move coda to imports and add packages needed for convergence code

ococrook · Oct 23, 2024 · 3e9a9b3 · 3e9a9b3
1 parent 80f9147
commit 3e9a9b3
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Showing 2 changed files with 41 additions and 13 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,9 +38,12 @@ Imports: Rcpp (>= 1.0.4.6),
     stats,
     utils,
     grDevices,
-    rlang
+    rlang,
+    RColorBrewer,
+    gtools, 
+    gridExtra,
+    coda (>= 0.19-4)
 Suggests: 
-    coda (>= 0.19-4),
     testthat,
     interp,
     fields,
@@ -51,7 +54,7 @@ Suggests:
 VignetteBuilder: knitr
 LinkingTo: Rcpp, RcppArmadillo, BH
 Roxygen: list(markdown=TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.3.2
 biocViews: Bayesian, Classification, Clustering, ImmunoOncology,
     QualityControl,DataImport, Proteomics, MassSpectrometry
 BugReports: https://github.com/ococrook/bandle/issues

diff --git a/NAMESPACE b/NAMESPACE
@@ -40,6 +40,11 @@ importFrom("circlize", "chordDiagram", "circos.trackPlotRegion", "CELL_META",
 importFrom("grDevices", "dev.off", "rainbow")
 importFrom("plyr", "id")
 importFrom("rlang", ".data")
+importFrom("RColorBrewer", "brewer.pal")
+importFrom("coda", "traceplot", "densplot", "gelman.diag")
+importFrom("gtools", "combinations")
+importFrom("gridExtra", "grid.arrange")
+
 
 exportClasses(bandleChains,
               bandleSummary,
@@ -55,14 +60,34 @@ exportMethods(posteriorEstimates,
 export(diffLoc,
        mcmc_plot_probs,
        spatial2D,
-       plotTranslocations, plotTable,
-       plotConvergence, plotGPmatern,
-       fitGP, fitGPmaternPC, fitGPmatern, 
-       bandle, bandlePredict, bandleProcess,
-       diffLocalisationProb, bootstrapdiffLocprob,
-       binomialDiffLocProb, EFDR,
-       meanOrganelle, prior_pred_dir,
-       prior_pred_pg, mrMethod, sim_dynamic,
-       summaries, StatStratum, dmvtCpp, Gumbel,
-       covOrganelle, pg_prior, kldirpg, kldir)
+       plotTranslocations, 
+       plotTable,
+       plotGPmatern,
+       fitGP, 
+       fitGPmaternPC, 
+       fitGPmatern, 
+       bandle, 
+       bandlePredict, 
+       bandleProcess,
+       diffLocalisationProb, 
+       bootstrapdiffLocprob, 
+       binomialDiffLocProb, 
+       EFDR,
+       meanOrganelle, 
+       prior_pred_dir, 
+       prior_pred_pg, 
+       mrMethod, 
+       sim_dynamic, 
+       kldirpg, 
+       kldir,
+       summaries, 
+       StatStratum, 
+       dmvtCpp, 
+       Gumbel,
+       covOrganelle, 
+       pg_prior, 
+       plotConvergence, 
+       plotOutliers,
+       bandle_get_outliers,
+       calculateGelman)