[R/bd_loglik_choosepar.R:1:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/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/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik_choosepar.R#L18) *style:* **Use <-, not =, for assignment.**
```r
         loglik = -Inf
                ^
```
[R/bd_loglik.R:2:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L2) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_loglik.R:6:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L6) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_loglik.R:7:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L7) *style:* **Trailing whitespace is superfluous.**
```r
#'
  ^
```
[R/bd_loglik.R:41:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' \cr \cr \code{pars2[4]} sets whether the parameters and likelihood should be shown
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:58:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
#' bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, missnumspec = 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:58:85:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L58) *style:* **Trailing whitespace is superfluous.**
```r
#' bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, missnumspec = 0)
                                                                                ^
```
[R/bd_loglik.R:60:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L60) *style:* **Use <-, not =, for assignment.**
```r
bd_loglik = function(pars1,pars2,brts,missnumspec,methode = 'lsoda')
          ^
```
[R/bd_loglik.R:60:28:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L60) *style:* **Commas should always have a space after.**
```r
bd_loglik = function(pars1,pars2,brts,missnumspec,methode = 'lsoda')
                           ^
```
[R/bd_loglik.R:60:34:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L60) *style:* **Commas should always have a space after.**
```r
bd_loglik = function(pars1,pars2,brts,missnumspec,methode = 'lsoda')
                                 ^
```
[R/bd_loglik.R:60:39:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L60) *style:* **Commas should always have a space after.**
```r
bd_loglik = function(pars1,pars2,brts,missnumspec,methode = 'lsoda')
                                      ^
```
[R/bd_loglik.R:60:51:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L60) *style:* **Commas should always have a space after.**
```r
bd_loglik = function(pars1,pars2,brts,missnumspec,methode = 'lsoda')
                                                  ^
```
[R/bd_loglik.R:60:61:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L60) *style:* **Only use double-quotes.**
```r
bd_loglik = function(pars1,pars2,brts,missnumspec,methode = 'lsoda')
                                                            ^~~~~~~
```
[R/bd_loglik.R:64:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
# - pars1[3] = la1 = parameter in exponential decay of speciation rate, OR K in diversity-dependence-like models (default 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:65:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
# - pars1[4] = mu1 = parameter in exponential decay of extinction rate (default 0)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:66:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
# - pars1[5] = T0 = age at which lambda is lambda0 (default T0 = age of phylogeny)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:71:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
# . tdmodel == 2: stepwise decline following diversity-dependence when extinction = 0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:72:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L72) *style:* **Lines should not be more than 80 characters.**
```r
# . tdmodel == 3: decline in speciation rate following deterministic logistic equation for ddmodel = 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:73:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
# . tdmodel == 4...8: change in speciation/extinction rate following ddmodel = 1...5, with n = expected number of species
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:74:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L74) *style:* **Lines should not be more than 80 characters.**
```r
# - pars2[2] = cond = conditioning on age (0), non-extinction of the clade and age (1), number of taxa and age (2), number of taxa (3)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:77:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L77) *style:* **Lines should not be more than 80 characters.**
```r
# - pars2[5] = likelihood is for a tree with crown age (2) or stem age (1) - stem age not yet implemented for tdmodel == 2
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:80:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L80) *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:81:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L81) *style:* **Use <-, not =, for assignment.**
```r
  rhotaut = function(tau,t1,pars)
          ^
```
[R/bd_loglik.R:81:26:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L81) *style:* **Commas should always have a space after.**
```r
  rhotaut = function(tau,t1,pars)
                         ^
```
[R/bd_loglik.R:81:29:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L81) *style:* **Commas should always have a space after.**
```r
  rhotaut = function(tau,t1,pars)
                            ^
```
[R/bd_loglik.R:82:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L82) *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:83:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L83) *style:* **Use <-, not =, for assignment.**
```r
    la0 = pars[1]
        ^
```
[R/bd_loglik.R:84:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L84) *style:* **Use <-, not =, for assignment.**
```r
    mu0 = pars[2]
        ^
```
[R/bd_loglik.R:85:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L85) *style:* **Use <-, not =, for assignment.**
```r
    la1 = pars[3]
        ^
```
