Add analyses chunks

generate_report.Rmd

 ---
 title: "MPGQuestionnaireReport"
 author: "Kleemeyer"
-date: "11/4/2020"
+date: "`r format(Sys.time(), '%d %B, %Y')`"
 output:
-  pdf_document: default
+#  pdf_document: default
   html_document: default
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
+knitr::opts_chunk$set(echo = TRUE, message = FALSE)
 library(knitr)
+library(kableExtra)
 library(ggplot2)
 library(dplyr)
 library(corrr)
+library(umx)
+library(matrixStats)
 
 source("get_data_exported.R")
 ```
 # Scale consistency
 
-* SCALE A: Group atmosphere
+## SCALE A: Group atmosphere
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_A <- responses_coded %>%
   select(A03:A05) %>%
   correlate() 
@@ -44,9 +47,9 @@ kable(output_A, caption = "Item statistics scale A")
 
 Cronbach's alpha for Scale A is `r rely_A$total$std.alpha`. 
 
-* SCALE B1: Leadership leadstyle
+## SCALE B1: Leadership leadstyle
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_B1 <- responses_coded %>%
   select(B02:B07) %>%
   correlate() 
@@ -70,9 +73,9 @@ kable(output_B1, caption = "Item statistics scale B1")
 
 Cronbach's alpha for Scale B1 is `r rely_B1$total$std.alpha`. 
 
-* SCALE B2: Leadership development
+## SCALE B2: Leadership development
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_B2 <- responses_coded %>%
   select(B09:B13) %>%
   correlate() 
@@ -96,9 +99,9 @@ kable(output_B2, caption = "Item statistics scale B2")
 
 Cronbach's alpha for Scale B2 is `r rely_B2$total$std.alpha`. 
 
-* SCALE C: Commitment
+## SCALE C: Commitment
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_C <- responses_coded %>%
   select(C02:C04) %>%
   correlate() 
@@ -122,9 +125,9 @@ kable(output_C, caption = "Item statistics scale C")
 
 Cronbach's alpha for Scale C is `r rely_C$total$std.alpha`. 
 
-* SCALE D: Bullying
+## SCALE D: Bullying
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_D <- responses_coded %>%
   select(D02:D06) %>%
   correlate() 
@@ -148,9 +151,9 @@ kable(output_D, caption = "Item statistics scale D")
 
 Cronbach's alpha for Scale D is `r rely_D$total$std.alpha`. 
 
-* SCALE E: Gender discrimination
+## SCALE E: Gender discrimination
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_E <- responses_coded %>%
   select(E03:E05) %>%
   correlate() 
@@ -174,9 +177,9 @@ kable(output_E, caption = "Item statistics scale E")
 
 Cronbach's alpha for Scale E is `r rely_E$total$std.alpha`. 
 
-* SCALE F: Sexual harassment
+## SCALE F: Sexual harassment
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_F <- responses_coded %>%
   select(F02:F08) %>%
   correlate() 
@@ -200,9 +203,9 @@ kable(output_F, caption = "Item statistics scale F")
 
 Cronbach's alpha for Scale F is `r rely_F$total$std.alpha`. 
 
-* SCALE H1: Work-life Balance
+## SCALE H1: Work-life Balance
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_H1 <- responses_coded %>%
   select(H02:H06) %>%
   correlate() 
@@ -226,9 +229,9 @@ kable(output_H1, caption = "Item statistics scale H1")
 
 Cronbach's alpha for Scale H1 is `r rely_H1$total$std.alpha`. 
 
-* SCALE H2: Work-family Balance
+## SCALE H2: Work-family Balance
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_H2 <- responses_coded %>%
   select(H09:H13) %>%
   correlate() 
@@ -252,9 +255,9 @@ kable(output_H2, caption = "Item statistics scale H2")
 
 Cronbach's alpha for Scale H2 is `r rely_H2$total$std.alpha`. 
 
-* SCALE H3: Parental leave - yes
+## SCALE H3: Parental leave - yes
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_H3 <- responses_coded %>%
   select(H17:H21) %>%
   correlate() 
@@ -278,9 +281,9 @@ kable(output_H3, caption = "Item statistics scale H3")
 
 Cronbach's alpha for Scale H3 is `r rely_H3$total$std.alpha`. 
 
-* SCALE H4: Parental leave - no
+## SCALE H4: Parental leave - no
 
-```{r echo = FALSE, message = FALSE}
+```{r echo = FALSE, results='asis'}
 interitem_H4 <- responses_coded %>%
   select(H23:H25) %>%
   correlate() 
@@ -304,61 +307,92 @@ kable(output_H4, caption = "Item statistics scale H4")
 
 Cronbach's alpha for Scale H4 is `r rely_H4$total$std.alpha`. 
 
-# Analyses
+# Factor Analyses
+
+```{r echo = FALSE, message = FALSE, include = FALSE}
+likert <- responses_coded %>%
+  select(A03:B13,C02:D06,E03:E05,F02:F08,H02:H06)
+
+efa <- umxEFA(likert, factors = 8, minManifests = 5)
+factors <- as.data.frame(loadings(efa))
+
+color.me <- rowMaxs(abs(loadings(efa)))
+```
+
+```{r echo = FALSE, message = FALSE}
+
+factors %>% 
+  mutate(items = row.names(.)) %>%
+  relocate(items) %>%
+  mutate_all(~cell_spec(
+    .x, 
+    color = ifelse(abs(.x) %in% color.me, "red", "black"))) %>%
+  kbl(format = "html", escape = F) %>%
+  kable_paper("striped") %>%
+  pack_rows("Scale A", 1, 3) %>%
+  pack_rows("Scale B", 4, 14) %>%
+  pack_rows("Scale C", 15, 17) %>%
+  pack_rows("Scale D", 18, 22) %>%
+  pack_rows("Scale E", 23, 25) %>%
+  pack_rows("Scale F", 26, 32) %>%
+  pack_rows("Scale H", 33, 37) %>%
+
+  kable_styling()
+
+```
+
+# General Analyses
 
 In total, `r nrow(responses)` participants (partly) completed the questionnaire.
 
 # Binary Questions
 
 * Do you work in a group?
-
-```{r echo = FALSE}
-table(responses$A01, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$A01, useNA = "ifany"))
 ```
 
