diff --git a/book/_quarto.yml b/book/_quarto.yml index 05bc62fd9e..eb29cba1bc 100644 --- a/book/_quarto.yml +++ b/book/_quarto.yml @@ -42,7 +42,7 @@ execute: knitr: opts_chunk: echo: true - fig.width: 15 + tidy: function(code, ...) gsub(pattern = "#\\s?nolint.*|#\\s?styler:.*", replacement = "", code) editor: visual highlight-style: github diff --git a/book/graphs/efficacy/fstg01.qmd b/book/graphs/efficacy/fstg01.qmd index fe0023f1ec..049f9cfb38 100644 --- a/book/graphs/efficacy/fstg01.qmd +++ b/book/graphs/efficacy/fstg01.qmd @@ -189,7 +189,7 @@ height <- 5 ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/graphs/efficacy/fstg02.qmd b/book/graphs/efficacy/fstg02.qmd index 19a9df5078..faf00793f1 100644 --- a/book/graphs/efficacy/fstg02.qmd +++ b/book/graphs/efficacy/fstg02.qmd @@ -170,7 +170,7 @@ plot_v3.width <- 8 ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/graphs/efficacy/mmrmg01.qmd b/book/graphs/efficacy/mmrmg01.qmd index 3421f7d506..c785c09f48 100644 --- a/book/graphs/efficacy/mmrmg01.qmd +++ b/book/graphs/efficacy/mmrmg01.qmd @@ -113,7 +113,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/graphs/other/brg01.qmd b/book/graphs/other/brg01.qmd index 1e4f9ea70d..6f77038e7a 100644 --- a/book/graphs/other/brg01.qmd +++ b/book/graphs/other/brg01.qmd @@ -298,7 +298,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/graphs/other/bwg01.qmd b/book/graphs/other/bwg01.qmd index bfd7035e62..76094e1836 100644 --- a/book/graphs/other/bwg01.qmd +++ b/book/graphs/other/bwg01.qmd @@ -336,7 +336,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.general) ## Data reproducible code diff --git a/book/graphs/other/cig01.qmd b/book/graphs/other/cig01.qmd index e151a6a564..f15d45f718 100644 --- a/book/graphs/other/cig01.qmd +++ b/book/graphs/other/cig01.qmd @@ -163,7 +163,7 @@ table ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/graphs/other/ippg01.qmd b/book/graphs/other/ippg01.qmd index b7ed7ed48e..330d15f9de 100644 --- a/book/graphs/other/ippg01.qmd +++ b/book/graphs/other/ippg01.qmd @@ -87,7 +87,7 @@ plots ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/graphs/other/kmg01.qmd b/book/graphs/other/kmg01.qmd index 6bb0bf1866..444983f82a 100644 --- a/book/graphs/other/kmg01.qmd +++ b/book/graphs/other/kmg01.qmd @@ -122,7 +122,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/graphs/other/ltg01.qmd b/book/graphs/other/ltg01.qmd index b7d3f05b76..82a7368894 100644 --- a/book/graphs/other/ltg01.qmd +++ b/book/graphs/other/ltg01.qmd @@ -217,7 +217,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/graphs/other/mng01.qmd b/book/graphs/other/mng01.qmd index 61ff248f05..e794c57e65 100644 --- a/book/graphs/other/mng01.qmd +++ b/book/graphs/other/mng01.qmd @@ -145,7 +145,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/graphs/pharmacokinetic/pkcg01.qmd b/book/graphs/pharmacokinetic/pkcg01.qmd index 16e1405b0d..02de58dcfc 100644 --- a/book/graphs/pharmacokinetic/pkcg01.qmd +++ b/book/graphs/pharmacokinetic/pkcg01.qmd @@ -91,7 +91,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/graphs/pharmacokinetic/pkcg02.qmd b/book/graphs/pharmacokinetic/pkcg02.qmd index 0d379e4e52..dd8f1771eb 100644 --- a/book/graphs/pharmacokinetic/pkcg02.qmd +++ b/book/graphs/pharmacokinetic/pkcg02.qmd @@ -92,7 +92,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/graphs/pharmacokinetic/pkcg03.qmd b/book/graphs/pharmacokinetic/pkcg03.qmd index 628ee8b145..bff256e818 100644 --- a/book/graphs/pharmacokinetic/pkcg03.qmd +++ b/book/graphs/pharmacokinetic/pkcg03.qmd @@ -104,7 +104,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/graphs/pharmacokinetic/pkpg01.qmd b/book/graphs/pharmacokinetic/pkpg01.qmd index 9c10e71350..8621f2c7c3 100644 --- a/book/graphs/pharmacokinetic/pkpg01.qmd +++ b/book/graphs/pharmacokinetic/pkpg01.qmd @@ -139,7 +139,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/graphs/pharmacokinetic/pkpg02.qmd b/book/graphs/pharmacokinetic/pkpg02.qmd index dbf056dc55..769a08cd88 100644 --- a/book/graphs/pharmacokinetic/pkpg02.qmd +++ b/book/graphs/pharmacokinetic/pkpg02.qmd @@ -144,7 +144,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/graphs/pharmacokinetic/pkpg06.qmd b/book/graphs/pharmacokinetic/pkpg06.qmd index 36bb4bf297..a321841e82 100644 --- a/book/graphs/pharmacokinetic/pkpg06.qmd +++ b/book/graphs/pharmacokinetic/pkpg06.qmd @@ -180,7 +180,7 @@ plot ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/ADA/adat01.qmd b/book/tables/ADA/adat01.qmd index 0efc9511c4..8930b29cd4 100644 --- a/book/tables/ADA/adat01.qmd +++ b/book/tables/ADA/adat01.qmd @@ -220,7 +220,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/ADA/adat02.qmd b/book/tables/ADA/adat02.qmd index cea03e9742..1e079edc30 100644 --- a/book/tables/ADA/adat02.qmd +++ b/book/tables/ADA/adat02.qmd @@ -141,7 +141,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/ADA/adat03.qmd b/book/tables/ADA/adat03.qmd index 09a11aa867..6b1f9ef4d2 100644 --- a/book/tables/ADA/adat03.qmd +++ b/book/tables/ADA/adat03.qmd @@ -121,7 +121,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/ADA/adat04a.qmd b/book/tables/ADA/adat04a.qmd index 48bc0a0b45..c0c966a26b 100644 --- a/book/tables/ADA/adat04a.qmd +++ b/book/tables/ADA/adat04a.qmd @@ -230,7 +230,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/ADA/adat04b.qmd b/book/tables/ADA/adat04b.qmd index 170714f485..722c2c35fe 100644 --- a/book/tables/ADA/adat04b.qmd +++ b/book/tables/ADA/adat04b.qmd @@ -213,7 +213,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/ECG/egt01.qmd b/book/tables/ECG/egt01.qmd index 2594585548..3f92f26194 100644 --- a/book/tables/ECG/egt01.qmd +++ b/book/tables/ECG/egt01.qmd @@ -83,7 +83,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/ECG/egt02.qmd b/book/tables/ECG/egt02.qmd index c18e19eabd..f41a298914 100644 --- a/book/tables/ECG/egt02.qmd +++ b/book/tables/ECG/egt02.qmd @@ -79,7 +79,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/ECG/egt03.qmd b/book/tables/ECG/egt03.qmd index 81b1702f53..ffe53c2583 100644 --- a/book/tables/ECG/egt03.qmd +++ b/book/tables/ECG/egt03.qmd @@ -142,7 +142,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/ECG/egt04.qmd b/book/tables/ECG/egt04.qmd index 9c1dc28c9f..307021c35f 100644 --- a/book/tables/ECG/egt04.qmd +++ b/book/tables/ECG/egt04.qmd @@ -89,7 +89,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/ECG/egt05_qtcat.qmd b/book/tables/ECG/egt05_qtcat.qmd index 5faf237c03..85e62e23ee 100644 --- a/book/tables/ECG/egt05_qtcat.qmd +++ b/book/tables/ECG/egt05_qtcat.qmd @@ -107,7 +107,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet01.qmd b/book/tables/adverse-events/aet01.qmd index 6c5df5b856..444b8975ef 100644 --- a/book/tables/adverse-events/aet01.qmd +++ b/book/tables/adverse-events/aet01.qmd @@ -338,7 +338,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet01_aesi.qmd b/book/tables/adverse-events/aet01_aesi.qmd index 8797369b95..8ddb1110a9 