Adjustment practice #2

Jiayue-He · 2021-06-07T11:44:17Z

No description provided.

invoke_wrapped: throwing std::runtime_error

…m/Logistic_Regression into adjustment_practice

Error in execCallbacks(timeoutSecs, all, loop$id) : invoke_wrapped: throwing std::runtime_error

…m/Logistic_Regression into adjustment_practice

shravanisamala

Hi Jiayue-He! Good job changing the ui.R. and server.R files to one app.R file! Just a few general things to consider:

I added many comments regarding the style because I was comparing the app side-by-side to the style guide. Make sure you go back in and add any necessary titles and remove and unnecessary details like the colons, strong(), and h4()s for bullet points.
Be sure to go through the whole code and add white space around = signs and other symbols where needed.
I would ask Dr. Neil and/or Mr. Carey about the huge chunks of code that are commented out and see if you can delete them.
Change the order of the tabs and fix the go buttons
Cite the packages you haven't cited yet. Check if all of them are used with the stale packages function we talked about today
Make sure your code is explicit everywhere and by this I mean the whole session = session, inputId = "" and so on
And for the overall code, I would try to go back when you have free time and fix the alignment and indenting of the code. I noticed that sometimes each line of text underneath the previous line was not consistently indented. For example, some lines are indented twice or thrice while some of the later lines are indented once. I would change them all to one just so we do not go past that 80 character guideline.

Overall, great job! You did a lot of great work to get the app to where it is now! I hope some of my comments will help!

shravanisamala · 2021-06-07T13:11:06Z

app.R

+
+library(dplyr)
+library(shinycssloaders)
+


Missing the BoastUtils package! When I tried running this code on my laptop, it says that the script function which is in BoastUtils was not found.

shravanisamala · 2021-06-07T13:12:22Z

app.R

+
+source("helpers.R") 
+
+ui <- dashboardPage(


According to the style guide, I believe this should be:

ui <- list(
dashboardPage( ...

shravanisamala · 2021-06-07T13:14:00Z

app.R

+      menuItem("References", tabName = "references", icon = icon("leanpub"))
+    ),
+
+    tags$div(


Here is the updated PSU button code from the style guide!

tags$div(
class = "sidebar-logo",
boastUtils::sidebarFooter()
)

shravanisamala · 2021-06-07T13:15:48Z

app.R

+    tabItems(
+      #Adding pre-requisites page to remove background from instructions page
+
+      tabItem(tabName="prereq",


The tab items are out of order. I think it should be Overview page, then prerequisites page

shravanisamala · 2021-06-07T13:18:02Z

app.R

+  ######### Could be combined but left separate so easily understood#####################
+
+  dashboardBody(
+    tags$head(


Not quite sure what lines 61 - 113 are supposed to do so I tried commenting it out and the app's background color for each page remained white! Consider asking Dr. Neil or Mr. Carey if it is ok to completely delete these lines of code.

shravanisamala · 2021-06-07T13:46:31Z

app.R

+          "Carey, R. (2019). boastUtils: BOAST Utilities, R Package.
+                             Available from https://github.com/EducationShinyAppTeam/boastUtils"
+        )
+      ) #end of tabItem


Don't forget the copyright info at the end of the references page!

br(), br(), br(), boastUtils::copyrightInfo()

shravanisamala · 2021-06-07T13:48:14Z

app.R

+
+
+        }
+      }


Check bracket alignment

shravanisamala · 2021-06-07T13:49:26Z

app.R

+
+  observeEvent(input$restart,{
+    updateButton(session, "submit", disabled = FALSE)
+    updateButton(session,"restart",disable =FALSE)


disabled not disable

shravanisamala · 2021-06-07T13:53:24Z

app.R

+    }
+    else{
+      if(length(index_list$list) == 1){
+        updateButton(session, "nextq", disabled = TRUE)


session = session etc.

shravanisamala · 2021-06-07T13:54:10Z

app.R

+
+  })
+
+  renderIcon()


I tried commenting this out and the app works without it. Was this something you were working on or can it be deleted?

lbednarczyk · 2021-06-16T16:16:20Z

DESCRIPTION

+URL: https://psu-eberly.shinyapps.io/Sample_App
+BugReports: https://github.com/EducationShinyAppTeam/Sample_App/issues


The website for URL and BugReports should be updated to say Logistic_Regression instead of Sample_App.

lbednarczyk · 2021-06-16T16:18:25Z

app.R

+#library(discrimARTs)
+library(leaflet)
+library(raster)
+library(DT)
+
+library(RColorBrewer) 
+#library(car)
+#library(rgdal)


You could delete the lines that have unused packages instead of leaving them commented out.

