diff --git a/DESCRIPTION b/DESCRIPTION index 31569b1..e8780ed 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: SummaryTables Title: Publication-Ready Summary Tables for Jamovi -Version: 1.2.1 +Version: 1.3.0 Authors@R: person("Nour Edin", "Darwish", , "nouredindarwish@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0009-0009-5527-4539")) @@ -32,6 +32,7 @@ Imports: cards (>= 0.7.1), cardx (>= 0.3.1), cli, + datawizard, dplyr, effectsize, flextable, @@ -50,7 +51,7 @@ Remotes: insightsengineering/cards@v0.7.1, insightsengineering/cardx@v0.3.1, ddsjoberg/gtsummary@952b665 +Config/roxygen2/version: 8.0.0 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 diff --git a/NEWS.md b/NEWS.md index bc28173..9944330 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +## SummaryTables 1.3.0 + +* Added Standardized Coefficients for Linear Regression analyses (both Univariable and Multivariable). +* Added a rounding option for 16 decimal places across all analyses. +* Enhanced UI labels. +* General bug-fixes and improvements. + ## SummaryTables 1.2.1 * Fixed an issue that caused an error when customizing the number of decimal places in the Continuous Table. diff --git a/R/regression.R b/R/regression.R index 6faad59..37c94c8 100644 --- a/R/regression.R +++ b/R/regression.R @@ -37,7 +37,7 @@ validateFactorPolynomials <- function(data, terms) { #' @param terms modelTerms list from self$options$modelTerms #' @return A formula object buildFormula <- function(y, terms) { - as.formula( + stats::as.formula( paste( y, "~", @@ -128,6 +128,54 @@ buildMultiRegTable <- function(model, options, b64Map) { } +# lmStd --------------------------------------------------------------------- + +#' Fit standard linear regression model on standardized variables +#' +#' @param formula Model formula +#' @param data Data frame +#' @param ... Extra arguments passed to lm +#' @return An lm model object fitted on standardized complete cases +lmStd <- function(formula, data, ...) { + # Goal: produce the same standardized coefficients (betas) as + # parameters::standardize_parameters(method = "refit"). + # + # How standardize_parameters(method = "refit") works internally: + # 1. Extracts the model frame via insight::get_data(model, source = "mf"), + # which is the data AFTER listwise deletion — rows with NA in ANY + # variable used by the model (numeric OR factor) are already gone. + + # 2. Standardizes that complete-case data with datawizard::standardize() + # (factors are left untouched by default since force = FALSE). + # 3. Refits the model on the standardized complete-case data. + # + # Previously we used: + # datawizard::standardize(data, select = select_vars, remove_na = "selected") + # This had a bug: with force = FALSE (default), datawizard internally + # excludes factor columns from the "selected" set, so remove_na = "selected" + # only checked numeric columns for NAs. Rows with NA in a factor (but not + # in any numeric column) were KEPT, meaning mean/SD was computed from MORE + # rows than lm() actually uses (lm() does its own listwise deletion). + # This produced different standardized coefficients than + # parameters::standardize_parameters(method = "refit"). + # + # We also cannot use remove_na = "all" on the full data frame, because + # "all" checks EVERY column — including ones not in the formula. NAs in + # unrelated columns would incorrectly drop rows. + # + # Fix: subset to formula columns first (data[select_vars]), then use + # remove_na = "all". This performs listwise deletion on exactly the + # variables the model uses, matching what lm() and + # parameters::standardize_parameters(method = "refit") do. + select_vars <- all.vars(formula) + data <- datawizard::standardize( + data[select_vars], + remove_na = "all" + ) + stats::lm(formula, data = data, ...) +} + + # buildUniRegTable ---------------------------------------------------------- #' Build a univariable tbl_uvregression table diff --git a/R/survival.R b/R/survival.R index 64e1e41..d9dac0a 100644 --- a/R/survival.R +++ b/R/survival.R @@ -78,7 +78,7 @@ buildSurvfitList <- function(data, elapsedB64, eventB64, strataB64, confInt) { survLHS <- sprintf("survival::Surv(%s, %s)", elapsedB64, eventB64) # Overall - overallF <- reformulate("1", response = survLHS) + overallF <- stats::reformulate("1", response = survLHS) fits <- list( rlang::inject(survival::survfit( !!overallF, @@ -89,7 +89,7 @@ buildSurvfitList <- function(data, elapsedB64, eventB64, strataB64, confInt) { # One fit per stratifying variable (each analyzed independently) for (s in strataB64) { - stratumF <- reformulate(s, response = survLHS) + stratumF <- stats::reformulate(s, response = survLHS) fits <- c( fits, list( diff --git a/R/tblcontinuous.h.R b/R/tblcontinuous.h.R index 0874a8b..98f4305 100644 --- a/R/tblcontinuous.h.R +++ b/R/tblcontinuous.h.R @@ -199,7 +199,8 @@ tblContinuousOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..addPvalue <- jmvcore::OptionBool$new( "addPvalue", diff --git a/R/tblcross.h.R b/R/tblcross.h.R index cb7544e..7d4c70f 100644 --- a/R/tblcross.h.R +++ b/R/tblcross.h.R @@ -88,7 +88,8 @@ tblCrossOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..margin <- jmvcore::OptionList$new( "margin", diff --git a/R/tbllikert.h.R b/R/tbllikert.h.R index 0f36907..8f6cf5a 100644 --- a/R/tbllikert.h.R +++ b/R/tbllikert.h.R @@ -81,7 +81,8 @@ tblLikertOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..levelOrder <- jmvcore::OptionList$new( "levelOrder", diff --git a/R/tblregcox.h.R b/R/tblregcox.h.R index 69ccfbf..9844036 100644 --- a/R/tblregcox.h.R +++ b/R/tblregcox.h.R @@ -114,7 +114,8 @@ tblRegCoxOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..confInt <- jmvcore::OptionBool$new( "confInt", diff --git a/R/tblreglinear.b.R b/R/tblreglinear.b.R index b909b89..1fcc9c7 100644 --- a/R/tblreglinear.b.R +++ b/R/tblreglinear.b.R @@ -67,7 +67,42 @@ tblRegLinearClass <- R6::R6Class( # Formula and model --------------------------------------------------- termsB64 <- lapply(terms, jmvcore::toB64) formula <- buildFormula(depB64, termsB64) - model <- runSafe(lm(formula, data = data), collector) + + if (self$options$standardize) { + # Goal: produce the same standardized coefficients (betas) as + # parameters::standardize_parameters(method = "refit"). + # + # How standardize_parameters(method = "refit") works internally: + # 1. Extracts the model frame (data AFTER listwise deletion — + # rows with NA in ANY variable, numeric OR factor, are gone). + # 2. Standardizes that complete-case data with + # datawizard::standardize() (factors untouched, force = FALSE). + # 3. Refits the model on the standardized complete-case data. + # + # Previously we used: + # standardize(data, select = ..., remove_na = "selected") + # Bug: with force = FALSE (default), datawizard excludes factors + # from the internal "selected" set, so remove_na = "selected" only + # checked numeric columns for NAs. Rows with NA in a factor (but + # not in any numeric) were KEPT, meaning mean/SD was computed from + # MORE rows than lm() actually uses — producing wrong betas. + # + # We also cannot use remove_na = "all" on the full data frame, + # because "all" checks EVERY column — including ones not in the + # formula. NAs in unrelated columns would incorrectly drop rows. + # + # Fix: subset to formula columns first (data[select_vars]), then + # use remove_na = "all". This performs listwise deletion on exactly + # the variables the model uses, matching what lm() and + # parameters::standardize_parameters(method = "refit") do. + select_vars <- all.vars(formula) + data <- datawizard::standardize( + data[select_vars], + remove_na = "all" + ) + } + + model <- runSafe(stats::lm(formula, data = data), collector) # Regression table ---------------------------------------------------- table <- runSafe( @@ -75,6 +110,15 @@ tblRegLinearClass <- R6::R6Class( collector ) + # Change header ------------------------------------------------------- + coefHeader <- if (self$options$standardize) { + "**Standardized Coefficient**" + } else { + "**Coefficient**" + } + table <- table |> + gtsummary::modify_header(estimate = coefHeader) + # Pipeline ------------------------------------------------------------ table <- pipeAddGlobalP( table, diff --git a/R/tblreglinear.h.R b/R/tblreglinear.h.R index e69f5f1..ef32e1e 100644 --- a/R/tblreglinear.h.R +++ b/R/tblreglinear.h.R @@ -12,6 +12,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas manualRun = FALSE, run = FALSE, modelTerms = NULL, + standardize = FALSE, digitsCoef = "auto", confInt = TRUE, confLevel = 95, @@ -83,6 +84,10 