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Summary table create r table format #116

Open

khansh01 wants to merge 13 commits into development from summary_table_create_r_table_format

khansh01 commented Oct 8, 2024

Created new R Markdown for flextable summary table

CliveWG and others added 10 commits

July 17, 2024 06:41


          Create basic kable table

af3e5bc


          add formats eg white font and other to headers

83b5952


          Add further formatting

b9d0c75


          Flextable for summary table

c3282b9


          Test file for demographics table output

edfdf21


          not sure when this ws or what the change was, sorry!

6db97c3


          Made use of down arrow next to Knit > Knit Directory > Project Direct…

5b7189c

…ory and hence......

Comment out setwd row 21

Change lp_path row 24 to my own working area - this change just for me and ooooops, left an old bit of copy and paste below.


          Hard code row 45 max_fy as function creates 2023/24 and as no data fo…

e9594e3

…r that year the markdown crashes - have only hardcoded as temp measure as I think James was looking into a function for this issue/


          updated summary table, fixing issue with the year in the household table

9baff9c


          commenting out code

adc041e

khansh01 requested review from Moohan, cfraser2020, RyanDuffy01, CliveWG, kenneo03git and JosieSteele

October 8, 2024 13:37

khansh01 linked an issue

that may be closed by this pull request

Summary table - Actual table in the final output #64

Open


          Merge branch 'main' into summary_table_create_r_table_format

4fc9114

Moohan changed the base branch from main to development

October 8, 2024 14:10


          Merge branch 'development' into summary_table_create_r_table_format

e881a81

Moohan requested changes

View reviewed changes

Member

Moohan left a comment

Great work!

I've made lots of suggestions, but nothing major 👍

I did notice a mix of pipes - I think |> is preferred now, so if unless there's something I missed where you're using a special ability of %>% could you swap them out to make it consistent please?

Summary Table/Summary Table Dev Flextable.Rmd

+              title: ''
+              output:
+                word_document:
+                  reference_docx: "//conf/LIST_analytics/West Hub/02 - Scaled Up Work/RMarkdown/Locality Profiles/Summary Table/ST_ref_doc.docx"

Member

Moohan Oct 8, 2024

Suggested change

      
                reference_docx: "//conf/LIST_analytics/West Hub/02 - Scaled Up Work/RMarkdown/Locality Profiles/Summary Table/ST_ref_doc.docx"
          
                reference_docx: "/conf/LIST_analytics/West Hub/02 - Scaled Up Work/RMarkdown/Locality Profiles/Summary Table/ST_ref_doc.docx"

Summary Table/Summary Table Dev Flextable.Rmd Outdated

+                word_document:
+                  reference_docx: "//conf/LIST_analytics/West Hub/02 - Scaled Up Work/RMarkdown/Locality Profiles/Summary Table/ST_ref_doc.docx"
+              ---
+              ;

Member

Moohan Oct 8, 2024

Think this is a typo?

Suggested change

;

Summary Table/Summary Table Dev Flextable.Rmd Outdated

+              # LOCALITY <- "Whalsay and Skerries"
+              # LOCALITY <- "Inverclyde East"
+              # setwd("~/list-localities-profiles/")

Member

Moohan Oct 8, 2024

We shouldn't ever need this?

Suggested change

# setwd("~/list-localities-profiles/")

Summary Table/Summary Table Dev Flextable.Rmd Outdated

Comment on lines 21 to 41

+              ## Project file path
+               lp_path <- "/conf/LIST_analytics/West Hub/02 - Scaled Up Work/RMarkdown/Locality Profiles/"
+              # Source in global functions/themes script
+               source("./Master RMarkdown Document & Render Code/Global Script.R")
+              # # demographics
+               source("./Demographics/1. Demographics - Population.R")
+               source("./Demographics/2. Demographics - SIMD.R")
+              #
+              # # housing
+               source("./Households/Households Code.R")
+              #
+              # # general health
+               source("./General Health/3. General Health Outputs.R")
+              #
+              # # lifestyle & risk factors
+               source("./Lifestyle & Risk Factors/2. Lifestyle & Risk Factors Outputs.R")
+              #
+              # # unscheduled care
+               source("./Unscheduled Care/2. Unscheduled Care outputs.R")

Member

Moohan Oct 8, 2024

I think these will need to be removed or commented out. I guess they were/are used for testing but we don't want them added uncommented?

