From 199a3a7eb417588275125d21a747cf672e264319 Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Sun, 5 Feb 2023 13:13:27 +0000
Subject: [PATCH 1/8] add gtsummary min version to description

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a9825a43..adf9cd9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -54,7 +54,7 @@ Imports:
     ggalluvial,
     ggplot2 (>= 3.0.0),
     ggspatial,
-    gtsummary,
+    gtsummary (>= 1.7.0),
     glue,
     here,
     janitor,

From 40d67029379e7dab93552b46173bb1e1fd888b35 Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Sun, 5 Feb 2023 13:13:45 +0000
Subject: [PATCH 2/8] add_ci for mortality

---
 .../templates/mortality/skeleton/skeleton.Rmd | 63 +++++++++----------
 1 file changed, 30 insertions(+), 33 deletions(-)

diff --git a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
index f45b88a8..64c34cd6 100644
--- a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
@@ -1649,13 +1649,13 @@ Note the possibility of negative confidence intervals if there are low counts
 ## weighted counts and proportion of dead
 death_props <- survey_design %>% 
   select(died) %>% 
-  tbl_svysummary() %>% 
+  ## note add_ci() does not allow logical variables 
+  ## type "categorical" changes to a character variable
+  tbl_svysummary(type = died ~ "categorical") %>% 
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1678,10 +1678,9 @@ CMR <- survey_design %>%
 
 
 During the recall period the weighted number and proportion of deaths in the 
-population was `r inline_text(death_props, variable = "died",  column = "stat_0")`,
+population was `r inline_text(death_props, variable = "died",  column = "stat_0", level = "TRUE")`,
 with a weighted confidence interval of
-`r #inline_text(death_props, variable = "died",  column = "add_stat_1")`, and a 
-design effect of `r #inline_text(death_props, variable = "died",  column = "add_stat_2")`.
+`r inline_text(death_props, variable = "died",  column = "ci_stat_0", level = "TRUE")`.
 This is a crude mortality rate of `r CMR` deaths per 10000 person-days. 
 
 
@@ -1705,13 +1704,12 @@ Note the possibility of negative confidence intervals if there are low counts
 ## weighted counts and proportion of dead
 death_props_strat <- survey_design %>% 
   select(died, health_district) %>%
-  tbl_svysummary(by = health_district) %>% 
+  tbl_svysummary(type = died ~ "categorical", 
+                 by = health_district) %>% 
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
-
-  ## add in deff 
-
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1737,16 +1735,14 @@ CMR_strat <- survey_design %>%
 ```
 
 
-In District A the weighted number of deaths was 
-`r inline_text(death_props_strat, variable = "died",  column = "stat_1")`, 
-which gives a weighted proportion of 
-`r #death_props_strat %>% pull("district_a ci")`, and a design effect of
-`r #death_props_strat %>% pull("district_a deff") %>% round(digits = 3)`.  
-In comparison, the weighted number of deaths in District B was
-`r inline_text(death_props_strat, variable = "died",  column = "stat_2")`, 
-the weighted proportion was 
-`r #death_props_strat %>% pull("district_b ci")` and the design effect was 
-`r #death_props_strat %>% pull("district_b deff") %>% round(digits = 3)`.  
+In District A the weighted number and proportion of deaths was
+`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "stat_1")`, 
+with a weighted confidence interval of
+`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "ci_stat_1")`.  
+In comparison, the weighted number and proportion of deaths in District B was
+`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "stat_2")`, 
+the weighted confidence interval was 
+`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "ci_stat_2")`.  