[R/bd_loglik.R:86:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L86) *style:* **Use <-, not =, for assignment.**
```r
    mu1 = pars[4]
        ^
```
[R/bd_loglik.R:86:18:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L86) *style:* **Trailing whitespace is superfluous.**
```r
    mu1 = pars[4]
                 ^~
```
[R/bd_loglik.R:87:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L87) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(la1 == 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0 * (tau - t1)}
      ^
```
[R/bd_loglik.R:87:29:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L87) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(la1 == 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0 * (tau - t1)}
                            ^
```
[R/bd_loglik.R:87:34:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L87) *style:* **Use <-, not =, for assignment.**
```r
    if(la1 == 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0 * (tau - t1)}
                                 ^
```
[R/bd_loglik.R:87:71:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L87) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if(la1 == 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0 * (tau - t1)}
                                                                      ^
```
[R/bd_loglik.R:88:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Lines should not be more than 80 characters.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:88:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
      ^
```
[R/bd_loglik.R:88:28:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                           ^
```
[R/bd_loglik.R:88:33:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Use <-, not =, for assignment.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                ^
```
[R/bd_loglik.R:88:57:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                       ~^~
```
[R/bd_loglik.R:88:73:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                       ~^~
```
[R/bd_loglik.R:88:88:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                                ~^~
```
[R/bd_loglik.R:88:94:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L88) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if(la1 > 0 & mu1 == 0) {rtt = mu0 * (tau - t1) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                                ^
```
[R/bd_loglik.R:89:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Lines should not be more than 80 characters.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:89:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
      ^
```
[R/bd_loglik.R:89:28:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
                           ^
```
[R/bd_loglik.R:89:33:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Use <-, not =, for assignment.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
                                ^
```
[R/bd_loglik.R:89:38:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Put spaces around all infix operators.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
                                    ~^~
```
[R/bd_loglik.R:89:54:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Put spaces around all infix operators.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
                                                    ~^~
```
[R/bd_loglik.R:89:69:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Put spaces around all infix operators.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
                                                                   ~^~
```
[R/bd_loglik.R:89:94:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L89) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if(la1 == 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0 * (tau - t1)}
                                                                                ^
```
[R/bd_loglik.R:90:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Lines should not be more than 80 characters.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:90:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
      ^
```
[R/bd_loglik.R:90:27:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                          ^
```
[R/bd_loglik.R:90:32:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Use <-, not =, for assignment.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                               ^
```
[R/bd_loglik.R:90:37:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                   ~^~
```
[R/bd_loglik.R:90:53:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                   ~^~
```
[R/bd_loglik.R:90:68:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                  ~^~
```
[R/bd_loglik.R:90:80:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                              ~^~
```
[R/bd_loglik.R:90:96:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                                ~^~
```
[R/bd_loglik.R:90:111:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Put spaces around all infix operators.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                                ~^~
```
[R/bd_loglik.R:90:117:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L90) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
    if(la1 > 0 & mu1 > 0) {rtt = mu0/mu1 * (exp(-mu1*t1) - exp(-mu1*tau)) - la0/la1 * (exp(-la1*t1) - exp(-la1*tau))}
                                                                                ^
```
[R/bd_loglik.R:93:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L93) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:94:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L94) *style:* **Variable or function name should be snake_case.**
```r
  PtTint = function(x,t1,pars)
  ^~~~~~
```
[R/bd_loglik.R:94:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L94) *style:* **Use <-, not =, for assignment.**
```r
  PtTint = function(x,t1,pars)
         ^
```
