Author: James Thorson

# Demonstration of selected features

#### James Thorson

    library(dsem)
    library(dynlm)
    library(ggplot2)
    library(reshape)
    library(gridExtra)
    library(phylopath)

`dsem` is an R package for fitting dynamic structural equation models (DSEMs) with a simple user-interface and generic specification of simultaneous and lagged effects in a non-recursive structure. We here highlight a few features in particular.

## Comparison with dynamic linear models

We first demonstrate that `dsem` gives identical results to `dynlm` for a well-known econometric model, the Klein-1 model.

    data(KleinI, package="AER")
    TS = ts(data.frame(KleinI, "time"=time(KleinI) - 1931))

    # dynlm
    fm_cons <- dynlm(consumption ~ cprofits + L(cprofits) + I(pwage + gwage), data = TS)
    fm_inv <- dynlm(invest ~ cprofits + L(cprofits) + capital, data = TS)                 #
    fm_pwage <- dynlm(pwage ~ gnp + L(gnp) + time, data = TS)

    # dsem
    sem = "
      # Link, lag, param_name
      cprofits -> consumption, 0, a1
      cprofits -> consumption, 1, a2
      pwage -> consumption, 0, a3
      gwage -> consumption, 0, a3

      cprofits -> invest, 0, b1
      cprofits -> invest, 1, b2
      capital -> invest, 0, b3

      gnp -> pwage, 0, c2
      gnp -> pwage, 1, c3
      time -> pwage, 0, c1
    "
    tsdata = TS[,c("time","gnp","pwage","cprofits",'consumption',
                   "gwage","invest","capital")]
    fit = dsem( sem=sem,
                tsdata = tsdata,
                estimate_delta0 = TRUE,
                control = dsem_control(
                  quiet = TRUE,
                  newton_loops = 0) )

    # Compile
    m1 = rbind( summary(fm_cons)$coef[-1,],
                summary(fm_inv)$coef[-1,],
                summary(fm_pwage)$coef[-1,] )[,1:2]
    m2 = summary(fit$sdrep)[1:9,]
    m = rbind(
      data.frame("var"=rownames(m1),m1,"method"="OLS","eq"=rep(c("C","I","Wp"),each=3)),
      data.frame("var"=rownames(m1),m2,"method"="GMRF","eq"=rep(c("C","I","Wp"),each=3))
    )
    m = cbind(m, "lower"=m$Estimate-m$Std..Error, "upper"=m$Estimate+m$Std..Error )

    # ggplot estimates

    longform = melt( as.data.frame(KleinI) )
      longform$year = rep( time(KleinI), 9 )
    p1 = ggplot( data=longform, aes(x=year, y=value) ) +
      facet_grid( rows=vars(variable), scales="free" ) +
      geom_line( )

    p2 = ggplot(data=m, aes(x=interaction(var,eq), y=Estimate, color=method)) +
      geom_point( position=position_dodge(0.9) ) +
      geom_errorbar( aes(ymax=as.numeric(upper),ymin=as.numeric(lower)),
                     width=0.25, position=position_dodge(0.9))  #

    p3 = plot( as_fitted_DAG(fit) ) +
         expand_limits(x = c(-0.2,1) )
    p4 = plot( as_fitted_DAG(fit, lag=1), text_size=4 ) +
         expand_limits(x = c(-0.2,1), y = c(-0.2,0) )

    p1

    p2

    grid.arrange( arrangeGrob(p3, p4, nrow=2) )

Results show that both packages provide (almost) identical estimates and standard errors.

We can also compare results using the Laplace approximation against those obtained via numerical integration of random effects using MCMC. In this example, MCMC results in somewhat higher estimates of exogenous variance parameters (presumably because those follow a chi-squared distribution with positive skewness), but otherwise the two produce similar estimates.

    library(tmbstan)

    # MCMC for both fixed and random effects
    mcmc = tmbstan( fit$obj, init="last.par.best" )
    summary_mcmc = summary(mcmc)

    # long-form data frame
    m1 = summary_mcmc$summary[1:17,c('mean','sd')]
    rownames(m1) = paste0( "b", seq_len(nrow(m1)) )
    m2 = summary(fit$sdrep)[1:17,c('Estimate','Std. Error')]
    m = rbind(
      data.frame('mean'=m1[,1], 'sd'=m1[,2], 'par'=rownames(m1), "method"="MCMC"),
      data.frame('mean'=m2[,1], 'sd'=m2[,2], 'par'=rownames(m1), "method"="LA")
    )
    m$lower = m$mean - m$sd
    m$upper = m$mean + m$sd

