[R/bd_loglik_choosepar.R:1:1:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L89) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:105:74:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L110) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:111:3:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L115) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:117:54:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L120) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:125:1:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L125) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:126:3:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L132) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:148:16:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L150) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bd_loglik.R:153:73:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L158) *style:* **Trailing whitespace is superfluous.**
```r
    } else {
            ^~~~~~~~
```
[R/bd_loglik.R:164:10:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L174) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:175:7:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L180) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:181:7:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L183) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:184:7:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L193) *style:* **Trailing whitespace is superfluous.**
```r
        }
         ^
```
[R/bd_loglik.R:196:9:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L200) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:201:9:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L205) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:207:1:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L207) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:208:9:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L295) *style:* **Trailing whitespace is superfluous.**
```r
          }
           ^
```
[R/bd_loglik.R:296:12:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L298) *style:* **Trailing whitespace is superfluous.**
```r
          #{
            ^
```
[R/bd_loglik.R:299:15:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L322) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:324:11:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L339) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:341:9:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L401) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:403:1:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_loglik.R#L403) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:405:11:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_ML.R#L3) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:8:3:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_ML.R#L8) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:14:3:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_ML.R#L14) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:40:1:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_ML.R#L87) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:88:1:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_ML.R#L91) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_ML.R:93:1:](https://github.com/rsetienne/DDD/blob/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/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/24813c6c29e59fb7c93b8bc63dd5865035fa05e4/R/bd_ML.R#L129) *style:* **Commas should always have a space after.**
```r
  namepars1 = c("lambda0","mu0","lambda1","mu1")


# Specs execution successful
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### Plans updated

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---|---|---
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this should be fixed since some times


请问该怎样准备测试数据，data/annotation/  data/images.pkl


tha big number song


So maybe I made a strange mistake somehow. Sorry about that.

I will imrove.


You are quite right. I think this is worth fixing so long as `nprocs` is still a valid option. Would you like to submit a PR, @saschadaehne ?


lgtm


а где его view?


typo: "ANother"


если это презентер, почему он исполняет обязанности GUI?


@krystian3w Tym razem obyło się bez opóźnień. Dostałem maila od CircleCI z przeprosinami, sporo większy ruch mieli niż zazwyczaj i dlatego zdarzały się opóźnienia :smile:.


Это не MVP, просто не мог подобрать более подходящее слово для названия


if *the*… *its*


declaMation ?


Yep, those are almost certainly the bug we predicted. Thanks, I'll make sure we get those working!


кем тогда является этот класс?


[](url)


It's not aligned!


so now it is declaim an not declare ?


Ok


- [ ] WE NEED BITCOINS


Test positions

Some examples from last TCEC seasons
3r4/p3r1pk/PpBb1pRp/1KpPpP1P/2P1P1R1/8/8/8 b - - 32 86
8/8/8/1k6/2p5/p1K5/N2B2r1/8 b - - 59 109
4r3/2r3p1/3kp2p/1p1pNp1P/p2PnP2/P1PK4/1P6/6RR w - - 22 101
1r4k1/1r1bq3/4p1p1/3pPpPp/pNpN1P1P/P1PnQ3/1PK5/1R3R2 b - - 13 82

Other draws
