diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..2e6adc6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+.Rhistory
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..e69de29
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..e69de29
diff --git a/R/getFinalSize.R b/R/getFinalSize.R
index 3d8e57d..b27884f 100644
--- a/R/getFinalSize.R
+++ b/R/getFinalSize.R
@@ -1,5 +1,6 @@
 library(deSolve)
 
+#' @export
 getFinalSizeAnalytic <- function(Rinit, Iinit, Vinit, N, R0, a, eps, q) {
 
   if (sum(Iinit) == 0) Iinit <- N / sum(N)
@@ -24,6 +25,7 @@ getFinalSizeAnalytic <- function(Rinit, Iinit, Vinit, N, R0, a, eps, q) {
   opt$par + Iinit + Rinit
 }
 
+#' @export
 exposure.SIR <- function(Time, state, Pars) {
   with(as.list(c(Time, state, Pars)), {
 
@@ -48,6 +50,7 @@ exposure.SIR <- function(Time, state, Pars) {
   })
 }
 
+#' @export
 rescale.R0 <- function(beta, gam, pop.p, N, R0.value) {
   NGM.unscaled <- N * pop.p * beta * 1 / gam
   dom.eigen <- as.numeric(eigen(NGM.unscaled)$values[1])
@@ -57,6 +60,7 @@ rescale.R0 <- function(beta, gam, pop.p, N, R0.value) {
   return(scaling.factor)
 }
 
+#' @export
 sim.exposure.SIR <- function(Rinit, Iinit, Vinit, tm, N, R0, gam, a, eps, q) {
 
   Ntot <- sum(N)
@@ -96,7 +100,7 @@ sim.exposure.SIR <- function(Rinit, Iinit, Vinit, tm, N, R0, gam, a, eps, q) {
   simulation
 }
 
-
+#' @export
 getFinalSize <- function(vacTime, vacPortion, popSize, R0, recoveryRate,
                          contactRatio, contactWithinGroup, suscRatio) {
   # vacTime: time after first case at which all vaccinations are delivered
@@ -125,6 +129,7 @@ getFinalSize <- function(vacTime, vacPortion, popSize, R0, recoveryRate,
 
