[R/ABC_SMC.R:2:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L2) *style:* **Use two spaces to indent, never tabs.**
```r
	sum <- 0;
^
```
[R/ABC_SMC.R:3:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L3) *style:* **Use two spaces to indent, never tabs.**
```r
	vals <- c();
^
```
[R/ABC_SMC.R:4:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L4) *style:* **Use two spaces to indent, never tabs.**
```r
	for(i in 1:length(P))
^
```
[R/ABC_SMC.R:7:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L7) *style:* **Use two spaces to indent, never tabs.**
```r
	    diff2 <- log(current[2]) - log(P[[i]][2]);
^
```
[R/ABC_SMC.R:24:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **lines should not be more than 80 characters.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:24:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Variable and function names should be all lowercase.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
^~~~~~~~~~~~
```
[R/ABC_SMC.R:24:31:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                              ^
```
[R/ABC_SMC.R:24:42:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                         ^
```
[R/ABC_SMC.R:24:42:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Variable and function names should be all lowercase.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                         ^~~~~~~
```
[R/ABC_SMC.R:24:50:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                 ^
```
[R/ABC_SMC.R:24:50:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Variable and function names should be all lowercase.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                 ^~~~~~~~~~~
```
[R/ABC_SMC.R:24:62:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                             ^
```
[R/ABC_SMC.R:24:72:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                                       ^
```
[R/ABC_SMC.R:24:83:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                                                ^
```
[R/ABC_SMC.R:24:83:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Variable and function names should be all lowercase.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                                                ^~~~~~~~~~~~
```
[R/ABC_SMC.R:24:96:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                                                ^
```
[R/ABC_SMC.R:24:107:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Commas should always have a space after.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                                                ^
```
[R/ABC_SMC.R:24:107:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L24) *style:* **Variable and function names should be all lowercase.**
```r
ABC_SMC_nLTT <- function(tree,statistics,simFunc,initEpsilon,PRIOR_GEN,PRIOR_DENS,numParticles,sigma=0.05,stopRate=1e-5) {
                                                                                ^~~~~~~~
```
[R/ABC_SMC.R:32:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L32) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[R/ABC_SMC.R:32:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L32) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:34:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L34) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:35:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L35) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:36:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L36) *style:* **lines should not be more than 80 characters.**
```r
  #generate a matrix with epsilon values, we assume that the SMC algorithm converges within 50 iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:37:25:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L37) *style:* **Put spaces around all infix operators.**
```r
  epsilon <- matrix(nrow=50,ncol=length(initEpsilon));
                       ~^~
```
[R/ABC_SMC.R:37:29:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L37) *style:* **Commas should always have a space after.**
```r
  epsilon <- matrix(nrow=50,ncol=length(initEpsilon));
                            ^
```
[R/ABC_SMC.R:37:33:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L37) *style:* **Put spaces around all infix operators.**
```r
  epsilon <- matrix(nrow=50,ncol=length(initEpsilon));
                               ~^~
```
[R/ABC_SMC.R:37:41:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L37) *style:* **Variable and function names should be all lowercase.**
```r
  epsilon <- matrix(nrow=50,ncol=length(initEpsilon));
                                        ^~~~~~~~~~~
```
[R/ABC_SMC.R:38:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L38) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(j in 1:length(initEpsilon)) {
     ^
```
[R/ABC_SMC.R:38:21:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
  for(j in 1:length(initEpsilon)) {
                    ^~~~~~~~~~~
```
[R/ABC_SMC.R:39:7:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L39) *style:* **Place a space before left parenthesis, except in a function call.**
```r
   for(i in 1:50) {
      ^
```
[R/ABC_SMC.R:40:15:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L40) *style:* **Commas should always have a space after.**
```r
    epsilon[i,j] <- initEpsilon[j] * exp(-0.5 * (i-1));
              ^
```
[R/ABC_SMC.R:40:21:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L40) *style:* **Variable and function names should be all lowercase.**
```r
    epsilon[i,j] <- initEpsilon[j] * exp(-0.5 * (i-1));
                    ^~~~~~~~~~~
```
[R/ABC_SMC.R:40:51:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L40) *style:* **Put spaces around all infix operators.**
```r
    epsilon[i,j] <- initEpsilon[j] * exp(-0.5 * (i-1));
                                                 ~^~
```
[R/ABC_SMC.R:43:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:45:3:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L45) *style:* **Variable and function names should be all lowercase.**
```r
  newWeights <- c();
  ^~~~~~~~~~
```
[R/ABC_SMC.R:46:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L46) *style:* **Use two spaces to indent, never tabs.**
```r
	   if(i == 1) { #in this initial step, generate parameters from the prior
^
```
[R/ABC_SMC.R:46:3:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L46) *style:* **Variable and function names should be all lowercase.**
```r
  newParams <- list(c(1:length(parameters)));
  ^~~~~~~~~
```
[R/ABC_SMC.R:47:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L47) *style:* **Use two spaces to indent, never tabs.**
```r
		  parameters <- PRIOR_GEN();
^~
```
[R/ABC_SMC.R:47:3:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L47) *style:* **Variable and function names should be all lowercase.**
```r
  previousWeights <- c();
  ^~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:48:3:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L48) *style:* **Variable and function names should be all lowercase.**
```r
  previousParams  <- list(c(1:length(parameters)));
  ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:49:16:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L49) *style:* **Variable and function names should be all lowercase.**
```r
  indices <- 1:numParticles;
               ^~~~~~~~~~~~
```
[R/ABC_SMC.R:51:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L51) *style:* **Use two spaces to indent, never tabs.**
```r
		for(p_index in 1:length(parameters)) {
^~
```
[R/ABC_SMC.R:51:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L51) *style:* **lines should not be more than 80 characters.**