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas private$..modelTerms <- jmvcore::OptionTerms$new( "modelTerms", modelTerms) + private$..standardize <- jmvcore::OptionBool$new( + "standardize", + standardize, + default=FALSE) private$..digitsCoef <- jmvcore::OptionList$new( "digitsCoef", digitsCoef, @@ -93,7 +98,8 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..confInt <- jmvcore::OptionBool$new( "confInt", @@ -275,6 +281,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas self$.addOption(private$..manualRun) self$.addOption(private$..run) self$.addOption(private$..modelTerms) + self$.addOption(private$..standardize) self$.addOption(private$..digitsCoef) self$.addOption(private$..confInt) self$.addOption(private$..confLevel) @@ -315,6 +322,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas manualRun = function() private$..manualRun$value, run = function() private$..run$value, modelTerms = function() private$..modelTerms$value, + standardize = function() private$..standardize$value, digitsCoef = function() private$..digitsCoef$value, confInt = function() private$..confInt$value, confLevel = function() private$..confLevel$value, @@ -354,6 +362,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas ..manualRun = NA, ..run = NA, ..modelTerms = NA, + ..standardize = NA, ..digitsCoef = NA, ..confInt = NA, ..confLevel = NA, @@ -445,6 +454,7 @@ tblRegLinearBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( #' @param manualRun . #' @param run . #' @param modelTerms . +#' @param standardize . #' @param digitsCoef . #' @param confInt . #' @param confLevel . @@ -498,6 +508,7 @@ tblRegLinear <- function( manualRun = FALSE, run = FALSE, modelTerms, + standardize = FALSE, digitsCoef = "auto", confInt = TRUE, confLevel = 95, @@ -554,6 +565,7 @@ tblRegLinear <- function( manualRun = manualRun, run = run, modelTerms = modelTerms, + standardize = standardize, digitsCoef = digitsCoef, confInt = confInt, confLevel = confLevel, diff --git a/R/tblreglogistic.h.R b/R/tblreglogistic.h.R index ffad326..7763f2d 100644 --- a/R/tblreglogistic.h.R +++ b/R/tblreglogistic.h.R @@ -100,7 +100,8 @@ tblRegLogisticOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..confInt <- jmvcore::OptionBool$new( "confInt", diff --git a/R/tblsummary.h.R b/R/tblsummary.h.R index e1ad8c2..be1adba 100644 --- a/R/tblsummary.h.R +++ b/R/tblsummary.h.R @@ -278,7 +278,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..statCatDefault <- jmvcore::OptionList$new( "statCatDefault", @@ -317,7 +318,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..percent <- jmvcore::OptionList$new( "percent", @@ -407,7 +409,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..diffDichotDefault <- jmvcore::OptionList$new( "diffDichotDefault", @@ -444,7 +447,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..diffDigitsCat <- jmvcore::OptionList$new( "diffDigitsCat", @@ -456,7 +460,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..addPvalue <- jmvcore::OptionBool$new( "addPvalue", @@ -623,7 +628,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..ciCatDefault <- jmvcore::OptionList$new( "ciCatDefault", @@ -670,7 +676,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..path <- jmvcore::OptionString$new( "path", diff --git a/R/tblsurvfit.h.R b/R/tblsurvfit.h.R index 0bc3bb2..df264a8 100644 --- a/R/tblsurvfit.h.R +++ b/R/tblsurvfit.h.R @@ -113,7 +113,8 @@ tblSurvfitOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class( "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..confLevel <- jmvcore::OptionNumber$new( "confLevel", diff --git a/R/tbluniregcox.h.R b/R/tbluniregcox.h.R index 7afaf28..664bdca 100644 --- a/R/tbluniregcox.h.R +++ b/R/tbluniregcox.h.R @@ -117,7 +117,8 @@ tblUniRegCoxOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..confInt <- jmvcore::OptionBool$new( "confInt", diff --git a/R/tblunireglinear.b.R b/R/tblunireglinear.b.R index e31698f..9935e1e 100644 --- a/R/tblunireglinear.b.R +++ b/R/tblunireglinear.b.R @@ -58,17 +58,27 @@ tblUniRegLinearClass <- R6::R6Class( depB64 <- jmvcore::toB64(dep) # Regression table ---------------------------------------------------- + method <- if (self$options$standardize) lmStd else stats::lm table <- runSafe( buildUniRegTable( data = data, y = depB64, include = jmvcore::toB64(self$options$varOrder), - method = lm, + method = method, options = self$options ), collector ) + # Change header ------------------------------------------------------- + coefHeader <- if (self$options$standardize) { + "**Standardized Coefficient**" + } else { + "**Coefficient**" + } + table <- table |> + gtsummary::modify_header(estimate = coefHeader) + # Pipeline ------------------------------------------------------------ table <- pipeAddGlobalP( table, diff --git a/R/tblunireglinear.h.R b/R/tblunireglinear.h.R index 019267b..77b3570 100644 --- a/R/tblunireglinear.h.R +++ b/R/tblunireglinear.h.R @@ -12,6 +12,7 @@ tblUniRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C varOrder = list(), manualRun = FALSE, run = FALSE, + standardize = FALSE, digitsCoef = "auto", confInt = TRUE, confLevel = 95, @@ -85,6 +86,10 @@ tblUniRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C private$..run <- jmvcore::OptionAction$new( "run", run) + private$..standardize <- jmvcore::OptionBool$new( + "standardize", + standardize, + default=FALSE) private$..digitsCoef <- jmvcore::OptionList$new( "digitsCoef", digitsCoef, @@ -95,7 +100,8 @@ tblUniRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..confInt <- jmvcore::OptionBool$new( "confInt", @@ -261,6 +267,7 @@ tblUniRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C self$.addOption(private$..varOrder) self$.addOption(private$..manualRun) self$.addOption(private$..run) + self$.addOption(private$..standardize) self$.addOption(private$..digitsCoef) self$.addOption(private$..confInt) self$.addOption(private$..confLevel) @@ -298,6 +305,7 @@ tblUniRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C varOrder = function() private$..varOrder$value, manualRun = function() private$..manualRun$value, run = function() private$..run$value, + standardize = function() private$..standardize$value, digitsCoef = function() private$..digitsCoef$value, confInt = function() private$..confInt$value, confLevel = function() private$..confLevel$value, @@ -334,6 +342,7 @@ tblUniRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6C ..varOrder = NA, ..manualRun = NA, ..run = NA, + ..standardize = NA, ..digitsCoef = NA, ..confInt = NA, ..confLevel = NA, @@ -422,6 +431,7 @@ tblUniRegLinearBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas #' @param varOrder . #' @param manualRun . #' @param run . +#' @param standardize . #' @param digitsCoef . #' @param confInt . #' @param confLevel . @@ -472,6 +482,7 @@ tblUniRegLinear <- function( varOrder = list(), manualRun = FALSE, run = FALSE, + standardize = FALSE, digitsCoef = "auto", confInt = TRUE, confLevel = 95, @@ -524,6 +535,7 @@ tblUniRegLinear <- function( varOrder = varOrder, manualRun = manualRun, run = run, + standardize = standardize, digitsCoef = digitsCoef, confInt = confInt, confLevel = confLevel, diff --git a/R/tblunireglogistic.h.R b/R/tblunireglogistic.h.R index cfed7b3..14a4816 100644 --- a/R/tblunireglogistic.h.R +++ b/R/tblunireglogistic.h.R @@ -102,7 +102,8 @@ tblUniRegLogisticOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R "2", "3", "4", - "5"), + "5", + "16"), default="auto") private$..confInt <- jmvcore::OptionBool$new( "confInt", diff --git a/docs/assets/standardized-coefficients.png b/docs/assets/standardized-coefficients.png new file mode 100644 index 0000000..a5f4147 Binary files /dev/null and b/docs/assets/standardized-coefficients.png differ diff --git a/docs/assets/stats-digits.png b/docs/assets/stats-digits.png index 077c911..014ea9c 100644 Binary files a/docs/assets/stats-digits.png and b/docs/assets/stats-digits.png differ diff --git a/docs/user-guide.md b/docs/user-guide.md index 572992e..3c539c7 100644 --- a/docs/user-guide.md +++ b/docs/user-guide.md @@ -67,7 +67,7 @@ You can independently set the rounding rules for various elements in your tables * **Auto (Default):** Typically uses adaptive decimal places, though certain themes may affect this behavior. -* **Fixed (0 to 5):** Uses a fixed number of decimal places. +* **Fixed (0-5, 16):** Uses a fixed number of decimal places. #### P-Values @@ -124,11 +124,11 @@ If you want specific tests for specific variables, you can manually select a dif When you select the **SMD** option as your **Difference** method, the values are calculated using the [`smd` R package](https://bsaul.github.io/smd/index.html).