 The crude mortality rate in District A was 
 `r CMR_strat %>% filter(health_district == "district_a") %>% pull(Mortality)`
 deaths per 10000 person-days and in District B was 
@@ -1861,8 +1857,9 @@ cause_of_death_prop <- survey_design %>%
   # proportions only among those who died
   filter(died) %>% 
   select(cause) %>% 
-  tbl_svysummary()
+  tbl_svysummary() %>% 
   ## add ci 
+  add_ci()
 
 ## weighted cause-specific mortality ratios
 cause_of_death_mort <- survey_design %>% 
@@ -1893,7 +1890,7 @@ cause_of_death_prop %>%
   ## modify the column headers
   modify_header(
     list(
-      stat_0 ~ "**Deaths \n N={round(N, digits = 0)}**", 
+      stat_0 ~ "Deaths \n N={round(N, digits = 0)}", 
       mortality ~ "**Mortality per 10,000 person/days (95% CI)**" 
     )
     ) %>% 
@@ -1929,7 +1926,7 @@ survey_design %>%
   select(cause, health_district) %>%
   tbl_svysummary(by = health_district) %>%   
   ## add in confidence intervals
-
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -2042,7 +2039,7 @@ survey_design %>%
   select(cause, age_group) %>%
   tbl_svysummary(by = age_group) %>%   
   ## add in confidence intervals
-
+  # add_ci() %>%
   ## modify the column headers
   modify_spanning_header(
     all_stat_cols() ~ "**Age group (years)**"
@@ -2079,7 +2076,7 @@ survey_design %>%
   select(cause, sex) %>%
   tbl_svysummary(by = sex) %>% 
   ## add in confidence intervals
-  
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format
@@ -2313,7 +2310,7 @@ survey_design %>%
   select(cause_illness) %>%
   tbl_svysummary() %>% 
   ## add in confidence intervals
-
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format
@@ -2344,7 +2341,7 @@ survey_design %>%
   select(cause_illness, age_group) %>%
   tbl_svysummary(by = age_group) %>%   
   ## add in confidence intervals
-
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format
@@ -2375,7 +2372,7 @@ survey_design %>%
   select(cause_illness, sex) %>%
   tbl_svysummary(by = sex) %>%   
   ## add in confidence intervals
-  
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format
@@ -2408,7 +2405,7 @@ survey_design %>%
   select(no_care_illness) %>%
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format
@@ -2440,7 +2437,7 @@ survey_design %>%
   select(violent_episodes_number, violence_nature, uniform, place_violence) %>%
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format
@@ -2473,7 +2470,7 @@ survey_design %>%
   select(fever_now, care_fever) %>%
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format
@@ -2504,7 +2501,7 @@ survey_design %>%
   select(reason_no_care) %>%
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
+  add_ci() %>% 
   ## make variable names bold 
   bold_labels() %>% 
   # change to flextable format

From 02298122c900b3b42694eafd12bdf629992f921d Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Sun, 5 Feb 2023 13:22:15 +0000
Subject: [PATCH 3/8] fix xaxis in alluvial plot mortality

---
 inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
index 64c34cd6..a02472fc 100644
--- a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
@@ -2211,7 +2211,7 @@ ggplot(data = flow_table,
        aes(axis1 = startcause, axis2 = endcause,
            y = n)) +
   ## define x axis limits and labels
-  scale_x_discrete(limits = c("Start\ncause", "End\ncause")) +
+  scale_x_discrete(limits = c("Start\ncause", "End\ncause"), expand = c(0,0)) +
   ## colour lines by sex 
   geom_alluvium(aes(fill = sex)) +
   ## fill in the label boxes grey

From 5fe66d6a5a4f33130fcc4236ddea0ea3cff2376a Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Sun, 5 Feb 2023 13:27:57 +0000
Subject: [PATCH 4/8] remove kable from options (using flextable)

---
 inst/rmarkdown/templates/ajs_outbreak/skeleton/skeleton.Rmd  | 3 ---
