diff --git a/DESCRIPTION b/DESCRIPTION
index a6368f98..e3aa12d1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -58,6 +58,6 @@ License: GPL (>=2)
 LazyLoad: yes
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 Remotes: reconverse/incidence2/pkg
+Config/roxygen2/version: 8.0.0
diff --git a/R/EpiEstim-package.R b/R/EpiEstim-package.R
index 695a2efd..999f1ae9 100644
--- a/R/EpiEstim-package.R
+++ b/R/EpiEstim-package.R
@@ -8,10 +8,10 @@
 #' \code{system.file("epiestimpapers.bib", package = "EpiEstim")}.
 #'
 #' @importFrom ggplot2 last_plot ggplot aes geom_step ggtitle
-#'   geom_ribbon geom_line xlab ylab xlim geom_hline ylim geom_histogram
-#'   scale_colour_manual scale_fill_manual scale_linetype_manual lims theme
-#'   margin element_rect theme_light %+replace% element_blank element_line
-#'   element_text scale_y_continuous
+#' @importFrom ggplot2 geom_ribbon geom_line xlab ylab xlim geom_hline ylim geom_histogram
+#' @importFrom ggplot2 scale_colour_manual scale_fill_manual scale_linetype_manual lims theme
+#' @importFrom ggplot2 margin element_rect theme_light %+replace% element_blank element_line
+#' @importFrom ggplot2 element_text scale_y_continuous
 #' 
 #' @importFrom rlang .data
 #' 
diff --git a/R/gibbs_draws.R b/R/gibbs_draws.R
index 9bffd8fd..982929ce 100644
--- a/R/gibbs_draws.R
+++ b/R/gibbs_draws.R
@@ -183,15 +183,6 @@ compute_lambda <- function(incid, si_distr) {
     msg2 <- "Use function 'process_I_multivariant' first"
     stop(msg1, msg2)
   }
-  if (any(si_distr[1,] != 0)){
-    stop("Values in the first row of si_distr must be 0")
-  }
-  if (any(abs(colSums(si_distr) - 1) > 0.01)) { # allow tolerance
-    stop("The sum of each column in si_distr should be equal to 1")
-  }
-  if (any(si_distr < 0)){
-    stop("si_distr must be >=0")
-  }
   lambda <- array(NA, dim = dim(incid$local))
   for(l in seq_len(dim(incid$local)[2])) {
     for(v in seq_len(dim(incid$local)[3])) {
@@ -242,6 +233,11 @@ compute_lambda <- function(incid, si_distr) {
 #'
 #' @param seed a numeric value used to fix the random seed
 #'
+#' @param validate_inputs a boolean value indicating whether to validate the
+#' inputs; default value is FALSE as inputs are validated in
+#' \code{estimate_advantage()}, where this function is called. Can be set to TRUE
+#' if this function is called directly for debugging or testing.
+#'
 #' @return A value or vector of values for epsilon for each non reference
 #'   pathogen/strain/variant, drawn from the marginal posterior distribution
 #'
@@ -263,26 +259,17 @@ compute_lambda <- function(incid, si_distr) {
 #' R <- matrix(1, nrow = T, ncol = n_loc)
 #' R[1, ] <- NA # no estimates of R on first time step
 #' draw_epsilon(R, incid$local, lambda, priors, seed = 1)
-
 draw_epsilon <- function(R, incid, lambda, priors,
                          shape_epsilon = NULL,
                          t_min = 2L, t_max = nrow(incid),
-                         seed = NULL) {
-  if (!is.integer(t_min) || !is.integer(t_max)){
-    stop("t_min and t_max must be integers")
-  }
-  if (t_min < 2 || t_max < 2){
-    stop("t_min and t_max must be >=2")
-  }
-  if(t_min > nrow(incid) || t_max > nrow(incid)){
-    stop("t_min and t_max must be <= nrow(incid)")
+                         seed = NULL, validate_inputs = FALSE) {
+  if (validate_inputs) {
+      eps_args <- as.list(environment())
+      do.call(check_estimate_advantage_inputs, args = eps_args)
   }
   if(any(R[!is.na(R)] < 0)) {
     stop("R must be >= 0")
   }
-  if (!is.null(seed) && !is.numeric(seed)){
-    stop("seed must be numeric")
-  }
   if (!is.null(seed)) set.seed(seed)
   t <- seq(t_min, t_max, 1)
   if (is.null(shape_epsilon)) {
@@ -333,6 +320,8 @@ draw_epsilon <- function(R, incid, lambda, priors,
 #'
 #' @param seed a numeric value used to fix the random seed
 #'
+#' @inheritParams draw_epsilon
+#' 
 #' @return a matrix of the instantaneous reproduction number R for the reference
 #'   pathogen/strain/variant for each time step (row) and each location (column)
 #'   drawn from the marginal posterior distribution
@@ -358,22 +347,15 @@ draw_epsilon <- function(R, incid, lambda, priors,
 draw_R <- function(epsilon, incid, lambda, priors,
                    shape_R_flat = NULL,
                    t_min = NULL, t_max = nrow(incid),
-                   seed = NULL) {
-  if (!is.integer(t_min) || !is.integer(t_max)){
-    stop("t_min and t_max must be integers")
-  }
-  if (t_min < 2 || t_max < 2){
-    stop("t_min and t_max must be >=2")
-  }
-  if(t_min > nrow(incid) || t_max > nrow(incid)){
-    stop("t_min and t_max must be <= nrow(incid)")
+                   seed = NULL, validate_inputs = FALSE) {
+  if (validate_inputs) {
+    R_args <- as.list(environment())
+    do.call(check_estimate_advantage_inputs, args = R_args)
   }
+
   if (any(epsilon < 0)){
     stop("epsilon must be > 0")
   }
-  if (!is.null(seed) && !is.numeric(seed)){
-    stop("seed must be numeric")
-  }
   if (!is.null(seed)) set.seed(seed)
   t <- seq(t_min, t_max, 1)
   if (is.null(shape_R_flat)) {
@@ -412,10 +394,7 @@ draw_R <- function(epsilon, incid, lambda, priors,
 #' @export
 
