Bugfix/remove trelli ddo

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FREDA
 Title: An app for the processing and visualization of Fourier-transform mass spectrometry data.
-Version: 1.2.4
+Version: 1.3.0
 Authors@R: c(person("Lisa", "Bramer", "lisa.bramer@pnnl.gov", role = "aut", "cre"),
     person("Daniel", "Claborne", "daniel.claborne@pnnl.gov", role = c("aut")))
 Description: A frontend application which exposes functionality of the ftmsRanalysis R package.  See 
@@ -22,8 +22,7 @@ Imports:
     markdown, 
     pander, 
     plotly, 
-    purrr, 
-    raster, 
+    purrr,
     RColorBrewer, 
     readr, 
     reshape2, 
@@ -47,6 +46,5 @@ Imports:
     xfun,
     MetaCycData, 
     mapDataAccess,
-    ftmsRanalysis,
-    datadr
+    ftmsRanalysis
 

Reactive_Variables/visualize_revals.R

@@ -149,7 +149,7 @@ plot_data <- eventReactive(input$plot_submit, {
     validate(need(input$summary_fxn %in% ftmsRanalysis:::getGroupComparisonSummaryFunctionNames(), "Please select a summary function"))
 
     # get the value of the single pairwise comparison
-    grpComparisonsObj <- divideByGroupComparisons(temp_data, comparisons = "all")[[1]]$value
+    grpComparisonsObj <- divideByGroupComparisons(temp_data, comparisons = "all")[[1]]
 
     # paramaters specific to uniqueness_gtest()
     if (input$summary_fxn == "uniqueness_gtest") {

calculation_options.csv

@@ -1,7 +1,7 @@
 "DisplayName","Function","Info"
 "Element Ratios","calc_element_ratios","Element ratios for each molecule"
 "Kendrick Mass and Defect","calc_kendrick","Kendrick Defect = Nominal Kendrick Mass - Kendrick Mass \n\n Kendrick MAss = IUPAC mass*(14/14.01565), where IUPAC mass is based on the 12C atomic mass as exactly 12 Da. <a href=""https://pubs.acs.org/doi/pdf/10.1021/ac010560w"">[Hughey et al., 2001]</a>"
-"NOSC","calc_nosc","Nominal oxidation state of carbon. <a href=""https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.2386"">[Koch \& Dittmar, 2006]</a><a href = ""https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.7433"">[Erratum]</a>"
+"NOSC","calc_nosc","Nominal oxidation state of carbon. <a href=""https://www.sciencedirect.com/science/article/pii/S0016703711000378"">[LaRowe &amp; Van Cappellen, 2011]</a>"
 "Gibbs Free Energy","calc_gibbs","Cox Gibbs Free Energy. Calculated as:60.3 - 28.5*NOSC <a href=""https://www.sciencedirect.com/science/article/pii/S0016703711000378"">[LaRowe &amp; Van Cappellen, 2011]</a>"
 "Aromaticity & Modified Aromaticity","calc_aroma","Aromaticity & Modified Aromaticity. <a href = ""https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.2386"">[Koch \& Dittmar, 2006]</a> <a href = ""https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.7433"">[Erratum]</a>"
 "DBE, DBE - O & DBE - AI","calc_dbe","DBE & DBE - O <a href = ""https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.2386"">[Koch \& Dittmar, 2006]</a> <a href = ""https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.7433"">[Erratum]</a>"

global.R

@@ -8,7 +8,6 @@ library(webshot)
 library(htmlwidgets)
 library(dplyr)
 library(markdown)
-library(raster)
 library(purrr)
 library(shinyBS)
 library(shinyjs)

renv.lock

@@ -281,16 +281,6 @@
       ],
       "Hash": "5edbbabab6ce0bf7900a74fd4358628e"
     },
-    "codetools": {
-      "Package": "codetools",
-      "Version": "0.2-19",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "c089a619a7fae175d149d89164f8c7d8"
-    },
     "colorspace": {
       "Package": "colorspace",
       "Version": "2.1-1",
@@ -368,28 +358,6 @@
       ],
       "Hash": "38bbf05fc2503143db4c734a7e5cab66"
     },
-    "datadr": {
-      "Package": "datadr",
-      "Version": "0.8.6",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "datadr",
-      "RemoteUsername": "delta-rho",
-      "RemoteRef": "HEAD",
-      "RemoteSha": "f3ffebd8e1c43a5d11cd3543bbe672c88f8c52f3",
-      "Requirements": [
-        "codetools",
-        "data.table",
-        "digest",
-        "dplyr",
-        "hexbin",
-        "magrittr",
-        "methods",
-        "parallel"
-      ],
-      "Hash": "4ddf60dd3cd5d3baf559f44d872fc74e"
-    },
     "digest": {
       "Package": "digest",
       "Version": "0.6.37",
@@ -487,13 +455,13 @@
       "Package": "ftmsRanalysis",
       "Version": "1.1.0",
       "Source": "GitHub",
-      "Remotes": "github::delta-rho/datadr, github::EMSL-Computing/MetaCycData",
+      "Remotes": "github::EMSL-Computing/MetaCycData",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteRepo": "ftmsRanalysis",
-      "RemoteUsername": "EMSL-Computing",
-      "RemoteRef": "8753cb08900045e0763e9be7aa293e98de62a490",
-      "RemoteSha": "8753cb08900045e0763e9be7aa293e98de62a490",
+      "RemoteUsername": "EMSL-computing",
+      "RemoteRef": "8590e0dea16084238c82364706db9855c00801de",
+      "RemoteSha": "8590e0dea16084238c82364706db9855c00801de",
       "Requirements": [
         "R",
         "RColorBrewer",
@@ -514,7 +482,7 @@
         "tidyr",
         "vegan"
       ],
-      "Hash": "0f4f9535c3cf1fcda1ad376ca0bcf0b4"
+      "Hash": "b973a46e6fe6ee30e4b8f03067dca5e2"
     },
     "generics": {
       "Package": "generics",
@@ -603,23 +571,6 @@
       ],
       "Hash": "24b224366f9c2e7534d2344d10d59211"
     },
-    "hexbin": {
-      "Package": "hexbin",
-      "Version": "1.28.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "124e384c01d8746f1c12f9dc1b80a161"
-    },
     "highr": {
       "Package": "highr",
       "Version": "0.11",
@@ -1176,20 +1127,6 @@
       ],
       "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
     },
-    "raster": {
-      "Package": "raster",
-      "Version": "3.6-26",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp",
-        "methods",
-        "sp",
-        "terra"
-      ],
-      "Hash": "7d6eda494f34a644420ac1bfd2a8023a"
-    },
     "readr": {
       "Package": "readr",
       "Version": "2.1.5",

ui.R

@@ -15,7 +15,7 @@ ui <- tagList(useShinyjs(),
   ),
 
   navbarPage(
-    title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.2.5")),
+    title = tags$div("FREDA", tags$span(style = "font-size:small", "v1.3.0")),
     windowTitle = 'FREDA',
     id = "top_page",
     theme = "yeti.css",
@@ -479,7 +479,7 @@ ui <- tagList(useShinyjs(),
             checkboxGroupInput("download_selection", label = "Check Download Selection",
               choices = c('Data File as one .csv and Molecular Identification File as another .csv' = "separate",
                 'Merged Data File and Molecular Identification File as a single .csv' = "merged",
-                'Data summaries for grouped plots' = "group_data"),
+                'Data summaries and comparison results for grouped plots' = "group_data"),
               width = "80%")
           )
         ),