JOSS review #1
Comments
40 tasks
|
Thank you so much for taking your time to give such a detailed review of the package. All your comments were valuable and will act accordingly.
|
Has the package been referenced anywhere? Meaning its usage has been in a peer reviewed journal article?
Yes, Thanks it works now, could you mention the requirements like such in the ReadMe? Will help users to navigate better.
Sorry I get this error in RStudio cloud as well. Could you check using RStudio cloud?
Yes please add all the necessary packages in Imports in DESCRIPTION. Also if you are making changes to your paper, please update it by calling whedon. |
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|
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Oh sure, please go to this page and comment Yes probably it is the ms office issue, can you please check what would can users do who do not have the latest ms office version? Thanks! |
9.When I choose the car.csv and try to use grapesAgri1::descApp() without header it shows me this error - please see this also Regards! |
You will have to add reference inside the paper.md as well, for which ever package you are referring to. Please refer to the submission guidelines of JOSS.
Can you please mention in the ReadMe file or any appropriate place that header is necessary in the file or it creates a confusion. I hope I made sense. Cheers! |
|
@adithirgis
😰 😌 |
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Hello! Can you please add the points corresponding to the list above, first issue I created. I see that you have almost completed the changes I asked except adding the reference. Thanks a lot. |
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@adithirgis paper.bib is not showing in References...no idea why |
|
Hi!
eg - where And also requesting you to add the numbers and the corresponding response to it as per my first list (since its difficult to keep track), so that I can check them off.
If this sounds correct change it to -
Thanks! |
- Problem cause by KableExtra as several apps are incoporated together. Removed PDF and Word download option, now only html, good to go!
- Validation added for unintended user inputs
- layout app generates field layout of experiments to perform experiment in field. Additional reading materials added in Readme
- Done
|
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R-cmd check seems ok. Screen shot in previous comment. |
|
Hello, Thanks for following up soon! Really appreciate it. I have a few things in my checklist now to end the review -
> devtools::test()
i Loading grapesAgri1
Registered S3 method overwritten by 'pryr':
method from
print.bytes Rcpp
i Testing grapesAgri1
√ | OK F W S | Context
x | 0 1 | app-file [70.3 s]
-------------------------------------------------------------------------------------------
Failure (testdesc.R:6:3): descApp_testing
Not all shinytest scripts passed for D:/Dropbox/ILKConsultancy/grapesAgri1/inst/desc: mytest
Diff output:
==== mytest ====
diff "C:\\Users\\Dell\\AppData\\Local\\Temp\\Rtmpo35dGe\\shinytest-diff-1eec7d913a59/mytest-expected/001.json" "C:\\Users\\Dell\\AppData\\Local\\Temp\\Rtmpo35dGe\\shinytest-diff-1eec7d913a59/mytest-current/001.json"
1,68c1,68
< {
< "input": {
< "dataset": "iris",
< "file1": null,
< "header": true,
< "req": "summary",
< "shiny_height": 744,
< "shiny_width": 992
< },
< "output": {
< "bygroup": null,
< "data_set": {
< "html": "<div class=\"form-group shiny-input-container\">\n <label class=\"control-label\" id=\"dataset-label\" for=\"dataset\">Choose a dataset:<\/label>\n <div>\n <select id=\"dataset\"><option value=\"iris\" selected>iris<\/option>\n<option value=\"pressure\">pressure<\/option>\n<option value=\"cars\">cars<\/option><\/select>\n <script type=\"application/json\" data-for=\"dataset\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script>\n <\/div>\n<\/div>\n<a id=\"downloadData\" class=\"btn btn-default shiny-download-link butt1\" href=\"\" target=\"_blank\" download>\n <i class=\"fa fa-download\" role=\"presentation\" aria-label=\"download icon\"><\/i>\n Download csv file to test\n<\/a>",