    # plot
    ggplot(data=m, aes(x=par, y=mean, col=method)) +
      geom_point( position=position_dodge(0.9) ) +
      geom_errorbar( aes(ymax=as.numeric(upper),ymin=as.numeric(lower)),
                     width=0.25, position=position_dodge(0.9))  #

## Comparison with vector autoregressive models

We next demonstrate that `dsem` gives similar results to a vector autoregressive (VAR) model. To do so, we analyze population abundance of wolf and moose populations on Isle Royale from 1959 to 2019, downloaded from their website (Vucetich, JA and Peterson RO. 2012. The population biology of Isle Royale wolves and moose: an overview. URL: www.isleroyalewolf.org).

This dataset was previously analyzed by in Chapter 14 of the User Manual for the R-package MARSS (Holmes, E. E., M. D. Scheuerell, and E. J. Ward (2023) Analysis of multivariate time-series using the MARSS package. Version 3.11.8. NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd E., Seattle, WA 98112, DOI: 10.5281/zenodo.5781847).

Here, we compare fits using `dsem` with `dynlm`, as well as a vector autoregressive model package `vars`, and finally with `MARSS`.

    data(isle_royale)
    data = ts( log(isle_royale[,2:3]), start=1959)

    sem = "
      # Link, lag, param_name
      wolves -> wolves, 1, arW
      moose -> wolves, 1, MtoW
      wolves -> moose, 1, WtoM
      moose -> moose, 1, arM
    "
    # initial first without delta0 (to improve starting values)
    fit0 = dsem( sem = sem,
                 tsdata = data,
                 estimate_delta0 = FALSE,
                 control = dsem_control(
                   quiet = FALSE,
                   getsd = FALSE) )
    #>   Coefficient_name Number_of_coefficients   Type
    #> 1           beta_z                      6  Fixed
    #> 2             mu_j                      2 Random

    #
    parameters = fit0$obj$env$parList()
      parameters$delta0_j = rep( 0, ncol(data) )

    # Refit with delta0
    fit = dsem( sem = sem,
                tsdata = data,
                estimate_delta0 = TRUE,
                control = dsem_control( quiet=TRUE,
                                        parameters = parameters ) )

    # dynlm
    fm_wolf = dynlm( wolves ~ 1 + L(wolves) + L(moose), data=data )   #
    fm_moose = dynlm( moose ~ 1 + L(wolves) + L(moose), data=data )   #

    # MARSS
    library(MARSS)
    z.royale.dat <- t(scale(data.frame(data),center=TRUE,scale=FALSE))
    royale.model.1 <- list(
      Z = "identity",
      B = "unconstrained",
      Q = "diagonal and unequal",
      R = "zero",
      U = "zero"
    )
    kem.1 <- MARSS(z.royale.dat, model = royale.model.1)
    #> Success! abstol and log-log tests passed at 16 iterations.
    #> Alert: conv.test.slope.tol is 0.5.
    #> Test with smaller values (<0.1) to ensure convergence.
    #>
    #> MARSS fit is
    #> Estimation method: kem
    #> Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
    #> Estimation converged in 16 iterations.
    #> Log-likelihood: -3.21765
    #> AIC: 22.4353   AICc: 23.70964
    #>
    #>                       Estimate
    #> B.(1,1)                 0.8669
    #> B.(2,1)                -0.1240
    #> B.(1,2)                 0.1417
    #> B.(2,2)                 0.8176
    #> Q.(X.wolves,X.wolves)   0.1341
    #> Q.(X.moose,X.moose)     0.0284
    #> x0.X.wolves             0.2324
    #> x0.X.moose             -0.6476
    #> Initial states (x0) defined at t=0
    #>
    #> Standard errors have not been calculated.
    #> Use MARSSparamCIs to compute CIs and bias estimates.
    SE <- MARSSparamCIs( kem.1 )

    # Using VAR package
    library(vars)
    var = VAR( data, type="const" )

    ### Compile
    m1 = rbind( summary(fm_wolf)$coef[-1,], summary(fm_moose)$coef[-1,] )[,1:2]
    m2 = summary(fit$sdrep)[1:4,]
    #m2 = cbind( "Estimate"=fit$opt$par, "Std. Error"=fit$sdrep$par.fixed )[1:4,]
    m3 = cbind( SE$parMean[c(1,3,2,4)], SE$par.se$B[c(1,3,2,4)] )
    colnames(m3) = colnames(m2)
    m4 = rbind( summary(var$varresult$wolves)$coef[-3,], summary(var$varresult$moose)$coef[-3,] )[,1:2]

