-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathREADME.Rmd
122 lines (74 loc) · 7.24 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
---
title: "SCBI Dendrometer bands"
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
[](https://zenodo.org/badge/latestdoi/150600455)
### Data collection errors to resolve
[](https://github.com/SCBI-ForestGEO/Dendrobands/actions)
**[Click here to view error reports.](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/testthat/reports)**
### warnings?
*These do not cause the tests to fail, but may indicate problems and should be reviewed.*
[](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/testthat/reports/warnings)
### Anomalous measurement report
```{r, echo=FALSE}
if(file.exists("testthat/reports/measurement_anomalies.png")){
knitr::include_graphics("testthat/reports/measurement_anomalies.png")
} else {
print("No anomalous measurements at the moment.")
}
```
## Overview
This repository contains dendrometer bands data for the SCBI ForestGEO plot. There are two sets of measurements:
1. *Biannual dendrometer bands* - dendrometer bands on >500 trees measured at start and end of growing season: 2010 - present
2. *Intra-annual (i.e. biweekly) dendrometer bands* - dendrometer bands on >150 trees measured around every 2 weeks during growing season: 2011 - present
This data exists in two forms:
1. [Raw data](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/resources/raw_data/) based on field collection forms.
1. [Post-processed data](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/data/) in the `scbi.dendroAll_YEAR.csv` files. This is the data to be used for analysis.
Whenever raw data is pushed to GitHub, GitHub Actions continuous integration follows the steps in [`.github/workflows/QA_QC_checks.yaml`](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/.github/workflows/QA_QC_checks.yaml), which automatically 1) takes the raw data and produces the post-processed data and 2) performs data QA/QC
To learn how to address both 1) code scripting and 2) data collection errors identified by GitHub Actions, watch this [screencast training video](https://sinet-my.sharepoint.com/:v:/g/personal/kimay_si_edu/EQ4BrXfDnk5MrtPihpFc4cYBMmn287nAxw6Rjn4P6Ruifg).
## Sampling location
[SCBI ForestGEO plot](https://forestgeo.si.edu/sites/north-america/smithsonian-conservation-biology-institute)
## Protocols and data management
1. *Biannual dendrometer bands* - In 2010, 243 bands were initially installed, additional bands were installed in 2011 and currently more than 515 stems of various DBH (5.5-152 cm) are being monitored. Protocols for band installations and remeasurement are published here ([original protocol](https://forestgeo.si.edu/sites/default/files/metal_band_dendrometer_protocol_done_1.pdf); [latest protocol](https://docs.google.com/document/d/1kCG22EAEnOVxw9Z-cPPvrHIzvRFE-j0U7anTmhJbkqM/edit)).
1. *Intra-annual dendrometer bands* - Since 2011, ~155 stems of DBH ranging from 6-148 cm are monitored biweekly during the growing season each year.
### Workflow
- [field_forms](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/resources/field_forms) and [raw_data](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/resources/raw_data) are pulled from the year's master file via R-scripts
- [maps](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/resources/maps) are generated based on the [current list of trees with dendrobands](https://github.com/SCBI-ForestGEO/Dendrobands/blob/master/data/dendro_trees.csv).
- data recorded in the field are entered in [raw_data](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/resources/raw_data) and immediately merged into the current year's master file using an R script.
### Data organization
A dataset for each year of collection is found in the [data folder](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/data). Each year has a master data set that includes both biannual and intra-annual surveys (with a file name format "scbi.dendroAll_YEAR.csv")
In the interest of keeping survey data entry simplified, each type of survey (biannual and intra-annual) has its own .csv for data entry for the current year. This is where the current year’s data will be entered during the growing season (March – November). When the growing season is finished and the November biannual survey is complete, data should be transferred to the scbi.dendroAll_YEAR.csv via joining/merging in R.
1. Metadata for these individual forms are consistent with the scbi.dendroAll_YEAR.csv [metadata](https://github.com/SCBI-ForestGEO/Dendrobands/blob/master/data/metadata/scbi.dendroALL_%5BYEAR%5D_metadata.csv) (the master).
## Tree data for dendro trees
A summary of tree species by survey type per year (ie. dbh range) are available [here](https://github.com/SCBI-ForestGEO/Dendrobands/tree/master/results/dendro_trees_dbhcount).
Some relevant data on dendrometer banded trees (geographic location, date started/end, mortalitity year, etc) is available here [dendro_trees.csv](https://github.com/SCBI-ForestGEO/Dendrobands/blob/master/data/dendro_trees.csv).
## Data Management
Collection of these data is a collaboration between the Anderson-Teixeira and McShea labs. These data formerly lived on the McShea V: drive (V:/SIGEO/DENDROMETRY/Dendrobands), and are now managed in this GitHub repository by the Anderson-Teixeira lab. Access is provided to any McShea lab member via SCBI-ForestGEO-guest, the password for which is stored in the V: drive.
## Data use
Contact [Kristina Anderson-Texeira](teixeirak@si.edu)
Note: Also relevant (for code, cross-site integration) is the [ForestGEO Dendro repository](https://github.com/forestgeo/dendro).
## Contributors
| name | GitHub ID| position* | role |
| -----| ---- | ---- |---- |
| Kristina Anderson-Teixeira | teixeirak | staff scientist, SCBI & STRI | plot PI |
| William McShea | | staff scientist, SCBI | plot PI |
| Erika Gonzalez-Akre | gonzalezeb | lab manager, SCBI | oversight of data collection |
| Victoria Meakem | | research assistant, SCBI | data collection |
| Ryan Helcoski | RHelcoski | research assistant, SCBI | data collection |
| Ian McGregor | mcgregorian1 | research assistant, SCBI | data collection, data organization, coding |
| Alyssa Terrell | terrella3 | research assistant, SCBI | data collection, data organization, coding |
| Cameron Dow | camerondow35 | research assistant, SCBI | data collection, data organization, coding |
| Albert Y. Kim | rudeboybert | research associate, SCBI | data organization, coding, continuous integration |
| Jess Shue | jess-shue | biological science technician, SERC | data collection, data organization, coding |
| Jennifer A. Jordan | jenajordan | intern, SCBI | data collection, data organization |
| Erin L. MacMonigle | | intern, SCBI | data collection, data organization |
*refers to position at time of main contribution to this repository
[List does not yet include field assistants/ students/ volunteers who helped collect data]
## Funding
ForestGEO
## Contact
Contact Erika Gonzalez-Akre or Albert Y. Kim for any inquiry on dendroband data collection at SCBI.