NEWS.md

In jsmodule: 'RStudio' Addins and 'Shiny' Modules for Medical Research

jsmodule 1.4.3

Update rocModule: Add accucary/ppv/npv with threshold

jsmodule 1.4.2

Update: Change default non-normal 2 group comparison test to wilcox.test

jsmodule 1.4.1

Error fix: jsBasicExtAddin, jsBasicGatget

jsmodule 1.4.0

Fix :

• update deprecated icon (Plot panel)

Update :

feature applies in jsBasicExtAddin (shiny app)

• Add description with callout

• Data , Table 1 panel

• modified some UI (with style.css)

• header color changed
• add zarathu & github page in header
• table 1's significant data changed

• Data's table column has color (when vairable is category)

• update DT function (Data)

• Column visiblity button added
• Column Reorder feature added
• may browse table with keyboard (arrow keys)

Refactor:

• csvfileInput.R Not use file's extension not name. (csv.txt will nor work)
• ggpairs.R apply theme with less if-else

jsmodule 1.3.6

Fix:

• kaplanModule PPT download

jsmodule 1.3.5

Fix:

• rocModule

• Change jsRepeatedGadjet to jsRepeatedGadget

jsmodule 1.3.4

Fix and Update: rocModule

• cutoff fix: rocModule

• Add "Show 1-specificity" option

jsmodule 1.3.3

New module (Thanks for Changwoo Lim)

• Histogram(histogramUI, histogramServer)

jsmodule 1.3.2

Update

• Add cutoff information to timerocModule, rocModule when 1 model, 1 indpendent variable.

Fix

• timerocModule: Invert plot when auc < 0.5

jsmodule 1.3.1

Fix

• Fix cutoff label of Kaplan-meier plot when continuous independent variable

jsmodule 1.3.0

New module (Thanks for Hyunki Lee)

• Boxplot(boxUI, boxServer), Lineplot(LineUI, LineServer), Barplot(BarUI, BarServer)

jsmodule 1.2.0

Update

• Add coxph ties option to coxModule: ties.coxph

Bugfix

• kaplanModule runs even if timeby = 1

jsmodule 1.1.9

Update

• Faster timerocModule: Change AUC/AUC difference 95%CI calculation method to survival::concordance

jsmodule 1.1.8

Update

• Change emf to pptx(editable) in figure download.

jsmodule 1.1.7

Bug fix

• Label info in subgroup analysis: regression, cox

jsmodule 1.1.6

Fix & update

• New module scatterplotUI & scatterplotServer: scatterplot using ggpubr: apply to Basic statistics

• timerocModule, rocModule: Compare ROC curve even if there are different sample size(na omit)

• Change timeby unit from 1 to 0.5 (when <365)

• Add surv.scale option to kaplan-meier plot

• Fix PS matching error with missing values

jsmodule 1.1.5

Fix

• Fix according to MatchIt 4.0 update.

• Erratum: Cumulative hazard -> Cumulative incidence

jsmodule 1.1.4

Update

• Show survival probabilities(%) at kaplan-meier plot. This requires jskm 0.4.2 or higher.

jsmodule 1.1.3

Update

• Choose time ranges: coxUI, coxModule.

jsmodule 1.1.2

Update

• Add No initial covariate option when ps calculation

jsmodule 1.1.1

Update

• Add landmark analysis to kaplan-meier analysis. Pease update jskm to 0.4.0 version.

• Add option hide 95%CI of AUC, NRIIDI to timerocModule. It reduces computation time.

jsmodule 1.1.0

• Apply AIC based stepwise selection to linear/logistic regression, cox model.

• Deprecated fucntion: regressModule & logisticModule, please use regressModule2 & logisticModule2

jsmodule 1.0.8

• Add option to tb1module1 ,tb1module2: get simulated p value in Fisher exact test when larger than 2 by 2 tables.

jsmodule 1.0.7

Dependency

• Add dependency: Cairo package

jsmodule 1.0.6

Bug fix

• PS matching: Duplicated independent variables UI in ROC/timeROC analysis.

Update

• Change minimum timeby in kaplan-meier plot: 1 to 0

jsmodule 1.0.5

Update

• PS matching: Change font size & color of the message with missing value information.

jsmodule 1.0.4

Bug fixes

• Cox model of Basic statistics module.

jsmodule 1.0.3

Bug fixes

• Incorrect p-value when applying cluster options.

• PS matching: allow continuous variables as Independent variables

Update

• PS matching: allow 1:N matching.

jsmodule 1.0.2

• Update: Stop running ShinyApps by closing the browser window.

jsmodule 1.0.1

Update

• Change reference of categorical variables

• Add line type option to kaplan-meier plot

Bug fixes

• Reactive error in propensity score matching.

jsmodule 1.0.0

Update

• Change UI: ROC/time-dependent ROC analysis.

