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Replace TealData with teal_data in the docs #845

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Replace TealData with teal_data in the docs #845

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b5c3b8a
refactoring cdisc_dataset() call to return teal_data()
kartikeyakirar Nov 7, 2023
d79eff1
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 7, 2023
2bfb054
adding code for reproducibility and updated news
kartikeyakirar Nov 8, 2023
3a11031
Merge branch '842_replace_tealdata@main' of https://github.com/insigh…
kartikeyakirar Nov 8, 2023
07fd195
fixing join_key issues.
kartikeyakirar Nov 8, 2023
f3d6296
included code vignettes and fixing notes
kartikeyakirar Nov 8, 2023
a5643f4
addressing comment.
kartikeyakirar Nov 8, 2023
bbbee71
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 8, 2023
cb4bccc
fixing styling and rd files
kartikeyakirar Nov 8, 2023
00ecbf5
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 8, 2023
b560850
'Empty-Commit'
kartikeyakirar Nov 9, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -68,7 +68,7 @@ Suggests:
knitr,
lubridate,
nestcolor (>= 0.1.0),
teal.data (>= 0.3.0),
teal.data (>= 0.3.0.9008),
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Usually, I guess we only work after the changes are merged into main and get the proper version. But, since in this case, we're working on top of unmerged changes the version will be higher than this. If everything goes well and we merge join_keys PR first it will be 0.3.0.9009 so I saw we wait for the version bump till the teal.data join_keys PR is merged.

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YEs, once join_keys PR is merged. will make consistent version bump to all the replace doc PR for teal.data

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I have the same in teal.modules.hermes https://github.com/insightsengineering/teal.modules.hermes/pull/342/files#r1386573062

testthat (>= 3.0)
VignetteBuilder:
knitr
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2 changes: 1 addition & 1 deletion NEWS.md
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Expand Up @@ -13,7 +13,7 @@
* Updated `tm_t_pp_basic_info`, `tm_t_pp_medical_history`, `tm_g_pp_therapy`, `tm_g_pp_adverse_events`, and `tm_t_pp_laboratory` to print patient ID above table.
* Updated `tm_t_pp_basic_info`, `tm_g_pp_therapy`, `tm_g_pp_adverse_events`, and `tm_t_pp_laboratory` to use `rlistings` to print data neatly in reports.
* Updated `tm_g_lineplot` to allow user to remove interval from plot.

* Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.

### Bug fixes
* Fixed bug in `tm_t_coxreg` preventing table from being displayed when no covariates are selected.
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41 changes: 22 additions & 19 deletions R/tm_a_gee.R
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Expand Up @@ -128,24 +128,27 @@ template_a_gee <- function(output_table,
#' @export
#'
#' @examples
#' adsl <- tmc_ex_adsl
#' adqs <- tmc_ex_adqs %>%
#' dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
#' dplyr::mutate(
#' AVISIT = as.factor(AVISIT),
#' AVISITN = rank(AVISITN) %>%
#' as.factor() %>%
#' as.numeric() %>%
#' as.factor(),
#' AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
#' ) %>%
#' droplevels()
#' data <- teal_data()
#' data <- within(data, {
#' ADSL <- tmc_ex_adsl
#' ADQS <- tmc_ex_adqs %>%
#' dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
#' dplyr::mutate(
#' AVISIT = as.factor(AVISIT),
#' AVISITN = rank(AVISITN) %>%
#' as.factor() %>%
#' as.numeric() %>%
#' as.factor(),
#' AVALBIN = AVAL < 50 #' Just as an example to get a binary endpoint.
#' ) %>%
#' droplevels()
#' })
#' datanames <- c("ADSL", "ADQS")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADQS", adqs)
Comment on lines -146 to -147
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I know this was not the case before, But I think we should make the teal_data object reproducible so that the code in the Show R code works. Right now it won't work because the data creation code is not specified.

@kartikeyakirar what do you think about adding it for all the examples so they are improved?

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I think its good idea. However, considering that these are for example for TMC modules and the preprocessing code be lengthy in some cases, which in turn might elongate the 'cdisc_data' call, I would lean towards not including it in for all the examples.
@gogonzo @donyunardi WDYT?

