Adding the latest

Author: Keith Goldfeld

Diff for: .gitignore

@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+src/*.o
+src/*.so
+src/*.dll

Diff for: DESCRIPTION

@@ -1,29 +1,31 @@
-Package: simstudy
-Type: Package
-Title: Simulation of Study Data
-Version: 0.0.0.9000
-Date: 2016-01-04
-Authors@R: person("Keith", "Goldfeld", email = "[email protected]",
-                  role = c("aut", "cre"))
-Author: Keith Goldfeld [aut]
-Mainainer: Keith Goldfeld <[email protected]>
-Description: A collection of functions that allow users to generate simulated
-    data sets in order to explore modeling techniques or better understand data
-    generating processes. The user specifies a set of relationships between
-    covariates, and generates data based on these specifications. The final data
-    sets can represent data from randomized control trials, repeated measure
-    (longitudinal) designs, and cluster randomized trials. Missingness can be
-    generated using various mechanisms (MCAR, MAR, NMAR).
-Depends:
-    R (>= 3.2.2),
-    data.table,
-    mvnfast
-License: GPL-3
-LazyData: TRUE
-Imports:
-    data.table
-RoxygenNote: 5.0.1
-Suggests: testthat,
-    knitr,
-    rmarkdown
-VignetteBuilder: knitr
+Package: simstudy
+Type: Package
+Title: Simulation of Study Data
+Version: 0.0.0.9000
+Date: 2016-01-04
+Authors@R: person("Keith", "Goldfeld", email = "[email protected]",
+                  role = c("aut", "cre"))
+Author: Keith Goldfeld [aut]
+Mainainer: Keith Goldfeld <[email protected]>
+Description: A collection of functions that allow users to generate simulated
+    data sets in order to explore modeling techniques or better understand data
+    generating processes. The user specifies a set of relationships between
+    covariates, and generates data based on these specifications. The final data
+    sets can represent data from randomized control trials, repeated measure
+    (longitudinal) designs, and cluster randomized trials. Missingness can be
+    generated using various mechanisms (MCAR, MAR, NMAR).
+Depends:
+    R (>= 3.2.2),
+    data.table,
+    mvnfast
+License: GPL-3
+LazyData: TRUE
+Imports:
+    data.table,
+    Rcpp
+RoxygenNote: 5.0.1
+Suggests: testthat,
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+LinkingTo: Rcpp

Diff for: LICENSE

@@ -1,12 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 export(addColumns)
-export(addDefs)
 export(addPeriods)
+export(defData)
 export(genCluster)
 export(genCorData)
 export(genData)
 export(genMiss)
 export(genObs)
-export(initDefs)
 export(mergeData)
+importFrom(Rcpp,sourceCpp)
+useDynLib(simstudy)

Diff for: NAMESPACE

@@ -0,0 +1,16 @@
+# This file was generated by Rcpp::compileAttributes
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' Multinomial
+#'
+vecMultinom <- function(probs) {
+    .Call('simstudy_vecMultinom', PACKAGE = 'simstudy', probs)
+}
+
+#' Matrix Multinomial
+#'
+#' @export
+matMultinom <- function(probmatrix) {
+    .Call('simstudy_matMultinom', PACKAGE = 'simstudy', probmatrix)
+}
+

Diff for: R/RcppExports.R

@@ -1,20 +1,25 @@
-#' Add columns to existing data set
-#'
-#' @param dtDefs Name of definitions for added columns
-#' @param dtOld Name of data table that is to be updated
-#' @return An updated data.table that contains the added simulated data
-#' @export
-#'
-
-addColumns <- function(dtDefs,dtOld) {
-
-  iter = nrow(dtDefs)
-  n = nrow(dtOld)
-  for (i in (1 : iter)) {
-    dtOld <- generate(dtDefs[i,], n, dtOld)
-  }
-
-  data.table::data.table(dtOld)
-
-}
-
+#' Add columns to existing data set
+#'
+#' @param dtDefs Name of definitions for added columns
+#' @param dtOld Name of data table that is to be updated
+#' @return An updated data.table that contains the added simulated data
+#' @export
+#'
+
+addColumns <- function(dtDefs,dtOld) {
+
+  oldkey <- data.table::key(dtOld)
+
+  iter = nrow(dtDefs)
+  n = nrow(dtOld)
+  for (i in (1 : iter)) {
+    dtOld <- generate(dtDefs[i,], n, dtOld)
+  }
+
+  dtOld <- data.table::data.table(dtOld)
+  data.table::setkeyv(dtOld, oldkey)
+
+  return(dtOld)
+
+}
+

