Monthly Archives: February 2014

GEOG 517 – Lab 3 – ArcGIS Network Analyst Tutorial

  • Exercise 1: Creating a network dataset
  • Exercise 2: Creating a multimodal network dataset
  • Exercise 3: Finding the best route using a network dataset
  • Exercise 4: Finding the closest fire stations
  • Exercise 5: Calculating service area and creating an OD cost matrix
  • Exercise 6: Creating a model for route analysis
  • Exercise 7: Servicing a set of orders with a fleet of vehicles
  • Exercise 8: Finding best routes to service a set of paired orders
  • Exercise 9: Choosing optimal store sites using location-allocation

Statistics for Data Science

Today’s lecture for Big Data Analytics included statistical tools for data analysis.

My Data Pro Tumble blog includes several listings and resources concerning statistics <http://mountainsol.tumblr.com/tagged/statistics>.

From the perspective of an information scientist, statistical analysis software is not just the computation done, but preservation of both the input, output, and processing.

One of the more popular statistical software packages is R, which actually does a lot more than work with statistics (as one of my recent tweets showed):

There’s a short introduction to R which explains:

R is a tool for statistics and data modeling. The R programming language is elegant, versatile, and has a highly expressive syntax designed around working with data. R is more than that, though — it also includes extremely powerful graphics capabilities. If you want to easily manipulate your data and present it in compelling ways, R is the tool for you.

http://tryr.codeschool.com/

It’s also possible to run R from the terminal in Mac OS X, but a nice interface for using R is R Studio <https://www.rstudio.com/>.

Other useful links:

http://ropensci.org/

http://cran.us.r-project.org/

http://www.statmethods.net/index.html

 

 

Environmental Layers for HPC Maximum Entropy Species Distribution Models in Great Smoky Mountains National Park

Currently there are 10 environmental layers that were used by Simmerman et. al in the demonstration project, “Exploring similarities among many species distributions.”

  1. Bedrock geology
  2. Digital elevation model
  3. Slope measured in degrees
  4. Solar radiation data
  5. Soil organic type
  6. Terrain shape index
  7. Topographic convergence index
  8. Leaf on canopy cover
  9. Understory density classes
  10. Vegetation classes

This slideshow requires JavaScript.

The contribution of environmental variables to each “Maximum Entropy” Species Distribution Model (MaxEnt SDM) environmental variables are accessible from each model under the “Environmental Layers” tab.

The help icon accompanying each model provides this text:

This is a species distribution model (SDM) produced by MaxEnt. This SDM is actually a composite from ten cross-validation runs for each species (see cross-validation results tab for more information). Original ATBI record locations are shown with black dots. The color scale goes from 0 probability of presence (dark brown) to 100% probability (dark green).

Color distribution depicting a probability between 0 (no chance of finding a species) and 1 (100% chance of finding a species)

Color distribution depicting a probability between 0 (no chance of finding a species) and 1 (100% chance of finding a species)

Below is a screen capture of the model generated for the Fraser fir (Abies fraseri). This model is based on 474 occurrence records.  The full size image is available online at <http://seelab.eecs.utk.edu/alltaxa/maps/Abies_fraseri.png>

Abies_fraseri

SDM model generated by the ATBI mapping project / University of Tennessee SEElab.

Interestingly, the MaxEnt model output suggests that the “Digital Elevation Model” contributed 88.8% to the Species Distribution Model for Abies frasieri.  This makes sense, since the Fraser fir is a species of conifer favoring cold environments that inhabits only the highest elevations of the Park.  The remaining layers contribute less than 5% to the model.

I’m copying out the taxonomic classification from Wikipedia:

Scientific classification
Kingdom: Plantae
Division: Pinophyta
Class: Pinopsida
Order: Pinales
Family: Pinaceae
Genus: Abies
Species: A. fraseri

The purpose is to access the records from the ATBI database, where I don’t see the Fraser fir listed in the ATBI “plants” kingdom. From <http://tremont22.campus.utk.edu/ATBI_Query.cfm> I searched by “order’ for “pinales.”