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@vedhav vedhav Nov 7, 2023 •
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I think there is no need to specify the code anymore, we have the new within() function. I think we need to document it as I believe it's the best practice.

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There are very few examples like that, and it's included in most of the tmg examples. I will make the update.

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@vedhav I think this qualifies to another issue. @kartikeyakirar feel free to make code reproducible or keep as reproducible as it was before. We need this soon on @main so I advise to make this branch ready as quick as possible.

#' ),
#' data = data,
#' modules = modules(
#' tm_a_gee(
#' label = "GEE",
Expand All @@ -155,7 +158,7 @@ template_a_gee <- function(output_table,
#' arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
#' visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
#' paramcd = choices_selected(
#' choices = value_choices(adqs, "PARAMCD", "PARAM"),
#' choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
#' selected = "FKSI-FWB"
#' ),
#' cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
Expand Down Expand Up @@ -444,14 +447,14 @@ srv_gee <- function(id,
datasets = data,
selector_list = selector_list,
merge_function = "dplyr::inner_join",
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

adsl_inputs <- teal.transform::merge_expression_module(
datasets = data,
data_extract = list(arm_var = arm_var),
anl_name = "ANL_ADSL",
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

anl_q <- shiny::reactive({
Expand Down
41 changes: 22 additions & 19 deletions R/tm_a_mmrm.R
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Expand Up @@ -452,30 +452,33 @@ template_mmrm_plots <- function(fit_name,
#' numerical precision.
#'
#' @examples
#' adsl <- tmc_ex_adsl
#' adqs <- tmc_ex_adqs %>%
#' dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
#' dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
#' dplyr::mutate(
#' AVISIT = as.factor(AVISIT),
#' AVISITN = rank(AVISITN) %>%
#' as.factor() %>%
#' as.numeric() %>%
#' as.factor() # making consecutive numeric factor
#' )
#'
#' arm_ref_comp <- list(
#' ARMCD = list(
#' ref = "ARM B",
#' comp = c("ARM A", "ARM C")
#' )
#' )
#'
#' data <- teal_data()
#' data <- within(data, {
#' ADSL <- tmc_ex_adsl
#' ADQS <- tmc_ex_adqs %>%
#' dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
#' dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
#' dplyr::mutate(
#' AVISIT = as.factor(AVISIT),
#' AVISITN = rank(AVISITN) %>%
#' as.factor() %>%
#' as.numeric() %>%
#' as.factor() #' making consecutive numeric factor
#' )
#' })
#'
#' datanames <- c("ADSL", "ADQS")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADQS", adqs)
#' ),
#' data = data,
#' modules = modules(
#' tm_a_mmrm(
#' label = "MMRM",
Expand All @@ -486,7 +489,7 @@ template_mmrm_plots <- function(fit_name,
#' visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
#' arm_ref_comp = arm_ref_comp,
#' paramcd = choices_selected(
#' choices = value_choices(adqs, "PARAMCD", "PARAM"),
#' choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
#' selected = "FKSI-FWB"
#' ),
#' cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
Expand Down Expand Up @@ -917,14 +920,14 @@ srv_mmrm <- function(id,
anl_inputs <- teal.transform::merge_expression_srv(
datasets = data,
selector_list = selector_list_without_cov,
join_keys = get_join_keys(data),
join_keys = teal.data::get_join_keys(data),
merge_function = "dplyr::inner_join"
)

adsl_merge_inputs <- teal.transform::merge_expression_module(
datasets = data,
data_extract = list(arm_var = arm_var),
join_keys = get_join_keys(data),
join_keys = teal.data::get_join_keys(data),
anl_name = "ANL_ADSL"
)

