Fix build (file dependencies)

DESCRIPTION

@@ -30,22 +30,19 @@ Collate:
     'mortalityTable.period.R'
     'mortalityTable.ageShift.R'
     'ageShift.R'
-    'fillAges.R'
-    'mortalityTable.mixed.R'
-    'mortalityTable.improvementFactors.R'
-    'mortalityTable.trendProjection.R'
-    'deathProbabilities.R'
-    'periodDeathProbabilities.R'
     'mortalityTable.joined.R'
-    'getOmega.R'
-    'pensionTable.R'
-    'utilityFunctions.R'
-    'mortalityTable.observed.R'
+    'mortalityTable.mixed.R'
     'ages.R'
     'baseTable.R'
     'baseYear.R'
+    'fillAges.R'
+    'pensionTable.R'
     'commutationNumbers.R'
+    'mortalityTable.improvementFactors.R'
+    'mortalityTable.trendProjection.R'
+    'deathProbabilities.R'
     'getCohortTable.R'
+    'getOmega.R'
     'getPeriodTable.R'
     'lifeTable.R'
     'makeQxDataFrame.R'
@@ -54,7 +51,10 @@ Collate:
     'mortalityTable.MakehamGompertz.R'
     'mortalityTable.Weibull.R'
     'mortalityTable.deMoivre.R'
+    'periodDeathProbabilities.R'
     'mortalityTable.jointLives.R'
+    'utilityFunctions.R'
+    'mortalityTable.observed.R'
     'mortalityTables.list.R'
     'mortalityTables.load.R'
     'plot.mortalityTable.R'

R/ages.R

-#' @include mortalityTable.period.R mortalityTable.mixed.R mortalityTable.joined.R mortalityTable.observed.R
+#' @include mortalityTable.period.R mortalityTable.mixed.R mortalityTable.joined.R
 NULL
 
 #' Return the defined ages of the life table
@@ -34,9 +34,3 @@ setMethod("ages", "mortalityTable.mixed",
 #               ages(object@table1);
 #           })
 
-# #' @describeIn ages Return the defined ages of the observed life table
-# setMethod("ages", "mortalityTable.observed",
-#           function(object, ...) {
-#               object@ages;
-#           })
-

R/getOmega.R

-#' @include mortalityTable.R mortalityTable.period.R mortalityTable.mixed.R mortalityTable.joined.R mortalityTable.observed.R
+#' @include mortalityTable.R mortalityTable.period.R mortalityTable.mixed.R mortalityTable.joined.R
 NULL
 
 #' Return the maximum age of the life table

R/mortalityTable.observed.R

-#' @include mortalityTable.R utilityFunctions.R getOmega.R periodDeathProbabilities.R deathProbabilities.R ages.R
+#' @include mortalityTable.R utilityFunctions.R ages.R getOmega.R periodDeathProbabilities.R deathProbabilities.R
 NULL
 
 #' Class mortalityTable.observed - Life table from actual observations
@@ -27,12 +27,13 @@ mortalityTable.observed = setClass(
  contains = "mortalityTable"
 )
 
-#' @describeIn ages Return the ages of the life table
+#' @describeIn ages Return the defined ages of the observed life table
 setMethod("ages", "mortalityTable.observed",
-          function(object) {
-              object@ages
+          function(object, ...) {
+              object@ages;
           })
 
+
 #' @describeIn getOmega Return the maximum age of the life table
 setMethod("getOmega", "mortalityTable.observed",
           function(object) {

man/ages.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ages.R, R/mortalityTable.jointLives.R
+% Please edit documentation in R/ages.R, R/mortalityTable.jointLives.R,
+%   R/mortalityTable.observed.R
 \docType{methods}
 \name{ages}
 \alias{ages}
 \alias{ages,mortalityTable.period-method}
 \alias{ages,mortalityTable.mixed-method}
 \alias{ages,mortalityTable.jointLives-method}
+\alias{ages,mortalityTable.observed-method}
 \title{Return the defined ages of the life table}
 \usage{
 ages(object, ...)
@@ -15,6 +17,8 @@ ages(object, ...)
 \S4method{ages}{mortalityTable.mixed}(object, ...)
 
 \S4method{ages}{mortalityTable.jointLives}(object, ...)
+
+\S4method{ages}{mortalityTable.observed}(object, ...)
 }
 \arguments{
 \item{object}{A life table object (instance of a \code{\linkS4class{mortalityTable}} class)}
@@ -31,6 +35,8 @@ Return the defined ages of the life table
 \item \code{mortalityTable.mixed}: Return the defined ages of the mixed life table
 
 \item \code{mortalityTable.jointLives}: Return the defined ages of the joint lives mortality table (returns the ages of the first table used for joint lives)
+
+\item \code{mortalityTable.observed}: Return the defined ages of the observed life table
 }}
 
 \examples{

man/deathProbabilities.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/deathProbabilities.R,
-%   R/mortalityTable.observed.R, R/mortalityTable.jointLives.R
+%   R/mortalityTable.jointLives.R, R/mortalityTable.observed.R
 \docType{methods}
 \name{deathProbabilities}
 \alias{deathProbabilities}
@@ -9,8 +9,8 @@
 \alias{deathProbabilities,mortalityTable.trendProjection-method}
 \alias{deathProbabilities,mortalityTable.improvementFactors-method}
 \alias{deathProbabilities,mortalityTable.mixed-method}
-\alias{deathProbabilities,mortalityTable.observed-method}
 \alias{deathProbabilities,mortalityTable.jointLives-method}
+\alias{deathProbabilities,mortalityTable.observed-method}
 \title{Return the (cohort) death probabilities of the life table given the birth year (if needed)}
 \usage{
 deathProbabilities(object, ..., ages = NULL, YOB = 1975)
@@ -30,11 +30,11 @@ deathProbabilities(object, ..., ages = NULL, YOB = 1975)
 \S4method{deathProbabilities}{mortalityTable.mixed}(object, ...,
   ages = NULL, YOB = 1975)
 