Fraser fir is accessible: <http://tremont22.campus.utk.edu/ATBI_Species.cfm?genus=Abies&epithet=fraseri&subspecies=%7E>.  Interestingly, the number of specimens in the database is 866.  Contrast this with the 474 records that were used to generate the model.  The model may simply be older (there does not appear to be a timestamp for the model; either from “Get Info” or opening up “Properties” in GIMP for both the large 299×1302 pixel PNG file and the small 600×269 pixel png) or, not all 866 occurrence records have spatial coordinates associated (e.g., they are “references from the literature.”)

Poster for North Carolina Partners in Amphibian and Reptile Conservation

Poster might highlight the MaxEnt model as an example of the outcome of research in the park and emphasize the need for more occurrence data to populate the ATBI database. 
As of Feb. 24, 2014, there are no reptile species modeled already by the All Taxa mapping project.
Some simple facts might help illustrate the need for more reptile data:
  • ​total herp species in park
  • total herp species in the ATBI database
  • total herp species in the ATBI database that have n = 30 or more
  • total herp species in the ATBI database that need more data to be modeled
I think n of 30 or more was settled on by convention in hopes of having a normal distribution (Central limit theorem).
I just looked at this issue for plants – ATBI has ~1,600 vascular plants, but only around 500 have data points that can be modeled.  And of those, 257 have the requisite 30 or more occurrence records.
Total herp species in the Park according to ATBI database:
Class Amphibia – 63 species
Class Reptilia – 41 species
I’m not sure where to get a “species checklist” for total herp species in the park.  Since the ATBI database is “All Taxa,” it seems that yes, all herp species would be included.  However I don’t know that this is true and it would be nice to verify against another source.
It is interesting that the species with the highest number of records is northern copperhead (Agkistrodon contortrix mokasen,) with 233 specimens, followed by the northern black racer (Coluber constrictor constrictor) at 181 specimens.
I took some .tiff images, saved in “Documents/NPS-NICS-Practicum/herpetofauna/ATBI-reptiles-022414” convert to PNG using GIMP (GNU Image Manipulation Program).
File – Export
(Command + Shift + E)
Dialog:
Select Filetype by Extension
-Choose PNG
Created files:
black-racer.png
northern-copperhead.png
Black racer species records in Great Smoky Mountains National Park.

Black racer species records in Great Smoky Mountains National Park.

Black racer species records in Great Smoky Mountains National Park.

Northern copperhead species records in Great Smoky Mountains National Park.

Total herp species in the ATBI database that have n = 30 or more

Total herp species in the ATBI database that need more data to be modeled

Vascular Plants Available to Model = 257

Vascular Plants in ATBI Database Suitable for MaxEnt SDM Modeling

This afternoon I have established a few facts concerning plants in the Smokies.

The ATBI database (available to me on public server) has 432 vascular plant species for which there are 30 or more occurrence records.

This is out of 2001 entries – although the ATBI database reports “1643 species” for subkingdom Tracheobionta. So, 432/2001 is about 21% species that have 30 or more records.

The SEElab already has maps for 225 plant species. (SeeLab-Plants-Mod)

I combined the SEElab plant list (n=225) with the ATBI vascular plants list of more than 30 records (n=432), then filtered for unique records based on scientific name.

This yielded a total of 257 scientific names, suggesting there are 257 plant species from the ATBI database that have NOT been modeled by SEElab.

I have attached this data in the .csv file, “Vasc-Plant-Unique.” Perhaps this is the roughly 257 species Keith Langdon mentioned to me on the phone?

I don’t yet have access to the Nautilus supercomputer so initial runs would need to be done on a PC. I can make my documentation for running individual models on a PC by doing these first runs.

With the refined list of ~257 plant species, is there a preference for particular species or species assemblages?

If there is no preference for a particular plant species (out of those that have the requisite number of 30 or more records) I could just do some species modelling for Hemlock forests, as there is literature available for me to reference and it is interesting to look at potential community impacts from the HWA.

I’m having some trouble forwarding the .csv file to NPS staff (filtering, probably a security risk).

