diff --git a/NAMESPACE b/NAMESPACE
index d981d8c4..8f136d21 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -228,8 +228,6 @@ S3method(update_inits_X,SIP)
 S3method(update_inits_X,SIS)
 S3method(update_inits_X,hMoI)
 S3method(update_inits_X,trace)
-S3method(xde_lines_X,SIP)
-S3method(xde_lines_X,SIS)
 S3method(xde_plot_X,SIP)
 S3method(xde_plot_X,SIS)
 S3method(xde_solve,aqua)
@@ -474,7 +472,8 @@ export(xDE_diffeqn_mosy)
 export(xde_lines_EIR)
 export(xde_lines_M)
 export(xde_lines_PR)
-export(xde_lines_X)
+export(xde_lines_X_SIP)
+export(xde_lines_X_SIS)
 export(xde_lines_YZ)
 export(xde_lines_YZ_fracs)
 export(xde_lines_aEIR)
diff --git a/R/adult-RM.R b/R/adult-RM.R
index fe657028..8a19ece7 100644
--- a/R/adult-RM.R
+++ b/R/adult-RM.R
@@ -54,7 +54,7 @@ F_eggs.RM <- function(t, y, pars, s) {
 #' @export
 dMYZdt.RM_ode <- function(t, y, pars, s) {
   Lambda = pars$Lambda[[s]]
-  kappa = pars$kappa [[s]]
+  kappa = pars$kappa[[s]]
 
   with(pars$ix$MYZ[[s]],{
     M <- y[M_ix]
@@ -83,7 +83,7 @@ dMYZdt.RM_ode <- function(t, y, pars, s) {
 dMYZdt.RM_dde <- function(t, y, pars, s){
 
   Lambda = pars$Lambda[[s]]
-  kappa = pars$kappa [[s]]
+  kappa = pars$kappa[[s]]
 
   with(pars$ix$MYZ[[s]],{
     M <- y[M_ix]
@@ -110,6 +110,7 @@ dMYZdt.RM_dde <- function(t, y, pars, s){
 
       Omega <- make_Omega(g, sigma, calK, nPatches)
       Omega_eip <- make_Omega(g_eip, sigma_eip, calK, nPatches)
+
       dMdt <- Lambda - (Omega %*% M)
       dPdt <- f*(M - P) - (Omega %*% P)
       dYdt <- f*q*kappa*(M - Y) - (Omega %*% Y)
diff --git a/R/aquatic-trace.R b/R/aquatic-trace.R
index d3899693..3dcd017c 100644
--- a/R/aquatic-trace.R
+++ b/R/aquatic-trace.R
@@ -15,8 +15,7 @@ LBionomics.trace <- function(t, y, pars, s) {
 #' @return a [numeric] vector of length `nHabitats`
 #' @export
 F_alpha.trace <- function(t, y, pars, s) {
-  Lp = pars$Lpar[[s]]
-  with(Lp, Lt(t, Lp))
+  pars$Lpar[[s]]$Lt(t)
 }
 
