ML.R:105:19:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L105) *style:* **Only use double-quotes.**
```r
    optimmethod = 'subplex',
                  ^~~~~~~~~
```
[R/bd_ML.R:107:15:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L107) *style:* **Only use double-quotes.**
```r
    methode = 'lsoda',
              ^~~~~~~
```
[R/bd_ML.R:109:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L109) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/bd_ML.R:110:4:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L110) *style:* **Commented code should be removed.**
```r
  #options(warn = -1)
   ^~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:111:8:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L111) *style:* **Use <-, not =, for assignment.**
```r
  brts = sort(abs(as.numeric(brts)),decreasing = TRUE)
       ^
```
[R/bd_ML.R:111:37:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L111) *style:* **Commas should always have a space after.**
```r
  brts = sort(abs(as.numeric(brts)),decreasing = TRUE)
                                    ^
```
[R/bd_ML.R:112:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L112) *style:* **Lines should not be more than 80 characters.**
```r
  out2 = invisible(data.frame(lambda0 = -1,mu0 = -1,lambda1 = -1, mu1 = -1, loglik = -1, df = -1, conv = -1))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:112:8:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L112) *style:* **Use <-, not =, for assignment.**
```r
  out2 = invisible(data.frame(lambda0 = -1,mu0 = -1,lambda1 = -1, mu1 = -1, loglik = -1, df = -1, conv = -1))
       ^
```
[R/bd_ML.R:112:44:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L112) *style:* **Commas should always have a space after.**
```r
  out2 = invisible(data.frame(lambda0 = -1,mu0 = -1,lambda1 = -1, mu1 = -1, loglik = -1, df = -1, conv = -1))
                                           ^
```
[R/bd_ML.R:112:53:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L112) *style:* **Commas should always have a space after.**
```r
  out2 = invisible(data.frame(lambda0 = -1,mu0 = -1,lambda1 = -1, mu1 = -1, loglik = -1, df = -1, conv = -1))
                                                    ^
```
[R/bd_ML.R:113:5:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L113) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.numeric(brts) == FALSE)
    ^
```
[R/bd_ML.R:114:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L114) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/bd_ML.R:118:10:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L118) *style:* **Use <-, not =, for assignment.**
```r
  idpars = sort(c(idparsopt,idparsfix))
         ^
```
[R/bd_ML.R:118:29:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L118) *style:* **Commas should always have a space after.**
```r
  idpars = sort(c(idparsopt,idparsfix))
                            ^
```
[R/bd_ML.R:119:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L119) *style:* **Lines should not be more than 80 characters.**
```r
  if((prod(idpars == (1:4)) != 1) || (length(initparsopt) != length(idparsopt)) || (length(parsfix) != length(idparsfix)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:119:5:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L119) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if((prod(idpars == (1:4)) != 1) || (length(initparsopt) != length(idparsopt)) || (length(parsfix) != length(idparsfix)))
    ^
```
[R/bd_ML.R:120:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L120) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/bd_ML.R:124:5:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L124) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(tdmodel == 0 & length(initparsopt) > 2)
    ^
```
[R/bd_ML.R:125:3:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L125) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  {
  ^
```
[R/bd_ML.R:126:1:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L126) *style:* **Lines should not be more than 80 characters.**
```r
     cat("tdmodel = 0 only accepts a constant speciation rate and extinction rate.\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_ML.R:129:13:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L129) *style:* **Use <-, not =, for assignment.**
```r
  namepars1 = c("lambda0","mu0","lambda1","mu1")
            ^
```
[R/bd_ML.R:129:27:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L129) *style:* **Commas should always have a space after.**
```r
  namepars1 = c("lambda0","mu0","lambda1","mu1")
                          ^
```
[R/bd_ML.R:129:33:](https://github.com/rsetienne/DDD/blob/a67c8897058b5fede2cc77290f8ffa89d04782ab/R/bd_ML.R#L129) *style:* **Commas should always have a space after.**
```r
  namepars1 = c("lambda0","mu0","lambda1","mu1")


Можно просто отсортировать массив и присвоить его элементы переменным:
```
cat_a, cat_b, hypotenuse = arr.sort
```


Лишние пустые строки, убери


This breaks the app. Do you know what should be put here instead?


les projets pour la prairie


#  jq-lau
jQuery的多语言切换

线上展示效果：HTTP：//jqlau.sjfaze.com/

在JQ-lau.js中：

var language = {
//中文内容
	ZH：{
		yan：'jq多语言'，//对应一个自定义属性
		哈哈： '语言'，
		优优： '切换'，
	}，
  //英文内容
	EN：{
		颜：'jq duo yu yan'，
		哈哈：“语言”，
		优优：“开关”，
	}

  在的index.html中：

语言
 //添加自定义data-lau属性：属性名为在jq-lau.js定义好的语言的yan
	切换 //添加自定义data-lau属性：属性名为在jq-lau.js定义好的语言的哈哈


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/119](https://github.com/JuliaRegistries/General/pull/119)

After the above pull request is merged, it is recommended that you create
a tag on this repository for the registered package version:
```
git tag -a v0.3.3 -m "<description of version>" f65b707ae2ce46ff1ae0edf66a5d44f79d87062e
git push origin v0.3.3
```


<details>

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

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and are missing the following scopes:

