refac: updated dates to agree with new dataset

epiverse-trace · Nov 24, 2024 · 758e7aa · 758e7aa
1 parent de630f3
commit 758e7aa
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Showing 18 changed files with 48 additions and 48 deletions.
diff --git a/R/estimate_vaccineff.R b/R/estimate_vaccineff.R
@@ -36,7 +36,7 @@
 #'   vaccinated_status = "v",
 #'   unvaccinated_status = "u",
 #'   immunization_delay = 15,
-#'   end_cohort = as.Date("2044-12-31"),
+#'   end_cohort = as.Date("2021-12-31"),
 #'   match = TRUE,
 #'   exact = c("age", "sex"),
 #'   nearest = NULL

diff --git a/R/make_vaccineff_data.R b/R/make_vaccineff_data.R
@@ -46,7 +46,7 @@
 #'   vaccinated_status = "v",
 #'   unvaccinated_status = "u",
 #'   immunization_delay = 15,
-#'   end_cohort = as.Date("2044-12-31"),
+#'   end_cohort = as.Date("2021-12-31"),
 #'   match = TRUE,
 #'   exact = c("age", "sex"),
 #'   nearest = NULL

diff --git a/README.Rmd b/README.Rmd
@@ -71,7 +71,7 @@ vaccineff_data <- make_vaccineff_data(
   vaccinated_status = "v",
   unvaccinated_status = "u",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = TRUE,
   exact = "sex",
   nearest = c(age = 1)

diff --git a/tests/testthat/_snaps/coh_immunization.md b/tests/testthat/_snaps/coh_immunization.md
@@ -3,19 +3,19 @@
     Code
       head(immunization_dose, 20)
     Output
-       [1] NA               NA               NA               NA              
-       [5] NA               "vaccine_date_2" NA               NA              
-       [9] "vaccine_date_2" "vaccine_date_2" NA               "vaccine_date_2"
-      [13] NA               NA               NA               NA              
-      [17] NA               "vaccine_date_2" "vaccine_date_2" "vaccine_date_2"
+       [1] NA               NA               NA               "vaccine_date_2"
+       [5] "vaccine_date_2" "vaccine_date_2" NA               "vaccine_date_2"
+       [9] NA               NA               NA               "vaccine_date_2"
+      [13] "vaccine_date_2" "vaccine_date_2" "vaccine_date_2" "vaccine_date_2"
+      [17] "vaccine_date_2" "vaccine_date_2" "vaccine_date_2" "vaccine_date_2"
 
 # `immunization_vaccine`: Basic expectations
 
     Code
       head(which_vaccine, 30)
     Output
-       [1] NA       NA       NA       NA       NA       "BRAND1" NA       NA      
-       [9] "BRAND1" "BRAND1" NA       "BRAND2" NA       NA       NA       NA      
-      [17] NA       "BRAND2" "BRAND1" "BRAND2" NA       "BRAND1" NA       NA      
-      [25] NA       NA       "BRAND2" NA       NA       NA      
+       [1] NA       NA       NA       "BRAND2" "BRAND1" "BRAND2" NA       "BRAND2"
+       [9] NA       NA       NA       "BRAND1" "BRAND1" "BRAND2" "BRAND2" "BRAND2"
+      [17] "BRAND1" "BRAND1" "BRAND1" "BRAND1" "BRAND2" "BRAND2" NA       NA      
+      [25] "BRAND2" "BRAND1" "BRAND2" NA       NA       "BRAND2"
 
diff --git a/tests/testthat/_snaps/coh_match.md b/tests/testthat/_snaps/coh_match.md
@@ -33,17 +33,17 @@
             {
               "type": "double",
               "attributes": {},
-              "value": [30.18416801, 0.5088853, 0.4911147]
+              "value": [63.23626374, 0.52197802, 0.47802198]
             },
             {
               "type": "double",
               "attributes": {},
-              "value": [47.51706037, 0.54855643, 0.45144357]
+              "value": [63.66823899, 0.59748428, 0.40251572]
             },
             {
               "type": "double",
               "attributes": {},
-              "value": [0.87245622, 0.0795363, -0.0795363]
+              "value": [0.03984279, 0.15254353, -0.15254353]
             }
           ]
         }
@@ -85,17 +85,17 @@
             {
               "type": "double",
               "attributes": {},
-              "value": [42.55192878, 0.54599407, 0.45400593]
+              "value": [63.2005571, 0.52089136, 0.47910864]
             },
             {
               "type": "double",
               "attributes": {},
-              "value": [44.90801187, 0.54599407, 0.45400593]
+              "value": [63.54038997, 0.52089136, 0.47910864]
             },
             {
               "type": "double",
               "attributes": {},
-              "value": [0.12717971, 0, 0]
+              "value": [0.03161695, 0, 0]
             }
           ]
         }
@@ -137,12 +137,12 @@
             {
               "type": "integer",
               "attributes": {},
-              "value": [619, 337, 282]
+              "value": [364, 359, 5]
             },
             {
               "type": "integer",
               "attributes": {},
-              "value": [381, 337, 44]
+              "value": [636, 359, 277]
             }
           ]
         }