Is sourcing all the scripts here the best way to test the summary table?

Summary Table/Summary Table Dev Flextable.Rmd Outdated

+              library(officer)
+              library(officedown)
+              # detach(package:tidylog, unload = TRUE)

Member

Moohan Oct 8, 2024

Suggested change

# detach(package:tidylog, unload = TRUE)

Summary Table/Summary Table Dev Flextable.Rmd Outdated

+                color(part = "header", color = "white") %>%
+                bg(part = "header", bg = "#3F3685") %>%
+                bg(j = 1:3, part = "body", bg = "grey90") |>
+               # width(j = 1, width = "22em") |>

Member

Moohan Oct 8, 2024

Suggested change

# width(j = 1, width = "22em") |>

Summary Table/Summary Table Dev Flextable.Rmd Outdated

		scot_values <- c(scot_alcohol_hosp, scot_alcohol_deaths, scot_drug_hosp, scot_bowel_screening)


		lifestyle_values <-data.frame(indicators, datatype, time, loc_values, other_loc_values,

Member

Moohan Oct 8, 2024

Suggested change

      
            lifestyle_values <-data.frame(indicators, datatype, time, loc_values, other_loc_values,
          
            lifestyle_values <- tibble(indicators, datatype, time, loc_values, other_loc_values,

Contributor

CliveWG Oct 9, 2024

Another random observation (that I looked up) - tibble preserves all of the variable types whereas in old versions of r data.frame may convert strings into factors.

Summary Table/Summary Table Dev Flextable.Rmd Outdated

Comment on lines 330 to 348

+              UC_values <-data.frame(indicators, datatype, time, loc_values, other_loc_values,
+                                        hscp_values, scot_values)
+              colnames(UC_values) <- headings
+              UC_table <- flextable(UC_values) %>%
+                bold(part = "header") %>%
+                bold(j = 1, bold = TRUE, part = "body") %>%
+                fontsize(part = "header", size = 12) %>%
+                font(part = "body", fontname = "Arial") |>
+                font(part = "header", fontname = "Arial") |>
+                color(part = "header", color = "white") %>%
+                bg(part = "header", bg = "#3F3685") %>%
+                bg(j = 1:3, part = "body", bg = "grey90") |>
+               # width(j = 1, width = "22em") |>
+                border(border = fp_border(color = "white", width = 1), part = "body") |>
+                set_table_properties(layout = "autofit")
+              UC_table

Member

Moohan Oct 8, 2024

Double check that UC_values and/or UC_table isn't used elsewhere before applying this suggestion.

Suggested change

      
            UC_values <-data.frame(indicators, datatype, time, loc_values, other_loc_values,
          
                                      hscp_values, scot_values)
          
            colnames(UC_values) <- headings
          
            UC_table <- flextable(UC_values) %>%
          
              bold(part = "header") %>%
          
              bold(j = 1, bold = TRUE, part = "body") %>%
          
              fontsize(part = "header", size = 12) %>%
          
              font(part = "body", fontname = "Arial") |>
          
              font(part = "header", fontname = "Arial") |> 
          
              color(part = "header", color = "white") %>%
          
              bg(part = "header", bg = "#3F3685") %>%
          
              bg(j = 1:3, part = "body", bg = "grey90") |>
          
             # width(j = 1, width = "22em") |> 
          
              border(border = fp_border(color = "white", width = 1), part = "body") |>
          
              set_table_properties(layout = "autofit")
          
            UC_table
          
            uc_values <- tibble(indicators, datatype, time, loc_values, other_loc_values,
          
                                      hscp_values, scot_values)
          
            colnames(uc_values) <- headings
          
            UC_table <- flextable(uc_values) %>%
          
              bold(part = "header") %>%
          
              bold(j = 1, bold = TRUE, part = "body") %>%
          
              fontsize(part = "header", size = 12) %>%
          
              font(part = "body", fontname = "Arial") |>
          
              font(part = "header", fontname = "Arial") |> 
          
              color(part = "header", color = "white") %>%
          
              bg(part = "header", bg = "#3F3685") %>%
          
              bg(j = 1:3, part = "body", bg = "grey90") |>
          
              border(border = fp_border(color = "white", width = 1), part = "body") |>
          
              set_table_properties(layout = "autofit")
          
