[R/create_beast2_input_beast.R:28:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_beast.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
    "namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_data.R:12:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_data.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("id=\"", beastscriptr::get_file_base_sans_ext(input_fasta_filenames), "\""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_data.R:14:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_data.R#L14) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, beastscriptr::create_beast2_input_data_sequences(input_fasta_filenames = input_fasta_filenames))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_data.R:22:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_data.R#L22) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_beast2_input_data_sequences <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:8:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L8) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_beast2_input_distribution <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:20:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"YuleModel.t:", ids, "\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:", ids, "\" tree=\"@Tree.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:21:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"YuleBirthRatePrior.t:", ids, "\" name=\"distribution\" x=\"@birthRate.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:22:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <Uniform id=\"Uniform.1\" name=\"distr\" upper=\"Infinity\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:25:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"BirthDeath.t:", ids, "\" spec=\"beast.evolution.speciation.BirthDeathGernhard08Model\" birthDiffRate=\"@BDBirthRate.t:", ids, "\" relativeDeathRate=\"@BDDeathRate.t:", ids, "\" tree=\"@Tree.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:26:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L26) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"BirthRatePrior.t:", ids, "\" name=\"distribution\" x=\"@BDBirthRate.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:27:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"1000.0\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:29:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"DeathRatePrior.t:", ids, "\" name=\"distribution\" x=\"@BDDeathRate.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:30:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <Uniform id=\"Uniform.4\" name=\"distr\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:36:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L36) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <populationModel id=\"ConstantPopulation.t:", ids, "\" spec=\"ConstantPopulation\" popSize=\"@popSize.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:49:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"BayesianSkyline.t:", ids, "\" spec=\"BayesianSkyline\" groupSizes=\"@bGroupSizes.t:", ids, "\" popSizes=\"@bPopSizes.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:50:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <treeIntervals id=\"BSPTreeIntervals.t:", ids, "\" spec=\"TreeIntervals\" tree=\"@Tree.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:52:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"MarkovChainedPopSizes.t:", ids, "\" spec=\"beast.math.distributions.MarkovChainDistribution\" jeffreys=\"true\" parameter=\"@bPopSizes.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:56:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"KappaPrior.s:", ids, "\" name=\"distribution\" x=\"@kappa.s:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:57:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <LogNormal id=\"LogNormalDistributionModel.0\" name=\"distr\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:58:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.1\" estimate=\"false\" name=\"M\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:59:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L59) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.2\" estimate=\"false\" name=\"S\">1.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:89:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L89) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <substModel id=\"JC69.s:", ids, "\" spec=\"JukesCantor\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:91:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L91) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <substModel id=\"hky.s:", ids, "\" spec=\"HKY\" kappa=\"@kappa.s:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:92:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_distribution.R#L92) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                        <frequencies id=\"estimatedFreqs.s:", ids, "\" spec=\"Frequencies\" frequencies=\"@freqParameter.s:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_loggers.R:46:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_loggers.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <log idref=\"BayesianSkyline.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_loggers.R:53:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_loggers.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <log idref=\"freqParameter.s:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:35:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"YuleBirthRateScaler.t:", ids, "\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:", ids, "\" scaleFactor=\"0.75\" weight=\"3.0\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:40:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"", operator_id_pre, "TreeScaler.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:46:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"", operator_id_pre, "TreeRootScaler.t:",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:52:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("    <operator id=\"", operator_id_pre, "UniformOperator.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:57:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"", operator_id_pre, "SubtreeSlide.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:63:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("    <operator id=\"", operator_id_pre, "Narrow.t:", ids, "\" spec=\"Exchange\" tree=\"@Tree.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:70:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("    <operator id=\"", operator_id_pre, "WilsonBalding.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:76:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L76) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"KappaScaler.s:", ids, "\" spec=\"ScaleOperator\" parameter=\"@kappa.s:", ids, "\" scaleFactor=\"0.5\" weight=\"0.1\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:78:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L78) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"FrequenciesExchanger.s:", ids, "\" spec=\"DeltaExchangeOperator\" delta=\"0.01\" weight=\"0.1\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:79:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter idref=\"freqParameter.s:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:100:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"popSizesScaler.t:", ids, "\" spec=\"ScaleOperator\" parameter=\"@bPopSizes.t:", ids, "\" scaleFactor=\"0.75\" weight=\"15.0\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:102:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"groupSizesDelta.t:", ids, "\" spec=\"DeltaExchangeOperator\" integer=\"true\" weight=\"6.0\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:103:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_operators.