100644 --- a/book/tables/adverse-events/aet01_aesi.qmd +++ b/book/tables/adverse-events/aet01_aesi.qmd @@ -493,7 +493,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet02.qmd b/book/tables/adverse-events/aet02.qmd index 899b695422..2ad8ae47d2 100644 --- a/book/tables/adverse-events/aet02.qmd +++ b/book/tables/adverse-events/aet02.qmd @@ -640,7 +640,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet02_smq.qmd b/book/tables/adverse-events/aet02_smq.qmd index ac36f7297d..567029c1a8 100644 --- a/book/tables/adverse-events/aet02_smq.qmd +++ b/book/tables/adverse-events/aet02_smq.qmd @@ -173,7 +173,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet03.qmd b/book/tables/adverse-events/aet03.qmd index fd1e80a590..97f685b19e 100644 --- a/book/tables/adverse-events/aet03.qmd +++ b/book/tables/adverse-events/aet03.qmd @@ -106,7 +106,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet04.qmd b/book/tables/adverse-events/aet04.qmd index 3be9f34b8f..63cfe96b70 100644 --- a/book/tables/adverse-events/aet04.qmd +++ b/book/tables/adverse-events/aet04.qmd @@ -561,7 +561,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet04_pi.qmd b/book/tables/adverse-events/aet04_pi.qmd index 75801a906a..0f3df3f34b 100644 --- a/book/tables/adverse-events/aet04_pi.qmd +++ b/book/tables/adverse-events/aet04_pi.qmd @@ -372,7 +372,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet05.qmd b/book/tables/adverse-events/aet05.qmd index cba8ce303d..8d6afa081a 100644 --- a/book/tables/adverse-events/aet05.qmd +++ b/book/tables/adverse-events/aet05.qmd @@ -72,7 +72,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet05_all.qmd b/book/tables/adverse-events/aet05_all.qmd index 3df59442f8..b9197f6e8b 100644 --- a/book/tables/adverse-events/aet05_all.qmd +++ b/book/tables/adverse-events/aet05_all.qmd @@ -73,7 +73,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet06.qmd b/book/tables/adverse-events/aet06.qmd index 551074d94a..47aa00838e 100644 --- a/book/tables/adverse-events/aet06.qmd +++ b/book/tables/adverse-events/aet06.qmd @@ -365,7 +365,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet06_smq.qmd b/book/tables/adverse-events/aet06_smq.qmd index 30af5f3aa8..d24b97b24a 100644 --- a/book/tables/adverse-events/aet06_smq.qmd +++ b/book/tables/adverse-events/aet06_smq.qmd @@ -239,7 +239,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet07.qmd b/book/tables/adverse-events/aet07.qmd index d7b33346a4..b0a53a76a6 100644 --- a/book/tables/adverse-events/aet07.qmd +++ b/book/tables/adverse-events/aet07.qmd @@ -109,7 +109,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet09.qmd b/book/tables/adverse-events/aet09.qmd index 9117b38516..a1205c41ac 100644 --- a/book/tables/adverse-events/aet09.qmd +++ b/book/tables/adverse-events/aet09.qmd @@ -173,7 +173,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet09_smq.qmd b/book/tables/adverse-events/aet09_smq.qmd index 53f3a5ac93..ab45fd1bb1 100644 --- a/book/tables/adverse-events/aet09_smq.qmd +++ b/book/tables/adverse-events/aet09_smq.qmd @@ -181,7 +181,7 @@ Note that filtering AEs for relatedness to study drug is not a necessary data pr It can be achieved using the `teal` module filter panel. The example here pre-sets the filters using `AEREL = "Y"` in `adae`. -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/adverse-events/aet10.qmd b/book/tables/adverse-events/aet10.qmd index c61fc615d1..d80d950d87 100644 --- a/book/tables/adverse-events/aet10.qmd +++ b/book/tables/adverse-events/aet10.qmd @@ -104,7 +104,7 @@ result The desired frequency is specified in `prune_freq`. For illustration, frequency is set to $\geq$ 35%. -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/concomitant-medications/cmt01.qmd b/book/tables/concomitant-medications/cmt01.qmd index 13d7c87832..e3bb458c33 100644 --- a/book/tables/concomitant-medications/cmt01.qmd +++ b/book/tables/concomitant-medications/cmt01.qmd @@ -231,7 +231,7 @@ result Here, `adcm` is processed to keep only one path per treatment. -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/concomitant-medications/cmt01a.qmd b/book/tables/concomitant-medications/cmt01a.qmd index 4a6a223490..df32f6131b 100644 --- a/book/tables/concomitant-medications/cmt01a.qmd +++ b/book/tables/concomitant-medications/cmt01a.qmd @@ -226,7 +226,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4") diff --git a/book/tables/concomitant-medications/cmt01b.qmd b/book/tables/concomitant-medications/cmt01b.qmd index 1bf1deee3e..e4e2908cc1 100644 --- a/book/tables/concomitant-medications/cmt01b.qmd +++ b/book/tables/concomitant-medications/cmt01b.qmd @@ -257,7 +257,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4") diff --git a/book/tables/concomitant-medications/cmt02_pt.qmd b/book/tables/concomitant-medications/cmt02_pt.qmd index 62e4f39b2e..db0b8205b9 100644 --- a/book/tables/concomitant-medications/cmt02_pt.qmd +++ b/book/tables/concomitant-medications/cmt02_pt.qmd @@ -69,7 +69,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4") diff --git a/book/tables/deaths/dtht01.qmd b/book/tables/deaths/dtht01.qmd index 90fe424868..23f3e23bb3 100644 --- a/book/tables/deaths/dtht01.qmd +++ b/book/tables/deaths/dtht01.qmd @@ -185,7 +185,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/demography/dmt01.qmd b/book/tables/demography/dmt01.qmd index 0297f7368d..1f5d030ec3 100644 --- a/book/tables/demography/dmt01.qmd +++ b/book/tables/demography/dmt01.qmd @@ -197,7 +197,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/disclosures/eudrat01.qmd b/book/tables/disclosures/eudrat01.qmd index ed44538123..afcf5923a9 100644 --- a/book/tables/disclosures/eudrat01.qmd +++ b/book/tables/disclosures/eudrat01.qmd @@ -94,7 +94,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/disclosures/eudrat02.qmd b/book/tables/disclosures/eudrat02.qmd index 93f48eb5c7..5005d20bee 100644 --- a/book/tables/disclosures/eudrat02.qmd +++ b/book/tables/disclosures/eudrat02.qmd @@ -71,7 +71,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/disposition/dst01.qmd b/book/tables/disposition/dst01.qmd index c66be2dc5d..4263a51386 100644 --- a/book/tables/disposition/dst01.qmd +++ b/book/tables/disposition/dst01.qmd @@ -118,7 +118,7 @@ result3 ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/disposition/pdt01.qmd b/book/tables/disposition/pdt01.qmd index 97132acc7b..86f987ffca 100644 --- a/book/tables/disposition/pdt01.qmd +++ b/book/tables/disposition/pdt01.qmd @@ -66,7 +66,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/disposition/pdt02.qmd b/book/tables/disposition/pdt02.qmd index 3ea04a5268..6471294966 100644 --- a/book/tables/disposition/pdt02.qmd +++ b/book/tables/disposition/pdt02.qmd @@ -67,7 +67,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/efficacy/aovt01.qmd b/book/tables/efficacy/aovt01.qmd index 9386fb097c..4ff5e528a9 100644 --- a/book/tables/efficacy/aovt01.qmd +++ b/book/tables/efficacy/aovt01.qmd @@ -63,7 +63,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/aovt02.qmd b/book/tables/efficacy/aovt02.qmd index 0a5cc03038..7f86ea47e8 100644 --- a/book/tables/efficacy/aovt02.qmd +++ b/book/tables/efficacy/aovt02.qmd @@ -70,7 +70,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/aovt03.qmd b/book/tables/efficacy/aovt03.qmd index 68338b5c3a..5fc9ec0170 100644 --- a/book/tables/efficacy/aovt03.qmd +++ b/book/tables/efficacy/aovt03.qmd @@ -71,7 +71,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/efficacy/cfbt01.qmd b/book/tables/efficacy/cfbt01.qmd index 6d14690007..a7da31e92f 100644 --- a/book/tables/efficacy/cfbt01.qmd +++ b/book/tables/efficacy/cfbt01.qmd @@ -91,7 +91,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/cmht01.qmd b/book/tables/efficacy/cmht01.qmd index a030310126..6920bf1286 100644 --- a/book/tables/efficacy/cmht01.qmd +++ b/book/tables/efficacy/cmht01.qmd @@ -138,7 +138,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/coxt01.qmd b/book/tables/efficacy/coxt01.qmd index 90eb4222f5..423787ba50 100644 --- a/book/tables/efficacy/coxt01.qmd +++ b/book/tables/efficacy/coxt01.qmd @@ -165,7 +165,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) arm_ref_comp <- list( diff --git a/book/tables/efficacy/coxt02.qmd b/book/tables/efficacy/coxt02.qmd index 5907f8f909..017f935275 100644 --- a/book/tables/efficacy/coxt02.qmd +++ b/book/tables/efficacy/coxt02.qmd @@ -136,7 +136,7 @@ See the *Multivariable Cox Regression with Interaction Term* tab. ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/dort01.qmd b/book/tables/efficacy/dort01.qmd index 69152657c1..edfbf9ba94 100644 --- a/book/tables/efficacy/dort01.qmd +++ b/book/tables/efficacy/dort01.qmd @@ -261,7 +261,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/lgrt02.qmd b/book/tables/efficacy/lgrt02.qmd index f917672a46..711c82306d 100644 --- a/book/tables/efficacy/lgrt02.qmd +++ b/book/tables/efficacy/lgrt02.qmd @@ -154,7 +154,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/mmrmt01.qmd b/book/tables/efficacy/mmrmt01.qmd index 39668a9773..a28cc42803 100644 --- a/book/tables/efficacy/mmrmt01.qmd +++ b/book/tables/efficacy/mmrmt01.qmd @@ -211,7 +211,7 @@ as.rtable(mmrm_results, type = "diagnostic") ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/onct05.qmd b/book/tables/efficacy/onct05.qmd index a5f25a5a37..7ea56596c1 100644 --- a/book/tables/efficacy/onct05.qmd +++ b/book/tables/efficacy/onct05.qmd @@ -135,7 +135,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} # Use table, embedded in response forest plot module. library(teal.modules.clinical) diff --git a/book/tables/efficacy/ratet01.qmd b/book/tables/efficacy/ratet01.qmd index a9e8ad7b3b..a59089735e 100644 --- a/book/tables/efficacy/ratet01.qmd +++ b/book/tables/efficacy/ratet01.qmd @@ -34,7 +34,7 @@ anl <- df_explicit_na(anl) ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In Progress diff --git a/book/tables/efficacy/rspt01.qmd b/book/tables/efficacy/rspt01.qmd index fb6339e111..ddcd8644f9 100644 --- a/book/tables/efficacy/rspt01.qmd +++ b/book/tables/efficacy/rspt01.qmd @@ -246,7 +246,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/efficacy/ttet01.qmd b/book/tables/efficacy/ttet01.qmd index 2f55c8090d..41ade0d57f 100644 --- a/book/tables/efficacy/ttet01.qmd +++ b/book/tables/efficacy/ttet01.qmd @@ -394,7 +394,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/exposure/ext01.qmd