[Pomp-commits] r1085 - in pkg/pomp: R man

[noreply at r-forge.r-project.org]

Author: kingaa
Date: 2015-02-22 20:43:12 +0100 (Sun, 22 Feb 2015)
New Revision: 1085

Modified:
   pkg/pomp/R/nlf.R
   pkg/pomp/man/nlf.Rd
Log:
- the transform.params argument is now deprecated in favor of the transform argument

Modified: pkg/pomp/R/nlf.R
===================================================================
--- pkg/pomp/R/nlf.R	2015-02-22 19:43:06 UTC (rev 1084)
+++ pkg/pomp/R/nlf.R	2015-02-22 19:43:12 UTC (rev 1085)
@@ -414,16 +414,16 @@
             verbose = getOption("verbose"),
             bootstrap = FALSE, bootsamp = NULL,
             lql.frac = 0.1, se.par.frac = 0.1,
-            eval.only = FALSE, transform.params = FALSE,
-            transform, ...)
+            eval.only = FALSE, transform.params,
+            transform = FALSE, ...)
           {
-            transform.params <- as.logical(transform.params)
-            if (!missing(transform)) {
-              warning("argument ",sQuote("transform"),
-                      " is deprecated and will change meaning in a future release.\n",
-                      "Use ",sQuote("transform.data")," instead.")
-              if (missing(transform.data)) transform.data <- transform
+            if (!missing(transform.params)) {
+              warning("argument ",sQuote("transform.params"),
+                      " is deprecated and will be removed in a future release.\n",
+                      "Use ",sQuote("transform")," instead.")
+              if (missing(transform)) transform <- transform.params
             }
+            transform <- as.logical(transform)
             if (missing(transform.data)) transform.data <- identity
             transform.data <- match.fun(transform.data)
             period <- as.numeric(period)
@@ -469,7 +469,7 @@
                          lql.frac=lql.frac,
                          se.par.frac=se.par.frac,
                          eval.only=eval.only,
-                         transform=transform.params,
+                         transform=transform,
                          transform.data=transform.data,
                          ...
                          )
@@ -482,7 +482,7 @@
           definition=function (object, start, est, lags,
             period, tensor, nconverge, nasymp, seed,
             transform.data, nrbf, method, lql.frac, se.par.frac,
-            transform.params, ...)
+            transform, ...)
           {            
             if (missing(start)) start <- coef(object)
             if (missing(est)) est <- object at est
@@ -492,7 +492,7 @@
             if (missing(nconverge)) nconverge <- object at nconverge
             if (missing(nasymp)) nasymp <- object at nasymp
             if (missing(seed)) seed <- object at seed
-            if (missing(transform.params)) transform.params <- object at transform
+            if (missing(transform)) transform <- object at transform
             if (missing(transform.data)) transform.data <- object at transform.data
             if (missing(nrbf)) nrbf <- object at nrbf
             if (missing(method)) method <- object at method
@@ -509,7 +509,7 @@
               tensor=tensor,
               nconverge=nconverge,
               seed=seed,
-              transform.params=transform.params,
+              transform=transform,
               transform.data=transform.data,
               nrbf=nrbf,
               method=method,

Modified: pkg/pomp/man/nlf.Rd
===================================================================
--- pkg/pomp/man/nlf.Rd	2015-02-22 19:43:06 UTC (rev 1084)
+++ pkg/pomp/man/nlf.Rd	2015-02-22 19:43:12 UTC (rev 1085)
@@ -22,10 +22,10 @@
      skip.se = FALSE, verbose = getOption("verbose"),
      bootstrap=FALSE, bootsamp = NULL,
      lql.frac = 0.1, se.par.frac = 0.1, eval.only = FALSE,
-     transform.params = FALSE, transform, \dots)
+     transform.params, transform = FALSE, \dots)
 \S4method{nlf}{nlfd.pomp}(object, start, est, lags, period, tensor,
      nconverge, nasymp, seed, transform.data, nrbf, method,
-     lql.frac, se.par.frac, transform.params, \dots)
+     lql.frac, se.par.frac, transform, \dots)
 }
 \arguments{
   \item{object}{
@@ -61,7 +61,16 @@
     When fitting, it is usually best to always run the simulations with the same sequence of random numbers, which is accomplished by setting \code{seed} to an integer.
     If you want a truly random simulation, set \code{seed=NULL}.
   }
-  \item{transform.data, transform}{
+  \item{transform.params}{
+    deprecated.
+    Will be removed in a future version.
+    Use \code{transform} instead.
+  }
+  \item{transform}{
+    logical;
+    if \code{TRUE}, parameters are optimized on the transformed scale.
+  }
+  \item{transform.data}{
     optional function.
     If specified, forecasting is performed using data and model simulations transformed by this function.
     By default, \code{transform.data} is the identity function, i.e., no transformation is performed.
@@ -97,10 +106,6 @@
   \item{eval.only}{
     logical; if \code{TRUE}, no optimization is attempted and the quasi-loglikelihood value is evaluated at the \code{start} parameters.
   } 
-  \item{transform.params}{
-    logical;
-    if \code{TRUE}, parameters are optimized on the transformed scale.
-  }
   \item{\dots}{
     Arguments that will be passed to \code{optim} or \code{subplex} in the \code{control} list.
   }