And, WordPress is not letting me upload any file other than a Microsoft .xls file. This is poor data management practice; I should archive a plain text or .csv file. So, my solution for the time being is that I believe I will paste the plain text here:

Saving the file on my local machine:

Documents/NPS-NICS-Practicum/ATBI-vasc-plant-021414/Vasc-Plant-Unique.txt

RecordNo,Kingdom,Class,Order,Family,Taxon,……,Data……………….,Type,Common Name 13413,,,,,Carex brunnescens sphaerostachya,,38,Specimens,Few flowered sedge 13432,,,,,Carex debilis variety,,75,Specimens, 13433,,,,,Carex digitalis,,43,Specimens,sedge 13449,,,,,Carex prasina,,30,Specimens,Drooping sedge 13456,,,,,Carex scabrata,,31,Specimens,Rough sedge 13460,,,,,Carex species,,291,Specimens, 13464,,,,,Carex swanii,,38,Specimens,Swan’s sedge 13471,,,,,Carex virescens,,31,Specimens,sedge 13513,,,,,Agrostis perennans,,42,Specimens,Upland bent 13522,,,,,Andropogon species,,71,Specimens, 13608,,,Ophioglossales,Ophioglossaceae,Botrychium biternatum,,58,Specimens,Southern grape fern 13610,,,,,Botrychium dissectum v. dissectum,,978,Specimens,”Cutleaf grapefern, dissectum” 13611,,,,,Botrychium dissectum v. obliquum,,155,Specimens,”Cutleaf grapefern, obliquum” 13617,,,,,Botrychium species,,38,Specimens, 13625,,,,,Asplenium rhizophyllum,,110,Specimens,Walking-fern spleenwort 13628,,,,,Asplenium trichomanes,,43,Specimens,Maiden-hair spleenwort 13630,,,,Blechnaceae,Woodwardia areolata,,126,Specimens,Netted chain fern 13633,,,,,Pteridium aquilinum,,1058,Specimens,Bracken fern 13634,,,,,Pteridium aquilinum subspecies,,78,Specimens, 13637,,,,,Pteridium aquilinum variety,,89,Specimens, 13638,,,,Dryopteridaceae,Athyrium asplenioides,,64,Specimens, 13639,,,,,Athyrium filix-femina angustum,,306,Specimens,Small northern lady fern 13640,,,,,Athyrium filix-femina asplenioides,,10129,Specimens,Southern lady fern 13648,,,,,Diplazium pycnocarpon,,66,Specimens,Glade fern 13652,,,,,Dryopteris cristata,,401,Specimens,”Crested wood fern,” 13656,,,,,Dryopteris species,,83,Specimens, 13658,,,,,Onoclea sensibilis,,43,Specimens,Sensitive fern 13665,,,,,Osmunda claytoniana,,42,Specimens,Interrupted fern 13666,,,,,Osmunda regalis,,66,Specimens,Royal fern 13669,,,,Polypodiaceae,Pleopeltis polypodioides,,63,Specimens,Resurrection fern 13671,,,,,Polypodium appalachianum,,3307,Specimens, 13768,,,,,Arisaema triphyllum triphyllum,,76,Specimens, 13772,,,Commelinales,Commelinaceae,Commelina communis,,39,Specimens,Common dayflower 13779,,,,,Tradescantia subaspera,,35,Specimens,Spiderwort 13788,,,,,Carex intumescens,,44,Specimens,Intumescent sedge 13794,,,,,Carex laxiflora v. laxiflora,,36,Specimens, 13802,,,,,Carex lurida,,30,Specimens,smaller hop sedge 13805,,,,,Carex nigromarginata,,42,Specimens,Black-margined sedge 13814,,,,,Arundinaria gigantea,,42,Specimens,Cane 13835,,,,,Spiranthes cernua,,38,Specimens,Nodding lady’s tresses 13839,,,,,Spiranthes species,,103,Specimens, 13843,,,,,Triphora trianthophora,,73,Specimens,Nodding Pogonia 13844,,,Liliales,Liliaceae,Trillium undulatum,,85,Specimens,Painted