Diff for: R/addColumns.R

@@ -1,56 +1,56 @@
-#' Create longitudinal/panel data
-#'
-#' @param dtName Name of existing data table
-#' @param nPeriods Number of time periods for each record
-#' @param idvars Names of index variables (in a string vector) that will be
-#' repeated during each time period
-#' @param timevars Names of time dependent variables. Defaults to NULL.
-#' @param timevarName Name of new time dependent varialbe
-#' @return An updated data.table that that has multiple rows 
-#' per observation in dtName
-#' @export
-#'
-
-# dtName must contain id for now
-
-addPeriods <- function(dtName, nPeriods, idvars = "id", 
-                       timevars = NULL, timevarName = "timevar") {
-  
-  dtX1 <- copy(dtName)
-  
-  if (!is.null(timevars)) {
-    dtX1[, eval(timevars) := NULL, with=TRUE] 
-  }
-  
-  dtTimes1 <- dtX1[, .(period = (0 : (nPeriods - 1))), keyby = idvars]
-  data.table::setkeyv(dtX1, idvars)
-  dtTimes1 <- dtTimes1[dtX1]
-  data.table::setkeyv(dtTimes1, c(idvars, "period"))
-  
-  if (!is.null(timevars)) {
-    
-    dtX2 <- copy(dtName)
-    varX2 <- names(dtX2)[!(names(dtX2) %in% c(idvars,timevars))]
-    
-    if (length(varX2)) {
-      dtX2[, eval(varX2) := NULL, with=TRUE]      
-    }
-    
-    dtTimes2 <- data.table::melt(dtX2,id.vars=idvars, 
-                                 value.name = timevarName,
-                                 variable.name = "period",
-                                 variable.factor = TRUE)
-    
-    dtTimes2[, period := factor(period, timevars)]
-    dtTimes2[, period := as.integer(period) - 1]
-    data.table::setkeyv(dtTimes2, c(idvars, "period"))
-    
-    return(dtTimes1[dtTimes2])
-    
-  } else {
-    
-    return(dtTimes1)
-    
-  }
-  
-}
+#' Create longitudinal/panel data
+#'
+#' @param dtName Name of existing data table
+#' @param nPeriods Number of time periods for each record
+#' @param idvars Names of index variables (in a string vector) that will be
+#' repeated during each time period
+#' @param timevars Names of time dependent variables. Defaults to NULL.
+#' @param timevarName Name of new time dependent varialbe
+#' @return An updated data.table that that has multiple rows 
+#' per observation in dtName
+#' @export
+#'
+
+# dtName must contain id for now
+
+addPeriods <- function(dtName, nPeriods, idvars = "id", 
+                       timevars = NULL, timevarName = "timevar") {
+  
+  dtX1 <- copy(dtName)
+  
+  if (!is.null(timevars)) {
+    dtX1[, eval(timevars) := NULL, with=TRUE] 
+  }
+  
+  dtTimes1 <- dtX1[, .(period = (0 : (nPeriods - 1))), keyby = idvars]
+  data.table::setkeyv(dtX1, idvars)
+  dtTimes1 <- dtTimes1[dtX1]
+  data.table::setkeyv(dtTimes1, c(idvars, "period"))
+  
+  if (!is.null(timevars)) {
+    
+    dtX2 <- copy(dtName)
+    varX2 <- names(dtX2)[!(names(dtX2) %in% c(idvars,timevars))]
+    
+    if (length(varX2)) {
+      dtX2[, eval(varX2) := NULL, with=TRUE]      
+    }
+    
+    dtTimes2 <- data.table::melt(dtX2,id.vars=idvars, 
+                                 value.name = timevarName,
+                                 variable.name = "period",
+                                 variable.factor = TRUE)
+    
+    dtTimes2[, period := factor(period, timevars)]
+    dtTimes2[, period := as.integer(period) - 1]
+    data.table::setkeyv(dtTimes2, c(idvars, "period"))
+    
+    return(dtTimes1[dtTimes2])
+    
+  } else {
+    
+    return(dtTimes1)
+    
+  }
+  
+}

Diff for: R/addPeriods.R

@@ -1,41 +1,39 @@
-#' Add single row to definitions table
-#'
-#' @param dtDefs Definition data.table to be modified
-#' @param varName test
-#' @param formula test
-#' @param variance test
-#' @param dist test
-#' @param link test
-#' @param nTrt test
-#' @param cMethod test
-#' @param missType test
-#' @return A data.table named dtName that is an updated data defnitions table
-#' @export
-
-addDefs <- function(dtDefs,
-                    varname = "",
-                    formula = "",
-                    variance = 0,
-                    dist = "Normal",
-                    link = "identity",
-                    nTrt = 0,
-                    cMethod = "",
-                    missType = "") {
-
-  dt.new <- data.table::data.table(varname,
-                                   formula,
-                                   variance,
-                                   dist,
-                                   link,
-                                   nTrt,
-                                   cMethod,
-                                   missType)
-
-  l = list(dtDefs,dt.new)
-
-  defNew <- data.table::rbindlist(l, use.names = TRUE, fill = TRUE)
-  attr(defNew, "id") <- attr(dtDefs, "id")
-
-  return(defNew)
-
-}
+#' Add single row to definitions table
+#'
+#' @param dtDefs Definition data.table to be modified
+#' @param varName test
+#' @param formula test
+#' @param variance test
+#' @param dist test
+#' @param link test
+#' @param id test
+#' @return A data.table named dtName that is an updated data defnitions table
+#' @export
+
+defData <- function(dtDefs = NULL,
+                    varname = "",
+                    formula = "",
+                    variance = 0,
+                    dist = "Normal",
+                    link = "identity",
+                    id="id") {
+
+  if (is.null(dtDefs)) {
+    dtDefs <- data.table::data.table()
+    attr(dtDefs,"id") <- id
+  }
+
+  dt.new <- data.table::data.table(varname,
+                                   formula,
+                                   variance,
+                                   dist,
+                                   link)
+
+  l = list(dtDefs,dt.new)
+
+  defNew <- data.table::rbindlist(l, use.names = TRUE, fill = TRUE)
+  attr(defNew, "id") <- attr(dtDefs, "id")
+
+  return(defNew)
+
+}