From ef2c0192d0f538ce32b31936489f19e53989c61f Mon Sep 17 00:00:00 2001 From: emilyvertosick <49212917+emilyvertosick@users.noreply.github.com> Date: Mon, 26 Jun 2023 18:11:11 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20MSKCC-Ep?= =?UTF-8?q?i-Bio/bstfun@532465ec4a7097d8cf2e4aea50f0add44f361320=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- dev/LICENSE-text.html | 2 +- dev/LICENSE.html | 2 +- dev/PULL_REQUEST_TEMPLATE.html | 2 +- dev/authors.html | 6 ++--- dev/index.html | 2 +- dev/news/index.html | 7 +++-- dev/pkgdown.yml | 2 +- dev/reference/add_cuminc_risktable.html | 17 ++++++++---- dev/reference/add_inline_forest_plot.html | 2 +- dev/reference/add_sparkline.html | 2 +- dev/reference/add_splines.html | 2 +- dev/reference/add_variable_grouping.html | 2 +- dev/reference/as_forest_plot.html | 2 +- dev/reference/as_ggplot.html | 2 +- dev/reference/assign_timepoint.html | 2 +- dev/reference/auc.html | 2 +- .../bold_italicize_group_labels.html | 2 +- dev/reference/bstfun-package.html | 2 +- dev/reference/cite_r.html | 2 +- dev/reference/clean_mrn.html | 2 +- dev/reference/count_map.html | 2 +- dev/reference/count_na.html | 2 +- dev/reference/create_project.html | 2 +- dev/reference/deprecated.html | 2 +- dev/reference/egfr.html | 2 +- .../figures/lifecycle-superseded.svg | 1 + dev/reference/fix_database_error.html | 2 +- dev/reference/followup_time.html | 2 +- dev/reference/get_mode.html | 2 +- dev/reference/ggcalibration.html | 2 +- dev/reference/here_data.html | 2 +- dev/reference/hpcc.html | 2 +- dev/reference/index.html | 2 +- dev/reference/list_labels.html | 10 ++++--- dev/reference/logistic_reg_adj_diff.html | 2 +- dev/reference/project_templates.html | 2 +- dev/reference/reexports.html | 2 +- dev/reference/rm_logs.html | 2 +- dev/reference/set_derived_variables.html | 2 +- dev/reference/style_tbl_compact.html | 26 ++++++++++++------- dev/reference/tbl_likert.html | 2 +- dev/reference/theme_gtsummary_msk.html | 2 +- dev/reference/trial.html | 2 +- dev/reference/use_bst_rstudio_prefs.html | 2 +- dev/reference/use_file.html | 2 +- dev/reference/use_varnames_as_labels.html | 2 +- 46 files changed, 85 insertions(+), 62 deletions(-) create mode 100644 dev/reference/figures/lifecycle-superseded.svg diff --git a/dev/LICENSE-text.html b/dev/LICENSE-text.html index 7f7b5393..0567d76f 100644 --- a/dev/LICENSE-text.html +++ b/dev/LICENSE-text.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/LICENSE.html b/dev/LICENSE.html index 55b99eff..1e776f7b 100644 --- a/dev/LICENSE.html +++ b/dev/LICENSE.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/PULL_REQUEST_TEMPLATE.html b/dev/PULL_REQUEST_TEMPLATE.html index dbb0e08c..9d4b203e 100644 --- a/dev/PULL_REQUEST_TEMPLATE.html +++ b/dev/PULL_REQUEST_TEMPLATE.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/authors.html b/dev/authors.html index 79e9f44c..49ad73b7 100644 --- a/dev/authors.html +++ b/dev/authors.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 @@ -113,13 +113,13 @@

Citation

Whiting K, Sjoberg D, Lavery J (2023). bstfun: Functions for the MSK Biostatistics Department. -R package version 0.5.1.9001, https://github.com/MSKCC-Epi-Bio/bstfun. +R package version 0.5.1.9002, https://github.com/MSKCC-Epi-Bio/bstfun. 

