1.8-5

alexanderrobitzsch · Feb 28, 2023 · 6f70f30 · 6f70f30
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mdmb
 Type: Package
 Title: Model Based Treatment of Missing Data
-Version: 1.8-1
-Date: 2023-02-17 22:38:37
+Version: 1.8-5
+Date: 2023-02-28 14:57:46
 Author: 
     Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
 Maintainer: 

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,5 +1,5 @@
 ## File Name: RcppExports.R
-## File Version: 1.008001
+## File Version: 1.008005
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 

diff --git a/R/frm_em.R b/R/frm_em.R
@@ -1,5 +1,5 @@
 ## File Name: frm_em.R
-## File Version: 0.961
+## File Version: 0.966
 
 
 frm_em <- function(dat, dep, ind, weights=NULL, verbose=TRUE,

diff --git a/R/frm_em_calc_likelihood.R b/R/frm_em_calc_likelihood.R
@@ -1,5 +1,5 @@
 ## File Name: frm_em_calc_likelihood.R
-## File Version: 1.387
+## File Version: 1.397
 
 #--- loop over models and predictions
 frm_em_calc_likelihood <- function( dat, ind0, NM, eps=1E-30, iter=NULL,
@@ -78,9 +78,13 @@ frm_em_calc_likelihood <- function( dat, ind0, NM, eps=1E-30, iter=NULL,
 
     post <- frm_normalize_posterior( post=post, case=dat$case)
     dat$weights <- dat$weights0 * post
+
     #--- compute total log likelihood
     ll <- frm_em_calc_total_likelihood(dat=dat, weights0=weights0,
-                like_obs=like_obs, post_miss=post_miss)
+                like_obs=like_obs, post_miss=post_miss, like=like)
+
+
+    #--- output
     res <- list( loglike=loglike, post=post, coefs=coefs,
                 model_results=model_results, ll=ll, post0=post0,
                 ind0=ind0, like=like, like0=like0  )

diff --git a/R/frm_em_calc_total_likelihood.R b/R/frm_em_calc_total_likelihood.R
@@ -1,13 +1,28 @@
 ## File Name: frm_em_calc_total_likelihood.R
-## File Version: 0.08
+## File Version: 0.123
 
 frm_em_calc_total_likelihood <- function(dat, weights0,
-    like_obs, post_miss)
+    like_obs, post_miss, like=NULL)
 {
     eps <- 1E-50
+
     # calculate total likelihood per case
-    like_case <- like_obs * post_miss
-    like_case <- rowsum( like_case, dat$case )[,1]
-    ll <- sum( log( like_case + eps ) * weights0 )
+    # like_case <- like_obs * post_miss
+    # like_case <- rowsum( like_case, dat$case )[,1]
+
+    #--- original computation
+    # like_case <- like_obs * post_miss
+    # like_case <- rowsum( like_case, dat$case )[,1]
+    # ll <- sum( log( like_case + eps ) * weights0 )
+
+    if (is.null(like)){
+        like_case <- like_obs * post_miss
+        like_case <- rowsum( like_case, dat$case )[,1]
+        ll <- sum( log( like_case + eps ) * weights0 )
+    } else {
+        like_case <- like * dat$delta_nodes
+        like_case <- rowsum( like_case, dat$case )[,1]
+        ll <- sum( log( like_case + eps ) * weights0 )
+    }
     return(ll)
 }
diff --git a/R/frm_prepare_data_em.R b/R/frm_prepare_data_em.R
@@ -1,5 +1,5 @@
 ## File Name: frm_prepare_data_em.R
-## File Version: 0.295
+## File Version: 0.303
 