b/book/tables/exposure/ext01.qmd index 32f1031bdc..44e16025b7 100644 --- a/book/tables/exposure/ext01.qmd +++ b/book/tables/exposure/ext01.qmd @@ -199,7 +199,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt01.qmd b/book/tables/lab-results/lbt01.qmd index c79a99febc..cd617f874e 100644 --- a/book/tables/lab-results/lbt01.qmd +++ b/book/tables/lab-results/lbt01.qmd @@ -87,7 +87,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt02.qmd b/book/tables/lab-results/lbt02.qmd index 04baf6582a..0d45f0d929 100644 --- a/book/tables/lab-results/lbt02.qmd +++ b/book/tables/lab-results/lbt02.qmd @@ -62,7 +62,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt03.qmd b/book/tables/lab-results/lbt03.qmd index 9730ac5f8d..18a2c39bb8 100644 --- a/book/tables/lab-results/lbt03.qmd +++ b/book/tables/lab-results/lbt03.qmd @@ -113,7 +113,7 @@ result Here, we pre-process and manually define the variable "Baseline or Absolute Change from Baseline". -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt04.qmd b/book/tables/lab-results/lbt04.qmd index 8cdc0b6536..ff172af6b6 100644 --- a/book/tables/lab-results/lbt04.qmd +++ b/book/tables/lab-results/lbt04.qmd @@ -58,7 +58,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt06.qmd b/book/tables/lab-results/lbt06.qmd index 0ef30ebb99..d1b0e7d277 100644 --- a/book/tables/lab-results/lbt06.qmd +++ b/book/tables/lab-results/lbt06.qmd @@ -94,7 +94,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/lab-results/lbt07.qmd b/book/tables/lab-results/lbt07.qmd index 7040933f02..d769bf4b9f 100644 --- a/book/tables/lab-results/lbt07.qmd +++ b/book/tables/lab-results/lbt07.qmd @@ -107,7 +107,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt08.qmd b/book/tables/lab-results/lbt08.qmd index e56953903d..800ce7a5bb 100644 --- a/book/tables/lab-results/lbt08.qmd +++ b/book/tables/lab-results/lbt08.qmd @@ -73,7 +73,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/lab-results/lbt09.qmd b/book/tables/lab-results/lbt09.qmd index da22c59c6f..7e34c7bd37 100644 --- a/book/tables/lab-results/lbt09.qmd +++ b/book/tables/lab-results/lbt09.qmd @@ -157,7 +157,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/lab-results/lbt10.qmd b/book/tables/lab-results/lbt10.qmd index cf914d395c..84c2ceeef3 100644 --- a/book/tables/lab-results/lbt10.qmd +++ b/book/tables/lab-results/lbt10.qmd @@ -93,7 +93,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/lab-results/lbt10_bl.qmd b/book/tables/lab-results/lbt10_bl.qmd index 7fcd3c4941..c119fc1d01 100644 --- a/book/tables/lab-results/lbt10_bl.qmd +++ b/book/tables/lab-results/lbt10_bl.qmd @@ -93,7 +93,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/lab-results/lbt11.qmd b/book/tables/lab-results/lbt11.qmd index 4795517392..91105964e2 100644 --- a/book/tables/lab-results/lbt11.qmd +++ b/book/tables/lab-results/lbt11.qmd @@ -134,7 +134,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt11_bl.qmd b/book/tables/lab-results/lbt11_bl.qmd index 52f7367bbc..994cc15b20 100644 --- a/book/tables/lab-results/lbt11_bl.qmd +++ b/book/tables/lab-results/lbt11_bl.qmd @@ -134,7 +134,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt12.qmd b/book/tables/lab-results/lbt12.qmd index 1939dc075c..59adc4da73 100644 --- a/book/tables/lab-results/lbt12.qmd +++ b/book/tables/lab-results/lbt12.qmd @@ -74,7 +74,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/lab-results/lbt12_bl.qmd b/book/tables/lab-results/lbt12_bl.qmd index