Trillium 13845,,,,,Trillium vaseyi,,35,Specimens,Vasey`s trillium 13863,,,,,Smilax species,,57,Specimens, 13876,,,,,Cypripedium acaule,,37,Specimens,Pink lady’s slipper 13881,,,,Typhaceae,Typha latifolia,,81,Specimens,wideleaf cattail 13887,,,,,Huperzia lucidula,,4103,Specimens,shining Club-moss 13908,,,,,Chaerophyllum tainturieri v. tainturieri,,10010,Specimens,wild chervil 13910,,,,,Cryptotaenia canadensis,,43,Specimens,Honewort 13924,,,,,Sanicula canadensis v. canadensis,,125,Specimens,Canada black snakeroot 13928,,,,,Sanicula smallii,,35,Specimens,small’s black snakeroot 13929,,,,,Sanicula species,,47,Specimens, 13931,,,,,Taenidia integerrima,,31,Specimens,Yellow pimpernel 13932,,,,,Thaspium barbinode,,30,Specimens,meadow-parsnip 13939,,,,,Cinna latifolia,,37,Specimens,woodreed 13944,,,,,Danthonia species,,44,Specimens, 13945,,,,,Danthonia spicata,,35,Specimens,Poverty grass 13950,,,,,Dichanthelium clandestinum,,41,Specimens,Deer-tongue witchgrass 13953,,,,,Dichanthelium dichotomum v. dichotomum,,36,Specimens, 13963,,,,,Dichanthelium species,,96,Specimens, 13976,,,,,Elymus riparius,,105,Specimens,wild rye 13993,,,,,Festuca subverticillata,,31,Specimens,Sheep`s-fescue 13995,,,,,Glyceria nubigena,,123,Specimens,Smoky Mountain Mannagrass 14003,,,,,Lolium arundinaceum,,76,Specimens, 14014,,,,,Muhlenbergia tenuiflora,,43,Specimens,Muhly 14026,,,,,Panicum species,,192,Specimens, 14042,,,,,Poa alsodes,,38,Specimens,wood bluegrass 14052,,,,,Poa species,,47,Specimens, 14055,,,,,Poaceae_genus species,,110,Specimens, 14058,,,,,Schizachyrium scoparium v. scoparium,,167,Specimens, 14087,,,,,Juncus effusus solutus,,37,Specimens,Soft rush 14093,,,,,Juncus tenuis,,103,Specimens,Larger path rush 14099,,,,,Luzula acuminata variety,,34,Specimens, 14110,,,,,Dioscorea quaternata,,221,Specimens,wild yam 14112,,,,,Dioscorea villosa,,47,Specimens, 14131,,,,,Allium tricoccum,,35,Specimens,”Ramps, wild leeks” 14135,,,,,Chamaelirium luteum,,50,Specimens,Fairy wand 14148,,,,,Erythronium umbilicatum umbilicatum,,154,Specimens, 14154,,,,,Lilium michauxii,,43,Specimens,Carolina lily 14157,,,,,Lilium superbum,,157,Specimens,Turk’s cap lily 14161,,,,,Maianthemum racemosum racemosum,,1292,Specimens, 14173,,,,,Polygonatum biflorum v. biflorum,,40,Specimens,Great Solomon’s seal 14175,,,,,Polygonatum biflorum variety,,126,Specimens, 14177,,,,,Polygonatum pubescens,,123,Specimens,hairy Solomon’s seal 14188,,,,,Trillium catesbaei,,78,Specimens,catesby’s trillium 14190,,,,,Trillium erectum,,122,Specimens,Wake robin 14191,,,,,Trillium grandiflorum,,34,Specimens,white trillium 14195,,,,,Trillium species,,80,Specimens, 14200,,,,,Galearis spectabilis,,58,Specimens,Showy orchis 14201,,,,,Goodyera pubescens,,292,Specimens,Downy rattlesnake-plantain 14202,,,,,Goodyera repens,,89,Specimens,Lesser rattlesnake-plantain 14285,,,Fagales,Betulaceae,Alnus serrulata,,111,Specimens,Common alder 14288,,,,,Thaspium trifoliatum variety,,45,Specimens, 14295,,,,,Aralia racemosa,,33,Specimens,wild spikenard 14297,,,,,Aralia spinosa,,53,Specimens,Devil’s