fixed initial values functions and added coverage

ropensci · Apr 1, 2024 · 6eeae83 · 6eeae83
1 parent 87de4bb
commit 6eeae83
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Showing 8 changed files with 25 additions and 3 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
 ^eDNAjoint\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
+^\.github$
diff --git a/.Rhistory b/.Rhistory
@@ -2,3 +2,7 @@ roxygen2::roxygenise()
 install.packages("codemetar")
 codemetar::write_codemeta()
 codemetar::give_opinions('C:\\Users\\abiga\\Documents\\WSG\\eDNAjoint')
+devtools::check()
+install.packages('roxygen2')
+devtools::check()
+.Last.error
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -48,3 +48,9 @@ jobs:
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: abigailkeller/eDNAjoint
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,8 @@ Imports:
     RcppParallel (>= 5.0.1),
     rstan (>= 2.26.23),
     rstantools (>= 2.3.1.1),
-    tidyr
+    tidyr, 
+    rlist
 LinkingTo: 
     BH (>= 1.66.0),
     Rcpp (>= 0.12.0),

diff --git a/R/jointModel.R b/R/jointModel.R
@@ -541,6 +541,7 @@ init_joint_cov <- function(n.chain,count_all,cov,initial_values){
         p10 <- stats::runif(1,log(0.0001),log(0.08)),
         alpha <- rep(0.1,length(cov)+1)
       )
+      names(A[[i]]) <- c('mu','p10','alpha')
     }
   }
 
@@ -589,6 +590,7 @@ init_joint_cov_catchability <- function(n.chain,count_all,q_names,cov,
         p10 <- stats::runif(1,log(0.0001),log(0.08)),
         alpha <- rep(0.1,length(cov)+1)
       )
+      names(A[[i]]) <- c('mu','q','p10','alpha')
     }
   }
 
@@ -636,6 +638,7 @@ init_joint_catchability <- function(n.chain,count_all,q_names,initial_values){
         p10 <- stats::runif(1,log(0.0001),log(0.08)),
         beta <- 0.5
       )
+      names(A[[i]]) <- c('mu','q','p10','beta')
     }
   }
 
@@ -676,6 +679,7 @@ init_joint <- function(n.chain,count_all,initial_values){
         p10 <- stats::runif(1,log(0.0001),log(0.08)),
         beta <- 0.5
       )
+      names(A[[i]]) <- c('mu','p10','beta')
     }
   }
 

diff --git a/R/traditionalModel.R b/R/traditionalModel.R
@@ -341,6 +341,7 @@ init_trad_catchability <- function(n.chain, count_all, q_names, initial_values){
         mu <- stats::runif(length(unique(count_all$L)), 0.01, 5),
         q <- as.data.frame(stats::runif(length(q_names),0.01,1))
       )
+      names(A[[i]]) <- c('mu','q')
     }
   }
 
@@ -367,6 +368,7 @@ init_trad <- function(n.chain, count_all, initial_values){
       A[[i]] <- list(
         mu <- stats::runif(length(unique(count_all$L)), 0.01, 5)
       )
+      names(A[[i]]) <- 'mu'
     }
   }
 

diff --git a/README.Rmd b/README.Rmd
@@ -14,11 +14,14 @@ knitr::opts_chunk$set(
 ```
 
 # eDNAjoint
-<img src="man/figures/logo.png" align="right" height="250" dpi="700" />
+<img src="man/figures/logo.png" align="right" height="200" dpi="700" />
 <!-- badges: start -->
+[![R-CMD-check](https://github.com/abigailkeller/eDNAjoint/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions/workflows/R-CMD-check.yaml)
+[![test-coverage](https://github.com/abigailkeller/eDNAjoint/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions/workflows/test-coverage.yaml)
+[![codecov](https://codecov.io/gh/abigailkeller/eDNAjoint/graph/badge.svg?token=AEVR9NSQ9Z)](https://codecov.io/gh/abigailkeller/eDNAjoint)
 <!-- badges: end -->
 
-```{r}
+```{r, echo=FALSE}
 #' @srrstats {BS1.2a} README with high-level overview and examples here
 ```