@Manual{,
   title = {bstfun: Functions for the MSK Biostatistics Department},
   author = {Karissa Whiting and Daniel D. Sjoberg and Jessica A. Lavery},
   year = {2023},
-  note = {R package version 0.5.1.9001},
+  note = {R package version 0.5.1.9002},
   url = {https://github.com/MSKCC-Epi-Bio/bstfun},
 }
diff --git a/dev/index.html b/dev/index.html index b380e4dd..34471a7f 100644 --- a/dev/index.html +++ b/dev/index.html @@ -35,7 +35,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/news/index.html b/dev/news/index.html index 6e35e2b3..71bf657b 100644 --- a/dev/news/index.html +++ b/dev/news/index.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 @@ -55,7 +55,10 @@

Changelog

bstfun (development version)

-
diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml index f33f643b..4927b0b0 100644 --- a/dev/pkgdown.yml +++ b/dev/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.19.2 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-06-26T17:35Z +last_built: 2023-06-26T18:10Z urls: reference: http://mskcc-epi-bio.github.io/bstfun/reference article: http://mskcc-epi-bio.github.io/bstfun/articles diff --git a/dev/reference/add_cuminc_risktable.html b/dev/reference/add_cuminc_risktable.html index ef4c1264..23c38893 100644 --- a/dev/reference/add_cuminc_risktable.html +++ b/dev/reference/add_cuminc_risktable.html @@ -1,6 +1,7 @@ -Add risk table to cuminc() plot — add_cuminc_risktable • bstfunAdd risk table to cuminc() plot — add_cuminc_risktable • bstfun @@ -18,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002
@@ -56,8 +57,9 @@

Add risk table to cuminc() plot

-

Plot cumulative incidence estimates with a risk table and estimates below -the figure.

+

[Deprecated]

+

See ggsurvfit::ggcuminc() for improved options for reporting cumulative +incidence estimates (e.g. add_quantile(x_value)).

@@ -112,6 +114,11 @@

Arguments

of plot legend. Default is 1 (black).

+
+

Details

+

Plot cumulative incidence estimates with a risk table and estimates below +the figure.

