Running examples in ‘phylosem-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: phylosem
> ### Title: Fit phylogenetic structural equation model
> ### Aliases: phylosem
> 
> ### ** Examples
> 
> # Load data set
> data(rhino, rhino_tree, package="phylopath")
> 
> # Run phylosem
> model = "
+   DD -> RS, p1
+   BM -> LS, p2
+   BM -> NL, p3
+   NL -> DD, p4
+ "
> psem = phylosem( sem = model,
+           data = rhino[,c("BM","NL","DD","RS","LS")],
+           tree = rhino_tree )
Read 4 records
NOTE: it is generally simpler to use specifyEquations() or cfa()
      see ?specifyEquations
1 regions found.
Using 1 threads
1 regions found.
Using 1 threads
List of estimated fixed and random effects:
  Coefficient_name Number_of_coefficients   Type
1           beta_z                      9  Fixed
2             x_vj                    495 Random
  0:     218940.22: 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000
  1:     8397.8060: 0.0842226 0.130623 0.120621 0.124798 0.347153 0.487021 0.538215 0.426241 0.798883
  2:     6354.4828: 0.0315557 0.151274 0.172831 0.173170 0.658033 0.551767 0.542706 0.578654 0.594083
  3:     3672.8577: 0.000303728 0.221429 0.224967 0.235152 0.725274 0.724685 0.748919 0.705591 0.856342
  4:     2740.3780: -0.102677 0.415193 0.403189 0.371336 0.731170 0.859963 0.790331 0.921711 0.951636
  5:     1998.5720: -0.126539 0.503355 0.465231 0.444702 0.930180 0.997626  1.00743  1.03020  1.14979
  6:     1603.6727: -0.156804 0.611920 0.546135 0.512778  1.10880  1.15370  1.19174  1.17670  1.34656
  7:     1378.4437: -0.184978 0.735384 0.635855 0.574242  1.28215  1.30788  1.36879  1.33950  1.53299
  8:     1246.1754: -0.205749 0.871125 0.727935 0.623959  1.45479  1.45790  1.54574  1.51056  1.71079
  9:     1168.3619: -0.217139  1.01403 0.814506 0.657424  1.62857  1.60494  1.72664  1.68772  1.88166
 10:     1123.9069: -0.220534  1.15457 0.885299 0.673319  1.80466  1.75160  1.91435  1.87091  2.04888
 11:     1100.3689: -0.220150  1.27536 0.928361 0.675635  1.98358  1.90047  2.11097  2.06073  2.21911
 12:     1089.9414: -0.220524  1.34559 0.935212 0.674388  2.16290  2.04937  2.31732  2.25655  2.40368
 13:     1088.5461: -0.220084  1.33812 0.932369 0.675458  2.21370  2.08811  2.38334  2.31655  2.47029
 14:     1087.8319: -0.220718  1.33618 0.933085 0.674475  2.26200  2.12267  2.45045  2.37612  2.54069
 15:     1087.7787: -0.220253  1.33642 0.932854 0.675008  2.26795  2.12603  2.46060  2.38452  2.55226
 16:     1087.7091: -0.220358  1.33673 0.932671 0.675146  2.27944  2.13226  2.48095  2.40115  2.57585
 17:     1087.7069: -0.217349  1.33044 0.940994 0.668413  2.28729  2.11448  2.49234  2.41721  2.59797
 18:     1087.6911: -0.222165  1.33489 0.932128 0.677383  2.28740  2.12316  2.49506  2.41681  2.59939
 19:     1087.6907: -0.214887  1.33792 0.933697 0.669999  2.28758  2.13505  2.49955  2.41615  2.60180
 20:     1087.6863: -0.221547  1.33726 0.932944 0.675110  2.28759  2.13517  2.49998  2.41611  2.60207
 21:     1087.6861: -0.220478  1.33704 0.932837 0.675081  2.28760  2.13522  2.50021  2.41608  2.60222
 22:     1087.6861: -0.220143  1.33645 0.932761 0.674901  2.28764  2.13538  2.50097  2.41602  2.60264
 23:     1087.6861: -0.220221  1.33658 0.932819 0.675126  2.28770  2.13531  2.50117  2.41601  2.60276
 24:     1087.6861: -0.220415  1.33670 0.932693 0.674998  2.28765  2.13538  2.50131  2.41596  2.60293
 25:     1087.6861: -0.220192  1.33683 0.932842 0.675013  2.28773  2.13544  2.50141  2.41587  2.60309
 26:     1087.6861: -0.220324  1.33674 0.932762 0.675074  2.28770  2.13543  2.50142  2.41588  2.60310
 27:     1087.6861: -0.220275  1.33670 0.932749 0.675068  2.28767  2.13543  2.50143  2.41589  2.60311
 28:     1087.6861: -0.220310  1.33668 0.932761 0.675067  2.28763  2.13543  2.50146  2.41592  2.60310
 29:     1087.6861: -0.220287  1.33668 0.932751 0.675069  2.28763  2.13543  2.50146  2.41592  2.60311
 30:     1087.6861: -0.220295  1.33668 0.932747 0.675069  2.28762  2.13542  2.50146  2.41592  2.60311
 31:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312
  0:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312
  1:     1087.6861: -0.220290  1.33668 0.932749 0.675069  2.28762  2.13542  2.50145  2.41592  2.60312
> 
> # Convert and plot using phylopath
> library(phylopath)

Attaching package: ‘phylopath’

The following objects are masked from ‘package:phylosem’:

    average, best, choice

> my_fitted_DAG = as_fitted_DAG(psem)
> coef_plot( my_fitted_DAG )
The fitted model does not contain confidence intervals, so showing standard errors instead. Fit the model with `boot` larger than 0 to get confidence intervals, or set `error_bar = "se"` to avoid this warning.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → NL' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'BM → LS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'NL → DD' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <e2>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <86>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'DD → RS' in 'mbcsToSbcs': dot substituted for <92>
> plot( my_fitted_DAG )
> 
> # Convert to phylo4d
> my_phylo4d = as_phylo4d(psem)
> 
> # Convert to sem
> library(sem)
> my_sem = as_sem(psem)
> pathDiagram( model = my_sem,
+                   style = "traditional",
+                   edge.labels = "values" )
Loading required namespace: DiagrammeR
> effects( my_sem )

 Total Effects (column on row)
           BM         NL         DD
DD  0.6296696  0.6750692  0.0000000
RS -0.1387108 -0.1487120 -0.2202914
LS  1.3366815  0.0000000  0.0000000
NL  0.9327482  0.0000000  0.0000000

 Direct Effects
          BM        NL         DD
DD 0.0000000 0.6750692  0.0000000
RS 0.0000000 0.0000000 -0.2202914
LS 1.3366815 0.0000000  0.0000000
NL 0.9327482 0.0000000  0.0000000

 Indirect Effects
              BM        NL DD
DD  6.296696e-01  0.000000  0
RS -1.387108e-01 -0.148712  0
LS  0.000000e+00  0.000000  0
NL -1.110223e-16  0.000000  0
> 
> # Convert and plot using semPlot
> library(semPlot)
> myplot = semPlotModel( my_sem )
> semPaths( my_sem,
+                    nodeLabels = myplot@Vars$name )
> 
> # Convert and plot using phylosignal
> library(phylosignal)
Error in library(phylosignal) : there is no package called ‘phylosignal’
Execution halted