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teal.data::datanames() is deprecated in favor of dot-prefix and names() (#324)
# Pull Request Part of insightsengineering/teal.data#333 Blocked by: - insightsengineering/teal.code#218 - insightsengineering/teal.data#347 - insightsengineering/teal#1402
1 parent d153e8d commit 4063d5a

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lines changed

‎DESCRIPTION‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -32,8 +32,8 @@ Depends:
3232
goshawk (>= 0.1.18),
3333
R (>= 3.6),
3434
shiny (>= 1.6.0),
35-
teal (>= 0.15.2),
36-
teal.transform (>= 0.5.0)
35+
teal (>= 0.15.2.9079),
36+
teal.transform (>= 0.5.0.9015)
3737
Imports:
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checkmate (>= 2.1.0),
3939
colourpicker,
@@ -47,7 +47,7 @@ Imports:
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shinyjs,
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shinyvalidate,
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stats,
50-
teal.code (>= 0.5.0),
50+
teal.code (>= 0.5.0.9012),
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teal.logger (>= 0.2.0.9011),
5252
teal.reporter (>= 0.2.0),
5353
teal.widgets (>= 0.4.0)
@@ -58,7 +58,7 @@ Suggests:
5858
rvest (>= 1.0.0),
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shinytest2,
6060
stringr (>= 1.4.1),
61-
teal.data (>= 0.5.0),
61+
teal.data (>= 0.6.0.9015),
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tern (>= 0.7.10),
6363
testthat (>= 3.0.4),
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utils

‎R/tm_g_gh_boxplot.R‎

Lines changed: 11 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -54,18 +54,18 @@
5454
#' library(stringr)
5555
#'
5656
#' # use non-exported function from goshawk
57-
#' h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
57+
#' .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
5858
#'
5959
#' # original ARM value = dose value
60-
#' arm_mapping <- list(
60+
#' .arm_mapping <- list(
6161
#' "A: Drug X" = "150mg QD",
6262
#' "B: Placebo" = "Placebo",
6363
#' "C: Combination" = "Combination"
6464
#' )
6565
#' set.seed(1)
6666
#' ADSL <- rADSL
6767
#' ADLB <- rADLB
68-
#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
68+
#' .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
6969
#' ADLB <- ADLB %>%
7070
#' mutate(
7171
#' AVISITCD = case_when(
@@ -86,9 +86,9 @@
8686
#' ARMCD == "ARM B" ~ 2,
8787
#' ARMCD == "ARM A" ~ 3
8888
#' ),
89-
#' ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
89+
#' ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
9090
#' ARM = factor(ARM) %>% reorder(TRTORD),
91-
#' ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
91+
#' ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
9292
#' ACTARM = factor(ACTARM) %>% reorder(TRTORD),
9393
#' ANRLO = 50,
9494
#' ANRHI = 75
@@ -105,20 +105,17 @@
105105
#' )) %>%
106106
#' ungroup()
107107
#'
108-
#' attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
109-
#' attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
108+
#' attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
109+
#' attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
110110
#' attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
111111
#' attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
112112
#'
113113
#' # add LLOQ and ULOQ variables
114-
#' ALB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
114+
#' ALB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL")
115115
#' ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")
116116
#' })
117117
#'
118-
#' datanames <- c("ADSL", "ADLB")
119-
#' datanames(data) <- datanames
120-
#'
121-
#' join_keys(data) <- default_cdisc_join_keys[datanames]
118+
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
122119
#'
123120
#' app <- init(
124121
#' data = data,
@@ -308,7 +305,7 @@ srv_g_boxplot <- function(id,
308305
moduleServer(id, function(input, output, session) {
309306
teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
310307
output$axis_selections <- renderUI({
311-
env <- shiny::isolate(as.list(data()@env))
308+
env <- shiny::isolate(as.list(data()))
312309
resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
313310
resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
314311
resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
@@ -508,7 +505,7 @@ srv_g_boxplot <- function(id,
508505

509506
joined_qenvs <- reactive({
510507
req(create_plot(), create_table())
511-
teal.code::join(create_plot(), create_table())
508+
c(create_plot(), create_table())
512509
})
513510

514511
code <- reactive(teal.code::get_code(joined_qenvs()))