- ![Jamovi interface showing the SMD method selected under the Difference options](assets/difference-smd.png){ loading=lazy width="500" } + ![jamovi interface showing the SMD method selected under the Difference options](assets/difference-smd.png){ loading=lazy width="500" }
!!! failure "Multiple P-Value Columns Error" - If you select a **Difference** method that generates a p-value and you also check **Add p-value** under the general **P-value** section, an error will occur. The table cannot display multiple p-value columns simultaneously. + If you select a **Difference** method that generates a p-value and you also check **P-value** under the general **P-value** section, an error will occur. The table cannot display multiple p-value columns simultaneously.
![Error message displayed in jamovi when attempting to add multiple p-value columns](assets/multiple-pvalues-error.png){ loading=lazy width="500" } @@ -141,12 +141,23 @@ It is important to understand the fundamental difference in how the **Univariabl * **Univariable Regression:** Fits *one separate model per predictor*. If you add 5 variables across the **Covariates** and **Factors** lists, the module will fit 5 distinct simple regression models (each predicting the dependent variable using just that one predictor) and combine the results into a single table. * **Multivariable Regression:** Fits *one single model containing all predictors*. If you add 5 variables across the **Covariates** and **Factors** lists, the module will fit a single model where all 5 variables are included simultaneously, adjusting for each other. +### Regression Tables: Standardized Coefficients + +For linear regression models, SummaryTables allows you to report standardized coefficients. + +
+ ![jamovi interface highlighting the Standardized Coefficients option in regression tables](assets/standardized-coefficients.png){ loading=lazy width="500" } +
+ +!!! info "Difference from SPSS" + If you are coming from SPSS, your results might look different because SPSS standardizes all variables, whereas we do not standardize **Factors**. We only standardize continuous variables (including **Covariates** and the **Dependent Variable**). This approach—which is also used by jamovi's default linear regression and GAMLj—is comparable to the "refit" method in the [`parameters` R package](https://easystats.github.io/parameters/reference/standardize_parameters.html#details). + ### Survival and Cox Regression: Event Variable Coding When using the **Survival Table** or **Cox Regression** analyses, the **Event variable** must be coded correctly:
- ![Jamovi interface showing the Event variable assignment and Event level selection](assets/event-variable-options.png){ loading=lazy width="500" } + ![jamovi interface showing the Event variable assignment and Event level selection](assets/event-variable-options.png){ loading=lazy width="500" }
* **If continuous:** You can use either `0` and `1` (0 = censored, 1 = event) OR `1` and `2` (1 = censored, 2 = event). Any other numeric values will cause an error. diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml index f015ed6..b70fbfb 100644 --- a/jamovi/0000.yaml +++ b/jamovi/0000.yaml @@ -1,12 +1,12 @@ --- title: Publication-Ready Summary Tables name: SummaryTables -version: 1.2.1 +version: 1.3.0 jms: '1.0' authors: - Nour Edin Darwish maintainer: Nour Edin Darwish -date: '2026-05-17' +date: '2026-05-23' type: R description: >- A comprehensive module for creating publication-ready summary and regression diff --git a/jamovi/tblcontinuous.a.yaml b/jamovi/tblcontinuous.a.yaml index b53d0e6..b1ec2b6 100644 --- a/jamovi/tblcontinuous.a.yaml +++ b/jamovi/tblcontinuous.a.yaml @@ -44,7 +44,7 @@ options: type: Action - name: addOverall - title: Add overall column (requires Grouping Variable) + title: Overall column (requires Grouping Variable) type: Bool default: false @@ -222,10 +222,12 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: addPvalue - title: Add p-value + title: P-value type: Bool default: false @@ -305,7 +307,7 @@ options: default: 0.05 - name: addQ - title: Add q-value (requires p-value) + title: Q-value (requires p-value) type: Bool default: false diff --git a/jamovi/tblcross.a.yaml b/jamovi/tblcross.a.yaml index 9824816..d88891b 100644 --- a/jamovi/tblcross.a.yaml +++ b/jamovi/tblcross.a.yaml @@ -77,10 +77,12 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: margin - title: Show + title: Totals type: List options: - title: Row & Column @@ -195,7 +197,7 @@ options: default: false - name: addPvalue - title: Add p-value + title: P-value type: Bool default: false @@ -240,7 +242,7 @@ options: default: 0.05 - name: sourceNote - title: Show p-value as source note + title: P-value as source note type: Bool default: false diff --git a/jamovi/tbllikert.a.yaml b/jamovi/tbllikert.a.yaml index e1b8b63..4ebfb39 100644 --- a/jamovi/tbllikert.a.yaml +++ b/jamovi/tbllikert.a.yaml @@ -77,6 +77,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: levelOrder @@ -90,7 +92,7 @@ options: default: asFirst - name: addN - title: Add N column + title: N column type: Bool default: false @@ -100,7 +102,7 @@ options: default: false - name: addNFootnote - title: Show footnote + title: Footnote type: Bool default: true diff --git a/jamovi/tblregcox.a.yaml b/jamovi/tblregcox.a.yaml index 5e61ee4..6ef95b6 100644 --- a/jamovi/tblregcox.a.yaml +++ b/jamovi/tblregcox.a.yaml @@ -64,7 +64,7 @@ options: type: Terms - name: exponentiate - title: Hazard ratio (exponentiate coefficients) + title: Hazard ratio (exponentiated coefficient) type: Bool default: true @@ -86,15 +86,17 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: confInt - title: Show confidence interval + title: Confidence interval type: Bool default: true - name: confLevel - title: Confidence level + title: Level type: Number min: 50 max: 99.9 @@ -106,12 +108,12 @@ options: default: false - name: addRefRowEstimate - title: Show reference value + title: Reference level coefficient type: Bool default: false - name: addN - title: Add N column + title: N column type: Bool default: false @@ -128,7 +130,7 @@ options: default: label - name: addNEvent - title: Add event N column + title: Event N column type: Bool default: false @@ -203,17 +205,17 @@ options: default: false - name: starsShowCi - title: Show confidence interval + title: Confidence interval type: Bool default: false - name: starsShowP - title: Show p-value + title: P-value type: Bool default: false - name: starsShowSe - title: Show standard error + title: Standard error type: Bool default: true @@ -297,7 +299,7 @@ options: default: false - name: addQ - title: Add q-value + title: Q-value type: Bool default: false diff --git a/jamovi/tblreglinear.a.yaml b/jamovi/tblreglinear.a.yaml index f53b0b2..78e65e0 100644 --- a/jamovi/tblreglinear.a.yaml +++ b/jamovi/tblreglinear.a.yaml @@ -48,6 +48,11 @@ options: title: Model Terms type: Terms + - name: standardize + title: Standardized coefficient + type: Bool + default: false + - name: digitsCoef title: Decimal places (coefficient & CI) type: List @@ -66,15 +71,17 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: confInt - title: Show confidence interval + title: Confidence interval type: Bool default: true - name: confLevel - title: Confidence level + title: Level type: Number min: 50 max: 99.9 @@ -86,17 +93,17 @@ options: default: false - name: intercept - title: Show intercept + title: Intercept row type: Bool default: false - name: addRefRowEstimate - title: Show reference value + title: Reference level coefficient type: Bool default: false - name: addN - title: Add N column + title: N column type: Bool default: false @@ -171,17 +178,17 @@ options: default: false - name: starsShowCi - title: Show confidence interval + title: Confidence interval type: Bool default: false - name: starsShowP - title: Show p-value + title: P-value type: Bool default: false - name: starsShowSe - title: Show standard error + title: Standard error type: Bool default: true @@ -265,7 +272,7 @@ options: default: false - name: addQ - title: Add q-value + title: Q-value type: Bool default: false diff --git a/jamovi/tblreglinear.u.yaml b/jamovi/tblreglinear.u.yaml index 06366fa..a6a1243 100644 --- a/jamovi/tblreglinear.u.yaml +++ b/jamovi/tblreglinear.u.yaml @@ -71,6 +71,8 @@ children: - type: Label label: General children: + - type: CheckBox + name: standardize - type: ComboBox name: digitsCoef - type: CheckBox diff --git a/jamovi/tblreglogistic.a.yaml b/jamovi/tblreglogistic.a.yaml index f19b241..debe961 100644 --- a/jamovi/tblreglogistic.a.yaml +++ b/jamovi/tblreglogistic.a.yaml @@ -50,7 +50,7 @@ options: type: Terms - name: exponentiate - title: Odds ratio (exponentiate coefficients) + title: Odds ratio (exponentiated coefficient) type: Bool default: true @@ -72,15 +72,17 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: confInt - title: Show confidence interval + title: Confidence interval type: Bool default: true - name: confLevel - title: Confidence level + title: Level type: Number min: 50 max: 99.9 @@ -92,17 +94,17 @@ options: default: false - name: intercept - title: Show intercept + title: Intercept row type: Bool default: false - name: addRefRowEstimate - title: Show reference value + title: Reference level coefficient type: Bool default: false - name: addN - title: Add N column + title: N column type: Bool default: false @@ -119,7 +121,7 @@ options: default: label - name: addNEvent - title: Add event N column + title: Event N column type: Bool default: false @@ -194,17 +196,17 @@ options: default: false - name: starsShowCi - title: Show confidence interval + title: Confidence interval type: Bool default: false - name: starsShowP - title: Show p-value + title: P-value type: Bool default: false - name: starsShowSe - title: Show standard error + title: Standard error type: Bool default: true @@ -288,7 +290,7 @@ options: default: false - name: addQ - title: Add q-value + title: Q-value type: Bool default: false diff --git a/jamovi/tblsummary.a.yaml b/jamovi/tblsummary.a.yaml index 77932b7..837a06f 100644 --- a/jamovi/tblsummary.a.yaml +++ b/jamovi/tblsummary.a.yaml @@ -52,7 +52,7 @@ options: type: Action - name: addN - title: Add N column + title: N column type: Bool default: false @@ -62,12 +62,12 @@ options: default: false - name: addNFootnote - title: Show footnote + title: Footnote type: Bool default: true - name: addOverall - title: Add overall column (requires Grouping Variable) + title: Overall column (requires Grouping Variable) type: Bool default: false @@ -278,6 +278,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: statCatDefault @@ -332,6 +334,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: percent @@ -347,7 +351,7 @@ options: default: column - name: addDifference - title: Add difference (requires Grouping Variable with exactly 2 levels) + title: Difference (requires Grouping Variable with exactly 2 levels) type: Bool default: false @@ -457,6 +461,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: diffDichotDefault @@ -506,6 +512,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: diffDigitsCat @@ -526,10 +534,12 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: addPvalue - title: Add p-value (requires Grouping Variable) + title: P-value (requires Grouping Variable) type: Bool default: false @@ -649,7 +659,7 @@ options: default: useDefault - name: addQ - title: Add q-value (requires p-value) + title: Q-value (requires p-value) type: Bool default: false @@ -686,7 +696,7 @@ options: default: 0.05 - name: addCi - title: Add confidence interval + title: Confidence interval type: Bool default: false @@ -698,7 +708,7 @@ options: default: 95 - name: ciMerge - title: Merge with statistic column + title: Merge CI with statistic column type: Bool default: false @@ -750,6 +760,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: ciCatDefault @@ -820,6 +832,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: path diff --git a/jamovi/tblsurvfit.a.yaml b/jamovi/tblsurvfit.a.yaml index d66a80d..252810f 100644 --- a/jamovi/tblsurvfit.a.yaml +++ b/jamovi/tblsurvfit.a.yaml @@ -99,6 +99,8 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: confLevel @@ -109,17 +111,17 @@ options: default: 95 - name: addN - title: Add N column + title: N column type: Bool default: false - name: addNEvent - title: Add event N column + title: Event N column type: Bool default: false - name: addPvalue - title: Add p-value (requires Stratifying Variables) + title: P-value (requires Stratifying Variables) type: Bool default: false @@ -191,7 +193,7 @@ options: default: 0.05 - name: addQ - title: Add q-value (requires p-value) + title: Q-value (requires p-value) type: Bool default: false diff --git a/jamovi/tbluniregcox.a.yaml b/jamovi/tbluniregcox.a.yaml index 89bf4d3..9a3bb3f 100644 --- a/jamovi/tbluniregcox.a.yaml +++ b/jamovi/tbluniregcox.a.yaml @@ -68,7 +68,7 @@ options: type: Action - name: exponentiate - title: Hazard ratio (exponentiate coefficients) + title: Hazard