Merge pull request #91 from ukhsa-collaboration/dsr_ci_non_independent

Dsr ci non independent

.github/workflows/R-CMD-check.yaml

@@ -21,7 +21,7 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
+         # - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}

.gitignore

@@ -33,3 +33,5 @@ vignettes/*.R
 inst/doc
 data-raw
 README.Rmd
+/doc/
+/Meta/

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: PHEindicatormethods
 Type: Package
-Version: 2.0.2
+Version: 2.1.0
 Title: Common Public Health Statistics and their Confidence Intervals 
 Description: Functions to calculate commonly used public health statistics and 
     their confidence intervals using methods approved for use in the production  
     of Public Health England indicators such as those presented via Fingertips 
-    (<http://fingertips.phe.org.uk/>). It provides functions for the generation 
+    (<https://fingertips.phe.org.uk/>). It provides functions for the generation 
     of proportions, crude rates, means, directly standardised rates, indirectly 
     standardised rates, standardised mortality ratios, slope and relative index
     of inequality and life expectancy. 
@@ -20,36 +20,39 @@ Description: Functions to calculate commonly used public health statistics and
     Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
     Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>.
     Low and Low (2004) <doi:10.1093/pubmed/fdh175>.
-Authors@R: c(person("Anderson",   "Georgina",  email = "[email protected]",  role = c("aut", "cre")),
-             person("Fox",        "Sebastian",                                           role = c("ctb")),
-             person("Francis",    "Matthew",                                             role = c("ctb")),
-             person("Fryers",     "Paul",      email = "[email protected]",        role = c("ctb")),
-             person("Clegg",      "Emma",                                                role = c("ctb")),
-             person("Westermann", "Annabel",   email = "[email protected]", role = c("ctb")),
-             person("Woolner",    "Joshua",                                              role = c("ctb")),
-             person("Fellows",    "Charlotte", email = "[email protected]",  role = c("ctb"))
+    Fingertips Public Health Technical Guide: <https://fingertips.phe.org.uk/static-reports/public-health-technical-guidance/>.
+Authors@R: c(person("Georgina", "Anderson", email = "[email protected]", role = c("aut", "cre")),
+             person("Sebastian", "Fox ", role = c("ctb")),
+             person("Matthew", "Francis ", role = c("ctb")),
+             person("Paul", "Fryers ", email = "[email protected]", role = c("ctb")),
+             person("Emma", "Clegg ",  role = c("ctb")),
+             person("Annabel", "Westermann ", role = c("ctb")),
+             person("Joshua", "Woolner ", role = c("ctb")),
+             person("Charlotte", "Fellows ", email = "[email protected]", role = c("ctb")),
+             person("Olivia", "Box Power", email = "[email protected]", role = c("ctb"))
              )
 BugReports: https://github.com/ukhsa-collaboration/PHEindicatormethods/issues
-Depends: R (>= 3.1.0)
+Depends: R (>= 4.3.0)
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Imports: 
-    broom,
+    broom (>= 1.0.0),
     dplyr (>= 1.1.0),
     purrr (>= 1.0.0),
-    rlang (>= 0.4.0),
+    rlang (>= 1.1.0),
     stats,
-    tibble,
+    tibble (>= 3.2.0),
     tidyselect (>= 1.2.0),
-    tidyr (>= 1.3.0)
+    tidyr (>= 1.3.0),
+    lifecycle
 Suggests: 
-    knitr,
-    readxl,
-    rmarkdown,
+    knitr (>= 1.48),
+    readxl (>= 1.4.0),
+    rmarkdown (>= 2.28),
     testthat (>= 3.0.0),
-    withr
+    withr (>= 3.0.0)
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -3,6 +3,7 @@
 export(assign_funnel_significance)
 export(calculate_ISRate)
 export(calculate_ISRatio)
+export(calculate_dsr)
 export(calculate_funnel_limits)
 export(calculate_funnel_points)
 export(phe_dsr)
@@ -14,6 +15,7 @@ export(phe_rate)
 export(phe_sii)
 import(broom)
 import(dplyr)
+importFrom(lifecycle,deprecated)
 importFrom(purrr,map)
 importFrom(purrr,map_chr)
 importFrom(rlang,":=")

NEWS.md

@@ -1,3 +1,11 @@
+## PHEindicatormethods v2.1.0
+This release makes changes to the DSR function
+* `calculate_dsr` function added to replace `phe_dsr`. The new calculate_dsr function has three new features:
+1. Users can now specify whether events are independent.  For non-independent events the data must be broken down by event frequency and the function will perform an adjustment to the confidence interval calculation. 
+2. The stdpoptype argument that was available in `phe_dsr` is not available in `calculate_dsr` and the user is now required to provide the standard populations as a field in the input dataframe. This is to negate the risk of incorrectly joining the standard population vector by position that was possible when using the function with stdpoptype = "vector".
+3. Because of point 2 above, users can now calculate DSRs for groups containing different numbers of age bands in a single execution (for example DSRs for all age populations and DSRs for under 75s).   
+* `phe_dsr` has been soft deprecated - please replace all calls to this function with `calculate_dsr` before September 2025, after which date the phe_dsr function will be removed from the package. Previous calls to `phe_dsr` with stdpoptype set to "field" can be replaced directly with `calculate_dsr`, however, the stdpoptype argument has been deprectaed so will need to be removed and the stdpop argument no longer has a default so this column name will need to be provided explicitly. For previous calls to `phe_dsr` with stdpoptype = "vector", the user will need to append the standard populations to their input data frame before calling the `calculate_dsr` function and provide the stdpop argument explicitly.
+
 ## PHEindicatormethods v2.0.2
 * Amended phe_quantile function so it will not produce quantiles when the number of small areas within a group is less than the number of quantiles requested. A warning will be generated when quantiles cannot be produced for this reason.
 * removed the highergeog argument from phe_quantile function, previously soft-deprecated in v1.2.0.