 #' @title Derivatives for aquatic stage mosquitoes
@@ -60,7 +59,8 @@ make_Lpar_trace = function(nHabitats, Lopts=list(), Lambda=1000, Lt = NULL){
     Lpar = list()
     class(Lpar) <- "trace"
     Lpar$Lambda = checkIt(Lambda, nHabitats)
-    if(is.null(Lt)) Lt = function(t, Lpar){Lpar$Lambda}
+    #if(is.null(Lt)) Lt = function(t, Lpar){Lpar$Lambda}
+    if(is.null(Lt)) Lt = function(t){Lambda}
     Lpar$Lt = Lt
     return(Lpar)
 })}
@@ -93,8 +93,8 @@ make_parameters_L_trace <- function(pars, Lambda, Lt=NULL) {
   stopifnot(is.numeric(Lambda))
   Lpar <- list()
   class(Lpar) <- 'trace'
-  Lpar$Lambda <- Lambda
-  if(is.null(Lt)) Lt = function(t, Lpar){Lpar$Lambda}
+  Lpar$Lambda = checkIt(Lambda, pars$nHabitats)
+  if(is.null(Lt)) Lt = function(t){Lambda}
   Lpar$Lt = Lt
   pars$Lpar[[1]] <- Lpar
   return(pars)
diff --git a/R/compute.R b/R/compute.R
index be01246d..05bf3bd3 100644
--- a/R/compute.R
+++ b/R/compute.R
@@ -19,11 +19,13 @@ compute_terms <- function(varslist, deout, pars, s, i) {
 #' @export
 compute_terms.xde <- function(varslist, deout, pars, s, i) {
   time = deout[,1]
+  eir = c()
+  kappa = c()
   for (ix in 1:length(time)){
-    yt = deout[i,-1]
-    pars = Transmission(time[i], yt, pars)
-    eir = pars$EIR[[1]]
-    kappa = pars$kappa[[1]]
+    yt = deout[ix,-1]
+    pars = Transmission(time[ix], yt, pars)
+    eir = c(eir, pars$EIR[[1]])
+    kappa = c(kappa, pars$kappa[[1]])
   }
   ni = compute_NI(deout, pars, i)
   fqZ = compute_fqZ(deout, pars, s)
@@ -56,10 +58,11 @@ compute_terms.cohort <- function(varslist, deout, pars, s, i) {
 #' @export
 compute_terms.human<- function(varslist, deout, pars, s, i) {
   time = deout[,1]
+  eir = c()
   for (ix in 1:length(time)){
     yt = deout[i,-1]
     pars = Transmission(time[i], yt, pars)
-    eir = pars$EIR[[1]]
+    eir = c(eir, pars$EIR[[1]])
   }
   ni = compute_NI(deout, pars)
   fqZ = compute_fqZ(deout, pars)
diff --git a/R/human-SIP.R b/R/human-SIP.R
index 90887229..2f1b87e2 100644
--- a/R/human-SIP.R
+++ b/R/human-SIP.R
@@ -250,7 +250,7 @@ get_inits_X.SIP <- function(pars, i){with(pars$Xinits[[i]],{
 #'
 #' @inheritParams xde_plot_X
 #' @export
-xde_plot_X.SIP = function(pars, i, clrs=c("darkblue", "darkred", "darkgreen"), llty=1, stable=FALSE, add_axes=TRUE){
+xde_plot_X.SIP = function(pars, i=1, clrs=c("darkblue", "darkred", "darkgreen"), llty=1, stable=FALSE, add_axes=TRUE){
   vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
 
   if(add_axes==TRUE)
@@ -258,16 +258,19 @@ xde_plot_X.SIP = function(pars, i, clrs=c("darkblue", "darkred", "darkgreen"), l
          plot(time, 0*time, type = "n", ylim = c(0, max(H)),
               ylab = "# Infected", xlab = "Time"))
 
-  xde_lines_X(vars$XH[[i]], pars, clrs, llty)
+  xde_lines_X_SIP(vars$XH[[i]], pars, clrs, llty)
 }
 
 
 #' Add lines for the density of infected individuals for the SIP model
 #'
-#' @inheritParams xde_lines_X
+#' @param XH a list with the outputs of parse_deout_X_SIS
+#' @param pars a list that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param clrs a vector of colors
+#' @param llty an integer (or integers) to set the `lty` for plotting
 #'
 #' @export
-xde_lines_X.SIP = function(XH, pars, clrs=c("darkblue", "darkred", "darkgreen"), llty=1){
+xde_lines_X_SIP = function(XH, pars, clrs=c("darkblue", "darkred", "darkgreen"), llty=1){
   with(XH,{
     if(pars$nStrata==1) {
       lines(time, S, col=clrs[1], lty = llty[1])
diff --git a/R/human-SIS.R b/R/human-SIS.R
index e1f32117..9bbd7d15 100644
--- a/R/human-SIS.R
+++ b/R/human-SIS.R
@@ -222,7 +222,7 @@ get_inits_X.SIS <- function(pars, i){
 #'
 #' @inheritParams xde_plot_X
 #' @export
-xde_plot_X.SIS = function(pars, i, clrs=c("darkblue","darkred"), llty=1, stable=FALSE, add_axes=TRUE){
+xde_plot_X.SIS = function(pars, i=1, clrs=c("darkblue","darkred"), llty=1, stable=FALSE, add_axes=TRUE){
   vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
 
   if(add_axes==TRUE)
@@ -230,27 +230,31 @@ xde_plot_X.SIS = function(pars, i, clrs=c("darkblue","darkred"), llty=1, stable=
          plot(time, 0*time, type = "n", ylim = c(0, max(H)),
               ylab = "# Infected", xlab = "Time"))
 
