diff --git a/404.html b/404.html index e2a51f3b..7304ab4f 100644 --- a/404.html +++ b/404.html @@ -27,7 +27,7 @@ DrugUtilisation - 0.8.0 + 0.8.1
library(DrugUtilisation)
+#> Error in get(paste0(generic, ".", class), envir = get_method_env()) :
+#> object 'type_sum.accel' not found
cdm <- mockDrugUtilisation(numberIndividuals = 100, seed = 1)
@@ -279,8 +281,8 @@ Create your cohort
cdm$drug_exposure |>
dplyr::filter(drug_concept_id %in% !!codes$acetaminophen & person_id == 69)
-#> # Source: SQL [4 x 23]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Source: SQL [?? x 23]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> drug_exposure_id person_id drug_concept_id drug_exposure_start_date
#> <int> <int> <int> <date>
#> 1 201 69 2905077 2002-01-29
@@ -297,8 +299,8 @@ Create your cohort
cdm$acetaminophen_cohort |>
dplyr::filter(subject_id == 69)
-#> # Source: SQL [1 x 4]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Source: SQL [?? x 4]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
#> 1 1 69 2001-03-04 2004-06-02
cdm$drug_exposure |>
dplyr::filter(drug_concept_id %in% !!codes$acetaminophen & person_id == 50)
-#> # Source: SQL [2 x 23]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Source: SQL [?? x 23]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> drug_exposure_id person_id drug_concept_id drug_exposure_start_date
#> <int> <int> <int> <date>
#> 1 143 50 1125360 2017-04-14
@@ -336,8 +338,8 @@ Create your cohort
cdm$acetaminophen_cohort |>
dplyr::filter(subject_id == 50)
-#> # Source: SQL [1 x 4]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Source: SQL [?? x 4]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
#> 1 1 50 2017-04-01 2017-04-23
@@ -399,19 +401,19 @@
cdm$acetaminophen_cohort
#> # Source: table<main.acetaminophen_cohort> [?? x 4]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
#> 1 1 35 2005-11-10 2006-09-09
-#> 2 1 73 2011-04-02 2011-06-19
-#> 3 1 23 2003-10-29 2003-11-27
-#> 4 1 44 2017-01-01 2018-03-30
-#> 5 1 57 2020-04-17 2020-11-19
-#> 6 1 77 1966-09-15 1966-12-27
-#> 7 1 99 2015-02-03 2020-11-01
-#> 8 1 45 2017-07-03 2018-07-06
-#> 9 1 25 2020-01-04 2020-02-05
-#> 10 1 87 2020-10-02 2021-01-02
+#> 2 1 23 2003-10-29 2003-11-27
+#> 3 1 44 2017-01-01 2018-03-30
+#> 4 1 73 2011-04-02 2011-06-19
+#> 5 1 45 2017-07-03 2018-07-06
+#> 6 1 25 2020-01-04 2020-02-05
+#> 7 1 87 2020-10-02 2021-01-02
+#> 8 1 57 2020-04-17 2020-11-19
+#> 9 1 77 1966-09-15 1966-12-27
+#> 10 1 99 2015-02-03 2020-11-01
#> # ℹ more rows
This would also get recorded in the attrition, counts and
settings.
@@ -508,19 +510,19 @@
cdm$acetaminophen_cohort
#> # Source: table<main.acetaminophen_cohort> [?? x 4]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
-#> 1 1 69 2001-03-04 2004-06-02
-#> 2 1 72 2009-12-10 2010-03-30
-#> 3 1 94 2000-10-10 2004-08-16
-#> 4 1 97 1991-02-09 1991-10-07
-#> 5 1 35 2005-11-10 2006-09-09
-#> 6 1 39 2022-02-09 2022-06-11
-#> 7 1 91 2022-09-15 2022-11-17
-#> 8 1 14 1990-04-27 1990-05-12
-#> 9 1 46 2004-06-27 2011-05-07
-#> 10 1 47 1963-12-22 1965-09-16
+#> 1 1 9 2016-03-17 2016-09-02
+#> 2 1 48 1972-04-14 1972-12-18
+#> 3 1 92 2012-12-03 2013-04-18
+#> 4 1 35 2005-11-10 2006-09-09
+#> 5 1 39 2022-02-09 2022-06-11
+#> 6 1 91 2022-09-15 2022-11-17
+#> 7 1 45 2017-07-03 2018-07-06
+#> 8 1 95 2001-06-13 2010-01-28
+#> 9 1 14 1990-04-27 1990-05-12
+#> 10 1 46 2004-06-27 2011-05-07
#> # ℹ more rows
This would also get recorded in the attrition, counts and settings on
top of the already exiting ones.
@@ -565,19 +567,19 @@
cdm$acetaminophen_cohort
#> # Source: table<main.acetaminophen_cohort> [?? x 4]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
-#> 1 1 97 1991-02-09 1991-10-07
+#> 1 1 48 1972-04-14 1972-12-18
#> 2 1 35 2005-11-10 2006-09-09
#> 3 1 91 2022-09-15 2022-11-17
-#> 4 1 14 1990-04-27 1990-05-12
-#> 5 1 46 2004-06-27 2011-05-07
-#> 6 1 47 1963-12-22 1965-09-16
-#> 7 1 3 1996-09-13 2008-07-15
-#> 8 1 42 2002-09-15 2007-12-19
-#> 9 1 75 2010-06-16 2011-09-20
-#> 10 1 48 1972-04-14 1972-12-18
+#> 4 1 45 2017-07-03 2018-07-06
+#> 5 1 95 2001-06-13 2010-01-28
+#> 6 1 14 1990-04-27 1990-05-12
+#> 7 1 46 2004-06-27 2011-05-07
+#> 8 1 47 1963-12-22 1965-09-16
+#> 9 1 97 1991-02-09 1991-10-07
+#> 10 1 17 2000-08-24 2003-02-19
#> # ℹ more rows
This would also get recorded in the attrition, counts and settings on
top of the already exiting ones.