```r
  for( i in 1:50 ) { #convergence is expected within 50 iterations, usually convergence occurs within 10 iterations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:51:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L51) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for( i in 1:50 ) { #convergence is expected within 50 iterations, usually convergence occurs within 10 iterations
     ^
```
[R/ABC_SMC.R:51:20:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L51) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  for( i in 1:50 ) { #convergence is expected within 50 iterations, usually convergence occurs within 10 iterations
                   ^
```
[R/ABC_SMC.R:51:41:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L51) *style:* **Use two spaces to indent, never tabs.**
```r
		for(p_index in 1:length(parameters)) {
                                        ^
```
[R/ABC_SMC.R:52:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L52) *style:* **Use two spaces to indent, never tabs.**
```r
			parameters[p_index] <- previousParams[[index]][p_index];
^~~
```
[R/ABC_SMC.R:52:50:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L52) *style:* **Commas should always have a space after.**
```r
    cat("\nGenerating Particles for iteration\t",i,"\n")
                                                 ^
```
[R/ABC_SMC.R:52:52:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L52) *style:* **Commas should always have a space after.**
```r
    cat("\nGenerating Particles for iteration\t",i,"\n")
                                                   ^
```
[R/ABC_SMC.R:53:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L53) *style:* **Use two spaces to indent, never tabs.**
```r
		}
^~
```
[R/ABC_SMC.R:54:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L54) *style:* **Use two spaces to indent, never tabs.**
```r
	if ((i)%%((iterations-burnin)/PRINT_FREQ) == 0) {
^
```
[R/ABC_SMC.R:55:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L55) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[R/ABC_SMC.R:58:5:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
    numberAccepted <- 0;
    ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:61:7:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(i > 1) { #replace all vectors
      ^
```
[R/ABC_SMC.R:61:15:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L61) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(i > 1) { #replace all vectors
              ^
```
[R/ABC_SMC.R:62:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L62) *style:* **lines should not be more than 80 characters.**
```r
     previousWeights <- newWeights / sum(newWeights); #normalize the weights and store them as previous weights.\
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:62:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
     previousWeights <- newWeights / sum(newWeights); #normalize the weights and store them as previous weights.\
     ^~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:62:25:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
     previousWeights <- newWeights / sum(newWeights); #normalize the weights and store them as previous weights.\
                        ^~~~~~~~~~
```
[R/ABC_SMC.R:62:42:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
     previousWeights <- newWeights / sum(newWeights); #normalize the weights and store them as previous weights.\
                                         ^~~~~~~~~~
```
[R/ABC_SMC.R:63:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L63) *style:* **Variable and function names should be all lowercase.**
```r
     newWeights <- c(); #remove all currently stored weights
     ^~~~~~~~~~
```
[R/ABC_SMC.R:64:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
     previousParams <- newParams; #store found params
     ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:64:24:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
     previousParams <- newParams; #store found params
                       ^~~~~~~~~
```
[R/ABC_SMC.R:65:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L65) *style:* **Use two spaces to indent, never tabs.**
```r

^~
```
[R/ABC_SMC.R:65:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L65) *style:* **Variable and function names should be all lowercase.**
```r
     newParams <- list(c(1:length(parameters))); #clear new params
     ^~~~~~~~~
```
[R/ABC_SMC.R:67:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L67) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~
```
[R/ABC_SMC.R:68:10:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    while(numberAccepted < numParticles) {
         ^
```
[R/ABC_SMC.R:68:11:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
    while(numberAccepted < numParticles) {
          ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:68:28:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
    while(numberAccepted < numParticles) {
                           ^~~~~~~~~~~~
```
[R/ABC_SMC.R:69:14:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	   if(i == 1) { #in this initial step, generate parameters from the prior
             ^
```
[R/ABC_SMC.R:69:17:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L69) *style:* **Put spaces around all infix operators.**
```r
	   if(i == 1) { #in this initial step, generate parameters from the prior
               ~^~~
```
[R/ABC_SMC.R:69:23:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L69) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
	   if(i == 1) { #in this initial step, generate parameters from the prior
                      ^
```
[R/ABC_SMC.R:70:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L70) *style:* **Use two spaces to indent, never tabs.**
```r

^~
```
[R/ABC_SMC.R:70:30:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L70) *style:* **Put spaces around all infix operators.**
```r
		  parameters <- PRIOR_GEN();
                            ~^~~
```
[R/ABC_SMC.R:71:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L71) *style:* **lines should not be more than 80 characters.**
```r
      } else { #if not in the initial step, generate parameters from the weighted previous distribution:
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:71:14:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L71) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      } else { #if not in the initial step, generate parameters from the weighted previous distribution:
             ^
```
[R/ABC_SMC.R:72:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L72) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/ABC_SMC.R:73:26:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Put spaces around all infix operators.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                        ~^~
```
[R/ABC_SMC.R:73:35:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Commas should always have a space after.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                                  ^
```
[R/ABC_SMC.R:73:39:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Put spaces around all infix operators.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                                     ~^~
```
[R/ABC_SMC.R:73:42:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Commas should always have a space after.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                                         ^
```
[R/ABC_SMC.R:73:49:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Put spaces around all infix operators.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                                               ~^~
```