```
{
  "AllOf": [
    "hooks:modify-hook:garbage/bugbug-test",
    "assume:hook-id:garbage/bugbug-test"
  ]
}
```

You have the scopes:

```
[
  "assume:project:relman:bugbug/build",
  "assume:project:taskcluster:mozilla-github-repository",
  "assume:repo:github.com/mozilla/bugbug:branch:pipeline-start-hook",
  "docker-worker:cache:bugbug-build",
  "docker-worker:capability:privileged",
  "notify:email:*",
  "notify:irc-channel:*",
  "notify:irc-user:*",
  "queue:create-task:aws-provisioner-v1/github-worker",
  "queue:create-task:aws-provisioner-v1/github-worker-windows",
  "queue:create-task:aws-provisioner-v1/releng-svc",
  "queue:create-task:aws-provisioner-v1/win2012r2",
  "queue:route:checks",
  "queue:route:garbage.*",
  "queue:route:index.garbage.*",
  "queue:route:notify.email.*",
  "queue:route:notify.irc-channel.*",
  "queue:route:notify.irc-user.*",
  "queue:route:statuses",
  "queue:scheduler-id:taskcluster-github",
  "secrets:get:garbage/*",
  "secrets:set:garbage/*"
]
```

This request requires you to satisfy this scope expression:

```
{
  "AllOf": [
    "hooks:modify-hook:garbage/bugbug-test",
    "assume:hook-id:garbage/bugbug-test",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/github-worker",
                "queue:create-task:very-high:aws-provisioner-v1/github-worker",
                "queue:create-task:high:aws-provisioner-v1/github-worker",
                "queue:create-task:medium:aws-provisioner-v1/github-worker",
                "queue:create-task:low:aws-provisioner-v1/github-worker",
                "queue:create-task:very-low:aws-provisioner-v1/github-worker",
                "queue:create-task:lowest:aws-provisioner-v1/github-worker"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/FXwNuvogRZWV6dyScGaUCA",
                "queue:schedule-task:taskcluster-github/FXwNuvogRZWV6dyScGaUCA/B-Ff0kd9SXKzA9i0c319Kg"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-04-18T09:53:15.956Z

</details>


<details>

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

Client ID project/taskcluster/tc-github/production-2 does not have sufficient scopes and are missing the following scopes:

```
{
  "AllOf": [
    "hooks:modify-hook:garbage/bugbug-test",
    "assume:hook-id:garbage/bugbug-test"
  ]
}
```

