Add CombPrev branch of EpiModelHIV

EpiModel · Mar 4, 2020 · 6983182 · 6983182
1 parent ff1f9ef
commit 6983182
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Showing 89 changed files with 2,864 additions and 5,811 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,12 +13,12 @@ Description: EpiModelHIV provides extensions to our general EpiModel package to
   sub-Saharan Africa.
 License: GPL-3
 Depends:
-    R (>= 3.2.0),
-    EpiModel (>= 1.6.5),
-    EpiModelHPC (>= 1.3.1),
+    R (>= 3.5.0),
+    EpiModel (>= 1.7.0),
+    EpiModelHPC (>= 2.0.0),
     ergm (>= 3.9.4),
     tergm (>= 3.5.2),
-    tergmLite (>= 1.1.0)
+    tergmLite (>= 1.2.0)
 Imports:
     bindata,
     network,
@@ -28,7 +28,6 @@ Suggests:
     knitr,
     testthat
 VignetteBuilder: knitr
-LinkingTo: ergm
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 LazyData: true
 Encoding: UTF-8
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,65 +1,48 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(print,nwstats)
-export(InitErgmTerm.absdiffby)
-export(InitErgmTerm.absdiffnodemix)
 export(acts_msm)
 export(aging_het)
 export(aging_msm)
-export(apportion_lr)
-export(assign_degree)
-export(base_nw_msm)
+export(arrival_msm)
 export(births_het)
-export(births_msm)
-export(calc_nwstats_msm)
 export(cd4_het)
 export(condoms_msm)
 export(control_het)
 export(control_msm)
 export(deaths_het)
-export(deaths_msm)
-export(disclose_msm)
+export(departure_msm)
 export(dx_het)
 export(edges_correct_het)
 export(edges_correct_msm)
-export(get_args)
-export(init_ccr5_msm)
+export(hivprogress_msm)
+export(hivtest_msm)
+export(hivtrans_msm)
+export(hivtx_msm)
+export(hivvl_msm)
 export(init_het)
 export(init_msm)
 export(init_status_msm)
+export(init_sti_msm)
 export(initialize_het)
 export(initialize_msm)
-export(make_nw_het)
 export(param_het)
 export(param_msm)
 export(position_msm)
 export(prep_msm)
 export(prevalence_het)
 export(prevalence_msm)
-export(progress_msm)
 export(reallocate_pcp)
 export(reinit_het)
 export(reinit_msm)
-export(remove_bad_roles_msm)
 export(riskhist_msm)
 export(simnet_het)
 export(simnet_msm)
-export(sourceDir)
-export(sti_recov)
-export(sti_trans)
-export(sti_tx)
-export(test_msm)
+export(stirecov_msm)
+export(stitrans_msm)
+export(stitx_msm)
 export(trans_het)
-export(trans_msm)
-export(truncate_sim)
 export(tx_het)
-export(tx_msm)
-export(update_aiclass_msm)
-export(update_roleclass_msm)
-export(verbose_het)
-export(verbose_msm)
 export(vl_het)
-export(vl_msm)
 import(EpiModel)
 import(EpiModelHPC)
 import(bindata)
@@ -71,11 +54,12 @@ import(tergmLite)
 importFrom(dplyr,group_by)
 importFrom(dplyr,summarise)
 importFrom(stats,plogis)
+importFrom(stats,predict)
 importFrom(stats,rbinom)
 importFrom(stats,rgeom)
 importFrom(stats,rmultinom)
 importFrom(stats,rnbinom)
 importFrom(stats,rpois)
 importFrom(stats,runif)
 importFrom(stats,simulate)
-useDynLib(EpiModelHIV, .registration = TRUE)
+importFrom(utils,tail)
diff --git a/R/EpiModelHIV-package.R b/R/EpiModelHIV-package.R
@@ -19,10 +19,9 @@
 #' @aliases EpiModelHIV
 #'
 #' @import EpiModel EpiModelHPC network networkDynamic tergmLite tergm ergm bindata
-#' @importFrom stats rbinom rgeom rmultinom rpois runif simulate rnbinom plogis
+#' @importFrom stats rbinom rgeom rmultinom rpois runif simulate rnbinom plogis predict
 #' @importFrom dplyr group_by summarise
-#'
-#' @useDynLib EpiModelHIV, .registration = TRUE
+#' @importFrom utils tail
 #'
 #' @docType package
 #' @keywords package msm het

diff --git a/R/ErgmTerms.R b/R/ErgmTerms.R
diff --git a/R/data.R b/R/data.R