Merge pull request #117 from nutriverse:dev

update CITATION

NAMESPACE

@@ -6,7 +6,7 @@ export(calculate_dead)
 export(calculate_default)
 export(calculate_los)
 export(calculate_los_median)
-export(calculate_median_muac)
+export(calculate_muac_median)
 export(calculate_no_response)
 export(calculate_performance)
 export(calculate_rout)

R/muac_at_admission.R

@@ -13,13 +13,14 @@
 #'   median mid-upper arm circumference with names from each level of `index`.
 #'
 #' @examples
-#' calculate_median_muac(otp_beneficiaries$muac)
-#' calculate_median_muac(otp_beneficiaries$muac, otp_beneficiaries$locality)
+#' calculate_muac_median(otp_beneficiaries$muac)
+#' calculate_muac_median(otp_beneficiaries$muac, otp_beneficiaries$locality)
 #' 
 #' @export
+#' @rdname calculate_muac
 #' 
 
-calculate_median_muac <- function(muac, index = NULL, na_values = NULL) {
+calculate_muac_median <- function(muac, index = NULL, na_values = NULL) {
   if (!is.null(na_values)) {
     muac <- ifelse(muac %in% na_values, NA_real_, muac)
   }
@@ -38,3 +39,22 @@ calculate_median_muac <- function(muac, index = NULL, na_values = NULL) {
 
   median_muac
 }
+
+
+calculate_muac_median_count <- function(muac, n, index = NULL) {
+  if (is.null(index)) {
+    Map(f = rep, x = muac, times = n) |>
+      unlist() |>
+      median(na.rm = TRUE)
+  } else {
+    split(data.frame(muac, n), f = index) |> 
+      lapply(
+        FUN = function(x) Map(f = rep, x = x$muac, times = x$n) |> unlist()
+      ) |> 
+      lapply(FUN = median, na.rm = TRUE) |> 
+      (\(x) do.call(rbind, x))() |>
+      (\(x) data.frame(
+        index = row.names(x), median_muac = x, row.names = NULL
+      ))()
+  }
+}

README.md

@@ -133,18 +133,18 @@ monitoring |>
 which results in the following:
 
     #> # A tibble: 72 × 7
-    #>    State        Year  total_discharge cure_rate default_rate death_rate
-    #>    <chr>        <chr>           <dbl>     <dbl>        <dbl>      <dbl>
-    #>  1 Blue Nile    2016             9693     0.889       0.0906    0.0151 
-    #>  2 Blue Nile    2017            10286     0.948       0.0399    0.00972
-    #>  3 Blue Nile    2018             8807     0.947       0.0404    0.00863
-    #>  4 Blue Nile    2019             9882     0.953       0.0366    0.00708
-    #>  5 Central Dar… 2016            13313     0.921       0.0440    0.0174 
-    #>  6 Central Dar… 2017            18098     0.935       0.0421    0.00912
-    #>  7 Central Dar… 2018            17600     0.939       0.0364    0.00955
-    #>  8 Central Dar… 2019            18573     0.952       0.0260    0.00549
-    #>  9 East Darfur  2016             9895     0.929       0.0550    0.0104 
-    #> 10 East Darfur  2017            12611     0.956       0.0327    0.00690
+    #>    State       Year  total_discharge cure_rate default_rate death_rate
+    #>    <chr>       <chr>           <dbl>     <dbl>        <dbl>      <dbl>
+    #>  1 Blue Nile   2016             9693     0.889       0.0906    0.0151 
+    #>  2 Blue Nile   2017            10286     0.948       0.0399    0.00972
+    #>  3 Blue Nile   2018             8807     0.947       0.0404    0.00863
+    #>  4 Blue Nile   2019             9882     0.953       0.0366    0.00708
+    #>  5 Central Da… 2016            13313     0.921       0.0440    0.0174 
+    #>  6 Central Da… 2017            18098     0.935       0.0421    0.00912
+    #>  7 Central Da… 2018            17600     0.939       0.0364    0.00955
+    #>  8 Central Da… 2019            18573     0.952       0.0260    0.00549
+    #>  9 East Darfur 2016             9895     0.929       0.0550    0.0104 
+    #> 10 East Darfur 2017            12611     0.956       0.0327    0.00690
     #> # ℹ 62 more rows
     #> # ℹ 1 more variable: non_response_rate <dbl>
 
