cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.gesmey
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Agave parviflora Torr."
 ]
}

 The dataset includes 69 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160731-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5bf9tf
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-116.09539 65.6806,-100.90747 62.08703,-74.73544 59.78173,-67.81952 63.91772,-72.29453 77.68177,-61.17481 80.93632,-60.36117 84.25867,-79.88849 83.44504,-105.45029 73.81698,-118.5363 68.12152,-116.09539 65.6806))",
 "TaxonKey is Ranunculus subrigidus W.B.Drew"
 ]
}

 The dataset includes 29 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0295226-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nrw2e8
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Actinodaphne semengohensis S.Julia"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0165741-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phte3u
title: Occurrence Download

description: A dataset containing 10868 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Allium sativum L."
 ]
}

 The dataset includes 10868 records from 337 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0295185-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n6bgfp
title: Occurrence Download

description: A dataset containing 305 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Camera trap database of Tiger from Rajaji National Park, Uttarakhand"
 ]
}

 The dataset includes 305 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0165770-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9yp65k
title: Occurrence Download

description: A dataset containing 1269 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acaena magellanica (Lam.) Vahl"
 ]
}

 The dataset includes 1269 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0295207-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.grudpt
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Puncturella noachina (Linnaeus, 1771)",
 "Geometry Polygon ((-0.81872320224334705 81.71335986952006181, 15.11673521981012946 82.94093416616939862, 55.03837845422534514 82.93072605576169565, 68.89890739424060939 82.76538423844311865, 68.23492995998834942 76.91672887805012238, 66.65798355363932615 76.41899886398434205, 58.35826562548645313 75.2830057792397298, 53.62742640643935488 72.27604926014167575, 56.51370019053020144 70.7184319212233703, 61.20731985535795161 69.33373585697623298, 61.03848461561595684 68.59378701793275468, 59.48520040998950265 68.17044220597425408, 56.31109790283980487 68.39555084581948563, 54.55521140952295411 67.98114593841629016, 51.6512452859604565 68.17044220597425408, 48.65267784747624091 67.02924254972219842, 40.94483653932162071 65.40948750740305684, 40.32919426231246263 64.38453675707305024, 38.06363068291878449 63.85719999959601267, 35.45330742839996674 63.59523518951031207, 32.17809051471124349 66.47463978769231119, 31.61169961986282928 67.35413577830914278, 38.21138482940098413 66.43524838936303922, 40.30456857123208891 66.65113196644773552, 40.03368596934806334 67.62779915964847532, 34.17277149222090316 68.8963607305246768, 27.46509718561969038 69.94367113526196533, 23.20588516082897712 69.84830520059951198, 19.77835359058319753 69.06055172175248913, 14.73786598728060149 67.08356056086624619, 12.041205119513684 67.75195906073822982, 8.34509648852492347 77.01326974603688313, -0.81872320224334705 \n 81.71335986952006181))",
 {
 "and" : [
 "Year is greater than 1980",
 "Year is less than or equal to 2000"
 ]
 }
 ]
}

 The dataset includes 46 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0159507-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kreruk
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liparis stolzii Schltr."
 ]
}

 The dataset includes 13 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011412-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xhxhaa
title: Occurrence Download

description: A dataset containing 26649 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Schisandraceae)"
 ]
}

 The dataset includes 26649 records from 342 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0161496-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/dqmtjs
title: GL MTU.mrk.json
DOI: 10.57745/lzgex2
title: GM MTU.mrk.json
DOI: 10.57745/wrxzp1
title: GAS2a.nrrd
DOI: 10.15468/dl.prb9tx
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallisneria spiralis",
 "Country is Hungary",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006866-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/wuqcev
title: Segmentation.seg.nrrd
DOI: 10.57745/i2pbzx
title: GM MTU.mrk.json
DOI: 10.57745/ojr5se
title: GL MTU.mrk.json
DOI: 10.57745/j66fbi
title: GAS2b.nrrd
DOI: 10.57745/55an2e
title: GM MTU.mrk.json
DOI: 10.57745/6bsl7q
title: Segmentation.seg.nrrd
DOI: 10.57745/tc0nae
title: GL MTU.mrk.json
DOI: 10.57745/b2ugwi
title: GAS3.nrrd
DOI: 10.57745/g89rpm
title: Segmentation.seg.nrrd
DOI: 10.57745/tfjmry
title: GL MTU.mrk.json
DOI: 10.57745/wvxiqz
title: GM MTU.mrk.json
DOI: 10.57745/5yv8pi
title: Segmentation.seg.nrrd
DOI: 10.57745/dcw6wf
title: GAS4.nrrd
DOI: 10.15468/dl.bsky67
title: Occurrence Download

description: A dataset containing 6276 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mayacaceae"
 ]
}

