bug fixed in tests (to continue)

lbbe-software · Sep 11, 2024 · ec9b4c5 · ec9b4c5
1 parent d604940
commit ec9b4c5
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Showing 3 changed files with 31 additions and 30 deletions.
diff --git a/tests/examplewithanchoringdata.R b/tests/examplewithanchoringdata.R
@@ -36,19 +36,6 @@ if (visualize)
 
 }
 
-# various plot of fitted curves (without data)
-if (visualize)
-{
-  curvesplot(f$fitres, xmax = max(f$omicdata$dose), 
-             facetby = "model", colorby = "model")
-  curvesplot(f$fitres, xmax = max(f$omicdata$dose), 
-             facetby = "typology")
-
-  # plot of selection of curves
-  curvesplot(f$fitres[f$fitres$trend == "U", ], xmax = max(f$omicdata$dose), 
-             facetby = "id")
-
-}
 
 
 # calculation of benchmark doses
@@ -62,6 +49,17 @@ if (visualize)
   bmdplotwithgradient(r$res, xmax = max(f$omicdata$dose))
 }
 
+# various plot of fitted curves (without data)
+if (visualize)
+{
+  curvesplot(r$res, xmax = max(f$omicdata$dose), 
+             facetby = "model", colorby = "model")
+  curvesplot(r$res, xmax = max(f$omicdata$dose), 
+             facetby = "typology")
+
+}
+
+
 # Calculation of confidence intervals on BMDs by Bootstrap
 if (doboot)
 {

diff --git a/tests/examplewithmetabolomic.R b/tests/examplewithmetabolomic.R
@@ -1,6 +1,6 @@
 library(DRomics)
-visualize <- FALSE # put to TRUE for a manual check of plots
-doboot <- FALSE
+visualize <- TRUE # put to TRUE for a manual check of plots
+doboot <- TRUE
 
 # importation and check of metabolomic data
 datafilename <- system.file("extdata", "metabolo_sample.txt", package="DRomics")
@@ -65,27 +65,14 @@ if (visualize)
 
 
 
-if (visualize) 
-{
-  # various plot of fitted curves (without data)
-  curvesplot(f$fitres, xmax = max(f$omicdata$dose), 
-             facetby = "model", colorby = "model")
-
-  curvesplot(f$fitres, xmax = max(f$omicdata$dose), 
-             facetby = "typology")
-
-  # plot of selection of curves
-  curvesplot(f$fitres[f$fitres$trend == "U", ], xmax = max(f$omicdata$dose), 
-             facetby = "id")
-
-}
 
 # calculation of benchmark doses
 # options in shiny : z (numerical positive value), x (numerical positive value : percentage)
 (r <- bmdcalc(f, z = 1, x = 10))
 if (visualize)
 (r.2 <- bmdcalc(f, z = 2, x = 50))
 
+
 # plot of BMD
 # options in shiny : BMDtype (2 possibilities), plottype (3 possibilities), by (3 possibilities)
 # hist.bins (integer for hist only)
@@ -101,6 +88,22 @@ if (visualize)
 
 }
 
+if (visualize) 
+{
+  # various plot of fitted curves (without data)
+  curvesplot(r$res, xmax = max(r$omicdata$dose), 
+             facetby = "model", colorby = "model")
+
+  curvesplot(r$res, xmax = max(r$omicdata$dose), 
+             facetby = "typology")
+
+  # plot of selection of curves
+  curvesplot(r$res[r$res$trend == "U", ], xmax = max(f$omicdata$dose), 
+             facetby = "id")
+
+}
+
+
 if (doboot)
 {
   niter <- 1000

diff --git a/tests/examplewithmicroarray.R b/tests/examplewithmicroarray.R
@@ -42,7 +42,7 @@ if (visualize)
   # with a chosen number of first items
   plot(f, items = 12) 
   # with chosen items in a specified order
-  plot(f, items = c("301.2", "363.1", "383.1"))
+  plot(f, items = c("15", "27.1", "7.1"))
   # residual plots
   plot(f, items = 12, plot.type = "fitted_residuals") 
   plot(f, items = 12, plot.type = "dose_residuals")