 }
 
+#' @export
 finalSizeExample <- getFinalSize(vacTime = 100, vacPortion = c(0.1, 0.1),
   popSize = c(800000, 200000), R0 = 1.5, recoveryRate = 1 / 7,
   contactRatio = 1.7, contactWithinGroup = c(0.4, 0.4), suscRatio = 1)
diff --git a/man/exposure.SIR.Rd b/man/exposure.SIR.Rd
new file mode 100644
index 0000000..209b93f
--- /dev/null
+++ b/man/exposure.SIR.Rd
@@ -0,0 +1,82 @@
+\name{exposure.SIR}
+\alias{exposure.SIR}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+A Capitalized Title (ideally limited to 65 characters)
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+exposure.SIR(Time, state, Pars)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{Time}{
+%%     ~~Describe \code{Time} here~~
+}
+  \item{state}{
+%%     ~~Describe \code{state} here~~
+}
+  \item{Pars}{
+%%     ~~Describe \code{Pars} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or standard data sets, see data().
+
+## The function is currently defined as
+function (Time, state, Pars)
+{
+    with(as.list(c(Time, state, Pars)), {
+        S <- c(S1, S2)
+        I <- c(I1, I2)
+        R <- c(R1, R2)
+        N <- c(N1, N2)
+        beta <- (1 - epsilon) * outer(activities, activities)/sum(c(N1,
+            N2) * activities) + epsilon * activities/c(N1, N2) *
+            diag(2)
+        beta <- beta/scaling.factor
+        dS <- -(beta \%*\% I) * S
+        dI <- (beta \%*\% I) * S - gam * I
+        dR <- gam * I
+        return(list(c(dS, dI, dR)))
+    })
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory (show via RShowDoc("KEYWORDS")):
+% \keyword{ ~kwd1 }
+% \keyword{ ~kwd2 }
+% Use only one keyword per line.
+% For non-standard keywords, use \concept instead of \keyword:
+% \concept{ ~cpt1 }
+% \concept{ ~cpt2 }
+% Use only one concept per line.
diff --git a/man/finalSizeExample.Rd b/man/finalSizeExample.Rd
new file mode 100644
index 0000000..8b9b832
--- /dev/null
+++ b/man/finalSizeExample.Rd
@@ -0,0 +1,28 @@
+\name{finalSizeExample}
+\alias{finalSizeExample}
+\docType{data}
+\title{
+A Capitalized Title for the Data Set
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of the dataset. ~~
+}
+\usage{data("finalSizeExample")}
+\format{
+  The format is:
+ num [1:2] 233224 102557
+}
+\details{
+%%  ~~ If necessary, more details than the __description__ above ~~
+}
+\source{
+%%  ~~ reference to a publication or URL from which the data were obtained ~~
+}
+\references{
+%%  ~~ possibly secondary sources and usages ~~
+}
+\examples{
+data(finalSizeExample)
+## maybe str(finalSizeExample) ; plot(finalSizeExample) ...
+}
+\keyword{datasets}
diff --git a/man/getFinalSize.Rd b/man/getFinalSize.Rd
new file mode 100644
index 0000000..3c34554
--- /dev/null
+++ b/man/getFinalSize.Rd
@@ -0,0 +1,97 @@
+\name{getFinalSize}
+\alias{getFinalSize}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+A Capitalized Title (ideally limited to 65 characters)
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+getFinalSize(vacTime, vacPortion, popSize, R0, recoveryRate, contactRatio, contactWithinGroup, suscRatio)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{vacTime}{
+%%     ~~Describe \code{vacTime} here~~
+}
+  \item{vacPortion}{
+%%     ~~Describe \code{vacPortion} here~~
+}
+  \item{popSize}{
+%%     ~~Describe \code{popSize} here~~
+}
+  \item{R0}{
+%%     ~~Describe \code{R0} here~~
+}
+  \item{recoveryRate}{
+%%     ~~Describe \code{recoveryRate} here~~
+}
+  \item{contactRatio}{
+%%     ~~Describe \code{contactRatio} here~~
+}
+  \item{contactWithinGroup}{
+%%     ~~Describe \code{contactWithinGroup} here~~
+}
+  \item{suscRatio}{
+%%     ~~Describe \code{suscRatio} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or standard data sets, see data().
+
+## The function is currently defined as
+function (vacTime, vacPortion, popSize, R0, recoveryRate, contactRatio,
+    contactWithinGroup, suscRatio)
+{
+    Isim1 <- c(0, 0)
+    Rsim1 <- c(0, 0)
+    if (vacTime > 0) {
+        sim1 <- sim.exposure.SIR(Rinit = c(0, 0), Iinit = c(0,
+            0), Vinit = c(0, 0), tm = vacTime, N = popSize, R0 = R0,
+            gam = recoveryRate, a = c(1, contactRatio), eps = contactWithinGroup,
+            q = c(1, suscRatio))
+        Isim1 <- as.numeric(sim1[nrow(sim1), c("I1", "I2")])
+        Rsim1 <- as.numeric(sim1[nrow(sim1), c("R1", "R2")])
+    }
+    getFinalSizeAnalytic(Rinit = Rsim1, Iinit = Isim1, Vinit = popSize *
+        vacPortion, N = popSize, R0 = R0, a = c(1, contactRatio),
+        eps = contactWithinGroup, q = c(1, suscRatio))
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory (show via RShowDoc("KEYWORDS")):
+% \keyword{ ~kwd1 }
+% \keyword{ ~kwd2 }
+% Use only one keyword per line.
+% For non-standard keywords, use \concept instead of \keyword:
+% \concept{ ~cpt1 }
+% \concept{ ~cpt2 }
+% Use only one concept per line.
diff --git a/man/getFinalSizeAnalytic.Rd b/man/getFinalSizeAnalytic.Rd
new file mode 100644
index 0000000..1bdd802
--- /dev/null
+++ b/man/getFinalSizeAnalytic.Rd
@@ -0,0 +1,100 @@
+\name{getFinalSizeAnalytic}
+\alias{getFinalSizeAnalytic}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+A Capitalized Title (ideally limited to 65 characters)
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+getFinalSizeAnalytic(Rinit, Iinit, Vinit, N, R0, a, eps, q)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{Rinit}{
