patchstat.Rmd

---
title: "White top Frequency"
author: "Amanda Stahlke"
date: "12/18/2019"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(scipen=999)
```

```{r libraries, message=FALSE, collapse=TRUE}
# data processing
library(dplyr)
library(SDMTools)
```


```{r}
freq_plot <- read.csv("Ldraba_raw_data_frequency.csv")
head(freq_plot, 20)
```

```{r}

freq_tots <- freq_plot %>%
  filter(cell_row=="Totals")
colnames(freq_tots)
dropcols <- c('date', 'recorder')
freq_tots <- freq_tots[,-which(colnames(freq_tots)==dropcols)]
freq_tots$site <- rep(1:6, each=3)
freq_tots$plot <- rep(1:3,  times=6)
freq_tots
freq_tots$site.plot <- paste0(freq_tots$site, ".", freq_tots$plot)

### These were calculated in Google sheet
colnames(freq_tots)[which(colnames(freq_tots)=="X")] <- "rowsum"

freq_tots %>%
  group_by(site.plot) %>%
  summarise(mean(rowsum)) %>%
  arrange(`mean(rowsum)`)

freq_tots %>%
  group_by(site) %>%
  summarise(mean(rowsum), sd(rowsum)) %>%
  arrange(`mean(rowsum)`)

freq_tots %>%
  # group_by(site) %>%
  summarise(mean(rowsum), sd(rowsum))
```
```{r}
freq_plot %>%
  filter(site==1) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  PatchStat(.,cellsize=1)

freq_plot %>%
  filter(site==1) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==2) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  # SDMTools::PatchStat(.,cellsize=1)
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==3) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==4) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==5) %>%
  dplyr::select(starts_with("col")) %>%
  # as.matrix() %>%SDMTools::ConnCompLabel() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==6) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  SDMTools::ConnCompLabel() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==4 & plot==1) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  # SDMTools::ConnCompLabel() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==4 & plot==2) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  # SDMTools::ConnCompLabel() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==4 & plot==3) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  ClassStat(.,cellsize=1)

freq_plot %>%
  filter(site==4 & plot==3) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  ConnCompLabel()

freq_plot %>%
  filter(site==4 & plot==3) %>%
  dplyr::select(starts_with("col")) %>%
  as.matrix() %>%
  ConnCompLabel() %>%
  ClassStat(.,cellsize=1)
```