walking stick 14298,,,,,Hedera helix,,402,Specimens,English Ivy 14299,,,,,Panax quinquefolius,,88,Specimens,Ginseng 14307,,,,,Hexastylis arifolia v. arifolia,,70,Specimens,Little brown jugs 14314,,,,,Ageratina altissima v. altissima,,119,Specimens,white snakeroot 14315,,,,,Ageratina altissima v. roanensis,,69,Specimens, 14321,,,,,Antennaria plantaginifolia,,46,Specimens,Plantain-leaved pussy toes 14335,,,,,Aster cordifolius,,44,Specimens, 14353,,,,,Aster species,,45,Specimens, 14359,,,,,Asteraceae_genus species,,137,Specimens,Aster family species 14366,,,,,Cacalia atriplicifolia,,33,Specimens, 14374,,,,,Chrysopsis mariana,,36,Specimens,Maryland golden aster 14387,,,,,Coreopsis major variety,,129,Specimens,wood Tickseed 14403,,,,,Erigeron pulchellus v. pulchellus,,33,Specimens,Robin’s-plantain 14406,,,,,Eupatorium album,,59,Specimens,white eupatorium 14409,,,,,Eupatorium fistulosum,,33,Specimens,Joe-Pye-weed 14411,,,,,Eupatorium maculatum,,32,Specimens,Joe-Pye-weed 14414,,,,,Eupatorium rotundifolium,,41,Specimens,Round-leaved snake-root 14418,,,,,Eupatorium species,,60,Specimens, 14424,,,,,Eurybia surculosa,,33,Specimens,Recurved aster 14426,,,,,Eutrochium purpureum v. pupureum,,42,Specimens, 14430,,,,,Gamochaeta purpureum,,33,Specimens,Purple Cudweed 14459,,,,,Iva annua,,153,Specimens,Iva 14469,,,,,Lactuca species,,32,Specimens, 14486,,,,,Polymnia laevigata,,2000,Specimens,Tennessee Leafcup 14492,,,,,Prenanthes species,,236,Specimens, 14493,,,,,Prenanthes trifoliolata,,36,Specimens,Lion’s foot 14506,,,,,Rugelia nudicaulis,,165,Specimens, 14508,,,,,Senecio anonymus,,43,Specimens,Yellow ragwort 14521,,,,,Solidago altissima v. altissima,,44,Specimens, 14523,,,,,Solidago arguta variety,,36,Specimens,Sharp-leaved goldenrod 14525,,,,,Solidago caesia,,42,Specimens,Curtis goldenrod 14546,,,,,Solidago species,,276,Specimens, 14547,,,,,Solidago speciosa v. rigidiuscula,,53,Specimens, 14552,,,,,Symphyotrichum concolor,,53,Specimens, 14570,,,,,Verbesina alternifolia,,57,Specimens,wingstem 14571,,,,,Verbesina occidentalis,,41,Specimens,wingstem 14582,,,,,Campanulastrum americanum,,33,Specimens, 14583,,,,,Lobelia cardinalis,,34,Specimens,Cardinal Flower 14584,,,,,Lobelia inflata,,68,Specimens,Indian tabacco 14595,,,Fagales,Fagaceae,Quercus montana,,408,Specimens,chestnut oak 14596,,,,,Quercus muehlenbergii,,31,Specimens,Yellow oak 14600,,,,,Quercus species,,72,Specimens, 14601,,,,,Quercus stellata,,39,Specimens,Post oak 14634,,,Geraniales,Balsaminaceae,Impatiens capensis,,71,Specimens,”Orange jewelweed, touch-me-not” 14636,,,,,Impatiens species,,44,Specimens, 14641,,,,,Geranium maculatum,,86,Specimens,wild geranium 14649,,,,,Oxalis stricta,,31,Specimens,Yellow wood-sorrel 14679,,,,,Silene virginica,,59,Specimens,Fire Pink 14682,,,,,Stellaria corei,,30,Specimens,Core’s chickweed 14700,,,Celastrales,Aquifoliaceae,Ilex ambigua,,36,Specimens, 14704,,,,,Ilex opaca v. opaca,,455,Specimens,American holly 14711,,,,,Euonymus americanus,,252,Specimens,American strawberry-bush 14718,,,,,Cornus amomum,,50,Specimens,Silky Dogwood 