 .../templates/cholera_outbreak/skeleton/skeleton.Rmd         | 3 ---
 .../templates/measles_outbreak/skeleton/skeleton.Rmd         | 3 ---
 .../templates/meningitis_outbreak/skeleton/skeleton.Rmd      | 3 ---
 inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd     | 2 --
 inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd     | 3 ---
 .../templates/vaccination_long/skeleton/skeleton.Rmd         | 3 ---
 .../templates/vaccination_short/skeleton/skeleton.Rmd        | 5 +----
 8 files changed, 1 insertion(+), 24 deletions(-)

diff --git a/inst/rmarkdown/templates/ajs_outbreak/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/ajs_outbreak/skeleton/skeleton.Rmd
index 3b53aa0b..6e525c40 100644
--- a/inst/rmarkdown/templates/ajs_outbreak/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/ajs_outbreak/skeleton/skeleton.Rmd
@@ -50,9 +50,6 @@ knitr::opts_chunk$set(echo = FALSE,       # hide all code chunks in output
 
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
-
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
      install.packages("pacman") }
diff --git a/inst/rmarkdown/templates/cholera_outbreak/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/cholera_outbreak/skeleton/skeleton.Rmd
index 9eac483d..00a8040a 100644
--- a/inst/rmarkdown/templates/cholera_outbreak/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/cholera_outbreak/skeleton/skeleton.Rmd
@@ -50,9 +50,6 @@ knitr::opts_chunk$set(echo = FALSE,       # hide all code chunks in output
 
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
-
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
      install.packages("pacman") }
diff --git a/inst/rmarkdown/templates/measles_outbreak/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/measles_outbreak/skeleton/skeleton.Rmd
index 92cfb63f..96ec4eef 100644
--- a/inst/rmarkdown/templates/measles_outbreak/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/measles_outbreak/skeleton/skeleton.Rmd
@@ -50,9 +50,6 @@ knitr::opts_chunk$set(echo = FALSE,       # hide all code chunks in output
 
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
-
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
      install.packages("pacman") }
diff --git a/inst/rmarkdown/templates/meningitis_outbreak/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/meningitis_outbreak/skeleton/skeleton.Rmd
index 3191ead3..97c7d3e2 100644
--- a/inst/rmarkdown/templates/meningitis_outbreak/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/meningitis_outbreak/skeleton/skeleton.Rmd
@@ -50,9 +50,6 @@ knitr::opts_chunk$set(echo = FALSE,       # hide all code chunks in output
 
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
-
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
      install.packages("pacman") }
diff --git a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
index a02472fc..e46f85a1 100644
--- a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
@@ -43,8 +43,6 @@ knitr::opts_chunk$set(echo = FALSE, error = TRUE, warning = FALSE, message = FAL
                       fig.width = 6*1.25, fig.height = 6)
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
 
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
diff --git a/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd
index c9b0e793..5af6463e 100644
--- a/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd
@@ -79,9 +79,6 @@ For help installing packages, please visit https://r4epis.netlify.com/welcome
 knitr::opts_chunk$set(echo = FALSE, error = TRUE, fig.width = 6*1.25, fig.height = 6)
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
-
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
      install.packages("pacman") }
diff --git a/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd
index cdadf2af..1ea87a00 100644
--- a/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd
@@ -46,9 +46,6 @@ For help installing packages, please visit https://r4epis.netlify.com/welcome
 knitr::opts_chunk$set(echo = FALSE, error = TRUE, fig.width = 6*1.25, fig.height = 6)
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
-
 
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
diff --git a/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd
index 698db93d..8fbd5250 100644
--- a/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd
@@ -46,9 +46,6 @@ For help installing packages, please visit https://r4epis.netlify.com/welcome
 knitr::opts_chunk$set(echo = FALSE, error = TRUE, fig.width = 6*1.25, fig.height = 6)
 
 
-## set default NA to - in output, define figure width/height
-options(knitr.kable.NA = "-")
-
 
 # Ensures the package "pacman" is installed
 if (!require("pacman")) {
@@ -1287,7 +1284,7 @@ left_join(ag, propcount, by = "age_group", suffix = c("", "_pop")) %>%
     "Source population (%)" = percent_pop,
     "P-value" = p.value
   ) %>%
-  kable(digits = 1)
+  qflextable()
 
 ```
 

From b1eb19938048cfc7de9566cf19086735e6ccccb7 Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Fri, 10 Feb 2023 11:15:04 +0000
Subject: [PATCH 5/8] update mort add_ci after gtsummary bugfix

---
 .../templates/mortality/skeleton/skeleton.Rmd   | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
index e46f85a1..f3e02729 100644
--- a/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/mortality/skeleton/skeleton.Rmd
@@ -1647,8 +1647,6 @@ Note the possibility of negative confidence intervals if there are low counts
 ## weighted counts and proportion of dead
 death_props <- survey_design %>% 
   select(died) %>% 
-  ## note add_ci() does not allow logical variables 
-  ## type "categorical" changes to a character variable
   tbl_svysummary(type = died ~ "categorical") %>% 
   ## add the weighted total
   add_n() %>%   
@@ -1702,8 +1700,7 @@ Note the possibility of negative confidence intervals if there are low counts
 ## weighted counts and proportion of dead
 death_props_strat <- survey_design %>% 
   select(died, health_district) %>%
-  tbl_svysummary(type = died ~ "categorical", 
-                 by = health_district) %>% 
+  tbl_svysummary(by = health_district) %>% 
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
@@ -1734,13 +1731,13 @@ CMR_strat <- survey_design %>%
 
 
 In District A the weighted number and proportion of deaths was
-`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "stat_1")`, 
+`r inline_text(death_props_strat, variable = "died", column = "stat_1")`, 
 with a weighted confidence interval of
-`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "ci_stat_1")`.  
+`r inline_text(death_props_strat, variable = "died", column = "ci_stat_1")`.  
 In comparison, the weighted number and proportion of deaths in District B was
-`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "stat_2")`, 
+`r inline_text(death_props_strat, variable = "died", column = "stat_2")`, 
 the weighted confidence interval was 
-`r inline_text(death_props_strat, variable = "died", level = "TRUE", column = "ci_stat_2")`.  
+`r inline_text(death_props_strat, variable = "died", column = "ci_stat_2")`.  
 The crude mortality rate in District A was 
 `r CMR_strat %>% filter(health_district == "district_a") %>% pull(Mortality)`
 deaths per 10000 person-days and in District B was 
@@ -2028,6 +2025,10 @@ by age group.
 Note that low counts or short observation times may lead to a confidence interval 
 that crosses zero (i.e. negative) for mortality ratios. These should be interpreted
 as if no deaths or recoded to zero (impossible to have negative deaths). 
+Note that confidence intervals would make this table crowded; in addition 
+groups with zero counts result in an error, from the original survey package. 