< "deps": [
< {
< "name": "selectize",
< "version": "0.12.4",
< "src": {
< "href": "shared/selectize"
< },
< "meta": null,
< "script": [
< "js/selectize.min.js",
< "accessibility/js/selectize-plugin-a11y.min.js"
< ],
< "stylesheet": "css/selectize.bootstrap3.css",
< "head": null,
< "attachment": null,
< "package": null,
< "all_files": true
< },
< {
< "name": "font-awesome",
< "version": "5.13.0",
< "src": {
< "href": "font-awesome-5.13.0"
< },
< "meta": null,
< "script": null,
< "stylesheet": [
< "css/all.min.css",
< "css/v4-shims.min.css"
< ],
< "head": null,
< "attachment": null,
< "all_files": true
< }
< ]
< },
< "image_down": null,
< "nort": "",
< "note": {
< "html": " <h4> To perform analysis using your own dataset prepare excel file in csv format by reading instruction below <\/h4>\n<p>\n<ui>\n<li>Open a new blank excel file<\/li>\n<li>Copy and paste observations into a new sheet (use only one sheet) of a new excel file<\/li>\n<li>Observations should be pasted as columns <\/li>\n<li>Don't type or delete anything on other cells without data<\/li>\n<li>You can use any names for your columns. No space is allowed in the Column name. If space is required use underscore ‘_’ or ‘.’ full stop; for example ‘Variable name’ should be written as Variable_name or Variable.name<\/li>\n<li>Data should be arranged towards upper left corner and row above the data should not be left blank <\/li>\n<li>Don't type and delete anything on other cells without data. If so select those cells, right click and click clear contents <\/li>\n<li>Give names to all column, Don't add any unnecessary columns that is not required for analysis<\/li>\n<li>Once all these are done, your file is ready. Now save it as CSV file. <\/li>\n<li><b>Upload file by clicking browse in the app <\/b><\/li>\n<\/ui>\n<\/p>\n<h5> You can download a model data set from below and test the App <\/h5>\n",
< "deps": [
<
< ]
< },
< "plot": null,
< "summaryout": null,
< "text3": null,
< "var": null,
< "var1": null,
< "var2": null
< },
< "export": {
<
< }
< }
---
> {
> "input": {
> "dataset": "iris",
> "file1": null,
> "header": true,
> "req": "summary",
> "shiny_height": 744,
> "shiny_width": 992
> },
> "output": {
> "bygroup": null,
> "data_set": {
> "html": "<div class=\"form-group shiny-input-container\">\n <label class=\"control-label\" id=\"dataset-label\" for=\"dataset\">Choose a dataset:<\/label>\n <div>\n <select id=\"dataset\"><option value=\"iris\" selected>iris<\/option>\n<option value=\"pressure\">pressure<\/option>\n<option value=\"cars\">cars<\/option><\/select>\n <script type=\"application/json\" data-for=\"dataset\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script>\n <\/div>\n<\/div>\n<a id=\"downloadData\" class=\"btn btn-default shiny-download-link butt1\" href=\"\" target=\"_blank\" download>\n <i class=\"fa fa-download\" role=\"presentation\" aria-label=\"download icon\"><\/i>\n Download csv file to test\n<\/a>",
> "deps": [
> {
> "name": "selectize",
> "version": "0.12.4",
> "src": {
> "href": "shared/selectize"
> },
> "meta": null,
> "script": [
> "js/selectize.min.js",
> "accessibility/js/selectize-plugin-a11y.min.js"
> ],
> "stylesheet": "css/selectize.bootstrap3.css",
> "head": null,
> "attachment": null,
> "package": null,
> "all_files": true
> },
> {
> "name": "font-awesome",
> "version": "5.13.0",
> "src": {
> "href": "font-awesome-5.13.0"
> },
> "meta": null,
> "script": null,
> "stylesheet": [
> "css/all.min.css",
> "css/v4-shims.min.css"
> ],
> "head": null,
> "attachment": null,
> "all_files": true
> }
> ]
> },
> "image_down": null,
> "nort": "",
> "note": {