14721,,,,,Cornus species,,58,Specimens, 14724,,,,,Galax urceolata,,307,Specimens, 14726,,,,,Diervilla sessilifolia,,33,Specimens,Sessile-leaved bush-honey-suck 14731,,,,,Lonicera japonica,,45,Specimens,Japanese Honeysuckle 14744,,,,,Sambucus racemosa v. racemosa,,49,Specimens, 14755,,,,,Viburnum nudum v. cassinoides,,41,Specimens,wild raisin 14783,,,,,Lyonia ligustrina v. ligustrina,,73,Specimens,Maleberry 14788,,,,,Rhododendron calendulaceum,,335,Specimens,Flame Azalea 14793,,,,,Rhododendron minus,,1134,Specimens,small-leaved rhododendron 14798,,,,,Rhododendron species,,2610,Specimens, 14801,,,,,Vaccinium arboreum,,54,Specimens,Sparkleberry 14809,,,,,Vaccinium simulatum,,58,Specimens, 14810,,,,,Vaccinium species,,63,Specimens, 14817,,,,,Monotropa uniflora,,99,Specimens,Indian pipe 14848,,,,,Cercis canadensis v. canadensis,,242,Specimens,redbud 14851,,,,,Cladrastis kentukea,,202,Specimens,Yellowwood 14869,,,,,Desmodium species,,45,Specimens, 14874,,,,,Gleditsia triacanthos,,58,Specimens,Honeylocust 14883,,,,,Lespedeza cuneata,,160,Specimens,Cuneate bush-clover 14884,,,,,Lespedeza hirta,,37,Specimens,hairy Bush-clover 14888,,,,,Lespedeza species,,60,Specimens, 14906,,,Fagales,Betulaceae,Betula alleghaniensis v. alleghaniensis,,65,Specimens, 14909,,,,,Betula lutea,,32,Specimens,Yellow Birch 14910,,,,,Betula nigra,,44,Specimens,River Birch 14912,,,,,Betula species,,231,Specimens, 14918,,,,,Vitis species,,126,Specimens, 14937,,,,,Hydrangea radiata,,96,Specimens,white-leaf hydrangea 14940,,,,,Philadelphus hirsutus,,118,Specimens,small-flowered hairy mock-orange 14952,,,,,Amelanchier species,,116,Specimens, 14953,,,,,Amelanchier stolonifera,,36,Specimens,Running serviceberry 14958,,,,,Aruncus dioicus,,39,Specimens,Goats beard 14971,,,,,Crataegus species,,56,Specimens, 14980,,,,,Phacelia dubia v. dubia,,203,Specimens,small-flowered phacelia 14998,,,,Fagaceae,Castanea dentata,,868,Specimens,American chestnut 15006,,,,,Quercus imbricaria,,92,Specimens,shingle oak 15021,,,,,Carya ovata,,41,Specimens,Shagbark hickory 15023,,,,,Carya species,,184,Specimens, 15025,,,,,Juglans cinerea,,313,Specimens,butternut 15028,,,Lamiales,Boraginaceae,Cynoglossum virginianum v. virginianum,,45,Specimens,wild comfrey 15057,,,,,Lycopus virginicus,,31,Specimens,Virginia water-horehound 15079,,,,,Pycnanthemum species,,49,Specimens, 15081,,,,,Salvia lyrata,,31,Specimens,Lyre-leaved sage 15093,,,,,Stachys nuttallii,,61,Specimens, 15111,,,,,Calycanthus floridus v. glaucus,,67,Specimens, 15112,,,,,Calycanthus floridus variety,,195,Specimens,Sweetshrub 15114,,,,Lauraceae,Lindera.Plantae benzoin,,209,Specimens,Spicebush 15118,,,Magnoliales,Annonaceae,Asimina triloba,,82,Specimens,Paw-paw 15131,,,,Tiliaceae,Tilia americana v. americana,,118,Specimens,American basswood 15132,,,,,Tilia americana v. heterophylla,,789,Specimens,white Basswood 15133,,,,,Tilia americana variety,,178,Specimens, 15134,,,,,Tilia species,,94,Specimens,Basswood species 15143,,,,Onagraceae,Circaea alpina alpina,,47,Specimens, 15163,,,,Thymelaceae,Dirca palustris,,105,Specimens, 