Merge pull request #29 from CSAFE-ISU/26-fix-warnings

26 fix warnings
CSAFE-ISU · Oct 30, 2024 · ea49204 · ea49204
2 parents e84ab90 + 8b49765
commit ea49204
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Showing 9 changed files with 68 additions and 32 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,7 +15,9 @@ LazyData: true
 Imports: 
     bslib,
     dplyr,
+    ggplot2,
     handwriter,
+    handwriterRF,
     magick,
     magrittr,
     rmarkdown,

diff --git a/R/app.R b/R/app.R
@@ -164,13 +164,13 @@ handwriterApp <- function(...){
     # placing the home page inside a module becomes quite complicated.
 
     # Switch to Scenario 1 tab
-    observeEvent(input$open_button, {
-      updateNavbarPage(session, "my-navbar", selected = "Scenario 1")
+    shiny::observeEvent(input$open_button, {
+      shiny::updateNavbarPage(session, "my-navbar", selected = "Scenario 1")
     })
 
     # Switch to Scenario 2 tab
-    observeEvent(input$closed_button, {
-      updateNavbarPage(session, "my-navbar", selected = "Scenario 2")
+    shiny::observeEvent(input$closed_button, {
+      shiny::updateNavbarPage(session, "my-navbar", selected = "Scenario 2")
     })
 
     openServer('open1')

diff --git a/R/closed-demo-preview.R b/R/closed-demo-preview.R
@@ -51,14 +51,14 @@ demoPreviewServer <- function(id, global) {
 
       # create a reactive for each model doc
       model_reactives <- lapply(model_docs, function(doc) {
-        reactive({
+        shiny::reactive({
           list(datapath = doc)
         })
       })
 
       # create a reactive for each questioned doc
       questioned_reactives <- lapply(questioned_docs, function(doc) {
-        reactive({
+        shiny::reactive({
           list(datapath = doc)
         })
       })

diff --git a/R/graphs.R b/R/graphs.R
@@ -39,7 +39,7 @@ graphsServer <- function(id, sample, graphs) {
     id,
     function(input, output, session) {
       output$path <- shiny::renderText({
-        req(sample()$datapath)
+        shiny::req(sample()$datapath)
         basename(sample()$datapath)
       })
 

diff --git a/R/home.R b/R/home.R
@@ -72,8 +72,8 @@ homeServer <- function(id){
   shiny::moduleServer(
     id,
     function(input, output, session){
-      observeEvent(input$open_button, {
-        updateNavbarPage(session, "my-navbar", selected = "Open-Set")
+      shiny::observeEvent(input$open_button, {
+        shiny::updateNavbarPage(session, "my-navbar", selected = "Open-Set")
       })
     }
   )

diff --git a/R/open-master.R b/R/open-master.R
@@ -68,7 +68,7 @@ openServer <- function(id){
     function(input, output, session){
 
       # ON / OFF BUTTON FOR RESULTS DISPLAY ----
-      display <- reactiveValues(show = FALSE)
+      display <- shiny::reactiveValues(show = FALSE)
 
       # graphs
       graphs <- shiny::reactiveValues(sample1 = NULL,
@@ -79,7 +79,7 @@ openServer <- function(id){
                                         sample2 = NULL)
 
       # LOAD ----
-      sample1 <- reactive({
+      sample1 <- shiny::reactive({
         cat(file=stderr(), "sample1 reactive \n")
 
         # turn off slr display
@@ -92,7 +92,7 @@ openServer <- function(id){
       }) %>% 
         shiny::bindEvent(input$open_upload1)
 
-      sample2 <- reactive({
+      sample2 <- shiny::reactive({
         cat(file=stderr(), "sample2 reactive \n")
 
         # turn off slr display
@@ -105,15 +105,15 @@ openServer <- function(id){
       }) %>% 
         shiny::bindEvent(input$open_upload2)
 
-      template_plot <- reactive({
+      template_plot <- shiny::reactive({
         x <- list()
         x$datapath <- system.file(file.path("extdata", "images", "template.png"), package = "handwriterApp")
         return(x)
       })
 
       # calculate slr
-      slr_df <- reactive({
-        req(sample1(), sample2())
+      slr_df <- shiny::reactive({
+        shiny::req(sample1(), sample2())
 
         cat(file=stderr(), "slr_df reactive \n")
 
@@ -149,7 +149,7 @@ openServer <- function(id){
       # RENDER ----
       # display handwriting samples
       output$samples_display <- shiny::renderUI({
-        req(sample1(), sample2())
+        shiny::req(sample1(), sample2())
         ns <- session$ns
 
         cat(file=stderr(), "render samples UI \n")
@@ -164,7 +164,7 @@ openServer <- function(id){
 
       # display hypotheses
       output$hypotheses_display <- shiny::renderUI({
-        req(sample1(), sample2())
+        shiny::req(sample1(), sample2())
         ns <- session$ns
 
         cat(file=stderr(), "render hypotheses UI \n")
@@ -185,7 +185,7 @@ openServer <- function(id){
 
       # display limitations
       output$limitations_display <- shiny::renderUI({
-        req(sample1(), sample2())
+        shiny::req(sample1(), sample2())
         ns <- session$ns
 
         cat(file=stderr(), "render limiations UI \n")
@@ -206,7 +206,7 @@ openServer <- function(id){
 