 compute_si_cutoff <- function(si_distr, miss_at_most = 0.05) {
-  if (any(colSums(si_distr) != 1)) {
-    warning("Input SI distributions should sum to 1. Normalising now")
-    si_distr <- si_distr / colSums(si_distr)
-  }
+
   cutoff <- 1 - miss_at_most
   cdf <- apply(si_distr, 2, cumsum)
   idx <- apply(
@@ -529,6 +508,10 @@ compute_t_min <- function(incid, si_distr, miss_at_most) {
 #'   is temporarily assigned to `[, , 1]` of the incidence array. We recommend the
 #'   default value of `TRUE` as we find this to stabilise inference.
 #'
+#' @param validate_inputs a boolean (defaulting to `TRUE`) indicating whether to
+#' validate the inputs before running the estimation. We recommned that this
+#' is set to `TRUE` as it will ensure any mistmatches in inputs are caught early.
+#'
 #' @return A list with the following elements:
 #' - `epsilon`: a matrix containing the MCMC chain (thinned and after burnin)
 #'   for the relative transmissibility of the "new" pathogen/strain/variant(s)
@@ -580,61 +563,32 @@ compute_t_min <- function(incid, si_distr, miss_at_most) {
 #' abline(h = 1, col = "red")
 #' plot(x$R[30, 3, ], type = "l",
 #'      xlab = "Iteration", ylab = "R time 30 location 3")
-
 estimate_advantage <- function(incid, si_distr, priors = default_priors(),
                            mcmc_control = default_mcmc_controls(),
                            t_min = NULL, t_max = nrow(incid),
                            seed = NULL,
                            incid_imported = NULL,
                            precompute = TRUE,
-                           reorder_incid = TRUE) {
+                           reorder_incid = TRUE,
+                           validate_inputs = TRUE) {
 
+  if (any(colSums(si_distr) != 1)) {
+    warning(
+      "Input SI distributions should sum to 1. Normalising now", call. = FALSE
+    )
+    si_distr <- normalise_si_distr(si_distr)
+  }
+  
   if (is.null(t_min)) {
     t_min <- compute_t_min(incid, si_distr)
   }
-  if (!is.integer(t_min) || !is.integer(t_max)) {
-    stop("t_min and t_max must be integers")
-  }
-  if (t_min < 2 || t_max < 2){
-    stop("t_min and t_max must be >=2")
-  }
-  if(t_min > nrow(incid) || t_max > nrow(incid)){
-    stop("t_min and t_max must be <= nrow(incid)")
-  }
-  if (any(si_distr[1,] != 0)){
-    stop("Values in the first row of si_distr must be 0")
-  }
-  if (any(abs(colSums(si_distr) - 1) > 0.01)) { # allow tolerance
-    stop("The sum of each column in si_distr should be equal to 1")
-  }
-  if (any(si_distr < 0)){
-    stop("si_distr must be >=0")
-  }
-  if (mcmc_control$n_iter < 0 || !is.integer(mcmc_control$n_iter)){
-    stop("n_iter in mcmc_control must be a positive integer")
-  }
-  if (mcmc_control$burnin < 0 || !is.integer(mcmc_control$burnin)){
-    stop("burnin in mcmc_control must be a positive integer")
-  }
-  if (mcmc_control$thin < 0 || !is.integer(mcmc_control$thin)){
-    stop("thin in mcmc_control must be a positive integer")
-  }
-  if (mcmc_control$n_iter < mcmc_control$burnin + mcmc_control$thin){
-    stop("In mcmc_control, n_iter must be greater than burnin + thin")
-  }
-  if (!is.null(seed) && !is.numeric(seed)){
-    stop("seed must be numeric")
-  }
-  if (!is.null(seed)) set.seed(seed)
 
