Vignette tables

NEWS.md

@@ -16,8 +16,12 @@
   namespaces is available, then the return from `comorbidities()` will be a
   `tibble` (or list of `tibble`s when `subconditions = TRUE`).
 
-  The tests were extended to consider the cases of passing in a data.table or
-  tibble to comorbidities when the associated namespaces are not available.
+  The tests were extended to consider the cases of passing in a `data.table` or
+  `tibble` to comorbidities when the associated namespaces are not available.
+
+## Other Changes
+
+* Improve formatting of vignettes/articles.
 
 # medicalcoder 0.6.0
 

vignettes/charlson.Rmd

@@ -84,12 +84,10 @@ Call `summary()` on the return object for a list of summary objects.  These can
 used to generate output tables to the end user's liking.
 
 ```{r}
-str(
-  summary(mdcr_results)
-)
+str(summary(mdcr_results))
 ```
 
-```{r, results = "asis"}
+```{r echo = FALSE, results = "asis"}
 x <- summary(mdcr_results)$conditions[, c("condition_description", "count", "percent")]
 tab <-
   kableExtra::kbl(
@@ -99,6 +97,7 @@ tab <-
     col.names = c("", "Count", "Percentage"),
     digits = 3
   )
+tab <- kableExtra::kable_styling(tab, bootstrap_options = c("striped"), font_size = 10)
 tab <- kableExtra::pack_rows(tab, group_label = "Comorbidity", start_row = 1, end_row = 17)
 tab <- kableExtra::pack_rows(tab, group_label = "Total Comorbidities", start_row = 18, end_row = nrow(x))
 tab

vignettes/comorbidities.Rmd

@@ -126,11 +126,7 @@ head(mdcr_longitudinal)
 ```
 
 A great level of detail for each of the comorbidity algorithms are provided in
-dedicated vignettes:
-
-```{r label = "other-vignettes", eval = FALSE}
-vignette(package = "medicalcoder")$results
-```
+dedicated vignettes.
 
 # When are conditions flag?
 
@@ -142,7 +138,7 @@ hospitalization.
 Implementation of Elixhauser comorbidities for 2022 and beyond [@ahrq2025]
 explicitly define the use of present on admission flags for specific conditions
 (see the `poa_required` flag reported in the data set returned by
-`get_elixhauser_poa`).
+`get_elixhauser_poa()`).
 ```{r}
 str(get_elixhauser_poa())
 ```
@@ -196,35 +192,45 @@ I50.40 intentionally marked as not present on admission.
 ```{r, label = "example-setup"}
 lookup_icd_codes(c("C78.4", "I50.40"))
 
-subset(get_pccc_codes(),
-       subset = full_code %in% c("C78.4", "I50.40"),
-       select = c("icdv", "dx", "code", "full_code", "condition", "pccc_v3.0"))
+codes <- c("C78.4", "I50.40")
+cols  <- c("icdv", "dx", "code", "full_code", "condition")
 
-subset(get_charlson_codes(),
-       subset = full_code %in% c("C78.4", "I50.40"),
-       select = c("icdv", "dx", "code", "full_code", "condition", "charlson_quan2011"))
+subset(
+  get_pccc_codes(),
+  subset = full_code %in% codes,
+  select = c(cols, "pccc_v3.0")
+)
 
-subset(get_elixhauser_codes(),
-       subset = full_code %in% c("C78.4", "I50.40") & elixhauser_ahrq2025 == 1L,
-       select = c("icdv", "dx", "code", "full_code", "condition", "elixhauser_ahrq2025"))
+subset(
+  get_charlson_codes(),
+  subset = full_code %in% codes,
+  select = c(cols, "charlson_quan2011")
+)
+
+subset(
+  get_elixhauser_codes(),
+  subset = full_code %in% codes & elixhauser_ahrq2025 == 1L,
+  select = c(cols, "elixhauser_ahrq2025")
+)
 
 record <-
-data.table::fread(text = "
-patid | encid | code   | poa
-A     | 1     | NA     | NA
-A     | 2     | C78.4  | 0
-A     | 3     | I50.40 | 1
-A     | 4     | NA     | NA
-A     | 5     | C78.4  | 1
-A     | 5     | I50.40 | 0
-A     | 6     | NA     | NA
-")
+  structure(
+    list(
+      patid = c("A", "A", "A", "A", "A", "A", "A"), 
+      encid = c(1L, 2L, 3L, 4L, 5L, 5L, 6L),
+      code = c(NA, "C78.4", "I50.40", NA, "C78.4", "I50.40", NA),
+      poa = c(NA, 0L, 1L, NA, 1L, 0L, NA)),
+    row.names = c(NA, -7L),
+    class = "data.frame"
+  )
 ```
 
-We will call `comorbidities` for the three methods using static POA flags and
-dynamic POA flags, and both flag methods.
+We will call `comorbidities()` for the three methods using static POA flags and
+dynamic POA flags, and both flag methods.  Results are shown in the following
+table.
 
