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Update docs to use the new teal_data instead of TealData #592

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Update docs to use the new teal_data instead of TealData #592

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eb7a07e
docs: update the examples to use the new teal_data object
vedhav Nov 7, 2023
d09651f
docs: update the vignettes to use the new teal_data object
vedhav Nov 7, 2023
d8a889e
chore: getting the data object using [[ instead of accessing the env …
vedhav Nov 7, 2023
4b064a0
docs: add changelog and fix lint error for real this time
vedhav Nov 7, 2023
c031262
chore: reduce example width to 100 chars
vedhav Nov 7, 2023
b5a6470
chore: call get_join_keys with pkg namespace
vedhav Nov 8, 2023
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4 changes: 4 additions & 0 deletions NEWS.md
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@@ -1,5 +1,9 @@
# teal.modules.general 0.2.16.9010

### Enhancements

* Updated the package docs and vignettes with the new way of specifying data for `teal::init()`. The `data` argument will accept a `teal_data` object

### Miscellaneous

* Specified minimal version of package dependencies.
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27 changes: 14 additions & 13 deletions R/tm_a_pca.R
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Expand Up @@ -24,24 +24,25 @@
#'
#' # ADSL example
#'
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#'
#' data <- teal_data()
#' data <- within(data, {
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#' })
#' datanames <- c("ADSL")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset(
#' "ADSL", ADSL,
#' code = "ADSL <- teal.modules.general::rADSL"
#' ),
#' check = TRUE
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_a_pca(
#' "PCA",
#' dat = teal.transform::data_extract_spec(
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' choices = teal.transform::variable_choices(data = ADSL, c("BMRKR1", "AGE", "EOSDY")),
#' choices = teal.transform::variable_choices(
#' data = data[["ADSL"]], c("BMRKR1", "AGE", "EOSDY")
#' ),
#' selected = c("BMRKR1", "AGE"),
#' multiple = TRUE
#' ),
Expand Down Expand Up @@ -257,7 +258,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
response[[i]]$select$choices <- var_labels(data[[response[[i]]$dataname]]())
response[[i]]$select$choices <- setdiff(
response[[i]]$select$choices,
unlist(get_join_keys(data)$get(response[[i]]$dataname))
unlist(teal.data::get_join_keys(data)$get(response[[i]]$dataname))
)
}

Expand Down Expand Up @@ -323,7 +324,7 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
anl_merged_input <- teal.transform::merge_expression_srv(
selector_list = selector_list,
datasets = data,
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

anl_merged_q <- reactive({
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18 changes: 11 additions & 7 deletions R/tm_a_regression.R
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Expand Up @@ -34,13 +34,17 @@
#' # Regression graphs from selected response variable (BMRKR1) and
#' # selected regressors (AGE)
#'
#' ADSL <- teal.modules.general::rADSL
#' data <- teal_data()
#' data <- within(data, {
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#' })
#' datanames <- c("ADSL")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
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I see the point now of waiting for change of the join_keys. Let's continue, maybe we will be able to merge them in the same time.

#'
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset("ADSL", ADSL, code = "ADSL <- teal.modules.general::rADSL"),
#' check = TRUE
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_a_regression(
#' label = "Regression",
Expand All @@ -58,7 +62,7 @@
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' label = "Select variables:",
#' choices = teal.transform::variable_choices(ADSL, c("AGE", "SEX", "RACE")),
#' choices = teal.transform::variable_choices(data[["ADSL"]], c("AGE", "SEX", "RACE")),
#' selected = "AGE",
#' multiple = TRUE,
#' fixed = FALSE
Expand Down Expand Up @@ -291,7 +295,7 @@ srv_a_regression <- function(id,
anl_merged_input <- teal.transform::merge_expression_srv(
selector_list = selector_list,
datasets = data,
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