-\S4method{deathProbabilities}{mortalityTable.observed}(object, ...,
-  ages = NULL, YOB = 1975)
-
 \S4method{deathProbabilities}{mortalityTable.jointLives}(object, ...,
   ageDifferences = c(), ages = NULL, YOB = 1975)
+
+\S4method{deathProbabilities}{mortalityTable.observed}(object, ...,
+  ages = NULL, YOB = 1975)
 }
 \arguments{
 \item{object}{The life table object (class inherited from mortalityTable)}
@@ -67,10 +67,10 @@ life table given the birth year (if needed)
 \item \code{mortalityTable.mixed}: Return the (cohort) death probabilities of the
 life table given the birth year (if needed)
 
-\item \code{mortalityTable.observed}: Return the (cohort) death probabilities of the
+\item \code{mortalityTable.jointLives}: Return the (cohort) death probabilities of the
 life table given the birth year (if needed)
 
-\item \code{mortalityTable.jointLives}: Return the (cohort) death probabilities of the
+\item \code{mortalityTable.observed}: Return the (cohort) death probabilities of the
 life table given the birth year (if needed)
 }}
 

man/getOmega.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/getOmega.R, R/mortalityTable.observed.R,
-%   R/mortalityTable.jointLives.R
+% Please edit documentation in R/getOmega.R, R/mortalityTable.jointLives.R,
+%   R/mortalityTable.observed.R
 \docType{methods}
 \name{getOmega}
 \alias{getOmega}
 \alias{getOmega,mortalityTable.period-method}
 \alias{getOmega,mortalityTable.mixed-method}
-\alias{getOmega,mortalityTable.observed-method}
 \alias{getOmega,mortalityTable.jointLives-method}
+\alias{getOmega,mortalityTable.observed-method}
 \title{Return the maximum age of the life table}
 \usage{
 getOmega(object)
@@ -16,9 +16,9 @@ getOmega(object)
 
 \S4method{getOmega}{mortalityTable.mixed}(object)
 
-\S4method{getOmega}{mortalityTable.observed}(object)
-
 \S4method{getOmega}{mortalityTable.jointLives}(object)
+
+\S4method{getOmega}{mortalityTable.observed}(object)
 }
 \arguments{
 \item{object}{A life table object (instance of a \code{mortalityTable} class)}
@@ -32,9 +32,9 @@ Return the maximum age of the life table
 
 \item \code{mortalityTable.mixed}: Return the maximum age of the mixed life table
 
-\item \code{mortalityTable.observed}: Return the maximum age of the period life table
-
 \item \code{mortalityTable.jointLives}: Return the maximum age of the joint lives mortality table (returns the maximum age of the first table used for joint lives, as the ages of the joint lives are now known to the function)
+
+\item \code{mortalityTable.observed}: Return the maximum age of the life table
 }}
 
 \examples{

man/periodDeathProbabilities.Rd

 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/periodDeathProbabilities.R,
-%   R/mortalityTable.observed.R, R/mortalityTable.jointLives.R
+%   R/mortalityTable.jointLives.R, R/mortalityTable.observed.R
 \docType{methods}
 \name{periodDeathProbabilities}
 \alias{periodDeathProbabilities}
@@ -9,8 +9,8 @@
 \alias{periodDeathProbabilities,mortalityTable.trendProjection-method}
 \alias{periodDeathProbabilities,mortalityTable.improvementFactors-method}
 \alias{periodDeathProbabilities,mortalityTable.mixed-method}
-\alias{periodDeathProbabilities,mortalityTable.observed-method}
 \alias{periodDeathProbabilities,mortalityTable.jointLives-method}
+\alias{periodDeathProbabilities,mortalityTable.observed-method}
 \title{Return the (period) death probabilities of the life table for a given
 observation year}
 \usage{
@@ -33,11 +33,11 @@ periodDeathProbabilities(object, ..., ages = NULL, Period = 1975)
 \S4method{periodDeathProbabilities}{mortalityTable.mixed}(object, ...,
   ages = NULL, Period = 1975)
 
-\S4method{periodDeathProbabilities}{mortalityTable.observed}(object, ...,
-  ages = NULL, Period = 1975)
-
 \S4method{periodDeathProbabilities}{mortalityTable.jointLives}(object, ...,
   ageDifferences = c(), ages = NULL, Period = 1975)
+
+\S4method{periodDeathProbabilities}{mortalityTable.observed}(object, ...,
+  ages = NULL, Period = 1975)
 }
 \arguments{
 \item{object}{The life table object (class inherited from mortalityTable)}
@@ -71,14 +71,14 @@ of the life table for a given observation year
 \item \code{mortalityTable.mixed}: Return the (period) death probabilities
 of the life table for a given observation year
 
+\item \code{mortalityTable.jointLives}: Return the (period) death probabilities
+of the joint lives mortality table for a given observation year
+
 \item \code{mortalityTable.observed}: Return the (period) death probabilities
 of the life table for a given observation year
 If the observed mortality table does not provide data
 for the desired period, the period closest to the
 `Period` argument will be used and a warning printed.
-
-\item \code{mortalityTable.jointLives}: Return the (period) death probabilities
-of the joint lives mortality table for a given observation year
 }}
 
 \examples{