c7c790f86e..a8c51494bf 100644 --- a/book/tables/lab-results/lbt12_bl.qmd +++ b/book/tables/lab-results/lbt12_bl.qmd @@ -74,7 +74,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/lab-results/lbt13.qmd b/book/tables/lab-results/lbt13.qmd index 6b86c4d1e1..cca87ba93c 100644 --- a/book/tables/lab-results/lbt13.qmd +++ b/book/tables/lab-results/lbt13.qmd @@ -416,7 +416,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt14.qmd b/book/tables/lab-results/lbt14.qmd index c900f4f888..ef9d06bba4 100644 --- a/book/tables/lab-results/lbt14.qmd +++ b/book/tables/lab-results/lbt14.qmd @@ -318,7 +318,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/lab-results/lbt15.qmd b/book/tables/lab-results/lbt15.qmd index 4312d376dd..67d50cf909 100644 --- a/book/tables/lab-results/lbt15.qmd +++ b/book/tables/lab-results/lbt15.qmd @@ -104,7 +104,7 @@ result The current module `tm_t_abnormality` is only displaying rows that are not all-zero, so the result could be a little different from static output where all-zero rows can be shown. -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/medical-history/mht01.qmd b/book/tables/medical-history/mht01.qmd index bcf2999b5a..4aeebbbd6f 100644 --- a/book/tables/medical-history/mht01.qmd +++ b/book/tables/medical-history/mht01.qmd @@ -164,7 +164,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/pharmacokinetic/pkct01.qmd b/book/tables/pharmacokinetic/pkct01.qmd index e246d199e1..5b047b3c31 100644 --- a/book/tables/pharmacokinetic/pkct01.qmd +++ b/book/tables/pharmacokinetic/pkct01.qmd @@ -148,7 +148,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt02.qmd b/book/tables/pharmacokinetic/pkpt02.qmd index f822a5a33b..9eb0a12451 100644 --- a/book/tables/pharmacokinetic/pkpt02.qmd +++ b/book/tables/pharmacokinetic/pkpt02.qmd @@ -86,7 +86,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt03.qmd b/book/tables/pharmacokinetic/pkpt03.qmd index 115b0093e3..d7e7afb762 100644 --- a/book/tables/pharmacokinetic/pkpt03.qmd +++ b/book/tables/pharmacokinetic/pkpt03.qmd @@ -164,7 +164,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt04.qmd b/book/tables/pharmacokinetic/pkpt04.qmd index 2bcd6184f9..eaadfcc737 100644 --- a/book/tables/pharmacokinetic/pkpt04.qmd +++ b/book/tables/pharmacokinetic/pkpt04.qmd @@ -86,7 +86,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt05.qmd b/book/tables/pharmacokinetic/pkpt05.qmd index d32dbe0c67..6c606fd165 100644 --- a/book/tables/pharmacokinetic/pkpt05.qmd +++ b/book/tables/pharmacokinetic/pkpt05.qmd @@ -104,7 +104,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt06.qmd b/book/tables/pharmacokinetic/pkpt06.qmd index ccd34f1ce1..20eed09cc0 100644 --- a/book/tables/pharmacokinetic/pkpt06.qmd +++ b/book/tables/pharmacokinetic/pkpt06.qmd @@ -87,7 +87,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt07.qmd b/book/tables/pharmacokinetic/pkpt07.qmd index c2574a8309..29cfe5838b 100644 --- a/book/tables/pharmacokinetic/pkpt07.qmd +++ b/book/tables/pharmacokinetic/pkpt07.qmd @@ -105,7 +105,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt08.qmd b/book/tables/pharmacokinetic/pkpt08.qmd index 4db386a85c..5c259dd3d9 100644 --- a/book/tables/pharmacokinetic/pkpt08.qmd +++ b/book/tables/pharmacokinetic/pkpt08.qmd @@ -89,7 +89,7 @@ cat(rtables::toString(result, indent_size = 10)) ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/pharmacokinetic/pkpt11.qmd b/book/tables/pharmacokinetic/pkpt11.qmd index 4d61ebcb7d..3209b88d47 