    # Bundle
    m = rbind(
      data.frame("var"=rownames(m1), m1, "method"="dynlm", "eq"=rep(c("Wolf","Moose"),each=2)),
      data.frame("var"=rownames(m1), m2, "method"="dsem", "eq"=rep(c("Wolf","Moose"),each=2)),
      data.frame("var"=rownames(m1), m3, "method"="MARSS", "eq"=rep(c("Wolf","Moose"),each=2)),
      data.frame("var"=rownames(m1), m4, "method"="vars", "eq"=rep(c("Wolf","Moose"),each=2))
    )
    #knitr::kable( m1, digits=3)
    #knitr::kable( m2, digits=3)

    m = cbind(m, "lower"=m$Estimate-m$Std..Error, "upper"=m$Estimate+m$Std..Error )

    # ggplot estimates ... interaction(x,y) causes an error sometimes
    library(ggplot2)
    library(ggpubr)
    library(ggraph)
    longform = reshape( isle_royale, idvar = "year", direction="long", varying=list(2:3), v.names="abundance", timevar="species", times=c("wolves","moose") )
    p1 = ggplot( data=longform, aes(x=year, y=abundance) ) +
      facet_grid( rows=vars(species), scales="free" ) +
      geom_point( )

    p2 = ggplot(data=m, aes(x=interaction(var,eq), y=Estimate, color=method)) +
      geom_point( position=position_dodge(0.9) ) +
      geom_errorbar( aes(ymax=as.numeric(upper),ymin=as.numeric(lower)),
                     width=0.25, position=position_dodge(0.9))  #
    p3 = plot( as_fitted_DAG(fit, lag=1), rotation=0 ) +
         geom_edge_loop( aes( label=round(weight,2), direction=0)) + #arrow=arrow(), , angle_calc="along", label_dodge=grid::unit(10,"points") )
         expand_limits(x = c(-0.1,0) )

    ggarrange( p1, p2, p3,
               labels = c("Time-series data", "Estimated effects", "Fitted path digram"),
               ncol = 1, nrow = 3)

Results again show that `dsem` can estimate parameters for a vector autoregressive model (VAM), and it exactly matches results from `vars`, using `dynlm`, or using `MARSS`.

## Multi-causal ecosystem synthesis

We next replicate an analysis involving climate, forage fishes, stomach contents, and recruitment of a predatory fish.

    data(bering_sea)
    Z = ts( bering_sea )
    family = rep('fixed', ncol(bering_sea))

    # Specify model
    sem = "
      # Link, lag, param_name
      log_seaice -> log_CP, 0, seaice_to_CP
      log_CP -> log_Cfall, 0, CP_to_Cfall
      log_CP -> log_Esummer, 0, CP_to_E
      log_PercentEuph -> log_RperS, 0, Seuph_to_RperS
      log_PercentCop -> log_RperS, 0, Scop_to_RperS
      log_Esummer -> log_PercentEuph, 0, Esummer_to_Suph
      log_Cfall -> log_PercentCop, 0, Cfall_to_Scop
      SSB -> log_RperS, 0, SSB_to_RperS

      log_seaice -> log_seaice, 1, AR1, 0.001
      log_CP -> log_CP, 1,  AR2, 0.001
      log_Cfall -> log_Cfall, 1, AR4, 0.001
      log_Esummer -> log_Esummer, 1, AR5, 0.001
      SSB -> SSB, 1, AR6, 0.001
      log_RperS ->  log_RperS, 1, AR7, 0.001
      log_PercentEuph -> log_PercentEuph, 1, AR8, 0.001
      log_PercentCop -> log_PercentCop, 1, AR9, 0.001
    "

    # Fit
    fit = dsem( sem = sem,
                tsdata = Z,
                family = family,
                control = dsem_control(use_REML=FALSE, quiet=TRUE) )
    ParHat = fit$obj$env$parList()
    # summary( fit )

