plotting

"trace" was renamed "trivial"
plotting was updated to match last parsing upgrade.
Getting Started Vignette.

NAMESPACE

@@ -31,32 +31,32 @@ S3method(F_H,SEISd)
 S3method(F_H,SIP)
 S3method(F_H,SIS)
 S3method(F_H,hMoI)
-S3method(F_H,trace)
+S3method(F_H,trivial)
 S3method(F_X,SEIS)
 S3method(F_X,SEISd)
 S3method(F_X,SIP)
 S3method(F_X,SIS)
 S3method(F_X,hMoI)
-S3method(F_X,trace)
+S3method(F_X,trivial)
 S3method(F_ar,nb)
 S3method(F_ar,pois)
 S3method(F_b,SEIS)
 S3method(F_b,SEISd)
 S3method(F_b,SIP)
 S3method(F_b,SIS)
 S3method(F_b,hMoI)
-S3method(F_b,trace)
+S3method(F_b,trivial)
 S3method(F_calK,static)
 S3method(F_eggs,RM)
 S3method(F_eggs,RM_dts)
 S3method(F_eggs,basicM)
 S3method(F_eggs,sei)
 S3method(F_eggs,si)
-S3method(F_eggs,trace)
+S3method(F_eggs,trivial)
 S3method(F_eip,fixedlag_dts)
 S3method(F_eip,static)
 S3method(F_emerge,basicL)
-S3method(F_emerge,trace)
+S3method(F_emerge,trivial)
 S3method(F_f,static)
 S3method(F_f,type2)
 S3method(F_foi,nb)
@@ -66,13 +66,13 @@ S3method(F_fqM,RM_dts)
 S3method(F_fqM,basicM)
 S3method(F_fqM,sei)
 S3method(F_fqM,si)
-S3method(F_fqM,trace)
+S3method(F_fqM,trivial)
 S3method(F_fqZ,RM)
 S3method(F_fqZ,RM_dts)
 S3method(F_fqZ,basicM)
 S3method(F_fqZ,sei)
 S3method(F_fqZ,si)
-S3method(F_fqZ,trace)
+S3method(F_fqZ,trivial)
 S3method(F_g,static)
 S3method(F_mu,static)
 S3method(F_ni,SEIS)
@@ -87,25 +87,25 @@ S3method(F_pr,SEISd)
 S3method(F_pr,SIP)
 S3method(F_pr,SIS)
 S3method(F_pr,hMoI)
-S3method(F_pr,trace)
+S3method(F_pr,trivial)
 S3method(F_pr_by_lm,SEIS)
 S3method(F_pr_by_lm,SEISd)
 S3method(F_pr_by_lm,SIP)
 S3method(F_pr_by_lm,SIS)
 S3method(F_pr_by_lm,hMoI)
-S3method(F_pr_by_lm,trace)
+S3method(F_pr_by_lm,trivial)
 S3method(F_pr_by_pcr,SEIS)
 S3method(F_pr_by_pcr,SEISd)
 S3method(F_pr_by_pcr,SIP)
 S3method(F_pr_by_pcr,SIS)
 S3method(F_pr_by_pcr,hMoI)
-S3method(F_pr_by_pcr,trace)
+S3method(F_pr_by_pcr,trivial)
 S3method(F_pr_by_rdt,SEIS)
 S3method(F_pr_by_rdt,SEISd)
 S3method(F_pr_by_rdt,SIP)
 S3method(F_pr_by_rdt,SIS)
 S3method(F_pr_by_rdt,hMoI)
-S3method(F_pr_by_rdt,trace)
+S3method(F_pr_by_rdt,trivial)
 S3method(F_q,dynamic)
 S3method(F_q,static)
 S3method(F_sigma,BQS)
@@ -124,7 +124,7 @@ S3method(IRS_EffectSizes,null)
 S3method(IRS_Effects,null)
 S3method(LBionomics,basicL)
 S3method(LBionomics,static)
-S3method(LBionomics,trace)
+S3method(LBionomics,trivial)
 S3method(LSM_EffectSizes,null)
 S3method(LSM_Effects,null)
 S3method(MBionomics,RM_func)
@@ -154,18 +154,18 @@ S3method(Transmission,setup)
 S3method(Transmission,static)
 S3method(TreatHabitats,null)
 S3method(Update_Lt,basicL)
-S3method(Update_Lt,trace)
+S3method(Update_Lt,trivial)
 S3method(Update_MYZt,RM)
 S3method(Update_MYZt,RM_dts)
 S3method(Update_MYZt,basicM)
 S3method(Update_MYZt,sei)
 S3method(Update_MYZt,si)
-S3method(Update_MYZt,trace)
+S3method(Update_MYZt,trivial)
 S3method(Update_Xt,SEIS)
 S3method(Update_Xt,SEISd)
 S3method(Update_Xt,SIP)
 S3method(Update_Xt,SIS)
-S3method(Update_Xt,trace)
+S3method(Update_Xt,trivial)
 S3method(UseBedNet,no_nets)
 S3method(VectorControl,control)
 S3method(VectorControl,no_control)
@@ -183,18 +183,18 @@ S3method(compute_Omega,dts)
 S3method(compute_Omega,xde)
 S3method(dHdt,zero)
 S3method(dLdt,basicL)
-S3method(dLdt,trace)
+S3method(dLdt,trivial)
 S3method(dMYZdt,RM)
