changed data loading

R/app_server.R

@@ -99,6 +99,7 @@ app_server <- function(input, output, session) {
                              ,plot3_efs = r$preds3_efs$plot
 
                              ,patprofile = r$pdatc$patdat_clean
+                             ,dat_fmtfun = dat_fmtfun
               )
               rmarkdown::render("R/report.Rmd"
                                 , output_file = file

R/app_ui.R

@@ -10,13 +10,12 @@ waiter::waiter_set_theme(html = waiter::spin_3()
 options(mc.cores = 8)
 
 # load data:
-zcta_hhinc     <- readRDS(file = "data/zcta_hhinc.RDS")
-patdat_default <- readRDS(file = "data/patdat_default.RDS")
-xtest_names    <- readRDS(file = "data/xtest_vnames.RDS")
-dat_fmtfun     <- readRDS(file = "data/dat_fmtfun.RDS")
-
-nft_os  <- readRDS(file = "data/deadcounter.rds")
-nft_efs <- readRDS(file = "data/efscounter.rds")
+# zcta_hhinc     <- readRDS(file = "data/zcta_hhinc.RDS")
+# patdat_default <- readRDS(file = "data/patdat_default.RDS")
+# xtest_names    <- readRDS(file = "data/xtest_vnames.RDS")
+# dat_fmtfun     <- readRDS(file = "data/dat_fmtfun.RDS")
+# nft_os  <- readRDS(file = "data/deadcounter.rds")
+# nft_efs <- readRDS(file = "data/efscounter.rds")
 
 #' The application User-Interface
 #'

R/report.Rmd

@@ -14,6 +14,7 @@ params:
   ptbl3_efs: NA
   plot3_efs: NA
   patprofile: NA
+  dat_fmtfun: NA
 ---
 
 # 1-Year Survival Estimates:
@@ -167,7 +168,8 @@ vnames <- c("age"
 
 ```{r echo = FALSE}
 
-dat_fmtfun <- readRDS("../data/dat_fmtfun.RDS")
+# dat_fmtfun <- readRDS("../data/dat_fmtfun.RDS")
+dat_fmtfun <- params$dat_fmtfun
 
 patdat <- dat_fmtfun(params$patprofile)
 

README.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "README for nmdp.asom"
 author: "Lisa Rein"
-date: "2024-08-23"
+date: "2024-10-15"
 output: html_document
 ---
 
@@ -14,16 +14,16 @@ setwd(mydir)
 
 list.files(mydir)
 
-# make sure that model objects deadcounter.rds and efscounter.rds are saved in data folder:
-list.files(paste0(mydir, "/data"))
+# internal app data, sysdata.rda, should be saved in R subfolder:
+list.files(paste0(mydir, "/R"))
 
