diff --git a/DESCRIPTION b/DESCRIPTION
index 393bb75..96b8c06 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Type: Package
Package: ClinicoPathDescriptives
Title: Descriptives Functions for Clinicopathological Research
-Version: 0.0.2.06
-Date: 2023-06-01
+Version: 0.0.2.07
+Date: 2023-07-02
Authors@R:
person(given = "Serdar",
family = "Balci",
@@ -47,10 +47,10 @@ Imports:
DiagrammeR,
DiagrammeRsvg,
rsvg,
- shiny
+ shiny,
+ gtsummary
Remotes:
- nbarrowman/vtree@ffa53d4ea5050fa9b26918f4bb30595e91a0f489,
- ddsjoberg/gtsummary@f43332fde6264ff95d092da644284dac739c4e17
+ nbarrowman/vtree@ffa53d4ea5050fa9b26918f4bb30595e91a0f489
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
diff --git a/R/alluvial.h.R b/R/alluvial.h.R
index 5b1dfe6..c736d88 100644
--- a/R/alluvial.h.R
+++ b/R/alluvial.h.R
@@ -8,7 +8,7 @@ alluvialOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
initialize = function(
vars = NULL,
condensationvar = NULL,
- excl = TRUE,
+ excl = FALSE,
marg = FALSE,
fill = "first_variable",
bin = "default",
@@ -31,7 +31,7 @@ alluvialOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
private$..excl <- jmvcore::OptionBool$new(
"excl",
excl,
- default=TRUE)
+ default=FALSE)
private$..marg <- jmvcore::OptionBool$new(
"marg",
marg,
@@ -205,7 +205,7 @@ alluvial <- function(
data,
vars,
condensationvar,
- excl = TRUE,
+ excl = FALSE,
marg = FALSE,
fill = "first_variable",
bin = "default",
diff --git a/R/crosstable.b.R b/R/crosstable.b.R
index a2ac351..a653d7b 100644
--- a/R/crosstable.b.R
+++ b/R/crosstable.b.R
@@ -17,8 +17,6 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
sty <- self$options$sty
-
-
if (is.null(self$options$vars) || is.null(self$options$group)) {
# ToDo Message ----
@@ -39,27 +37,32 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
todo <- ""
html <- self$results$todo
html$setContent(todo)
+ }
if (sty == "finalfit") {
-
- todo <- glue::glue("
+ todo2 <- glue::glue("
finalfit uses
aov (analysis of variance) or t.test for Welch two sample t-test. Note continuous non-parametric test is always Kruskal Wallis (kruskal.test) which in two-group setting is equivalent to Mann-Whitney U /Wilcoxon rank sum test. See full documentation here.
"
)
+ }
- html <- self$results$todo
- html$setContent(todo)
+ if (sty != "finalfit") {
+
+ todo2 <- glue::glue("")
}
+ html <- self$results$todo2
+ html$setContent(todo2)
+
# Error Message ----
- if (nrow(self$data) == 0) stop("Data contains no (complete) rows")
+ if (nrow(self$data) == 0) stop("Data contains no (complete) rows")
# Prepare Data ----
@@ -149,41 +152,48 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
na_include = FALSE,
na_to_p = FALSE,
cont = self$options$cont,
+ cont_nonpara = NULL,
+ cont_cut = 5,
cont_range = TRUE,
-
p_cont_para = "aov",
p_cat = self$options$pcat,
-
-
-
-
-
-
-
- cont_nonpara = NULL,
- cont_cut = 5,
dependent_label_prefix = "Dependent: ",
dependent_label_suffix = "",
row_totals_colname = "Total N",
row_missing_colname = "Missing N",
-
-
column = TRUE,
+
orderbytotal = FALSE,
- digits = c(1, 1, 3, 1),
+ digits = c(1, 1, 3, 1, 0),
+
+