-  if (t_min > t_max) {
-    stop("t_min is greater than t_max. You can specify a smaller t_min or increase t_max.")
+  estimate_advantage_args <- as.list(environment())
+  estimate_advantage_args$si_distr <- si_distr # normalized value
+  if (validate_inputs) {
+     do.call(check_estimate_advantage_inputs, args = estimate_advantage_args)
   }
   
-  if (!identical(priors, default_priors())) {
-    warning("Priors where the mean of epsilon is different from 1 are not currently supported.")
-  }
-
   T <- nrow(incid)
   n_loc <- ncol(incid)
 
@@ -820,6 +774,8 @@ process_I_multivariant <- function(incid, incid_imported = NULL) {
   res
 }
 
+
+
 ## TODO: check dimensions of objects is correct everywhere
 ## TODO: fix number of variants to be 2
 
diff --git a/R/utilities.R b/R/utilities.R
index 72154d4d..84c2ecec 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -518,3 +518,9 @@ si_from_data_valid_distrs <- function(dist) {
   list(is_dist_valid = dist %in% valid_names, all_valid_distrs = valid_names)
 }
 
+#' Normalise a serial interval distribution
+#' @keywords internal
+#' @noRd
+normalise_si_distr <- function(si_distr) {
+  sweep(si_distr, 2, colSums(si_distr), "/")
+}
diff --git a/R/validate_mv_epiestim_inputs.R b/R/validate_mv_epiestim_inputs.R
new file mode 100644
index 00000000..446a8695
--- /dev/null
+++ b/R/validate_mv_epiestim_inputs.R
@@ -0,0 +1,154 @@
+#' Check incidence input for MV-EpiEstim
+#'
+#' Check that incid is a 3-dimensional array with non-negatuve enteries.
+#' 
+#' @inheritParams estimate_advantage
+#' @returns Silently returns TRUE if the checks are passed, otherwise throws an
+#' error.
+#' @author Sangeeta Bhatia
+#' @keywords internal
+check_incidence <- function(incid) {
+  if (any(incid < 0)) {
+    stop("incid must be >=0")
+  }
+  if (!is.array(incid) || length(dim(incid)) != 3) {
+    stop(
+      "incid must be a 3-dimensional array with dimensions time, location, variant",
+      .call = FALSE
+    )
+  }
+  invisible(TRUE)
+}
+
+
+#' Check priors  for MV-EpiEstim
+#'
+#' Check that priors is a list of the correct format and that the mean of the
+#' prior for epsilon is 1 (as currently only priors with mean of epsilon equal
+#' to 1 is supported).
+#' 
+#' @inheritParams estimate_advantage
+#' @returns Silently returns TRUE if the checks are passed, otherwise throws an
+#' error.
+#' @author Sangeeta Bhatia
+#' @keywords internal
+check_priors <- function(priors) {
+  
+  if (!identical(priors, default_priors())) {
+    warning(
+      "Priors where the mean of epsilon is different from 1 are not currently supported.",
+      .call = FALSE
+    )
+  }
+  invisible(TRUE)
+}
+
+#' Check MCMC control parameters for MV-EpiEstim
+#'
+#' Check that (1) mcmc_control is a list of the correct format, (2) n_iter, burnin
+#' and thin are positive integers and (3) n_iter is greater than burnin + thin.
+#' 
+#' @inheritParams estimate_advantage
+#' @returns Silently returns TRUE if the checks are passed, otherwise throws an
+#' error.
+#' @author Sangeeta Bhatia
+#' @keywords internal
+check_mcmc_control <- function(mcmc_control) {
+
+  if (mcmc_control$n_iter < 0 || !is.integer(mcmc_control$n_iter)) {
+    stop("n_iter in mcmc_control must be a positive integer", .call = FALSE)
+  }
+  if (mcmc_control$burnin < 0 || !is.integer(mcmc_control$burnin)) {
+    stop("burnin in mcmc_control must be a positive integer", .call = FALSE)