       # display writer profiles
       output$profiles_display <- shiny::renderUI({
-        req(clusters$sample1, clusters$sample2, display$show)
+        shiny::req(clusters$sample1, clusters$sample2, display$show)
         ns <- session$ns
 
         cat(file=stderr(), "render writer profiles UI \n")
@@ -237,15 +237,15 @@ openServer <- function(id){
 
       # display similarity score
       output$score <- shiny::renderText({
-        req(slr_df(), display$show)
+        shiny::req(slr_df(), display$show)
 
         cat(file=stderr(), "render score \n")
         slr_df()$score
       })
 
       # display slr
       output$slr <- shiny::renderText({
-        req(slr_df(), display$show)
+        shiny::req(slr_df(), display$show)
 
         cat(file=stderr(), "render slr \n")
 
@@ -264,26 +264,26 @@ openServer <- function(id){
 
       # display slr interpretation
       output$slr_interpretation <- shiny::renderText({
-        req(slr_df(), display$show)
+        shiny::req(slr_df(), display$show)
         cat(file=stderr(), "render interpretation \n")
         handwriterRF::interpret_slr(slr_df())
       })
 
       # display slr results
       output$slr_display <- shiny::renderUI({
-        req(sample1(), sample2(), slr_df(), display$show)
+        shiny::req(sample1(), sample2(), slr_df(), display$show)
         ns <- session$ns
 
         cat(file=stderr(), "render slr UI \n")
 
         shiny::tagList(
           shiny::h1("COMPARISON RESULTS"),
           shiny::HTML("<p>Handwriter measures the similarity between the two writer profiles using a random forest trained 
-          on handwriting samples from the <a href='https://data.csafe.iastate.edu/HandwritingDatabase/'>CSAFE Handwriting Database</a>. 
-          The result is a <i>similarity score</i> between the two writer profiles. Next, handwriter calculates the likelihood of observing the similarity score if the 'same writer' hypothesis is true and the likelihood 
+                      on handwriting samples from the <a href='https://data.csafe.iastate.edu/HandwritingDatabase/'>CSAFE Handwriting Database</a>. 
+                      The result is a <i>similarity score</i> between the two writer profiles. Next, handwriter calculates the likelihood of observing the similarity score if the 'same writer' hypothesis is true and the likelihood 
                       of observing the similarity score if the 'different writers' hypothesis is true. The <i>score-based likelihood ratio</i> is the ratio of these
                       two likelihoods. For more information, see <cite><a hrer='https://doi.org/10.1002/sam.11566'>Handwriting identification using random forests 
-                      and score‐based likelihood ratios.</a></cite></p>
+                      and score-based likelihood ratios.</a></cite></p>
                       "
                       ),
           shiny::h2("Similarity Score"),
@@ -302,12 +302,12 @@ openServer <- function(id){
       singleImageServer("sample1", sample1)
       singleImageServer("sample2", sample2)
 
-      graphsServer("sample1_graphs", sample1, reactive(graphs$sample1))
-      graphsServer("sample2_graphs", sample2, reactive(graphs$sample2))
+      graphsServer("sample1_graphs", sample1, shiny::reactive(graphs$sample1))
+      graphsServer("sample2_graphs", sample2, shiny::reactive(graphs$sample2))
 
       singleImageServer("template1", template_plot, title = "Clusters")
 
-      writerProfileServer("writer_profiles", sample1, sample2, reactive(clusters))
+      writerProfileServer("writer_profiles", sample1, sample2, shiny::reactive(clusters))
     }
   )
 }
diff --git a/R/plots.R b/R/plots.R
@@ -1,4 +1,38 @@
+# The 'handwriterApp' R package performs writership analysis of handwritten
+# documents. Copyright (C) 2024 Iowa State University of Science and Technology
+# on behalf of its Center for Statistics and Applications in Forensic Evidence
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License along with
+# this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# Internal Functions ------------------------------------------------------
+
+#' Plot Writer Profiles
+#'
+#' Create a line plot of cluster fill rates for one or more documents, where the
+#' cluster fill rates serve as writer profiles. Each cluster fill rates for each
+#' document are plotted as different colored lines.
+#'
+#' @param rates A data frame of cluster fill rates created with
+#'   \code{\link[handwriterRF]{get_cluster_fill_rates}}
+#'
+#' @return A line plot
+#'
+#' @noRd
+#' 
 plot_writer_profiles <- function(rates) {
+  # prevent note: "no visible binding for global variable"
+  docname <- cluster <- rate <- NULL
 
   rates <- rates %>% 
     tidyr::pivot_longer(cols = -tidyr::any_of(c("docname", "total_graphs")), names_to = "cluster", values_to = "rate") %>%

diff --git a/R/single-image.R b/R/single-image.R
@@ -22,13 +22,13 @@ singleImageServer <- function(id, sample, title = NULL) {
         if (!is.null(title)){
           title
         } else {
-          req(sample()$datapath)
+          shiny::req(sample()$datapath)
           basename(sample()$datapath)
         }
       })
 
       output$image <- shiny::renderImage({
-        req(sample()$datapath)
+        shiny::req(sample()$datapath)
 
         image <- magick::image_read(sample()$datapath)
         tmp <- image %>%

diff --git a/R/writer-profile.R b/R/writer-profile.R
@@ -20,7 +20,7 @@ writerProfileServer <- function(id, sample1, sample2, clusters) {
     id,
     function(input, output, session) {
       output$path <- shiny::renderText({
-        req(sample1()$datapath, sample2()$datapath)
+        shiny::req(sample1()$datapath, sample2()$datapath)
         paste(basename(sample1()$datapath), "and", basename(sample2()$datapath))
       })