15174,,,,Papaveraceae,Sanguinaria canadensis,,91,Specimens,Bloodroot 15177,,,,,Plantago major,,86,Specimens,Plantain 15211,,,,,Polygonum sagittatum,,33,Specimens,tearthumb 15235,,,,,Caulophyllum thalictroides,,129,Specimens,Blue cohosh 15239,,,,,Podophyllum peltatum,,48,Specimens,May-apple 15246,,,,,Actaea podocarpa,,40,Specimens, 15248,,,,,Actaea racemosa v. racemosa,,117,Specimens, 15255,,,,,Cimicifuga racemosa,,31,Specimens, 15265,,,,,Hepatica nobilis v. acuta,,46,Specimens,Round-lobed hepatica 15275,,,,,Ranunculus hispidus,,34,Specimens,Carolina buttercup 15282,,,,,Thalictrum clavatum,,37,Specimens,Brook meadowrue 15290,,,,,Thalictrum species,,31,Specimens, 15309,,,Theales,Theaceae,Stewartia ovata,,32,Specimens,Mountain stewartia 15314,,,,,Morus rubra,,107,Specimens,red Mulberry 15319,,,,,Ulmus alata,,37,Specimens,winged elm 15320,,,,,Ulmus americana,,156,Specimens,American elm 15326,,,,,Pilea pumila,,35,Specimens,”Richweed, clearweed” 15336,,,,,Passiflora lutea,,44,Specimens,Yellow passion-flower 15338,,,,Violaceae,Hybanthus concolor,,62,Specimens,green violet 15342,,,,,Viola canadensis v. canadensis,,673,Specimens,Canadian violet 15344,,,,,Viola cucullata,,453,Specimens,Marsh blue violet 15346,,,,,Viola hirsutula,,238,Specimens,Southern wood violet 15348,,,,,Viola labradorica,,784,Specimens, 15349,,,,,Viola lanceolata,,200,Specimens,Lance-leaved violet 15352,,,,,Viola palmata,,85,Specimens,Three-lobed violet 15353,,,,,Viola pedata,,145,Specimens,Birds foot violet 15357,,,,,Geum canadense,,33,Specimens,white Avens 15373,,,,,Physocarpus opulifolius v. opulifolius,,30,Specimens,Ninebark 15382,,,,,Prunus americana,,42,Specimens,wild plum 15391,,,,,Prunus serotina v. serotina,,1257,Specimens,Black cherry 15413,,,,,Rubus flagellaris,,40,Specimens,Northern Dewberry 15419,,,,,Rubus phoenicolasius,,93,Specimens,wineberry 15420,,,,,Rubus species,,430,Specimens, 15430,,,,Saxifragaceae,Astilbe biternata,,38,Specimens,false goats beard 15433,,,,,Heuchera americana,,38,Specimens,Alumroot 15442,,,,,Mitella diphylla,,41,Specimens,Bishops cap 15443,,,,,Parnassia asarifolia,,108,Specimens,grass-of-Parnassus 15449,,,,,Tiarella cordifolia,,233,Specimens, 15459,,,,,Galium circaezans v. circaezans,,76,Specimens,wild Licorice 15465,,,,,Galium pilosum variety,,30,Specimens, 15466,,,,,Galium species,,75,Specimens, 15474,,,,,Houstonia purpurea v. purpurea,,65,Specimens,woodland bluets 15475,,,,,Houstonia purpurea variety,,97,Specimens, 15480,,,,,Mitchella repens,,359,Specimens,Partridgeberry 15493,,,,,Salix nigra,,52,Specimens,Black willow 15494,,,,,Salix sericea,,39,Specimens,Silky willow 15498,,,,,Phoradendron leucarpum,,55,Specimens, 15501,,,,,Acer negundo,,41,Specimens,Box-elder 15506,,,,,Acer rubrum v. rubrum,,92,Specimens,Trident maple 15508,,,,,Acer rubrum variety,,9526,Specimens, 15516,,,,,Rhus copallinum variety,,102,Specimens, 15517,,,,,Rhus glabra,,34,Specimens,Smooth Sumac 15521,,,,,Toxicodendron radicans radicans,,274,Specimens,Poison ivy 15529,,,,Simaroubaceae,Ailanthus altissima,,37,Specimens,tree-Of-Heaven