+  }
+  if (mcmc_control$thin < 0 || !is.integer(mcmc_control$thin)) {
+    stop("thin in mcmc_control must be a positive integer", .call = FALSE)
+  }
+  if (mcmc_control$n_iter < mcmc_control$burnin + mcmc_control$thin) {
+    stop("In mcmc_control, n_iter must be greater than burnin + thin", .call = FALSE)
+  }
+  invisible(TRUE)
+}
+
+#' Validate t_min and t_max inputs for MV-EpiEstim
+#'
+#' Check that (1) t_min and t_max are integers, (2) that they are >= 2, that 
+#' they are <= nrow(incid) and (3) t_min is not greater than t_max.
+#' 
+#' @inheritParams estimate_advantage
+#' @returns Silently returns TRUE if the checks are passed, otherwise throws an
+#' error.
+#' @author Sangeeta Bhatia
+#' @keywords internal
+check_t_min_t_max <- function(t_min, t_max, incid) {
+    if (!is.integer(t_min) || !is.integer(t_max)) {
+      stop("t_min and t_max must be integers", .call = FALSE)
+    }
+    if (t_min < 2 || t_max < 2) {
+      stop("t_min and t_max must be >=2", .call = FALSE)
+    }
+    if (t_min > nrow(incid) || t_max > nrow(incid)) {
+      stop("t_min and t_max must be <= nrow(incid)", .call = FALSE)
+    }
+    if (t_min > t_max) {
+      stop(
+        "t_min is greater than t_max. You can specify a smaller t_min or increase t_max.",
+        .call = FALSE
+      )
+    }
+    invisible(TRUE)
+}
+
+
+#' Validate seed input for MV-EpiEstim
+#'
+#' Validate that the seed is not null and is numeric
+#' 
+#' @inheritParams estimate_advantage
+#' @return Silently returns TRUE if the checks are passed, otherwise throws an error.
+#' @author Sangeeta Bhatia
+#' @keywords internal
+check_seed <- function(seed) {
+  if (!is.null(seed) && !is.numeric(seed)) {
+    stop("supplied seed is not a valid integer", .call = FALSE)
+  }
+  if (!is.null(seed)) set.seed(seed)
+  invisible(TRUE)
+}
+
+
+#' Validate inputs to estimate_advantage
+#'
+#' Runs all available input checks for \code{\link{estimate_advantage}} based on
+#' the supplied arguments. Each check is called only if the corresponding
+#' argument is present.
+#'
+#' @param ... Named arguments passed to \code{\link{estimate_advantage}}.
+#' @returns Invisibly returns \code{NULL}; throws an error if any input check
+#' fails.
+#' @author Sangeeta Bhatia
+#' @keywords internal
+check_estimate_advantage_inputs <- function(...) {
+  estimate_advantage_args <- list(...)
+  arg_names <- names(estimate_advantage_args)
+  if ("incid" %in% arg_names) 
+    check_incidence(estimate_advantage_args$incid)
+
+  if ("si" %in% arg_names)
+    apply(estimate_advantage_args$si_distr, 2, check_si_distr)
+
+  if ("priors" %in% arg_names)
+    check_priors(estimate_advantage_args$priors)
+  
+  if ("mcmc_control" %in% arg_names)
+    check_mcmc_control(estimate_advantage_args$mcmc_control)
+  
+  if (all(c("t_min", "t_max", "incid") %in% arg_names)) {
+    check_t_min_t_max(
+      estimate_advantage_args$t_min, estimate_advantage_args$t_max,
+      estimate_advantage_args$incid
+    )
+  }
+  if ("seed" %in% arg_names)
+    check_seed(estimate_advantage_args$seed)
+}
diff --git a/man/EpiEstim-package.Rd b/man/EpiEstim-package.Rd
index a5efc74c..b7b766bf 100644
--- a/man/EpiEstim-package.Rd
+++ b/man/EpiEstim-package.Rd
@@ -26,6 +26,11 @@ Useful links:
 \author{
 \strong{Maintainer}: Anne Cori \email{a.cori@imperial.ac.uk} (\href{https://orcid.org/0000-0002-8443-9162}{ORCID})
 