• Choose cut-off value in kaplan-meier analysis with continuous independent variable.

• Add some icons.

• Choose multiple conditions when subsetting data.

• Add caliper option when propensity score matching.

• Make binary variables from contiuous variables.

• Non-normal variables can be summarized with [min,max].

• Add line color, x-axis label option to kaplan-meier plot

Bug fixes

• Encoding error when csv file upload.

jsmodule 0.9.9

New addins

• Basic statistics with external file: jsBasicExtAddin

• Propensity score analysis with external file: jsPropensityExtAddin

• Repeated measure analysis with external file: jsRepeatedExtAddin

• Survey data analysis with external file: jsSurveyExtAddin

Bug fixes

• Regression/Logistic model in jsSurveyAddin.

• Id issue in repeated measure analysis.

jsmodule 0.9.3

Update: Propensity score analysis

• Add scatterplot, ROC/time-dependent ROC analysis.

Bug fixes: repeated measure analysis

• Error if repeated measure variable is id.

• Error if there are missing values.

Bug fixes: survey data analysis

• Error in ROC analysis

Bug fixes: Table 1

• data.frame vs data.table issue.

jsmodule 0.9.2

• Bug fixes: Apply nested survey design to jsSurveyGadget and FileSurveyInput

jsmodule 0.9.1

Bug fixes

• Encoding issues when reading sav/sas7bdat/dta formats.

• Default independent variables when running regression/logistic/cox analysis

Update

• Add limit.unires option to regression/logistic/cox analysis to prevent computation burden.

jsmodule 0.9.0

New module

• Shiny module forROC analysis : rocUI rocModule.

• Add this module to jsBasicGadget and jsRepeatedGadjet.

Update

• Apply time-dependent ROC to survey data analysis(jsSurveyGadget)

jsmodule 0.8.6

Update

• Change candidate time variables in survival analysis : allow only > 0

• Add option to change legend, p-value position in kaplan-meier plot

Bug fixes

• Time-dependent ROC analysis can allow 1 model.

jsmodule 0.8.5

• Keep original variable's name in tables/figures

jsmodule 0.8.4

• Change default step of x-axis range.

jsmodule 0.8.3

• Bug fix: time-dependent ROC analysis.

jsmodule 0.8.2.1

• Bug fix: emf format can recognize figure's line.

jsmodule 0.8.2

• Add emf format to the plot download modules. You can customize the plot in MS powerpoint.

jsmodule 0.8.1

• Change default time when time-dependent ROC analysis.

jsmodule 0.8.0

New module

• Shiny module for time-dependent ROC analysis : timerocUI timerocModule.

• Add this module to jsBasicGadget and jsRepeatedGadjet.

jsmodule 0.7.10

• Add Kaplan-meier plot options: timeby, x/y-axis ranges.

jsmodule 0.7.9

Update

• Add progress bar to download handlers of scatterplot and kaplan-meier plot.

• Kaplan-meier plot in Basic statistics can use continuous variables as group variables. The module suggest best 5 cuts based on the p-values of logrank test.

• Add number at risk table option to weighted kalan-meier plot.

Bug fixes

• Add namespace survival::cluster for marginal cox model.

jsmodule 0.7.8

Update

• Add sub-group analysis based on the range of continuous variable.

• Add multiple factor choice option when doing sub-group analysis based on categorical variable.

jsmodule 0.7.7

• Fix NOTE and examples for cran upload

jsmodule 0.7.6

• You can get Subset data based on the range of continuous variables.

jsmodule 0.7.5

Update

• Add Subset data feature to all Addins and input modules. You can select subset data before analysis.

Bug fixes

• Fix warn variable error in regressModule, logisticModule.

• Fix list of except variables in ggpairsModule.

jsmodule 0.6.9

Bug fixes

• Fix some spell for cran release.

Update

• Update travis-ci.

• Add appveyor CI to test window environment.

jsmodule 0.6.8

Update

• Warning if there are stongly correlated independent variables in regressModule, jsBasicGadget.

jsmodule 0.6.7

Update

• Show unweighted & weighted table 1 at same tab in jsSurveyGadget

Bug fixes

• Initial cluster variable state in jsSurveyGadget

jsmodule 0.6.6

Update

• Add unweighted table 1 to jsSurveyGadget

Bug fixes

• Apply list tye independent variables to regressModule, logisticModule, GEEModuleLinear and GEEModuleLogistic

• Change sub-group analysis's reactive methods: regressModule, logisticModule, GEEModuleLinear and GEEModuleLogistic

jsmodule 0.6.5

Update

• Add marginal cox model option to coxModule, kaplanModule and jsRepeatedGadget

• Add Overall kaplan-meier plot to kaplanModule

• Set default cluster, strata and weights to None in jsSurveyGadget, FileSurveyInput

