Automated build.

.setup/latex/pdf/.gitignore

@@ -0,0 +1,5 @@
+*
+*/
+!*.pdf
+!.gitignore
+!bib.bib

.setup/vignettes/fit-ct-var-dynr.Rmd.orig

@@ -31,7 +31,7 @@ knitr::opts_chunk$set(
 ```{r}
 #| echo = FALSE
 set.seed(42)
-n <- 5
+n <- 50
 time <- 100
 delta_t <- 0.10
 k <- p <- 3

.setup/vignettes/fit-ct-var-mx.Rmd.orig

@@ -32,7 +32,7 @@ knitr::opts_chunk$set(
 ```{r}
 #| echo = FALSE
 set.seed(42)
-n <- 5
+n <- 50
 time <- 100
 delta_t <- 0.10
 k <- p <- 3

.setup/vignettes/med-boot.Rmd.orig

@@ -34,7 +34,7 @@ The `cTMed` package provides a bootstrap approach, in addition to the delta and
 ```{r}
 #| include = FALSE
 set.seed(42)
-n <- 5
+n <- 50
 time <- 100
 delta_t <- 0.10
 k <- p <- 3

.setup/vignettes/med-std.Rmd.orig

@@ -139,7 +139,7 @@ mc <- MCMedStd(
   from = "x",
   to = "y",
   med = "m",
-  R = 1000L,
+  R = 20000L,
   ncores = parallel::detectCores() # use multiple cores
 )
 plot(mc)

.setup/vignettes/med.Rmd.orig

@@ -97,7 +97,7 @@ mc <- MCMed(
   from = "x",
   to = "y",
   med = "m",
-  R = 1000L,
+  R = 20000L,
   ncores = parallel::detectCores() # use multiple cores
 )
 plot(mc)

CITATION.cff

@@ -8,7 +8,7 @@ message: 'To cite package "cTMed" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'cTMed: Continuous Time Mediation'
-version: 1.0.4.9000
+version: 1.0.5
 identifiers:
 - type: doi
   value: 10.32614/CRAN.package.cTMed
@@ -31,7 +31,7 @@ preferred-citation:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4818-8420
   year: '2024'
-  notes: R package version 1.0.4.9000
+  notes: R package version 1.0.5
 repository: https://CRAN.R-project.org/package=cTMed
 repository-code: https://github.com/jeksterslab/cTMed
 url: https://jeksterslab.github.io/cTMed/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cTMed
 Title: Continuous Time Mediation
-Version: 1.0.4.9000
+Version: 1.0.5
 Authors@R: 
     person(given = "Ivan Jacob Agaloos",
            family = "Pesigan",

NAMESPACE

@@ -23,8 +23,10 @@ S3method(summary,ctmedposteriorphi)
 S3method(summary,ctmedtraj)
 export(BootBeta)
 export(BootBetaStd)
+export(BootIndirectCentral)
 export(BootMed)
 export(BootMedStd)
+export(BootTotalCentral)
 export(DeltaBeta)
 export(DeltaBetaStd)
 export(DeltaIndirectCentral)

NEWS.md

@@ -1,10 +1,9 @@
-# cTMed 1.0.4.9000
+# cTMed 1.0.5
 
 ## Patch
 
-* Latest development version.
 * Added the `MCPhiSigma()` function.
-* Minor edits to tests.
+* Added the `BootIndirectCentral()` and `BootTotalCentral()` functions.
 
 # cTMed 1.0.4
 

R/cTMed-boot-central-dot.R

@@ -0,0 +1,153 @@
+.BootCentral <- function(phi,
+                         phi_hat,
+                         delta_t,
+                         total,
+                         ncores = NULL) {
+  if (total) {
+    Fun <- .TotalCentral
+  } else {
+    Fun <- .IndirectCentral
+  }
+  # nocov start
+  par <- FALSE
+  if (!is.null(ncores)) {
+    ncores <- as.integer(ncores)
+    R <- length(phi)
+    if (ncores > R) {
+      ncores <- R
+    }
+    if (ncores > 1) {
+      par <- TRUE
+    }
+  }
+  if (par) {
+    os_type <- Sys.info()["sysname"]
+    if (os_type == "Darwin") {
+      fork <- TRUE
+    } else if (os_type == "Linux") {
+      fork <- TRUE
+    } else {
+      fork <- FALSE
+    }
+    if (fork) {
+      output <- lapply(
+        X = delta_t,
+        FUN = function(i) {
+          thetahatstar <- parallel::mclapply(
+            X = phi,
+            FUN = Fun,
+            delta_t = i,
+            mc.cores = ncores
+          )
+          thetahatstar <- do.call(
+            what = "rbind",
+            args = thetahatstar
+          )
+          colnames(thetahatstar) <- colnames(phi_hat)
+          thetahatstar <- cbind(
+            thetahatstar,
+            interval = i
+          )
+          est <- c(
+            Fun(
+              phi = phi_hat,
+              delta_t = i
+            ),
+            i
+          )
+          names(est) <- c(
+            colnames(phi_hat),
+            "interval"
+          )
+          out <- list(
+            delta_t = i,
+            est = est,
+            thetahatstar = thetahatstar
+          )
+          return(out)
+        }
+      )
+    } else {
+      cl <- parallel::makeCluster(ncores)
+      on.exit(
+        parallel::stopCluster(cl = cl)
+      )
+      output <- lapply(
+        X = delta_t,
+        FUN = function(i) {
+          thetahatstar <- parallel::parLapply(
+            cl = cl,
+            X = phi,
+            fun = Fun,
+            delta_t = i
+          )
+          thetahatstar <- do.call(
+            what = "rbind",
+            args = thetahatstar
+          )
+          colnames(thetahatstar) <- colnames(phi_hat)
+          thetahatstar <- cbind(
+            thetahatstar,
+            interval = i
+          )
+          est <- c(
+            Fun(
+              phi = phi_hat,
+              delta_t = i
+            ),
+            i
+          )
+          names(est) <- c(
+            colnames(phi_hat),
+            "interval"
+          )
+          out <- list(
+            delta_t = i,
+            est = est,
+            thetahatstar = thetahatstar
+          )
+          return(out)
+        }
+      )
+    }
+    # nocov end
+  } else {
+    output <- lapply(
+      X = delta_t,
+      FUN = function(i) {
+        thetahatstar <- lapply(
+          X = phi,
+          FUN = Fun,
+          delta_t = i
+        )
+        thetahatstar <- do.call(
+          what = "rbind",
+          args = thetahatstar
+        )
+        colnames(thetahatstar) <- colnames(phi_hat)
+        thetahatstar <- cbind(
+          thetahatstar,
+          interval = i
+        )
+        est <- c(
+          Fun(
+            phi = phi_hat,
+            delta_t = i
+          ),
+          i
+        )
+        names(est) <- c(
+          colnames(phi_hat),
+          "interval"
+        )
+        out <- list(
+          delta_t = i,
+          est = est,
+          thetahatstar = thetahatstar
+        )
+        return(out)
+      }
+    )
+  }
+  return(output)
+}