+If you would like to have confidence intervals we suggest only showing a subset
+of the levels or groups in your data. 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -->
 
 ```{r weighted_death_cause_by_age, warning = FALSE}

From edf1743ca530b0c63c561949fb0819ff4453fa95 Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Fri, 10 Feb 2023 13:49:32 +0000
Subject: [PATCH 6/8] add confidence int to nutrition

---
 .../templates/nutrition/skeleton/skeleton.Rmd | 43 +++++++++++++------
 1 file changed, 29 insertions(+), 14 deletions(-)

diff --git a/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd
index 5af6463e..ddec7395 100644
--- a/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/nutrition/skeleton/skeleton.Rmd
@@ -905,9 +905,9 @@ study_data_cleaned <- study_data_cleaned %>%
   mutate(
     across(
       .cols = c(stunting_haz, 
-                         moderate_stunting_haz, 
-                         severe_stunting_haz), # select the indicator variables
-      .funs = ~if_else(!is.na(flen) & flen == 1, NA, .))) # NA if flagged, else leave as is
+                moderate_stunting_haz, 
+                severe_stunting_haz), # select the indicator variables
+      .fns = ~if_else(!is.na(flen) & flen == 1, NA, .))) # NA if flagged, else leave as is
 
 
 
@@ -1993,7 +1993,9 @@ overall <- survey_design %>%
   select(all_of(MUAC)) %>% 
   ## only show the row with TRUE
   tbl_svysummary(missing = "no", 
-                 value = everything() ~ TRUE)
+                 value = everything() ~ TRUE) %>% 
+  ## add confidence intervals
+  add_ci()
 
 age_strat <- survey_design %>% 
   ## tabulate multiple variables with same values
@@ -2010,7 +2012,8 @@ tbl_merge(list(overall, age_strat)) %>%
     list(
       ## rename the spanning header
       ## you can see what the columns are called by putting in an object and inspecting table_body
-      stat_0_1    ~ "**Overall**", 
+      c(stat_0_1, 
+        ci_stat_0_1) ~ "**Overall**",  
       c(stat_1_2,
         stat_2_2, 
         stat_3_2,
@@ -2049,7 +2052,9 @@ overall <- survey_design %>%
   select(all_of(MUAC)) %>% 
   ## only show the row with TRUE
   tbl_svysummary(missing = "no", 
-                 value = everything() ~ TRUE)
+                 value = everything() ~ TRUE) %>% 
+  ## add confidence intervals
+  add_ci()
 
 age_strat <- survey_design %>% 
   ## only keep children less than 87cm
@@ -2060,7 +2065,7 @@ age_strat <- survey_design %>%
   tbl_svysummary(missing = "no", 
                  value = everything() ~ TRUE, 
                  ## stratify by age group
-                 by = age_group)
+                 by = age_group) 
 
 ## combine the overall and stratified tables 
 tbl_merge(list(overall, age_strat)) %>% 
@@ -2068,7 +2073,8 @@ tbl_merge(list(overall, age_strat)) %>%
     list(
       ## rename the spanning header
       ## you can see what the columns are called by putting in an object and inspecting table_body
-      stat_0_1    ~ "**Overall**", 
+      c(stat_0_1, 
+        ci_stat_0_1) ~ "**Overall**", 
       c(stat_1_2,
         stat_2_2, 
         stat_3_2,
@@ -2107,7 +2113,9 @@ overall <- survey_design %>%
   select(all_of(HAZ)) %>% 
   ## only show the row with TRUE
   tbl_svysummary(missing = "no", 
-                 value = everything() ~ TRUE)
+                 value = everything() ~ TRUE) %>% 
+  ## add confidence intervals
+  add_ci()
 
 age_strat <- survey_design %>% 
   ## tabulate multiple variables with same values
@@ -2124,7 +2132,8 @@ tbl_merge(list(overall, age_strat)) %>%
     list(
       ## rename the spanning header
       ## you can see what the columns are called by putting in an object and inspecting table_body
-      stat_0_1    ~ "**Overall**", 
+      c(stat_0_1, 
+        ci_stat_0_1) ~ "**Overall**",  
       c(stat_1_2,
         stat_2_2, 
         stat_3_2,
@@ -2162,7 +2171,9 @@ overall <- survey_design %>%
   select(all_of(WAZ)) %>% 
   ## only show the row with TRUE
   tbl_svysummary(missing = "no", 
-                 value = everything() ~ TRUE)
+                 value = everything() ~ TRUE) %>% 
+  ## add confidence intervals
+  add_ci()
 
 age_strat <- survey_design %>% 
   ## tabulate multiple variables with same values
@@ -2179,7 +2190,8 @@ tbl_merge(list(overall, age_strat)) %>%
     list(
       ## rename the spanning header
       ## you can see what the columns are called by putting in an object and inspecting table_body