> "html": " <h4> To perform analysis using your own dataset prepare excel file in csv format by reading instruction below <\/h4>\n<p>\n<ui>\n<li>Open a new blank excel file<\/li>\n<li>Copy and paste observations into a new sheet (use only one sheet) of a new excel file<\/li>\n<li>Observations should be pasted as columns <\/li>\n<li>Don't type or delete anything on other cells without data<\/li>\n<li>You can use any names for your columns. No space is allowed in the Column name. If space is required use underscore ‘_’ or ‘.’ full stop; for example ‘Variable name’ should be written as Variable_name or Variable.name<\/li>\n<li>Data should be arranged towards upper left corner and row above the data should not be left blank <\/li>\n<li>Don't type and delete anything on other cells without data. If so select those cells, right click and click clear contents <\/li>\n<li>Give names to all column, Don't add any unnecessary columns that is not required for analysis<\/li>\n<li>Once all these are done, your file is ready. Now save it as CSV file. <\/li>\n<li><b>Upload file by clicking browse in the app <\/b><\/li>\n<\/ui>\n<\/p>\n<h5> You can download a model data set from below and test the App <\/h5>\n",
> "deps": [
>
> ]
> },
> "plot": null,
> "summaryout": null,
> "text3": null,
> "var": null,
> "var1": null,
> "var2": null
> },
> "export": {
>
> }
> }
If this is expected, use `snapshotUpdate('D:/Dropbox/ILKConsultancy/grapesAgri1/inst/desc')` to update
-------------------------------------------------------------------------------------------
x | 0 1 | app-file [21.4 s]
-------------------------------------------------------------------------------------------
Failure (testttest.R:6:3): ttest_testing
Not all shinytest scripts passed for D:/Dropbox/ILKConsultancy/grapesAgri1/inst/comp_mean: mytest
Diff output:
==== mytest ====
diff "C:\\Users\\Dell\\AppData\\Local\\Temp\\Rtmpo35dGe\\shinytest-diff-1eec37707b35/mytest-expected/001.json" "C:\\Users\\Dell\\AppData\\Local\\Temp\\Rtmpo35dGe\\shinytest-diff-1eec37707b35/mytest-current/001.json"
1,81c1,81
< {
< "input": {
< "dataset": "iris",
< "file1": null,
< "header": true,
< "req1": "ttest"
< },
< "output": {
< "data_set": {
< "html": "<div class=\"form-group shiny-input-container\">\n <label class=\"control-label\" id=\"dataset-label\" for=\"dataset\">Choose a dataset:<\/label>\n <div>\n <select id=\"dataset\"><option value=\"iris\" selected>iris<\/option>\n<option value=\"rock\">rock<\/option>\n<option value=\"pressure\">pressure<\/option><\/select>\n <script type=\"application/json\" data-for=\"dataset\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script>\n <\/div>\n<\/div>\n<a id=\"downloadData\" class=\"btn btn-default shiny-download-link butt1\" href=\"\" target=\"_blank\" download>\n <i class=\"fa fa-download\" role=\"presentation\" aria-label=\"download icon\"><\/i>\n Download csv file to test\n<\/a>",
< "deps": [
< {
< "name": "selectize",
< "version": "0.12.4",
< "src": {
< "href": "shared/selectize"
< },
< "meta": null,
< "script": [
< "js/selectize.min.js",
< "accessibility/js/selectize-plugin-a11y.min.js"
< ],
< "stylesheet": "css/selectize.bootstrap3.css",
< "head": null,
< "attachment": null,
< "package": null,
< "all_files": true
< },
< {
< "name": "font-awesome",
< "version": "5.13.0",
< "src": {
< "href": "font-awesome-5.13.0"
< },
< "meta": null,
< "script": null,
< "stylesheet": [
< "css/all.min.css",
< "css/v4-shims.min.css"
< ],
< "head": null,
< "attachment": null,
< "all_files": true
< }
< ]
< },
< "ftest": null,
< "image_down": null,
< "note1": null,
< "note2": null,
< "note3": null,
< "note4": null,
< "note5": null,
< "ottest": null,
< "plot": null,
< "pttest": null,
< "slider": null,
< "start_note": {