 S3method(dMYZdt,basicM)
 S3method(dMYZdt,sei)
 S3method(dMYZdt,si)
-S3method(dMYZdt,trace)
+S3method(dMYZdt,trivial)
 S3method(dXdt,SEIS)
 S3method(dXdt,SEISd)
 S3method(dXdt,SIP)
 S3method(dXdt,SIS)
 S3method(dXdt,hMoI)
-S3method(dXdt,trace)
+S3method(dXdt,trivial)
 S3method(d_F_eip_dt,static)
 S3method(dts_steady_state_X,SEIS)
 S3method(dts_steady_state_X,SIP)
@@ -211,35 +211,35 @@ S3method(get_MYZinits,RM_dts)
 S3method(get_MYZinits,basicM)
 S3method(get_MYZinits,sei)
 S3method(get_MYZinits,si)
-S3method(get_MYZinits,trace)
+S3method(get_MYZinits,trivial)
 S3method(get_Xinits,SEIS)
 S3method(get_Xinits,SEISd)
 S3method(get_Xinits,SIP)
 S3method(get_Xinits,SIS)
 S3method(get_Xinits,hMoI)
-S3method(get_Xinits,trace)
+S3method(get_Xinits,trivial)
 S3method(get_f,RM)
 S3method(get_f,basicM)
 S3method(get_f,sei)
 S3method(get_f,si)
-S3method(get_f,trace)
+S3method(get_f,trivial)
 S3method(get_g,RM)
 S3method(get_g,basicM)
 S3method(get_g,sei)
 S3method(get_g,si)
-S3method(get_g,trace)
+S3method(get_g,trivial)
 S3method(get_q,RM)
 S3method(get_q,basicM)
 S3method(get_q,sei)
 S3method(get_q,si)
-S3method(get_q,trace)
+S3method(get_q,trivial)
 S3method(get_sigma,RM)
 S3method(get_sigma,basicM)
 S3method(get_sigma,sei)
 S3method(get_sigma,si)
-S3method(get_sigma,trace)
+S3method(get_sigma,trivial)
 S3method(list_Lvars,basicL)
-S3method(list_Lvars,trace)
+S3method(list_Lvars,trivial)
 S3method(list_MYZvars,RM)
 S3method(list_MYZvars,RM_dts)
 S3method(list_MYZvars,basicM)
@@ -250,20 +250,20 @@ S3method(list_Xvars,SEISd)
 S3method(list_Xvars,SIP)
 S3method(list_Xvars,SIS)
 S3method(make_Linits,basicL)
-S3method(make_Linits,trace)
+S3method(make_Linits,trivial)
 S3method(make_Lpar,basicL)
-S3method(make_Lpar,trace)
+S3method(make_Lpar,trivial)
 S3method(make_MYZinits,RM)
 S3method(make_MYZinits,RM_dts)
 S3method(make_MYZinits,basicM)
 S3method(make_MYZinits,sei)
 S3method(make_MYZinits,si)
-S3method(make_MYZinits,trace)
+S3method(make_MYZinits,trivial)
 S3method(make_MYZpar,RM)
 S3method(make_MYZpar,basicM)
 S3method(make_MYZpar,sei)
 S3method(make_MYZpar,si)
-S3method(make_MYZpar,trace)
+S3method(make_MYZpar,trivial)
 S3method(make_Omega,dts)
 S3method(make_Omega,xde)
 S3method(make_TimeSpent,as_matrix)
@@ -274,47 +274,47 @@ S3method(make_X_indices,SEISd)
 S3method(make_X_indices,SIP)
 S3method(make_X_indices,SIS)
 S3method(make_X_indices,hMoI)
-S3method(make_X_indices,trace)
+S3method(make_X_indices,trivial)
 S3method(make_Xinits,SEIS)
 S3method(make_Xinits,SEISd)
 S3method(make_Xinits,SIP)
 S3method(make_Xinits,SIS)
 S3method(make_Xinits,hMoI)
-S3method(make_Xinits,trace)
+S3method(make_Xinits,trivial)
 S3method(make_Xpar,SEIS)
 S3method(make_Xpar,SEISd)
 S3method(make_Xpar,SIP)
 S3method(make_Xpar,SIS)
 S3method(make_Xpar,hMoI)
-S3method(make_Xpar,trace)
+S3method(make_Xpar,trivial)
 S3method(make_calK,as_matrix)
 S3method(make_calK,herethere)
 S3method(make_calK,xy)
 S3method(make_indices_L,basicL)
-S3method(make_indices_L,trace)
+S3method(make_indices_L,trivial)
 S3method(make_indices_MYZ,RM)
 S3method(make_indices_MYZ,RM_dts)
 S3method(make_indices_MYZ,basicM)
 S3method(make_indices_MYZ,sei)
 S3method(make_indices_MYZ,si)
-S3method(make_indices_MYZ,trace)
+S3method(make_indices_MYZ,trivial)
 S3method(make_runtime,dts)