 The dataset includes 6276 records from 315 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006863-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/tlpzjf
title: RF MTU.mrk.json
DOI: 10.57745/nezbqd
title: RF1.nrrd
DOI: 10.57745/hnocna
title: RF2.nrrd
DOI: 10.57745/qahgzs
title: Segmentation.seg.nrrd
DOI: 10.57745/uarrni
title: RF MTU.mrk.json
DOI: 10.57745/pfakbj
title: RF3.nrrd
DOI: 10.57745/n3eawh
title: Segmentation.seg.nrrd
DOI: 10.15468/dl.t479gt
title: Occurrence Download

description: A dataset containing 29841 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'ZM'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence."year" &gt;= 2001 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 29841 records were derived from 171 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006837-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/c48lsm
title: RF MTU.mrk.json
DOI: 10.57745/0hayno
title: RF MTU.mrk.json
DOI: 10.57745/lo3nvk
title: Segmentation.seg.nrrd
DOI: 10.57745/gmvqp7
title: RF4.nrrd
DOI: 10.15468/dl.exchu3
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallisneria spiralis",
 "Country is Germany",
 "HasCoordinate is true"
 ]
}

 The dataset includes 73 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006865-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/pnkvhz
title: Segmentation.seg.nrrd
DOI: 10.57745/fh5d46
title: MTU RF.mrk.json
DOI: 10.57745/zlhl4m
title: RF5.nrrd
DOI: 10.57745/qqrw9c
title: SM MTU.mrk.json
DOI: 10.57745/rmqigo
title: BF MTU.mrk.json
DOI: 10.57745/fw8gbp
title: ST MTU.mrk.json
DOI: 10.57745/1ktiw5
title: IJ1.nrrd
DOI: 10.57745/r0osdo
title: IJ2.nrrd
DOI: 10.15468/dl.ffmv24
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vallisneria spiralis",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 41 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006867-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/aejes9
title: ST MTU.mrk.json
DOI: 10.57745/ynakjr
title: BF MTU.mrk.json
DOI: 10.57745/r9jxvu
title: Segmentation.seg.nrrd
DOI: 10.57745/ulmo3q
title: SM MTU.mrk.json
DOI: 10.57745/6bboru
title: IJ3.nrrd
DOI: 10.57745/bpu6ky
title: ST MTU.mrk.json
DOI: 10.57745/wydvuo
title: BF MTU.mrk.json
DOI: 10.57745/lpyqko
title: Segmentation.seg.nrrd
DOI: 10.57745/5iengy
title: SM MTU.mrk.json
DOI: 10.57745/lo0ido
title: BF MTU.mrk.json
DOI: 10.57745/clr8g3
title: ST MTU.mrk.json
DOI: 10.57745/lpc2at
title: SM MTU.mrk.json
DOI: 10.57745/nltl3s
title: IJ4.nrrd
DOI: 10.57745/r33sxj
title: ST MTU.mrk.json
DOI: 10.57745/l26qjt
title: BF MTU.mrk.json
DOI: 10.57745/ty4cwm
title: Segmentation.seg.nrrd
DOI: 10.57745/w60iqj
title: SM MTU.mrk.json
DOI: 10.57745/qytucq
title: IJ5.nrrd
DOI: 10.57745/ahcvvi
title: Segmentation.seg.nrrd
DOI: 10.57745/fo15np
title: GL MTU.mrk.json
DOI: 10.57745/xd6f3q
title: GM MTU.mrk.json
DOI: 10.57745/ty0vfq
title: GAS5.nrrd
DOI: 10.57745/oalawp
title: Segmentation.seg.nrrd
DOI: 10.57745/bh38ed
title: GM MTU.mrk.json
DOI: 10.57745/igas0f
title: GL MTU.mrk.json
DOI: 10.57745/imtcbo
title: GAS1.nrrd
DOI: 10.57745/brn54l
title: Segmentation.seg.nrrd
DOI: 10.57745/to7vmj
title: GL MTU.mrk.json
DOI: 10.57745/vxmz5v
title: GM MTU.mrk.json
DOI: 10.57745/7umqvn
title: GAS2a.nrrd
DOI: 10.57745/gyghdt
title: Segmentation.seg.nrrd
DOI: 10.57745/h3fhyj
title: GL MTU.mrk.json
DOI: 10.57745/o6yfpc
title: GAS2b.nrrd
DOI: 10.57745/xnaew9
title: GM MTU.mrk.json
DOI: 10.57745/1kfa20
title: Segmentation.seg.nrrd
DOI: 10.57745/sdo2jh
title: GL MTU.mrk.json
DOI: 10.57745/b03bdx
title: GM MTU.mrk.json
DOI: 10.57745/ang1hc
title: Segmentation.seg.nrrd
DOI: 10.57745/daxcpm
title: GAS3.nrrd
DOI: 10.57745/cmaadr
title: GL MTU.mrk.json
DOI: 10.57745/gbkjiv
title: GM MTU.mrk.json
DOI: 10.57745/qtfo9j
title: GAS4.nrrd
DOI: 10.57745/nbeyn5
title: RF MTU.mrk.json
DOI: 10.57745/vfec2d
title: Segmentation.seg.nrrd
DOI: 10.57745/pzlfb2
title: RF1.nrrd
DOI: 10.57745/is6lzn
title: RF2.nrrd
DOI: 10.57745/hh9fmq
title: Segmentation.seg.nrrd
DOI: 10.57745/rvjusf
title: RF MTU.mrk.json
DOI: 10.57745/sga2ma
title: RF3.nrrd
DOI: 10.57745/eax6xs
title: Segmentation.seg.nrrd
DOI: 10.57745/ecl9a0
title: RF MTU.mrk.json
DOI: 10.5281/zenodo.17132505
title: Scalable Steady-State Entanglement with Floquet-Engineered Stabilizer Pumping in Neutral Atom Arrays
DOI: 10.5281/zenodo.17132506
title: Scalable Steady-State Entanglement with Floquet-Engineered Stabilizer Pumping in Neutral Atom Arrays
DOI: 10.57745/bvt6ll
title: Segmentation.seg.nrrd
DOI: 10.57745/rpr8qt
title: RF MTU.mrk.json
DOI: 10.57745/976ax6
title: Segmentation.seg.nrrd
DOI: 10.57745/shxjop
title: RF4.nrrd
DOI: 10.57745/d3m9y4
title: RF MTU.mrk.json
DOI: 10.57745/hzbbaq
title: RF5.nrrd
DOI: 10.57745/n4kcpc
title: BF MTU.mrk.json
DOI: 10.15468/dl.rtkd6w
title: Occurrence Download

