Add covr yaml file

_pkgdown.yml

@@ -25,25 +25,27 @@ reference:
   - '`Wang2007`'
   - '`pump`'
   - '`rats`'
+  - '`warfarin`'
 - title: Options for fitting and output
   contents:
-  - '`nmSave`'
-  - '`nmDocx`'
-  - '`saemControl`'
   - '`foceiControl`'
   - '`nlmeControl`'
+  - '`nmDocx`'
+  - '`nmSave`'
+  - '`saemControl`'
   - '`tableControl`'
 - title: Low level estimation routines
   contents:
-  - '`gnlmm`'
-  - '`foceiFit`'
-  - '`saem.fit`'
-  - '`dynmodel`'
+  - '`as.dynmodel`'
+  - '`as.focei.dynmodel`'
   - '`dynmodel.mcmc`'
+  - '`dynmodelControl`'
+  - '`dynmodel`'
+  - '`foceiFit`'
+  - '`gnlmm`'
   - '`nlme_lin_cmpt`'
   - '`nlme_ode`'
-  - '`as.dynmodel`'
-  - '`as.focei.dynmodel`'
+  - '`saem.fit`'
 - title: Unit tests and validation functions
   contents:
   - '`nlmixrValidate`'
@@ -74,6 +76,7 @@ reference:
   - '`stat_cens`'
 - title: Internal functions
   contents:
+  - '`VarCorr.nlmixrNlme'`
   - '`as.focei`'
   - '`bootdata`'
   - '`calc.2LL`'
@@ -96,37 +99,51 @@ reference:
   - '`metabolite`'
   - '`model`'
   - '`nlme_gof`'
-  - '`nlmixr`'
   - '`nlmixrAugPred`'
   - '`nlmixrBounds.eta.names`'
   - '`nlmixrBounds.focei.upper.lower`'
+  - '`nlmixrBoundsParser`'
+  - '`nlmixrBounds`'
+  - '`nlmixrDynmodelConvert`'
+  - '`nlmixrEst`'
+  - '`nlmixrEval_`'
+  - '`nlmixrGill83`'
+  - '`nlmixrHess`'
   - '`nlmixrLogo`'
   - '`nlmixrPred`'
   - '`nlmixrSim`'
+  - '`nlmixrTest`'
+  - '`nlmixrUI.dynmodelfun2`'
+  - '`nlmixrUI.dynmodelfun`'
   - '`nlmixrUI.focei.fixed`'
   - '`nlmixrUI.focei.inits`'
   - '`nlmixrUI.nlme.specs`'
   - '`nlmixrUI.rxode.pred`'
   - '`nlmixrUI.saem.ares`'
   - '`nlmixrUI.saem.bres`'
+  - '`nlmixrUI.saem.cres`'
   - '`nlmixrUI.saem.distribution`'
   - '`nlmixrUI.saem.eta.trans`'
   - '`nlmixrUI.saem.fit`'
   - '`nlmixrUI.saem.fixed`'
-  - '`nlmixrUI.saem.init`'
   - '`nlmixrUI.saem.init.omega`'
   - '`nlmixrUI.saem.init.theta`'
+  - '`nlmixrUI.saem.init`'
   - '`nlmixrUI.saem.log.eta`'
-  - '`nlmixrUI.saem.model`'
   - '`nlmixrUI.saem.model.omega`'
+  - '`nlmixrUI.saem.model`'
   - '`nlmixrUI.saem.res.mod`'
   - '`nlmixrUI.saem.res.name`'
+  - '`nlmixrUI.saem.rx1`'
   - '`nlmixrUI.saem.theta.name`'
   - '`nlmixrUI.theta.pars`'
   - '`nlmixrVersion`'
   - '`nlmixr_fit`'
+  - '`nlmixr`'
+  - '`nmLst`'
   - '`nmsimplex`'
   - '`ofv`'
+  - '`pheno_sd`'
   - '`plot.dyn.ID`'
   - '`plot.dyn.mcmc`'
   - '`plot.nlmixrFitData`'
@@ -139,6 +156,7 @@ reference:
   - '`print.saemFit`'
   - '`residuals.nlmixrFitData`'
   - '`saem.cleanup`'
+  - '`setCov`'
   - '`setOfv`'
   - '`sqrtm`'
   - '`summary.dyn.ID`'
@@ -150,22 +168,6 @@ reference:
   - '`vpc_saemFit`'
   - '`vpc_ui`'
   - '`yeoJohnson`'
-  - '`nlmixrBounds`'
-  - '`nlmixrBoundsParser`'
-  - '`nlmixrDynmodelConvert`'
-  - '`nlmixrEst`'
-  - '`nlmixrGill83`'
-  - '`nlmixrEval_`'
-  - '`nlmixrHess`'
-  - '`nlmixrTest`'
-  - '`nlmixrUI.dynmodelfun`'
-  - '`nlmixrUI.dynmodelfun2`'
-  - '`nlmixrUI.saem.cres`'
-  - '`nlmixrUI.saem.rx1`'
-  - '`nmLst`'
-  - '`pheno_sd`'
-  - '`setCov`'
-  - '`warfarin `'
 navbar:
   left:
   - text: Articles

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true