[R/ABC_SMC.R:73:55:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Commas should always have a space after.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                                                      ^
```
[R/ABC_SMC.R:73:59:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Put spaces around all infix operators.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                                                         ~^~
```
[R/ABC_SMC.R:73:60:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L73) *style:* **Variable and function names should be all lowercase.**
```r
        index <- sample(x=indices,size=1,replace=TRUE,prob=previousWeights);
                                                           ^~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:74:41:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L74) *style:* **Trailing whitespace is superfluous.**
```r
		for(p_index in 1:length(parameters)) {
                                        ^
```
[R/ABC_SMC.R:75:45:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L75) *style:* **Put spaces around all infix operators.**
```r
			parameters[p_index] <- previousParams[[index]][p_index];
                                           ~^~~
```
[R/ABC_SMC.R:75:48:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L75) *style:* **Variable and function names should be all lowercase.**
```r
			parameters[p_index] <- previousParams[[index]][p_index];
                                               ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:78:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L78) *style:* **lines should not be more than 80 characters.**
```r
        toChange <- sample(1:length(parameters),1);  #only perturb one parameter, to avoid extremely low acceptance rates due to simultaneous perturbation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:78:9:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L78) *style:* **Variable and function names should be all lowercase.**
```r
        toChange <- sample(1:length(parameters),1);  #only perturb one parameter, to avoid extremely low acceptance rates due to simultaneous perturbation
        ^~~~~~~~
```
[R/ABC_SMC.R:78:49:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L78) *style:* **Commas should always have a space after.**
```r
        toChange <- sample(1:length(parameters),1);  #only perturb one parameter, to avoid extremely low acceptance rates due to simultaneous perturbation
                                                ^
```
[R/ABC_SMC.R:79:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L79) *style:* **lines should not be more than 80 characters.**
```r
        eta <- log(parameters[toChange]) + rnorm(1,0,sigma); # perturb the parameter a little bit, on log scale, so parameter doesn't go < 0.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:79:31:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L79) *style:* **Variable and function names should be all lowercase.**
```r
        eta <- log(parameters[toChange]) + rnorm(1,0,sigma); # perturb the parameter a little bit, on log scale, so parameter doesn't go < 0.
                              ^~~~~~~~
```
[R/ABC_SMC.R:79:52:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L79) *style:* **Commas should always have a space after.**
```r
        eta <- log(parameters[toChange]) + rnorm(1,0,sigma); # perturb the parameter a little bit, on log scale, so parameter doesn't go < 0.
                                                   ^
```
[R/ABC_SMC.R:79:54:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L79) *style:* **Commas should always have a space after.**
```r
        eta <- log(parameters[toChange]) + rnorm(1,0,sigma); # perturb the parameter a little bit, on log scale, so parameter doesn't go < 0.
                                                     ^
```
[R/ABC_SMC.R:80:20:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L80) *style:* **Variable and function names should be all lowercase.**
```r
        parameters[toChange] <- exp(eta)
                   ^~~~~~~~
```
[R/ABC_SMC.R:80:41:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L80) *style:* **Trailing whitespace is superfluous.**
```r
        parameters[toChange] <- exp(eta)
                                        ^
```
[R/ABC_SMC.R:81:7:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L81) *style:* **Trailing whitespace is superfluous.**
```r
     }
      ^~
```
[R/ABC_SMC.R:82:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L82) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:83:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L83) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~
```
[R/ABC_SMC.R:84:8:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L84) *style:* **Place a space before left parenthesis, except in a function call.**
```r
     if(PRIOR_DENS(parameters) > 0) #reject if outside the prior
       ^
```
[R/ABC_SMC.R:84:65:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L84) *style:* **Trailing whitespace is superfluous.**
```r
     if(PRIOR_DENS(parameters) > 0) #reject if outside the prior
                                                                ^
```
[R/ABC_SMC.R:85:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L85) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
     {
     ^
```
[R/ABC_SMC.R:86:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L86) *style:* **lines should not be more than 80 characters.**
```r
        new_tree <- simFunc(parameters); #simulate a new tree, given the proposed parameters
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:86:21:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L86) *style:* **Variable and function names should be all lowercase.**
```r
        new_tree <- simFunc(parameters); #simulate a new tree, given the proposed parameters
                    ^~~~~~~
```
[R/ABC_SMC.R:88:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L88) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~
```
[R/ABC_SMC.R:89:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L89) *style:* **Use two spaces to indent, never tabs.**
```r
		}
^~
```
[R/ABC_SMC.R:89:12:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L89) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        for(k in 1:length(statistics)) {
           ^
```
[R/ABC_SMC.R:90:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L90) *style:* **Use two spaces to indent, never tabs.**
```r
	 }
^
```
[R/ABC_SMC.R:91:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L91) *style:* **Use two spaces to indent, never tabs.**
```r

^
```
[R/ABC_SMC.R:91:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L91) *style:* **lines should not be more than 80 characters.**
```r
          if(is.na(stats[k])) stats[k] <- Inf;     #calculate the summary statistics for the simulated tree
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:91:13:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L91) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if(is.na(stats[k])) stats[k] <- Inf;     #calculate the summary statistics for the simulated tree
            ^
```
[R/ABC_SMC.R:93:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L93) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/ABC_SMC.R:94:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L94) *style:* **lines should not be more than 80 characters.**
```r
        for (k in 1:length(statistics)) {    #check if the summary statistics are sufficiently close to the observed summary statistics
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:94:41:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L94) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        for (k in 1:length(statistics)) {    #check if the summary statistics are sufficiently close to the observed summary statistics