            uc_table

Summary Table/Summary Table Dev Flextable.Rmd Outdated

Comment on lines 375 to 396

+              UC_MH_values <-data.frame(indicators, datatype, time, loc_values, other_loc_values,
+                                        hscp_values, scot_values)
+              colnames(UC_MH_values) <- headings
+              UC_MH_table <- flextable(UC_MH_values) %>%
+                bold(part = "header") %>%
+                bold(j = 1, bold = TRUE, part = "body") %>%
+                fontsize(part = "header", size = 12) %>%
+                font(part = "body", fontname = "Arial") |>
+                font(part = "header", fontname = "Arial") |>
+                color(part = "header", color = "white") %>%
+                bg(part = "header", bg = "#3F3685") %>%
+                bg(j = 1:3, part = "body", bg = "grey90") |>
+               # width(j = 1, width = "22em") |>
+                border(border = fp_border(color = "white", width = 1), part = "body") |>
+                set_table_properties(layout = "autofit")
+              UC_MH_table

Member

Moohan Oct 8, 2024

Suggested change

      
            UC_MH_values <-data.frame(indicators, datatype, time, loc_values, other_loc_values,
          
                                      hscp_values, scot_values)
          
            colnames(UC_MH_values) <- headings
          
            UC_MH_table <- flextable(UC_MH_values) %>%
          
              bold(part = "header") %>%
          
              bold(j = 1, bold = TRUE, part = "body") %>%
          
              fontsize(part = "header", size = 12) %>%
          
              font(part = "body", fontname = "Arial") |>
          
              font(part = "header", fontname = "Arial") |> 
          
              color(part = "header", color = "white") %>%
          
              bg(part = "header", bg = "#3F3685") %>%
          
              bg(j = 1:3, part = "body", bg = "grey90") |>
          
             # width(j = 1, width = "22em") |> 
          
              border(border = fp_border(color = "white", width = 1), part = "body") |> 
          
              set_table_properties(layout = "autofit")
          
            UC_MH_table
          
            uc_mh_values <- tibble(indicators, datatype, time, loc_values, other_loc_values,
          
                                      hscp_values, scot_values)
          
            colnames(uc_mh_values) <- headings
          
            uc_mh_table <- flextable(uc_mh_values) %>%
          
              bold(part = "header") %>%
          
              bold(j = 1, bold = TRUE, part = "body") %>%
          
              fontsize(part = "header", size = 12) %>%
          
              font(part = "body", fontname = "Arial") |>
          
              font(part = "header", fontname = "Arial") |> 
          
              color(part = "header", color = "white") %>%
          
              bg(part = "header", bg = "#3F3685") %>%
          
              bg(j = 1:3, part = "body", bg = "grey90") |>
          
              border(border = fp_border(color = "white", width = 1), part = "body") |> 
          
              set_table_properties(layout = "autofit")
          
            uc_mh_table

Summary Table/Summary-Table-Markdown-Development.html Outdated

Member

Moohan Oct 8, 2024

I don't think this file should have been committed. We can add HTML files to the .gitignore so git ignores them in the future but can you delete this please?

CliveWG reviewed

View reviewed changes

Unscheduled Care/2. Unscheduled Care outputs.R

@@ @@ -34,15 +34,15 @@ library(reshape2) @@
               # LOCALITY <- "Ayr North and Former Coalfield Communities"
               # LOCALITY <- "Whalsay and Skerries"
               # LOCALITY <- "North Perthshire"
+              #LOCALITY <- "Inverclyde East"
               # Set date limit for financial year
               # Unless we're in Q4 use the previous FY as the max
               max_fy <- ifelse(

Contributor

CliveWG Oct 9, 2024

I'm not sure whether I've commented on this before hmmmmmm. Would it be better having the max_fy as a function in Global?


          making suggested changes, commenting out code, making code more consi…

a632fd8

…stent

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Reviewers

Moohan Moohan requested changes

CliveWG CliveWG left review comments

cfraser2020 Awaiting requested review from cfraser2020

RyanDuffy01 Awaiting requested review from RyanDuffy01

kenneo03git Awaiting requested review from kenneo03git

JosieSteele Awaiting requested review from JosieSteele

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