[R/bd_loglik.R:94:23:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L94) *style:* **Commas should always have a space after.**
```r
  PtTint = function(x,t1,pars)
                      ^
```
[R/bd_loglik.R:94:26:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L94) *style:* **Commas should always have a space after.**
```r
  PtTint = function(x,t1,pars)
                         ^
```
[R/bd_loglik.R:95:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L95) *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:95:4:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L95) *style:* **Trailing whitespace is superfluous.**
```r
  {
   ^
```
[R/bd_loglik.R:96:5:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L96) *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:96:12:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L96) *style:* **Use <-, not =, for assignment.**
```r
    PtTint = pars[2] * exp(-pars[4] * x) * exp(rhotaut(x,t1,pars))
           ^
```
[R/bd_loglik.R:96:58:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L96) *style:* **Commas should always have a space after.**
```r
    PtTint = pars[2] * exp(-pars[4] * x) * exp(rhotaut(x,t1,pars))
                                                         ^
```
[R/bd_loglik.R:96:61:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L96) *style:* **Commas should always have a space after.**
```r
    PtTint = pars[2] * exp(-pars[4] * x) * exp(rhotaut(x,t1,pars))
                                                            ^
```
[R/bd_loglik.R:99:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L99) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:100:6:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L100) *style:* **Use <-, not =, for assignment.**
```r
  ff = function(t1,pars)
     ^
```
[R/bd_loglik.R:100:20:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L100) *style:* **Commas should always have a space after.**
```r
  ff = function(t1,pars)
                   ^
```
[R/bd_loglik.R:101:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L101) *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:102:8:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L102) *style:* **Use <-, not =, for assignment.**
```r
    ff = 1/pars[3] + (1/2 - 1/pars[3]) * exp(-(pars[1] - pars[2]) * t1)
       ^
```
[R/bd_loglik.R:102:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L102) *style:* **Put spaces around all infix operators.**
```r
    ff = 1/pars[3] + (1/2 - 1/pars[3]) * exp(-(pars[1] - pars[2]) * t1)
         ~^~
```
[R/bd_loglik.R:102:24:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L102) *style:* **Put spaces around all infix operators.**
```r
    ff = 1/pars[3] + (1/2 - 1/pars[3]) * exp(-(pars[1] - pars[2]) * t1)
                      ~^~
```
[R/bd_loglik.R:102:30:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L102) *style:* **Put spaces around all infix operators.**
```r
    ff = 1/pars[3] + (1/2 - 1/pars[3]) * exp(-(pars[1] - pars[2]) * t1)
                            ~^~
```
[R/bd_loglik.R:102:47:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L102) *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:105:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L105) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:106:15:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L106) *style:* **Use <-, not =, for assignment.**
```r
  exprhotaut2 = function(tau,t1,pars)
              ^
```
[R/bd_loglik.R:106:30:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L106) *style:* **Commas should always have a space after.**
```r
  exprhotaut2 = function(tau,t1,pars)
                             ^
```
[R/bd_loglik.R:106:33:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L106) *style:* **Commas should always have a space after.**
```r
  exprhotaut2 = function(tau,t1,pars)
                                ^
```
[R/bd_loglik.R:107:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L107) *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:107:4:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L107) *style:* **Trailing whitespace is superfluous.**
```r
  {
   ^~~
```
[R/bd_loglik.R:108:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L108) *style:* **Use <-, not =, for assignment.**
```r
    rtt = ff(tau,pars)/ff(t1,pars)
        ^
```
[R/bd_loglik.R:108:18:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L108) *style:* **Commas should always have a space after.**
```r
    rtt = ff(tau,pars)/ff(t1,pars)
                 ^
```
[R/bd_loglik.R:108:23:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L108) *style:* **Put spaces around all infix operators.**
```r
    rtt = ff(tau,pars)/ff(t1,pars)
                     ~^~
```
[R/bd_loglik.R:108:30:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L108) *style:* **Commas should always have a space after.**
```r
    rtt = ff(tau,pars)/ff(t1,pars)
                             ^
```
[R/bd_loglik.R:111:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L111) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:112:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L112) *style:* **Variable or function name should be snake_case.**
```r
  intPtTint2 = function(t1,T,pars)
  ^~~~~~~~~~
```
[R/bd_loglik.R:112:14:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L112) *style:* **Use <-, not =, for assignment.**
```r
  intPtTint2 = function(t1,T,pars)
             ^
```
[R/bd_loglik.R:112:28:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L112) *style:* **Commas should always have a space after.**
```r
  intPtTint2 = function(t1,T,pars)
                           ^
```
[R/bd_loglik.R:112:30:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L112) *style:* **Commas should always have a space after.**
```r
  intPtTint2 = function(t1,T,pars)
                             ^
```
[R/bd_loglik.R:113:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L113) *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:114:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:114:5:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Variable or function name should be snake_case.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
