# README

The following is a description of the files within this resource:

**Chagrin_Methods.pdf**: This document provides supplementary info for the methods used in collecting and processing samples.

**Chagrin2023_Analysis.RMD**: This document is an R markdown file containing the code used for the statistical analysis of the data within the Data Folder.

## Data Folder

* **Chagrin_DataSummary.csv**: This CSV file contains all the data points that were measured from biofilm samples. Nitrogen fixation was measured on intact biofilms, while all other endpoints where measured after the biofilms were scrubbed from the unglazed ceramic tile.
    * Variables  

| Variable Name | Definition | Units |
| -------- | ------- |------- |
| Stream_ID  | Mesocosm ID number    | Unitless |
| Chla |  Chlorophyll a concentration normalized to surface area from each mesocosm   |  μg Chla/cm^2 |
| AFDM |  Ash free dry mass (AFDM) normalized to surface area   |  g/cm^2 |
| AFDM_mg_cm2 |  Ash free dry mass (AFDM) normalized to surface area converted to mg/cm^2  |  mg/cm^2 |
| Regeneration Rate    | The rate that ammonium entered  into the water column.   |nmol N/hr |
| Uptake Rate    | The rate that ammonium was removed from the water column.   |nmol N/hr |
| Regen_SA    | The rate that ammonium entered into the water column normalized for surface area.   |nmol N/cm^2/hr |
| Uptake_SA    | The rate that ammonium was removed from the water column normalized for surface area.   |nmol N/cm^2/hr |
| Regen_Chla    | The rate that ammonium entered into the water column normalized for algal biomass.   |nmol N/μg Chla/cm^2/hr |
| Uptake_Chla   | The rate that ammonium was removed from the water columnnormalized for algal biomass.   |nmol N/μg Chla/cm^2/hr |
| Regen_AFDM    | The rate that ammonium entered into the water column normalized for AFDM.   |nmol N/μg AFDM/cm^2/hr |
| Uptake_AFDM   | The rate that ammonium was removed from the water columnnormalized for AFDM.   |nmol N/μg AFDM/cm^2/hr |
| Nfix sqcm    | Nitrogen fixation rates normalized for surface area   |μmol N/cm^2/hr |
| Corrected_Rates_ugN/ugChla/hr  | Nitrogen fixation rates normalized for Chla concentration   |μmol N/μg Chla/hr |
| LAP_Activity  | Leucine aminopeptidase (LAP) activity measured using a fluorescent substrate   |nmol N/hr |
| LAP_Activity_Chla  | Leucine aminopeptidase (LAP) activity measured using a fluorescent substrate normalized for Chla concentration   |nmol N/μg Chla/cm^2/hr |
| LAP_Activity_AFDM  | Leucine aminopeptidase (LAP) activity measured using a fluorescent substrate normalized for AFDM    |nmol N/μg AFDM/cm^2/hr |
| AAP_Activity  | Arginine aminopeptidase (AAP) activity measured using a fluorescent substrate   |nmol N/hr |
| AAP_Activity_Chla  | Arginine aminopeptidase (AAP) activity measured using a fluorescent substrate normalized for Chla concentration   |nmol N/μg Chla/cm^2/hr |
| AAP_Activity_AFDM  | Arginine aminopeptidase (AAP) activity measured using a fluorescent substrate normalized for AFDM    |nmol N/μg AFDM/cm^2/hr |
| Treatment |  Nutrient ammendment treatment the mesocosm received. N indicates nitrogen, P indicates phosphorus, Fe indicates iron, and "+" indicates a combination treatment.     | Unitless |
| N   | Indicates whether the mesocosm received N. A value of 1 indicates yes, 0 indicates no. | Unitless |
| P   | Indicates whether the mesocosm received P. A value of 1 indicates yes, 0 indicates no. | Unitless |
| Fe   | Indicates whether the mesocosm received Fe. A value of 1 indicates yes, 0 indicates no. | Unitless |
| Block   | Indicates which treatment block the mesocosm was placed within. | Unitless |


* **Bentho_Data.csv** : This file contains the algal biomass data obtained using BenthoTorch measurements over the study period which was used to calculate the growth curves for each of the mesocosms.
    * Variables 

| Variable Name    | Definition | Units |
| -------- | ------- |------- |
| streamID | Mesocosm ID number    | Unitless |
| Date  | Date that the measurement was taken    | Month/Day/Year |
| Diatoms  | Total diatom biomass estimated by the BenthoTorch    | μg/cm^2 |
| Cyanos  | Total cyanobacteria biomass estimated by the BenthoTorch    | μg/cm^2 |
| Green  | Total green algae biomass estimated by the BenthoTorch    | μg/cm^2 |
| Total_Biomass  | Total biomass obtained by pooling the biomass estimates of all three algal groups    | μg/cm^2 |
| Treatment |  Nutrient ammendment treatment the mesocosm received. N indicates nitrogen, P indicates phosphorus, Fe indicates iron, and "+" indicates a combination treatment.     | Unitless |
| N   | Indicates whether the mesocosm received N. A value of 1 indicates yes, 0 indicates no. | Unitless |
| P   | Indicates whether the mesocosm received P. A value of 1 indicates yes, 0 indicates no. | Unitless |
| Fe   | Indicates whether the mesocosm received Fe. A value of 1 indicates yes, 0 indicates no. | Unitless |
| Block   | Indicates which treatment block the mesocosm was placed within. | Unitless |


* **Growth_Rate_3.csv** : This file contains the logistic growth rate model outputs for each mesocosm except for the three where a model was unable to be fitted.
    * Variables 

| Variable Name    | Definition | Units |
| -------- | ------- |------- |
| streamID | Mesocosm ID number    | Unitless |
| Asym  | The carrying capacity of the mesocosm    | K |
| scal| The inverse of the intrinsic growth rate   | 1/r |
| xmid| The initial population size divided by the intrinsic growth rate  | P_0/r|