You have the scopes:

```
[
  "assume:project:relman:bugbug/build",
  "assume:project:taskcluster:mozilla-github-repository",
  "assume:repo:github.com/mozilla/bugbug:pull-request",
  "docker-worker:cache:bugbug-build",
  "docker-worker:capability:privileged",
  "notify:email:*",
  "notify:irc-channel:*",
  "notify:irc-user:*",
  "queue:create-task:aws-provisioner-v1/github-worker",
  "queue:create-task:aws-provisioner-v1/github-worker-windows",
  "queue:create-task:aws-provisioner-v1/releng-svc",
  "queue:create-task:aws-provisioner-v1/win2012r2",
  "queue:route:checks",
  "queue:route:garbage.*",
  "queue:route:index.garbage.*",
  "queue:route:notify.email.*",
  "queue:route:notify.irc-channel.*",
  "queue:route:notify.irc-user.*",
  "queue:route:statuses",
  "queue:scheduler-id:taskcluster-github",
  "secrets:get:garbage/*",
  "secrets:set:garbage/*"
]
```

This request requires you to satisfy this scope expression:

```
{
  "AllOf": [
    "hooks:modify-hook:garbage/bugbug-test",
    "assume:hook-id:garbage/bugbug-test",
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/github-worker",
                "queue:create-task:very-high:aws-provisioner-v1/github-worker",
                "queue:create-task:high:aws-provisioner-v1/github-worker",
                "queue:create-task:medium:aws-provisioner-v1/github-worker",
                "queue:create-task:low:aws-provisioner-v1/github-worker",
                "queue:create-task:very-low:aws-provisioner-v1/github-worker",
                "queue:create-task:lowest:aws-provisioner-v1/github-worker"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/DS3Q4KwCSAmXtmx3YqSqaA",
                "queue:schedule-task:taskcluster-github/DS3Q4KwCSAmXtmx3YqSqaA/WBzuxWIcQnKK0Wb8p4mi_Q"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-04-18T09:53:16.496Z

</details>


When the processbrowser is just opened, "self processBrowser" is nil, and an error will occur if I press the shortcut. (maybe I can change to choose the first process)
Currently the shortcut key can not be used, so I refer to the original processbrowser.


It really depends on where the `-` is, eg. https://regex101.com/r/8kgBzi/1 fails, while https://regex101.com/r/8kgBzi/2 would work.


aa


@chelmuth @nfeske sorry for this avoidable compile error on sel4 tonight. The famous last small refactoring without a re-compiling caused this. Please apply above small fixup to staging.


Should be good, but you have another method.

```
psbt.AddKeyPaths(accountPubKey, relativeKeyPaths);
psbt.RebaseKeyPaths(accountPubKey.PubKey.GetHDFingerprint(), masterFP, pathToAccountPubKey);
```
So if you have a coin: `0'/0'/0'/1/10`
then `relativeKeyPaths` should be `1/10` and `pathToAccountPubKey` should be `0'/0'/0'`.

After this your inputs should be set correctly. (also, `psbt.ToString()` is nice now! so you can debug easily)


Tower of Hanoi using 3 pegs
- Stack as underlying data structure.
- Time complexity needs to be evaluated yet


Registration pull request created: [JuliaRegistries/General/120](https://github.com/JuliaRegistries/General/pull/120)

After the above pull request is merged, it is recommended that you create
a tag on this repository for the registered package version:
```
git tag -a v0.4.4 -m "<description of version>" 7f0609bb765e17a3c8f0743f7d24b29ac0fef304
git push origin v0.4.4
```


yeah, it depends on where you put the `-`, if you put it on the end, it is clear that you do not meant to specify a range, if you place it on other places it may try to create a range from it.


Now could not deploy this pull request since the `now.json` file is empty.
It should be a valid JSON file.

    For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


It should be. Recent PHP versions upgraded to PCRE 2 that is more strict about `-` in character groups.


Sorry, it was a mistake. I will remove your name.


In this solution, you managed to get rid of the `Integer` boxing overhead, but the arrays you create are still quite large.

I think that the original solution, with `BitSet` instead of `List`, has the best chance of working. If even that has a memory problem, then we'll have to find a smarter solution which does not require us to store so much data in memory.


what if `doc == null`? This happened on my first attempt to run it.


I can't find any other usages of `demos` and it doesn't seem to be used anywhere outside DocData either.


<img src="https://media1.tenor.com/images/93d11bc59526ce49f60766f0045d819b/tenor.gif?itemid=11500735" alt="https://www.youtube.com/"


should have been named wip prim_to_con!


FBI OPEN UP


Deployment failed with the following error:

~~~
Builds rate limit exceeded (0 of 32 remaining). Try again in 60m
~~~


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-3157-nerdologues-composer.pantheonsite.io/)

Created multidev environment [ci-3157](https://dashboard.pantheon.io/sites/f8b6bd4b-bde6-45de-b354-3bf2c6c1f757#ci-3157) for nerdologues-composer.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-3158-nerdologues-composer.pantheonsite.io/)

Created multidev environment [ci-3158](https://dashboard.pantheon.io/sites/f8b6bd4b-bde6-45de-b354-3bf2c6c1f757#ci-3158) for nerdologues-composer.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-5-dig-pantheon-d8-composer-project.pantheonsite.io/)

Created multidev environment [pr-5](https://dashboard.pantheon.io/sites/f00aaaee-f0c1-4385-9ade-ac6d58cf1375#pr-5) for dig-pantheon-d8-composer-project.


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

Created multidev environment [pr-8](https://dashboard.pantheon.io/sites/20f4f1ae-f932-489c-a1ae-43ae865f206c#pr-8) for resourcehub.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-1-sb-demo-04182019.pantheonsite.io/)

Created multidev environment [pr-1](https://dashboard.pantheon.io/sites/9bca1edf-01ae-4da6-9bf6-2ca9b4b23e31#pr-1) for sb-demo-04182019.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-5-topperstation.pantheonsite.io/)

Created multidev environment [pr-5](https://dashboard.pantheon.io/sites/db5fb5e4-3225-46f0-b0a9-1cc803600c48#pr-5) for topperstation.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-1-drupal-v8.pantheonsite.io/)

Created multidev environment [pr-1](https://dashboard.pantheon.io/sites/d424071d-85b4-41be-bb05-9050909c1c6c#pr-1) for drupal-v8.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-4-erp4edu.pantheonsite.io/)

Created multidev environment [pr-4](https://dashboard.pantheon.io/sites/dd66d777-8d0e-4efd-8adf-e9d768b1687e#pr-4) for erp4edu.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-7-yan-playground-d8.pantheonsite.io/)

Created multidev environment [pr-7](https://dashboard.pantheon.io/sites/fd99cb00-efb7-453c-b5a5-5f125d8bcba9#pr-7) for yan-playground-d8.


Speaking of
```latex
\mathrm{d}x
```
Which is better of the following?
```latex
\int \! \ln x \, \mathrm{d}x
```
```latex
\int    \ln x \, \mathrm{d}x
```
```latex
\int \! \ln x    \mathrm{d}x
```
```latex
\int    \ln x    \mathrm{d}x
```


### Visual regression report:

[![Visual report](https://circleci.com/gh/stevector/nerdologues-d8/3159/artifacts/0/artifact/backstop_data/bitmaps_test/20190419-000632/0600294051_clip_2_0_document_0_desktop.png)](https://circleci.com/gh/stevector/nerdologues-d8/3159/artifacts/0/artifact/backstop_data/html_report/index.html)


Looks great!


hi @xhebox i'm currently playing around with wine... i wonder if we could have a chat about it


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-2-ncu-demo.pantheonsite.io/)

Created multidev environment [pr-2](https://dashboard.pantheon.io/sites/62b1d444-d704-491e-8168-bcabd8479ae7#pr-2) for ncu-demo.


cc @godotengine/documentation


FBI OPEN UP


ORIGINAL DATA FROM
https://www.esrl.noaa.gov/psd/gcos_wgsp/Timeseries/Data/sunspot.long.data


test


Neat! I have this done similar in each file. This can be fixed later as clean up.


## Jenkins Build Summary

Built from [this commit](https://github.com/mellery451/rippled/commit/80493b02e29f1f59696e6e621b277860e0c37c43)

Built at __20190419 - 00:17:13__

### Test Results

Build Type | Log | Result | Status
---------- | --- | ------ | ------
rpm | [logfile](http://ci.ops.ripple.com/job/mellery-rippled/job/pkg-ub19/2//artifact/rpm.txt) | 1158 cases, 0 failed, t: n/a | PASS :white_check_mark:


Seems to work fine besides infection and gungame, Both of these cause the game to lock up on map load.


test ok?


@purplelady105 Yeah what she said.


# Specs execution successful
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### Plans updated

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

Project | Plan | Build
---|---|---
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[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

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## Jenkins Build Summary

Built from [this commit](https://github.com/ximinez/rippled/commit/6070383ce9ebc4ec485a771a99d5b1a4eb981449)

Built at __20190419 - 00:21:31__

### Test Results

Build Type | Log | Result | Status
---------- | --- | ------ | ------
rpm | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/rpm.txt) | 1158 cases, 0 failed, t: n/a | PASS :white_check_mark:
msvc.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/msvc.Debug.txt) | 1155 cases, 0 failed, t: 614s | PASS :white_check_mark:
msvc.Debug,
NINJA_BUILD=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/msvc.Debug_NINJA_BUILD_true.txt) | 1155 cases, 0 failed, t: 637s | PASS :white_check_mark:
msvc.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/msvc.Debug_Dunity_OFF.txt) | 1155 cases, 0 failed, t: 1171s | PASS :white_check_mark:
msvc.Release | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/msvc.Release.txt) | 1155 cases, 0 failed, t: 422s | PASS :white_check_mark:
gcc.Release
-Dassert=ON,
MANUAL_TESTS=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Release_Dassert_ON_MANUAL_TESTS_true.txt) | 951 cases, 0 failed, t: 6m8s | PASS :white_check_mark:
docs,
TARGET=docs | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/docs_TARGET_docs.txt) | 1 cases, 0 failed, t: 0m2s | PASS :white_check_mark:
clang.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/clang.Debug.txt) | 1158 cases, 0 failed, t: 3m14s | PASS :white_check_mark:
gcc.Debug
-Dcoverage=ON,
TARGET=coverage_report,
SKIP_TESTS=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Debug_Dcoverage_ON_TARGET_coverage_report_SKIP_TESTS_true.txt) | 1158 cases, 0 failed, t: 17m26s | PASS :white_check_mark:
clang.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/clang.Debug_Dunity_OFF.txt) | 1158 cases, 0 failed, t: 10m59s | PASS :white_check_mark:
gcc.Debug | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Debug.txt) | 1158 cases, 0 failed, t: 3m30s | PASS :white_check_mark:
clang.Release
-Dassert=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/clang.Release_Dassert_ON.txt) | 1158 cases, 0 failed, t: 5m42s | PASS :white_check_mark:
gcc.Debug
-Dunity=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Debug_Dunity_OFF.txt) | 1158 cases, 0 failed, t: 11m49s | PASS :white_check_mark:
gcc.Release
-Dassert=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Release_Dassert_ON.txt) | 1158 cases, 0 failed, t: 6m12s | PASS :white_check_mark:
gcc.Debug
-Dstatic=OFF | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Debug_Dstatic_OFF.txt) | 1158 cases, 0 failed, t: 3m29s | PASS :white_check_mark:
gcc.Debug
-Dstatic=OFF -DBUILD_SHARED_LIBS=ON | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Debug_Dstatic_OFF_DBUILD_SHARED_LIBS_ON.txt) | 1158 cases, 0 failed, t: 3m29s | PASS :white_check_mark:
gcc.Debug,
NINJA_BUILD=true | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/gcc.Debug_NINJA_BUILD_true.txt) | 1158 cases, 0 failed, t: 3m2s | PASS :white_check_mark:
clang.Debug
-Dunity=OFF -Dsan=address,
PARALLEL_TESTS=false,
DEBUGGER=false | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/clang.Debug_Dunity_OFF_Dsan_address_PARALLEL_TESTS_false_DEBUGGER_false.txt) | 1158 cases, 0 failed, t: 11m26s | PASS :white_check_mark:
clang.Debug
-Dunity=OFF -Dsan=undefined,
PARALLEL_TESTS=false | [logfile](http://ci.ops.ripple.com/job/ed-rippled/job/ss--ticket-handle/1//artifact/clang.Debug_Dunity_OFF_Dsan_undefined_PARALLEL_TESTS_false.txt) | 1158 cases, 0 failed, t: 12m27s | PASS :white_check_mark:


Successfully aliased the URL <https://docs-r7uq97y7t.zeit.sh> to the following aliases.

* https://docs.zeit.sh
* https://docs-git-master.zeit.sh


Yeah...


That was fast!


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Created multidev environment [ci-3162](https://dashboard.pantheon.io/sites/f8b6bd4b-bde6-45de-b354-3bf2c6c1f757#ci-3162) for nerdologues-composer.


### Visual regression report:

[![Visual report](https://circleci.com/gh/stevector/nerdologues-d8/3166/artifacts/0/artifact/backstop_data/bitmaps_test/20190419-002909/0600294051_Nerd_bio_2_MBS_0_document_0_desktop.png)](https://circleci.com/gh/stevector/nerdologues-d8/3166/artifacts/0/artifact/backstop_data/html_report/index.html)


### Visual regression report:

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The behavioral typecheck would happen once, before the contract is deployed. And a type signature something like `<ret!>true <=> not <err!>true` doesn't seem prohibitive (using the syntax from [the SLMC manual](http://ctp.di.fct.unl.pt/SLMC/manual.pdf))

The repeated `@Either` calls impact the transaction cost of every REV transfer, including every deployment, right?

I'm all for "make it work, then make it fast" but we should eventually pay attention to cost accounting overhead, right?


Updated and opened a PR: https://github.com/ros2/rosidl/pull/363


非常好


It's easy when you give a reproducible example, a screenshot, and a correct guess at what the problem is!


The following doc(s) have been deployed to the [sgmysqlsl](https://sgmysqlsl-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/mysql-slow-log](https://sgmysqlsl-static-docs.pantheonsite.io/docs/mysql-slow-log)


Added a few comments inline.


Very minor suggestion. `onlyOwner` is a de facto standard naming convention for this concern. It will also avoid conflicts if you decide to make a `function isOwner() public view returns(bool) { ...`


test ok?


So we really shouldn't include test source into the library.  The reference functions are just that.  They should only be linked or included with the tests.


just call them crc16_t10dif_copy_ref()


Let's just change the check to compare the multi-binary, main function against the reference function.  We would like to stop exposing the base functions altogether eventually and have only one entry point for each function.


This table was already in crc_base.c.  Leave it in there and just add the other tables and table versions into it.  In the _ref file put a bitwize version of iscsi called crc32_iscsi_ref()  (_base_ref is a bit redundant).  Since all the ref functions are small I would suggest just putting them in a header called crc_ref.h and including in the tests.  This will keep you from having to add a dependency rule to all the tests but don't forget to add the line in the makefile:
`other_src += crc/crc_ref.h`
to make sure it gets into the build.


Build version: __`0.10.0-renovate/node-8.15.711`__ :crossed_fingers: [`renovate/node-8.15`](https://github.com/streamich/ci-scripts/tree/renovate/node-8.15) on [*CircleCI*](https://circleci.com/gh/streamich/ci-scripts/711) :tada:


Main


Build version: __`0.10.0-renovate/node-8.15.1100`__ :crossed_fingers: [`renovate/node-8.15`](https://github.com/streamich/ci-scripts/tree/renovate/node-8.15) on [*Travis*](https://travis-ci.org/streamich/ci-scripts/builds/521974778) :tada:


dljfdljf


Oops, #3523 not #3533


cached numcols


I posted edited version in my repo, please check. comp_slices has some discrepancy in var names, I guess it's not done yet?


`ServerPreformReload` should be `ServerPerformReload` (spelling error).


Im going to delete that function anyway but thanks.


> It's easy when you give a reproducible example, a screenshot, and a correct guess at a simple solution!

Doesn't everybody always do that?  🤷♂


`private` is good for making sure a child contract that inherits from this doesn't accidentally overwrite important data. Another side effect is it means there is no "free" getter. If it was `public` the "free" getter would look like:

```
function balances(address a) public view returns(uint) {
  return balances[a];
}
```

`private` does not protect confidentiality as is often assumed. Miners and nodes _need_ access to the storage trie to correctly process the contract functions and this means the data is easily inspectable by anyone with knowledge of how that works.

Since it is not possible to safeguard confidentiality (efforts to do so will merely inconvenience a determined adversary) it is usually best to ensure that the contract state is easily discoverable - keeping in mind that the data access you create needs to be satisfactory for all future use-cases.

All to say, as a good habit, I would manually add a function that mimics the "free" function whenever I make a private state variable.


Fancy!


``` file abs-true
abs-true: broken symbolic link to /home/lramage/repos/proot/tests//rootfs/bin/abs-true
```


Successfully aliased the URL <https://twitter-avatar-bilszeerki.now.sh> to the following alias.

* https://twitter-avatar.now.sh


Рецепт лучше получить из таблицы машины-рецепты, там просто смотрим id машины и он нам отдаем все рецепты на ней


Oops ... here it is ... I would pass in an address so anyone can inspect anything. I would also remove `isRunning` so that the state can be inspected during an emergency stop. As a general heuristic, use guards on state-changing functions. It's safe to remove them from read-only functions.


Successfully aliased the URL <https://twitter-avatar-ivukvieozs.now.sh> to the following alias.

* https://twitter-avatar.now.sh


Missed the opportunity to `Revert "Revert "add rubygem-kubernetes-deploy to extrapackages""`


Build version: __`3.1.1-master.286`__ :crossed_fingers: [`master`](https://github.com/streamich/md-mdast/tree/master) on [*CircleCI*](https://circleci.com/gh/streamich/md-mdast/286) :tada:


❌ quinCI run of 'master' failed. Exit code was 127.
<details>
<summary>Log output:</summary>