    ^~~~~~~~~~
```
[R/bd_loglik.R:114:16:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Use <-, not =, for assignment.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
               ^
```
[R/bd_loglik.R:114:25:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Put spaces around all infix operators.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                       ~^~
```
[R/bd_loglik.R:114:32:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Commas should always have a space after.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                               ^
```
[R/bd_loglik.R:114:41:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                                        ^
```
[R/bd_loglik.R:114:50:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Put spaces around all infix operators.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                                                ~^~
```
[R/bd_loglik.R:114:68:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Commas should always have a space after.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                                                                   ^
```
[R/bd_loglik.R:114:81:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Commas should always have a space after.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                                                                                ^
```
[R/bd_loglik.R:114:87:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Put spaces around all infix operators.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                                                                                ~^~
```
[R/bd_loglik.R:114:88:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                                                                                ^
```
[R/bd_loglik.R:114:107:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    intPtTint2 = pars[2]/ff(t1,pars) * ( (T - t1)/pars[3] + (ff(t1,pars) - ff(T,pars))/(pars[1] - pars[2]) )
                                                                                ^
```
[R/bd_loglik.R:117:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L117) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/bd_loglik.R:118:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L118) *style:* **Use <-, not =, for assignment.**
```r
  tdmodel = pars2[1]
          ^
```
[R/bd_loglik.R:119:5:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L119) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(min(pars1) < 0 | (tdmodel == 4 & pars1[1] <= pars1[2]))
    ^
```
[R/bd_loglik.R:120:3:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.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_loglik.R:122:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L122) *style:* **Use <-, not =, for assignment.**
```r
     loglik = -Inf
            ^
```
[R/bd_loglik.R:125:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L125) *style:* **Use <-, not =, for assignment.**
```r
    cond = pars2[2]
         ^
```
[R/bd_loglik.R:126:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L126) *style:* **Use <-, not =, for assignment.**
```r
    soc = pars2[5]
        ^
```
[R/bd_loglik.R:127:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L127) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(cond == 3)
      ^
```
[R/bd_loglik.R:128:5:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L128) *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:129:12:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L129) *style:* **Use <-, not =, for assignment.**
```r
       soc = 2
           ^
```
[R/bd_loglik.R:131:12:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L131) *style:* **Use <-, not =, for assignment.**
```r
    btorph = pars2[3]
           ^
```
[R/bd_loglik.R:132:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L132) *style:* **Use <-, not =, for assignment.**
```r
    verbose = pars2[4]
            ^
```
[R/bd_loglik.R:133:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L133) *style:* **Use <-, not =, for assignment.**
```r
    m = missnumspec
      ^
```
[R/bd_loglik.R:134:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L134) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.na(pars2[6]))
      ^
```
[R/bd_loglik.R:135:5:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L135) *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:136:17:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L136) *style:* **Use <-, not =, for assignment.**
```r
       pars2[6] = Inf
                ^
```
[R/bd_loglik.R:137:6:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L137) *style:* **Trailing whitespace is superfluous.**
```r
    }
     ^~
```
[R/bd_loglik.R:138:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L138) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/bd_loglik.R:139:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L139) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(soc == 1 & tdmodel == 2)
      ^
```
[R/bd_loglik.R:140:5:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L140) *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:141:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L141) *style:* **Lines should not be more than 80 characters.**
```r
      cat("Stem age and conditioning on extant taxa only have not yet been implemented for this model. Use dd_loglik instead\n")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/bd_loglik.R:142:14:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L142) *style:* **Use <-, not =, for assignment.**
```r
      loglik = -Inf
             ^
```
[R/bd_loglik.R:144:12:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L144) *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:144:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L144) *style:* **Trailing whitespace is superfluous.**
```r
