Changelog • jsmodule

Update

Added an option to the Kaplan-Meier, Cox, and ForestCox modules that allows the outcome (event) and time variables to be linked when the user specifies vec.event and vec.time. When this option is enabled, selecting an event variable automatically updates the corresponding time variable, and vice versa.

Update

Add options to customize x axis ticks in forest plot

Update

Add function to allow adjusting cutoff for a single independent variable and observing model’s metrics in rocModule, rocModule2.
Add option to turn pairwise p value option on in case level of stratified group >= 3, in tb1moduleUI.
Add subgroup analysis for propensity score matching/repeated/survey.

Update

Add competing risk analysis in subgroup, Kaplan-meier, regression tab.

Update:

Change Boxplot fill type

Bugfix:

sav file load in FilePSInput.R, FileRepeatedInput.R, FileSurveyInput.R

Update

Add label option on lineplot

Bugfix:

Fix 2 group factor not working problem in forestcoxServer

Bugfix:

Fix var_label displaying incorrectly when loading .sav file

Update

Download table as word document (Thanks for Jinhwan Kim)

Update

Apply SPSS label info (Thanks for Jinhwan Kim)

Bugfix:

dropdown button & p value options: barplot, boxplot and lineplot

Update:

Add P value option to barplot, boxplot and lineplot
Add dropdown button for graphical option to barplot, boxplot and lineplot

Update:

Add Subgroupanalysis to jsBasicGadget
Add figure in subgroup analysis with forestplot
Add family ‘poisson’ in forestglm
Add “line size” “point size” to lineplot

New module:

Subgroup analysis with forestplot (Thanks for Yoonkyoung Jeon)
forestcox (forestcoxUI, forestcoxServer)
forestglm (forestglmUI, forestglmServer)

Update:

Add “reverse y-axis” option to lineplot

Update

rocModule: Add accucary/ppv/npv with threshold

Update:

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

Error fix: `jsBasicExtAddin`, `jsBasicGatget`

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

Fix:

kaplanModule PPT download

Fix:

rocModule
Change jsRepeatedGadjet to jsRepeatedGadget

Fix and Update: `rocModule`

cutoff fix: rocModule
Add “Show 1-specificity” option

New module (Thanks for Changwoo Lim)

Histogram(histogramUI, histogramServer)

Update

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

Fix

timerocModule: Invert plot when auc < 0.5

Fix

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

New module (Thanks for Hyunki Lee)

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

Update

Add coxph ties option to coxModule: ties.coxph

Bugfix

kaplanModule runs even if timeby = 1

Update

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

Update

Change emf to pptx(editable) in figure download.

Bug fix

Label info in subgroup analysis: regression, cox

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

Fix

Fix according to MatchIt 4.0 update.
Erratum: Cumulative hazard -> Cumulative incidence

Update

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

Update

Choose time ranges: coxUI, coxModule.

Update

Add No initial covariate option when ps calculation

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.

Apply AIC based stepwise selection to linear/logistic regression, cox model.
Deprecated fucntion: regressModule & logisticModule, please use regressModule2 & logisticModule2

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

Dependency

Add dependency: Cairo package

Bug fix

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

Update

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

Update

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

Bug fixes

Cox model of Basic statistics module.

Bug fixes

Incorrect p-value when applying cluster options.
PS matching: allow continuous variables as Independent variables

Update

PS matching: allow 1:N matching.

Update: Stop running ShinyApps by closing the browser window.

Update

Change reference of categorical variables
Add line type option to kaplan-meier plot

Bug fixes

Reactive error in propensity score matching.

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.

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.

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.

Bug fixes: Apply nested survey design to jsSurveyGadget and FileSurveyInput

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.

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)

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.

Keep original variable’s name in tables/figures

Change default step of x-axis range.

Bug fix: time-dependent ROC analysis.

Bug fix: emf format can recognize figure’s line.

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

Change default time when time-dependent ROC analysis.

New module

Shiny module for time-dependent ROC analysis : timerocUI timerocModule.
Add this module to jsBasicGadget and jsRepeatedGadjet.

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

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.

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.

Fix NOTE and examples for cran upload

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

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.

Bug fixes

Fix some spell for cran release.

Update

Update travis-ci.
Add appveyor CI to test window environment.

Update

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

Update

Show unweighted & weighted table 1 at same tab in jsSurveyGadget

Bug fixes

Initial cluster variable state in jsSurveyGadget

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

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

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

Bug fixes : Label information in regressModule, logisticModule
Update: default.unires option to regressModule, logisticModule

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

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

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

Add testthat.

New module

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

New Gadget

Shiny Gadget for repeated measure analysis: jsRepeatedGadget

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.

Update: Upload Stata .dta format.

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

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.

Bug fixes

IPTW table in tb1simple and tb1simple2 modules.
Kaplan-meier UI in jsPropensityGadget

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

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

Update : csvFile module can remove empty columns.

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

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.

New module

tb1simpleUI, tb1simple, tb1simple2 for propensity score analysis

Bug fixes

factor variable criteria in csvInput, tb1module and tb1module2

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

New gadget

jsBasicGadget : Basic statistics

Minor update

csvFile changes variable name including / to _ and etc.

Bug fixes

Dependency issue with jstable package

Minor update

Support sav/sas7bdat formats

Bug fixes:

tbmoduleUI, tbmoduleUI2 : some error

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.

Update

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

New module

tb1moduleUI2 can deal reactive data

New module: tb1moduleUI, tb1module

Update: csvFile can deal label information

File upload: csvFileInput, csvFile