Last updated: 2021-11-11

Checks: 7 0

Knit directory: 2019-feature-selection/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20190522)

The command set.seed(20190522) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

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File paths: relative

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Repository version: 25bf2db

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The results in this page were generated with repository version 25bf2db. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    .Ruserdata/
    Ignored:    .drake/
    Ignored:    .vscode/
    Ignored:    analysis/rosm.cache/
    Ignored:    data/
    Ignored:    inst/Benchmark for Filter Methods for Feature Selection in High-Dimensional  Classification Data.pdf
    Ignored:    inst/study-area-map/._study-area.qgs
    Ignored:    inst/study-area-map/study-area.qgs~
    Ignored:    log/
    Ignored:    renv/library/
    Ignored:    renv/local/
    Ignored:    renv/staging/
    Ignored:    reviews/
    Ignored:    rosm.cache/

Unstaged changes:
    Modified:   R/01-fun-download.R
    Modified:   R/03-fun-hyperspectral.R
    Modified:   _drake.R
    Modified:   code/010-download.R
    Modified:   code/020-hyperspectral-processing.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/eda.Rmd) and HTML (docs/eda.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	25bf2db	pat-s	2021-11-11	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	16d6a74	pat-s	2021-11-02	Build site.
Rmd	547c3de	pat-s	2021-11-02	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
Rmd	b2df0fb	pat-s	2021-11-02	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	d9e2d9c	pat-s	2021-04-12	Build site.
Rmd	d83e8cf	pat-s	2021-04-12	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	af4e9aa	pat-s	2021-04-05	Build site.
Rmd	ab68766	pat-s	2021-04-01	restore old observation counts
html	5820967	pat-s	2021-03-30	Build site.
Rmd	67ae6cf	pat-s	2021-03-30	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
Rmd	4d87520	pat-s	2021-03-29	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
Rmd	c46d8bb	pat-s	2021-03-11	object name fixes
Rmd	632ad43	pat-s	2021-03-07	eda: 95% for PCA instead of 90%
html	b1e5802	pat-s	2021-02-10	Build site.
Rmd	250c984	pat-s	2021-02-10	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	8dc0133	pat-s	2021-02-09	Build site.
Rmd	bb8195d	pat-s	2021-02-09	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	fd3acb5	pat-s	2020-12-26	Build site.
Rmd	82ed31e	pat-s	2020-12-26	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	06f8310	pat-s	2020-12-26	Build site.
Rmd	d690cc0	pat-s	2020-12-26	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	b65821e	pat-s	2020-12-26	Build site.
Rmd	97711ce	pat-s	2020-12-26	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	0328965	pat-s	2020-12-26	Build site.
Rmd	0c854fe	pat-s	2020-12-26	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	875226f	pat-s	2020-12-26	Build site.
Rmd	e8b7487	pat-s	2020-12-26	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	ea4e83e	pat-s	2020-12-26	Build site.
Rmd	084bb6d	pat-s	2020-12-26	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	a016ad6	pat-s	2020-12-25	Build site.
Rmd	1143bc1	pat-s	2020-12-25	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
html	a953299	pat-s	2020-08-12	Build site.
html	8b5e422	pat-s	2020-08-05	Build site.
html	2be34b0	pat-s	2020-03-22	Build site.
Rmd	f40ac65	pat-s	2020-03-22	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose = TRUE)
Rmd	8794c9d	pat-s	2020-03-03	remove copy_figures() from eda.Rmd
Rmd	2e9f8a1	pat-s	2020-02-24	do everything for buffer of 2m and no buffer
html	3cab82e	pat-s	2020-02-15	Build site.
Rmd	5b2fa27	pat-s	2020-02-15	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose =
html	f2c521e	pat-s	2020-02-14	Build site.
Rmd	4f44b92	pat-s	2020-02-14	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose =
html	b1f675f	pat-s	2020-01-08	Build site.
html	f93458f	pat-s	2019-12-21	Build site.
html	6f633ff	pat-s	2019-09-02	Build site.
Rmd	518d0cb	pat-s	2019-09-01	style files using tidyverse style
html	7582c67	pat-s	2019-08-31	Build site.
html	caafca3	pat-s	2019-08-29	Build site.
html	abed0ec	pat-s	2019-08-12	Build site.
html	df85aba	pat-s	2019-07-12	Build site.
html	3a44a95	pat-s	2019-07-10	Build site.
html	4f6bc44	pat-s	2019-07-02	Build site.
Rmd	888dc6b	pat-s	2019-07-02	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose =
Rmd	24e318f	pat-s	2019-07-01	update reports
Rmd	b1f8fd7	pat-s	2019-07-01	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE, verbose =
Rmd	0969776	pat-s	2019-06-28	misc
html	32d5be0	pat-s	2019-06-27	Build site.
Rmd	185d576	pat-s	2019-06-27	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)
Rmd	ca7205f	pat-s	2019-06-27	add new report
Rmd	f49f020	pat-s	2019-06-26	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)
html	3110e18	pat-s	2019-06-24	Build site.
Rmd	13b04f0	pat-s	2019-06-24	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)
html	8b7af59	pat-s	2019-06-22	Build site.
Rmd	6402961	pat-s	2019-06-22	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)
html	b5ca114	pat-s	2019-06-21	Build site.
Rmd	7b1372a	pat-s	2019-06-21	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)
Rmd	2ffcc3b	pat-s	2019-06-19	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)
Rmd	4cf247a	pat-s	2019-06-18	fix git
html	4cf247a	pat-s	2019-06-18	fix git
Rmd	48817ef	pat-s	2019-06-15	move figure
html	4c3422d	pat-s	2019-06-15	Build site.
html	55e63a8	pat-s	2019-06-15	Build site.
Rmd	21871f7	pat-s	2019-06-15	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)
Rmd	6e2989d	pat-s	2019-06-15	update reports
Rmd	eaa444a	pat-s	2019-06-15	add EDA and spectral signatures report
html	5230081	pat-s	2019-06-15	Build site.
Rmd	a036319	pat-s	2019-06-15	wflow_publish(knitr_in(“analysis/eda.Rmd”), view = FALSE)

