Merge pull request #30 from nutriverse/dev

edit oedema chapter; fix #16
nutriverse · Dec 9, 2024 · d6af25b · d6af25b
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diff --git a/05-oedema.qmd b/05-oedema.qmd
@@ -1,34 +1,35 @@
+---
+output-file: oedema.html
+engine: knitr
+---
+
 # Checking for oedema {#sec-test-oedema}
 
-Nutritional oedema, manifested as bilateral pitting oedema, is a sign of severe acute malnutrition. Nutritional oedema always starts from the feet and extends upwards to other parts of the body. Children with nutritional oedema are at high risk of mortality hence require immediate therapeutic care. This [chapter](#oedema) describes how to check nutritional oedema.
+Nutritional oedema, manifested as bilateral pitting oedema, is a sign of severe acute malnutrition. Nutritional oedema always starts from the feet and extends upwards to other parts of the body. Children with nutritional oedema are at high risk of mortality hence require immediate therapeutic care. This chapter describes how to check nutritional oedema.
 
-## Equipment
+## Equipment {#sec-test-oedema-equipment}
 
 No tool or equipment is needed for checking for nutritional oedema.
 
-## Personnel
+## Personnel {#sec-test-oedema-personnel}
 
 Oedema check can be performed by a single person.
 
-## Steps in checking for nutritional oedema
+## Steps in checking for nutritional oedema {#sec-test-oedema-steps}
 
 1. Press both feet with thumbs
 
-Using both thumbs of your hands, apply normal pressure on top of both feet of the child for about three seconds as shown below. You can estimate three seconds by counting ***‘one thousand and one, one thousand and two, one thousand and three’*** in English. It takes roughly 3 seconds to be able to say these words.
+Using both thumbs of your hands, apply normal pressure on top of both feet of the child for about three seconds as shown in @fig-test-oedema-step1. You can estimate three seconds by counting ***‘one thousand and one, one thousand and two, one thousand and three’*** in English. It takes roughly 3 seconds to be able to say these words.
 
-```{r oedemaStep1, fig.cap = "Press both feet with thumbs", echo = FALSE, fig.align = "center", fig.retina = 1}
-knitr::include_graphics("images/oedemaStep1.jpg")
-```
+![Press both feet with thumbs](images/oedemaStep1.jpg){#fig-test-oedema-step1 fig-align="center"}
 
 2. Release pressure from feet
 
 After three seconds, release the pressure you are applying on the child’s feet. Observe the resulting effect on the child’s feet.
 
 If there is oedema, an impression remains on both feet for a few seconds as shown below.
 
-```{r oedemaStep2, fig.cap = "Bilateral pitting oedema observed after releasing thumbs", echo = FALSE, fig.align = "center", fig.retina = 1}
-knitr::include_graphics("images/oedemaStep2.jpg")
-```
+![Bilateral pitting oedema observed after releasing thumbs](images/oedemaStep2.jpg){#fig-test-oedema-step2 fig-align="center"}
 
 3. Move up to check on the lower legs
 If there is nutritional oedema present on the feet, perform the same test described in step 2 but now move up to the lower legs.
@@ -38,30 +39,41 @@ If there is nutritional oedema present on the lower legs, perform the same test
 
 **Step 3** and **Step 4** are performed to be able to grade or classify the level of nutritional oedema the child is suffering from (if present).
 
-+------------------------------------------------------------+---------------+
-| **Oedema Description**                                     | **Grade**     |
-+============================================================+===============+
-| Oedema below the knees                                     | `+`           |
-+------------------------------------------------------------+---------------+
-| Oedema in both feet and legs, below the knees              | `++`          |
-+------------------------------------------------------------+---------------+
-| Oedema in both feet, legs, arms and sacral pad and eyelids | `+++`         |
-+------------------------------------------------------------+---------------+
+```{r}
+#| label: tbl-oedema-grade
+#| tbl-cap: Nutritional oedema classification
+#| echo: false
+
+data.frame(
+  description = c(
+    "Oedema below the knees",
+    "Oedema in both feet and legs",
+    "Oedema in both feet, legs, arms, and sacral pad and eyelids"
+  ),
+  grade = c("+", "++", "+++")
+) |>
+  knitr::kable(col.names = c("Oedema Description", "Grade")) |>
+  kableExtra::kable_styling(
+    bootstrap_options = c("bordered", "striped"),
+    full_width = FALSE, 
+    position = "center"
+  )
+```
 
 5. Record on the paper questionnaire or the mobile device the presence or absence of oedema. If oedema is present, record also the grade of the oedema.
 
-&nbsp;
+::: {.callout-warning}
 
-::: {.callout-note}
+## Referring cases of nutritional oedema
 
 Children with oedema (any grade) are at a high risk of dying and should be immediately referred to a health care facility (ideally a facility that manages severe acute undernutrition).
 
 :::
 
-&nbsp;
-
 ::: {.callout-important}
 
+## Reminders
+
 * Oedema is a very rare event.
 
 * It is the most common source of errors.

diff --git a/_quarto.yml b/_quarto.yml
@@ -46,6 +46,7 @@ format:
     number-sections: true
     crossref:
       chapters: true
+    html-table-processing: none
   pdf:
     documentclass: scrreprt
     papersize: a4

diff --git a/packages.R b/packages.R
@@ -1,3 +1,5 @@
 # Load dependencies ------------------------------------------------------------
 
 library(quarto)
+library(kableExtra)
+
diff --git a/renv.lock b/renv.lock
@@ -23,6 +23,16 @@
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@@ -197,6 +238,31 @@
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@@ -213,6 +279,17 @@
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@@ -237,6 +314,16 @@
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@@ -258,6 +345,17 @@
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@@ -377,6 +475,80 @@
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@@ -387,6 +559,30 @@
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@@ -400,6 +596,19 @@
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