From e194f5404ca8fbbe37c92c3b969fcd5b7404e924 Mon Sep 17 00:00:00 2001
From: Jim Thorson <James.T.Thorson@gmail.com>
Date: Mon, 30 Dec 2024 12:05:08 -0800
Subject: [PATCH] fix merge

---
 DESCRIPTION | 2 +-
 NEWS.md     | 2 ++
 R/dsem.R    | 5 +++++
 man/dsem.Rd | 7 +++++++
 4 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4c89021..df6ebfb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,7 +14,7 @@ Imports:
     Matrix,
     sem,
     igraph,
-    RTMB
+    RTMB,
     ggraph,
     grid,
     methods
diff --git a/NEWS.md b/NEWS.md
index a5fe77c..d5a4724 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,6 +6,8 @@
   option
 * Adding `convert_equations` to extend `sem::specifyEquations` and simplify
   specification for large models
+* Adding argument `prior_negloglike` as interface to specify Bayesian priors
+  and/or likelihood penalties
 
 # dsem 1.3.0
 
diff --git a/R/dsem.R b/R/dsem.R
index 00928eb..f6b7b8f 100644
--- a/R/dsem.R
+++ b/R/dsem.R
@@ -20,6 +20,11 @@
 #'        while covs=c("x1", "x2") specifies the variance of x1 and the variance of x2 but not their covariance.
 #'        These same covariances can be added manually via argument `sem`, but using argument `covs` might
 #'        save time for models with many variables.
+#' @param prior_negloglike A user-provided function that takes as input the vector of fixed effects out$obj$par
+#'        returns the negative log-prior probability. For example
+#'        \code{prior_negloglike = function(par) -1 * dnorm( par[1], mean=0, sd=0.1, log=TRUE)}
+#'        specifies a normal prior probability
+#'        for the for the first fixed effect with mean of zero and logsd of 0.1
 #' @param control Output from \code{\link{dsem_control}}, used to define user
 #'        settings, and see documentation for that function for details.
 #'
diff --git a/man/dsem.Rd b/man/dsem.Rd
index 93d2cc1..8f084bf 100644
--- a/man/dsem.Rd
+++ b/man/dsem.Rd
@@ -9,6 +9,7 @@ dsem(
   tsdata,
   family = rep("fixed", ncol(tsdata)),
   estimate_delta0 = FALSE,
+  prior_negloglike = NULL,
   control = dsem_control(),
   covs = colnames(tsdata)
 )
@@ -29,6 +30,12 @@ Other options correspond to different specifications of measurement error.}
 as fixed effects, or alternatively to assume that dynamics start at some stochastic draw away from
 the stationary distribution}
 
+\item{prior_negloglike}{A user-provided function that takes as input the vector of fixed effects out$obj$par
+returns the negative log-prior probability. For example
+\code{prior_negloglike = function(par) -1 * dnorm( par[1], mean=0, sd=0.1, log=TRUE)}
+specifies a normal prior probability
+for the for the first fixed effect with mean of zero and logsd of 0.1}
+
 \item{control}{Output from \code{\link{dsem_control}}, used to define user
 settings, and see documentation for that function for details.}