    # Timeseries plot
    oldpar <- par(no.readonly = TRUE)
    par( mfcol=c(3,3), mar=c(2,2,2,0), mgp=c(2,0.5,0), tck=-0.02 )
    for(i in 1:ncol(bering_sea)){
      tmp = bering_sea[,i,drop=FALSE]
      tmp = cbind( tmp, "pred"=ParHat$x_tj[,i] )
      SD = as.list(fit$sdrep,what="Std.")$x_tj[,i]
      tmp = cbind( tmp, "lower"=tmp[,2] - ifelse(is.na(SD),0,SD),
                        "upper"=tmp[,2] + ifelse(is.na(SD),0,SD) )
      #
      plot( x=rownames(bering_sea), y=tmp[,1], ylim=range(tmp,na.rm=TRUE),
            type="p", main=colnames(bering_sea)[i], pch=20, cex=2 )
      lines( x=rownames(bering_sea), y=tmp[,2], type="l", lwd=2,
             col="blue", lty="solid" )
      polygon( x=c(rownames(bering_sea),rev(rownames(bering_sea))),
               y=c(tmp[,3],rev(tmp[,4])), col=rgb(0,0,1,0.2), border=NA )
    }
    par(oldpar)

    #
    library(phylopath)
    library(ggplot2)
    library(ggpubr)
    library(reshape)
    library(gridExtra)
    longform = melt( bering_sea )
      longform$year = rep( 1963:2023, ncol(bering_sea) )
    p0 = ggplot( data=longform, aes(x=year, y=value) ) +
      facet_grid( rows=vars(variable), scales="free" ) +
      geom_point( )

    p1 = plot( (as_fitted_DAG(fit)), edge.width=1, type="width",
               text_size=4, show.legend=FALSE,
               arrow = grid::arrow(type='closed', 18, grid::unit(10,'points')) ) +
         scale_x_continuous(expand = c(0.4, 0.1))
    p1$layers[[1]]$mapping$edge_width = 1
    p2 = plot( (as_fitted_DAG(fit, what="p_value")), edge.width=1, type="width",
               text_size=4, show.legend=FALSE, colors=c('black', 'black'),
               arrow = grid::arrow(type='closed', 18, grid::unit(10,'points')) ) +
         scale_x_continuous(expand = c(0.4, 0.1))
    p2$layers[[1]]$mapping$edge_width = 0.5

    #grid.arrange( arrangeGrob( p0+ggtitle("timeseries"),
    #              arrangeGrob( p1+ggtitle("Estimated path diagram"),
    #                           p2+ggtitle("Estimated p-values"), nrow=2), ncol=2 ) )
    ggarrange(p1, p2, labels = c("Simultaneous effects", "Two-sided p-value"),
                        ncol = 1, nrow = 2)

These results are further discussed in the paper describing dsem.

## Site-replicated trophic cascade

Finally, we replicate an analysis involving a trophic cascade involving sea stars predators, sea urchin consumers, and kelp producers.

    data(sea_otter)
    Z = ts( sea_otter[,-1] )

    # Specify model
    sem = "
      Pycno_CANNERY_DC -> log_Urchins_CANNERY_DC, 0, x2
      log_Urchins_CANNERY_DC -> log_Kelp_CANNERY_DC, 0, x3
      log_Otter_Count_CANNERY_DC -> log_Kelp_CANNERY_DC, 0, x4

      Pycno_CANNERY_UC -> log_Urchins_CANNERY_UC, 0, x2
      log_Urchins_CANNERY_UC -> log_Kelp_CANNERY_UC, 0, x3
      log_Otter_Count_CANNERY_UC -> log_Kelp_CANNERY_UC, 0, x4

      Pycno_HOPKINS_DC -> log_Urchins_HOPKINS_DC, 0, x2
      log_Urchins_HOPKINS_DC -> log_Kelp_HOPKINS_DC, 0, x3
      log_Otter_Count_HOPKINS_DC -> log_Kelp_HOPKINS_DC, 0, x4

      Pycno_HOPKINS_UC -> log_Urchins_HOPKINS_UC, 0, x2
      log_Urchins_HOPKINS_UC -> log_Kelp_HOPKINS_UC, 0, x3
      log_Otter_Count_HOPKINS_UC -> log_Kelp_HOPKINS_UC, 0, x4

      Pycno_LOVERS_DC -> log_Urchins_LOVERS_DC, 0, x2
      log_Urchins_LOVERS_DC -> log_Kelp_LOVERS_DC, 0, x3
      log_Otter_Count_LOVERS_DC -> log_Kelp_LOVERS_DC, 0, x4

      Pycno_LOVERS_UC -> log_Urchins_LOVERS_UC, 0, x2
      log_Urchins_LOVERS_UC -> log_Kelp_LOVERS_UC, 0, x3
      log_Otter_Count_LOVERS_UC -> log_Kelp_LOVERS_UC, 0, x4