+%%     ~~Describe \code{Rinit} here~~
+}
+  \item{Iinit}{
+%%     ~~Describe \code{Iinit} here~~
+}
+  \item{Vinit}{
+%%     ~~Describe \code{Vinit} here~~
+}
+  \item{N}{
+%%     ~~Describe \code{N} here~~
+}
+  \item{R0}{
+%%     ~~Describe \code{R0} here~~
+}
+  \item{a}{
+%%     ~~Describe \code{a} here~~
+}
+  \item{eps}{
+%%     ~~Describe \code{eps} here~~
+}
+  \item{q}{
+%%     ~~Describe \code{q} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or standard data sets, see data().
+
+## The function is currently defined as
+function (Rinit, Iinit, Vinit, N, R0, a, eps, q)
+{
+    if (sum(Iinit) == 0)
+        Iinit <- N/sum(N)
+    Sinit <- N - Rinit - Iinit - Vinit
+    fn <- (1 - eps) * a * N
+    f <- fn/sum(fn)
+    cij <- diag(eps) + outer((1 - eps), f)
+    R0i <- R0/eigen(a * q * cij)$values[1] * a * q
+    Zrhs <- function(Z) c(Sinit * (1 - exp(-R0i * cij \%*\% ((Z +
+        Iinit)/N))))
+    optfn <- function(x) ifelse(all(x > 0), max(abs(x - Zrhs(x))),
+        Inf)
+    optVal <- Inf
+    while (optVal > 1) {
+        opt <- optim((0.01 + 0.98 * runif(length(N))) * N, optfn)
+        optVal <- opt$value
+    }
+    opt$par + Iinit + Rinit
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory (show via RShowDoc("KEYWORDS")):
+% \keyword{ ~kwd1 }
+% \keyword{ ~kwd2 }
+% Use only one keyword per line.
+% For non-standard keywords, use \concept instead of \keyword:
+% \concept{ ~cpt1 }
+% \concept{ ~cpt2 }
+% Use only one concept per line.
diff --git a/man/rescale.R0.Rd b/man/rescale.R0.Rd
new file mode 100644
index 0000000..096008d
--- /dev/null
+++ b/man/rescale.R0.Rd
@@ -0,0 +1,79 @@
+\name{rescale.R0}
+\alias{rescale.R0}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+A Capitalized Title (ideally limited to 65 characters)
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+rescale.R0(beta, gam, pop.p, N, R0.value)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{beta}{
+%%     ~~Describe \code{beta} here~~
+}
+  \item{gam}{
+%%     ~~Describe \code{gam} here~~
+}
+  \item{pop.p}{
+%%     ~~Describe \code{pop.p} here~~
+}
+  \item{N}{
+%%     ~~Describe \code{N} here~~
+}
+  \item{R0.value}{
+%%     ~~Describe \code{R0.value} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or standard data sets, see data().
+
+## The function is currently defined as
+function (beta, gam, pop.p, N, R0.value)
+{
+    NGM.unscaled <- N * pop.p * beta * 1/gam
+    dom.eigen <- as.numeric(eigen(NGM.unscaled)$values[1])
+    NGM.scaled <- NGM.unscaled/dom.eigen * R0.value
+    scaling.factor <- beta/(NGM.scaled/(N * pop.p) * gam)
+    return(scaling.factor)
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory (show via RShowDoc("KEYWORDS")):
+% \keyword{ ~kwd1 }
+% \keyword{ ~kwd2 }
+% Use only one keyword per line.
+% For non-standard keywords, use \concept instead of \keyword:
+% \concept{ ~cpt1 }
+% \concept{ ~cpt2 }
+% Use only one concept per line.
diff --git a/man/sim.exposure.SIR.Rd b/man/sim.exposure.SIR.Rd
new file mode 100644
index 0000000..b49e8a2
--- /dev/null
+++ b/man/sim.exposure.SIR.Rd
@@ -0,0 +1,109 @@
+\name{sim.exposure.SIR}
+\alias{sim.exposure.SIR}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+A Capitalized Title (ideally limited to 65 characters)
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+sim.exposure.SIR(Rinit, Iinit, Vinit, tm, N, R0, gam, a, eps, q)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{Rinit}{
+%%     ~~Describe \code{Rinit} here~~
+}
+  \item{Iinit}{
+%%     ~~Describe \code{Iinit} here~~
+}
+  \item{Vinit}{
+%%     ~~Describe \code{Vinit} here~~
+}
+  \item{tm}{
+%%     ~~Describe \code{tm} here~~
+}
+  \item{N}{
+%%     ~~Describe \code{N} here~~
+}
+  \item{R0}{
+%%     ~~Describe \code{R0} here~~
+}
+  \item{gam}{
+%%     ~~Describe \code{gam} here~~
+}
+  \item{a}{
+%%     ~~Describe \code{a} here~~
+}
+  \item{eps}{
+%%     ~~Describe \code{eps} here~~
+}
+  \item{q}{
+%%     ~~Describe \code{q} here~~
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or standard data sets, see data().
+
+## The function is currently defined as
+function (Rinit, Iinit, Vinit, tm, N, R0, gam, a, eps, q)
+{
+    Ntot <- sum(N)
+    beta <- (1 - eps) * outer(a, a)/sum(N * a) + eps * a/(N) *
+        diag(2)
+    scaling.factor <- rescale.R0(beta = beta, gam = gam, pop.p = N/Ntot,
+        N = Ntot, R0.value = R0)
+    pars <- list(N = Ntot, N1 = N[1], N2 = N[2], activities = a,
+        epsilon = eps, gam = gam, scaling.factor = scaling.factor)
+    times <- c(0, tm)
+    S.init <- c(S1 = N[1] - Rinit[1] - Iinit[1] - Vinit[1], S2 = N[2] -
+        Rinit[2] - Iinit[2] - Vinit[2])
+    I.init <- c(I1 = Iinit[1], I2 = Iinit[2])
+    R.init <- c(R1 = Rinit[1], R2 = Rinit[2])
+    if (sum(I.init) == 0) {
+        I.init <- c(I1 = N[1]/Ntot, I2 = N[2]/Ntot)
+        S.init <- S.init - I.init
+    }
+    y0 <- c(S.init, I.init, R.init)
+    simulation <- as.data.frame(ode(y0, times, exposure.SIR,
+        pars))
+    simulation
+  }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory (show via RShowDoc("KEYWORDS")):
+% \keyword{ ~kwd1 }
+% \keyword{ ~kwd2 }
+% Use only one keyword per line.
+% For non-standard keywords, use \concept instead of \keyword:
+% \concept{ ~cpt1 }
+% \concept{ ~cpt2 }
+% Use only one concept per line.