-  xde_lines_X(vars$XH[[i]], pars, clrs, llty)
+  xde_lines_X_SIS(vars$XH[[i]], pars, clrs, llty)
 }
 
 
 #' Add lines for the density of infected individuals for the SIS model
 #'
-#' @inheritParams xde_lines_X
+#' @param XH a list with the outputs of parse_deout_X_SIS
+#' @param pars a list that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param clrs a vector of colors
+#' @param llty an integer (or integers) to set the `lty` for plotting
 #'
 #' @export
-xde_lines_X.SIS = function(XH, pars, clrs=c("darkblue","darkred"), llty=1){
+xde_lines_X_SIS = function(XH, pars, clrs=c("darkblue","darkred"), llty=1){
   with(XH,{
     if(pars$nStrata==1) {
       lines(time, S, col=clrs[1], lty = llty[1])
       lines(time, I, col=clrs[2], lty = llty[1])
     }
     if(pars$nStrata>1){
-      if (length(clrs)==1) clrs=matrix(clrs, 2, pars$nStrata)
+      if (length(clrs)==2) clrs=matrix(clrs, 2, pars$nStrata)
       if (length(llty)==1) llty=rep(llty, pars$nStrata)
+
       for(i in 1:pars$nStrata){
-        lines(time, S[,i], col=clrs[i,1], lty = llty[i])
-        lines(time, I[,i], col=clrs[i,2], lty = llty[i])
+        lines(time, S[,i], col=clrs[1,i], lty = llty[i])
+        lines(time, I[,i], col=clrs[2,i], lty = llty[i])
       }
     }
   })}
diff --git a/R/human-interface.R b/R/human-interface.R
index 741d17e3..e8f64377 100644
--- a/R/human-interface.R
+++ b/R/human-interface.R
@@ -144,19 +144,6 @@ HTC <- function(pars, i) {
 #' @param add_axes a logical: plot axes only if TRUE
 #'
 #' @export
-xde_plot_X = function(pars, i, clrs="black", llty=1, stable=FALSE, add_axes=TRUE){
+xde_plot_X = function(pars, i=1, clrs="black", llty=1, stable=FALSE, add_axes=TRUE){
   UseMethod("xde_plot_X", pars$Xpar[[i]])
 }
-
-#' Add lines for basic outputs of epidemiological models
-#'
-#' @param XH a list with the outputs of `exDE::parse_deout()`
-#' @param pars a list that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
-#' @param clrs a vector of colors
-#' @param llty an integer (or integers) to set the `lty` for plotting
-#'
-#' @export
-xde_lines_X = function(XH, pars, clrs="black", llty=1){
-  UseMethod("xde_lines_X", pars$Xpar)
-}
-
diff --git a/R/plot-MYZ.R b/R/plot-MYZ.R
index 8f73631e..7a2f4a15 100644
--- a/R/plot-MYZ.R
+++ b/R/plot-MYZ.R
@@ -2,20 +2,21 @@
 #' Plot adult mosquito population density
 #'
 #' @param pars a list that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param s the vector species index
 #' @param clrs a vector of colors
 #' @param llty an integer (or integers) to set the `lty` for plotting
 #' @param stable a logical: set to FALSE for `orbits` and TRUE for `stable_orbits`
 #' @param add_axes a logical: plot axes only if TRUE
 #'
 #' @export
-xde_plot_M = function(pars, clrs="darkblue", llty=1, stable=FALSE, add_axes=TRUE){
+xde_plot_M = function(pars, s=1, clrs="darkblue", llty=1, stable=FALSE, add_axes=TRUE){
   vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
 