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <intparameter idref=\"bGroupSizes.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:37:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L37) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"birthRate.t:", ids, "\" name=\"stateNode\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:39:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"BDBirthRate.t:", ids, "\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:40:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"BDDeathRate.t:", ids, "\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:42:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"popSize.t:", ids, "\" name=\"stateNode\">0.3</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:44:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"bPopSizes.t:", ids, "\" dimension=\"5\" lower=\"0.0\" name=\"stateNode\" upper=\"380000.0\">380.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:45:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <stateNode id=\"bGroupSizes.t:", ids, "\" spec=\"parameter.IntegerParameter\" dimension=\"5\">1</stateNode>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:48:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"kappa.s:", ids, "\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:49:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"freqParameter.s:", ids, "\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:51:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"kappa1.s:", ids, "\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:52:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"kappa2.s:", ids, "\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:53:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/create_beast2_input_state.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"freqParameter.s:", ids, "\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_cbs_tree_prior.R:2:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/is_cbs_tree_prior.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @param x an object, to be determined if it is a valid constant coalescent Bayesian skyline prior
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_cbs_tree_prior.R:3:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/is_cbs_tree_prior.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @return TRUE if x is a valid constant coalescent Bayesian skyline prior, FALSE otherwise
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_ccp_tree_prior.R:2:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/is_ccp_tree_prior.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @param x an object, to be determined if it is a valid constant coalescence population tree prior
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_ccp_tree_prior.R:3:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/R/is_ccp_tree_prior.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @return TRUE if x is a valid constant coalescence population tree prior, FALSE otherwise
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input_data.R:8:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input_data.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
  expected <- "                    <sequence id=\"seq_t1\" taxon=\"t1\" totalcount=\"4\" value=\"acttgttgcgactgcgcctg\"/>"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input_data.R:19:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input_data.R#L19) *style:* **Lines should not be more than 80 characters.**
```r
  expected <- "                    <sequence id=\"seq_t1\" taxon=\"t1\" totalcount=\"4\" value=\"acttgttgcgactgcgcctg\"/>"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:51:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:68:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "birth_death_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:82:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    tree_priors = beastscriptr::create_tree_prior(name = "coalescent_constant_population")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:85:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "coalescent_constant_population_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:101:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L101) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "yule_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:114:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
    tree_priors = beastscriptr::create_tree_prior(name = "coalescent_bayesian_skyline")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:117:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "coalescent_bayesian_skyline_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:128:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L128) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "jc69_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:139:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L139) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "hky_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:152:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L152) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "tn93_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:180:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L180) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "gtr_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:182:5:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L182) *style:* **Commented code should be removed.**
```r
  # write.csv(created_lines, "~/created.csv")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:183:5:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L183) *style:* **Commented code should be removed.**
```r
  # write.csv(expected_lines, "~/expected.csv")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:188:7:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-create_beast2_input.R#L188) *style:* **Commented code should be removed.**
```r
  #   print(paste0(i, " / ", length(expected_lines)))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-is_yule_tree_prior.R:6:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3dd00e5d34d96e938902800d0dc8010e56acc38e/tests/testthat/test-is_yule_tree_prior.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
  testthat::expect_false(is_yule_tree_prior(create_tree_prior(name = "birth_death")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Bluemix [toolchain](https://console.bluemix.net/devops/toolchains/dd1eda5f-ea15-4f78-8235-461f8ec39446 "archive-lab"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/e743c5c0-3d7c-4c19-8f52-f4079e61eca0 "archive-lab") deployed [archive-lab](https://github.com/jesiels/archive-lab/releases/tag/deploy-ibm-yp-us-south-jesiels-br.ibm.com-dev-20171019-101917 "deploy-ibm-yp-us-south-jesiels-br.ibm.com-dev-20171019-101917") to [dev](https://console.bluemix.net/apps/9bef1c64-daad-4901-a521-8d3ca4508119?env_id=ibm:yp:us-south "ibm:yp:us-south:jesiels@br.ibm.com:dev"), including this commit


So we
1. bumped version to 0.5.0
2. released 0.5.0
3. bumped version to 0.5.1
4. yanked 0.5.0
5. downgraded the version to 0.5.0
6. bumped version to 0.5.1
(Next 7. Release 0.5.1)

What did we gain by the "downgrade" here?