na_include_dependent = FALSE,
na_complete_cases = FALSE,
fit_id = FALSE,
- add_col_totals = FALSE,
+
+ na_to_prop = TRUE,
+
+
+ add_col_totals = TRUE,
include_col_totals_percent = TRUE,
col_totals_rowname = NULL,
col_totals_prefix = "",
add_row_totals = FALSE,
- include_row_missing_col = TRUE
+ include_row_totals_percent = TRUE,
+ include_row_missing_col = TRUE,
+
+ catTest = NULL,
+ weights = NULL
+
+
+
+
+
+
) -> tablefinalfit
@@ -213,10 +223,22 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
tablegtsummary <-
gtsummary::tbl_summary(data = mydata,
- by = self$options$group) %>%
- gtsummary::modify_header(stat_by =
- gt::md("**{level}** N = {n} ({style_percent(p)}%)")) %>%
+ by = self$options$group,
+ statistic = list(
+ gtsummary::all_continuous() ~ "{mean} ({sd})",
+ gtsummary::all_categorical() ~ "{n} / {N} ({p}%)"
+ ),
+ digits = gtsummary::all_continuous() ~ 2,
+ missing_text = "(Missing)"
+
+ ) %>%
+ gtsummary::modify_header(
+ update = gtsummary::all_stat_cols() ~ structure("**{level}** N = {n} ({style_percent(p)}%)", class = "from_markdown")
+ # stat_by =
+ # gt::md("**{level}** N = {n} ({style_percent(p)}%)")
+ ) %>%
gtsummary::add_n(x = .) %>%
+ gtsummary::add_overall() %>%
gtsummary::bold_labels(x = .) %>%
gtsummary::add_p(x = .,
pvalue_fun =
@@ -225,6 +247,11 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
digits = 2)
) %>%
gtsummary::add_q()
+ # %>%
+ # gtsummary::bold_labels() %>%
+ # gtsummary::bold_levels() %>%
+ # gtsummary::bold_p()
+
tablegtsummary <-
gtsummary::as_kable_extra(tablegtsummary)
@@ -284,5 +311,5 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
# tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
}
- })
+ )
)
diff --git a/R/crosstable.h.R b/R/crosstable.h.R
index 1a11a1d..118dab7 100644
--- a/R/crosstable.h.R
+++ b/R/crosstable.h.R
@@ -9,7 +9,7 @@ crosstableOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
vars = NULL,
group = NULL,
sty = "nejm",
- excl = TRUE,
+ excl = FALSE,
cont = "mean",
pcat = "chisq", ...) {
@@ -44,7 +44,7 @@ crosstableOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
private$..excl <- jmvcore::OptionBool$new(
"excl",
excl,
- default=TRUE)
+ default=FALSE)
private$..cont <- jmvcore::OptionList$new(
"cont",
cont,
@@ -88,6 +88,7 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
inherit = jmvcore::Group,
active = list(
todo = function() private$.items[["todo"]],
+ todo2 = function() private$.items[["todo2"]],
tablestyle1 = function() private$.items[["tablestyle1"]],
tablestyle2 = function() private$.items[["tablestyle2"]],
tablestyle3 = function() private$.items[["tablestyle3"]],
@@ -109,14 +110,26 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"vars",
"group",
"cont",
- "pcat")))
+ "pcat",
+ "sty")))
+ self$add(jmvcore::Html$new(
+ options=options,
+ name="todo2",
+ title="To Do",
+ clearWith=list(
+ "vars",
+ "group",
+ "cont",
+ "pcat",
+ "sty")))
self$add(jmvcore::Html$new(
options=options,
name="tablestyle1",
title="`Cross Table - ${group}`",
clearWith=list(
"vars",
- "group"),
+ "group",
+ "sty"),
visible="(sty:arsenal)",
refs="arsenal"))