``````
sh: 1: git: not found
``````
</details>


Shouldn't this be fixed on Transifex instead, @awesomerobot?


это подходит для всего, кроме процедур, там надо вызывать так: cursor.callproc(procname, args=())
Вот документация: https://pymysql.readthedocs.io/en/latest/modules/cursors.html
Здесь есть пример: https://o7planning.org/ru/11463/connecting-mysql-database-in-python-using-pymysql#a7889084


Capitalization of variables!


We will see sender contract event first then our SplitEvent.
I'll put the .transfer at the bottom then we'll see our SplitEvent first.


Separate function arguments with spaces: eg `AddAmmo(Loaded, 0)`


@rejon


This broke the shell. `yarn start` now runs in prod mode.


Successfully aliased the URL <https://jameswlanecom-hgu6qf5yi.now.sh> to the following aliases.

* https://jameswlane.com
* https://www.jameswlane.com
* https://jameswlanecom-git-master.jameswlane.now.sh


@JacksonTenor did this too


K. Easy to fix.


> @rejon


@JacksonTenor and @leahy089 did this as well


❌ quinCI run of 'master' failed. Exit code was 128.
<details>
<summary>Log output:</summary>

``````
Warning: Permanently added 'github.com,140.82.118.4' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
``````
</details>


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Created multidev environment [pr-11](https://dashboard.pantheon.io/sites/5dc54081-9ac4-47f3-96ea-b84d100dbf19#pr-11) for bjennings-drupalcon-seattle-2019.


I can't solve this problem for you, you're going to have to figure it out on your own. Nothing in the code you posted seems wrong.

However, some quick math based on the number you posted (4-6M operations a second):

4M operations per second so let's assume we're trying to emit 4M metrics per second. Each metric is a counter so assume 25 bytes per metric (something like `'some.whatever.counter:1|c'`, random example, could be longer, could be shorter). That's 100 MB/sec of metrics you're trying to send (25 bytes * 4M operations / 1048576 bytes per megabyte). Put another way, it's 750 Mb/sec, or **75% of the network bandwidth on a 1Gbps network card in metrics alone**, not counting whatever real work this application is doing.

I'm not surprised enabling metrics makes things slower. Maybe try not emitting a metric each time you perform an operation, keep track of a count in a local variable outside your hot loop and emit a single metric afterward.

As I said, this is just a guess and I can't solve this for you.


Saw this while looking at the servercert-wg list, shouldn't this be `SYNTAX: contactphone <rfc3966 Global Number>` @dougbeattie?


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