description: A dataset containing 887826 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen, Fossil, Living Specimen, Occurrence evidence)",
 "Continent is one of (North America, South America)",
 "TaxonKey is Cactaceae"
 ]
}

 The dataset includes 887826 records from 913 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006815-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/dosfdw
title: ST MTU.mrk.json
DOI: 10.57745/xdkgu0
title: SM MTU.mrk.json
DOI: 10.15468/dl.fww92f
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.05811 -16.93503,-28.94189 -16.93503,-28.94189 9.93503,-96.05811 9.93503,-96.05811 -16.93503))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Brachyplatystoma rousseauxii"
 ]
}

 The dataset includes 94 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006870-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/ag1az7
title: IJ1.nrrd
DOI: 10.57745/nkwcmu
title: IJ2.nrrd
DOI: 10.57745/fqf8zp
title: ST MTU.mrk.json
DOI: 10.57745/6syzgy
title: BF MTU.mrk.json
DOI: 10.57745/eumsi7
title: Segmentation.seg.nrrd
DOI: 10.57745/f9ouyk
title: SM MTU.mrk.json
DOI: 10.57745/qtwsjj
title: IJ3.nrrd
DOI: 10.57745/ccmyc8
title: ST MTU.mrk.json
DOI: 10.57745/98oxjl
title: BF MTU.mrk.json
DOI: 10.57745/z9aada
title: Segmentation.seg.nrrd
DOI: 10.57745/hjlzeq
title: SM MTU.mrk.json
DOI: 10.57745/1ktqol
title: ST MTU.mrk.json
DOI: 10.15468/dl.rudv8x
title: Occurrence Download

description: A dataset containing 502 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Indotestudo elongata"
 ]
}

 The dataset includes 502 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006871-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0bige1
title: Occurrence Download

description: A dataset containing 748 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 {
 "or" : [
 "Issue is Coordinate rounded",
 "Issue is Geodetic datum invalid",
 "Issue is Geodetic datum assumed WGS84",
 "Issue is Country derived from coordinates",
 "Issue is Individual count invalid"
 ]
 },
 "Year 1900-2019",
 "HasCoordinate is true",
 "TaxonKey is Arbutus unedo L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 748 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002771-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aiohon
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002774-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12806280
title: Bark Beetle outbreak module dev into ORCHIDEE - simulation results and quantitative evaluation

description: This R script runs simulations of a bark beetle outbreak module, collects results, and then creates a plot to visualize these results. Here is an overview of the script:


1. Library Import and Variable Initialization


The script begins by importing several libraries necessary for the operations carried out:



	
ncdf4: For working with NetCDF files, a format commonly used to store array-oriented scientific data.
	
chron: For handling chronological objects like dates and times.
	
lattice and ggplot2: For data visualization.
	
gridExtra: For arranging multiple grid-based plots on a page.
	
plyr: For data manipulation.
	
RColorBrewer: For color palettes.
	
reshape2: For restructuring and aggregating data.



Several variables are then initialized, most of which seem to represent various environmental and simulation parameters (e.g., latitude, mean annual temperature, mean growth rate, mean annual precipitation, radiation, and elevation for different locations, etc.)


Libraries


library(ncdf4)
library(chron)
library(lattice)
library(ggplot2)
library(gridExtra)
library(plyr)
library(RColorBrewer)
library(reshape2)


2. Simulation Loop


This part of the script is where the main loop of the simulation happens. The loop goes through each location (ncname), each experiment (exp), each intervention (int), and each file (file). For each combination, it checks if the corresponding NetCDF file exists. If it does, it opens the file and retrieves the data associated with the variable names present in the file, excluding the first three variables.


For the variable named WOOD_VOL_PIX_CUT, it applies a function across the second dimension (columns) of the matrix and stores the result in the ext_value variable. Then, it calculates cumsum(seqBPI)[period] and statel for different conditions.


3. Data Processing and Visualization


After the simulations are complete, the script reshapes the results data using the melt function from the reshape2 library, keeping certain variables as identifiers. It then removes rows where value equals 0.


Finally, the script creates a bar plot of the processed results using ggplot2. The bars are filled based on the variable field, the width is set by outbreak_int, and the plot is faceted by MAT+Fluxnet_Site~wind. The plot is saved as a PNG file named "figure_3.png".


In summary, this code is designed to run simulations for a bark beetle outbreak model across different sites, scenarios, interventions, and parameters, collect the results, process the data, and create a plot to visualize the results.
DOI: 10.5281/zenodo.8004953
title: Bark Beetle outbreak module dev into ORCHIDEE - simulation results and quantitative evaluation

description: This R script runs simulations of a bark beetle outbreak module, collects results, and then creates a plot to visualize these results. Here is an overview of the script:


1. Library Import and Variable Initialization


The script begins by importing several libraries necessary for the operations carried out:



	
ncdf4: For working with NetCDF files, a format commonly used to store array-oriented scientific data.
	
chron: For handling chronological objects like dates and times.
	
lattice and ggplot2: For data visualization.
	
gridExtra: For arranging multiple grid-based plots on a page.
	
plyr: For data manipulation.
	
RColorBrewer: For color palettes.
	
reshape2: For restructuring and aggregating data.



Several variables are then initialized, most of which seem to represent various environmental and simulation parameters (e.g., latitude, mean annual temperature, mean growth rate, mean annual precipitation, radiation, and elevation for different locations, etc.)


Libraries


library(ncdf4)
library(chron)
library(lattice)
library(ggplot2)
library(gridExtra)
library(plyr)
library(RColorBrewer)
library(reshape2)


2. Simulation Loop


This part of the script is where the main loop of the simulation happens. The loop goes through each location (ncname), each experiment (exp), each intervention (int), and each file (file). For each combination, it checks if the corresponding NetCDF file exists. If it does, it opens the file and retrieves the data associated with the variable names present in the file, excluding the first three variables.


For the variable named WOOD_VOL_PIX_CUT, it applies a function across the second dimension (columns) of the matrix and stores the result in the ext_value variable. Then, it calculates cumsum(seqBPI)[period] and statel for different conditions.


3. Data Processing and Visualization


After the simulations are complete, the script reshapes the results data using the melt function from the reshape2 library, keeping certain variables as identifiers. It then removes rows where value equals 0.


Finally, the script creates a bar plot of the processed results using ggplot2. The bars are filled based on the variable field, the width is set by outbreak_int, and the plot is faceted by MAT+Fluxnet_Site~wind. The plot is saved as a PNG file named "figure_3.png".


In summary, this code is designed to run simulations for a bark beetle outbreak model across different sites, scenarios, interventions, and parameters, collect the results, process the data, and create a plot to visualize the results.