self$add(jmvcore::Html$new(
@@ -127,7 +140,8 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"vars",
"group",
"cont",
- "pcat"),
+ "pcat",
+ "sty"),
visible="(sty:finalfit)",
refs="finalfit"))
self$add(jmvcore::Html$new(
@@ -136,7 +150,8 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
title="`Cross Table - ${group}`",
clearWith=list(
"vars",
- "group"),
+ "group",
+ "sty"),
visible="(sty:gtsummary)",
refs="gtsummary"))
self$add(jmvcore::Html$new(
@@ -145,7 +160,8 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
title="`Cross Table - ${group}`",
clearWith=list(
"vars",
- "group"),
+ "group",
+ "sty"),
visible="(sty:nejm || sty:lancet || sty:hmisc)",
refs="tangram"))}))
@@ -188,6 +204,7 @@ crosstableBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
+#' \code{results$todo2} \tab \tab \tab \tab \tab a html \cr
#' \code{results$tablestyle1} \tab \tab \tab \tab \tab a html \cr
#' \code{results$tablestyle2} \tab \tab \tab \tab \tab a html \cr
#' \code{results$tablestyle3} \tab \tab \tab \tab \tab a html \cr
@@ -200,7 +217,7 @@ crosstable <- function(
vars,
group,
sty = "nejm",
- excl = TRUE,
+ excl = FALSE,
cont = "mean",
pcat = "chisq") {
diff --git a/R/tableone.h.R b/R/tableone.h.R
index 2c106d4..7077937 100644
--- a/R/tableone.h.R
+++ b/R/tableone.h.R
@@ -8,7 +8,7 @@ tableoneOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
initialize = function(
vars = NULL,
sty = "t1",
- excl = TRUE, ...) {
+ excl = FALSE, ...) {
super$initialize(
package="ClinicoPathDescriptives",
@@ -31,7 +31,7 @@ tableoneOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
private$..excl <- jmvcore::OptionBool$new(
"excl",
excl,
- default=TRUE)
+ default=FALSE)
self$.addOption(private$..vars)
self$.addOption(private$..sty)
@@ -160,7 +160,7 @@ tableone <- function(
data,
vars,
sty = "t1",
- excl = TRUE) {
+ excl = FALSE) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("tableone requires jmvcore to be installed (restart may be required)")
diff --git a/R/vartree.h.R b/R/vartree.h.R
index 3cd3653..c0c9529 100644
--- a/R/vartree.h.R
+++ b/R/vartree.h.R
@@ -16,7 +16,7 @@ vartreeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
follow = NULL,
followLevel1 = NULL,
followLevel2 = NULL,
- excl = TRUE,
+ excl = FALSE,
vp = TRUE,
horizontal = FALSE,
sline = TRUE,
@@ -105,7 +105,7 @@ vartreeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
private$..excl <- jmvcore::OptionBool$new(
"excl",
excl,
- default=TRUE)
+ default=FALSE)
private$..vp <- jmvcore::OptionBool$new(
"vp",
vp,
@@ -360,7 +360,7 @@ vartree <- function(
follow,
followLevel1,
followLevel2,
- excl = TRUE,
+ excl = FALSE,
vp = TRUE,
horizontal = FALSE,
sline = TRUE,
diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml
index 8c03a36..f4eed31 100644
--- a/jamovi/0000.yaml
+++ b/jamovi/0000.yaml
@@ -1,12 +1,12 @@
---
title: Descriptives Functions for Clinicopathological Research
name: ClinicoPathDescriptives
-version: 0.0.2.06
+version: 0.0.2.07
jms: '1.0'
authors:
- Serdar Balci
maintainer: Serdar Balci
-date: '2023-06-01'
+date: '2023-07-02'
type: R
description: >-