-      stat_0_1    ~ "**Overall**", 
+      c(stat_0_1, 
+        ci_stat_0_1) ~ "**Overall**",   
       c(stat_1_2,
         stat_2_2, 
         stat_3_2,
@@ -2218,7 +2230,9 @@ overall <- survey_design %>%
   select(all_of(WHZ)) %>% 
   ## only show the row with TRUE
   tbl_svysummary(missing = "no", 
-                 value = everything() ~ TRUE)
+                 value = everything() ~ TRUE) %>% 
+  ## add confidence intervals
+  add_ci()
 
 age_strat <- survey_design %>% 
   ## tabulate multiple variables with same values
@@ -2235,7 +2249,8 @@ tbl_merge(list(overall, age_strat)) %>%
     list(
       ## rename the spanning header
       ## you can see what the columns are called by putting in an object and inspecting table_body
-      stat_0_1    ~ "**Overall**", 
+      c(stat_0_1, 
+        ci_stat_0_1) ~ "**Overall**", 
       c(stat_1_2,
         stat_2_2, 
         stat_3_2,

From 0f179a51ee869cd23f32f0c5a54f0f4001d214d5 Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Fri, 10 Feb 2023 15:41:42 +0000
Subject: [PATCH 7/8] add ci for vacc long

---
 .../vaccination_long/skeleton/skeleton.Rmd    | 30 +++++--------------
 1 file changed, 8 insertions(+), 22 deletions(-)

diff --git a/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd
index 1ea87a00..5a14dac8 100644
--- a/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/vaccination_long/skeleton/skeleton.Rmd
@@ -1574,9 +1574,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1626,9 +1624,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1696,9 +1692,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1748,9 +1742,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1799,9 +1791,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1851,9 +1841,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1898,13 +1886,11 @@ survey_design %>%
   select(reason_vars$option_name) %>% 
   tbl_svysummary(value = list(everything() ~ 1)) %>% 
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
-      stat_0 ~ "**Weighted Count (n) \n (N={round(N, digits = 0)})**"
+      stat_0 ~ "Weighted Count (n) \n (N={round(N, digits = 0)})"
     )
     ) %>% 
   ## make variable names bold 

From 18a05f9d9dc84a8d74defdea0ea7dd36976caf18 Mon Sep 17 00:00:00 2001
From: Alex Spina <alexfspina@gmail.com>
Date: Fri, 10 Feb 2023 15:50:10 +0000
Subject: [PATCH 8/8] add ci to vacc short

---
 .../vaccination_short/skeleton/skeleton.Rmd   | 48 +++++--------------
 1 file changed, 12 insertions(+), 36 deletions(-)

diff --git a/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd
index 8fbd5250..a3ed6f50 100644
--- a/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/vaccination_short/skeleton/skeleton.Rmd
@@ -1507,9 +1507,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1544,9 +1542,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1584,9 +1580,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
-   
-  ## add in deff 
-   
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1626,9 +1620,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
-   
-  ## add in deff 
-   
+  add_ci() %>%  
   ## modify the column headers
   modify_header(
     list(
@@ -1665,9 +1657,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
-   
-  ## add in deff 
-   
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1707,9 +1697,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
-   
-  ## add in deff 
-   
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1749,9 +1737,7 @@ survey_design %>%
   ## add the weighted total
   add_n() %>%   
   ## add in confidence intervals
-   
-  ## add in deff 
-   
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1787,9 +1773,7 @@ survey_design %>%
   select(reason_route_vacc) %>% 
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1822,9 +1806,7 @@ survey_design %>%
   select(reason_msf_vacc) %>% 
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1856,9 +1838,7 @@ survey_design %>%
   select(reason_sia_vacc) %>% 
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1889,9 +1869,7 @@ survey_design %>%
   select(diagnosis_disease) %>% 
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(
@@ -1925,9 +1903,7 @@ survey_design %>%
   select(time_since_group) %>% 
   tbl_svysummary() %>% 
   ## add in confidence intervals
-  
-  ## add in deff 
-  
+  add_ci() %>% 
   ## modify the column headers
   modify_header(
     list(