+

Author

Meier Hsu

diff --git a/dev/reference/add_inline_forest_plot.html b/dev/reference/add_inline_forest_plot.html index 709cfd6a..cb59ccc4 100644 --- a/dev/reference/add_inline_forest_plot.html +++ b/dev/reference/add_inline_forest_plot.html @@ -18,7 +18,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002
diff --git a/dev/reference/add_sparkline.html b/dev/reference/add_sparkline.html index f62ab696..cc0364e3 100644 --- a/dev/reference/add_sparkline.html +++ b/dev/reference/add_sparkline.html @@ -19,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/add_splines.html b/dev/reference/add_splines.html index f81dd705..b2fbd646 100644 --- a/dev/reference/add_splines.html +++ b/dev/reference/add_splines.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/add_variable_grouping.html b/dev/reference/add_variable_grouping.html index 1150f710..3756001e 100644 --- a/dev/reference/add_variable_grouping.html +++ b/dev/reference/add_variable_grouping.html @@ -22,7 +22,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/as_forest_plot.html b/dev/reference/as_forest_plot.html index 2466106f..7a41cd12 100644 --- a/dev/reference/as_forest_plot.html +++ b/dev/reference/as_forest_plot.html @@ -20,7 +20,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/as_ggplot.html b/dev/reference/as_ggplot.html index e2bab8f0..46a20d42 100644 --- a/dev/reference/as_ggplot.html +++ b/dev/reference/as_ggplot.html @@ -19,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/assign_timepoint.html b/dev/reference/assign_timepoint.html index 3d1ccdd7..69241fa8 100644 --- a/dev/reference/assign_timepoint.html +++ b/dev/reference/assign_timepoint.html @@ -19,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/auc.html b/dev/reference/auc.html index 83601604..db8aed30 100644 --- a/dev/reference/auc.html +++ b/dev/reference/auc.html @@ -24,7 +24,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/bold_italicize_group_labels.html b/dev/reference/bold_italicize_group_labels.html index 42798c89..21a83f28 100644 --- a/dev/reference/bold_italicize_group_labels.html +++ b/dev/reference/bold_italicize_group_labels.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/bstfun-package.html b/dev/reference/bstfun-package.html index aa277e9b..81c717e1 100644 --- a/dev/reference/bstfun-package.html +++ b/dev/reference/bstfun-package.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/cite_r.html b/dev/reference/cite_r.html index d7115598..6d2b88df 100644 --- a/dev/reference/cite_r.html +++ b/dev/reference/cite_r.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/clean_mrn.html b/dev/reference/clean_mrn.html index 58a37b25..9d0db158 100644 --- a/dev/reference/clean_mrn.html +++ b/dev/reference/clean_mrn.html @@ -25,7 +25,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/count_map.html b/dev/reference/count_map.html index 3dd43dce..d73fb217 100644 --- a/dev/reference/count_map.html +++ b/dev/reference/count_map.html @@ -18,7 +18,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/count_na.html b/dev/reference/count_na.html index 0f198a03..17710168 100644 --- a/dev/reference/count_na.html +++ b/dev/reference/count_na.html @@ -18,7 +18,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/create_project.html b/dev/reference/create_project.html index 1629241f..3ddcf31e 100644 --- a/dev/reference/create_project.html +++ b/dev/reference/create_project.html @@ -21,7 +21,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/deprecated.html b/dev/reference/deprecated.html index ba2b8a73..65d88874 100644 --- a/dev/reference/deprecated.html +++ b/dev/reference/deprecated.html @@ -20,7 +20,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/egfr.html b/dev/reference/egfr.html index 7d7d98f6..9e5fd95d 100644 --- a/dev/reference/egfr.html +++ b/dev/reference/egfr.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/figures/lifecycle-superseded.svg b/dev/reference/figures/lifecycle-superseded.svg new file mode 100644 index 00000000..75f24f55 --- /dev/null +++ b/dev/reference/figures/lifecycle-superseded.svg @@ -0,0 +1 @@ + lifecyclelifecyclesupersededsuperseded \ No newline at end of file diff --git a/dev/reference/fix_database_error.html b/dev/reference/fix_database_error.html index 4645f08f..50ea9f6c 100644 --- a/dev/reference/fix_database_error.html +++ b/dev/reference/fix_database_error.html @@ -22,7 +22,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/followup_time.html b/dev/reference/followup_time.html index 981e5a31..9b6b1448 100644 --- a/dev/reference/followup_time.html +++ b/dev/reference/followup_time.html @@ -20,7 +20,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/get_mode.html b/dev/reference/get_mode.html index 3a39e8c7..2586345d 100644 --- a/dev/reference/get_mode.html +++ b/dev/reference/get_mode.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/ggcalibration.html b/dev/reference/ggcalibration.html index f9d45e5c..c736482d 100644 --- a/dev/reference/ggcalibration.html +++ b/dev/reference/ggcalibration.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/here_data.html b/dev/reference/here_data.html index 0ad88511..188fe5ad 100644 --- a/dev/reference/here_data.html +++ b/dev/reference/here_data.html @@ -21,7 +21,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/hpcc.html b/dev/reference/hpcc.html index 9809802e..481d97d7 100644 --- a/dev/reference/hpcc.html +++ b/dev/reference/hpcc.html @@ -23,7 +23,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/index.html b/dev/reference/index.html index d6fa63e7..dc3f89b2 100644 --- a/dev/reference/index.html +++ b/dev/reference/index.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/list_labels.html b/dev/reference/list_labels.html index 65b24cae..3dd00e94 100644 --- a/dev/reference/list_labels.html +++ b/dev/reference/list_labels.html @@ -1,5 +1,6 @@ -Get variable labels and store in named list — list_labels • bstfunGet variable labels and store in named list — list_labels • bstfun @@ -17,7 +18,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 @@ -55,7 +56,8 @@

Get variable labels and store in named list

-

Get variable labels and store in named list

+

[Deprecated]

+

Use map(data, ~ attr(.x, "label")) instead.