+Authors:
+\itemize{
+  \item Anne Cori \email{a.cori@imperial.ac.uk} (\href{https://orcid.org/0000-0002-8443-9162}{ORCID})
+}
+
 Other contributors:
 \itemize{
   \item Simon Cauchemez [contributor]
diff --git a/man/check_estimate_advantage_inputs.Rd b/man/check_estimate_advantage_inputs.Rd
new file mode 100644
index 00000000..aaa3f3c1
--- /dev/null
+++ b/man/check_estimate_advantage_inputs.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate_mv_epiestim_inputs.R
+\name{check_estimate_advantage_inputs}
+\alias{check_estimate_advantage_inputs}
+\title{Validate inputs to estimate_advantage}
+\usage{
+check_estimate_advantage_inputs(...)
+}
+\arguments{
+\item{...}{Named arguments passed to \code{\link{estimate_advantage}}.}
+}
+\value{
+Invisibly returns \code{NULL}; throws an error if any input check
+fails.
+}
+\description{
+Runs all available input checks for \code{\link{estimate_advantage}} based on
+the supplied arguments. Each check is called only if the corresponding
+argument is present.
+}
+\author{
+Sangeeta Bhatia
+}
+\keyword{internal}
diff --git a/man/check_incidence.Rd b/man/check_incidence.Rd
new file mode 100644
index 00000000..a79349e9
--- /dev/null
+++ b/man/check_incidence.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate_mv_epiestim_inputs.R
+\name{check_incidence}
+\alias{check_incidence}
+\title{Check incidence input for MV-EpiEstim}
+\usage{
+check_incidence(incid)
+}
+\arguments{
+\item{incid}{a multidimensional array containing values of the incidence
+for each time step (1st dimension), location (2nd dimension) and
+pathogen/strain/variant (3rd dimension)}
+}
+\value{
+Silently returns TRUE if the checks are passed, otherwise throws an
+error.
+}
+\description{
+Check that incid is a 3-dimensional array with non-negatuve enteries.
+}
+\author{
+Sangeeta Bhatia
+}
+\keyword{internal}
diff --git a/man/check_mcmc_control.Rd b/man/check_mcmc_control.Rd
new file mode 100644
index 00000000..0e0972ca
--- /dev/null
+++ b/man/check_mcmc_control.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate_mv_epiestim_inputs.R
+\name{check_mcmc_control}
+\alias{check_mcmc_control}
+\title{Check MCMC control parameters for MV-EpiEstim}
+\usage{
+check_mcmc_control(mcmc_control)
+}
+\arguments{
+\item{mcmc_control}{a list of default MCMC control parameters, obtained by
+default from \code{\link[=default_mcmc_controls]{default_mcmc_controls()}}}
+}
+\value{
+Silently returns TRUE if the checks are passed, otherwise throws an
+error.
+}
+\description{
+Check that (1) mcmc_control is a list of the correct format, (2) n_iter, burnin
+and thin are positive integers and (3) n_iter is greater than burnin + thin.
+}
+\author{
+Sangeeta Bhatia
+}
+\keyword{internal}
diff --git a/man/check_priors.Rd b/man/check_priors.Rd
new file mode 100644
index 00000000..d3109e8d
--- /dev/null
+++ b/man/check_priors.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate_mv_epiestim_inputs.R
+\name{check_priors}
+\alias{check_priors}
+\title{Check priors  for MV-EpiEstim}
+\usage{
+check_priors(priors)
+}
+\arguments{
+\item{priors}{a list of prior parameters (shape and scale of a gamma
+distribution) for epsilon and R; can be obtained from the function
+\code{\link[=default_priors]{default_priors()}}. The prior for R is assumed to be the same for all
+time steps and all locations}
+}
+\value{
+Silently returns TRUE if the checks are passed, otherwise throws an
+error.
+}
+\description{