‎R/tm_g_gh_correlationplot.R‎

Lines changed: 10 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -57,22 +57,22 @@
5757
#' library(stringr)
5858
#'
5959
#' # use non-exported function from goshawk
60-
#' h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
60+
#' .h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
6161
#'
6262
#' # original ARM value = dose value
63-
#' arm_mapping <- list(
63+
#' .arm_mapping <- list(
6464
#' "A: Drug X" = "150mg QD",
6565
#' "B: Placebo" = "Placebo",
6666
#' "C: Combination" = "Combination"
6767
#' )
68-
#' color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")
68+
#' .color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")
6969
#' # assign LOQ flag symbols: circles for "N" and triangles for "Y", squares for "NA"
70-
#' shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
70+
#' .shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
7171
#'
7272
#' set.seed(1)
7373
#' ADSL <- rADSL
7474
#' ADLB <- rADLB
75-
#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
75+
#' .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
7676
#' ADLB <- ADLB %>%
7777
#' mutate(AVISITCD = case_when(
7878
#' AVISIT == "SCREENING" ~ "SCR",
@@ -102,7 +102,7 @@
102102
#' ifelse(grepl("A", ARMCD), 3, NA)
103103
#' )
104104
#' )) %>%
105-
#' mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
105+
#' mutate(ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))])) %>%
106106
#' mutate(ARM = factor(ARM) %>%
107107
#' reorder(TRTORD)) %>%
108108
#' mutate(
@@ -130,19 +130,16 @@
130130
#' paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
131131
#' )) %>%
132132
#' ungroup()
133-
#' attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
133+
#' attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
134134
#' attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
135135
#' attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
136136
#'
137137
#' # add LLOQ and ULOQ variables
138-
#' ADLB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
138+
#' ADLB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL")
139139
#' ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")
140140
#' })
141141
#'
142-
#' datanames <- c("ADSL", "ADLB")
143-
#' datanames(data) <- datanames
144-
#'
145-
#' join_keys(data) <- default_cdisc_join_keys[datanames]
142+
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
146143
#'
147144
#' app <- init(
148145
#' data = data,
@@ -374,7 +371,7 @@ srv_g_correlationplot <- function(id,
374371
moduleServer(id, function(input, output, session) {
375372
teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
376373
output$axis_selections <- renderUI({
377-
env <- shiny::isolate(as.list(data()@env))
374+
env <- shiny::isolate(as.list(data()))
378375
resolved_x_param <- teal.transform::resolve_delayed(module_args$xaxis_param, env)
379376
resolved_x_var <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
380377
resolved_y_param <- teal.transform::resolve_delayed(module_args$yaxis_param, env)

‎R/tm_g_gh_density_distribution_plot.R‎

Lines changed: 9 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -40,14 +40,14 @@
4040
#' library(stringr)
4141
#'
4242
#' # original ARM value = dose value
43-
#' arm_mapping <- list(
43+
#' .arm_mapping <- list(
4444
#' "A: Drug X" = "150mg QD",
4545
#' "B: Placebo" = "Placebo",
4646
#' "C: Combination" = "Combination"
4747
#' )
4848
#' ADSL <- rADSL
4949
#' ADLB <- rADLB
50-
#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
50+
#' .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
5151
#' ADLB <- ADLB %>%
5252
#' mutate(
5353
#' AVISITCD = case_when(
@@ -68,19 +68,17 @@
6868
#' ARMCD == "ARM B" ~ 2,
6969
#' ARMCD == "ARM A" ~ 3
7070
#' ),
71-
#' ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
71+
#' ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
7272
#' ARM = factor(ARM) %>% reorder(TRTORD),
73-
#' ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
73+
#' ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
7474
#' ACTARM = factor(ACTARM) %>% reorder(TRTORD)
7575
#' )
7676
#'
77-
#' attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
78-
#' attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
77+
#' attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
78+
#' attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
7979
#' })
8080
#'
81-
#' datanames <- c("ADSL", "ADLB")
82-
#' datanames(data) <- datanames
83-
#' join_keys(data) <- default_cdisc_join_keys[datanames]
81+
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
8482
#'
8583
#' app <- init(
8684
#' data = data,
@@ -256,7 +254,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
256254
moduleServer(id, function(input, output, session) {
257255
teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
258256
output$axis_selections <- renderUI({
259-
env <- shiny::isolate(as.list(data()@env))
257+
env <- shiny::isolate(as.list(data()))
260258
resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
261259
resolved_param <- teal.transform::resolve_delayed(module_args$param, env)
262260
resolved_trt <- teal.transform::resolve_delayed(module_args$trt_group, env)
@@ -416,7 +414,7 @@ srv_g_density_distribution_plot <- function(id, # nolint
416414