-  if(add_axes == TRUE) with(vars$MYZ,
+  if(add_axes == TRUE) with(vars$MYZ[[s]],
                             plot(time, 0*time, type = "n", ylim = range(0,max(M)),
                                  ylab = "Mosquito Density", xlab = "Time"))
 
-  xde_lines_M(vars$MYZ, pars, clrs, llty)
+  xde_lines_M(vars$MYZ[[s]], pars, clrs, llty)
 }
 
 #' Add lines for adult mosquito population density
@@ -41,6 +42,7 @@ xde_lines_M = function(MYZ, pars, clrs="darkblue", llty=1){
 #' Plot the density of infected and infective mosquitoes
 #'
 #' @param pars a list that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param s the vector species index
 #' @param Yclrs a vector of colors for infected mosquitoes
 #' @param Zclrs a vector of colors for infective mosquitoes
 #' @param llty an integer (or integers) to set the `lty` for plotting
@@ -48,15 +50,15 @@ xde_lines_M = function(MYZ, pars, clrs="darkblue", llty=1){
 #' @param add_axes to plot axes only if TRUE
 #'
 #' @export
-xde_plot_YZ = function(pars, Yclrs = "purple", Zclrs="darkred", llty=1, stable=FALSE, add_axes=TRUE){
+xde_plot_YZ = function(pars, s=1, Yclrs = "purple", Zclrs="darkred", llty=1, stable=FALSE, add_axes=TRUE){
   vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
 
   if(add_axes == TRUE)
-    with(vars$MYZ,
+    with(vars$MYZ[[s]],
          plot(time, 0*time, type = "n", ylim = range(0,max(Y)),
               ylab = "Mosquito Density", xlab = "Time"))
 
-  xde_lines_YZ(vars$MYZ, pars, Yclrs, Zclrs, llty)
+  xde_lines_YZ(vars$MYZ[[s]], pars, Yclrs, Zclrs, llty)
 }
 
 #' Add lines for the density of infected and infective mosquitoes
@@ -89,6 +91,7 @@ xde_lines_YZ = function(MYZ, pars, Yclrs="purple", Zclrs = "darkred", llty=1){
 #' Plot the fraction of infected and infective mosquitoes
 #'
 #' @param pars a list that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param s the vector species index
 #' @param Yclrs a vector of colors for infected mosquitoes
 #' @param Zclrs a vector of colors for infective mosquitoes
 #' @param llty an integer (or integers) to set the `lty` for plotting
@@ -96,15 +99,15 @@ xde_lines_YZ = function(MYZ, pars, Yclrs="purple", Zclrs = "darkred", llty=1){
 #' @param add_axes a logical to plot axes only if TRUE
 #'
 #' @export
-xde_plot_YZ_fracs = function(pars, Yclrs = "purple", Zclrs = "darkred", llty=1, stable=FALSE, add_axes=TRUE){
+xde_plot_YZ_fracs = function(pars, s=1, Yclrs = "purple", Zclrs = "darkred", llty=1, stable=FALSE, add_axes=TRUE){
   vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
 
   if(add_axes == TRUE)
-    with(vars$MYZ,
+    with(vars$MYZ[[s]],
          plot(time, 0*time, type = "n", ylim = range(0,1),
               ylab = "Fraction Infected", xlab = "Time"))
 
-  xde_lines_YZ_fracs(vars$MYZ, pars, Yclrs, Zclrs, llty)
+  xde_lines_YZ_fracs(vars$MYZ[[s]], pars, Yclrs, Zclrs, llty)
 }
 
 #' Add lines for the fraction of infected and infective mosquitoes
diff --git a/R/setup.R b/R/setup.R
index 3be59982..04160a3b 100644
--- a/R/setup.R
+++ b/R/setup.R
@@ -25,7 +25,7 @@
 #' @param Lopts a list to configure the L model
 #' @return a [list]
 #' @export
-xde_setup = function(modelName,
+xde_setup = function(modelName = "unnamed",
 
                      # Dynamical Components
                      MYZname = "RM",
@@ -117,7 +117,7 @@ xde_setup = function(modelName,
 #' @param kappa values -- net infectivity to force adult infection dynamics
 #' @return a [list]
 #' @export
-xde_setup_mosy = function(modelName,
+xde_setup_mosy = function(modelName = "unnamed",
 
