Change .mard refs to .msm

EpiModel · Feb 18, 2016 · 65e8d7d · 65e8d7d
1 parent fe01487
commit 65e8d7d
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Showing 53 changed files with 262 additions and 268 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,39 +2,39 @@
 
 S3method(print,nwstats)
 export(InitErgmTerm.absdiffnodemix)
-export(acts.mard)
-export(aging.mard)
+export(acts.msm)
+export(aging.msm)
 export(apportion_lr)
 export(assign_degree)
-export(base_nw.mard)
-export(births.mard)
-export(calc_nwstats.mard)
-export(condoms.mard)
-export(control.mard)
-export(deaths.mard)
-export(disclose.mard)
-export(edges_correct.mard)
+export(base_nw.msm)
+export(births.msm)
+export(calc_nwstats.msm)
+export(condoms.msm)
+export(control.msm)
+export(deaths.msm)
+export(disclose.msm)
+export(edges_correct.msm)
 export(get_args)
-export(init.mard)
-export(initialize.mard)
-export(param.mard)
-export(position.mard)
-export(prep.mard)
-export(prevalence.mard)
-export(progress.mard)
+export(init.msm)
+export(initialize.msm)
+export(param.msm)
+export(position.msm)
+export(prep.msm)
+export(prevalence.msm)
+export(progress.msm)
 export(reallocate_pcp)
-export(reinit.mard)
-export(riskhist.mard)
-export(simnet.mard)
-export(test.mard)
-export(trans.mard)
-export(tx.mard)
-export(update_aiclass.mard)
+export(reinit.msm)
+export(riskhist.msm)
+export(simnet.msm)
+export(test.msm)
+export(trans.msm)
+export(tx.msm)
+export(update_aiclass.msm)
 export(update_degree)
-export(update_roleclass.mard)
-export(update_vl.mard)
-export(updatenwp.mard)
-export(verbose.mard)
+export(update_roleclass.msm)
+export(update_vl.msm)
+export(updatenwp.msm)
+export(verbose.msm)
 import(EpiModel)
 import(EpiModelHPC)
 import(bindata)

diff --git a/R/estimation.R b/R/estimation.R
@@ -63,13 +63,13 @@
 #' calculated externally to the package in a setup scenario file.
 #'
 #' @seealso
-#' Network statistics calculated here are entered into \code{\link{base_nw.mard}}
+#' Network statistics calculated here are entered into \code{\link{base_nw.msm}}
 #' to construct the base network, and then into the parameters in
-#' \code{\link{param.mard}}.
+#' \code{\link{param.msm}}.
 #'
 #' @export
 #'
-calc_nwstats.mard <- function(time.unit = 7, method = 2,
+calc_nwstats.msm <- function(time.unit = 7, method = 2,
                               num.B, num.W, deg.mp.B, deg.mp.W,
                               mdeg.inst.B, mdeg.inst.W,
                               qnts.B, qnts.W,
@@ -359,10 +359,10 @@ calc_nwstats.mard <- function(time.unit = 7, method = 2,
 #'              \code{netest}.
 #'
 #' @param nwstats An object of class \code{nwstats}, as output from
-#'        \code{\link{calc_nwstats.mard}}.
+#'        \code{\link{calc_nwstats.msm}}.
 #'
 #' @details
-#' This function takes the output of \code{\link{calc_nwstats.mard}} and constructs
+#' This function takes the output of \code{\link{calc_nwstats.msm}} and constructs
 #' an empty network with the necessary attributes for race, square root of age,
 #' and sexual role class. This base network is used for all three network
 #' estimations.
@@ -373,7 +373,7 @@ calc_nwstats.mard <- function(time.unit = 7, method = 2,
 #'
 #' @export
 #'
-base_nw.mard <- function(nwstats) {
+base_nw.msm <- function(nwstats) {
 
   num.B <- nwstats$num.B
   num.W <- nwstats$num.W

diff --git a/R/mod.acts.R b/R/mod.acts.R
@@ -4,7 +4,7 @@
 #' @description Module function for setting the number of sexual acts on the
 #'              discordant edgelist.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' The number of acts at each time step is specified as a function of the race of
@@ -22,7 +22,7 @@
 #' @keywords module
 #' @export
 #'
-acts.mard <- function(dat, at) {
+acts.msm <- function(dat, at) {
 
   for (type in c("main", "pers", "inst")) {
 

diff --git a/R/mod.aging.R b/R/mod.aging.R
@@ -15,7 +15,7 @@
 #' @keywords module
 #' @export
 #'
-aging.mard <- function(dat, at) {
+aging.msm <- function(dat, at) {
 
   time.unit <- dat$param$time.unit
 

diff --git a/R/mod.births.R b/R/mod.births.R
@@ -4,7 +4,7 @@
 #' @description Module function for births or entries into the sexually active
 #'              population.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' New population members are added based on expected numbers of entries among
@@ -21,7 +21,7 @@
 #' @keywords module
 #' @export
 #'
-births.mard <- function(dat, at){
+births.msm <- function(dat, at){
 