    } else {
            ^~~~~~~~
```
[R/bd_loglik.R:145:12:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L145) *style:* **Use <-, not =, for assignment.**
```r
      brts = sort(abs(as.numeric(brts)),decreasing = TRUE)
           ^
```
[R/bd_loglik.R:145:41:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L145) *style:* **Commas should always have a space after.**
```r
      brts = sort(abs(as.numeric(brts)),decreasing = TRUE)
                                        ^
```
[R/bd_loglik.R:146:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L146) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(brts[length(brts)] == 0)
        ^
```
[R/bd_loglik.R:147:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L147) *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:148:15:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L148) *style:* **Use <-, not =, for assignment.**
```r
         brts = brts[-length(brts)]
              ^
```
[R/bd_loglik.R:150:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L150) *style:* **Use <-, not =, for assignment.**
```r
      brts2 = c(-sort(abs(as.numeric(brts)),decreasing = TRUE),0)
            ^
```
[R/bd_loglik.R:150:45:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L150) *style:* **Commas should always have a space after.**
```r
      brts2 = c(-sort(abs(as.numeric(brts)),decreasing = TRUE),0)
                                            ^
```
[R/bd_loglik.R:150:64:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L150) *style:* **Commas should always have a space after.**
```r
      brts2 = c(-sort(abs(as.numeric(brts)),decreasing = TRUE),0)
                                                               ^
```
[R/bd_loglik.R:151:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L151) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(i in 2:length(brts2))
         ^
```
[R/bd_loglik.R:152:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L152) *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:153:12:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L153) *style:* **Place a space before left parenthesis, except in a function call.**
```r
         if(brts2[i] == brts2[i - 1])
           ^
```
[R/bd_loglik.R:154:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L154) *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:155:22:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L155) *style:* **Use <-, not =, for assignment.**
```r
            brts2[i] = brts2[i] + 1E-10
                     ^
```
[R/bd_loglik.R:158:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L158) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(soc == 2)
        ^
```
[R/bd_loglik.R:159:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L159) *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:160:14:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L160) *style:* **Use <-, not =, for assignment.**
```r
        brts = c(brts[1],brts)
             ^
```
[R/bd_loglik.R:160:26:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L160) *style:* **Commas should always have a space after.**
```r
        brts = c(brts[1],brts)
                         ^
```
[R/bd_loglik.R:162:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L162) *style:* **Variable or function name should be snake_case.**
```r
      TT = brts[1]
      ^~
```
[R/bd_loglik.R:162:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L162) *style:* **Use <-, not =, for assignment.**
```r
      TT = brts[1]
         ^
```
[R/bd_loglik.R:163:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L163) *style:* **Use <-, not =, for assignment.**
```r
      t = TT - brts
        ^
```
[R/bd_loglik.R:164:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L164) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:165:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L165) *style:* **Variable or function name should be snake_case.**
```r
      S = length(brts)
      ^
```
[R/bd_loglik.R:165:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L165) *style:* **Use <-, not =, for assignment.**
```r
      S = length(brts)
        ^
```
[R/bd_loglik.R:166:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L166) *style:* **Variable or function name should be snake_case.**
```r
      N = S + m
      ^
```
[R/bd_loglik.R:166:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L166) *style:* **Use <-, not =, for assignment.**
```r
      N = S + m
        ^
```
[R/bd_loglik.R:167:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L167) *style:* **Use <-, not =, for assignment.**
```r
      np = length(brts2)
         ^
```
[R/bd_loglik.R:168:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L168) *style:* **Variable or function name should be snake_case.**
```r
      PtT = rep(0,S)
      ^~~
```
[R/bd_loglik.R:168:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L168) *style:* **Use <-, not =, for assignment.**
```r
      PtT = rep(0,S)
          ^
```
[R/bd_loglik.R:168:19:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L168) *style:* **Commas should always have a space after.**
```r
      PtT = rep(0,S)
                  ^
```
[R/bd_loglik.R:169:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L169) *style:* **Use <-, not =, for assignment.**
```r
      ux = rep(0,S)
         ^
```
[R/bd_loglik.R:169:18:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L169) *style:* **Commas should always have a space after.**
```r
      ux = rep(0,S)
                 ^
```
[R/bd_loglik.R:170:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L170) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:171:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L171) *warning:* **local variable ‘abstol’ assigned but may not be used**
```r
      abstol = 1e-16
      ^~~~~~
```
[R/bd_loglik.R:171:14:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L171) *style:* **Use <-, not =, for assignment.**
```r
      abstol = 1e-16
             ^
```
[R/bd_loglik.R:172:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L172) *warning:* **local variable ‘reltol’ assigned but may not be used**