                                        ^
```
[R/ABC_SMC.R:95:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L95) *style:* **Use two spaces to indent, never tabs.**
```r
			output <- c();
^~~
```
[R/ABC_SMC.R:95:28:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L95) *style:* **Put spaces around all infix operators.**
```r
          if ( abs(stats[k]-obs_statistics[k]) > epsilon[i,k] ) {
                          ~^~
```
[R/ABC_SMC.R:95:60:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L95) *style:* **Commas should always have a space after.**
```r
          if ( abs(stats[k]-obs_statistics[k]) > epsilon[i,k] ) {
                                                           ^
```
[R/ABC_SMC.R:96:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L96) *style:* **Use two spaces to indent, never tabs.**
```r
			for(k in 1:length(parameters)) {
^~~
```
[R/ABC_SMC.R:97:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L97) *style:* **Use two spaces to indent, never tabs.**
```r
			  add <- c();
^~~
```
[R/ABC_SMC.R:97:15:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L97) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            if(i == 1) accept <- TRUE  #the first step always accepts
              ^
```
[R/ABC_SMC.R:98:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L98) *style:* **Use two spaces to indent, never tabs.**
```r
			  for(m in 1:length(previousParams[[k]])) {
^~~
```
[R/ABC_SMC.R:99:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L99) *style:* **Use two spaces to indent, never tabs.**
```r
					add <- c(add,previousParams[[k]][m]);
^~~~~
```
[R/ABC_SMC.R:100:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L100) *style:* **Use two spaces to indent, never tabs.**
```r
			  }
^~~
```
[R/ABC_SMC.R:101:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L101) *style:* **Use two spaces to indent, never tabs.**
```r
			  output <- rbind(output,add);
^~~
```
[R/ABC_SMC.R:102:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L102) *style:* **Use two spaces to indent, never tabs.**
```r
			}
^~~
```
[R/ABC_SMC.R:103:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L103) *style:* **Use two spaces to indent, never tabs.**
```r
			return( output);
^~~
```
[R/ABC_SMC.R:103:11:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L103) *style:* **Variable and function names should be all lowercase.**
```r
          numberAccepted <- numberAccepted + 1
          ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:103:20:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L103) *style:* **Use two spaces to indent, never tabs.**
```r
			return( output);
                   ^
```
[R/ABC_SMC.R:103:29:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L103) *style:* **Variable and function names should be all lowercase.**
```r
          numberAccepted <- numberAccepted + 1
                            ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:104:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L104) *style:* **Use two spaces to indent, never tabs.**
```r

^~~
```
[R/ABC_SMC.R:104:11:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L104) *style:* **Variable and function names should be all lowercase.**
```r
          newParams[[numberAccepted]] <- parameters;
          ^~~~~~~~~
```
[R/ABC_SMC.R:104:22:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L104) *style:* **Variable and function names should be all lowercase.**
```r
          newParams[[numberAccepted]] <- parameters;
                     ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:105:27:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L105) *style:* **Use <-, not =, for assignment.**
```r
          weight_accepted = 1;
                          ^
```
[R/ABC_SMC.R:106:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **lines should not be more than 80 characters.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:106:13:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
            ^
```
[R/ABC_SMC.R:106:38:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Use <-, not =, for assignment.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                     ^
```
[R/ABC_SMC.R:106:40:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Variable and function names should be all lowercase.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                       ^~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:106:40:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *warning:* **no visible global function definition for ‘calculateWeight’**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                       ^~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:106:56:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Variable and function names should be all lowercase.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                                       ^~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:106:72:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Commas should always have a space after.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                                                       ^
```
[R/ABC_SMC.R:106:72:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Variable and function names should be all lowercase.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                                                       ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:106:87:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Commas should always have a space after.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                                                                ^
```
[R/ABC_SMC.R:106:98:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Commas should always have a space after.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                                                                ^
```
[R/ABC_SMC.R:106:104:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L106) *style:* **Commas should always have a space after.**
```r
          if( i > 1) weight_accepted = calculateWeight(previousWeights,previousParams,parameters,sigma,PRIOR_DENS); #calculate the weight
                                                                                ^
```
[R/ABC_SMC.R:107:11:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L107) *style:* **Variable and function names should be all lowercase.**
```r
          newWeights[numberAccepted] = weight_accepted;
          ^~~~~~~~~~
```
[R/ABC_SMC.R:107:22:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L107) *style:* **Variable and function names should be all lowercase.**
```r
          newWeights[numberAccepted] = weight_accepted;
                     ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:107:38:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L107) *style:* **Use <-, not =, for assignment.**
```r
          newWeights[numberAccepted] = weight_accepted;
                                     ^
```
[R/ABC_SMC.R:108:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L108) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~
```
[R/ABC_SMC.R:109:15:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L109) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if ((numberAccepted)%%(numParticles/PRINT_FREQ) == 0) {
              ^
```
[R/ABC_SMC.R:109:16:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
          if ((numberAccepted)%%(numParticles/PRINT_FREQ) == 0) {
               ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:109:31:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L109) *style:* **Put spaces around all infix operators.**
```r
          if ((numberAccepted)%%(numParticles/PRINT_FREQ) == 0) {
                             ~^~~
```
[R/ABC_SMC.R:109:33:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L109) *style:* **Place a space before left parenthesis, except in a function call.**
```r
          if ((numberAccepted)%%(numParticles/PRINT_FREQ) == 0) {
                                ^
```
[R/ABC_SMC.R:109:34:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
          if ((numberAccepted)%%(numParticles/PRINT_FREQ) == 0) {
                                 ^~~~~~~~~~~~
```
[R/ABC_SMC.R:109:46:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L109) *style:* **Put spaces around all infix operators.**
```r
          if ((numberAccepted)%%(numParticles/PRINT_FREQ) == 0) {
                                            ~^~
```
[R/ABC_SMC.R:110:52:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L110) *style:* **Trailing whitespace is superfluous.**
```r
                        cat("**"); flush.console();
                                                   ^
```
[R/ABC_SMC.R:114:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L114) *style:* **Use two spaces to indent, never tabs.**
```r
	for(m in 1:length(previousParams[[k]])) {
^
```
[R/ABC_SMC.R:114:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L114) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~
```
[R/ABC_SMC.R:115:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L115) *style:* **Use two spaces to indent, never tabs.**
```r
		add <- c(add,previousParams[[k]][m]);
^~
```
[R/ABC_SMC.R:116:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L116) *style:* **Use two spaces to indent, never tabs.**
```r
	}
^
```
[R/ABC_SMC.R:116:9:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L116) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(tried > (1/stopRate)) {
        ^
```
[R/ABC_SMC.R:116:20:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L116) *style:* **Put spaces around all infix operators.**
```r
      if(tried > (1/stopRate)) {
                  ~^~
```
[R/ABC_SMC.R:116:21:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L116) *style:* **Variable and function names should be all lowercase.**
```r
      if(tried > (1/stopRate)) {
                    ^~~~~~~~
```
[R/ABC_SMC.R:116:32:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L116) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      if(tried > (1/stopRate)) {
                               ^
```
[R/ABC_SMC.R:116:33:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L116) *style:* **Trailing whitespace is superfluous.**
```r
      if(tried > (1/stopRate)) {
                                ^
```
[R/ABC_SMC.R:117:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L117) *style:* **Use two spaces to indent, never tabs.**
```r
	output <- rbind(output,add);
^
```
[R/ABC_SMC.R:117:11:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L117) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if((numberAccepted / tried) < stopRate) {
          ^
```
[R/ABC_SMC.R:117:12:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L117) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        if((numberAccepted / tried) < stopRate) {
           ^
```
[R/ABC_SMC.R:117:13:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L117) *style:* **Variable and function names should be all lowercase.**
```r
        if((numberAccepted / tried) < stopRate) {
            ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:117:39:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L117) *style:* **Variable and function names should be all lowercase.**
```r
        if((numberAccepted / tried) < stopRate) {
                                      ^~~~~~~~
```
[R/ABC_SMC.R:119:19:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L119) *style:* **Use two spaces to indent, never tabs.**
```r
  return( output);
                  ^
```
[R/ABC_SMC.R:119:28:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L119) *style:* **Place a space before left parenthesis, except in a function call.**
```r
			for(k in 1:length(parameters)) {
                           ^
```
[R/ABC_SMC.R:121:30:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L121) *style:* **Place a space before left parenthesis, except in a function call.**
```r
			  for(m in 1:length(previousParams[[k]])) {
                             ^
```
[R/ABC_SMC.R:121:45:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
			  for(m in 1:length(previousParams[[k]])) {
                                            ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:122:54:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
					add <- c(add,previousParams[[k]][m]);
                                                     ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:124:34:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L124) *style:* **Put spaces around all infix operators.**
```r
			  output <- rbind(output,add);
                                ~^~~
```
[R/ABC_SMC.R:126:20:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L126) *style:* **Trailing whitespace is superfluous.**
```r
			return( output);
                   ^
```
[R/ABC_SMC.R:127:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L127) *style:* **Trailing whitespace is superfluous.**
```r

^~~
```
[R/ABC_SMC.R:132:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L132) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:133:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L133) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/ABC_SMC.R:135:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L135) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(k in 1:length(parameters)) {
     ^
```
[R/ABC_SMC.R:137:12:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L137) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	for(m in 1:length(previousParams[[k]])) {
           ^
```
[R/ABC_SMC.R:137:27:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L137) *style:* **Variable and function names should be all lowercase.**
```r
	for(m in 1:length(previousParams[[k]])) {
                          ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:138:21:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L138) *style:* **Put spaces around all infix operators.**
```r
		add <- c(add,previousParams[[k]][m]);
                   ~^~~
```
[R/ABC_SMC.R:138:30:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L138) *style:* **Variable and function names should be all lowercase.**
```r
		add <- c(add,previousParams[[k]][m]);
                             ^~~~~~~~~~~~~~
```
[R/ABC_SMC.R:140:16:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L140) *style:* **Put spaces around all infix operators.**
```r
	output <- rbind(output,add);
              ~^~~
```
[R/ABC_SMC.R:142:19:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L142) *style:* **Trailing whitespace is superfluous.**
```r
  return( output);
                  ^
```
[R/ABC_SMC.R:165:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L165) *style:* **Variable and function names should be all lowercase.**
```r
calculateWeight <- function(W,P,current,S,PRIOR_DENS) {
^~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:165:31:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L165) *style:* **Commas should always have a space after.**
```r
calculateWeight <- function(W,P,current,S,PRIOR_DENS) {
                              ^
```
[R/ABC_SMC.R:165:33:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L165) *style:* **Commas should always have a space after.**
