Merge branch '6-checklist' [#14]

Portfolio.md

@@ -1,6 +1,6 @@
 ---
 title: 'Time-adjusted effect of socioeconomic status in mortality rates after brain injury: cohort study'
-date: ""
+date: "2023-12-19"
 permalink: /portfolio/SAR-2023-016/
 redirect_from:
   - /portfolio/SAR-2023-016-BH/

report/SAR-2023-016-BH-v01.Rmd

@@ -2,7 +2,7 @@
 title: "Time-adjusted effect of socioeconomic status in mortality rates after brain injury: cohort study"
 subtitle: 'DOCUMENT: SAR-2023-016-BH-v01'
 author: '**From:** Felipe Figueiredo **To:** Brennan Hickson'
-date: "`r Sys.Date()`"
+date: "2023-12-19"
 output:
   html_document:
     fig_caption: yes
@@ -123,7 +123,7 @@ tab_desc %>%
   # as_flex_table(       # only for DOCX
   # ) %>%
   # flextable::set_caption(
-    caption = "**Table 1** Epidemiological, demographic and clinical characteristics of study participants."
+    caption = "**Table 1** Epidemiological, demographic and clinical characteristics of study participants at the time of discharge."
   )
 ```
 
@@ -200,7 +200,7 @@ tab_m6 %>%
   # as_flex_table(       # only for DOCX
   # ) %>%
   # flextable::set_caption(
-    caption = "**Table 2** Effect of SES on mortality; HR estimates were adjusted for sex, race, age, education, employment status, residence after rehab discharge, urbanization, rehabilitation payer, spinal cord injury, substance abuse, days from injury to rehabe, FIM scores quartiles and interactions between FIM scores and the exposure."
+    caption = "**Table 2** Effect of SES on mortality; HR estimates were adjusted for sex, race, age, education, employment status, residence after rehab discharge, urbanization, rehabilitation payer, spinal cord injury, substance abuse, days from injury to rehab, FIM scores quartiles and interactions between FIM scores and the exposure."
   )
 
 range_crude <- tab_inf$tbls[[1]]$table_body$estimate %>% range(na.rm = TRUE) %>% style_number(2)
@@ -236,7 +236,7 @@ All observational studies are recommended to be reported following the STROBE gu
 
 # Conclusions
 
-The epidemiological profile of the study participant is an 31 years old white male, that has greater than high school level of education, is actively employed and lives in an urban setting.
+The epidemiological profile of the study participant is a 31 years old white male, that has greater than high school level of education, is actively employed and lives in an urban setting.
 
 <!-- There appears to be a crude effect of SES on mortality, where participants that were discharged to either a comfortable or a distressed neighborhood had increased risk of death when compared to those discharged to a prosperous neighborhood. -->
 After controlling for

report/SAR-2023-016-BH-v01.md

@@ -104,7 +104,7 @@ A total of 334 (60%) were employed and
 287 (53%) participants lived in an urban area.
 
 
-Table: **Table 1** Epidemiological, demographic and clinical characteristics of study participants.
+Table: **Table 1** Epidemiological, demographic and clinical characteristics of study participants at the time of discharge.
 
 |                                        **Characteristic**                                        | **N = 564** |
 |:------------------------------------------------------------------------------------------------:|:-----------:|
@@ -252,7 +252,7 @@ The effect of SES of the neighborhood to which the individuals were discharged w
 No level of FIM motor function appears to be protective, but participants with the highest functional scores (within the fourth quartile) had a significant increased risk of dying in all neighborhoods, compared to the prosperous neighborhoods.
 
 
-Table: **Table 2** Effect of SES on mortality; HR estimates were adjusted for sex, race, age, education, employment status, residence after rehab discharge, urbanization, rehabilitation payer, spinal cord injury, substance abuse, days from injury to rehabe, FIM scores quartiles and interactions between FIM scores and the exposure.
+Table: **Table 2** Effect of SES on mortality; HR estimates were adjusted for sex, race, age, education, employment status, residence after rehab discharge, urbanization, rehabilitation payer, spinal cord injury, substance abuse, days from injury to rehab, FIM scores quartiles and interactions between FIM scores and the exposure.
 
 |**Characteristic**                                       | **HR** |  **95% CI**  | **p-value** |
 |:--------------------------------------------------------|:------:|:------------:|:-----------:|
@@ -317,7 +317,7 @@ All observational studies are recommended to be reported following the STROBE gu
 
 # Conclusions
 
-The epidemiological profile of the study participant is an 31 years old white male, that has greater than high school level of education, is actively employed and lives in an urban setting.
+The epidemiological profile of the study participant is a 31 years old white male, that has greater than high school level of education, is actively employed and lives in an urban setting.
 
 <!-- There appears to be a crude effect of SES on mortality, where participants that were discharged to either a comfortable or a distressed neighborhood had increased risk of death when compared to those discharged to a prosperous neighborhood. -->
 After controlling for

scripts/tables-save.R

@@ -74,6 +74,9 @@ tab_inf <- tbl_merge(
   tab_spanner = c("Model 1", "Model 2", "Model 3", "Model 4", "Model 5", "Model 6")
   )
 
+# simplified version of T2
+tab_m6 <- model6 %>% tab() %>% modify_footnote(estimate ~ model6.lab)
+
 # table A1 ----------------------------------------------------------------
 
 # use SE instead of CI
@@ -102,4 +105,4 @@ theme_gtsummary_compact()
 write_rds(tab_desc, "dataset/tab_desc_016.rds")
 write_rds(tab_inf, "dataset/tab_inf_016.rds")
 write_rds(tab_app, "dataset/tab_app_016.rds")
-model6 %>% tab() %>% modify_footnote(estimate ~ model6.lab) %>% write_rds("dataset/tab_m6_016.rds")
+tab_m6 %>% write_rds("dataset/tab_m6_016.rds")