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33 changes: 20 additions & 13 deletions R/tm_g_barchart_simple.R
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Expand Up @@ -16,14 +16,21 @@
#' @examples
#' library(nestcolor)
#'
#' adsl <- tmc_ex_adsl %>% dplyr::mutate(ITTFL = factor("Y") %>%
#' formatters::with_label("Intent-To-Treat Population Flag"))
#' adae <- tmc_ex_adae %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
#' ADSL <- tmc_ex_adsl %>%
#' dplyr::mutate(ITTFL = factor("Y") %>%
#' formatters::with_label("Intent-To-Treat Population Flag"))
#' ADAE <- tmc_ex_adae %>%
#' dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADAE", adae)
#' ADSL = ADSL,
#' ADAE = ADAE,
#' code = "ADSL <- tmc_ex_adsl %>%
#' dplyr::mutate(ITTFL = factor(\"Y\") %>%
#' formatters::with_label(\"Intent-To-Treat Population Flag\"))
#' ADAE <- tmc_ex_adae %>%
#' dplyr::filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))"
#' ),
#' modules = modules(
#' tm_g_barchart_simple(
Expand All @@ -32,7 +39,7 @@
#' dataname = "ADSL",
#' select = select_spec(
#' choices = variable_choices(
#' adsl,
#' ADSL,
#' c(
#' "ARM", "ACTARM", "SEX",
#' "RACE", "ITTFL", "SAFFL", "STRATA2"
Expand All @@ -47,7 +54,7 @@
#' dataname = "ADSL",
#' select = select_spec(
#' choices = variable_choices(
#' adsl,
#' ADSL,
#' c(
#' "ARM", "ACTARM", "SEX",
#' "RACE", "ITTFL", "SAFFL", "STRATA2"
Expand All @@ -60,7 +67,7 @@
#' data_extract_spec(
#' dataname = "ADAE",
#' select = select_spec(
#' choices = variable_choices(adae, c("AETOXGR", "AESEV", "AESER")),
#' choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
#' selected = NULL,
#' multiple = FALSE
#' )
Expand All @@ -70,7 +77,7 @@
#' data_extract_spec(
#' dataname = "ADAE",
#' select = select_spec(
#' choices = variable_choices(adae, c("AETOXGR", "AESEV", "AESER")),
#' choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
#' selected = "AETOXGR",
#' multiple = FALSE
#' )
Expand All @@ -79,7 +86,7 @@
#' dataname = "ADSL",
#' select = select_spec(
#' choices = variable_choices(
#' adsl,
#' ADSL,
#' c(
#' "ARM", "ACTARM", "SEX",
#' "RACE", "ITTFL", "SAFFL", "STRATA2"
Expand All @@ -94,7 +101,7 @@
#' data_extract_spec(
#' dataname = "ADAE",
#' select = select_spec(
#' choices = variable_choices(adae, c("AETOXGR", "AESEV", "AESER")),
#' choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
#' selected = "AESEV",
#' multiple = FALSE
#' )
Expand All @@ -103,7 +110,7 @@
#' dataname = "ADSL",
#' select = select_spec(
#' choices = variable_choices(
#' adsl,
#' ADSL,
#' c(
#' "ARM", "ACTARM", "SEX",
#' "RACE", "ITTFL", "SAFFL", "STRATA2"
Expand Down Expand Up @@ -374,7 +381,7 @@ srv_g_barchart_simple <- function(id,

anl_inputs <- teal.transform::merge_expression_srv(
datasets = data,
join_keys = get_join_keys(data),
join_keys = teal.data::get_join_keys(data),
selector_list = selector_list
)

