import namespace from exDE

dd-harp · Dec 14, 2023 · 1a1103f · 1a1103f
1 parent 1a5edc5
commit 1a1103f
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Showing 16 changed files with 524 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,9 +13,11 @@ RoxygenNote: 7.2.3
 URL: https://dd-harp.github.io/mobwork/
 BugReports: https://github.com/dd-harp/mobwork/issues
 Roxygen: list(markdown = TRUE)
+Depends:
+  exDE
 Imports:
-  exDE,
   stats
 Suggests:
-    knitr
+    knitr,
+    rmarkdown 
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,25 +1,29 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(F_eggs,RMG)
+S3method(F_fqZ,RMG)
+S3method(MBionomics,RMG)
+S3method(dMYZdt,RMG)
+S3method(get_inits_MYZ,RMG)
 S3method(lines_M,RM)
 S3method(lines_M,RMG)
 S3method(lines_X,SIS)
 S3method(lines_YZ,RM)
 S3method(lines_YZ,RMG)
 S3method(lines_YZ_fracs,RM)
 S3method(lines_YZ_fracs,RMG)
+S3method(make_indices_MYZ,RMG)
+S3method(parse_deout_MYZ,RMG)
 S3method(plot_M,RM)
 S3method(plot_M,RMG)
 S3method(plot_X,SIS)
 S3method(plot_YZ,RM)
 S3method(plot_YZ,RMG)
 S3method(plot_YZ_fracs,RM)
 S3method(plot_YZ_fracs,RMG)
+S3method(setup_MYZ,RMG)
 S3method(split_stratum_by_biting,SIS)
-export(F_eggs.RMG)
-export(F_fqZ.RMG)
-export(MBionomics.RMG)
-export(dMYZdt.RMG)
-export(get_inits_MYZ.RMG)
+S3method(update_inits_MYZ,RMG)
 export(lines_EIR)
 export(lines_M)
 export(lines_PR)
@@ -31,10 +35,8 @@ export(lines_eirVpr)
 export(lines_eirpr)
 export(make_MYZinits_RMG)
 export(make_MYZpar_RMG)
-export(make_indices_MYZ.RMG)
 export(make_inits_MYZ_RMG)
 export(make_parameters_MYZ_RMG)
-export(parse_deout_MYZ.RMG)
 export(plot_EIR)
 export(plot_M)
 export(plot_PR)
@@ -45,10 +47,8 @@ export(plot_aEIR)
 export(plot_eirVpr)
 export(plot_eirpr)
 export(pr2Lambda)
-export(setup_MYZ.RMG)
 export(split_stratum_by_biting)
 export(ssMYZ)
-export(update_inits_MYZ.RMG)
 export(xde_eir2ni)
 export(xde_eir2pr)
 export(xde_pr2eir)
@@ -57,4 +57,5 @@ export(xde_scaling)
 export(xde_scaling_Z)
 export(xde_scaling_eir)
 export(xde_scaling_lambda)
+import("exDE")
 importFrom(utils,tail)
diff --git a/R/MYZmod-RMG.R b/R/MYZmod-RMG.R
@@ -278,7 +278,6 @@ get_inits_MYZ.RMG <- function(pars) {with(pars$MYZinits,{
   c(U0, Gu0, Y0, Gy0, Z0, Gz0)
 })}
 
-
 #' Basic plotting: plot mosquito population density for the "RMG" model
 #'
 #' @inheritParams plot_M

diff --git a/R/mobwork-package.R b/R/mobwork-package.R
@@ -0,0 +1,8 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @import "exDE"
+## usethis namespace: end
+NULL
+#>NULL
diff --git a/man/F_eggs.RMG.Rd b/man/F_eggs.RMG.Rd
diff --git a/man/F_fqZ.RMG.Rd b/man/F_fqZ.RMG.Rd
diff --git a/man/MBionomics.RMG.Rd b/man/MBionomics.RMG.Rd
diff --git a/man/dMYZdt.RMG.Rd b/man/dMYZdt.RMG.Rd
diff --git a/man/get_inits_MYZ.RMG.Rd b/man/get_inits_MYZ.RMG.Rd
diff --git a/man/make_indices_MYZ.RMG.Rd b/man/make_indices_MYZ.RMG.Rd
diff --git a/man/mobwork-package.Rd b/man/mobwork-package.Rd
diff --git a/man/parse_deout_MYZ.RMG.Rd b/man/parse_deout_MYZ.RMG.Rd
diff --git a/man/setup_MYZ.RMG.Rd b/man/setup_MYZ.RMG.Rd
diff --git a/man/update_inits_MYZ.RMG.Rd b/man/update_inits_MYZ.RMG.Rd
diff --git a/vignettes/Xmod-SIS.Rmd b/vignettes/Xmod-SIS.Rmd
@@ -4,8 +4,10 @@ date: "`r format(Sys.time(), '%B %d, %Y')`"
 output:
   html_document: 
     theme: paper 
-  pdf_document: default
-split_by: section+number
+vignette: >
+  %\VignetteIndexEntry{The Generalized Ross-Macdonald Adult Mosquito Model}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r, echo=FALSE, warning=FALSE, messages=FALSE, purl=F}

diff --git a/vignettes/Xmod-SIS.html b/vignettes/Xmod-SIS.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -278,7 +278,6 @@ get_inits_MYZ.RMG <- function(pars) {with(pars$MYZinits,{ @@
       c(U0, Gu0, Y0, Gy0, Z0, Gz0)
     })}
     #' Basic plotting: plot mosquito population density for the "RMG" model
     #'
     #' @inheritParams plot_M
@@ Expand Down @@