calculate_k.Rmd

---
title: "calculate k"
author: "Melanie K. Taylor"
date: "2024-07-16"
output: pdf_document
---

```{r}
#if needed install tidyverse and litterfitter
library(litterfitter)
library(tidyverse)
library(dplyr)

#set working directory
setwd("C:/Users/melanietaylor/Desktop")

#load litter values
lit <- read.csv("C:/Users/melanietaylor/Desktop/k_values_g_per_g_with_duration_in_days_cornelissen.csv")
```

```{r}
#calculate proportion litter remaining
#calculate time in years
lit <- lit %>% 
  drop_na(proportion_mass_loss) %>%
  mutate(p_litter_remaining = 1 - proportion_mass_loss,
         length_yr = length_decomp_days/365)
  

#Get unique species
all_species <- unique(lit$speciesname)

output <- data.frame(species = character(),
                     k = double())

#started to try to write loop:
for (species in all_species) {

  df <- filter(lit, speciesname == species)
  
  fit <- fit_litter(time=c(0, df$length_yr),
                    mass.remaining = c(1, df$p_litter_remaining),
                    model = "neg.exp",
                    iters = 500)
  line_output <- data.frame(species=species, 
                            k=coef(fit))
  
  output <- rbind(output, line_output)
}

write.csv(output, "k_values_cornelissen.csv")

```