Bug fixes

• Some error comments in coxModule and kaplanModule

• Change default candidate dependent variables to categorical variables with 0, 1 in GEEModuleLogistic, jsRepeatedGadget

jsmodule 0.6.4

New module

• Module for Survival analysis: coxUI, coxModule, kaplanUI and kaplanModule

• Module for ggplot download UI: ggplotdownUI

Update

• Add survival analysis to jsBasicGadget, jsSurveyGadget

Bug fixes

• jsPropensityGadget

jsmodule 0.6.2

• Bug fixes : Label information in regressModule, logisticModule

• Update: default.unires option to regressModule, logisticModule

jsmodule 0.6.1

• Update : Apply complex survey design to FileSurvey, regressModule, logisticModule and jsSurveyGadget

jsmodule 0.6.0

New Gadget

• Shiny Gadget for survey data analysis: jsSurveyGadget

New module

• Module for survey data analysis: FileSurvey

Update

• Survey analysis option to regressModule, logisticModule and tb1

jsmodule 0.5.7

• Bug fixes: sub-group option in regressModule, logisticModule, jsPropensityGadget, GEEModuleLinear and GEEModuleLogistic

jsmodule 0.5.6

• Add testthat.

jsmodule 0.5.5

New module

• Modules for repeated measure analysis: FileRepeated, GEEModuleUI, GEEModuleLinear and GEEModuleLogistic

New Gadget

• Shiny Gadget for repeated measure analysis: jsRepeatedGadget

jsmodule 0.5.3

Update

• New option: nfactor.limit in regressModule, logisticModule, jsBasicGadget, csvFileInput and FilePsInput

Bug fixes

• regressModule, logisticModule, jsPropensityGadget can deal missing data issue.

• csvFileInput, FilePSInput change variable class integer64 to double.

jsmodule 0.5.2

• Update: Upload Stata .dta format.

jsmodule 0.5.1

• Modify tb1module, tb1module2, tb1simple ,tb1simple2: compatible with updated jstable

jsmodule 0.5.0

Update

• Add sub-group analysis to regressModule, logisticModule and jsPropensityGadget.

• Apply the updated cox2.display function in jstable package to jsPropensityGadget.

Typo

• Strata variable in ggpairsModule, ggpairsModule2.

jsmodule 0.4.9

Bug fixes

• IPTW table in tb1simple and tb1simple2 modules.

• Kaplan-meier UI in jsPropensityGadget

jsmodude 0.4.8

• tb1module and tb1module2 can control the maximum factor levels to include.

jsmodule 0.4.6

• Bug fixes : Modules for regression exclude NA when selecting binary variables.

jsmodule 0.4.5

• Update : csvFile module can remove empty columns.

jsmodule 0.4.4

• Change regression table function to glmshow.display in jstable package.

jsmodule 0.4.3

New gadget

• jsPropensityGadget : Propensity score analysis

Update

• Excluded non-normal variable selection feature from tb1simple module.

• Apply original variable names to label information : csvFileInput & FilePsInput functions.

jsmodule 0.4.0

New module

• tb1simpleUI, tb1simple, tb1simple2 for propensity score analysis

jsmodule 0.3.7

Bug fixes

• factor variable criteria in csvInput, tb1module and tb1module2

jsmodule 0.3.6

New module

• FilePsInput, FilePs are modules of data input for propensity score calculation.

Minor update

• Change default data.table & fread check.names option to TRUE

jsmodule 0.3.5

New gadget

• jsBasicGadget : Basic statistics

Minor update

• csvFile changes variable name including / to _ and etc.

Bug fixes

• Dependency issue with jstable package

jsmodule 0.3.1

Minor update

• Support sav/sas7bdat formats

Bug fixes:

• tbmoduleUI, tbmoduleUI2 : some error

jsmodule 0.3.0

Bug fixes:

• tbmoduleUI, tbmoduleUI2 : Apply shapiro.test

New module

• regressModuleUI, regressModule, regressModule2

• logisticModuleUI, logisticModule, logisticModule2

• ggpairsModuleUI1, ggpairsModuleUI2, ggpairsModule

New function

• regress.display2, logistic.display2 : Regression table for reactive data.

jsmodule 0.2.5

Update

• csvFile : Add n_ to column names that begin with a number.

New module

• tb1moduleUI2 can deal reactive data

jsmodule 0.2.0

• New module: tb1moduleUI, tb1module

jsmodule 0.1.0

• Update: csvFile can deal label information

jsmodule 0.0.1

• File upload: csvFileInput, csvFile

jsmodule documentation built on Oct. 18, 2023, 9:08 a.m.