regression_var <- reactive({
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14 changes: 9 additions & 5 deletions R/tm_data_table.R
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Expand Up @@ -25,13 +25,17 @@
#' @export
#' @examples
#'
#' ADSL <- teal.modules.general::rADSL
#' data <- teal_data()
#' data <- within(data, {
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#' })
#' datanames <- c("ADSL")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#'
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset("ADSL", ADSL, code = "ADSL <- teal.modules.general::rADSL"),
#' check = TRUE
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_data_table(
#' variables_selected = list(ADSL = c("STUDYID", "USUBJID", "SUBJID", "SITEID", "AGE", "SEX")),
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11 changes: 7 additions & 4 deletions R/tm_file_viewer.R
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Expand Up @@ -13,11 +13,14 @@
#' @export
#'
#' @examples
#' data <- data.frame(1)
#' data <- teal_data()
#' data <- within(data, {
#' data <- data.frame(1)
#' })
#' datanames(data) <- c("data")
#'
#' app <- teal::init(
#' data = teal_data(
#' dataset("data", data)
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_file_viewer(
#' input_path = list(
Expand Down
18 changes: 10 additions & 8 deletions R/tm_front_page.R
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Expand Up @@ -17,6 +17,15 @@
#' @export
#' @examples
#'
#' data <- teal_data()
#' data <- within(data, {
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#' })
#' datanames <- c("ADSL")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#'
#' table_1 <- data.frame(Info = c("A", "B"), Text = c("A", "B"))
#' table_2 <- data.frame(`Column 1` = c("C", "D"), `Column 2` = c(5.5, 6.6), `Column 3` = c("A", "B"))
#' table_3 <- data.frame(Info = c("E", "F"), Text = c("G", "H"))
Expand All @@ -27,15 +36,8 @@
#' "Table 3" = table_3
#' )
#'
#' ADSL <- teal.modules.general::rADSL
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset("ADSL", ADSL,
#' code = "ADSL <- teal.modules.general::rADSL",
#' metadata = list("Author" = "NEST team", "data_source" = "synthetic data")
#' ),
#' check = TRUE
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_front_page(
#' header_text = c(
Expand Down
21 changes: 12 additions & 9 deletions R/tm_g_association.R
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Expand Up @@ -25,22 +25,25 @@
#' @examples
#' # Association plot of selected reference variable (SEX)
#' # against other selected variables (BMRKR1)
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#' data <- teal_data()
#' data <- within(data, {
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#' })
#' datanames <- c("ADSL")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#'
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset("ADSL", ADSL, code = "ADSL <- teal.modules.general::rADSL"),
#' check = TRUE
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_g_association(
#' ref = teal.transform::data_extract_spec(
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' label = "Select variable:",
#' choices = teal.transform::variable_choices(
#' ADSL,
#' data[["ADSL"]],
#' c("SEX", "RACE", "COUNTRY", "ARM", "STRATA1", "STRATA2", "ITTFL", "BMRKR2")
#' ),
#' selected = "RACE",
Expand All @@ -52,7 +55,7 @@
#' select = teal.transform::select_spec(
#' label = "Select variables:",
#' choices = teal.transform::variable_choices(
#' ADSL,
#' data[["ADSL"]],
#' c("SEX", "RACE", "COUNTRY", "ARM", "STRATA1", "STRATA2", "ITTFL", "BMRKR2")
#' ),
#' selected = "BMRKR2",
Expand Down Expand Up @@ -248,7 +251,7 @@ srv_tm_g_association <- function(id,
anl_merged_input <- teal.transform::merge_expression_srv(
datasets = data,
selector_list = selector_list,
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