 frm_prepare_data_em <- function(dat, dep, ind, weights0, dat0, update_model=NULL)
 {
@@ -9,6 +9,7 @@ frm_prepare_data_em <- function(dat, dep, ind, weights0, dat0, update_model=NULL
     dat$weights0 <- weights0
     dat$weights <- 1
     dat$resp_all <- 1
+    dat$delta_nodes <- 1
     # vector of dependent variables
     dv_vars <- c()
     for (mm in 1:NM){
@@ -20,6 +21,7 @@ frm_prepare_data_em <- function(dat, dep, ind, weights0, dat0, update_model=NULL
         dat <- frm_prepare_data_include_latent_data( dat=dat, var_mm=var_mm,
                         nodes_mm=nodes_mm, ind_mm=ind[[mm]] )
     }
+
     #** prepare dependent variables
     dat <- frm_prepare_data_include_latent_data( dat=dat,
                     var_mm=dep$dv_vars, nodes_mm=dep$nodes, ind_mm=dep )

diff --git a/R/frm_prepare_data_include_latent_data.R b/R/frm_prepare_data_include_latent_data.R
@@ -1,5 +1,5 @@
 ## File Name: frm_prepare_data_include_latent_data.R
-## File Version: 0.21
+## File Version: 0.224
 
 
 ##################################################################
@@ -30,6 +30,14 @@ frm_prepare_data_include_latent_data <- function( dat, var_mm,
         dat11 <- dat0[ rep_ind,  ]
         dat11[,var_mm] <- rep( nodes_mm, each=N0 )
         dat11$weights <- dat11$weights * rep( ind_mm$nodes_weights, each=N0 )
+        #*** include delta_nodes for some models
+        model_mm <- ind_mm$model
+        models0 <- c("linreg", "yjtreg", "bctreg")
+        if (sum( model_mm %in% models0 )> 0 ){
+            d1 <- cbind( c( diff(nodes_mm), NA), c(NA, diff(nodes_mm) ) )
+            diff_nodes <- rowMeans(d1, na.rm=TRUE)
+            dat11$delta_nodes <- dat11$delta_nodes * rep( diff_nodes, each=N0 )
+        }
         dat12 <- rbind( dat12, dat11 )
     }
     dat12 <- dat12[ order(dat12$case), ]

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 If you use `mdmb` and have suggestions for improvement or have found bugs, please email me at robitzsch@leibniz-ipn.de.
 Please always provide a minimal dataset, necessary to demonstrate the problem, 
 a minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and
-all necessary information on the used librarys, the R version, and the OS it is run on, perhaps a sessionInfo().
+all necessary information on the used librarys, the R version, and the OS it is run on, perhaps a `sessionInfo()`.
 
 #### Manual
 
@@ -25,9 +25,9 @@ The CRAN version can be installed from within R using:
 utils::install.packages("mdmb")
 ```
 
-#### GitHub version `mdmb` 1.8-1 (2023-02-17)
+#### GitHub version `mdmb` 1.8-5 (2023-02-28)
 
-[![](https://img.shields.io/badge/github%20version-1.8--1-orange.svg)](https://github.com/alexanderrobitzsch/mdmb)&#160;&#160;
+[![](https://img.shields.io/badge/github%20version-1.8--5-orange.svg)](https://github.com/alexanderrobitzsch/mdmb)&#160;&#160;
 
 The version hosted [here](https://github.com/alexanderrobitzsch/mdmb) is the development version of `mdmb`. 
 The GitHub version can be installed using `devtools` as:

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 1.13.1
 pkgdown: 1.5.1
 pkgdown_sha: ~
 articles: []
-last_built: 2023-02-17T21:45Z
+last_built: 2023-02-28T14:03Z
 
diff --git a/inst/NEWS b/inst/NEWS
@@ -30,10 +30,12 @@ CHANGELOG mdmb
 
 
 ---------------------------------------------------------------------
-VERSIONS mdmb 1.8  |  2023-02-17  |  Last: mdmb 1.8-1
+VERSIONS mdmb 1.8  |  2023-02-28  |  Last: mdmb 1.8-5
 ---------------------------------------------------------------------
 
-xxxx  *
+FIXED * now ouput observed log-likelihood value and not expected 
+        log-likelihood (thanks to Paul Allison)
+
 
 
 DATA  * included/modified datasets: ---

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -1,5 +1,5 @@
 //// File Name: RcppExports.cpp
-//// File Version: 1.008001
+//// File Version: 1.008005
 // Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393