< "html": " <h4> To perform analysis using your own dataset, prepare excel file in csv format by reading instruction below <\/h4>\n<p>\n<ui>\n<li>Open a new blank excel file<\/li>\n<li>Copy and paste observations into a new sheet (use only one sheet) of a new excel file<\/li>\n<li>Groups to be compared should be pasted as columns <\/li>\n<li>Don't type or delete anything on other cells without data<\/li>\n<li>You can use any names for your columns. No space is allowed in the Column name. If space is required use underscore ‘_’ or ‘.’ full stop; for example ‘Variable name’ should be written as Variable_name or Variable.name<\/li>\n<li>Data should be arranged towards upper left corner and row above the data should not be left blank <\/li>\n<li>Type 'NA' in the cell with no observation<\/li>\n<li>Don't type and delete anything on other cells without data. If so select those cells, right click and click clear contents <\/li>\n<li>Give names to all column, Don't add any unnecessary columns that is not required for analysis<\/li>\n<li>Once all these are done, your file is ready. Now save it as CSV file. <\/li>\n<li><b>Upload file by clicking browse in the app <\/b><\/li>\n<\/ui>\n<\/p>\n<p>\n<b> Things to remember while doing t-test<\/b>\n<li>Note that, unpaired two-samples t-test can be used only under certain conditions: <\/li>\n<li>First condition: each of the two groups of samples being compared, should be normally distributed. This can be checked using Shapiro-Wilk test and other data visualization techniques [use grapes::descApp()]<\/li>\n<li>Second condition: Variances of the two groups should be equal.\nThis can be checked using Homogenity of variance test (F test) available\nwith in the app. <\/li>\n<li>If the variances of the two groups being compared are different (heteroscedasticity), it’s possible to use the Welch t test, an adaptation of Student t-test. <\/li>\n<li>Welch t test and F-test are available within the app<\/li>\n<\/p>\n<b> You can download a model data set from below and test the App <\/b>\n",
< "deps": [
<
< ]
< },
< "summary1": null,
< "summary2": null,
< "summary3": null,
< "summary4": null,
< "summary5": null,
< "ttest": null,
< "var": null,
< "var1": null,
< "var2": null,
< "var3": null,
< "var4": null,
< "var5": null,
< "wttest": null
< },
< "export": {
<
< }
< }
---
> {
> "input": {
> "dataset": "iris",
> "file1": null,
> "header": true,
> "req1": "ttest"
> },
> "output": {
> "data_set": {
> "html": "<div class=\"form-group shiny-input-container\">\n <label class=\"control-label\" id=\"dataset-label\" for=\"dataset\">Choose a dataset:<\/label>\n <div>\n <select id=\"dataset\"><option value=\"iris\" selected>iris<\/option>\n<option value=\"rock\">rock<\/option>\n<option value=\"pressure\">pressure<\/option><\/select>\n <script type=\"application/json\" data-for=\"dataset\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script>\n <\/div>\n<\/div>\n<a id=\"downloadData\" class=\"btn btn-default shiny-download-link butt1\" href=\"\" target=\"_blank\" download>\n <i class=\"fa fa-download\" role=\"presentation\" aria-label=\"download icon\"><\/i>\n Download csv file to test\n<\/a>",
> "deps": [
> {
> "name": "selectize",
> "version": "0.12.4",
> "src": {
> "href": "shared/selectize"
> },
> "meta": null,
> "script": [
> "js/selectize.min.js",
> "accessibility/js/selectize-plugin-a11y.min.js"
> ],
> "stylesheet": "css/selectize.bootstrap3.css",
> "head": null,
> "attachment": null,
> "package": null,
> "all_files": true
> },
> {
> "name": "font-awesome",
> "version": "5.13.0",
> "src": {
> "href": "font-awesome-5.13.0"
> },
> "meta": null,
> "script": null,
> "stylesheet": [
> "css/all.min.css",
> "css/v4-shims.min.css"
> ],
> "head": null,
> "attachment": null,
> "all_files": true
> }
> ]
> },
> "ftest": null,
> "image_down": null,
> "note1": null,
> "note2": null,
> "note3": null,
> "note4": null,
> "note5": null,
> "ottest": null,
> "plot": null,
> "pttest": null,
> "slider": null,
> "start_note": {