+Check that priors is a list of the correct format and that the mean of the
+prior for epsilon is 1 (as currently only priors with mean of epsilon equal
+to 1 is supported).
+}
+\author{
+Sangeeta Bhatia
+}
+\keyword{internal}
diff --git a/man/check_seed.Rd b/man/check_seed.Rd
new file mode 100644
index 00000000..db56ac74
--- /dev/null
+++ b/man/check_seed.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate_mv_epiestim_inputs.R
+\name{check_seed}
+\alias{check_seed}
+\title{Validate seed input for MV-EpiEstim}
+\usage{
+check_seed(seed)
+}
+\arguments{
+\item{seed}{a numeric value used to fix the random seed}
+}
+\value{
+Silently returns TRUE if the checks are passed, otherwise throws an error.
+}
+\description{
+Validate that the seed is not null and is numeric
+}
+\author{
+Sangeeta Bhatia
+}
+\keyword{internal}
diff --git a/man/check_t_min_t_max.Rd b/man/check_t_min_t_max.Rd
new file mode 100644
index 00000000..c836b0de
--- /dev/null
+++ b/man/check_t_min_t_max.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/validate_mv_epiestim_inputs.R
+\name{check_t_min_t_max}
+\alias{check_t_min_t_max}
+\title{Validate t_min and t_max inputs for MV-EpiEstim}
+\usage{
+check_t_min_t_max(t_min, t_max, incid)
+}
+\arguments{
+\item{t_min}{an integer > 1 giving the minimum time step to consider in the
+estimation.
+If \code{NULL}, \code{t_min} is calculated using the function \code{\link[=compute_si_cutoff]{compute_si_cutoff()}}
+which gets the maximum (across all variants) of the 95th percentile of the
+SI distribution.}
+
+\item{t_max}{an integer > \code{t_min} and <= \code{nrow(incid)} giving the maximum time
+step to consider in the estimation. Default value is \code{nrow(incid)}.}
+
+\item{incid}{a multidimensional array containing values of the incidence
+for each time step (1st dimension), location (2nd dimension) and
+pathogen/strain/variant (3rd dimension)}
+}
+\value{
+Silently returns TRUE if the checks are passed, otherwise throws an
+error.
+}
+\description{
+Check that (1) t_min and t_max are integers, (2) that they are >= 2, that
+they are <= nrow(incid) and (3) t_min is not greater than t_max.
+}
+\author{
+Sangeeta Bhatia
+}
+\keyword{internal}
diff --git a/man/default_priors.Rd b/man/default_priors.Rd
index 9ab5ae84..762c2b3e 100644
--- a/man/default_priors.Rd
+++ b/man/default_priors.Rd
@@ -9,8 +9,8 @@ default_priors()
 \value{
 a list of default parameters for the priors.
 Values can then be manually edited as in the examples below.
-Users could use functions \code{\link[epitrix:gamma_tools]{epitrix::gamma_shapescale2mucv()}} and
-\code{\link[epitrix:gamma_tools]{epitrix::gamma_mucv2shapescale()}} to set the shape and scale corresponding
+Users could use functions \code{\link[epitrix:gamma_shapescale2mucv]{epitrix::gamma_shapescale2mucv()}} and
+\code{\link[epitrix:gamma_mucv2shapescale]{epitrix::gamma_mucv2shapescale()}} to set the shape and scale corresponding
 to the desired prior mean and coefficient of variation.
 }
 \description{
diff --git a/man/draw_R.Rd b/man/draw_R.Rd
index 3b947147..790bb9c0 100644
--- a/man/draw_R.Rd
+++ b/man/draw_R.Rd
@@ -12,7 +12,8 @@ draw_R(
   shape_R_flat = NULL,
   t_min = NULL,
   t_max = nrow(incid),
-  seed = NULL
+  seed = NULL,
+  validate_inputs = FALSE
 )
 }
 \arguments{
@@ -52,6 +53,11 @@ observations at time step 1 and can therefore only start at time step 2).}
 step to consider in the estimation. Default value is \code{nrow(incid)}.}
 