VI = Vegetation Indices
NRI = Normalized Ratio Indices
HR = Hyperspectral reflectances (image bands)

Datasets

VI

Overview

Name	Value
Rows	1,808
Columns	90
Discrete columns	0
Continuous columns	90
All missing columns	0
Missing observations	0
Complete Rows	1,808
Total observations	162,720

Histograms

Version	Author	Date
16d6a74	pat-s	2021-11-02
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
16d6a74	pat-s	2021-11-02
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
8dc0133	pat-s	2021-02-09
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
3a44a95	pat-s	2019-07-10
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
4c3422d	pat-s	2019-06-15
5230081	pat-s	2019-06-15

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
3a44a95	pat-s	2019-07-10
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
4c3422d	pat-s	2019-06-15
5230081	pat-s	2019-06-15

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
3a44a95	pat-s	2019-07-10
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
4c3422d	pat-s	2019-06-15
5230081	pat-s	2019-06-15

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
3a44a95	pat-s	2019-07-10
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
4c3422d	pat-s	2019-06-15
5230081	pat-s	2019-06-15

PCA

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
b1e5802	pat-s	2021-02-10
8dc0133	pat-s	2021-02-09
fd3acb5	pat-s	2020-12-26
06f8310	pat-s	2020-12-26
b65821e	pat-s	2020-12-26
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
8b5e422	pat-s	2020-08-05
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
3a44a95	pat-s	2019-07-10
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
4c3422d	pat-s	2019-06-15
5230081	pat-s	2019-06-15

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
8dc0133	pat-s	2021-02-09
fd3acb5	pat-s	2020-12-26
06f8310	pat-s	2020-12-26
b65821e	pat-s	2020-12-26
0328965	pat-s	2020-12-26
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25

      pc        var         pct   cum_pct
 1:  PC1 42.4131654 0.476552420 0.4765524
 2:  PC2 22.4594889 0.252353808 0.7289062
 3:  PC3  5.3988741 0.060661506 0.7895677
 4:  PC4  3.5094306 0.039431805 0.8289995
 5:  PC5  2.6970006 0.030303378 0.8593029
 6:  PC6  1.7125059 0.019241640 0.8785446
 7:  PC7  1.2014343 0.013499262 0.8920438
 8:  PC8  1.1551886 0.012979647 0.9050235
 9:  PC9  1.0728365 0.012054342 0.9170778
10: PC10  0.9912339 0.011137459 0.9282153
11: PC11  0.8577122 0.009637215 0.9378525
12: PC12  0.7408468 0.008324121 0.9461766

Corr

Version	Author	Date
16d6a74	pat-s	2021-11-02
d9e2d9c	pat-s	2021-04-12
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
8b5e422	pat-s	2020-08-05
3cab82e	pat-s	2020-02-15
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

NRI

Overview

Name	Value
Rows	1,808
Columns	7,382
Discrete columns	0
Continuous columns	7,382
All missing columns	0
Missing observations	0
Complete Rows	1,808
Total observations	13,346,656

Histograms

No histograms for NRI -> too many features.