Wrong url: https://wordpress.org/plugins/gf-block-ips/


お疲れ様です！
オブジェクト指向OKです！


I think this is a related, but different issue, since @peircej's change actually _catches_ a `UnicodeDecodeError`, albeit apparently at a different place!


[R/create_beast2_input_beast.R:28:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_beast.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
    "namespace=\"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\" ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_data.R:12:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_data.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("id=\"", beastscriptr::get_file_base_sans_ext(input_fasta_filenames), "\""))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_data.R:14:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_data.R#L14) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, beastscriptr::create_beast2_input_data_sequences(input_fasta_filenames = input_fasta_filenames))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_data.R:22:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_data.R#L22) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_beast2_input_data_sequences <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:8:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L8) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_beast2_input_distribution <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:20:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"YuleModel.t:", ids, "\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:", ids, "\" tree=\"@Tree.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:21:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L21) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"YuleBirthRatePrior.t:", ids, "\" name=\"distribution\" x=\"@birthRate.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:22:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <Uniform id=\"Uniform.1\" name=\"distr\" upper=\"Infinity\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:25:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L25) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"BirthDeath.t:", ids, "\" spec=\"beast.evolution.speciation.BirthDeathGernhard08Model\" birthDiffRate=\"@BDBirthRate.t:", ids, "\" relativeDeathRate=\"@BDDeathRate.t:", ids, "\" tree=\"@Tree.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:26:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L26) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"BirthRatePrior.t:", ids, "\" name=\"distribution\" x=\"@BDBirthRate.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:27:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"1000.0\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:29:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"DeathRatePrior.t:", ids, "\" name=\"distribution\" x=\"@BDDeathRate.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:30:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <Uniform id=\"Uniform.4\" name=\"distr\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:33:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"CoalescentConstant.t:", ids, "\" spec=\"Coalescent\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:34:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L34) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <populationModel id=\"ConstantPopulation.t:", ids, "\" spec=\"ConstantPopulation\" popSize=\"@popSize.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:47:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"BayesianSkyline.t:", ids, "\" spec=\"BayesianSkyline\" groupSizes=\"@bGroupSizes.t:", ids, "\" popSizes=\"@bPopSizes.t:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:48:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <treeIntervals id=\"BSPTreeIntervals.t:", ids, "\" spec=\"TreeIntervals\" tree=\"@Tree.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:50:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L50) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <distribution id=\"MarkovChainedPopSizes.t:", ids, "\" spec=\"beast.math.distributions.MarkovChainDistribution\" jeffreys=\"true\" parameter=\"@bPopSizes.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:55:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L55) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"KappaPrior.s:", ids, "\" name=\"distribution\" x=\"@kappa.s:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:56:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <LogNormal id=\"LogNormalDistributionModel.0\" name=\"distr\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:57:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.1\" estimate=\"false\" name=\"M\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:58:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.2\" estimate=\"false\" name=\"S\">1.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:62:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L62) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"kappa1Prior.s:", ids, "\" name=\"distribution\" x=\"@kappa1.s:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:63:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <LogNormal id=\"LogNormalDistributionModel.1\" name=\"distr\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:64:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.3\" estimate=\"false\" name=\"M\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:65:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.4\" estimate=\"false\" name=\"S\">1.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:68:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("            <prior id=\"kappa2Prior.s:", ids, "\" name=\"distribution\" x=\"@kappa2.s:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:69:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                <LogNormal id=\"LogNormalDistributionModel.2\" name=\"distr\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:70:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.5\" estimate=\"false\" name=\"M\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:71:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <parameter id=\"RealParameter.6\" estimate=\"false\" name=\"S\">1.