   ## Variables
 
@@ -48,7 +48,7 @@ births.mard <- function(dat, at){
 
   ## Update Attr
   if (nBirths > 0) {
-    dat <- setBirthAttr.mard(dat, at, nBirths.B, nBirths.W)
+    dat <- setBirthAttr.msm(dat, at, nBirths.B, nBirths.W)
   }
 
 
@@ -67,7 +67,7 @@ births.mard <- function(dat, at){
 }
 
 
-setBirthAttr.mard <- function(dat, at, nBirths.B, nBirths.W) {
+setBirthAttr.msm <- function(dat, at, nBirths.B, nBirths.W) {
 
   nBirths <- nBirths.B + nBirths.W
 

diff --git a/R/mod.condoms.R b/R/mod.condoms.R
@@ -4,7 +4,7 @@
 #' @description Module function stochastically simulates potential condom use
 #'              for each act on the discordant edgelist.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' For each act on the discordant edgelist, condom use is stochastically simulated
@@ -20,7 +20,7 @@
 #' @keywords module
 #' @export
 #'
-condoms.mard <- function(dat, at) {
+condoms.msm <- function(dat, at) {
 
   for (type in c("main", "pers", "inst")) {
 

diff --git a/R/mod.death.R b/R/mod.death.R
@@ -4,7 +4,7 @@
 #' @description Module function for simulting both general and disease-related
 #'              deaths among population members.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' Deaths are divided into two categories: general deaths, for which demographic
@@ -19,13 +19,13 @@
 #' This function returns the updated \code{dat} object accounting for deaths.
 #' The deaths are deactivated from the main and casual networks, as those are in
 #' \code{networkDynamic} class objects; dead nodes are not deleted from the
-#' instant network until the \code{\link{simnet.mard}} module for bookkeeping
+#' instant network until the \code{\link{simnet.msm}} module for bookkeeping
 #' purposes.
 #'
 #' @keywords module
 #' @export
 #'
-deaths.mard <- function(dat, at) {
+deaths.msm <- function(dat, at) {
 
   ## General deaths
   age <- floor(dat$attr$age)

diff --git a/R/mod.disclose.R b/R/mod.disclose.R
@@ -4,7 +4,7 @@
 #' @description Module function for disclosure of HIV status to partners given
 #'              non-disclosure in the past.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' Persons who are infected may disclose their status to partners at three
@@ -20,7 +20,7 @@
 #' @keywords module
 #' @export
 #'
-disclose.mard <- function(dat, at){
+disclose.msm <- function(dat, at){
 
   for (type in c("main", "pers", "inst")) {
 

diff --git a/R/mod.edgescorr.R b/R/mod.edgescorr.R
@@ -4,7 +4,7 @@
 #' @description Adjusts the edges coefficients in a dynamic network model
 #'              to preserve the mean degree.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' In HIV/STI modeling, there is typically an assumption that changes in
@@ -27,7 +27,7 @@
 #' @keywords module
 #' @export
 #'
-edges_correct.mard <- function(dat, at) {
+edges_correct.msm <- function(dat, at) {
 
   old.num <- dat$epi$num[at - 1]
   new.num <- sum(dat$attr$active == 1, na.rm = TRUE)

diff --git a/R/mod.init.R b/R/mod.init.R
@@ -6,9 +6,9 @@
 #'              simulates disease status and other attributes.
 #'
 #' @param x An \code{EpiModel} object of class \code{\link{netest}}.
-#' @param param An \code{EpiModel} object of class \code{\link{param.mard}}.
-#' @param init An \code{EpiModel} object of class \code{\link{init.mard}}.
-#' @param control An \code{EpiModel} object of class \code{\link{control.mard}}.
+#' @param param An \code{EpiModel} object of class \code{\link{param.msm}}.
+#' @param init An \code{EpiModel} object of class \code{\link{init.msm}}.
+#' @param control An \code{EpiModel} object of class \code{\link{control.msm}}.
 #' @param s Simulation number, used for restarting dependent simulations.
 #'
 #' @return
@@ -18,7 +18,7 @@
 #' @export
 #' @keywords module
 #'
-initialize.mard <- function(x, param, init, control, s) {
+initialize.msm <- function(x, param, init, control, s) {
 