PCA

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
b1e5802	pat-s	2021-02-10
fd3acb5	pat-s	2020-12-26
06f8310	pat-s	2020-12-26
b65821e	pat-s	2020-12-26
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
8b5e422	pat-s	2020-08-05
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
6f633ff	pat-s	2019-09-02
7582c67	pat-s	2019-08-31
abed0ec	pat-s	2019-08-12
3a44a95	pat-s	2019-07-10
4f6bc44	pat-s	2019-07-02
32d5be0	pat-s	2019-06-27
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
4c3422d	pat-s	2019-06-15
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
b1e5802	pat-s	2021-02-10
fd3acb5	pat-s	2020-12-26
06f8310	pat-s	2020-12-26
b65821e	pat-s	2020-12-26
0328965	pat-s	2020-12-26
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25

Corr

No correlation plot for NRI -> too many features.

HR

Overview

Name	Value
Rows	1,808
Columns	123
Discrete columns	0
Continuous columns	123
All missing columns	0
Missing observations	0
Complete Rows	1,808
Total observations	222,384

Histograms

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

PCA

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
b1e5802	pat-s	2021-02-10
fd3acb5	pat-s	2020-12-26
06f8310	pat-s	2020-12-26
b65821e	pat-s	2020-12-26
0328965	pat-s	2020-12-26
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
8b5e422	pat-s	2020-08-05
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
0328965	pat-s	2020-12-26
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
b1e5802	pat-s	2021-02-10
fd3acb5	pat-s	2020-12-26
06f8310	pat-s	2020-12-26
b65821e	pat-s	2020-12-26
0328965	pat-s	2020-12-26
875226f	pat-s	2020-12-26

Corr

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
875226f	pat-s	2020-12-26
a016ad6	pat-s	2020-12-25
8b5e422	pat-s	2020-08-05
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
b1f675f	pat-s	2020-01-08
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
5230081	pat-s	2019-06-15

Custom plots

Mean defoliation per plot

# A tibble: 4 x 2
  plot     `mean(defoliation)`
* <fct>                  <dbl>
1 Laukiz 1                57.2
2 Laukiz 2                13.5
3 Luiando                 68.4
4 Oiartzun                69.1

Coefficient of variation

# A tibble: 4 x 2
  plot     `(sd(defoliation)/mean(defoliation)) * 100`
* <fct>                                          <dbl>
1 Laukiz 1                                        34.5
2 Laukiz 2                                       125. 
3 Luiando                                         12.2
4 Oiartzun                                        20.2

sd / skewness

# A tibble: 4 x 2
  plot     `((sd(defoliation)/mean(defoliation)) * 100)/e1071::skewness(defolia…
* <fct>                                                                    <dbl>
1 Laukiz 1                                                                -40.7 
2 Laukiz 2                                                                 55.0 
3 Luiando                                                                  -3.19
4 Oiartzun                                                                -21.5

# A tibble: 4 x 2
  plot     `sd(defoliation)`
* <fct>                <dbl>
1 Laukiz 1             19.8 
2 Laukiz 2             16.9 
3 Luiando               8.32
4 Oiartzun             14.0

Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Warning in is.na(x): is.na() applied to non-(list or vector) of type
'expression'

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
8dc0133	pat-s	2021-02-09
a016ad6	pat-s	2020-12-25
2be34b0	pat-s	2020-03-22
f2c521e	pat-s	2020-02-14
f93458f	pat-s	2019-12-21
4f6bc44	pat-s	2019-07-02
b5ca114	pat-s	2019-06-21
4cf247a	pat-s	2019-06-18
55e63a8	pat-s	2019-06-15

Point density

Mean average distance between all trees in a given plot.

Calculated via raster::pointDistance(allpairs = TRUE).