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:101:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L101) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <substModel id=\"JC69.s:", ids, "\" spec=\"JukesCantor\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:103:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                    <substModel id=\"hky.s:", ids, "\" spec=\"HKY\" kappa=\"@kappa.s:", ids, "\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distribution.R:104:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_distribution.R#L104) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("                        <frequencies id=\"estimatedFreqs.s:", ids, "\" spec=\"Frequencies\" frequencies=\"@freqParameter.s:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_loggers.R:46:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_loggers.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <log idref=\"BayesianSkyline.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_loggers.R:53:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_loggers.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <log idref=\"freqParameter.s:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:35:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"YuleBirthRateScaler.t:", ids, "\" spec=\"ScaleOperator\" parameter=\"@birthRate.t:", ids, "\" scaleFactor=\"0.75\" weight=\"3.0\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:40:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"", operator_id_pre, "TreeScaler.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:46:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"", operator_id_pre, "TreeRootScaler.t:",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:52:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("    <operator id=\"", operator_id_pre, "UniformOperator.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:57:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L57) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"", operator_id_pre, "SubtreeSlide.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:63:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("    <operator id=\"", operator_id_pre, "Narrow.t:", ids, "\" spec=\"Exchange\" tree=\"@Tree.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:70:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L70) *style:* **Lines should not be more than 80 characters.**
```r
  text <- c(text, paste0("    <operator id=\"", operator_id_pre, "WilsonBalding.t:", ids,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:76:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L76) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"KappaScaler.s:", ids, "\" spec=\"ScaleOperator\" parameter=\"@kappa.s:", ids, "\" scaleFactor=\"0.5\" weight=\"0.1\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:78:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L78) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"FrequenciesExchanger.s:", ids, "\" spec=\"DeltaExchangeOperator\" delta=\"0.01\" weight=\"0.1\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:79:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter idref=\"freqParameter.s:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:100:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"popSizesScaler.t:", ids, "\" spec=\"ScaleOperator\" parameter=\"@bPopSizes.t:", ids, "\" scaleFactor=\"0.75\" weight=\"15.0\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:102:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L102) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("    <operator id=\"groupSizesDelta.t:", ids, "\" spec=\"DeltaExchangeOperator\" integer=\"true\" weight=\"6.0\">"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:103:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_operators.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <intparameter idref=\"bGroupSizes.t:", ids, "\"/>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:37:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L37) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"birthRate.t:", ids, "\" name=\"stateNode\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:39:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"BDBirthRate.t:", ids, "\" lower=\"0.0\" name=\"stateNode\" upper=\"10000.0\">1.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:40:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"BDDeathRate.t:", ids, "\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.5</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:42:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"popSize.t:", ids, "\" name=\"stateNode\">0.3</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:44:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L44) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"bPopSizes.t:", ids, "\" dimension=\"5\" lower=\"0.0\" name=\"stateNode\" upper=\"380000.0\">380.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:45:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <stateNode id=\"bGroupSizes.t:", ids, "\" spec=\"parameter.IntegerParameter\" dimension=\"5\">1</stateNode>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:48:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L48) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"kappa.s:", ids, "\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:49:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L49) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"freqParameter.s:", ids, "\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:51:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"kappa1.s:", ids, "\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:52:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L52) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"kappa2.s:", ids, "\" lower=\"0.0\" name=\"stateNode\">2.0</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:53:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/create_beast2_input_state.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