5k2/3b4/5p2/p1p1pPp1/PpPpP1Pp/1P1P3P/8/3R1K2 w - - 20 1
5k2/8/5p2/p1p1pPp1/PbPpP1Pp/3P3P/8/3R1K2 w - - 20 1

Blocked in infinite loop before last commit :
q1B5/1P1q4/8/8/8/6R1/8/1K1k4 w - - 0 1

hard cases (not solved)
8/8/6b1/8/p7/Pp6/1P1K1k2/8 w - - 10 171 (very difficult one even if obvious for human brain)
1r6/4p1k1/p2p1p1p/P1pP1Pn1/1rN1P1P1/1PKP4/1R6/5R2 w - - 34 74
8/8/8/B6b/p2p1p2/Pp1p1k2/1P6/4K3 b - - 17 165
1r4k1/6p1/q3prp1/2Pn4/1p1P1P1P/pQ1R2P1/8/B3R1K1 w - - 79 96
3q2k1/1r3p1p/3pbPpb/p1p1p3/P2nP2P/1PRP2P1/3N1R1K/3BQ3 b - - 29 43

Verification (non draw, long zugzwang that SF should still find):
8/1b2P3/5k2/p7/Pp1K3p/1P6/2Bp3P/8 b - - 0 49
8/5k2/1r4p1/6Pp/R7/6K1/8/8 b - - 51 78


Здесь я обьявляю счетчик и передаю его по указателю в функцию bSort(), отладчиком проверил в теле функции считает., но назад сюда не передает. С qSort() аналогично...


лучше вынести GUI отдельно или просто не называть подобный класс презентером?


ct vreman nul


На сколько профитно хранить в Person номер телефона? есть ли тогда смысл в использовании множества и переопределении `equals` и `hashCode`?


Здесь в лямбду вообще не заходит...


<details>

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

InterpreterError at template.tasks[0].payload.env["GIT_REPOSITORY"]: object has no property pull_request

</details>


Fa manina le zavatra asaiko atao tsy atao fa zavatra hafa ndray no ataonao ? Io AchatOrpailleur io zao tsy mety io ? Ina n objectif amin'io ?


I think I did this right


Thanks! I had the same thing in Sublime Text, but somehow after an upgrade the configuration got reset and it was not autosaving `.es6` files.


tu devrais juste checker avec les ancestors de brand aussi, tant qu'a ca, non?


The message should say this commit is {{ commit.index }} commits behind


@battlemidget Scapestack doesn't fall under the jenkins firewall umbrella does it? I'm pretty sure we still need these there.


Be careful with blank space


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

* https://linronglang.com
* https://www.linronglang.com
* https://linronglang-git-master.linronglang1.now.sh


JS youtube


Is this a part of the DDS demo, or accidentally committed?


This commit has been mentioned on **Nix community**. There might be relevant details there:

https://discourse.nixos.org/t/no-font-droid-in-19-03/2663/2


A


los cambios funcionaron a la perfección 🍄


;knp


Successfully aliased the URL <https://linronglang-ip8xk11ca.now.sh> to the following aliases.

* https://linronglang.com
* https://www.linronglang.com
* https://linronglang-git-master.linronglang1.now.sh


Good


Ito ange no asaiko ovainao alohan'izy rehetra !!!


Successfully aliased the URL <https://nicollis-b2owfa962.now.sh> to the following aliases.

* https://nick.oll.is
* https://nic.oll.is
* https://nicholas.oll.is
* https://nicollis-git-master.nicollis.now.sh


Oh this is nice. Thank you!


### [Codacy](https://app.codacy.com/app/hyperiumjailbreak/client/commit?cid=346451079) detected an issue:
#### Message: `Use one line for each declaration, it enhances code readability.`

#### Currently on:
+ **Commit**:  e3d09021e0f21fdf7626f76356e94c6a8e1e97a1
+ **File**:    [src/main/java/cc/hyperium/addons/customcrosshair/gui/GuiCustomCrosshairEditColour.java](https://github.com/hyperiumjailbreak/client/blob/e3d09021e0f21fdf7626f76356e94c6a8e1e97a1/src/main/java/cc/hyperium/addons/customcrosshair/gui/GuiCustomCrosshairEditColour.java)
+ **LineNum**: [111](https://github.com/hyperiumjailbreak/client/blob/e3d09021e0f21fdf7626f76356e94c6a8e1e97a1/src/main/java/cc/hyperium/addons/customcrosshair/gui/GuiCustomCrosshairEditColour.java#L111)


hj


.log files by nemali byt v git repositari, delete -> commit-push -> add into .gitignore


While I agree with the _content_ of the patch, :+1: on that suggestion.

If you're looking for a way to make this visible to users that potentially have the skills to port from ar71xx to ath79, then you might consider changing
```
Atheros AR7xxx/AR9xxx
```
to
```
ar71xx (DEPRECATED)
```
You then would need to know what "ar71xx" was to even explore it, and the fact that the world as you know it is coming to an end would be at least vaguely evident when in `menuconfig`.


The bugfixes:
- Rook findLegalMovesOnSameFile() was consistently missing 1 legal move, due to incorrect condition in for loop.
- King isInCheck() was behaving incorrectly when the King was checking for possible moves (if the King captured a piece, the boardstate was not updated and any checks that were previously blocked by the captured piece were missed).


.iml  files by nemali byt git repositari -> delete-> commit-push -> add to .gitignore


FYI this gives the following warning at compile-time:
```c++
.piolibdeps/ESP Async WebServer/src/AsyncJson.h:39:33: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
constexpr char* JSON_MIMETYPE = "application/json"```


right. Can you fix that please? I need to go


встретимся в следующем году)


Done


Commit #59cc965 does multi course support
And this fixes the delete

[https://github.com/ullfindsmit/learnpress/commit/59cc96535a2ff39e0f8a5e26c26cf5ee4505014d](url)