Updating addPeriods

Author: Keith Goldfeld

NEWS.md

@@ -1,8 +1,8 @@
 # simstudy (development version)
 
 ## New features
-*`addPeriods` has a new argument `periodVec` that allows user to specify 
-specific measurement time periods as a vector.
+*`addPeriods` now includes a new argument `periodVec` that allows users to designate 
+specific measurement time periods using vector.
 
 ## Minor fix
 * Function `logisticCoefs` now correctly handles double dot notation.

R/group_data.R

@@ -8,25 +8,25 @@
 #' @param timevarName Name of new time dependent variable
 #' @param timeid Variable name for new index field. Defaults to "timevar"
 #' @param perName Variable name for period field. Defaults to "period"
-#' @param perVec Vector of period times. Defaults to NULL
+#' @param periodVec Vector of period times. Defaults to NULL
 #' @details It is possible to generate longitudinal data with varying 
 #' numbers of measurement periods as well as varying time intervals between 
 #' each measurement period. This is done by defining specific variables \emph{in} the 
 #' data set that define the number of observations per subject and the average 
 #' interval time between each observation. \bold{\emph{nCount}} defines the number of 
 #' measurements for an individual; \bold{\emph{mInterval}} specifies the average time between 
-#' intervals for a subject; and vInterval specifies the variance of those 
-#' interval times. If \bold{\emph{vInterval}} is set to 0 or is not defined, the interval for
+#' intervals for a subject; and \bold{\emph{vInterval}} specifies the variance of those 
+#' interval times. If \bold{\emph{mInterval}} is not defined, no intervals are used. If \bold{\emph{vInterval}} is set to 0 or is not defined, the interval for
 #' a subject is determined entirely by the mean interval. If \bold{\emph{vInterval}} is 
 #' greater than 0, time intervals are generated using a gamma distribution 
 #' with specified mean and dispersion. If either \bold{\emph{nPeriods}} or \bold{\emph{timevars}} 
 #' is specified, that will override any \bold{\emph{nCount}}, \bold{\emph{mInterval}}, and 
 #' \bold{\emph{vInterval}} data.
 #' 
-#' \bold\emph{{perVec}} is used to specify measurement periods that are different
-#' the default counting variables. If \bold\emph{{perVec}} is not specified, 
+#' \bold{\emph{periodVec}} is used to specify measurement periods that are different
+#' the default counting variables. If \bold{\emph{periodVec}} is not specified, 
 #' the periods default to \emph{0, 1, ... n-1}, with \emph{n} periods. If 
-#' \bold\emph{{perVec}} is specified as \emph{c(x_1, x_2, ... x_n)}, then
+#' \bold{\emph{periodVec}} is specified as \emph{c(x_1, x_2, ... x_n)}, then
 #' \emph{x_1, x_2, ... x_n} represent the measurement periods.
 #' @return An updated data.table that that has multiple rows
 #' per observation in dtName
@@ -98,10 +98,13 @@ addPeriods <- function(dtName,
   if (!is.null(nPeriods)) { # same number for each subject
 
     dtTimes1 <- dtX1[, list(.period = (0:(nPeriods - 1))), keyby = idvars]
+
   } else {
+    
     if ("nCount" %in% names(dtX1)) { # specified for each subject
 
       dtTimes1 <- dtX1[, list(.period = (0:(nCount - 1))), keyby = idvars]
+
     } else { # not specified for each subject or for all
 
       stop("No period or count parameter provided")
@@ -113,6 +116,12 @@ addPeriods <- function(dtName,
   data.table::setkeyv(dtX1, idvars)
   dtTimes1 <- dtTimes1[dtX1]
   data.table::setkeyv(dtTimes1, c(idvars, ".period"))
+  
+  # Remove nCount if it was included
+  
+  if ("nCount" %in% names(dtX1)) {
+    dtTimes1[, nCount := NULL]
+  }
 
   # Create code for final index assignment
 
@@ -152,14 +161,11 @@ addPeriods <- function(dtName,
       eval(cmd)
       data.table::setkeyv(dtTimes1, timeid)
 
-      data.table::setnames(dtTimes1, old = ".period", new = perName)
-
     } else { # if time dependent variables not specified
 
       eval(cmd)
       data.table::setkeyv(dtTimes1, timeid)
 