   # Master data list
   dat <- list()
@@ -146,7 +146,7 @@ initialize.mard <- function(x, param, init, control, s) {
   dat$attr$ins.quot <- ins.quot
 
   # HIV-related attributes
-  dat <- init_status.mard(dat)
+  dat <- init_status.msm(dat)
 
   # CCR5
   dat <- init_ccr5(dat)
@@ -161,7 +161,7 @@ initialize.mard <- function(x, param, init, control, s) {
   dat$temp$discl.list <- matrix(NA, nrow = 0, ncol = 3)
   colnames(dat$temp$discl.list) <- c("pos", "neg", "discl.time")
 
-  dat <- prevalence.mard(dat, at = 1)
+  dat <- prevalence.msm(dat, at = 1)
 
   class(dat) <- "dat"
   return(dat)
@@ -193,7 +193,7 @@ remove_bad_roles <- function(nw) {
 }
 
 
-init_status.mard <- function(dat) {
+init_status.msm <- function(dat) {
 
   num.B <- dat$init$num.B
   num.W <- dat$init$num.W
@@ -675,7 +675,7 @@ init_ccr5 <- function(dat) {
 #'              specified time step given an input \code{netsim} object.
 #'
 #' @param x An \code{EpiModel} object of class \code{\link{netsim}}.
-#' @inheritParams initialize.mard
+#' @inheritParams initialize.msm
 #'
 #' @return
 #' This function resets the data elements on the \code{dat} master data object
@@ -684,7 +684,7 @@ init_ccr5 <- function(dat) {
 #' @export
 #' @keywords module
 #'
-reinit.mard <- function(x, param, init, control, s) {
+reinit.msm <- function(x, param, init, control, s) {
 
   if (any(c("param", "control", "nwparam", "epi", "attr", "temp",
     "riskh", "el", "p") %in% names(x)) == FALSE) {

diff --git a/R/mod.position.R b/R/mod.position.R
@@ -4,7 +4,7 @@
 #' @description Module function for establishing sexual role or position in each
 #'              act on the discordant edgelist.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' The sexual role within each act is determined by each nodes "role identity"
@@ -22,7 +22,7 @@
 #' @keywords module
 #' @export
 #'
-position.mard <- function(dat, at) {
+position.msm <- function(dat, at) {
 
   ## Variables
   al <- dat$temp$al

diff --git a/R/mod.prep.R b/R/mod.prep.R
@@ -4,11 +4,11 @@
 #' @description Module function for implementation and uptake of pre-exposure
 #'              prophylaxis (PrEP) to prevent HIV infection.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @export
 #'
-prep.mard <- function(dat, at) {
+prep.msm <- function(dat, at) {
 
   if (at < dat$param$prep.start) {
     return(dat)

diff --git a/R/mod.prevalence.R b/R/mod.prevalence.R
@@ -4,7 +4,7 @@
 #' @description This module calculates demographic, transmission, and clinical
 #'              statistics at each time step within the simulation.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' Summary statistic calculations are of two broad forms: prevalence and
@@ -21,7 +21,7 @@
 #' @keywords module
 #' @export
 #'
-prevalence.mard <- function(dat, at) {
+prevalence.msm <- function(dat, at) {
 
   active <- dat$attr$active
   race <- dat$attr$race
@@ -110,7 +110,7 @@ prevalence.mard <- function(dat, at) {
 }
 
 
-prev.full.mard <- function(dat, at) {
+prev.full.msm <- function(dat, at) {
 
   active <- dat$attr$active
   race <- dat$attr$race

diff --git a/R/mod.progress.R b/R/mod.progress.R
@@ -4,7 +4,7 @@
 #' @description Module function for HIV disease progression through acute, chronic
 #'              and AIDS stages.
 #'
-#' @inheritParams aging.mard
+#' @inheritParams aging.msm
 #'
 #' @details
 #' HIV disease is divided into four stages: acute rising, acute falling, chronic
@@ -30,7 +30,7 @@
 #' @keywords module
 #' @export
 #'
-progress.mard <- function(dat, at) {
+progress.msm <- function(dat, at) {
 
   ## Variables