Merge pull request #7 from atsa-es/marxss2

fixed to pass RCMD check

Author: eeholmes

DESCRIPTION

@@ -13,12 +13,14 @@ Description: Work on TMB files to fit MARSS models with TMB.
 URL: https://atsa-es.github.io/marssTMB, https://github.com/atsa-es/marssTMB
 BugReports: https://github.com/atsa-es/marssTMB/issues
 License: GPL (>= 2)
+Depends: R (>= 3.5.0)
 Imports: 
     TMB (>= 1.9.3),
     stats,
-    MARSS
+    MARSS (>= 3.11.4)
 Suggests: 
     ggplot2,
+    dplyr,
     tidyr,
     knitr,
     rmarkdown,

NAMESPACE

@@ -7,4 +7,5 @@ export(create.varcov.maps)
 export(dfaTMB)
 export(uniTMB)
 import(MARSS)
+importFrom(stats,coef)
 useDynLib(marssTMB, .registration=TRUE); useDynLib(marssTMB_TMBExports)

NEWS.md

@@ -1,8 +1,8 @@
 # marssTMB 0.0.7
 
 * updated `marxss.hpp` to be in MARSS format with X and Y as mxT and nxT
-* added Q estimation to `marxss.hpp` (note `MARSS_tmp()` will block this until this is tested)
-* added C estimation to `marxss.hpp` (note `MARSS_tmp()` will block this until this is tested)
+* added Q estimation to `marxss.hpp` (note `MARSS_tmb()` will block this until this is tested)
+* added C estimation to `marxss.hpp` (note `MARSS_tmb()` will block this until this is tested)
 
 # marssTMB 0.0.6
 

R/MARSS-TMB.R

@@ -17,11 +17,13 @@
 #'    * tinitx = 1 (must be)
 #'    * (if form="dfa") m the number of states (factors). default is 1
 #' @param inits list of initial conditions
+#' @param miss.value A parameter for backcompatibility. Not used.
 #' @param method must be "TMB" (case sensitive)
 #' @param form The equation form used in the marssTMB() call. The default is "dfa". 
 #' @param fit Whether to fit the model.
 #' @param silent Show TMB output when fitting
 #' @param control list for the optimization function. [stats::nlminb()] or [stats::optim()], `control$fun.opt` allows you to choose optim or nlminb as the optimization function. `control$optim.method` allows you to choose method for `optim()`.
+#' @param ... Extra parameters. Not used.
 #' 
 #' @return The output list from [MARSStmb()]
 #' @example inst/examples/MARSS_TMB_example.R

R/MARSStmb.R

@@ -1,7 +1,5 @@
 #' Internal function: Parameter estimation using TMB
 #'
-#' Status 5/1/23 fits model. Now working on [to_marssMLE()] to format a [MARSS::marssMLE] object.
-#'
 #' Minimal error checking is done in this function.
 #' Normal calling function is [MARSS_tmb()] which in
 #' turn calls this function. Note when MARSS is updated, the
@@ -13,20 +11,19 @@
 #' * Q is fixed (not estimated)
 #'
 #' @details
-#' This function returns a list which is passed to [to_marssMLE()] for further
-#' processing.
+#' This function returns [MARSS::marssMLE] object. For the `iter.record` element
+#' of the object, the following are returned as a list:
 #'
 #' * `obj.function` is the raw output from the [TMB::MakeADFun()] call.
 #' * `opt.output` is the raw output from the optimization call (optim or nlminb)
-#' * `MLEobj` is the unfitted (no par element) [MARSS::marssMLE] object. Has all the parameters and correct structure.
 #'
 #'
 #' @param MLEobj A properly formatted MARSS model as output by [MARSS_tmb()]
 
 #' @return A [MARSS::marssMLE] object
-#' @example inst/examples/dfa_example.R
+#' @example inst/examples/MARSStmb_example.R
 #' @author Eli Holmes. This function is inspired by dfaTMB.R written by Tim Cline while a graduate student in the Fish 507 Time Series Analysis course.
-#' @seealso [MARSS::MARSSoptim()], [MARSS::MARSSkem()], [to_marssMLE()]
+#' @seealso [MARSS::MARSSoptim()], [MARSS::MARSSkem()]
 #' @export
 MARSStmb <- function(MLEobj) {
   pkg <- "MARSStmb"

