---
title: "analyses"
output: html_document
date: "2025-03-03"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(dplyr)
library(kableExtra)
library(ggplot2)
library(officer)
library(flextable)
library(openxlsx)
```

## Binom test



```{r tabelka, include=FALSE}


proportions_binom <- data.frame(
                 species = character(),
                 stage = character(),
                 M = numeric(),
                 F = numeric(),
                 M_F = numeric(),
                 prop = numeric(),
                 p_val = numeric(),
                 ci_min = numeric(),
                 ci_max = numeric(),
                 stringsAsFactors = FALSE)
```

```{r funkcje, echo=FALSE}



describe_binom <- function(df, species, stage, Mn, Fn) {
  all <- (Mn+Fn)
  #tab <- matrix(c(Mn, all/2, Fn, all/2), nrow = 2)
  pt <- binom.test(x = Mn, n = all, p = 0.5)
  df <- rbind(df, data.frame(
                 species = species,
                 stage = stage,
                 M = Mn,
                 F = Fn,
                 M_F = round(Mn/Fn, 2),
                 prop = round(pt$estimate, 2),
                 p_val = round(pt$p.value, 4),
                 ci_min = round(pt$conf.int[1], 2),
                 ci_max = round(pt$conf.int[2], 2)
  )
  )
return(df)  
}
```

```{r ra-seeds, echo=FALSE}
Fn <- 62
Mn <- 38
seeds <- c(Fn, Mn)
all_n <- sum(seeds)


proportions_binom <- describe_binom(proportions_binom, "R. acetosa", "seeds", Mn, Fn)
```


```{r ra-seedlings, echo=FALSE}
Fs <- 18
Ms <- 17
seedlings <- c(Fs, Ms)
all_s <- sum(seedlings)

proportions_binom <- describe_binom(proportions_binom, "R. acetosa", "plants", Ms, Fs)
```




```{r rt-seeds, echo=FALSE}
Fn <- 40+38+38+41
Mn <- 18+21+22+19
seeds <- c(Fn, Mn)
all_n <- sum(seeds)


proportions_binom <- describe_binom(proportions_binom, "R. thyrsiflorus", "seeds", Mn, Fn)
```


```{r rt-seedlings, echo=FALSE}
Fs <- 17
Ms <- 9
seedlings <- c(Fs, Ms)
all_s <- sum(seedlings)


proportions_binom <- describe_binom(proportions_binom, "R. thyrsiflorus", "plants", Ms, Fs)

```

```{r plot-proportions, echo=FALSE}



proportions_binom$group <- paste(proportions_binom$species, proportions_binom$stage, sep = " - ")
knitr::kable(proportions_binom) %>% kable_styling(full_width = FALSE, position = "center")
proportions_binom$group <- factor(proportions_binom$group, levels = c("R. acetosa - seeds", 
                                        "R. acetosa - plants",
                                        "R. thyrsiflorus - seeds",
                                        "R. thyrsiflorus - plants"))

write.table(proportions_binom, file = "proportions_binom.tsv", 
            sep = "\t",           
            row.names = FALSE,    
            quote = FALSE,        
            na = "NA")

write.xlsx(proportions_binom, file = "proportions_binom.xlsx", rowNames = FALSE)

doc <- read_docx()
doc <- doc %>%
  body_add_flextable(flextable(proportions_binom))
print(doc, target = "proportions_binom.docx")


p <- ggplot(proportions_binom, aes(x = group, y = prop, fill = stage)) +
  geom_bar(stat = "identity", width = 0.7, color = "black") +
  geom_errorbar(aes(ymin = ci_min, ymax = ci_max), width = 0.2, size = 0.8) +
  scale_fill_manual(values = c("seeds" = "gray80", "plants" = "gray90")) +
  ylim(0, 1) +
  labs(x = "Species and Stage", y = "Frequency of males", 
       title = "Frequency of males in seeds and plants") +
  theme_minimal() +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
p
ggsave(filename = "box_binom.svg", plot = p, width = 8, height = 6, dpi = 300, bg = "transparent")
ggsave(filename = "box_binom.pdf", plot = p, width = 8, height = 6, bg = "transparent")
ggsave(filename = "box_binom.png", plot = p, width = 8, height = 6, dpi = 300, bg = "transparent")
```