re render upon pass devtools::check()

afsc-assessments · Dec 17, 2024 · d4be9aa · d4be9aa
1 parent 71833c2
commit d4be9aa
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Showing 210 changed files with 14,143 additions and 167 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,5 +2,3 @@
 .Rhistory
 .RData
 .Ruserdata
-inst/doc
-docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -31,7 +31,8 @@ Imports:
     gridExtra,
     here
 LinkingTo:
-    TMB
+    TMB,
+    RcppEigen
 Suggests: 
     knitr,
     rmarkdown

diff --git a/NAMESPACE b/NAMESPACE
@@ -7,5 +7,3 @@ export(confint_Deriv)
 export(get_Breaks)
 export(refit_Growth)
 import(mgcv)
-useDynLib(growthbreaks, .registration=TRUE); useDynLib(growthbreaks_TMBExports)
-useDynLib(src, .registration=TRUE); useDynLib(src_TMBExports)
diff --git a/R/growthbreaks-package.R b/R/growthbreaks-package.R
diff --git a/R/misc.R b/R/misc.R
@@ -23,5 +23,5 @@ vonB_optim <- function(pars, ages_use, obs){
 
 }
 
-# TMB::compile(here::here("src","sptlVB_Sel_Sigma.cpp"))
-# dyn.load(TMB::dynlib(here::here("src","sptlVB_Sel_Sigma")))
+# TMB::compile(here::here("src", "growthbreaks.cpp"))
+# dyn.load(TMB::dynlib(here::here("src", "growthbreaks")))
diff --git a/R/refit_Growth.R b/R/refit_Growth.R
@@ -66,7 +66,7 @@ refit_Growth <- function(dat = simulated_data, breakpoints, selex = FALSE, showP
 
   # TMB::compile(here::here("TMB","sptlVB_Sel_Sigma.cpp"))
   # dyn.load(TMB::dynlib(here::here("TMB","sptlVB_Sel_Sigma")))
-  model <- TMB::MakeADFun(data, parameters,  DLL="sptlVB_Sel_Sigma",silent=T,map=map)
+  model <- TMB::MakeADFun(data, parameters,  DLL="growthbreaks",silent=T,map=map)
   fit <- nlminb(
     model$par,
     model$fn,

diff --git a/R/src-package.R b/R/src-package.R
diff --git a/docs/.nojekyll b/docs/.nojekyll
@@ -0,0 +1 @@
+
diff --git a/docs/404.html b/docs/404.html