> "html": " <h4> To perform analysis using your own dataset, prepare excel file in csv format by reading instruction below <\/h4>\n<p>\n<ui>\n<li>Open a new blank excel file<\/li>\n<li>Copy and paste observations into a new sheet (use only one sheet) of a new excel file<\/li>\n<li>Groups to be compared should be pasted as columns <\/li>\n<li>Don't type or delete anything on other cells without data<\/li>\n<li>You can use any names for your columns. No space is allowed in the Column name. If space is required use underscore ‘_’ or ‘.’ full stop; for example ‘Variable name’ should be written as Variable_name or Variable.name<\/li>\n<li>Data should be arranged towards upper left corner and row above the data should not be left blank <\/li>\n<li>Type 'NA' in the cell with no observation<\/li>\n<li>Don't type and delete anything on other cells without data. If so select those cells, right click and click clear contents <\/li>\n<li>Give names to all column, Don't add any unnecessary columns that is not required for analysis<\/li>\n<li>Once all these are done, your file is ready. Now save it as CSV file. <\/li>\n<li><b>Upload file by clicking browse in the app <\/b><\/li>\n<\/ui>\n<\/p>\n<p>\n<b> Things to remember while doing t-test<\/b>\n<li>Note that, unpaired two-samples t-test can be used only under certain conditions: <\/li>\n<li>First condition: each of the two groups of samples being compared, should be normally distributed. This can be checked using Shapiro-Wilk test and other data visualization techniques [use grapes::descApp()]<\/li>\n<li>Second condition: Variances of the two groups should be equal.\nThis can be checked using Homogenity of variance test (F test) available\nwith in the app. <\/li>\n<li>If the variances of the two groups being compared are different (heteroscedasticity), it’s possible to use the Welch t test, an adaptation of Student t-test. <\/li>\n<li>Welch t test and F-test are available within the app<\/li>\n<\/p>\n<b> You can download a model data set from below and test the App <\/b>\n",
> "deps": [
>
> ]
> },
> "summary1": null,
> "summary2": null,
> "summary3": null,
> "summary4": null,
> "summary5": null,
> "ttest": null,
> "var": null,
> "var1": null,
> "var2": null,
> "var3": null,
> "var4": null,
> "var5": null,
> "wttest": null
> },
> "export": {
>
> }
> }
If this is expected, use `snapshotUpdate('D:/Dropbox/ILKConsultancy/grapesAgri1/inst/comp_mean')` to update
-------------------------------------------------------------------------------------------
== Results ================================================================================
Duration: 91.8 s
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
If this sounds correct change it to -
Thanks! |
**
**
- ok
- styler Thank you. |
|
Hello, Thanks! Could you please check this again? This is from the latest pull. Let me know if this is my system issue. devtools::test()
i Loading grapesAgri1
i Testing grapesAgri1
√ | OK F W S | Context
x | 0 1 | app-file [9.9 s]
-------------------------------------------------------------------------------------------
Error (testdesc.R:6:3): descApp_testing
Error: Cannot find shiny port number. Error:
Loading required package: shiny
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: grid
Attaching package: 'kableExtra'
The following object is masked from 'package:dplyr':
group_rows
Attaching package: 'pastecs'
The following object is masked from 'package:magrittr':
extract
The following objects are masked from 'package:dplyr':
first, last
Loading required package: ggplot2
Registered S3 method overwritten by 'pryr':
method from
print.bytes Rcpp
Backtrace:
1. shinytest::expect_pass(testApp(appDir, compareImages = FALSE)) testdesc.R:6:2
2. shinytest::testApp(appDir, compareImages = FALSE)
3. base::lapply(...)
4. shinytest:::FUN(X[[i]], ...)
5. base::source(testname, local = env)
7. [ base::eval(...) ] with 1 more call
9. ShinyDriver$new("../../")
10. shinytest:::initialize(...)
11. shinytest:::sd_initialize(...)
12. private$startShiny(...)
13. shinytest:::sd_startShiny(...)