```r
calculateWeight <- function(W,P,current,S,PRIOR_DENS) {
                                ^
```
[R/ABC_SMC.R:165:41:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L165) *style:* **Commas should always have a space after.**
```r
calculateWeight <- function(W,P,current,S,PRIOR_DENS) {
                                        ^
```
[R/ABC_SMC.R:165:43:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L165) *style:* **Commas should always have a space after.**
```r
calculateWeight <- function(W,P,current,S,PRIOR_DENS) {
                                          ^
```
[R/ABC_SMC.R:167:14:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L167) *style:* **Put spaces around all infix operators.**
```r
	vals <- c();
            ~^~~
```
[R/ABC_SMC.R:168:12:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L168) *style:* **Place a space before left parenthesis, except in a function call.**
```r
	for(i in 1:length(P))
           ^
```
[R/ABC_SMC.R:169:5:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L169) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    {
    ^
```
[R/ABC_SMC.R:169:6:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L169) *style:* **Trailing whitespace is superfluous.**
```r
    {
     ^
```
[R/ABC_SMC.R:171:19:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L171) *style:* **Put spaces around all infix operators.**
```r
	    diff2 <- log(current[2]) - log(P[[i]][2]);
                 ~^~~
```
[R/ABC_SMC.R:171:38:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L171) *style:* **Put spaces around all infix operators.**
```r
	    diff2 <- log(current[2]) - log(P[[i]][2]);
                                    ~^~
```
[R/ABC_SMC.R:172:37:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Commas should always have a space after.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                    ^
```
[R/ABC_SMC.R:172:41:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Put spaces around all infix operators.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                       ~^~
```
[R/ABC_SMC.R:172:44:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Commas should always have a space after.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                           ^
```
[R/ABC_SMC.R:172:46:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Put spaces around all infix operators.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                            ~^~
```
[R/ABC_SMC.R:172:64:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Commas should always have a space after.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                                               ^
```
[R/ABC_SMC.R:172:68:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Put spaces around all infix operators.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                                                  ~^~
```
[R/ABC_SMC.R:172:71:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Commas should always have a space after.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                                                      ^
```
[R/ABC_SMC.R:172:73:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Put spaces around all infix operators.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                                                       ~^~
```
[R/ABC_SMC.R:172:77:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L172) *style:* **Trailing whitespace is superfluous.**
```r
      vals[i] <- W[i] * dnorm(diff1,mean=0,sd=S) * dnorm(diff2,mean=0,sd=S);
                                                                            ^~~
```
[R/ABC_SMC.R:174:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L174) *style:* **Trailing whitespace is superfluous.**
```r

^~~
```
[R/ABC_SMC.R:176:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L176) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/ABC_SMC.R:202:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **lines should not be more than 80 characters.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:202:1:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Variable and function names should be all lowercase.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
^~~~~~~~~
```
[R/ABC_SMC.R:202:27:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Commas should always have a space after.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                          ^
```
[R/ABC_SMC.R:202:27:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Variable and function names should be all lowercase.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                          ^~~~~~~~~~~~~~~~~~
```
[R/ABC_SMC.R:202:46:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Commas should always have a space after.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                             ^
```
[R/ABC_SMC.R:202:57:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Commas should always have a space after.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                                        ^
```
[R/ABC_SMC.R:202:57:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Variable and function names should be all lowercase.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                                        ^~~~~~~~~~~~~
```
[R/ABC_SMC.R:202:71:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Commas should always have a space after.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                                                      ^
```
[R/ABC_SMC.R:202:82:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Commas should always have a space after.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                                                                ^
```
[R/ABC_SMC.R:202:105:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Put spaces around all infix operators.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                                                                ~^~
```
[R/ABC_SMC.R:202:109:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Commas should always have a space after.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                                                                ^
```
[R/ABC_SMC.R:202:120:](https://github.com/richelbilderbeek/nLTT/blob/2c3a4e06335d8b0a4057c0c53f1ea17b472319b8/R/ABC_SMC.R#L202) *style:* **Commas should always have a space after.**
```r
MCMC_nLTT <- function(phy,likelihoodFunction,parameters,logTransforms,iterations,burnin=round(iterations/3),thinning=1,sigma=1) {
                                                                                ^
```


typo here? - texNormalOffsets


你的这个测试是成功的么?


ButtonGroup is much more accessible. If  a Buttongroup is used depends on the number and text length of the options.
Have a look at the new global settings now - it looks much better.


@thijsjanzen : could you satisfy the beloved @lintr-bot ?


not be url snooper?


Good catch. It was an attempt that is not required anymore.


sorry, github cut off my explanation. Here is the rest of what I said...
"(i.e. cursorOverlay02bd00 tells that I used the color 02bd00 to tint the image). Next, I'll be working on background/s and ideas :DD"


Yes, this is still required, without it (using slibtool merged from your main branch as of now) attempting to build databases/db4:

```
clibtool: link: ln -s db_archive db_archive.exe.wrapper
./libtool --mode=execute true db_archive
clibtool: execute: db_archive.exe.wrapper true .libs/db_archive
*** Error code 2
```

With it the build completes successfully.


