Updated assign calls to inherits = !TRUE to avoid problems in global …

…environment
Auburngrads · Sep 9, 2020 · 7131dd3 · 7131dd3
1 parent 7e845c9
commit 7131dd3
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Showing 11 changed files with 18 additions and 18 deletions.
diff --git a/R/ADDTsim.R b/R/ADDTsim.R
@@ -147,7 +147,7 @@ function (ADDT.test.plan, ADDT.plan.values, number.sim = 3, plotem = F,
         }
         data.ddd[, response.column] <- the.response
         cat("\nStart simulation", i, "of", number.sim, "\n")
-        assign(envir = .frame0,  inherits = TRUE,"last.sim.ADDT.ddd", data.ddd)
+        assign(envir = .frame0, inherits = !TRUE,"last.sim.ADDT.ddd", data.ddd)
         if (i <= as.numeric(plotem)) {
             dest.degrad.mle.out <- groupm.Dest.Degrad(data.ddd,
                 distribution = distribution, transformation.response = transformation.response,
@@ -173,7 +173,7 @@ function (ADDT.test.plan, ADDT.plan.values, number.sim = 3, plotem = F,
                   collapse = ",")))
             file.name <- paste("ProblemData", floor(runif(1) *
                 1e+07), ".ddd", sep = "")
-            assign(envir = .frame0,  inherits = TRUE,file.name, data.ddd)
+            assign(envir = .frame0, inherits = !TRUE,file.name, data.ddd)
             cat("\nCheck stored data in", file.name, "\n")
         }
         else {

diff --git a/R/ComputeSummarizeMultiple.SimRMDOverTime.R b/R/ComputeSummarizeMultiple.SimRMDOverTime.R
@@ -34,7 +34,7 @@ function (RMD.pv, RMD.plan.vec, EvaluateEndTimes, begin.time = 1,
                 MysetOldClass(attr(plan.results, "class"))
                 cat("Saving simulations results", results.object.name,
                   "\n")
-                assign(envir = .frame0,  inherits = TRUE,results.object.name, plan.results)
+                assign(envir = .frame0, inherits = !TRUE,results.object.name, plan.results)
             }
             results.matrix[, j] <- SummarizeMultiple.SimRMDOverTime
             SimulatedQuantileSummary(plan.results, p = p, plot.stuff = plot.stuff,

diff --git a/R/FillRegion.R b/R/FillRegion.R
@@ -112,7 +112,7 @@ function (gmle.out,
       dir.vector <- x/sqrt(sum(x^2))
       return(dir.vector)
     }
-    assign(envir = .frame0,  inherits = TRUE,"iter.count", 0 )
+    assign(envir = .frame0, inherits = !TRUE,"iter.count", 0 )
     start.date <- date()
     theta.hat <- gmle.out$est.out$x
     dim <- length(theta.hat)
@@ -144,10 +144,10 @@ function (gmle.out,
     debug1 <- 1
     log.like <- gmle.out$log.like
     std.error <- gmle.out$t.standard.error
-    assign(envir = .frame0,  inherits = TRUE,"model", value = gmle.out$model)
-    assign(envir = .frame0,  inherits = TRUE,"debug1", value = debug1)
-    assign(envir = .frame0,  inherits = TRUE,"log.like", value = gmle.out$log.like)
-    assign(envir = .frame0,  inherits = TRUE,"data.ld", value = gmle.out$data.ld)
+    assign(envir = .frame0, inherits = !TRUE,"model", value = gmle.out$model)
+    assign(envir = .frame0, inherits = !TRUE,"debug1", value = debug1)
+    assign(envir = .frame0, inherits = !TRUE,"log.like", value = gmle.out$log.like)
+    assign(envir = .frame0, inherits = !TRUE,"data.ld", value = gmle.out$data.ld)
     sim.bound <- log.like(theta.hat) + 0.5 * qchisq(conf.level,dim)
     pt.bound <- log.like(theta.hat) + 0.5 * qchisq(conf.level,1)
     size <- trunc(iter/cull)
@@ -290,6 +290,6 @@ function (gmle.out,
         upper.2close = upper.2close, lower.2close = lower.2close,
         conf.level = conf.level, gmle.out = gmle.out, date = gmle.out$date)
     oldClass(return.list) <- "FillRegion.out"
-    assign(envir = .frame0,  inherits = TRUE,jcrname, value = return.list)
+    assign(envir = .frame0, inherits = !TRUE,jcrname, value = return.list)
     return(gmle.out)
 }
diff --git a/R/FitLinearDegradationData.R b/R/FitLinearDegradationData.R
@@ -14,7 +14,7 @@ function (PassedData, print.stuff = T, plot.stuff = T, observation.time.range =
         if (plot.stuff)
             PlotData.rmd(PassedGroupedData)
     }
-    assign(envir = .frame0,  inherits = TRUE,"RMD.data.grouped", PassedGroupedData)
+    assign(envir = .frame0, inherits = !TRUE,"RMD.data.grouped", PassedGroupedData)
     control.list <- lmeControl(maxIter = maxIter, msMaxIter = msMaxIter,
         msVerbose = msVerbose, niterEM = niterEM)
     rmd.fit <- lme(RMD.data.grouped, random = ~Time, control = control.list)