```r
      reltol = 1e-10
      ^~~~~~
```
[R/bd_loglik.R:172:14:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L172) *style:* **Use <-, not =, for assignment.**
```r
      reltol = 1e-10
             ^
```
[R/bd_loglik.R:172:21:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L172) *style:* **Trailing whitespace is superfluous.**
```r
      reltol = 1e-10
                    ^
```
[R/bd_loglik.R:173:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L173) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:174:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L174) *style:* **Variable or function name should be snake_case.**
```r
      T0 = TT
      ^~
```
[R/bd_loglik.R:174:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L174) *style:* **Use <-, not =, for assignment.**
```r
      T0 = TT
         ^
```
[R/bd_loglik.R:175:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L175) *style:* **Use <-, not =, for assignment.**
```r
      la0 = pars1[1]
          ^
```
[R/bd_loglik.R:176:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L176) *style:* **Use <-, not =, for assignment.**
```r
      mu0 = pars1[2]
          ^
```
[R/bd_loglik.R:177:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L177) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(length(pars1) > 2)
        ^
```
[R/bd_loglik.R:178:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L178) *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:179:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L179) *style:* **Use <-, not =, for assignment.**
```r
        la1 = pars1[3]
            ^
```
[R/bd_loglik.R:180:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L180) *style:* **Variable or function name should be snake_case.**
```r
        K = pars1[3]
        ^
```
[R/bd_loglik.R:180:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L180) *style:* **Use <-, not =, for assignment.**
```r
        K = pars1[3]
          ^
```
[R/bd_loglik.R:181:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L181) *style:* **Use <-, not =, for assignment.**
```r
        mu1 = pars1[4]
            ^
```
[R/bd_loglik.R:182:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L182) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(length(pars1) == 5)
          ^
```
[R/bd_loglik.R:183:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L183) *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:184:12:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L184) *style:* **Variable or function name should be snake_case.**
```r
           T0 = pars1[5]
           ^~
```
[R/bd_loglik.R:184:15:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L184) *style:* **Use <-, not =, for assignment.**
```r
           T0 = pars1[5]
              ^
```
[R/bd_loglik.R:185:10:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L185) *style:* **Trailing whitespace is superfluous.**
```r
        }
         ^
```
[R/bd_loglik.R:187:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L187) *style:* **Use <-, not =, for assignment.**
```r
        la1 = 0
            ^
```
[R/bd_loglik.R:188:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L188) *style:* **Variable or function name should be snake_case.**
```r
        K = Inf
        ^
```
[R/bd_loglik.R:188:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L188) *style:* **Use <-, not =, for assignment.**
```r
        K = Inf
          ^
```
[R/bd_loglik.R:189:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L189) *style:* **Use <-, not =, for assignment.**
```r
        mu1 = 0
            ^
```
[R/bd_loglik.R:190:15:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L190) *style:* **Use <-, not =, for assignment.**
```r
        pars1 = c(pars1,c(0,0))
              ^
```
[R/bd_loglik.R:190:25:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L190) *style:* **Commas should always have a space after.**
```r
        pars1 = c(pars1,c(0,0))
                        ^
```
[R/bd_loglik.R:190:29:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L190) *style:* **Commas should always have a space after.**
```r
        pars1 = c(pars1,c(0,0))
                            ^
```
[R/bd_loglik.R:192:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L192) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:193:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L193) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(tdmodel == 1)
        ^
```
[R/bd_loglik.R:194:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L194) *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:195:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L195) *style:* **Use <-, not =, for assignment.**
```r
        la0 = la0 * exp(-la1 * (T0 - TT))
            ^
```
[R/bd_loglik.R:196:13:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L196) *style:* **Use <-, not =, for assignment.**
```r
        mu0 = mu0 * exp(-mu1 * (T0 - TT))
            ^
```
[R/bd_loglik.R:197:8:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L197) *style:* **Trailing whitespace is superfluous.**
```r
      }
       ^
```
[R/bd_loglik.R:198:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L198) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:199:14:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L199) *style:* **Use <-, not =, for assignment.**
```r
      loglik = (btorph == 0) * lgamma(S)
             ^
```
[R/bd_loglik.R:200:1:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L200) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[R/bd_loglik.R:201:9:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L201) *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:202:7:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L202) *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:203:11:](https://github.com/rsetienne/DDD/blob/b3d1d7584ba26fcf2e56e22fca909c980afcf257/R/bd_loglik.R#L203) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if(abs(la0 - mu0) < 1E-10)