100644 --- a/book/tables/pharmacokinetic/pkpt11.qmd +++ b/book/tables/pharmacokinetic/pkpt11.qmd @@ -161,7 +161,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/risk-management-plan/rmpt01.qmd b/book/tables/risk-management-plan/rmpt01.qmd index 921129be5c..8d88d74394 100644 --- a/book/tables/risk-management-plan/rmpt01.qmd +++ b/book/tables/risk-management-plan/rmpt01.qmd @@ -82,7 +82,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/risk-management-plan/rmpt03.qmd b/book/tables/risk-management-plan/rmpt03.qmd index 7e89e57a78..5d1aec4951 100644 --- a/book/tables/risk-management-plan/rmpt03.qmd +++ b/book/tables/risk-management-plan/rmpt03.qmd @@ -115,7 +115,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/risk-management-plan/rmpt04.qmd b/book/tables/risk-management-plan/rmpt04.qmd index f72c1972a3..907a3df4f0 100644 --- a/book/tables/risk-management-plan/rmpt04.qmd +++ b/book/tables/risk-management-plan/rmpt04.qmd @@ -71,7 +71,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/risk-management-plan/rmpt05.qmd b/book/tables/risk-management-plan/rmpt05.qmd index b1c7218856..3ce0c24878 100644 --- a/book/tables/risk-management-plan/rmpt05.qmd +++ b/book/tables/risk-management-plan/rmpt05.qmd @@ -73,7 +73,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/risk-management-plan/rmpt06.qmd b/book/tables/risk-management-plan/rmpt06.qmd index cf72deccc1..d5a422ec26 100644 --- a/book/tables/risk-management-plan/rmpt06.qmd +++ b/book/tables/risk-management-plan/rmpt06.qmd @@ -324,7 +324,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} #| code-fold: show # In progress diff --git a/book/tables/safety/enrollment01.qmd b/book/tables/safety/enrollment01.qmd index 0c981d293f..ac8e897d52 100644 --- a/book/tables/safety/enrollment01.qmd +++ b/book/tables/safety/enrollment01.qmd @@ -126,7 +126,7 @@ result Note that for this module application, only the variables passed into `by_vars` are used when `row_groups` is selected. Variables passed into `analyze_vars` are additionally used when `row_groups` is deselected. -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/vital-signs/vst01.qmd b/book/tables/vital-signs/vst01.qmd index ce1880a6ff..297bb532c4 100644 --- a/book/tables/vital-signs/vst01.qmd +++ b/book/tables/vital-signs/vst01.qmd @@ -125,7 +125,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/tables/vital-signs/vst02.qmd b/book/tables/vital-signs/vst02.qmd index 3c0fe1ecf0..1208524a79 100644 --- a/book/tables/vital-signs/vst02.qmd +++ b/book/tables/vital-signs/vst02.qmd @@ -81,7 +81,7 @@ result ## `teal` App -```{r teal, message=FALSE, opts.label=c('skip_if_testing', 'app')} +```{r teal, opts.label=c('skip_if_testing', 'app')} library(teal.modules.clinical) ## Data reproducible code diff --git a/book/test-utils/envir_hook.qmd b/book/test-utils/envir_hook.qmd index 39a1d301ad..e2ccfd87aa 100644 --- a/book/test-utils/envir_hook.qmd +++ b/book/test-utils/envir_hook.qmd @@ -2,6 +2,9 @@ #| renv.ignore: TRUE knitr::knit_hooks$set(test = function(options, envir, before = FALSE) { + if (isFALSE(testthat::is_checking() || testthat::is_testing())) { + return(NULL) + } if (isFALSE(before)) { if (!exists("tenv", envir = envir)) { envir$tenv <- new.env() @@ -27,7 +30,11 @@ knitr::opts_template$set( screenshot.opts = list(delay = 5), dev = "png", fig.width = 15, - cache = FALSE + cache = FALSE, + message = FALSE, + R.options = list( + teal.log_level = "FATAL" + ) ) ) ```