Update_vars_dict

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sitrep
 Title: Report Templates and Helper Functions for Applied Epidemiology
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Alexander", "Spina", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8425-1867")),

NEWS.md

@@ -1,3 +1,6 @@
+# sitrep 0.4.0
+* minor changes to variables in templates 
+
 # sitrep 0.3.0
 
 * bump version of epidict package to latest - allowing for msf_dict_rename() helper function

cran-comments.md

@@ -13,4 +13,4 @@ Ubuntu-latest, R-oldrel-1
 
 0 errors | 0 warnings | 0 note
 
-* minor release to include latest version of package dependency 
+* minor release with changes to templates

inst/rmarkdown/templates/ajs_intersectional_outbreak/skeleton/skeleton.Rmd

@@ -241,10 +241,10 @@ linelist_raw |>
          adm2_residence,
          adm3_residence,
          status,
-         vacci_hev_dose1_yn, 
-         vacci_hev_dose2_yn,
-         vacci_hev_dose3_yn,
-         hev_rt_result,
+         vacci_HEV_dose1_yn, 
+         vacci_HEV_dose2_yn,
+         vacci_HEV_dose3_yn,
+         HEV_RT_result,
          pregnant_yn,
          post_partum,
          outcome,
@@ -396,27 +396,27 @@ linelist_cleaned <- linelist_cleaned |>
 ## Vaccination columns combined into 1
 linelist_cleaned <- linelist_cleaned |> 
   mutate(
-    vacci_hev_dose1 = str_detect(vacci_hev_dose1_yn, "Yes"),
-    vacci_hev_dose2 = str_detect(vacci_hev_dose2_yn, "Yes"),
-    vacci_hev_dose3 = str_detect(vacci_hev_dose3_yn, "Yes"),
+    vacci_HEV_dose1 = str_detect(vacci_HEV_dose1_yn, "Yes"),
+    vacci_HEV_dose2 = str_detect(vacci_HEV_dose2_yn, "Yes"),
+    vacci_HEV_dose3 = str_detect(vacci_HEV_dose3_yn, "Yes"),
 
-    vacci_hev_doses = case_when(
-      vacci_hev_dose1 & vacci_hev_dose2 & vacci_hev_dose3 ~ "3 doses",
-      vacci_hev_dose1 & vacci_hev_dose2 ~ "2 doses",
-      vacci_hev_dose1 ~ "1 dose",
-      vacci_hev_dose1_yn == "No" & (is.na(vacci_hev_dose2_yn) & is.na(vacci_hev_dose3_yn)) ~ "0 doses",
-      vacci_hev_dose1_yn == "No" & vacci_hev_dose2_yn == "No" & is.na(vacci_hev_dose3_yn) ~ "0 doses",
-      vacci_hev_dose1_yn == "No" & vacci_hev_dose2_yn == "No" & vacci_hev_dose3_yn == "No" ~ "0 doses",
-      is.na(vacci_hev_dose1_yn) & is.na(vacci_hev_dose2_yn) & is.na(vacci_hev_dose3_yn) ~ NA,
+    vacci_HEV_doses = case_when(
+      vacci_HEV_dose1 & vacci_HEV_dose2 & vacci_HEV_dose3 ~ "3 doses",
+      vacci_HEV_dose1 & vacci_HEV_dose2 ~ "2 doses",
+      vacci_HEV_dose1 ~ "1 dose",
+      vacci_HEV_dose1_yn == "No" & (is.na(vacci_HEV_dose2_yn) & is.na(vacci_HEV_dose3_yn)) ~ "0 doses",
+      vacci_HEV_dose1_yn == "No" & vacci_HEV_dose2_yn == "No" & is.na(vacci_HEV_dose3_yn) ~ "0 doses",
+      vacci_HEV_dose1_yn == "No" & vacci_HEV_dose2_yn == "No" & vacci_HEV_dose3_yn == "No" ~ "0 doses",
+      is.na(vacci_HEV_dose1_yn) & is.na(vacci_HEV_dose2_yn) & is.na(vacci_HEV_dose3_yn) ~ NA,
       TRUE ~ "Unclear"  # fallback for any mixed or inconsistent case
     )
   ) |> 
-  select(-vacci_hev_dose1, -vacci_hev_dose2, -vacci_hev_dose3)
+  select(-vacci_HEV_dose1, -vacci_HEV_dose2, -vacci_HEV_dose3)
 
 ##  Test results
 linelist_cleaned <- linelist_cleaned |> 
 
-  mutate(hev_rt_result = factor(hev_rt_result,
+  mutate(HEV_RT_result = factor(HEV_RT_result,
                              levels = c("Positive",
                                         "Negative", 
                                         "Not done"))) |> 
@@ -772,11 +772,11 @@ _Percentages calculated among those with non-missing vaccine or rapid test infor
 ```{r vaccination_test}
 
 linelist_cleaned |> 
-  select(vacci_hev_doses, age_group, hev_rt_result) |> 
+  select(vacci_HEV_doses, age_group, HEV_RT_result) |> 
   tbl_summary(percent = "column",
               by = "age_group",
-              label = list(vacci_hev_doses = "Number of HEV vaccine doses",
-                           hev_rt_result = "HEV Rapid Test results "),
+              label = list(vacci_HEV_doses = "Number of HEV vaccine doses",
+                           HEV_RT_result = "HEV Rapid Test results "),
               missing_text = "[Missing]") |> 
   add_overall()  |>
   ## make variable names bold