[R/add_alignments.R:7:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_alignments.R#L7) *warning:* **no visible global function definition for ‘is_valid_file’**
```r
  testit::assert(is_valid_file(filename))
                 ^~~~~~~~~~~~~
```
[R/add_alignments.R:8:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_alignments.R#L8) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/add_pbd_output.R:10:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_pbd_output.R#L10) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/add_posteriors.R:13:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_posteriors.R#L13) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/add_posteriors.R:29:22:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_posteriors.R#L29) *warning:* **no visible global function definition for ‘is_alignment’**
```r
      testit::assert(is_alignment(alignment))
                     ^~~~~~~~~~~~
```
[R/add_posteriors.R:51:22:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_posteriors.R#L51) *style:* **Variable and function names should not be longer than 30 characters.**
```r
        posterior <- convert_alignment_to_beast_posterior(
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_species_trees_with_outgroup.R:7:1:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_species_trees_with_outgroup.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
add_species_trees_with_outgroup <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/add_species_trees_with_outgroup.R:20:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_species_trees_with_outgroup.R#L20) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/add_species_trees_with_outgroup.R:42:21:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/add_species_trees_with_outgroup.R#L42) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    species_tree <- sample_species_trees_from_pbd_sim_output(
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/branch_sorter.R:8:12:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/branch_sorter.R#L8) *warning:* **no visible global function definition for ‘branch_sorter’**
```r
    return(branch_sorter(ape::read.tree(filename)))
           ^~~~~~~~~~~~~
```
[R/branch_sorter.R:10:12:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/branch_sorter.R#L10) *warning:* **no visible global function definition for ‘read_file’**
```r
    return(read_file(filename)$species_tree_with_outgroup[[1]][[1]])
           ^~~~~~~~~
```
[R/collect_file_gammas.R:40:26:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_file_gammas.R#L40) *warning:* **no visible global function definition for ‘collect_species_tree_gammas’**
```r
  species_tree_gammas <- collect_species_tree_gammas(filename)
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/collect_file_gammas.R:41:23:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_file_gammas.R#L41) *warning:* **no visible global function definition for ‘collect_posterior_gammas’**
```r
  posterior_gammas <- collect_posterior_gammas(filename)
                      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/collect_file_nltts.R:44:25:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_file_nltts.R#L44) *warning:* **no visible global function definition for ‘collect_species_tree_nltts’**
```r
  species_tree_nltts <- collect_species_tree_nltts(filename = filename, dt = dt)
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/collect_file_nltts.R:45:22:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_file_nltts.R#L45) *warning:* **no visible global function definition for ‘collect_posterior_nltts’**
```r
  posterior_nltts <- collect_posterior_nltts(filename = filename, dt = dt)
                     ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/collect_parameters.R:32:13:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_parameters.R#L32) *warning:* **no visible global function definition for ‘read_file’**
```r
    file <- read_file(filename)
            ^~~~~~~~~
```
[R/collect_posterior_filenames.R:31:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_posterior_filenames.R#L31) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(parameter_filename)
          ^~~~~~~~~
```
[R/collect_posterior_gammas.R:20:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_posterior_gammas.R#L20) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/collect_posterior_gammas.R:46:29:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_posterior_gammas.R#L46) *warning:* **no visible global function definition for ‘collect_gamma_statistics’**
```r
        gamma_statistics <- collect_gamma_statistics(phylogenies)
                            ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/collect_posterior_nllts.R:15:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_posterior_nllts.R#L15) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/collect_species_tree_gammas.R:28:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_species_tree_gammas.R#L28) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/collect_species_tree_nltts.R:24:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_species_tree_nltts.R#L24) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/collect_species_tree_n_taxa.R:30:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_species_tree_n_taxa.R#L30) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/collect_species_tree_n_taxa.R:47:10:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/collect_species_tree_n_taxa.R#L47) *warning:* **no visible global function definition for ‘collect_n_taxa’**
```r
    g <- collect_n_taxa(c(phylogeny))
         ^~~~~~~~~~~~~~
```
[R/convert_alignment_to_beast_input_file.R:10:1:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/convert_alignment_to_beast_input_file.R#L10) *style:* **Variable and function names should not be longer than 30 characters.**
```r
convert_alignment_to_beast_input_file <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convert_alignment_to_beast_input_file.R:27:3:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/convert_alignment_to_beast_input_file.R#L27) *warning:* **no visible global function definition for ‘convert_alignment_to_fasta’**
```r
  convert_alignment_to_fasta(alignment_dnabin, temp_fasta_filename)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convert_alignment_to_beast_posterior.R:12:1:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/convert_alignment_to_beast_posterior.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
convert_alignment_to_beast_posterior <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convert_alignment_to_beast_posterior.R:78:3:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/convert_alignment_to_beast_posterior.R#L78) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  convert_alignment_to_beast_input_file(
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/convert_alignment_to_beast_posterior.R:132:22:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/convert_alignment_to_beast_posterior.R#L132) *warning:* **no visible global function definition for ‘is_beast_posterior’**
```r
      testit::assert(is_beast_posterior(posterior))
                     ^~~~~~~~~~~~~~~~~~
```
[R/convert_alignment_to_beast_posterior.R:155:22:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/convert_alignment_to_beast_posterior.R#L155) *warning:* **no visible global function definition for ‘is_beast_posterior’**