                      # Dynamical Components
                      MYZname = "basicM",
@@ -186,7 +186,7 @@ xde_setup_mosy = function(modelName,
 #' @param LSMname is a character string defining a LSM model
 #' @return a [list]
 #' @export
-xde_setup_aquatic = function(modelName,
+xde_setup_aquatic = function(modelName = "unnamed",
                      nHabitats = 1,
                      nVectors = 1,
                      Lname = "basic",
@@ -235,7 +235,7 @@ xde_setup_aquatic = function(modelName,
 #' @param TaRopts are the options to setup TaR
 #' @return a [list]
 #' @export
-xde_setup_human = function(modelName,
+xde_setup_human = function(modelName = "unnamed",
 
                      # Dynamical Components
                      Xname = "SIS",
@@ -286,8 +286,8 @@ xde_setup_human = function(modelName,
 }
 
 #' @title Set up a model for xde_diffeqn_cohort
-#' @param modelName is a name for the model (arbitrary)
 #' @param F_eir is a function F_eir(t, pars) that returns the daily FoI
+#' @param modelName is a name for the model (arbitrary)
 #' @param Xname is a character string defining a X model
 #' @param HPop is the number of humans in each patch
 #' @param searchB is a vector of search weights for blood feeding
@@ -295,7 +295,8 @@ xde_setup_human = function(modelName,
 #' @param Hopts a list to configure the H model
 #' @return a [list]
 #' @export
-xde_setup_cohort = function(modelName, F_eir,
+xde_setup_cohort = function(F_eir,
+                           modelName = "unnamed",
 
                            # Dynamical Components
                            Xname = "SIS",
diff --git a/R/transmission.R b/R/transmission.R
index 97fd24f9..b87de930 100644
--- a/R/transmission.R
+++ b/R/transmission.R
@@ -90,6 +90,6 @@ F_kappa <- function(t, y, pars, beta, i) {
 #' @export
 compute_beta = function(H, wts_f, TaR){
   W <- as.vector(TaR %*% (wts_f*H))
-  beta <- diag(wts_f, length(H)) %*% t(TaR) %*% diag(1/W, dim(TaR)[1])
+  beta <- diag(wts_f, length(H)) %*% t(TaR) %*% diag(1/W, length(W))
   return(beta)
 }
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 5570b22c..6165812c 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -317,7 +317,6 @@ reference:
   - update_inits_X
   - HTC
   - xde_plot_X
-  - xde_lines_X
 - subtitle: trace
   desc: |
     Specialized methods for a human trace model to pass kappa as a parameter
@@ -377,7 +376,7 @@ reference:
   - make_parameters_X_SIS
   - HTC.SIS
   - xde_plot_X.SIS
-  - xde_lines_X.SIS
+  - xde_lines_X_SIS
 - subtitle: SIP
   desc: |
     Specialized methods for the SIP (Susceptible-Infected-Prophylaxis) model of human dynamics.
@@ -399,7 +398,7 @@ reference:
   - make_parameters_X_SIP
   - HTC.SIP
   - xde_plot_X.SIP
-  - xde_lines_X.SIP
+  - xde_lines_X_SIP
 - title: Human Population Dynamics
   desc: |
     Generic methods for the human demography and aging
diff --git a/man/xde_lines_X.Rd b/man/xde_lines_X.Rd
deleted file mode 100644
index 2f60b1af..00000000
--- a/man/xde_lines_X.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/human-interface.R
-\name{xde_lines_X}
-\alias{xde_lines_X}
-\title{Add lines for basic outputs of epidemiological models}
-\usage{
-xde_lines_X(XH, pars, clrs = "black", llty = 1)
-}
-\arguments{
-\item{XH}{a list with the outputs of \code{exDE::parse_deout()}}
-
-\item{pars}{a list that defines an \code{exDE} model (\emph{e.g.},  generated by \code{xde_setup()})}
-
-\item{clrs}{a vector of colors}
-
-\item{llty}{an integer (or integers) to set the \code{lty} for plotting}
-}
-\description{
-Add lines for basic outputs of epidemiological models
-}
diff --git a/man/xde_lines_X.SIP.Rd b/man/xde_lines_X_SIP.Rd
similarity index 70%
rename from man/xde_lines_X.SIP.Rd
rename to man/xde_lines_X_SIP.Rd
index 71024a3c..b2cd9373 100644
--- a/man/xde_lines_X.SIP.Rd
+++ b/man/xde_lines_X_SIP.Rd
@@ -1,13 +1,18 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/human-SIP.R
-\name{xde_lines_X.SIP}
-\alias{xde_lines_X.SIP}
+\name{xde_lines_X_SIP}
+\alias{xde_lines_X_SIP}
 \title{Add lines for the density of infected individuals for the SIP model}
 \usage{
-\method{xde_lines_X}{SIP}(XH, pars, clrs = c("darkblue", "darkred", "darkgreen"), llty = 1)
+xde_lines_X_SIP(
+  XH,
+  pars,
+  clrs = c("darkblue", "darkred", "darkgreen"),
+  llty = 1
+)
 }
 \arguments{
-\item{XH}{a list with the outputs of \code{exDE::parse_deout()}}
+\item{XH}{a list with the outputs of parse_deout_X_SIS}
 