-------------------------------------------------------------------------------------------
x | 0 1 | app-file [27.7 s]
-------------------------------------------------------------------------------------------
Failure (testttest.R:6:3): ttest_testing
Not all shinytest scripts passed for D:/Dropbox/ILKConsultancy/grapesAgri1/inst/comp_mean: mytest
Diff output:
==== mytest ====
diff "C:\\Users\\Dell\\AppData\\Local\\Temp\\RtmpiSn5IW\\shinytest-diff-a3c7be07fc/mytest-expected/001.json" "C:\\Users\\Dell\\AppData\\Local\\Temp\\RtmpiSn5IW\\shinytest-diff-a3c7be07fc/mytest-current/001.json"
1,81c1,81
< {
< "input": {
< "dataset": "iris",
< "file1": null,
< "header": true,
< "req1": "ttest"
< },
< "output": {
< "data_set": {
< "html": "<div class=\"form-group shiny-input-container\">\n <label class=\"control-label\" id=\"dataset-label\" for=\"dataset\">Choose a dataset:<\/label>\n <div>\n <select id=\"dataset\"><option value=\"iris\" selected>iris<\/option>\n<option value=\"rock\">rock<\/option>\n<option value=\"pressure\">pressure<\/option><\/select>\n <script type=\"application/json\" data-for=\"dataset\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script>\n <\/div>\n<\/div>\n<a id=\"downloadData\" class=\"btn btn-default shiny-download-link butt1\" href=\"\" target=\"_blank\" download>\n <i class=\"fa fa-download\" role=\"presentation\" aria-label=\"download icon\"><\/i>\n Download csv file to test\n<\/a>",
< "deps": [
< {
< "name": "selectize",
< "version": "0.12.4",
< "src": {
< "href": "shared/selectize"
< },
< "meta": null,
< "script": [
< "js/selectize.min.js",
< "accessibility/js/selectize-plugin-a11y.min.js"
< ],
< "stylesheet": "css/selectize.bootstrap3.css",
< "head": null,
< "attachment": null,
< "package": null,
< "all_files": true
< },
< {
< "name": "font-awesome",
< "version": "5.13.0",
< "src": {
< "href": "font-awesome-5.13.0"
< },
< "meta": null,
< "script": null,
< "stylesheet": [
< "css/all.min.css",
< "css/v4-shims.min.css"
< ],
< "head": null,
< "attachment": null,
< "all_files": true
< }
< ]
< },
< "ftest": null,
< "image_down": null,
< "note1": null,
< "note2": null,
< "note3": null,
< "note4": null,
< "note5": null,
< "ottest": null,
< "plot": null,
< "pttest": null,
< "slider": null,
< "start_note": {
< "html": " <h4> To perform analysis using your own dataset, prepare excel file in csv format by reading instruction below <\/h4>\n<p>\n<ui>\n<li>Open a new blank excel file<\/li>\n<li>Copy and paste observations into a new sheet (use only one sheet) of a new excel file<\/li>\n<li>Groups to be compared should be pasted as columns <\/li>\n<li>Don't type or delete anything on other cells without data<\/li>\n<li>You can use any names for your columns. No space is allowed in the Column name. If space is required use underscore ‘_’ or ‘.’ full stop; for example ‘Variable name’ should be written as Variable_name or Variable.name<\/li>\n<li>Data should be arranged towards upper left corner and row above the data should not be left blank <\/li>\n<li>Type 'NA' in the cell with no observation<\/li>\n<li>Don't type and delete anything on other cells without data. If so select those cells, right click and click clear contents <\/li>\n<li>Give names to all column, Don't add any unnecessary columns that is not required for analysis<\/li>\n<li>Once all these are done, your file is ready. Now save it as CSV file. <\/li>\n<li><b>Upload file by clicking browse in the app <\/b><\/li>\n<\/ui>\n<\/p>\n<p>\n<b> Things to remember while doing t-test<\/b>\n<li>Note that, unpaired two-samples t-test can be used only under certain conditions: <\/li>\n<li>First condition: each of the two groups of samples being compared, should be normally distributed. This can be checked using Shapiro-Wilk test and other data visualization techniques [use grapes::descApp()]<\/li>\n<li>Second condition: Variances of the two groups should be equal.\nThis can be checked using Homogenity of variance test (F test) available\nwith in the app. <\/li>\n<li>If the variances of the two groups being compared are different (heteroscedasticity), it’s possible to use the Welch t test, an adaptation of Student t-test. <\/li>\n<li>Welch t test and F-test are available within the app<\/li>\n<\/p>\n<b> You can download a model data set from below and test the App <\/b>\n",
< "deps": [
<
< ]
< },
< "summary1": null,
< "summary2": null,
< "summary3": null,
< "summary4": null,
< "summary5": null,
< "ttest": null,
< "var": null,
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---
> {
> "input": {
> "dataset": "iris",
> "file1": null,
> "header": true,
> "req1": "ttest"
> },
> "output": {
> "data_set": {