      Pycno_MACABEE_DC -> log_Urchins_MACABEE_DC, 0, x2
      log_Urchins_MACABEE_DC -> log_Kelp_MACABEE_DC, 0, x3
      log_Otter_Count_MACABEE_DC -> log_Kelp_MACABEE_DC, 0, x4

      Pycno_MACABEE_UC -> log_Urchins_MACABEE_UC, 0, x2
      log_Urchins_MACABEE_UC -> log_Kelp_MACABEE_UC, 0, x3
      log_Otter_Count_MACABEE_UC -> log_Kelp_MACABEE_UC, 0, x4

      Pycno_OTTER_PT_DC -> log_Urchins_OTTER_PT_DC, 0, x2
      log_Urchins_OTTER_PT_DC -> log_Kelp_OTTER_PT_DC, 0, x3
      log_Otter_Count_OTTER_PT_DC -> log_Kelp_OTTER_PT_DC, 0, x4

      Pycno_OTTER_PT_UC -> log_Urchins_OTTER_PT_UC, 0, x2
      log_Urchins_OTTER_PT_UC -> log_Kelp_OTTER_PT_UC, 0, x3
      log_Otter_Count_OTTER_PT_UC -> log_Kelp_OTTER_PT_UC, 0, x4

      Pycno_PINOS_CEN -> log_Urchins_PINOS_CEN, 0, x2
      log_Urchins_PINOS_CEN -> log_Kelp_PINOS_CEN, 0, x3
      log_Otter_Count_PINOS_CEN -> log_Kelp_PINOS_CEN, 0, x4

      Pycno_SIREN_CEN -> log_Urchins_SIREN_CEN, 0, x2
      log_Urchins_SIREN_CEN -> log_Kelp_SIREN_CEN, 0, x3
      log_Otter_Count_SIREN_CEN -> log_Kelp_SIREN_CEN, 0, x4

      # AR1
      Pycno_CANNERY_DC -> Pycno_CANNERY_DC, 1, ar1
      log_Urchins_CANNERY_DC -> log_Urchins_CANNERY_DC, 1, ar2
      log_Otter_Count_CANNERY_DC -> log_Otter_Count_CANNERY_DC, 1, ar3
      log_Kelp_CANNERY_DC -> log_Kelp_CANNERY_DC, 1, ar4

      Pycno_CANNERY_UC -> Pycno_CANNERY_UC, 1, ar1
      log_Urchins_CANNERY_UC -> log_Urchins_CANNERY_UC, 1, ar2
      log_Otter_Count_CANNERY_UC -> log_Otter_Count_CANNERY_UC, 1, ar3
      log_Kelp_CANNERY_UC -> log_Kelp_CANNERY_UC, 1, ar4

      Pycno_HOPKINS_DC -> Pycno_HOPKINS_DC, 1, ar1
      log_Urchins_HOPKINS_DC -> log_Urchins_HOPKINS_DC, 1, ar2
      log_Otter_Count_HOPKINS_DC -> log_Otter_Count_HOPKINS_DC, 1, ar3
      log_Kelp_HOPKINS_DC -> log_Kelp_HOPKINS_DC, 1, ar4

      Pycno_HOPKINS_UC -> Pycno_HOPKINS_UC, 1, ar1
      log_Urchins_HOPKINS_UC -> log_Urchins_HOPKINS_UC, 1, ar2
      log_Otter_Count_HOPKINS_UC -> log_Otter_Count_HOPKINS_UC, 1, ar3
      log_Kelp_HOPKINS_UC -> log_Kelp_HOPKINS_UC, 1, ar4

      Pycno_LOVERS_DC -> Pycno_LOVERS_DC, 1, ar1
      log_Urchins_LOVERS_DC -> log_Urchins_LOVERS_DC, 1, ar2
      log_Otter_Count_LOVERS_DC -> log_Otter_Count_LOVERS_DC, 1, ar3
      log_Kelp_LOVERS_DC -> log_Kelp_LOVERS_DC, 1, ar4

      Pycno_LOVERS_UC -> Pycno_LOVERS_UC, 1, ar1
      log_Urchins_LOVERS_UC -> log_Urchins_LOVERS_UC, 1, ar2
      log_Otter_Count_LOVERS_UC -> log_Otter_Count_LOVERS_UC, 1, ar3
      log_Kelp_LOVERS_UC -> log_Kelp_LOVERS_UC, 1, ar4