 \item{pars}{a list that defines an \code{exDE} model (\emph{e.g.},  generated by \code{xde_setup()})}
 
diff --git a/man/xde_lines_X.SIS.Rd b/man/xde_lines_X_SIS.Rd
similarity index 71%
rename from man/xde_lines_X.SIS.Rd
rename to man/xde_lines_X_SIS.Rd
index 32f32094..ab83a7a3 100644
--- a/man/xde_lines_X.SIS.Rd
+++ b/man/xde_lines_X_SIS.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/human-SIS.R
-\name{xde_lines_X.SIS}
-\alias{xde_lines_X.SIS}
+\name{xde_lines_X_SIS}
+\alias{xde_lines_X_SIS}
 \title{Add lines for the density of infected individuals for the SIS model}
 \usage{
-\method{xde_lines_X}{SIS}(XH, pars, clrs = c("darkblue", "darkred"), llty = 1)
+xde_lines_X_SIS(XH, pars, clrs = c("darkblue", "darkred"), llty = 1)
 }
 \arguments{
-\item{XH}{a list with the outputs of \code{exDE::parse_deout()}}
+\item{XH}{a list with the outputs of parse_deout_X_SIS}
 
 \item{pars}{a list that defines an \code{exDE} model (\emph{e.g.},  generated by \code{xde_setup()})}
 
diff --git a/man/xde_plot_M.Rd b/man/xde_plot_M.Rd
index 514417ff..d0c71897 100644
--- a/man/xde_plot_M.Rd
+++ b/man/xde_plot_M.Rd
@@ -4,11 +4,20 @@
 \alias{xde_plot_M}
 \title{Plot adult mosquito population density}
 \usage{
-xde_plot_M(pars, clrs = "darkblue", llty = 1, stable = FALSE, add_axes = TRUE)
+xde_plot_M(
+  pars,
+  s = 1,
+  clrs = "darkblue",
+  llty = 1,
+  stable = FALSE,
+  add_axes = TRUE
+)
 }
 \arguments{
 \item{pars}{a list that defines an \code{exDE} model (\emph{e.g.},  generated by \code{xde_setup()})}
 