@@ -630,19 +632,19 @@
cdm$acetaminophen_cohort
#> # Source: table<main.acetaminophen_cohort> [?? x 4]
-#> # Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> # Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> cohort_definition_id subject_id cohort_start_date cohort_end_date
#> <int> <int> <date> <date>
#> 1 1 35 2005-11-10 2006-09-09
-#> 2 1 46 2004-06-27 2011-05-07
-#> 3 1 42 2002-09-15 2007-12-19
-#> 4 1 75 2010-06-16 2011-09-20
-#> 5 1 29 2020-12-08 2021-01-09
-#> 6 1 93 2014-01-09 2016-06-21
-#> 7 1 36 2018-06-17 2018-10-24
-#> 8 1 17 2000-08-24 2003-02-19
-#> 9 1 87 2020-10-02 2021-01-02
-#> 10 1 96 2011-05-25 2013-01-23
+#> 2 1 45 2017-07-03 2018-07-06
+#> 3 1 95 2001-06-13 2010-01-28
+#> 4 1 46 2004-06-27 2011-05-07
+#> 5 1 17 2000-08-24 2003-02-19
+#> 6 1 87 2020-10-02 2021-01-02
+#> 7 1 96 2011-05-25 2013-01-23
+#> 8 1 29 2020-12-08 2021-01-09
+#> 9 1 93 2014-01-09 2016-06-21
+#> 10 1 88 2015-08-19 2016-05-09
#> # ℹ more rows
This would also get recorded in the attrition, counts and settings on
top of the already exiting ones.
diff --git a/articles/daily_dose_calculation.html b/articles/daily_dose_calculation.html
index 38df1acc..bd9d23d6 100644
--- a/articles/daily_dose_calculation.html
+++ b/articles/daily_dose_calculation.html
@@ -26,7 +26,7 @@
DrugUtilisation
- 0.8.0
+ 0.8.1
@@ -96,24 +96,26 @@ Daily dose
library(DrugUtilisation)
+#> Error in get(paste0(generic, ".", class), envir = get_method_env()) :
+#> object 'type_sum.accel' not found
cdm <- mockDrugUtilisation(numberIndividuals = 100, seed = 123456)
cdm$drug_strength |>
dplyr::glimpse()
#> Rows: ??
#> Columns: 12
-#> Database: DuckDB v1.1.3 [unknown@Linux 6.5.0-1025-azure:R 4.4.2/:memory:]
+#> Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1017-azure:R 4.4.2/:memory:]
#> $ drug_concept_id <int> 1125315, 1125360, 1503297, 1503327, 150332…
#> $ ingredient_concept_id <int> 1125315, 1125315, 1503297, 1503297, 150329…
-#> $ amount_value <dbl> NA, 5.0e+02, NA, 1.0e+03, 5.0e+02, NA, NA,…
-#> $ amount_unit_concept_id <int> 8576, 8576, 8576, 8576, 8576, 8510, NA, NA…
-#> $ numerator_value <dbl> NA, NA, NA, NA, NA, NA, 100, 300, NA, NA, …
-#> $ numerator_unit_concept_id <int> NA, NA, NA, NA, NA, NA, 8510, 8510, NA, NA…
-#> $ denominator_value <dbl> NA, NA, NA, NA, NA, NA, NA, 3, NA, NA, NA,…
-#> $ denominator_unit_concept_id <int> NA, NA, NA, NA, NA, NA, 8587, 8587, NA, NA…
-#> $ box_size <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
+#> $ amount_value <dbl> NA, 5.0e+02, NA, 1.0e+03, 5.0e+02, NA, NA,…
+#> $ amount_unit_concept_id <int> 8576, 8576, 8576, 8576, 8576, 8510, NA, NA…
+#> $ numerator_value <dbl> NA, NA, NA, NA, NA, NA, 100, 300, NA, NA, …
+#> $ numerator_unit_concept_id <int> NA, NA, NA, NA, NA, NA, 8510, 8510, NA, NA…
+#> $ denominator_value <dbl> NA, NA, NA, NA, NA, NA, NA, 3, NA, NA, NA,…
+#> $ denominator_unit_concept_id <int> NA, NA, NA, NA, NA, NA, 8587, 8587, NA, NA…
+#> $ box_size <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
#> $ valid_start_date <date> 1-01-19, 1-01-19, 1-01-19, 1-01-19, 1-01-…
#> $ valid_end_date <date> 31-12-20, 31-12-20, 31-12-20, 31-12-20, 3…
-#> $ invalid_reason <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
+#> $ invalid_reason <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
You can read the documentation of the drug strength table and description of the different fields here: https://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:drug_strength.
Not all drug concept ids and ingredient concept ids can be related, @@ -152,44 +154,44 @@