diff --git a/R/Gamma.mle.R b/R/Gamma.mle.R
@@ -68,8 +68,8 @@ Gamma.mle <-
       names(thetaorig) <- model$orig.param.names
       return(thetaorig)
     }
-    assign(envir = .frame0,  inherits = TRUE,"iter.count", 0 )
-    assign(envir = .frame0,  inherits = TRUE,"debug1", debug1)
+    assign(envir = .frame0, inherits = !TRUE,"iter.count", 0 )
+    assign(envir = .frame0, inherits = !TRUE,"debug1", debug1)
     probs <- cdfest(data.ld)$prob
     p1 <- min(probs[probs > 0])/2
     p2 <- 0.9 * max(probs)

diff --git a/R/GetAxesRange.R b/R/GetAxesRange.R
@@ -21,7 +21,7 @@ SetAxesRange <- function (type, x.axis, xlim, xlab, y.axis, ylim, ylab)
                                         sep = ""))
         the.list[[the.axes.name]] <- list(xlim = xlim, x.axis = x.axis,
                                           xlab = xlab, ylim = ylim, y.axis = y.axis, ylab = ylab)
-        assign(envir = .frame0,  inherits = TRUE,file.name, the.list)
+        assign(envir = .frame0, inherits = !TRUE,file.name, the.list)
         invisible()
       }
 

diff --git a/R/MakeMultipleRdu.R b/R/MakeMultipleRdu.R
@@ -8,6 +8,6 @@ function (frame.names, ID.column, time.column, event.column)
                 "Data"))
         file.name <- paste(frame.names[i], "rdu", sep = ".")
         cat("Saving subset", file.name, "\n")
-        assign(envir = .frame0,  inherits = TRUE,file.name, value = frame.rdu)
+        assign(envir = .frame0, inherits = !TRUE,file.name, value = frame.rdu)
     }
 }
diff --git a/R/MysetOldClass.R b/R/MysetOldClass.R
@@ -21,6 +21,6 @@ function (Classes, where = 1)
 
     allOldClasses <- sort(unique(c(Classes[[1]], allOldClasses)))
 
-    assign(envir = .frame0,  inherits = TRUE, "oldClasses", allOldClasses)
+    assign(envir = .frame0, inherits = !TRUE, "oldClasses", allOldClasses)
     invisible()
 }
diff --git a/R/NHPP.mle.R b/R/NHPP.mle.R
@@ -31,7 +31,7 @@ function (data.rdu,
           theta.start = c(NA,NA),
           kprint = 0,...)
 {
-    assign(envir = .frame0,  inherits = TRUE,"debug1", debug1)
+    assign(envir = .frame0, inherits = !TRUE,"debug1", debug1)
 
     options(digits = 5)
     func.call <- match.call()

diff --git a/R/SetAxesRange.R b/R/SetAxesRange.R
@@ -18,6 +18,6 @@ function (type, x.axis, xlim, xlab, y.axis, ylim, ylab)
         sep = ""))
     the.list[[the.axes.name]] <- list(xlim = xlim, x.axis = x.axis, 
         xlab = xlab, ylim = ylim, y.axis = y.axis, ylab = ylab)
-    assign(envir = .frame0,  inherits = TRUE,file.name, the.list)
+    assign(envir = .frame0, inherits = !TRUE,file.name, the.list)
     invisible()
 }
diff --git a/R/SplitFrame.R b/R/SplitFrame.R
@@ -8,7 +8,7 @@ function (frame, split.variable, name.prefix = deparse(substitute(frame)),
         file.name <- paste(name.prefix, SubFrameListNames[i],
             sep = sepChars)
         cat("Saving subset", file.name, "\n")
-        assign(envir = .frame0,  inherits = TRUE,file.name, value = SubFrameList[[i]])
+        assign(envir = .frame0, inherits = !TRUE,file.name, value = SubFrameList[[i]])
     }
     namesOfObjects <- paste(name.prefix, SubFrameListNames, sep = sepChars)
     invisible(namesOfObjects)