+\item{s}{the vector species index}
+
 \item{clrs}{a vector of colors}
 
 \item{llty}{an integer (or integers) to set the \code{lty} for plotting}
diff --git a/man/xde_plot_X.Rd b/man/xde_plot_X.Rd
index 52657aa1..b7c82860 100644
--- a/man/xde_plot_X.Rd
+++ b/man/xde_plot_X.Rd
@@ -4,7 +4,14 @@
 \alias{xde_plot_X}
 \title{Basic plotting for epidemiological models}
 \usage{
-xde_plot_X(pars, i, clrs = "black", llty = 1, stable = FALSE, add_axes = TRUE)
+xde_plot_X(
+  pars,
+  i = 1,
+  clrs = "black",
+  llty = 1,
+  stable = FALSE,
+  add_axes = TRUE
+)
 }
 \arguments{
 \item{pars}{a list that defines an \code{exDE} model (\emph{e.g.},  generated by \code{xde_setup()})}
diff --git a/man/xde_plot_X.SIP.Rd b/man/xde_plot_X.SIP.Rd
index be55b2b0..290b3f98 100644
--- a/man/xde_plot_X.SIP.Rd
+++ b/man/xde_plot_X.SIP.Rd
@@ -6,7 +6,7 @@
 \usage{
 \method{xde_plot_X}{SIP}(
   pars,
-  i,
+  i = 1,
   clrs = c("darkblue", "darkred", "darkgreen"),
   llty = 1,
   stable = FALSE,
diff --git a/man/xde_plot_X.SIS.Rd b/man/xde_plot_X.SIS.Rd
index 7a8a1ff8..4164890b 100644
--- a/man/xde_plot_X.SIS.Rd
+++ b/man/xde_plot_X.SIS.Rd
@@ -6,7 +6,7 @@
 \usage{
 \method{xde_plot_X}{SIS}(
   pars,
-  i,
+  i = 1,
   clrs = c("darkblue", "darkred"),
   llty = 1,
   stable = FALSE,
diff --git a/man/xde_plot_YZ.Rd b/man/xde_plot_YZ.Rd
index 8343ed2d..5afa754d 100644
--- a/man/xde_plot_YZ.Rd
+++ b/man/xde_plot_YZ.Rd
@@ -6,6 +6,7 @@
 \usage{
 xde_plot_YZ(
   pars,
+  s = 1,
   Yclrs = "purple",
   Zclrs = "darkred",
   llty = 1,
@@ -16,6 +17,8 @@ xde_plot_YZ(
 \arguments{
 \item{pars}{a list that defines an \code{exDE} model (\emph{e.g.},  generated by \code{xde_setup()})}
 
+\item{s}{the vector species index}
+
 \item{Yclrs}{a vector of colors for infected mosquitoes}
 
 \item{Zclrs}{a vector of colors for infective mosquitoes}
diff --git a/man/xde_plot_YZ_fracs.Rd b/man/xde_plot_YZ_fracs.Rd
index bb7d9897..0df45ea9 100644
--- a/man/xde_plot_YZ_fracs.Rd
+++ b/man/xde_plot_YZ_fracs.Rd
@@ -6,6 +6,7 @@
 \usage{
 xde_plot_YZ_fracs(
   pars,
+  s = 1,
   Yclrs = "purple",
   Zclrs = "darkred",
   llty = 1,
@@ -16,6 +17,8 @@ xde_plot_YZ_fracs(
 \arguments{
 \item{pars}{a list that defines an \code{exDE} model (\emph{e.g.},  generated by \code{xde_setup()})}
 
+\item{s}{the vector species index}
+
 \item{Yclrs}{a vector of colors for infected mosquitoes}
 
 \item{Zclrs}{a vector of colors for infective mosquitoes}
diff --git a/man/xde_setup.Rd b/man/xde_setup.Rd
index d3df059c..e78bb6a3 100644
--- a/man/xde_setup.Rd
+++ b/man/xde_setup.Rd
@@ -5,7 +5,7 @@
 \title{Set up a model for xde_diffeqn}
 \usage{
 xde_setup(
-  modelName,
+  modelName = "unnamed",
   MYZname = "RM",
   Xname = "SIS",
   Lname = "trace",
diff --git a/man/xde_setup_aquatic.Rd b/man/xde_setup_aquatic.Rd
index ed14fa3f..6f1001c5 100644
--- a/man/xde_setup_aquatic.Rd
+++ b/man/xde_setup_aquatic.Rd
@@ -5,7 +5,7 @@
 \title{Set up a model for xde_diffeqn_aqua}
 \usage{
 xde_setup_aquatic(
-  modelName,
+  modelName = "unnamed",
   nHabitats = 1,
   nVectors = 1,
   Lname = "basic",
diff --git a/man/xde_setup_cohort.Rd b/man/xde_setup_cohort.Rd
index 74274c24..42ff218d 100644
--- a/man/xde_setup_cohort.Rd
+++ b/man/xde_setup_cohort.Rd
@@ -5,8 +5,8 @@
 \title{Set up a model for xde_diffeqn_cohort}
 \usage{
 xde_setup_cohort(
-  modelName,
   F_eir,
+  modelName = "unnamed",
   Xname = "SIS",
   HPop = 1000,
   searchB = 1,
@@ -15,10 +15,10 @@ xde_setup_cohort(
 )
 }
 \arguments{
-\item{modelName}{is a name for the model (arbitrary)}
-
 \item{F_eir}{is a function F_eir(t, pars) that returns the daily FoI}
 