@@ -76,6 +78,8 @@

Author

Examples

list_labels(trial)
+#> Warning: `list_labels()` was deprecated in bstfun 0.5.2.
+#> ℹ Please use `map(data, ~ attr(.x, 'label'))`
 #> $trt
 #> [1] "Chemotherapy Treatment"
 #> 
diff --git a/dev/reference/logistic_reg_adj_diff.html b/dev/reference/logistic_reg_adj_diff.html
index c87f6d1c..8658fce2 100644
--- a/dev/reference/logistic_reg_adj_diff.html
+++ b/dev/reference/logistic_reg_adj_diff.html
@@ -26,7 +26,7 @@
       
       
         bstfun
-        0.5.1.9001
+        0.5.1.9002
diff --git a/dev/reference/project_templates.html b/dev/reference/project_templates.html index 6901468d..e509120f 100644 --- a/dev/reference/project_templates.html +++ b/dev/reference/project_templates.html @@ -18,7 +18,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002
diff --git a/dev/reference/reexports.html b/dev/reference/reexports.html index 5c55974f..75ca0aa2 100644 --- a/dev/reference/reexports.html +++ b/dev/reference/reexports.html @@ -32,7 +32,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002
diff --git a/dev/reference/rm_logs.html b/dev/reference/rm_logs.html index 0095c3c1..87c9b1a1 100644 --- a/dev/reference/rm_logs.html +++ b/dev/reference/rm_logs.html @@ -19,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/set_derived_variables.html b/dev/reference/set_derived_variables.html index 98bb2eb5..c35d543f 100644 --- a/dev/reference/set_derived_variables.html +++ b/dev/reference/set_derived_variables.html @@ -19,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/style_tbl_compact.html b/dev/reference/style_tbl_compact.html index 4b311340..2ca45cf4 100644 --- a/dev/reference/style_tbl_compact.html +++ b/dev/reference/style_tbl_compact.html @@ -1,8 +1,7 @@ -Compact Table Styling — style_tbl_compact • bstfunCompact Table Styling — style_tbl_compact • bstfun @@ -20,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 @@ -58,10 +57,9 @@

Compact Table Styling

-

Apply the same compact styling available from -gtsummary::theme_gtsummary_compact() to any -gt, flextable, huxtable, or knitr::kable() table. -knitr::kable() stlying uses the kableExtra package

+

[Deprecated]

+

Use gtsummary::theme_gtsummary_compact() +and gtreg::tbl_listing() to apply gtsummary compact formatting to any type of table.

@@ -74,6 +72,13 @@

Arguments

a gt, flextable, huxtable, or knitr::kable() table.

+
+

Details

+

Apply the same compact styling available from +gtsummary::theme_gtsummary_compact() to any +gt, flextable, huxtable, or knitr::kable() table. +knitr::kable() stlying uses the kableExtra package

+

Example Output

@@ -99,6 +104,9 @@

Examples

head(trial) %>% gt::gt() %>% style_tbl_compact() +#> Warning: `style_tbl_compact()` was deprecated in bstfun 0.5.2. +#> ℹ Set `gtsummary::theme_gtsummary_compact()` and use `gtreg::tbl_listing()` to +#> apply {gtsummary} compact formatting to any type of table.
diff --git a/dev/reference/tbl_likert.html b/dev/reference/tbl_likert.html index 484429ed..e275e055 100644 --- a/dev/reference/tbl_likert.html +++ b/dev/reference/tbl_likert.html @@ -21,7 +21,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/theme_gtsummary_msk.html b/dev/reference/theme_gtsummary_msk.html index 7c82c4ee..f194ae99 100644 --- a/dev/reference/theme_gtsummary_msk.html +++ b/dev/reference/theme_gtsummary_msk.html @@ -18,7 +18,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/trial.html b/dev/reference/trial.html index 5e1dc376..12815eeb 100644 --- a/dev/reference/trial.html +++ b/dev/reference/trial.html @@ -19,7 +19,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/use_bst_rstudio_prefs.html b/dev/reference/use_bst_rstudio_prefs.html index def5c30f..fde17f12 100644 --- a/dev/reference/use_bst_rstudio_prefs.html +++ b/dev/reference/use_bst_rstudio_prefs.html @@ -35,7 +35,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/use_file.html b/dev/reference/use_file.html index c3eee861..47dcee8d 100644 --- a/dev/reference/use_file.html +++ b/dev/reference/use_file.html @@ -20,7 +20,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002 diff --git a/dev/reference/use_varnames_as_labels.html b/dev/reference/use_varnames_as_labels.html index 01f8ee4e..130c9e39 100644 --- a/dev/reference/use_varnames_as_labels.html +++ b/dev/reference/use_varnames_as_labels.html @@ -17,7 +17,7 @@ bstfun - 0.5.1.9001 + 0.5.1.9002