Expand Down
22 changes: 13 additions & 9 deletions R/tm_g_ci.R
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Expand Up @@ -192,13 +192,17 @@ template_g_ci <- function(dataname, # nolint
#' @examples
#' library(nestcolor)
#'
#' adsl <- tmc_ex_adsl
#' adlb <- tmc_ex_adlb
#' ADSL <- tmc_ex_adsl
#' ADLB <- tmc_ex_adlb
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADLB", adlb)
#' ADSL = ADSL,
#' ADLB = ADLB,
#' code = "
#' ADSL <- tmc_ex_adsl
#' ADLB <- tmc_ex_adlb
#' "
#' ),
#' modules = modules(
#' tm_g_ci(
Expand All @@ -217,15 +221,15 @@ template_g_ci <- function(dataname, # nolint
#' filter = list(
#' filter_spec(
#' vars = "PARAMCD",
#' choices = levels(adlb$PARAMCD),
#' selected = levels(adlb$PARAMCD)[1],
#' choices = levels(ADLB$PARAMCD),
#' selected = levels(ADLB$PARAMCD)[1],
#' multiple = FALSE,
#' label = "Select lab:"
#' ),
#' filter_spec(
#' vars = "AVISIT",
#' choices = levels(adlb$AVISIT),
#' selected = levels(adlb$AVISIT)[1],
#' choices = levels(ADLB$AVISIT),
#' selected = levels(ADLB$AVISIT)[1],
#' multiple = FALSE,
#' label = "Select visit:"
#' )
Expand Down Expand Up @@ -399,7 +403,7 @@ srv_g_ci <- function(id, # nolint

anl_inputs <- teal.transform::merge_expression_srv(
datasets = data,
join_keys = get_join_keys(data),
join_keys = teal.data::get_join_keys(data),
selector_list = selector_list
)

Expand Down
27 changes: 17 additions & 10 deletions R/tm_g_forest_rsp.R
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Expand Up @@ -217,8 +217,8 @@ template_forest_rsp <- function(dataname = "ANL",
#' @examples
#' library(nestcolor)
#'
#' adsl <- tmc_ex_adsl
#' adrs <- tmc_ex_adrs %>%
#' ADSL <- tmc_ex_adsl
#' ADRS <- tmc_ex_adrs %>%
#' dplyr::mutate(AVALC = tern::d_onco_rsp_label(AVALC) %>%
#' formatters::with_label("Character Result/Finding")) %>%
#' dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
Expand All @@ -236,28 +236,35 @@ template_forest_rsp <- function(dataname = "ANL",
#'
#' app <- init(
#' data = cdisc_data(
#' cdisc_dataset("ADSL", adsl),
#' cdisc_dataset("ADRS", adrs)
#' ADSL = ADSL,
#' ADRS = ADRS,
#' code = "
#' ADSL <- tmc_ex_adsl
#' ADRS <- tmc_ex_adrs %>%
#' dplyr::mutate(AVALC = tern::d_onco_rsp_label(AVALC) %>%
#' formatters::with_label(\"Character Result/Finding\")) %>%
#' dplyr::filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")
#' "
#' ),
#' modules = modules(
#' tm_g_forest_rsp(
#' label = "Forest Response",
#' dataname = "ADRS",
#' arm_var = choices_selected(
#' variable_choices(adsl, c("ARM", "ARMCD")),
#' variable_choices(ADSL, c("ARM", "ARMCD")),
#' "ARMCD"
#' ),
#' arm_ref_comp = arm_ref_comp,
#' paramcd = choices_selected(
#' value_choices(adrs, "PARAMCD", "PARAM"),
#' value_choices(ADRS, "PARAMCD", "PARAM"),
#' "INVET"
#' ),
#' subgroup_var = choices_selected(
#' variable_choices(adsl, names(adsl)),
#' variable_choices(ADSL, names(ADSL)),
#' c("BMRKR2", "SEX")
#' ),
#' strata_var = choices_selected(
#' variable_choices(adsl, c("STRATA1", "STRATA2")),
#' variable_choices(ADSL, c("STRATA1", "STRATA2")),
#' "STRATA2"
#' ),
#' plot_height = c(600L, 200L, 2000L),
Expand Down Expand Up @@ -514,13 +521,13 @@ srv_g_forest_rsp <- function(id,
datasets = data,
selector_list = selector_list,
merge_function = "dplyr::inner_join",
join_keys = get_join_keys(data)
join_keys = teal.data::get_join_keys(data)
)

adsl_inputs <- teal.transform::merge_expression_module(
datasets = data,
data_extract = list(arm_var = arm_var, subgroup_var = subgroup_var, strata_var = strata_var),
join_keys = get_join_keys(data),
join_keys = teal.data::get_join_keys(data),
anl_name = "ANL_ADSL"
)

Expand Down
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