 \item{seed}{a numeric value used to fix the random seed}
+
+\item{validate_inputs}{a boolean value indicating whether to validate the
+inputs; default value is FALSE as inputs are validated in
+\code{estimate_advantage()}, where this function is called. Can be set to TRUE
+if this function is called directly for debugging or testing.}
 }
 \value{
 a matrix of the instantaneous reproduction number R for the reference
diff --git a/man/draw_epsilon.Rd b/man/draw_epsilon.Rd
index 84b0a3bd..1ee96f15 100644
--- a/man/draw_epsilon.Rd
+++ b/man/draw_epsilon.Rd
@@ -12,7 +12,8 @@ draw_epsilon(
   shape_epsilon = NULL,
   t_min = 2L,
   t_max = nrow(incid),
-  seed = NULL
+  seed = NULL,
+  validate_inputs = FALSE
 )
 }
 \arguments{
@@ -51,6 +52,11 @@ observations at time step 1 and can therefore only start at time step 2).}
 step to consider in the estimation. Default value is \code{nrow(incid)}.}
 
 \item{seed}{a numeric value used to fix the random seed}
+
+\item{validate_inputs}{a boolean value indicating whether to validate the
+inputs; default value is FALSE as inputs are validated in
+\code{estimate_advantage()}, where this function is called. Can be set to TRUE
+if this function is called directly for debugging or testing.}
 }
 \value{
 A value or vector of values for epsilon for each non reference
diff --git a/man/estimate_R.Rd b/man/estimate_R.Rd
index 17c1342a..3d6b9db7 100644
--- a/man/estimate_R.Rd
+++ b/man/estimate_R.Rd
@@ -15,7 +15,7 @@ estimate_R(
   dt_out = 7L,
   recon_opt = "naive",
   iter = 10L,
-  tol = 1e-06,
+  tol = 0.000001,
   grid = list(precision = 0.001, min = -1, max = 1),
   backimputation_window = 0,
   date_convention = NULL
diff --git a/man/estimate_R_agg.Rd b/man/estimate_R_agg.Rd
index f39e7b0e..8711e794 100644
--- a/man/estimate_R_agg.Rd
+++ b/man/estimate_R_agg.Rd
@@ -9,7 +9,7 @@ estimate_R_agg(
   dt = 7L,
   dt_out = 7L,
   iter = 10L,
-  tol = 1e-06,
+  tol = 0.000001,
   recon_opt = "naive",
   config = make_config(),
   method = c("non_parametric_si", "parametric_si"),
diff --git a/man/estimate_advantage.Rd b/man/estimate_advantage.Rd
index a7566640..a08ac722 100644
--- a/man/estimate_advantage.Rd
+++ b/man/estimate_advantage.Rd
@@ -14,7 +14,8 @@ estimate_advantage(
   seed = NULL,
   incid_imported = NULL,
   precompute = TRUE,
-  reorder_incid = TRUE
+  reorder_incid = TRUE,
+  validate_inputs = TRUE
 )
 }
 \arguments{
@@ -63,6 +64,10 @@ incidence array can be internally reordered during the estimation of the
 transmission advantage. If \code{TRUE}, the most transmissible pathogen/strain/variant
 is temporarily assigned to \verb{[, , 1]} of the incidence array. We recommend the
 default value of \code{TRUE} as we find this to stabilise inference.}
+
+\item{validate_inputs}{a boolean (defaulting to \code{TRUE}) indicating whether to
+validate the inputs before running the estimation. We recommned that this
+is set to \code{TRUE} as it will ensure any mistmatches in inputs are caught early.}
 }
 \value{
 A list with the following elements:
diff --git a/tests/testthat/test-multivariant-input.R b/tests/testthat/test-multivariant-input.R
index ef1d5823..44490a69 100644
--- a/tests/testthat/test-multivariant-input.R
+++ b/tests/testthat/test-multivariant-input.R
@@ -19,11 +19,11 @@ sidistr_3=cbind(c(0,-0.1,0.7,0.4),c(0,0.2,0.5,0.3)) # negative value
 
 test_that("si_distr is specified correctly", {
   expect_error(compute_lambda(incid=incid_processed, si_distr=sidistr_1),
-               "Values in the first row of si_distr must be 0")
-  expect_error(compute_lambda(incid=incid_processed, si_distr=sidistr_2),
-               "The sum of each column in si_distr should be equal to 1")
+               "si_distr should be so that si_distr[1] = 0.", fixed = TRUE)
+  expect_warning(compute_lambda(incid=incid_processed, si_distr=sidistr_2),
+               "si_distr does not sum to 1.")
   expect_error(compute_lambda(incid=incid_processed, si_distr=sidistr_3),
-               "si_distr must be >=0")
+               "si_distr must be a positive vector.")
 })
 
 ##############################
@@ -45,15 +45,15 @@ tmin3 <- as.integer(nrow(incid)+1) # greater than nrow(incid)
 test_that("tmin and tmax are specified correctly", {
   expect_error(draw_epsilon(R=R, incid=incid, lambda=lambda, priors=priors,
                               t_min = tmin1, t_max = nrow(incid),
-                              seed = NULL),
+                              seed = NULL, validate_inputs = TRUE),
                "t_min and t_max must be integers")
   expect_error(draw_epsilon(R=R, incid=incid, lambda=lambda, priors=priors,
                             t_min = tmin2, t_max = nrow(incid),
-                            seed = NULL),
+                            seed = NULL, validate_inputs = TRUE),
                "t_min and t_max must be >=2")
   expect_error(draw_epsilon(R=R, incid=incid, lambda=lambda, priors=priors,
                             t_min = tmin3, t_max = nrow(incid),
-                            seed = NULL),
+                            seed = NULL, validate_inputs = TRUE),
                "t_min and t_max must be <= nrow(incid)", fixed=TRUE)
 })
 
