PLD_interface: no visible global function definition for ‘read.table’
PLD_interface: no visible global function definition for ‘write.table’
PLD_loc_mrca: no visible global function definition for ‘barplot’
PLD_plot_stat_mig: no visible global function definition for ‘density’
PLD_plot_stat_mig: no visible global function definition for ‘rainbow’
PLD_plot_stat_mig: no visible global function definition for ‘plot’
PLD_plot_stat_mig: no visible global function definition for ‘lines’
PLD_plot_stat_mig: no visible global function definition for ‘legend’
PLD_plot_trees: no visible global function definition for ‘par’
break_node_height_tie: no visible global function definition for
  ‘qnorm’
break_node_height_tie: no visible global function definition for
  ‘runif’
break_node_height_tie: no visible global function definition for
  ‘pnorm’
effSaSize: no visible global function definition for ‘acf’
effSaSize: no visible global function definition for ‘sd’
mcmc_phyloland: no visible global function definition for ‘write.table’
mcmc_phyloland: no visible global function definition for ‘par’
mcmc_phyloland: no visible global function definition for ‘barplot’
mcmc_phyloland: no visible global function definition for ‘hist’
mcmc_phyloland: no visible global function definition for ‘title’
mcmc_phyloland: no visible global function definition for ‘runif’
read_loc: no visible global function definition for ‘read.table’
read_space: no visible global function definition for ‘read.table’
sigma_upperlim: no visible global function definition for ‘pnorm’
space_dist: no visible global function definition for ‘dist’
stat_phyloland: no visible global function definition for ‘density’
stat_phyloland: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  acf barplot density dist hist legend lines par plot pnorm qnorm
  quantile rainbow read.table runif sd title write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "hist", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "acf", "density", "dist", "pnorm", "qnorm",
             "quantile", "runif", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.