R/dfaTMB.R

@@ -1,6 +1,11 @@
 #' Tim Cline's original code to Fit a DFA model with TMB.
 #' 
 #' This can be called to fit a DFA with his syntax, but generally no work should be done here.
+#' 
+#' @details
+#' The control defaults for [stats::nlminb()] are `iter.max = 2000` and `eval.max = 2000`. 
+#' For [stats::optim()], the defaults are `reltol = 1e-12` and `maxit = 2000`.
+#' 
 #'
 #' @param y Vector of observations n x T.
 #' @param model list with 
@@ -16,8 +21,8 @@
 #' @param silent Show TMB output when fitting, defaults to TRUE
 #' @param fun.opt function to use for optimization: `stats::nlminb()` or `stats::optim()`
 #' @param method to pass to optim call; ignored for `fun="nlminb"`
-#' @param form The equation form used in the marssTMB() call. The default is "dfa". 
-
+#' @param form The equation form used in the marssTMB() call. The default is "dfa".
+#' @param control a list with the control settings for the optimatization function. See details for the defaults.
 #' @return A list with Optimization, Estimates, Fits, and AIC
 #' @example inst/examples/dfa_example.R
 #' @author Tim Cline wrote most of this while a graduate student in the Fish 507 Time Series Analysis course. Eli Holmes later modified it to replicate the MARSS(x, form="dfa") model.
@@ -146,10 +151,9 @@ dfaTMB <- function(y,
   }
   pl1 <- obj1$env$parList() # This contains all of your parameter estimates RAW as they come out of the optimizer
   if (EstSE) {
-    sdr <- sdreport(obj1)
+    sdr <- TMB::sdreport(obj1)
   }
 
-  # ScaleFac<-as.vector(apply(pl1$u,2,FUN=sd))
   # pl1$u<-t(t(pl1$u)/ScaleFac)
   # pl1$Z<-t(t(pl1$Z)*ScaleFac)
 
@@ -176,6 +180,8 @@ dfaTMB <- function(y,
 
   # Standard Errors for parameters
   if (EstSE) {
+    # ScaleFac<-as.vector(apply(pl1$u,2,FUN=sd))
+    ScaleFac <- 1
     SES <- list(
       D = sdr$sd[which(names(sdr$value) == "D")],
       Z = sdr$sd[which(names(sdr$value) == "Z")] * ScaleFac,

R/marssTMB-package.R

@@ -1,5 +1,6 @@
 #' @rawNamespace useDynLib(marssTMB, .registration=TRUE); useDynLib(marssTMB_TMBExports)
 #' @import MARSS
+#' @importFrom stats coef
 #' @keywords internal
 "_PACKAGE"
 

inst/examples/MARSS_TMB_example.R

@@ -8,4 +8,4 @@ dat <- as.data.frame(lakeWAplanktonTrans) |>
   MARSS::zscore()
 
 #fit with MARSS
-fit <- MARSS_tmb(dat, model=list(m=3))
+fit <- MARSS_tmb(dat, model=list(m=3, tinitx=1), form="dfa")

inst/examples/MARSStmb_example.R

@@ -0,0 +1,14 @@
+library(MARSS)
+data(lakeWAplankton, package = "MARSS")
+phytoplankton <- c("Cryptomonas", "Diatoms", "Greens", "Unicells", "Other.algae")
+dat <- as.data.frame(lakeWAplanktonTrans) |>
+  subset(Year >= 1980 & Year <= 1989) |>
+  subset(select=phytoplankton) |>
+  t() |>
+  MARSS::zscore()
+
+# set-up the model
+mod <- MARSS_tmb(dat, model=list(m=3, tinitx=1), form="dfa", fit=FALSE)
+# fit
+fit <- MARSStmb(mod)
+