anl_merged_q <- reactive({
Expand Down
24 changes: 14 additions & 10 deletions R/tm_g_bivariate.R
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Expand Up @@ -45,20 +45,24 @@
#'
#' @examples
#' # Bivariate plot of selected variable (AGE) against selected (SEX)
#' ADSL <- teal.modules.general::rADSL
#' data <- teal_data()
#' data <- within(data, {
#' library(nestcolor)
#' ADSL <- teal.modules.general::rADSL
#' })
#' datanames <- c("ADSL")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#'
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset("ADSL", ADSL, code = "ADSL <- teal.modules.general::rADSL"),
#' check = TRUE
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_g_bivariate(
#' x = teal.transform::data_extract_spec(
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' label = "Select variable:",
#' choices = teal.transform::variable_choices(ADSL),
#' choices = teal.transform::variable_choices(data[["ADSL"]]),
#' selected = "AGE",
#' fixed = FALSE
#' )
Expand All @@ -67,7 +71,7 @@
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' label = "Select variable:",
#' choices = teal.transform::variable_choices(ADSL),
#' choices = teal.transform::variable_choices(data[["ADSL"]]),
#' selected = "SEX",
#' multiple = FALSE,
#' fixed = FALSE
Expand All @@ -77,7 +81,7 @@
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' label = "Select variable:",
#' choices = teal.transform::variable_choices(ADSL),
#' choices = teal.transform::variable_choices(data[["ADSL"]]),
#' selected = "ARM",
#' fixed = FALSE
#' )
Expand All @@ -86,7 +90,7 @@
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' label = "Select variable:",
#' choices = teal.transform::variable_choices(ADSL),
#' choices = teal.transform::variable_choices(data[["ADSL"]]),
#' selected = "COUNTRY",
#' fixed = FALSE
#' )
Expand Down Expand Up @@ -437,7 +441,7 @@ srv_g_bivariate <- function(id,
anl_merged_input <- teal.transform::merge_expression_srv(
selector_list = selector_list,
datasets = data,
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

anl_merged_q <- reactive({
Expand Down
32 changes: 22 additions & 10 deletions R/tm_g_distribution.R
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Expand Up @@ -29,8 +29,15 @@
#'
#' @examples
#' # Example with non-clinical data
#'
#' data <- teal_data()
#' data <- within(data, {
#' iris <- iris
#' })
#' datanames(data) <- c("iris")
#'
#' app <- teal::init(
#' data = teal_data(dataset("iris", iris)),
#' data = data,
#' modules = list(
#' teal.modules.general::tm_g_distribution(
#' dist_var = teal.transform::data_extract_spec(
Expand All @@ -48,22 +55,27 @@
#' }
#'
#' # Example with clinical data
#' ADSL <- teal.modules.general::rADSL
#' data <- teal_data()
#' data <- within(data, {
#' ADSL <- teal.modules.general::rADSL
#' })
#' datanames <- c("ADSL")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#'
#' vars1 <- choices_selected(variable_choices(ADSL, c("ARM", "COUNTRY", "SEX")), selected = NULL)
#' vars1 <- choices_selected(
#' variable_choices(data[["ADSL"]], c("ARM", "COUNTRY", "SEX")),
#' selected = NULL
#' )
#'
#' app <- teal::init(
#' data = teal.data::cdisc_data(
#' teal.data::cdisc_dataset("ADSL", ADSL),
#' code = "ADSL <- teal.modules.general::rADSL",
#' check = FALSE
#' ),
#' data = data,
#' modules = teal::modules(
#' teal.modules.general::tm_g_distribution(
#' dist_var = teal.transform::data_extract_spec(
#' dataname = "ADSL",
#' select = teal.transform::select_spec(
#' choices = teal.transform::variable_choices(ADSL, c("AGE", "BMRKR1")),
#' choices = teal.transform::variable_choices(data[["ADSL"]], c("AGE", "BMRKR1")),
#' selected = "BMRKR1",
#' multiple = FALSE,
#' fixed = FALSE
Expand Down Expand Up @@ -435,7 +447,7 @@ srv_distribution <- function(id,
anl_merged_input <- teal.transform::merge_expression_srv(
selector_list = selector_list,
datasets = data,
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

anl_merged_q <- reactive({
Expand Down
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