417415
joined_qenvs <- reactive({
418416
req(create_plot(), create_table())
419-
teal.code::join(create_plot(), create_table())
417+
c(create_plot(), create_table())
420418
})
421419

422420
code <- reactive(teal.code::get_code(joined_qenvs()))

‎R/tm_g_gh_lineplot.R‎

Lines changed: 8 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -60,15 +60,15 @@
6060
#' library(nestcolor)
6161
#'
6262
#' # original ARM value = dose value
63-
#' arm_mapping <- list(
63+
#' .arm_mapping <- list(
6464
#' "A: Drug X" = "150mg QD",
6565
#' "B: Placebo" = "Placebo",
6666
#' "C: Combination" = "Combination"
6767
#' )
6868
#'
6969
#' ADSL <- rADSL
7070
#' ADLB <- rADLB
71-
#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
71+
#' .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
7272
#' ADLB <- ADLB %>%
7373
#' mutate(
7474
#' AVISITCD = case_when(
@@ -89,18 +89,16 @@
8989
#' ARMCD == "ARM B" ~ 2,
9090
#' ARMCD == "ARM A" ~ 3
9191
#' ),
92-
#' ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
92+
#' ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
9393
#' ARM = factor(ARM) %>% reorder(TRTORD),
94-
#' ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
94+
#' ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
9595
#' ACTARM = factor(ACTARM) %>% reorder(TRTORD)
9696
#' )
97-
#' attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
98-
#' attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
97+
#' attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
98+
#' attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
9999
#' })
100100
#'
101-
#' datanames <- c("ADSL", "ADLB")
102-
#' datanames(data) <- datanames
103-
#' join_keys(data) <- default_cdisc_join_keys[datanames]
101+
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
104102
#'
105103
#' app <- init(
106104
#' data = data,
@@ -349,7 +347,7 @@ srv_lineplot <- function(id,
349347
ns <- session$ns
350348

351349
output$axis_selections <- renderUI({
352-
env <- shiny::isolate(as.list(data()@env))
350+
env <- shiny::isolate(as.list(data()))
353351
resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
354352
resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
355353
resolved_param <- teal.transform::resolve_delayed(module_args$param, env)

‎R/tm_g_gh_scatterplot.R‎

Lines changed: 8 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -45,15 +45,15 @@
4545
#' library(stringr)
4646
#'
4747
#' # original ARM value = dose value
48-
#' arm_mapping <- list(
48+
#' .arm_mapping <- list(
4949
#' "A: Drug X" = "150mg QD",
5050
#' "B: Placebo" = "Placebo",
5151
#' "C: Combination" = "Combination"
5252
#' )
5353
#'
5454
#' ADSL <- rADSL
5555
#' ADLB <- rADLB
56-
#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
56+
#' .var_labels <- lapply(ADLB, function(x) attributes(x)$label)
5757
#' ADLB <- ADLB %>%
5858
#' mutate(
5959
#' AVISITCD = case_when(
@@ -74,18 +74,16 @@
7474
#' ARMCD == "ARM B" ~ 2,
7575
#' ARMCD == "ARM A" ~ 3
7676
#' ),
77-
#' ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
77+
#' ARM = as.character(.arm_mapping[match(ARM, names(.arm_mapping))]),
7878
#' ARM = factor(ARM) %>% reorder(TRTORD),
79-
#' ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
79+
#' ACTARM = as.character(.arm_mapping[match(ACTARM, names(.arm_mapping))]),
8080
#' ACTARM = factor(ACTARM) %>% reorder(TRTORD)
8181
#' )
82-
#' attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
83-
#' attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
82+
#' attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
83+
#' attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
8484
#' })
8585
#'
86-
#' datanames <- c("ADSL", "ADLB")
87-
#' datanames(data) <- datanames
88-
#' join_keys(data) <- default_cdisc_join_keys[datanames]
86+
#' join_keys(data) <- default_cdisc_join_keys[names(data)]
8987
#'
9088
#'
9189
#' app <- init(
@@ -257,7 +255,7 @@ srv_g_scatterplot <- function(id,
257255
moduleServer(id, function(input, output, session) {
258256
teal.logger::log_shiny_input_changes(input, namespace = "teal.goshawk")
259257
output$axis_selections <- renderUI({
260-
env <- shiny::isolate(as.list(data()@env))
258+
env <- shiny::isolate(as.list(data()))
261259
resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env)
262260
resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env)
263261
resolved_param <- teal.transform::resolve_delayed(module_args$param, env)

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