@@ -256,25 +256,25 @@ citation provided by a call to the `citation` function as follows:
 
 ``` r
 citation("squeacr")
-#> To cite squeacr in publications use:
+#> To cite sleacr in publications use:
 #> 
-#>   Myatt, Mark, Guevarra, Ernest, Fieschi, Lionella, Norris,
-#>   Allison, Guerrero, Saul, Schofield, Lilly, Jones, Daniel,
-#>   Emru, Ephrem, Sadler, Kate (2012). _Semi-Quantitative
-#>   Evaluation of Access and Coverage (SQUEAC)/Simplified Lot
-#>   Quality Assurance Sampling Evaluation of Access and Coverage
-#>   (SLEAC) Technical Reference_.
+#>   Mark Myatt, Ernest Guevarra, Lionella Fieschi, Allison
+#>   Norris, Saul Guerrero, Lilly Schofield, Daniel Jones, Ephrem
+#>   Emru, Kate Sadler (2012). _Semi-Quantitative Evaluation of
+#>   Access and Coverage (SQUEAC)/Simplified Lot Quality
+#>   Assurance Sampling Evaluation of Access and Coverage (SLEAC)
+#>   Technical Reference_. FHI 360/FANTA, Washington, DC.
 #>   <https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
-#>   @Manual{,
-#>     location = {Washington, DC},
+#>   @Book{,
 #>     title = {Semi-Quantitative Evaluation of Access and Coverage ({SQUEAC})/Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage ({SLEAC}) Technical Reference},
-#>     url = {https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf},
-#>     publisher = {FHI 360/FANTA},
-#>     author = {{Myatt} and {Mark} and {Guevarra} and {Ernest} and {Fieschi} and {Lionella} and {Norris} and {Allison} and {Guerrero} and {Saul} and {Schofield} and {Lilly} and {Jones} and {Daniel} and {Emru} and {Ephrem} and {Sadler} and {Kate}},
+#>     author = {{Mark Myatt} and {Ernest Guevarra} and {Lionella Fieschi} and {Allison Norris} and {Saul Guerrero} and {Lilly Schofield} and {Daniel Jones} and {Ephrem Emru} and {Kate Sadler}},
 #>     year = {2012},
+#>     publisher = {FHI 360/FANTA},
+#>     address = {Washington, DC},
+#>     url = {https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf},
 #>   }
 ```
 

inst/CITATION

@@ -1,10 +1,10 @@
 bibentry(
-  bibtype   = "Manual",
-  header    = "To cite squeacr in publications use:",
-	location  = "Washington, DC",
+  bibtype   = "Book",
+  header    = "To cite sleacr in publications use:",
 	title     = "Semi-Quantitative Evaluation of Access and Coverage ({SQUEAC})/Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage ({SLEAC}) Technical Reference",
-	url       = "https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf",
-	publisher = "FHI 360/FANTA",
-	author    = "Myatt, Mark and Guevarra, Ernest and Fieschi, Lionella and Norris, Allison and Guerrero, Saul and Schofield, Lilly and Jones, Daniel and Emru, Ephrem and Sadler, Kate",
-	year      = "2012"
-)
+	author    = c(person("Mark Myatt"), person("Ernest Guevarra"), person("Lionella Fieschi"), person("Allison Norris"), person("Saul Guerrero"), person("Lilly Schofield"), person("Daniel Jones"), person("Ephrem Emru"), person("Kate Sadler")),
+  year      = "2012",
+  publisher = "FHI 360/FANTA",
+  address   = "Washington, DC",
+	url       = "https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf"
+)

pkgdown/_pkgdown.yml

@@ -61,7 +61,7 @@ reference:
 
   - title: MUAC-at-admission
     contents:
-    - calculate_median_muac
+    - calculate_muac_median
 
   - title: Length of stay
     contents:

tests/testthat/test-muac_at_admission.R

@@ -1,9 +1,9 @@
 # Tests for calculate_median_muac function -------------------------------------
 
 test_that("calculate_median_muac works as expected", {
-  expect_type(calculate_median_muac(otp_beneficiaries$muac), "double")
+  expect_type(calculate_muac_median(otp_beneficiaries$muac), "double")
   expect_type(
-    calculate_median_muac(otp_beneficiaries$muac, otp_beneficiaries$locality),
+    calculate_muac_median(otp_beneficiaries$muac, otp_beneficiaries$locality),
     "double"
   )
 })