New option --date-outlier for -e option in LSD2

main/timetree.cpp

@@ -237,6 +237,11 @@ void runLSD2(PhyloTree *tree) {
  arg.push_back(convertDoubleToString(Params::getInstance().clock_stddev));
  }
  }
+
+ if (Params::getInstance().date_outlier >= 0) {
+ arg.push_back("-e");
+ arg.push_back(convertIntToString(Params::getInstance().date_outlier));
+ }
 
  if (Params::getInstance().root) {
  // print outgroup file for LSD

utils/tools.cpp

@@ -1121,6 +1121,7 @@ void parseArg(int argc, char *argv[], Params &params) {
  params.date_debug = false;
  params.date_replicates = 0;
  params.clock_stddev = -1.0;
+ params.date_outlier = -1.0;
 
  params.matrix_exp_technique = MET_EIGEN3LIB_DECOMPOSITION;
 
@@ -4118,6 +4119,16 @@ void parseArg(int argc, char *argv[], Params &params) {
  continue;
  }
 
+ if (strcmp(argv[cnt], "--date-outlier") == 0) {
+ cnt++;
+ if (cnt >= argc)
+ throw "Use --date-outlier <z_score_for_removing_outlier_nodes>";
+ params.date_outlier = convert_double(argv[cnt]);
+ if (params.date_outlier < 0)
+ throw "--date-outlier must be non-negative";
+ continue;
+ }
+
  if (strcmp(argv[cnt], "--date-debug") == 0) {
  params.date_debug = true;
  continue;
@@ -4582,6 +4593,7 @@ void usage_iqtree(char* argv[], bool full_command) {
  << " --date-ci NUM Number of replicates to compute confidence interval" << endl
  << " --clock-sd NUM Std-dev for lognormal relaxed clock (default: 0.2)" << endl
  << " --date-outgroup Include outgroup in time tree (default: no)" << endl
+ << " --date-outlier NUM Z-score cutoff to exclude outlier nodes (e.g. 3)" << endl
  << " --date-options \"..\" Extra options passing directly to LSD2" << endl
  << " --dating STRING Dating method: LSD for least square dating (default)" << endl
 #endif

utils/tools.h

@@ -2203,6 +2203,9 @@ class Params {
 
  /** standard deviation of lognormal relaxed clock model for confidence interval estimate */
  double clock_stddev;
+
+ /** z-score for detecting outlier nodes */
+ double date_outlier;
 };
 
 /**