> "html": "<div class=\"form-group shiny-input-container\">\n <label class=\"control-label\" id=\"dataset-label\" for=\"dataset\">Choose a dataset:<\/label>\n <div>\n <select id=\"dataset\"><option value=\"iris\" selected>iris<\/option>\n<option value=\"rock\">rock<\/option>\n<option value=\"pressure\">pressure<\/option><\/select>\n <script type=\"application/json\" data-for=\"dataset\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script>\n <\/div>\n<\/div>\n<a id=\"downloadData\" class=\"btn btn-default shiny-download-link butt1\" href=\"\" target=\"_blank\" download>\n <i class=\"fa fa-download\" role=\"presentation\" aria-label=\"download icon\"><\/i>\n Download csv file to test\n<\/a>",
> "deps": [
> {
> "name": "selectize",
> "version": "0.12.4",
> "src": {
> "href": "shared/selectize"
> },
> "meta": null,
> "script": [
> "js/selectize.min.js",
> "accessibility/js/selectize-plugin-a11y.min.js"
> ],
> "stylesheet": "css/selectize.bootstrap3.css",
> "head": null,
> "attachment": null,
> "package": null,
> "all_files": true
> },
> {
> "name": "font-awesome",
> "version": "5.13.0",
> "src": {
> "href": "font-awesome-5.13.0"
> },
> "meta": null,
> "script": null,
> "stylesheet": [
> "css/all.min.css",
> "css/v4-shims.min.css"
> ],
> "head": null,
> "attachment": null,
> "all_files": true
> }
> ]
> },
> "ftest": null,
> "image_down": null,
> "note1": null,
> "note2": null,
> "note3": null,
> "note4": null,
> "note5": null,
> "ottest": null,
> "plot": null,
> "pttest": null,
> "slider": null,
> "start_note": {
> "html": " <h4> To perform analysis using your own dataset, prepare excel file in csv format by reading instruction below <\/h4>\n<p>\n<ui>\n<li>Open a new blank excel file<\/li>\n<li>Copy and paste observations into a new sheet (use only one sheet) of a new excel file<\/li>\n<li>Groups to be compared should be pasted as columns <\/li>\n<li>Don't type or delete anything on other cells without data<\/li>\n<li>You can use any names for your columns. No space is allowed in the Column name. If space is required use underscore ‘_’ or ‘.’ full stop; for example ‘Variable name’ should be written as Variable_name or Variable.name<\/li>\n<li>Data should be arranged towards upper left corner and row above the data should not be left blank <\/li>\n<li>Type 'NA' in the cell with no observation<\/li>\n<li>Don't type and delete anything on other cells without data. If so select those cells, right click and click clear contents <\/li>\n<li>Give names to all column, Don't add any unnecessary columns that is not required for analysis<\/li>\n<li>Once all these are done, your file is ready. Now save it as CSV file. <\/li>\n<li><b>Upload file by clicking browse in the app <\/b><\/li>\n<\/ui>\n<\/p>\n<p>\n<b> Things to remember while doing t-test<\/b>\n<li>Note that, unpaired two-samples t-test can be used only under certain conditions: <\/li>\n<li>First condition: each of the two groups of samples being compared, should be normally distributed. This can be checked using Shapiro-Wilk test and other data visualization techniques [use grapes::descApp()]<\/li>\n<li>Second condition: Variances of the two groups should be equal.\nThis can be checked using Homogenity of variance test (F test) available\nwith in the app. <\/li>\n<li>If the variances of the two groups being compared are different (heteroscedasticity), it’s possible to use the Welch t test, an adaptation of Student t-test. <\/li>\n<li>Welch t test and F-test are available within the app<\/li>\n<\/p>\n<b> You can download a model data set from below and test the App <\/b>\n",
> "deps": [
>
> ]
> },
> "summary1": null,
> "summary2": null,
> "summary3": null,
> "summary4": null,
> "summary5": null,
> "ttest": null,
> "var": null,
> "var1": null,
> "var2": null,
> "var3": null,
> "var4": null,
> "var5": null,
> "wttest": null
> },
> "export": {
>
> }
> }
If this is expected, use `snapshotUpdate('D:/Dropbox/ILKConsultancy/grapesAgri1/inst/comp_mean')` to update
-------------------------------------------------------------------------------------------
== Results ================================================================================
Duration: 37.7 s
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]I completed most of the review. Will wait for this one. Thank you! |
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Ok I got it; hopefully a 'loadTimeout ' in ShinyDriver$new will resolve the issue. Will get back to you shortly. Thank you for all the support! |
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Hi! ==> devtools::check() i Updating grapesAgri1 documentation
v checking for file 'D:\PERMANENT ASSETS\R package\grapesAgri1/DESCRIPTION' ...