 S3method(make_runtime,xde)
 S3method(parse_Lorbits,basicL)
-S3method(parse_Lorbits,trace)
+S3method(parse_Lorbits,trivial)
 S3method(parse_MYZorbits,RM)
 S3method(parse_MYZorbits,RM_dts)
 S3method(parse_MYZorbits,basicM)
 S3method(parse_MYZorbits,sei)
 S3method(parse_MYZorbits,si)
-S3method(parse_MYZorbits,trace)
+S3method(parse_MYZorbits,trivial)
 S3method(parse_Xorbits,SEIS)
 S3method(parse_Xorbits,SEISd)
 S3method(parse_Xorbits,SIP)
 S3method(parse_Xorbits,SIS)
 S3method(parse_Xorbits,hMoI)
-S3method(parse_Xorbits,trace)
-S3method(put_Lvars,trace)
+S3method(parse_Xorbits,trivial)
+S3method(put_Lvars,trivial)
 S3method(put_MYZvars,RM_dts)
 S3method(put_MYZvars,sei)
 S3method(put_MYZvars,si)
@@ -336,13 +336,13 @@ S3method(trigger_setup,dynamic)
 S3method(trigger_setup,setup)
 S3method(trigger_setup,static)
 S3method(update_Linits,basicL)
-S3method(update_Linits,trace)
+S3method(update_Linits,trivial)
 S3method(update_MYZinits,RM)
 S3method(update_MYZinits,RM_dts)
 S3method(update_MYZinits,basicM)
 S3method(update_MYZinits,sei)
 S3method(update_MYZinits,si)
-S3method(update_MYZinits,trace)
+S3method(update_MYZinits,trivial)
 S3method(update_MYZpar_RM,modified)
 S3method(update_MYZpar_RM,unmodified)
 S3method(update_Omega,dts)
@@ -352,7 +352,7 @@ S3method(update_Xinits,SEISd)
 S3method(update_Xinits,SIP)
 S3method(update_Xinits,SIS)
 S3method(update_Xinits,hMoI)
-S3method(update_Xinits,trace)
+S3method(update_Xinits,trivial)
 S3method(xde_derivatives,aquatic)
 S3method(xde_derivatives,cohort)
 S3method(xde_derivatives,full)
@@ -363,18 +363,18 @@ S3method(xde_solve,ode)
 S3method(xde_steady,dde)
 S3method(xde_steady,ode)
 S3method(xde_steady_state_L,basicL)
-S3method(xde_steady_state_L,trace)
+S3method(xde_steady_state_L,trivial)
 S3method(xde_steady_state_M,basicM)
 S3method(xde_steady_state_MYZ,RM)
 S3method(xde_steady_state_MYZ,sei)
 S3method(xde_steady_state_MYZ,si)
-S3method(xde_steady_state_MYZ,trace)
+S3method(xde_steady_state_MYZ,trivial)
 S3method(xde_steady_state_X,SEIS)
 S3method(xde_steady_state_X,SEISd)
 S3method(xde_steady_state_X,SIP)
 S3method(xde_steady_state_X,SIS)
 S3method(xde_steady_state_X,hMoI)
-S3method(xde_steady_state_X,trace)
+S3method(xde_steady_state_X,trivial)
 S3method(xds_plot_X,SEIS)
 S3method(xds_plot_X,SEISd)
 S3method(xds_plot_X,SIP)
@@ -486,15 +486,15 @@ export(compute_kappa)
 export(compute_local_frac)
 export(create_Linits_basicL)
 export(create_Lpar_basicL)
-export(create_Lpar_trace)
+export(create_Lpar_trivial)
 export(create_MYZinits_RM)
 export(create_MYZinits_RM_dts)
 export(create_MYZinits_basicM)
 export(create_MYZinits_sei)
 export(create_MYZinits_si)
 export(create_MYZpar_RM_static)
 export(create_MYZpar_RMfunc)
-export(create_MYZpar_trace)
+export(create_MYZpar_trivial)
 export(create_TimeSpent_athome)
 export(create_TimeSpent_xy)
 export(create_Xinits_SEIS)
@@ -507,7 +507,7 @@ export(create_Xpar_SEISd)
 export(create_Xpar_SIP)
 export(create_Xpar_SIS)
 export(create_Xpar_hMoI)
-export(create_Xpar_trace)
+export(create_Xpar_trivial)
 export(create_calK_herethere)
 export(create_calK_xy)
 export(create_habitat_matrix)
@@ -531,6 +531,7 @@ export(dts_update_Xt)
 export(eir2fqZ)
 export(foi2eir)
 export(fqZ2eir)
+export(get_EIR)
 export(get_H)
 export(get_Linits)
 export(get_MYZinits)