```r
      testit::assert(is_beast_posterior(posterior))
                     ^~~~~~~~~~~~~~~~~~
```
[R/convert_phylogeny_to_alignment.R:43:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/convert_phylogeny_to_alignment.R#L43) *warning:* **no visible global function definition for ‘is_alignment’**
```r
  testit::assert(is_alignment(alignment_dnabin))
                 ^~~~~~~~~~~~
```
[R/find_paths.R:86:1:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/find_paths.R#L86) *style:* **Variable and function names should not be longer than 30 characters.**
```r
find_beast_posterior_test_filename <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_paths.R:88:10:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/find_paths.R#L88) *warning:* **no visible global function definition for ‘find_path’**
```r
  return(find_path(filename = "is_beast_posterior.trees"))
         ^~~~~~~~~
```
[R/normalized_rooted_branch_score.R:14:32:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/normalized_rooted_branch_score.R#L14) *warning:* **no visible global function definition for ‘branch_sorter’**
```r
    filename                <- branch_sorter(filename)
                               ^~~~~~~~~~~~~
```
[R/plot_alignments.R:11:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_alignments.R#L11) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/plot_extant_incipient_tree.R:13:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_extant_incipient_tree.R#L13) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/plot_gene_tree.R:3:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_gene_tree.R#L3) *warning:* **no visible global function definition for ‘is_valid_file’**
```r
  testit::assert(is_valid_file(filename))
                 ^~~~~~~~~~~~~
```
[R/plot_gene_tree.R:5:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_gene_tree.R#L5) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/plot_posterior_sample_nltts.R:12:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_posterior_sample_nltts.R#L12) *warning:* **no visible global function definition for ‘is_valid_file’**
```r
  testit::assert(is_valid_file(filename))
                 ^~~~~~~~~~~~~
```
[R/plot_posterior_sample_nltts.R:14:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_posterior_sample_nltts.R#L14) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/plot_posterior_samples.R:7:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_posterior_samples.R#L7) *warning:* **no visible global function definition for ‘is_valid_file’**
```r
  testit::assert(is_valid_file(filename))
                 ^~~~~~~~~~~~~
```
[R/plot_posterior_samples.R:9:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_posterior_samples.R#L9) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/plot_species_tree_with_outgroup_nltt.R:7:1:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_species_tree_with_outgroup_nltt.R#L7) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_species_tree_with_outgroup_nltt <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_species_tree_with_outgroup_nltt.R:11:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_species_tree_with_outgroup_nltt.R#L11) *warning:* **no visible global function definition for ‘is_valid_file’**
```r
  testit::assert(is_valid_file(filename))
                 ^~~~~~~~~~~~~
```
[R/plot_species_tree_with_outgroup.R:6:1:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_species_tree_with_outgroup.R#L6) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_species_tree_with_outgroup <- function(filename) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_species_tree_with_outgroup.R:7:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_species_tree_with_outgroup.R#L7) *warning:* **no visible global function definition for ‘is_valid_file’**
```r
  testit::assert(is_valid_file(filename))
                 ^~~~~~~~~~~~~
```
[R/plot_species_tree_with_outgroup.R:8:11:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/plot_species_tree_with_outgroup.R#L8) *warning:* **no visible global function definition for ‘read_file’**
```r
  file <- read_file(filename)
          ^~~~~~~~~
```
[R/sample_species_trees_from_pbd_sim_output.R:8:1:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/sample_species_trees_from_pbd_sim_output.R#L8) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sample_species_trees_from_pbd_sim_output <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sample_species_trees_from_pbd_sim_output.R:13:5:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/sample_species_trees_from_pbd_sim_output.R#L13) *warning:* **no visible global function definition for ‘is_pbd_sim_output’**
```r
    is_pbd_sim_output(pbd_sim_output, verbose = TRUE)
    ^~~~~~~~~~~~~~~~~
```
[R/sample_species_trees_from_pbd_sim_output.R:19:16:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/sample_species_trees_from_pbd_sim_output.R#L19) *warning:* **no visible global function definition for ‘get_phylogeny_crown_age’**
```r
  crown_age <- get_phylogeny_crown_age(pbd_sim_output$tree)
               ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/save_parameters_to_file.R:113:18:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/R/save_parameters_to_file.R#L113) *warning:* **no visible global function definition for ‘is_valid_file’**
```r
  testit::assert(is_valid_file(filename))
                 ^~~~~~~~~~~~~
```
[tests/testthat/test-add_species_trees_with_outgroup.R:27:3:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/tests/testthat/test-add_species_trees_with_outgroup.R#L27) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  add_species_trees_with_outgroup(
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-convert_alignment_to_beast_input_file.R:19:3:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/tests/testthat/test-convert_alignment_to_beast_input_file.R#L19) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  convert_alignment_to_beast_input_file(
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-is_beast_posterior.R:4:15:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/tests/testthat/test-is_beast_posterior.R#L4) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  filename <- find_beast_posterior_test_filename()
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-is_beast_posterior.R:11:5:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/tests/testthat/test-is_beast_posterior.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    find_beast_posterior_test_filename()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-is_beast_posterior.R:18:5:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/tests/testthat/test-is_beast_posterior.R#L18) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    find_beast_posterior_test_filename()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-is_beast_posterior.R:33:5:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/tests/testthat/test-is_beast_posterior.R#L33) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    find_beast_posterior_test_filename()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-is_beast_posterior.R:44:5:](https://github.com/richelbilderbeek/Cer2016/blob/16b585c2af7972879cc655ef18069466b8e781a1/tests/testthat/test-is_beast_posterior.R#L44) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    find_beast_posterior_test_filename()
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```