@@ -64,7 +64,7 @@ test_that("R is specified correctly",{
   Rneg[1,1] <- -1
   expect_error(draw_epsilon(R=Rneg, incid=incid, lambda=lambda, priors=priors,
                             t_min = 2L, t_max = nrow(incid),
-                            seed = NULL),
+                            seed = NULL, validate_inputs = TRUE),
                "R must be >= 0")
 })
 
@@ -75,8 +75,8 @@ seed <- "a"
 test_that("seed is specified correctly",{
   expect_error(draw_epsilon(R=R, incid=incid, lambda=lambda, priors=priors,
                             t_min = 2L, t_max = nrow(incid),
-                            seed = "a"),
-               "seed must be numeric")
+                            seed = "a", validate_inputs = TRUE),
+               "supplied seed is not a valid integer")
 })
 
 ########################
@@ -100,15 +100,15 @@ tmin3 <- as.integer(nrow(incid)+1) # greater than nrow(incid)
 test_that("tmin and tmax are specified correctly", {
   expect_error(draw_R(epsilon=epsilon, incid=incid, lambda=lambda, priors=priors,
                             t_min = tmin1, t_max = nrow(incid),
-                            seed = NULL),
+                            seed = NULL, validate_inputs = TRUE),
                "t_min and t_max must be integers")
   expect_error(draw_R(epsilon=epsilon, incid=incid, lambda=lambda, priors=priors,
                             t_min = tmin2, t_max = nrow(incid),
-                            seed = NULL),
+                            seed = NULL, validate_inputs = TRUE),
                "t_min and t_max must be >=2")
   expect_error(draw_R(epsilon=epsilon, incid=incid, lambda=lambda, priors=priors,
                             t_min = tmin3, t_max = nrow(incid),
-                            seed = NULL),
+                            seed = NULL, validate_inputs = TRUE),
                "t_min and t_max must be <= nrow(incid)", fixed=TRUE)
 })
 
@@ -120,8 +120,8 @@ seed <- "a"
 test_that("seed is specified correctly",{
   expect_error(draw_R(epsilon=epsilon, incid=incid, lambda=lambda, priors=priors,
                             t_min = 2L, t_max = nrow(incid),
-                            seed = seed),
-               "seed must be numeric")
+                            seed = seed, validate_inputs = TRUE),
+               "supplied seed is not a valid integer")
 })
 
 
@@ -132,7 +132,7 @@ epsilon <- -1
 test_that("epsilon is specified correctly",{
   expect_error(draw_R(epsilon=epsilon, incid=incid, lambda=lambda, priors=priors,
                       t_min = 2L, t_max = nrow(incid),
-                      seed = NULL),
+                      seed = NULL, validate_inputs = TRUE),
                "epsilon must be > 0")
 })
 
@@ -183,17 +183,17 @@ test_that("si_distr is specified correctly", {
                               mcmc_control = default_mcmc_controls(),
                               t_min = 2L, t_max = nrow(incid),
                               seed = NULL),
-               "Values in the first row of si_distr must be 0")
-  expect_error(estimate_advantage(incid=incid, si_distr=sidistr_2, priors=priors,
+               "si_distr should be so that si_distr[1] = 0.", fixed=TRUE)
+  expect_warning(estimate_advantage(incid=incid, si_distr=sidistr_2, priors=priors,
                               mcmc_control = default_mcmc_controls(),
                               t_min = 2L, t_max = nrow(incid),
                               seed = NULL),
-               "The sum of each column in si_distr should be equal to 1")
+               "Input SI distributions should sum to 1. Normalising now")
   expect_error(estimate_advantage(incid=incid, si_distr=sidistr_3, priors=priors,
                               mcmc_control = default_mcmc_controls(),
                               t_min = 2L, t_max = nrow(incid),
                               seed = NULL),
-               "si_distr must be >=0")
+               "si_distr must be a positive vector.")
 })
 
 
@@ -245,7 +245,7 @@ test_that("seed is specified correctly",{
                               mcmc_control = default_mcmc_controls(),
                               t_min = 2L, t_max = nrow(incid),
                               seed = seed),
-               "seed must be numeric")
+               "supplied seed is not a valid integer")
 })
 
   # convergence check
@@ -327,4 +327,5 @@ test_that("the Rt of the reference variant is returned both with and without inc
                              seed = NULL, reorder_incid = FALSE)
   
   expect_equal(stats::median(out$R, na.rm = T), stats::median(out2$R, na.rm = T), tolerance = 0.001)
-})
\ No newline at end of file
+})
+