-
 * Did you have a personal conversation with your supervisor?
-
-```{r echo = FALSE}
-table(responses$B14, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$B14, useNA = "ifany"))
 ```
 
 * Have you been subjected to bullying during the past 12 months?
-```{r echo = FALSE}
-table(responses$D12, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$D12, useNA = "ifany"))
 ```
 
 * Have you been subjected to gender discrimination during the past 12 months?
-```{r echo = FALSE}
-table(responses$E05, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$E05, useNA = "ifany"))
 ```
 
 * Have you been subjected to sexual harassment during the past 12 months?
-```{r echo = FALSE}
-table(responses$F11, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$F11, useNA = "ifany"))
 ```
 
 * Do children under the age of 18 live in your household?
-```{r echo = FALSE}
-table(responses$H07, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$H07, useNA = "ifany"))
 ```
 
 * Do people with care needs live in your household?
-```{r echo = FALSE}
-table(responses$H30, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$H30, useNA = "ifany"))
 ```
 
 * Have you taken parental leave?
-```{r echo = FALSE}
-table(responses$H14, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$H14, useNA = "ifany"))
 ```
 
-* Ehat is your gender?
-```{r echo = FALSE}
-table(responses$I02, useNA = "ifany")
+* What is your gender?
+```{r echo = FALSE, results='asis'}
+kable(table(responses$I02, useNA = "ifany"))
 ```
 
 * What is your position in the MPG?
-```{r echo = FALSE}
-table(responses$I03, useNA = "ifany")
+```{r echo = FALSE, results='asis'}
+kable(table(responses$I03, useNA = "ifany"))
 ```