-- Checking ---------------------------- grapesAgri1 --
-- R CMD check results ---------------------------------- grapesAgri1 1.0.0 ---- 0 errors v | 0 warnings v | 0 notes v R CMD check succeeded ==> devtools::test() i Loading grapesAgri1
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Hello, I still get the error, I think its screen shot issue which can arises if the size of the screens differ (this is an issue with shinytest package). I will wrap up the review now. Congratulations! And three optional comments -
Thanks! |
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Hi, I just realised you could also check why the Thanks! |
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Hi, |
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Hi, phew!! 😌 I think issue is I should keep my git config core.autocrlf false, so you can clone in to a windows system without any issues. Thank You |
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Hi |
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Hi, I checked again but I still get the errors, but I am pretty sure its because the sizes of the image issue. I think its not resolvable as of now using shinytest. Check this - rstudio/shinytest#300 and rstudio/shinytest#315. Thanks |
|
I will close this issue now. All the best. Adithi |
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Thank you for submitting to JOSS, I enjoyed reviewing this package. Congratulations!
Starting my review here. To avoid system errors I tried to run this package on RStudio cloud.
Can you please add references in paper.md using paper.bib.
Can you please mention whether
grapesAgri1has been cited or referenced anywhere and if yes where please add it.As mentioned in the paper.md -
"Scientist and research students were in trouble to find a suitable platform for their data analysis and also to publish the research output in quality journals. Most of the softwares available for data analysis are proprietary or lacks a simple user interface. Though several online platforms were available for data analysis, they are not much updated up to the current publication standards at international level."
Can the authors please mention software name they have come across which are proprietary, lack simple user interface or not updated to current standards and do not provide graphs, thus providing a comparative study.
Also in the DESCRIPTION of the package, please add the version number of the packages which are being imported, this might resolve the conflict of versions.
Styling of the code is not uniform , please refer to this guide for styling or you could also use
stylerpackage, sometimes=is used for assignment and in other places<-is used (recommend choosing one style and sticking with it)eg -
result=as.data.frame( anova(anvaTable) ); trtmeans<-out$meansSpacing in code is inconsistent. Also the code lines stretch very long, beyond the recommended 80 characters or 120 characters. Here is a resource which could be helpful - https://devguide.ropensci.org/building.html#code-style, http://adv-r.had.co.nz/Style.html and https://www.tidyverse.org/blog/2017/12/styler-1.0.0/.
Can you please point me to the tests folder of this application? I do not seem to find the test folder in the package. Please add test units for automatically testing your application. Tests for functions will also be required. Examples from JOSS - https://github.com/michaellevy/gwdegree/tree/master/tests/testthat, https://github.com/PsyChiLin/EFAshiny/tree/master/tests/testthat, https://github.com/OttaviaE/DscoreApp/tree/master/tests, https://github.com/pmcharrison/psychTestR/tree/master/tests/testthat.
I got three notes while checking the package using
devtools::check(). I would suggest adding.biband.mdextensions to the.Rbuildignorefile. And another problem I faced is that I requirekableExtraas an import not suggests, because I tried installing the package and it still says I need to install thekableExtra,summarytools, and forgrapesAgri1::ttApp()it requiredPairedData.checking package dependencies ... NOTE Packages suggested but not available for checking: 'kableExtra', 'summarytools', 'desplot', 'PairedData'.When I choose the car.csv and try to use
grapesAgri1::descApp()without header it shows me this error -For correlation analysis report download in
grapesAgri1::corrApp()function for Simple_corelation, for html version the formatting looks fine, while the word/docx version does not seem very intuitive, is there a way to format it correctly, and the pdf version is not downloaded in my windows 10 system. Error for pdf version is -Warning in system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2) : '"pdflatex"' not found Warning: Error in : LaTeX failed to compile report.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.-For this function
grapesAgri1::crdApp()for the below selected parameters I am not able to generate the table is there some mistake I am making, please explain the data used hereunequal_replication.csvand others to understand the functionality better -It would be great if these functions -
grapesAgri1::layoutApp()andgrapesAgri1::rbdApp()and its application are explained in the ReadMe file. And to add both the apps work well with themango data.csv.Paper suggestions - I will pr, please feel free to ignore some if you feel its not grammatically correct. Changes are in bold and strikeout.
Extra suggestion, if possible the Community guidelines can be mentioned in the documentation or the ReadMe file instead of paper.md
Let me know if you have questions.
Cheers!
Adithi
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