      Pycno_MACABEE_DC -> Pycno_MACABEE_DC, 1, ar1
      log_Urchins_MACABEE_DC -> log_Urchins_MACABEE_DC, 1, ar2
      log_Otter_Count_MACABEE_DC -> log_Otter_Count_MACABEE_DC, 1, ar3
      log_Kelp_MACABEE_DC -> log_Kelp_MACABEE_DC, 1, ar4

      Pycno_MACABEE_UC -> Pycno_MACABEE_UC, 1, ar1
      log_Urchins_MACABEE_UC -> log_Urchins_MACABEE_UC, 1, ar2
      log_Otter_Count_MACABEE_UC -> log_Otter_Count_MACABEE_UC, 1, ar3
      log_Kelp_MACABEE_UC -> log_Kelp_MACABEE_UC, 1, ar4

      Pycno_OTTER_PT_DC -> Pycno_OTTER_PT_DC, 1, ar1
      log_Urchins_OTTER_PT_DC -> log_Urchins_OTTER_PT_DC, 1, ar2
      log_Otter_Count_OTTER_PT_DC -> log_Otter_Count_OTTER_PT_DC, 1, ar3
      log_Kelp_OTTER_PT_DC -> log_Kelp_OTTER_PT_DC, 1, ar4

      Pycno_OTTER_PT_UC -> Pycno_OTTER_PT_UC, 1, ar1
      log_Urchins_OTTER_PT_UC -> log_Urchins_OTTER_PT_UC, 1, ar2
      log_Otter_Count_OTTER_PT_UC -> log_Otter_Count_OTTER_PT_UC, 1, ar3
      log_Kelp_OTTER_PT_UC -> log_Kelp_OTTER_PT_UC, 1, ar4

      Pycno_PINOS_CEN -> Pycno_PINOS_CEN, 1, ar1
      log_Urchins_PINOS_CEN -> log_Urchins_PINOS_CEN, 1, ar2
      log_Otter_Count_PINOS_CEN -> log_Otter_Count_PINOS_CEN, 1, ar3
      log_Kelp_PINOS_CEN -> log_Kelp_PINOS_CEN, 1, ar4

      Pycno_SIREN_CEN -> Pycno_SIREN_CEN, 1, ar1
      log_Urchins_SIREN_CEN -> log_Urchins_SIREN_CEN, 1, ar2
      log_Otter_Count_SIREN_CEN -> log_Otter_Count_SIREN_CEN, 1, ar3
      log_Kelp_SIREN_CEN -> log_Kelp_SIREN_CEN, 1, ar4
    "

    # Fit model
    fit = dsem( sem = sem,
                tsdata = Z,
                control = dsem_control(use_REML=FALSE, quiet=TRUE) )
    # summary( fit )

    #
    library(phylopath)
    library(ggplot2)
    library(ggpubr)
    get_part = function(x){
      vars = c("log_Kelp","log_Otter","log_Urchin","Pycno")
      index = sapply( vars, FUN=\(y) grep(y,rownames(x$coef))[1] )
      x$coef = x$coef[index,index]
      dimnames(x$coef) = list( vars, vars )
      return(x)
    }
    p1 = plot( get_part(as_fitted_DAG(fit)), type="width", show.legend=FALSE)
    p1$layers[[1]]$mapping$edge_width = 0.5
    p2 = plot( get_part(as_fitted_DAG(fit, what="p_value" )), type="width",
               show.legend=FALSE, colors=c('black', 'black'))
    p2$layers[[1]]$mapping$edge_width = 0.1

    longform = melt( sea_otter[,-1], as.is=TRUE )
    longform$X1 = 1999:2019[longform$X1]
    longform$Site = gsub( "log_Kelp_", "",
                    gsub( "log_Urchins_", "",
                    gsub( "Pycno_", "",
                    gsub( "log_Otter_Count_", "", longform$X2))))
    longform$Species = sapply( seq_len(nrow(longform)), FUN=\(i)gsub(longform$Site[i],"",longform$X2[i]) )
    p3 = ggplot( data=longform, aes(x=X1, y=value, col=Species) ) +
      facet_grid( rows=vars(Site), scales="free" ) +
      geom_line( )

    ggarrange(p1 + scale_x_continuous(expand = c(0.3, 0)),
                        p2 + scale_x_continuous(expand = c(0.3, 0)),
                        labels = c("Simultaneous effects", "Two-sided p-value"),
                        ncol = 1, nrow = 2)

Again, these results are further discussed in the paper describing dsem.