+\item{modelName}{is a name for the model (arbitrary)}
+
 \item{Xname}{is a character string defining a X model}
 
 \item{HPop}{is the number of humans in each patch}
diff --git a/man/xde_setup_human.Rd b/man/xde_setup_human.Rd
index 5261f9a3..e864e830 100644
--- a/man/xde_setup_human.Rd
+++ b/man/xde_setup_human.Rd
@@ -5,7 +5,7 @@
 \title{Set up a model for xde_diffeqn_human}
 \usage{
 xde_setup_human(
-  modelName,
+  modelName = "unnamed",
   Xname = "SIS",
   HPop = 1000,
   MYZopts = list(),
diff --git a/man/xde_setup_mosy.Rd b/man/xde_setup_mosy.Rd
index 5b56c724..24923f3b 100644
--- a/man/xde_setup_mosy.Rd
+++ b/man/xde_setup_mosy.Rd
@@ -5,7 +5,7 @@
 \title{Set up a model for xde_diffeqn_mosy}
 \usage{
 xde_setup_mosy(
-  modelName,
+  modelName = "unnamed",
   MYZname = "basicM",
   Lname = "basic",
   nPatches = 1,
diff --git a/vignettes/human_hmoi.Rmd b/vignettes/human_hmoi.Rmd
index 68263baa..9234e856 100644
--- a/vignettes/human_hmoi.Rmd
+++ b/vignettes/human_hmoi.Rmd
@@ -156,11 +156,11 @@ F_eir1 = fF_eir1(EIR)
 ```
 
 ```{r}
-xde_setup_cohort("test_hMoI", F_eir1, "hMoI", HPop=Hpop, Xopts = Xo) ->test_hMoI
+xde_setup_cohort(F_eir1, Xname="hMoI", HPop=Hpop, Xopts = Xo) ->test_hMoI
 ```
 
 ```{r}
-xde_solve(test_hMoI, 365, 365)$outputs$deout -> out2
+xde_solve(test_hMoI, 365, 365)$outputs$orbits$deout -> out2
 approx_equal(out2, out1)
 ```
 
diff --git a/vignettes/human_sip.Rmd b/vignettes/human_sip.Rmd
index 05680637..76a0a40c 100644
--- a/vignettes/human_sip.Rmd
+++ b/vignettes/human_sip.Rmd
@@ -138,7 +138,7 @@ F_eir1 = fF_eir1(EIR)
 ```
 
 ```{r}
-xde_setup_cohort("test_SIP", F_eir1, "SIP", HPop=Hpop, Xopts = Xo) -> test_SIP
+xde_setup_cohort(F_eir1, Xname="SIP", HPop=Hpop, Xopts = Xo) -> test_SIP
 ```
 
 ```{r}
diff --git a/vignettes/human_sis.Rmd b/vignettes/human_sis.Rmd
index d82bc337..4d2ba877 100644
--- a/vignettes/human_sis.Rmd
+++ b/vignettes/human_sis.Rmd
@@ -154,7 +154,7 @@ F_eir1 = fF_eir1(EIR)
 ```
 
 ```{r}
-xde_setup_cohort("test_SIS", F_eir1, "SIS", HPop=Hpop, Xopts = Xo) -> test_SIS
+xde_setup_cohort(F_eir1, Xname="SIS", HPop=Hpop, Xopts = Xo) -> test_SIS
 ```
 
 ```{r}