 ```{r, include = FALSE}
+data.table::setDT(record)
 args <-
   list(data = record,
        icd.codes = "code",
@@ -283,6 +289,7 @@ tab <-
     rtn,
     row.names = FALSE,
     escape = FALSE,
+    align = rep("c", nrow(rtn)),
     caption = "Indicators for when a comorbidity is flagged based on the algorithm, present on admission (poa), and flag.method. The two ICD codes,C78.4 and I50.40, map to cancer and cardiovascular disease respectively."
   )
 tab <-
@@ -292,6 +299,8 @@ tab <-
     general = "C78.4 does not need to be POA to count for Elixhauser. I50.40 does need to be POA to count for Elixhauser."
   )
 
+tab <- kable_styling(tab, bootstrap_options = c("striped", "bordered"), full_width = FALSE, font_size = 8)
+#tab <- scroll_box(tab, height = "600px")
 tab <- pack_rows(tab, "flag.method = 'current'", 1L, 6L)
 tab <- pack_rows(tab, "flag.method = 'cumulative'", 7L, 12L)
 tab <- add_header_above(tab, c(" " = 2L, rep(c("PCCC" = 2L, "Charlson" = 2L, "Elixhauser" = 2L), 3L)))

vignettes/elixhauser.Rmd

@@ -129,7 +129,7 @@ tables.
 summary(mdcr_results)
 ```
 
-```{r, results = "asis"}
+```{r echo = FALSE, results = "asis"}
 x <- summary(mdcr_results)$conditions
 tab <-
   kableExtra::kbl(
@@ -139,7 +139,8 @@ tab <-
     col.names = c("", "Count", "Percentage"),
     digits = 3
   )
-tab <- kableExtra::pack_rows(tab, group_label = "Comorbidity", start_row = 1, end_row = 39)
+tab <- kableExtra::kable_styling(tab, bootstrap_options = c("striped"), font_size = 10)
+tab <- kableExtra::pack_rows(tab, group_label = "Comorbidity", start_row = 1, end_row = 38)
 tab <- kableExtra::pack_rows(tab, group_label = "Total Comorbidities", start_row = 39, end_row = nrow(x))
 tab
 ```

vignettes/icd.Rmd

@@ -36,9 +36,6 @@ Centers for Disease Control (CDC) and from the Centers for Medicare & Medicaid
 Services (CMS).  The specific links to the source data sets can be found in the
 source code for the `medicalcoder` package on
 [GitHub](https://github.com/dewittpe/medicalcoder).
-```{r label = "medicalcoder-url"}
-cat(packageDescription('medicalcoder')$URL)
-```
 
 End users can get a `data.frame` with
 ICD-9 diagnostic, ICD-9 procedure, ICD-10 diagnostic, and ICD-10 procedure codes.
@@ -96,6 +93,8 @@ d4
 
 * `assignable_end`: The last year the code was assignable.
 
+## with.descriptions
+
 To get the descriptions of the ICD codes call `get_icd_codes()` with
 `with.descriptions = TRUE`.
 ```{r, label = "icd-codes-with-descriptions"}
@@ -108,28 +107,49 @@ The return has the additional columns:
 * `desc_end`: the last fiscal_year that the description was documented
 
 Over time the descriptions for some ICD codes were modified within sources.
-There are also many differences between sources.  The table below has several
+There are also many differences between sources.  The tables below have several
 examples.
 
 ```{r, label = "deltas-in-desc", results = "hide"}
 delta_in_desc <-
-  subset(get_icd_codes(with.descriptions = TRUE),
-         subset = full_code %in% c("Z88.7", "010.93", "V76.49"),
-         select = c("full_code", "src", "desc", "desc_start", "desc_end"))
+  subset(
+    get_icd_codes(with.descriptions = TRUE),
+    subset = full_code %in% c("Z88.7", "010.93", "V76.49"),
+    select = c("full_code", "src", "desc", "desc_start", "desc_end")
+  )
 ```
 
-```{r, label = "deltas-in-desc-show", echo = FALSE, results = "asis"}
-knitr::kable(delta_in_desc, row.names = FALSE)
+The only difference in the description for 010.93 is a comma.
+
+```{r, label = "deltas-in-desc-show-010.93", echo = FALSE, results = "asis"}
+knitr::kable(
+  subset(delta_in_desc, subset = full_code == "010.93"),
+  row.names = FALSE
+)
 ```
 
-* Z88.7 has differences in the description over time within `cms` source and
-  between `cms` and `who`.
+ICD-10-CM Z88.7 has differences in the description over time within `cms` source
+and between `cms` and `who`.
 
-* The only difference in the description for 010.93 is a comma.
+```{r, label = "deltas-in-desc-show-Z88.7", echo = FALSE, results = "asis"}
+knitr::kable(
+  subset(delta_in_desc, subset = full_code == "Z88.7"),
+  row.names = FALSE
+)
+```
+
+ICD-9-CM V79.49 had the description of 'other' which would require exploration
+of the header codes to understand. Even when the most verbose description may
+still require consideration of the header codes to fullye understand.
+
+```{r, label = "deltas-in-desc-show-v79.49", echo = FALSE, results = "asis"}
+knitr::kable(
+  subset(delta_in_desc, subset = full_code == "V76.49"),
+  row.names = FALSE
+)
+```
 
-* ICD-9-CM V79.49 had the description of 'other' which would require exploration
-  of the header codes to understand. Even when the most verbose description may
-  still require consideration of the header codes to fully understand.
+## with.hierarchy
 
 Lastly, the `get_icd_codes()` function includes the argument `with.hierarchy`
 which will provide additional details for the codes.