diff --git a/tests/testthat/_snaps/coh_match_utils.md b/tests/testthat/_snaps/coh_match_utils.md
@@ -4,7 +4,7 @@
       summary
     Output
                   u   v
-      All       619 381
-      Matched   337 337
-      Unmatched 282  44
+      All       364 636
+      Matched   359 359
+      Unmatched   5 277
 
diff --git a/tests/testthat/_snaps/coh_time_to_event.md b/tests/testthat/_snaps/coh_time_to_event.md
@@ -3,6 +3,6 @@
     Code
       head(exposition_time, 20)
     Output
-       [1] 280 280 162 171 169 280 280  37 280 280 280 280 280 280 280 280 171 213 280
-      [20]  98
+       [1] 152 161 167 224 221 242 281 183 281 250 165 281 194 281 123 225 281 281 281
+      [20] 281
 
diff --git a/tests/testthat/test-coh_eff_plot.R b/tests/testthat/test-coh_eff_plot.R
@@ -17,7 +17,7 @@ vaccineff_data <- make_vaccineff_data(
   vaccinated_status = "v",
   unvaccinated_status = "u",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = FALSE
 )
 

diff --git a/tests/testthat/test-coh_immunization.R b/tests/testthat/test-coh_immunization.R
@@ -1,16 +1,16 @@
 #### Tests for coh_immunization.R module ####
 #### Prepare data for all the tests ####
 data("cohortdata")
-start_cohort <- as.Date("2044-01-01")
-end_cohort <- as.Date("2044-12-31")
+start_cohort <- as.Date("2021-01-01")
+end_cohort <- as.Date("2021-12-31")
 # calculate immunization date
 cohortdata$immunization <- get_immunization_date(
   data_set = cohortdata,
   outcome_date_col = "death_date",
   censoring_date_col = "death_other_causes",
   immunization_delay = 14,
   vacc_date_col = c("vaccine_date_1", "vaccine_date_2"),
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   take_first = FALSE
 )
 
@@ -103,7 +103,7 @@ test_that("`make_immunization`: vaccine names provided", {
 test_that("`get_immunization_date`: Basic expectations", {
   # get immunization dates
   vacc_date_col <- c("vaccine_date_1", "vaccine_date_2")
-  tf <- as.Date("2044-12-31")
+  tf <- as.Date("2021-12-31")
   immunization_delay <- 45 # use extreme outcome delay to test expectations
   limit_delta <- immunization_delay
   cohortdata$immunization <- get_immunization_date(
@@ -208,7 +208,7 @@ test_that("`get_immunization_date`: Basic expectations", {
 test_that("`get_immunization_date`: Take first vaccination", {
   # get immunization dates
   vacc_date_col <- c("vaccine_date_1", "vaccine_date_2")
-  tf <- as.Date("2044-12-31")
+  tf <- as.Date("2021-12-31")
   immunization_delay <- 45 # use extreme outcome delay to test expectations
   limit_delta <- immunization_delay
   cohortdata$immunization <- get_immunization_date(
@@ -273,8 +273,8 @@ test_that("`get_immunization_date`: Take first vaccination", {
 # Test coherence immunization date and end_cohort date
 test_that("`get_immunization_date`: end_cohort > immunization", {
   date_format <- "%Y-%m-%d"
-  t0 <- as.Date("2044-01-01", date_format)
-  tf <- as.Date("2044-12-31", date_format)
+  t0 <- as.Date("2021-01-01", date_format)
+  tf <- as.Date("2021-12-31", date_format)
   immunization_delay <- 14
   data(cohortdata)
 

diff --git a/tests/testthat/test-coh_match.R b/tests/testthat/test-coh_match.R
@@ -1,8 +1,8 @@
 #### Tests for coh_match.R module ####
 #### Prepare data for all the tests ####
 data("cohortdata")
-start_cohort <- as.Date("2044-01-01")
-end_cohort <- as.Date("2044-12-31")
+start_cohort <- as.Date("2021-01-01")
+end_cohort <- as.Date("2021-12-31")
 