 ```
 
 
 ```{r eval = FALSE}
 
 # To run the app:
-# Note the model objects are large and the initial load could take a long time:
+# Note the internal app data (includes model objects) is large and the initial load could take a while:
 library(shiny)
 shiny::runApp()
 
@@ -36,6 +36,8 @@ shiny::runApp()
 
 # Dependent packages should automatically be installed/loaded but just in case,
 # app dependencies (also noted in NAMESPACE):
+
+# export(run_app)
 # import(bslib)
 # import(flextable)
 # import(ggplot2)

README.html

@@ -11,7 +11,7 @@
 
 <meta name="author" content="Lisa Rein" />
 
-<meta name="date" content="2024-08-23" />
+<meta name="date" content="2024-10-15" />
 
 <title>README for nmdp.asom</title>
 
@@ -352,7 +352,7 @@
 
 <h1 class="title toc-ignore">README for nmdp.asom</h1>
 <h4 class="author">Lisa Rein</h4>
-<h4 class="date">2024-08-23</h4>
+<h4 class="date">2024-10-15</h4>
 
 </div>
 
@@ -363,21 +363,35 @@ <h4 class="date">2024-08-23</h4>
 setwd(mydir)
 
 list.files(mydir)</code></pre>
-<pre><code>##  [1] &quot;app.R&quot;           &quot;data&quot;            &quot;DESCRIPTION&quot;     &quot;dev&quot;            
-##  [5] &quot;inst&quot;            &quot;man&quot;             &quot;NAMESPACE&quot;       &quot;nmdp.asom.Rproj&quot;
-##  [9] &quot;R&quot;               &quot;README.html&quot;     &quot;README.Rmd&quot;</code></pre>
-<pre class="r"><code># make sure that model objects deadcounter.rds and efscounter.rds are saved in data folder:
-list.files(paste0(mydir, &quot;/data&quot;))</code></pre>
-<pre><code>## [1] &quot;dat_fmtfun.RDS&quot;     &quot;deadcounter.rds&quot;    &quot;efscounter.rds&quot;    
-## [4] &quot;patdat_default.RDS&quot; &quot;xtest_vnames.RDS&quot;   &quot;zcta_hhinc.RDS&quot;</code></pre>
+<pre><code>##  [1] &quot;app.R&quot;           &quot;DESCRIPTION&quot;     &quot;dev&quot;             &quot;inst&quot;           
+##  [5] &quot;man&quot;             &quot;NAMESPACE&quot;       &quot;nmdp.asom.Rproj&quot; &quot;R&quot;              
+##  [9] &quot;README.html&quot;     &quot;README.Rmd&quot;</code></pre>
+<pre class="r"><code># internal app data, sysdata.rda, should be saved in R subfolder:
+list.files(paste0(mydir, &quot;/R&quot;))</code></pre>
+<pre><code>##  [1] &quot;_disable_autoload.R&quot;       &quot;app_config.R&quot;             
+##  [3] &quot;app_server.R&quot;              &quot;app_ui.R&quot;                 
+##  [5] &quot;golem_utils_server.R&quot;      &quot;golem_utils_ui.R&quot;         
+##  [7] &quot;mod_assemble_patprofile.R&quot; &quot;mod_clean_patprofile.R&quot;   
+##  [9] &quot;mod_enter_demo.R&quot;          &quot;mod_enter_disease.R&quot;      
+## [11] &quot;mod_enter_disease_all.R&quot;   &quot;mod_enter_disease_aml.R&quot;  
+## [13] &quot;mod_enter_disease_cll.R&quot;   &quot;mod_enter_disease_cml.R&quot;  
+## [15] &quot;mod_enter_disease_hd.R&quot;    &quot;mod_enter_disease_mds.R&quot;  
+## [17] &quot;mod_enter_disease_mm.R&quot;    &quot;mod_enter_disease_nhl.R&quot;  
+## [19] &quot;mod_enter_donor.R&quot;         &quot;mod_enter_transplant.R&quot;   
+## [21] &quot;mod_predict_efs.R&quot;         &quot;mod_predict_os.R&quot;         
+## [23] &quot;mod_save_patprofile.R&quot;     &quot;mod_upload_patprofile.R&quot;  
+## [25] &quot;report.Rmd&quot;                &quot;run_app.R&quot;                
+## [27] &quot;sysdata.rda&quot;</code></pre>
 <pre class="r"><code># To run the app:
-# Note the model objects are large and the initial load could take a long time:
+# Note the internal app data (includes model objects) is large and the initial load could take a while:
 library(shiny)
 shiny::runApp()
 
 # you should see a message in the console if the app is successfully loading: &#39;Loading nmdp.asom&#39;</code></pre>
 <pre class="r"><code># Dependent packages should automatically be installed/loaded but just in case,
 # app dependencies (also noted in NAMESPACE):
+
+# export(run_app)
 # import(bslib)
 # import(flextable)
 # import(ggplot2)

nmdp.asom.Rproj

@@ -1,23 +1,23 @@
-Version: 1.0
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: No
-
-EnableCodeIndexing: No
-UseSpacesForTab: Yes
-NumSpacesForTab: 4
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-LineEndingConversion: Posix
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-
-QuitChildProcessesOnExit: Yes
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: No
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+
+QuitChildProcessesOnExit: Yes