Descriptives Functions for Clinicopathological Research Descriptive functions
diff --git a/jamovi/alluvial.a.yaml b/jamovi/alluvial.a.yaml
index 3a5fd8a..7fd0416 100644
--- a/jamovi/alluvial.a.yaml
+++ b/jamovi/alluvial.a.yaml
@@ -30,7 +30,7 @@ options:
- name: excl
title: Exclude missing (NA)
type: Bool
- default: true
+ default: false
- name: marg
title: Marginal plots
diff --git a/jamovi/crosstable.a.yaml b/jamovi/crosstable.a.yaml
index 289adc5..3c3f21f 100644
--- a/jamovi/crosstable.a.yaml
+++ b/jamovi/crosstable.a.yaml
@@ -59,7 +59,7 @@ options:
- name: excl
title: Exclude Missing (NA)
type: Bool
- default: true
+ default: false
- name: cont
diff --git a/jamovi/crosstable.r.yaml b/jamovi/crosstable.r.yaml
index 35fb488..e3bc596 100644
--- a/jamovi/crosstable.r.yaml
+++ b/jamovi/crosstable.r.yaml
@@ -11,8 +11,15 @@ items:
clearWith:
- vars
- group
- - cont
- - pcat
+
+ - name: todo2
+ title: To Do
+ type: Html
+ clearWith:
+ - vars
+ - group
+ - sty
+
# - name: tablearsenal_output
# title: tablearsenal_output
@@ -27,6 +34,7 @@ items:
clearWith:
- vars
- group
+ - sty
visible: (sty:arsenal)
refs: arsenal
@@ -39,6 +47,7 @@ items:
- group
- cont
- pcat
+ - sty
visible: (sty:finalfit)
refs: finalfit
@@ -49,6 +58,7 @@ items:
clearWith:
- vars
- group
+ - sty
visible: (sty:gtsummary)
refs: gtsummary
@@ -59,6 +69,7 @@ items:
clearWith:
- vars
- group
+ - sty
visible: (sty:nejm || sty:lancet || sty:hmisc)
refs: tangram
diff --git a/jamovi/tableone.a.yaml b/jamovi/tableone.a.yaml
index b490eff..6547cff 100644
--- a/jamovi/tableone.a.yaml
+++ b/jamovi/tableone.a.yaml
@@ -54,7 +54,7 @@ options:
- name: excl
title: Exclude Missing (NA)
type: Bool
- default: true
+ default: false
# - name: alllevels
diff --git a/jamovi/vartree.a.yaml b/jamovi/vartree.a.yaml
index 03b5378..4bebb2e 100644
--- a/jamovi/vartree.a.yaml
+++ b/jamovi/vartree.a.yaml
@@ -83,7 +83,7 @@ options:
- name: excl
title: Exclude Missing (NA)
type: Bool
- default: true
+ default: false
- name: vp
title: Valid Percentages
diff --git a/man/alluvial.Rd b/man/alluvial.Rd
index 3f663e6..beb180f 100644
--- a/man/alluvial.Rd
+++ b/man/alluvial.Rd
@@ -8,7 +8,7 @@ alluvial(
data,
vars,
condensationvar,
- excl = TRUE,
+ excl = FALSE,
marg = FALSE,
fill = "first_variable",
bin = "default",
diff --git a/man/crosstable.Rd b/man/crosstable.Rd
index 9aeda7e..eaae228 100644
--- a/man/crosstable.Rd
+++ b/man/crosstable.Rd
@@ -9,7 +9,7 @@ crosstable(
vars,
group,
sty = "nejm",
- excl = TRUE,
+ excl = FALSE,
cont = "mean",
pcat = "chisq"
)
diff --git a/man/tableone.Rd b/man/tableone.Rd
index 690dfed..2c34a95 100644
--- a/man/tableone.Rd
+++ b/man/tableone.Rd
@@ -4,7 +4,7 @@
\alias{tableone}
\title{Table One}
\usage{
-tableone(data, vars, sty = "t1", excl = TRUE)
+tableone(data, vars, sty = "t1", excl = FALSE)
}
\arguments{
\item{data}{The data as a data frame.}
diff --git a/man/vartree.Rd b/man/vartree.Rd
index 9b815b4..182dd5e 100644
--- a/man/vartree.Rd
+++ b/man/vartree.Rd
@@ -16,7 +16,7 @@ vartree(
follow,
followLevel1,
followLevel2,
- excl = TRUE,
+ excl = FALSE,
vp = TRUE,
horizontal = FALSE,
sline = TRUE,