 # Sample cohort to make tests faster - take a bigger sample
 sample_size <- 1000

diff --git a/tests/testthat/test-coh_match_iterate.R b/tests/testthat/test-coh_match_iterate.R
@@ -1,8 +1,8 @@
 #### Tests for coh_match_iterate.R module ####
 #### Prepare data for all the tests ####
 data("cohortdata")
-start_cohort <- as.Date("2044-01-01")
-end_cohort <- as.Date("2044-12-31")
+start_cohort <- as.Date("2021-01-01")
+end_cohort <- as.Date("2021-12-31")
 
 # sample cohort to make tests faster - take a bigger sample
 sample_size <- 10000

diff --git a/tests/testthat/test-coh_match_utils.R b/tests/testthat/test-coh_match_utils.R
@@ -1,8 +1,8 @@
 #### Tests for coh_match_utils.R module ####
 #### Prepare data for all tests ####
 data("cohortdata")
-start_cohort <- as.Date("2044-01-01")
-end_cohort <- as.Date("2044-12-31")
+start_cohort <- as.Date("2021-01-01")
+end_cohort <- as.Date("2021-12-31")
 
 # tests for match_cohort_() and match_summary can use the small data
 sample_size <- 1000

diff --git a/tests/testthat/test-coh_time_to_event.R b/tests/testthat/test-coh_time_to_event.R
@@ -1,7 +1,7 @@
 #### Tests for coh_time_to_event.R module ####
 #### Prepare data for all the tests ####
 data("cohortdata")
-end_cohort <- as.Date("2044-12-31")
+end_cohort <- as.Date("2021-12-31")
 
 # sample cohort to make tests faster - take a bigger sample
 sample_size <- 10000

diff --git a/tests/testthat/test-estimate_vaccineff.R b/tests/testthat/test-estimate_vaccineff.R
@@ -17,7 +17,7 @@ vaccineff_data <- make_vaccineff_data(
   vaccinated_status = "v",
   unvaccinated_status = "u",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = TRUE,
   exact = c("age", "sex"),
   nearest = NULL

diff --git a/tests/testthat/test-handler_validations.R b/tests/testthat/test-handler_validations.R
@@ -10,8 +10,8 @@ vacc_name_col <- "vaccine_2"
 vaccinated_status <- "v"
 unvaccinated_status <- "u"
 immunization_delay <- 0
-start_cohort <- as.Date("2044-01-31")
-end_cohort <- as.Date("2044-12-31")
+start_cohort <- as.Date("2021-01-31")
+end_cohort <- as.Date("2021-12-31")
 match <- NULL
 nearest <- NULL
 exact <- NULL

diff --git a/tests/testthat/test-utils_coverage.R b/tests/testthat/test-utils_coverage.R
@@ -17,7 +17,7 @@ vaccineff_data <- make_vaccineff_data(
   vaccinated_status = "1 vacc",
   unvaccinated_status = "0 unvacc",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = TRUE,
   exact = c("age", "sex"),
   nearest = NULL

diff --git a/vignettes/cohort_design.Rmd b/vignettes/cohort_design.Rmd
@@ -59,7 +59,7 @@ vaccineff_data <- make_vaccineff_data(
   vaccinated_status = "v",
   unvaccinated_status = "u",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = FALSE
 )
 
@@ -111,7 +111,7 @@ vaccineff_data_matched <- make_vaccineff_data(
   vaccinated_status = "v",
   unvaccinated_status = "u",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = TRUE,
   exact = c("age", "sex"),
   nearest = NULL
@@ -158,7 +158,7 @@ vaccineff_data_matched2 <- make_vaccineff_data(
   vaccinated_status = "v",
   unvaccinated_status = "u",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = TRUE,
   exact = "sex",
   nearest = c(age = 2)

diff --git a/vignettes/vaccineff.Rmd b/vignettes/vaccineff.Rmd
@@ -94,7 +94,7 @@ vaccineff_data <- make_vaccineff_data(
   vaccinated_status = "v",
   unvaccinated_status = "u",
   immunization_delay = 15,
-  end_cohort = as.Date("2044-12-31"),
+  end_cohort = as.Date("2021-12-31"),
   match = TRUE,
   exact = c("age", "sex"),
   nearest = NULL