Re-gen docs and prevent genning of internal functions

[Rnaught] / man / IDEA.Rd

diff --git a/man/IDEA.Rd b/man/IDEA.Rd
index 2dc8240d20cb847a98dfb401555eee8f3e328956..f4c7d143181af3364c6eab6809d127f04e7f3835 100644 (file)
--- a/man/IDEA.Rd
+++ b/man/IDEA.Rd
@@ -9,42 +9,40 @@ IDEA(NT, mu)
 \arguments{
 \item{NT}{Vector of case counts.}
 
 \arguments{
 \item{NT}{Vector of case counts.}
 

-\item{mu}{Mean of the serial distribution. This needs to match case counts in time units. For example, if case counts
-are weekly and the serial distribution has a mean of seven days, then \code{mu} should be set to one. If case
-counts are daily and the serial distribution has a mean of seven days, then \code{mu} should be set to seven.}
+\item{mu}{Mean of the serial distribution. This needs to match case counts in
+time units. For example, if case counts are weekly and the serial
+distribution has a mean of seven days, then \code{mu} should be set
+to one. If case counts are daily and the serial distribution has a
+mean of seven days, then \code{mu} should be set to seven.}

 }
 \value{
 \code{IDEA} returns a single value, the estimate of R0.
 }
 \description{
 }
 \value{
 \code{IDEA} returns a single value, the estimate of R0.
 }
 \description{

-This function implements a least squares estimation method of R0 due to Fisman et al. (PloS One, 2013).
-See details for implementation notes.
+This function implements a least squares estimation method of R0 due to
+Fisman et al. (PloS One, 2013). See details for implementation notes.

 }
 \details{
 }
 \details{

-This method is closely related to that implemented in \code{ID}. The method is based on an incidence decay model.
-The estimate of R0 is the value which minimizes the sum of squares between observed case counts and cases counts
+This method is closely related to that implemented in \code{ID}. The method
+is based on an incidence decay model. The estimate of R0 is the value which
+minimizes the sum of squares between observed case counts and cases counts

 expected under the model.
 
 expected under the model.
 

-This method is based on an approximation of the SIR model, which is most valid at the beginning of an epidemic.
-The method assumes that the mean of the serial distribution (sometimes called the serial interval) is known.
-The final estimate can be quite sensitive to this value, so sensitivity testing is strongly recommended.
-Users should be careful about units of time (e.g., are counts observed daily or weekly?) when implementing.
+This method is based on an approximation of the SIR model, which is most
+valid at the beginning of an epidemic. The method assumes that the mean of
+the serial distribution (sometimes called the serial interval) is known. The
+final estimate can be quite sensitive to this value, so sensitivity testing
+is strongly recommended. Users should be careful about units of time (e.g.,
+are counts observed daily or weekly?) when implementing.

 }
 \examples{
 }
 \examples{

-## ===================================================== ##
-## Illustrate on weekly data                             ##
-## ===================================================== ##
-
+# Weekly data.

 NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4)
 NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4)

-## obtain Rhat when serial distribution has mean of five days
-IDEA(NT=NT, mu=5/7)
-## obtain Rhat when serial distribution has mean of three days
-IDEA(NT=NT, mu=3/7)

 
 

-## ========================================================= ##
-## Compute Rhat using only the first five weeks of data      ##
-## ========================================================= ##
+# Obtain R0 when the serial distribution has a mean of five days.
+IDEA(NT, mu = 5 / 7)

 
 

-IDEA(NT=NT[1:5], mu=5/7) # serial distribution has mean of five days
+# Obtain R0 when the serial distribution has a mean of three days.
+IDEA(NT, mu = 3 / 7)

 
 }
 
 }