cooccurrence_analysis.Rmd

---
title: "cooccurrence_analysis"
output: html_document
---

# format data into a species/site matrix! (in our case, OTU/subject matrix)
```{r}
# library(cooccur)
# library(xlsx)

# example analysis w/ finches data and cooccur package
# data(finches)
# View(finches)

# now, to check out the dataframe we're working with!
# srm_pos_hgm_subject_df <- subset(hgm_subject_df, SRM_present == "TRUE")
# subject_OTU_matrix <- srm_pos_hgm_subject_df[,c("merged_subject_id",OTU_names)]
# row.names(subject_OTU_matrix) <- subject_OTU_matrix$merged_subject_id

# write.xlsx2(subject_OTU_matrix, "subject_OTU_matrix.xlsx")
# manually remove merged_subject_id column in excel here!!!
subject_OTU_matrix <- read.xlsx2("subject_OTU_matrix.xlsx", row.names=1, sheetIndex = 1, colClasses = c("character", rep("numeric", 55)), endRow = 1295)

# subject_OTU_matrix_num <- as.matrix(apply(subject_OTU_matrix, 2, as.numeric))

# typeof(subject_OTU_matrix[1,1])
View(subject_OTU_matrix)
# DONE FUCKING FINALLY
```

# cooccurrence analysis on finches data (example)
```{r}
# example on finches data
# co <- print(cooccur(finches, spp_names = TRUE))
```

# cooccurrence analysis on our data!
```{r}
# small_matrix <- subject_OTU_matrix[1:9,1:3]
cooccur(mat=small_matrix, spp_names = T, type = "site_spp", thresh = T)
# subject_OTU_co <- print(cooccur(small_matrix, spp_names = T, type = "site_spp"))

# cooccur(finches, spp_names = T)
```