    text <- c(text, paste0("        <parameter id=\"freqParameter.s:", ids, "\" dimension=\"4\" lower=\"0.0\" name=\"stateNode\" upper=\"1.0\">0.25</parameter>"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_cbs_tree_prior.R:2:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/is_cbs_tree_prior.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @param x an object, to be determined if it is a valid constant coalescent Bayesian skyline prior
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_cbs_tree_prior.R:3:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/is_cbs_tree_prior.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @return TRUE if x is a valid constant coalescent Bayesian skyline prior, FALSE otherwise
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_ccp_tree_prior.R:2:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/is_ccp_tree_prior.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @param x an object, to be determined if it is a valid constant coalescence population tree prior
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_ccp_tree_prior.R:3:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/R/is_ccp_tree_prior.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @return TRUE if x is a valid constant coalescence population tree prior, FALSE otherwise
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input_data.R:8:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input_data.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
  expected <- "                    <sequence id=\"seq_t1\" taxon=\"t1\" totalcount=\"4\" value=\"acttgttgcgactgcgcctg\"/>"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input_data.R:19:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input_data.R#L19) *style:* **Lines should not be more than 80 characters.**
```r
  expected <- "                    <sequence id=\"seq_t1\" taxon=\"t1\" totalcount=\"4\" value=\"acttgttgcgactgcgcctg\"/>"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:51:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:68:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L68) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "birth_death_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:82:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L82) *style:* **Lines should not be more than 80 characters.**
```r
    tree_priors = beastscriptr::create_tree_prior(name = "coalescent_constant_population")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:85:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "coalescent_constant_population_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:101:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L101) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "yule_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:114:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
    tree_priors = beastscriptr::create_tree_prior(name = "coalescent_bayesian_skyline")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:117:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L117) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "coalescent_bayesian_skyline_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:128:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L128) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "jc69_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:139:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L139) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "hky_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:152:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L152) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "tn93_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:180:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L180) *style:* **Lines should not be more than 80 characters.**
```r
  expected_lines <- readLines(system.file("extdata", "gtr_2_4.xml", package = "beastscriptr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:182:5:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L182) *style:* **Commented code should be removed.**
```r
  # write.csv(created_lines, "~/created.csv")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:183:5:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L183) *style:* **Commented code should be removed.**
```r
  # write.csv(expected_lines, "~/expected.csv")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_beast2_input.R:188:7:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-create_beast2_input.R#L188) *style:* **Commented code should be removed.**
```r
  #   print(paste0(i, " / ", length(expected_lines)))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-is_yule_tree_prior.R:6:1:](https://github.com/richelbilderbeek/beastscriptr/blob/3f7f88f68258d49e13000630b9324f0ab0ceb4d4/tests/testthat/test-is_yule_tree_prior.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
  testthat::expect_false(is_yule_tree_prior(create_tree_prior(name = "birth_death")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Ohh right, sorry I missed that.
But in fact, `rangeElements` can be used on composite spaces. It's just that we already use the subspace. So either `v.functionSpace()->template rangeElements< 0 >()` or `M_composite_v.functionSpace()->template rangeElements< T::value >()`


お疲れ様です！
クラスの継承 OKです！　継承に関しては別ファイルから継承するとファイル内がコンパクトになるのでやって見てください！


@CDRandom Why is that suggestion a comment on this commit?


Ok, cool. I'll do that.


load the MNIST data


test hello world


修改代码太多，我周末详细看一下。另外，你把版本直接升级到`3.1`了，这可能不太合适


it's not exacly what happened: Initially it was bumped to 0.5.1 and it happened on a branch that got never merged to master, which means this version was never published to rubygems!  The branch with 0.5.1 was unfinished (and that's why e.g. ascalon useses a git reference to one of its commits, not the version)

0.5.0 was released with the missing encoding comment and despite 'bundle install' worked fine in rspec-hive and socialguide projects on my local machine, it failed along with our docker build so in my opinion there was no point to keep this buggy version in rubygems. Sadly I discovered the problem after it got released to rubygems so I decided to yank it, fix the gem, bump the version to 0.5.1 and release it as an official gem to rubygems