lbednarczyk · 2021-06-16T16:48:44Z

app.R

+                                                where data is divided into recommended 10 groups. The p-value can 
+                                                determine the significance of the result.")),
+              br(),
+              h4(tags$li("Hosmer-Lemeshow Test Statstics")),


There is a typo in Statistics here.

lbednarczyk · 2021-06-16T16:49:49Z

app.R

+                                                                            \\over exp_{ij}}$$')),
+              br(),
+              br(),
+              div(style = "text-align: center",bsButton("start","Go to the overview",


After you update the order of tabs to be first overview and then prerequisites, the label on this button should be changed to Explore.

lbednarczyk · 2021-06-16T16:50:19Z

app.R

+              br(),
+              div(style = "text-align: center",bsButton("start","Go to the overview",
+                                                        icon("bolt"),style = "danger",
+                                                        size = "large",class="circle grow"))


None of the buttons should have the class = circle grow argument.

lbednarczyk · 2021-06-16T16:56:35Z

app.R

+                      tableOutput("lemeshowDF"),
+                      tableOutput("obsexpDF"),


I was getting errors on the page where these outputs were supposed to be shown, the packages ResourceSelection and data.table should be added at the top of the app so that these outputs will run properly.

lbednarczyk · 2021-06-16T16:57:43Z

app.R

+                  ),
+                  #set continue button
+                  div(style = "text-align: center",
+                      bsButton(inputId = "go1", label =  "Play the game!", icon("bolt"), style= "danger", size= "large", class='circle grow')


You could change the label on this button to just say "Play!".

lbednarczyk · 2021-06-16T17:03:35Z

app.R

+                        selectInput(inputId="MedYvar", label="Select Response Variable Y",
+                                    choices = c("Acceptance"),
+                                    selected = 'Acceptance'),


Not sure if this selection is needed since there is only one option for the response variable for each of the possible data sets.

lbednarczyk · 2021-06-16T17:04:16Z

app.R

+                    mainPanel(
+                      plotOutput("empericalLogitPlot", width = "100%")%>% withSpinner(color="#ffa500")


This plot wouldn't load until I added the Stat2Data package at the beginning of the code.

lbednarczyk

Good job overall! Other than the comments that I left throughout the code, I would just make sure to go through the code and fix spacing issues and make all of the arguments explicit like Shravani said. Also make sure to add the missing packages so that everything runs smoothly.

rpc5102 · 2022-01-04T15:29:42Z

6aaa28d was deployed to shinyapps.io to resolve an SSL Expiry error although I suggest further work to clean up.

Maxinewsu

Recommended Priority: Urgent

Issues are all addressed.
The link of URL and Bugreports on DESCRIPTION is not correct
Missing screenshot on README.
Add a citation on the overview page.
Add a line "This app was last updated by xxx" at the bottom of the overview page.
Switch the order of Prerequisite and Overview pages.
The last three referenes on Reference page are not cited using the required format.
The font size is too big compared to other shiny apps.

"Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred" may not be fixable the way the app is made.

tarynmch

Good work with updating the app. The UI looks good, but in the server, I noticed that some of the IDs are not camelcase (like gamescore), some things are not individually indented (line 749 and 755), the chapter name should be changed, and there is no alt text for some of the plots and images in the game. The only thing I suggest is to go through the question bank excel and make the capitalization consistent for the choices.
I also noticed that when using the Single Logistic Regression sliders, it said in the console, "glm.fit: fitted probabilities numerically 0 or 1 occurred."

Made fixes to code including the addition of alt texts, naming of objects, indentation, and deletion of unused code. Made updates to the question bank file. Removed unused images. Fixed Chapter in description

Sburke26 · 2023-07-10T18:42:16Z

Thank you for the review.
I made additional fixes to the app.
The "glm.fit: fitted probabilities numerically 0 or 1 occurred." message can't be removed due to the current way the data is simulated.
I think I added alt text to everything but the logistic plot which uses renderPlotly() instead of renderPlot().
Please let me know if you notice anything else.

tarynmch

Looks good. The main thing I noticed was that when you click game it says, "Select your answer from below" but after you click next it says, "pick an answer from below." I would just make sure that is concise. Then make sure randNum is camelcase. I also suggest that for the game, if you want to get to 20 points within 10 questions, you could add a question counter. Otherwise, the app looks great!

Sburke26 · 2023-07-21T18:33:30Z

Thank you for the review. I made some changes and added a question counter. Please let me know if you see anything else.

tarynmch

Looks good! The only thing I suggest is that on the Overview page in the instructions, be sure to mention that the New Sample button is within the Explore tab. Otherwise, be sure to get rid of the unnecessary code in the app.R before you merge the branches. Great work.

