get dsemRTMB working as package

NAMESPACE

@@ -15,6 +15,7 @@ export(cAIC)
 export(classify_variables)
 export(convert_equations)
 export(dsem)
+export(dsemRTMB)
 export(dsem_control)
 export(list_parameters)
 export(loo_residuals)
@@ -59,3 +60,6 @@ importFrom(stats,simulate)
 importFrom(stats,time)
 importFrom(stats,vcov)
 useDynLib(dsem, .registration = TRUE)
+
+# Edited by hand
+import("RTMB")

R/compute_nll.R

@@ -72,9 +72,6 @@ function( parlist,
     # Hadamard squared LU-decomposition
     # See: https://eigen.tuxfamily.org/dox/group__QuickRefPage.html
     squared_invIminusRho_kk = invIminusRho_kk
-    #print(class(squared_invIminusRho_kk))
-    #print(invIminusRho_kk)
-    #REPORT( invIminusRho_kk )
     squared_invIminusRho_kk@x = squared_invIminusRho_kk@x^2
 
     if( options[2] == 1 ){

R/dsemRTMB.R

@@ -1,5 +1,23 @@
-
-
+#' @title Fit dynamic structural equation model
+#'
+#' @description Fits a dynamic structural equation model
+#'
+#' @inheritParams dsem
+#'
+#' @param log_prior A user-provided function that takes as input the list of
+#'        parameters \code{out$obj$env$parList()} where \code{out} is the output from
+#'        \code{dsemRTMB()}, and returns the log-prior probability.  For example
+#'        \code{log_prior = function(p) dnorm( p$beta_z[1], mean=0, sd=0.1, log=TRUE)}
+#'        specifies a normal prior probability for the first path coefficient
+#'        with mean of zero and sd of 0.1
+#'
+#' @details
+#' See \code{\link{dsem}} for details
+#'
+#' @return
+#' An object (list) of class `dsem`, fitted using RTMB
+#'
+#' @export
 dsemRTMB <-
 function( sem,
           tsdata,

R/read_model.R

@@ -10,10 +10,7 @@
 #' @param quiet Boolean indicating whether to print messages to terminal
 #'
 #' @details
-#' \strong{RAM specification using arrow-and-lag notation}
-#'
-#'
-#' @export
+#' See \code{\link{make_dsem_ram.R}} for details
 read_model <-
 function( sem,
           times,