specify location for function 'posterior'

This is complex because posterior is an S4 method that relies on
topicmodels and modeltools (and methods, probably). Unclear which will
work yet, so this is a first attempt.

Author: mjwestgate

DESCRIPTION

@@ -6,5 +6,5 @@ Author: Martin J. Westgate <[email protected]>
 Maintainer: Martin J. Westgate <[email protected]>
 Description: Tools to support literature review and evidence synthesis in R.
 Depends: R (>= 3.1.0)
-Imports: ade4, plotly, shiny, shinycssloaders, shinydashboard, SnowballC, stringdist, tm, topicmodels, viridisLite, magrittr
+Imports: ade4, plotly, shiny, shinycssloaders, shinydashboard, SnowballC, stringdist, tm, topicmodels, viridisLite, magrittr, methods, modeltools
 License: GPL-2

NAMESPACE

@@ -7,11 +7,13 @@ S3method(print, bibliography)
 S3method(summary, bibliography)
 S3method(summary, review_info)
 importFrom(grDevices, grey)
+importFrom(magrittr,"%>%")
+importFrom(modeltools, posterior)
 importFrom(plotly, renderPlotly, event_data)
 importFrom(shiny, sliderInput, selectInput, textInput, actionButton, tableOutput, uiOutput, reactiveValues, observeEvent, observe, renderPrint, isolate, fluidRow, strong, column, icon, p)
 importFrom(shinydashboard, sidebarMenu, menuItem, menuSubItem)
 importFrom(stats, xtabs)
 importFrom(tm, removePunctuation, removeWords, removeNumbers, stemDocument, tm_map, Corpus, VectorSource, DocumentTermMatrix, removeSparseTerms, stopwords, content_transformer, weightTf)
+importFrom(topicmodels, LDA, CTM)
 importFrom(utils, head, tail, write.csv, write.table)
 importFrom(viridisLite, magma, viridis, inferno, plasma)
-importFrom(magrittr,"%>%")

R/start_review_window.R

@@ -25,8 +25,8 @@ if(class(x)=="review_info"){
 palette_initial <-viridisLite::magma(n=model@k, alpha=0.9, begin=0, end=0.9)
 
 # data to send to plotinfo
-x_matrix<-topicmodels::posterior(model)$topics # article x topic
-y_matrix<-t(topicmodels::posterior(model)$terms)
+x_matrix<-modeltools::posterior(model)$topics # article x topic
+y_matrix<-t(modeltools::posterior(model)$terms)
 plot_list<-list(
 	x=data.frame(
 		id=rownames(dtm),
@@ -460,8 +460,8 @@ observeEvent(input$go_LDA, {
 		topic_model=sidebar_tracker$model_type,
 		n_topics=input$n_topics,
 		iterations=input$iterations)
-	x_matrix<-posterior(infostore$model)$topics
-	y_matrix<-t(posterior(infostore$model)$terms)
+	x_matrix<-modeltools::posterior(infostore$model)$topics
+	y_matrix<-t(modeltools::posterior(infostore$model)$terms)
 	keep_cols<-c("id", "caption", "abstract")
 	initial_captions<-plotinfo$x[, keep_cols[which(keep_cols %in% colnames(plotinfo$x))]]
 	# update plotinfo