updated roxygen

ropensci · Dec 31, 2024 · faf4cf4 · faf4cf4
1 parent 3db3f78
commit faf4cf4
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Showing 52 changed files with 8,332 additions and 18,923 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,21 +2,7 @@
 inst/doc
 src/eDNAjoint.so
 src/RcppExports.o
-src/stanExports_joint_binary_catchability_gamma.o
-src/stanExports_joint_binary_catchability_negbin.o
-src/stanExports_joint_binary_catchability_pois.o
-src/stanExports_joint_binary_cov_catchability_gamma.o
-src/stanExports_joint_binary_cov_catchability_negbin.o
-src/stanExports_joint_binary_cov_catchability_pois.o
-src/stanExports_joint_binary_cov_gamma.o
-src/stanExports_joint_binary_cov_negbin.o
-src/stanExports_joint_binary_cov_pois.o
-src/stanExports_joint_binary_gamma.o
-src/stanExports_joint_binary_negbin.o
-src/stanExports_joint_binary_pois.o
-src/stanExports_traditional_catchability_gamma.o
-src/stanExports_traditional_catchability_negbin.o
-src/stanExports_traditional_catchability_pois.o
-src/stanExports_traditional_gamma.o
-src/stanExports_traditional_negbin.o
-src/stanExports_traditional_pois.o
+src/stanExports_joint_continuous.o
+src/stanExports_joint_count.o
+src/stanExports_traditional_count.o
+src/stanExports_traditional_continuous.o
diff --git a/.ipynb_checkpoints/Untitled-checkpoint.ipynb b/.ipynb_checkpoints/Untitled-checkpoint.ipynb
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,7 +13,7 @@ URL: https://github.com/ropensci/eDNAjoint, https://docs.ropensci.org/eDNAjoint/
 BugReports: https://github.com/ropensci/eDNAjoint/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd", "srr::srr_stats_roclet"))
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Biarch: true
 Depends: 
     R (>= 3.4.0)

diff --git a/R/stanmodels.R b/R/stanmodels.R
@@ -1,27 +1,13 @@
 # Generated by rstantools.  Do not edit by hand.
 
 # names of stan models
-stanmodels <- c("joint_binary_catchability_gamma", "joint_binary_catchability_negbin", "joint_binary_catchability_pois", "joint_binary_cov_catchability_gamma", "joint_binary_cov_catchability_negbin", "joint_binary_cov_catchability_pois", "joint_binary_cov_gamma", "joint_binary_cov_negbin", "joint_binary_cov_pois", "joint_binary_gamma", "joint_binary_negbin", "joint_binary_pois", "traditional_catchability_gamma", "traditional_catchability_negbin", "traditional_catchability_pois", "traditional_gamma", "traditional_negbin", "traditional_pois")
+stanmodels <- c("joint_continuous", "joint_count", "traditional_continuous", "traditional_count")
 
 # load each stan module
-Rcpp::loadModule("stan_fit4joint_binary_catchability_gamma_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_catchability_negbin_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_catchability_pois_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_cov_catchability_gamma_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_cov_catchability_negbin_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_cov_catchability_pois_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_cov_gamma_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_cov_negbin_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_cov_pois_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_gamma_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_negbin_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4joint_binary_pois_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4traditional_catchability_gamma_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4traditional_catchability_negbin_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4traditional_catchability_pois_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4traditional_gamma_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4traditional_negbin_mod", what = TRUE)
-Rcpp::loadModule("stan_fit4traditional_pois_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4joint_continuous_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4joint_count_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4traditional_continuous_mod", what = TRUE)
+Rcpp::loadModule("stan_fit4traditional_count_mod", what = TRUE)
 
 # instantiate each stanmodel object
 stanmodels <- sapply(stanmodels, function(model_name) {

diff --git a/man/detectionCalculate.Rd b/man/detectionCalculate.Rd
diff --git a/man/detectionPlot.Rd b/man/detectionPlot.Rd
diff --git a/man/jointModel.Rd b/man/jointModel.Rd
diff --git a/man/jointSelect.Rd b/man/jointSelect.Rd
diff --git a/man/jointSummarize.Rd b/man/jointSummarize.Rd
diff --git a/man/muCritical.Rd b/man/muCritical.Rd
diff --git a/man/traditionalModel.Rd b/man/traditionalModel.Rd
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -12,44 +12,16 @@ Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
 
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4joint_binary_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_catchability_pois_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_gamma_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_negbin_mod();
-RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_pois_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_continuous_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4joint_count_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_continuous_mod();
+RcppExport SEXP _rcpp_module_boot_stan_fit4traditional_count_mod();
 
 static const R_CallMethodDef CallEntries[] = {
-    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_catchability_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_catchability_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_cov_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4joint_binary_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_binary_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_catchability_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_catchability_pois_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_gamma_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_gamma_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_negbin_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_negbin_mod, 0},
-    {"_rcpp_module_boot_stan_fit4traditional_pois_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_pois_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_continuous_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_continuous_mod, 0},
+    {"_rcpp_module_boot_stan_fit4joint_count_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4joint_count_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_continuous_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_continuous_mod, 0},
+    {"_rcpp_module_boot_stan_fit4traditional_count_mod", (DL_FUNC) &_rcpp_module_boot_stan_fit4traditional_count_mod, 0},
     {NULL, NULL, 0}
 };
 

diff --git a/src/stanExports_joint_binary_catchability_gamma.cc b/src/stanExports_joint_binary_catchability_gamma.cc