Remove an problematic install.packages command

Cleaning up the explore page to improve efficiency and table accessibility

Remove unnecessary packages and code from the app; deleted helpers file that contained elements counter to the Style Guide.

Clean up of alt text

Reorganizing Game Server code

Initial work towards reformatting the game page of the app

Jiayue He added 15 commits June 7, 2021 06:46

complete revising app

d74e2ca

complete description file

313917b

adding feedback

ddad429

Create docs

b18b57a

Delete docs

1fc64cc

Delete server.R

1431acd

Delete ui.R

ee45278

add docs file

bba0eac

Delete rsconnect/shinyapps.io/psu-eberly directory

20a2d2b

fix Error in execCallbacks(timeoutSecs, all, loop$id) :

49d0a1d

invoke_wrapped: throwing std::runtime_error

Merge branch 'adjustment_practice' of github.com:EducationShinyAppTea…

ffd3ecb

…m/Logistic_Regression into adjustment_practice

Delete README.md

1ccf6e0

fix the error, not sure,

64a612e

Error in execCallbacks(timeoutSecs, all, loop$id) : invoke_wrapped: throwing std::runtime_error

Merge branch 'adjustment_practice' of github.com:EducationShinyAppTea…

566ea33

…m/Logistic_Regression into adjustment_practice

adding reference

6fa28d8

Jiayue-He requested review from lbednarczyk and shravanisamala June 7, 2021 11:44

shravanisamala previously requested changes Jun 7, 2021

View reviewed changes

lbednarczyk reviewed Jun 16, 2021

View reviewed changes

lbednarczyk previously requested changes Jun 16, 2021

View reviewed changes

Jiayue He and others added 4 commits June 20, 2021 19:05

fix "could not find hoslem.test() function"

ebf31c3

fix "could not find setDT() function"

632db54

Cleaned up unused packages and applied styler formatting

6aaa28d

Updated .gitignore

70b7913

neilhatfield requested a review from Maxinewsu May 27, 2022 20:54

Maxinewsu previously requested changes May 30, 2022

View reviewed changes

updated

bf911cf

Maxinewsu requested review from a team and removed request for a team June 9, 2022 23:51

Sburke26 added 4 commits June 12, 2023 09:48

Update ToDoList.txt

f47fd54

"Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred" may not be fixable the way the app is made.

Update app.R

e04c019

Update app.R

1dc990a

Add to Acknowledgements

4da22d2

Sburke26 requested a review from tarynmch June 27, 2023 16:46

tarynmch suggested changes Jul 10, 2023

View reviewed changes

Post-Review updates

3ba2a43

Made fixes to code including the addition of alt texts, naming of objects, indentation, and deletion of unused code. Made updates to the question bank file. Removed unused images. Fixed Chapter in description

Sburke26 requested a review from tarynmch July 11, 2023 13:33

tarynmch suggested changes Jul 18, 2023

View reviewed changes

Sburke26 added 2 commits July 20, 2023 17:37

Update app.R

1e09380

Update app.R

0ffb0e5

Sburke26 requested a review from tarynmch July 21, 2023 18:34

Sburke26 added 4 commits July 27, 2023 17:27

minor updates

0f6623c

Update Logistic Plot

dc4fb39

Update app.R

235162d

Update app.R

51505bf

tarynmch previously approved these changes Aug 1, 2023

View reviewed changes

updates

3184243

Sburke26 dismissed tarynmch’s stale review via 3184243 August 3, 2023 20:16

Sburke26 and others added 9 commits August 7, 2023 11:47

Update app.R

cc1933a

Update app.R

06e21f6

Update app.R

a54fbe0

Remove an problematic install.packages command

First set of final updates

c4e184b

Clean Up Explore Page

b06013e

Cleaning up the explore page to improve efficiency and table accessibility

Remove Unnecessary Packages and Commands

a619afb

Remove unnecessary packages and code from the app; deleted helpers file that contained elements counter to the Style Guide.

Update app.R

937acca

Clean up of alt text

Update app.R

17f528f

Reorganizing Game Server code

Reformatting Game

ce3c779

Initial work towards reformatting the game page of the app

Provide feedback

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Adjustment practice #2

Adjustment practice #2

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		URL: https://psu-eberly.shinyapps.io/Sample_App
		BugReports: https://github.com/EducationShinyAppTeam/Sample_App/issues

		mainPanel(
		plotOutput("empericalLogitPlot", width = "100%")%>% withSpinner(color="#ffa500")


		library(dplyr)
		library(shinycssloaders)


		source("helpers.R")

		ui <- dashboardPage(

Adjustment practice #2

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Adjustment practice #2

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Jiayue-He commented Jun 7, 2021

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