-      data.table::setnames(dtTimes1, old = ".period", new = perName)
     }
 
     # if specified different measurement intervals:
@@ -169,30 +175,26 @@ addPeriods <- function(dtName,
       assertNumeric(periodVec = periodVec)
       assertLength(periodVec = periodVec, length = nPeriods) # Need to make sure
 
-      dtTimes1[, period := periodVec[period + 1]]
+      dtTimes1[, .period := periodVec[.period + 1]]
     }
 
   } else { # is.null(nPeriods) == TRUE
 
-    if (all(c("nCount", "mInterval") %in% names(dtX1))) {
+    if ( "mInterval" %in% names(dtX1) ) {
       if (!("vInterval" %in% names(dtX1))) dtTimes1[, vInterval := 0]
 
       dtTimes1[, timeElapsed := .genPosSkew(1, mInterval, vInterval), keyby = c(idvars, ".period")]
       dtTimes1[.period == 0, timeElapsed := 0]
 
       dtTimes1[, time := round(cumsum(timeElapsed)), keyby = idvars]
-      dtTimes1[, c("timeElapsed", "nCount", "mInterval", "vInterval") := NULL]
+      dtTimes1[, c("timeElapsed", "mInterval", "vInterval") := NULL]
 
       eval(cmd)
       data.table::setkeyv(dtTimes1, timeid)
-
-      data.table::setnames(dtTimes1, old = ".period", new = perName)
-      
-    } else { 
-      stop("No period or count parameter provided")
-    }
+    } 
   }
 
+  data.table::setnames(dtTimes1, old = ".period", new = perName)
   dtTimes1[]
 
 }

man/addPeriods.Rd

@@ -1,3 +1,69 @@
+# addPariods
+test_that("addPeriods works", {
+  skip_on_cran()
+  
+  tdef <- defData(varname = "T", dist = "binary", formula = 0.5)
+  tdef <- defData(tdef, varname = "Y0", dist = "normal", formula = 10, variance = 1)
+  tdef <- defData(tdef, varname = "Y1", dist = "normal", formula = "Y0 + 5 + 5 * T", variance = 1)
+  tdef <- defData(tdef, varname = "Y2", dist = "normal", formula = "Y0 + 10 + 5 * T", variance = 1)
+
+  n <- ceiling(runif(1, 10, 20))
+  dtTrial <- genData(n, tdef)
+  
+  p <- ceiling(runif(1, 3, 8))
+  dtTime <- addPeriods(
+    dtTrial,
+    nPeriods = p, idvars = "id"
+  )
+  
+  expect_equal(nrow(dtTime), n*p)
+  
+  expect_silent(
+    addPeriods(dtTrial,
+      nPeriods = 3, idvars = "id",
+      timevars = c("Y0", "Y1", "Y2"), timevarName = "Y",
+      periodVec = c(0, 3, 5)
+    )
+  )
+  
+  expect_warning(
+    addPeriods(dtTrial,
+               nPeriods = 2, idvars = "id",
+               timevars = c("Y0", "Y1", "Y2"), timevarName = "Y"
+    )
+  )
+  
+  testthat::expect_silent(
+    addPeriods(dtTrial,
+               nPeriods = 3, idvars = "id",
+               timevars = c("Y0", "Y1", "Y2"), 
+               timevarName = "Y"
+    )
+  )
+  
+  def <- defData(varname = "xbase", dist = "normal", formula = 20, variance = 3)
+  def <- defData(def, varname = "nCount", dist = "noZeroPoisson", formula = 6)
+  def <- defData(def, varname = "mInterval", dist = "gamma", formula = 30, variance = .01)
+  def <- defData(def, varname = "vInterval", dist = "nonrandom", formula = .07)
+
+  dt <- genData(50, def)
+  expect_silent(addPeriods(dt))
+  
+  
+  def <- defData(varname = "xbase", dist = "normal", formula = 20, variance = 3)
+  def <- defData(def, varname = "nCount", dist = "noZeroPoisson", formula = 6)
+  def <- defData(def, varname = "mInterval", dist = "gamma", formula = 30, variance = .01)
+
+  dt <- genData(50, def)
+  expect_silent(addPeriods(dt))
+  
+  def <- defData(varname = "xbase", dist = "normal", formula = 20, variance = 3)
+  
+  dt <- genData(50, def)
+  expect_error(addPeriods(dt))
+  
+})
+
 # .addStrataCode ----
 test_that("strata codes are added as expected.", {
   skip_on_cran()