$`Laukiz 1`
[1] 34.3363

$`Laukiz 2`
[1] 61.5862

$Luiando
[1] 33.75951

$Oiartzun
[1] 35.09547

PCA feature set comparison

Comparing the “proportion of variance explained” (POV) for all feature sets.

Version	Author	Date
af4e9aa	pat-s	2021-04-05
5820967	pat-s	2021-03-30
b1e5802	pat-s	2021-02-10
8dc0133	pat-s	2021-02-09
fd3acb5	pat-s	2020-12-26
06f8310	pat-s	2020-12-26
b65821e	pat-s	2020-12-26
0328965	pat-s	2020-12-26
875226f	pat-s	2020-12-26

Buffer extraction scenario sketches

Standard scenario (somewhere within the pixel)

Extreme scenario (at the border of one or multiple pixels)

R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /opt/spack/opt/spack/linux-centos7-x86_64/gcc-9.2.0/r-4.0.4-udi7a3ahhtokdcoyqdbndhebeupt7hid/rlib/R/lib/libRblas.so
LAPACK: /opt/spack/opt/spack/linux-centos7-x86_64/gcc-9.2.0/r-4.0.4-udi7a3ahhtokdcoyqdbndhebeupt7hid/rlib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] here_1.0.1         patchwork_1.1.1    fs_1.5.0           raster_3.4-5      
 [5] sp_1.4-5           purrr_0.3.4        knitr_1.31         ggpubr_0.4.0      
 [9] ggplot2_3.3.3      ggsci_2.9          dplyr_1.0.4        DataExplorer_0.8.2
[13] usethis_2.0.0      magrittr_2.0.1     drake_7.13.2      

loaded via a namespace (and not attached):
 [1] tidyr_1.1.2       carData_3.0-4     R.utils_2.10.1    highr_0.8        
 [5] base64url_1.4     renv_0.13.2       cellranger_1.1.0  yaml_2.2.1       
 [9] progress_1.2.2    pillar_1.4.7      backports_1.2.1   lattice_0.20-41  
[13] glue_1.4.2        digest_0.6.27     promises_1.1.1    ggsignif_0.6.0   
[17] colorspace_2.0-0  plyr_1.8.6        htmltools_0.5.1.1 httpuv_1.5.5     
[21] R.oo_1.24.0       pkgconfig_2.0.3   broom_0.7.4       haven_2.3.1      
[25] scales_1.1.1      whisker_0.4       openxlsx_4.2.3    later_1.1.0.1    
[29] rio_0.5.16        git2r_0.28.0      tibble_3.0.6      txtq_0.2.3       
[33] farver_2.0.3      generics_0.1.0    car_3.0-10        ellipsis_0.3.1   
[37] withr_2.4.1       cli_2.4.0         crayon_1.4.0      readxl_1.3.1     
[41] evaluate_0.14     storr_1.2.5       R.methodsS3_1.8.1 fansi_0.4.2      
[45] class_7.3-18      rstatix_0.6.0     forcats_0.5.1     foreign_0.8-81   
[49] tools_4.0.4       data.table_1.13.6 prettyunits_1.1.1 hms_1.0.0        
[53] lifecycle_0.2.0   stringr_1.4.0     munsell_0.5.0     zip_2.1.1        
[57] e1071_1.7-4       networkD3_0.4     compiler_4.0.4    rlang_0.4.10     
[61] grid_4.0.4        rstudioapi_0.13   htmlwidgets_1.5.3 igraph_1.2.6     
[65] labeling_0.4.2    rmarkdown_2.6     gtable_0.3.0      codetools_0.2-18 
[69] abind_1.4-5       curl_4.3          reshape2_1.4.4    R6_2.5.0         
[73] gridExtra_2.3     rgdal_1.5-23      utf8_1.1.4        filelock_1.0.2   
[77] workflowr_1.6.2   rprojroot_2.0.2   stringi_1.5.3     parallel_4.0.4   
[81] Rcpp_1.0.6        vctrs_0.3.6       tidyselect_1.1.0  xfun_0.20

Exploratory data analysis

Patrick Schratz

Datasets

VI

Overview

Histograms

PCA

Corr

NRI

Overview

Histograms

PCA

Corr

HR

Overview

Histograms

PCA

Corr

Custom plots

Mean defoliation per plot

Coefficient of variation

sd / skewness

Point density

PCA feature set comparison

Buffer extraction scenario sketches