ratio (exponentiated coefficient) type: Bool default: true @@ -90,15 +90,17 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: confInt - title: Show confidence interval + title: Confidence interval type: Bool default: true - name: confLevel - title: Confidence level + title: Level type: Number min: 50 max: 99.9 @@ -110,12 +112,12 @@ options: default: false - name: addRefRowEstimate - title: Show reference value + title: Reference level coefficient type: Bool default: false - name: addN - title: Add N column + title: N column type: Bool default: true @@ -132,7 +134,7 @@ options: default: label - name: addNEvent - title: Add event N column + title: Event N column type: Bool default: false @@ -190,17 +192,17 @@ options: default: false - name: starsShowCi - title: Show confidence interval + title: Confidence interval type: Bool default: false - name: starsShowP - title: Show p-value + title: P-value type: Bool default: false - name: starsShowSe - title: Show standard error + title: Standard error type: Bool default: true @@ -284,7 +286,7 @@ options: default: false - name: addQ - title: Add q-value + title: Q-value type: Bool default: false diff --git a/jamovi/tblunireglinear.a.yaml b/jamovi/tblunireglinear.a.yaml index 90b6471..262a508 100644 --- a/jamovi/tblunireglinear.a.yaml +++ b/jamovi/tblunireglinear.a.yaml @@ -52,6 +52,11 @@ options: title: Run type: Action + - name: standardize + title: Standardized coefficient + type: Bool + default: false + - name: digitsCoef title: Decimal places (coefficient & CI) type: List @@ -70,15 +75,17 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: confInt - title: Show confidence interval + title: Confidence interval type: Bool default: true - name: confLevel - title: Confidence level + title: Level type: Number min: 50 max: 99.9 @@ -90,12 +97,12 @@ options: default: false - name: addRefRowEstimate - title: Show reference value + title: Reference level coefficient type: Bool default: false - name: addN - title: Add N column + title: N column type: Bool default: true @@ -153,17 +160,17 @@ options: default: false - name: starsShowCi - title: Show confidence interval + title: Confidence interval type: Bool default: false - name: starsShowP - title: Show p-value + title: P-value type: Bool default: false - name: starsShowSe - title: Show standard error + title: Standard error type: Bool default: true @@ -247,7 +254,7 @@ options: default: false - name: addQ - title: Add q-value + title: Q-value type: Bool default: false diff --git a/jamovi/tblunireglinear.u.yaml b/jamovi/tblunireglinear.u.yaml index 4ab4192..dc54374 100644 --- a/jamovi/tblunireglinear.u.yaml +++ b/jamovi/tblunireglinear.u.yaml @@ -48,6 +48,8 @@ children: - type: Label label: General children: + - type: CheckBox + name: standardize - type: ComboBox name: digitsCoef - type: CheckBox diff --git a/jamovi/tblunireglogistic.a.yaml b/jamovi/tblunireglogistic.a.yaml index dc61241..3c80fe5 100644 --- a/jamovi/tblunireglogistic.a.yaml +++ b/jamovi/tblunireglogistic.a.yaml @@ -54,7 +54,7 @@ options: type: Action - name: exponentiate - title: Odds ratio (exponentiate coefficients) + title: Odds ratio (exponentiated coefficient) type: Bool default: true @@ -76,15 +76,17 @@ options: name: "4" - title: "5" name: "5" + - title: "16" + name: "16" default: auto - name: confInt - title: Show confidence interval + title: Confidence interval type: Bool default: true - name: confLevel - title: Confidence level + title: Level type: Number min: 50 max: 99.9 @@ -96,12 +98,12 @@ options: default: false - name: addRefRowEstimate - title: Show reference value + title: Reference level coefficient type: Bool default: false - name: addN - title: Add N column + title: N column type: Bool default: true @@ -118,7 +120,7 @@ options: default: label - name: addNEvent - title: Add event N column + title: Event N column type: Bool default: false @@ -176,17 +178,17 @@ options: default: false - name: starsShowCi - title: Show confidence interval + title: Confidence interval type: Bool default: false - name: starsShowP - title: Show p-value + title: P-value type: Bool default: false - name: starsShowSe - title: Show standard error + title: Standard error type: Bool default: true @@ -270,7 +272,7 @@ options: default: false - name: addQ - title: Add q-value + title: Q-value type: Bool default: false