 

Spring 2014 Practicum Application

Student’s SIS Advisor’s Name: Dr. Suzie Allard
Name Student’s Practicum Supervisor: Tom Colson; Scott Simmerman
Number of Credit Hours for which you wish to be enrolled in the practicum: 3 hours
Semester during which you wish to be enrolled in the practicum: Spring 2014
Briefly describe prior and/or current information or library work experience:
I am interested in a career in environmental information management,
particularly in a governmental natural resource management agency. My course work to date includes classes in geographic information science,
environmental information management, and data visualization for
environmental science.
Indicate the type of information organization in which you wish to take the
practicum: Environmental Information Management Org
Practicum Location: Great Smoky Mountains National Park; National Institute for Computational Sciences

Practicum Objectives:
I would like to develop advanced environmental information processing and
data visualization skills by working with species occurrence records and a
high performance computing environment as part of a technology transfer
project between the University of Tennessee and the National Park Service.

The following four practicum goals and associated outcomes are proposed for
this project:

(1) Develop proficiency in running the MaxEnt species distribution modelling
program in a PC environment for determining probability of species
distribution given environmental variables and demonstrate acquired
proficiency by providing training and instruction to Park Service staff in
use of the MaxEnt program on Park resources configured to run MaxEnt.
Training materials and sessions will be produced as an outcome of the
practicum.
(2) Gain skills with workflow and parallel processing in a high performance
computing environment on a single-system-image supercomputer and demonstrate these skills by generating species distribution models as requested by practicum supervisor. There are currently 540 species models out of ~36,000 species in the park. A collection of new models will demonstrate the outcome of the practicum.
(3) Create documentation for running the MaxEnt model in a PC environment using appropriate technology such as a wiki with walkthroughs, screen captures, or video screencasts as appropriate. A URL will be provided to the final online documentation to demonstrate the outcome of the practicum.
(4) Practice sound data curation principles in managing both model inputs and model outputs by successfully building on the store of models available at . An HPC data management system such as XSEDE (XSEDE.org) will be used to manage the inputs and outputs to demonstrate the outcome of the practicum.

In a rough estimation, I expect to spend about a 1/3 of the required 150
hours learning MaxEnt on PC and HPC environments, 1/3 writing documentation, and 1/3 creating and delivering training (to commence in March, 2014) to enable NPS staff to implement MaxEnt modelling on both PC and HPC platforms.

Presentation – Geocoding in Geographic Information Retrieval Systems

I presented this paper at the Geographic Information Systems II (GIS II) session at the 2014 Geography Symposium (See UT Geography Symposium Program 2014)

I represented The University of Tennessee School of Information Sciences at this interdisciplinary conference themed “Mapping outside the lines: Geography as a nexus for interdisciplinary and collaborative research.”

Tanner Jessel, School of Information Sciences, University of Tennessee. “Geocoding in Geographic Information Retrieval Systems.”

Information with a geographic component is among the most valuable and sought after types of information. However, the majority of geographical information exists as indirectly referenced locational information within unstructured text. Even among well-annotated, spatially explicit datasets, existing metadata can be of sparse, inconsistent, or otherwise of poor quality due to time and budgetary constraints. For these reasons, automated annotation of spatially explicit coordinates, a process known as geocoding, is an active area of research in geographic infor- mation science. Research concerning geocoding represents a long-term effort with a body of knowledge that has grown across several decades. Unfortunately, funding cycles are not always long-term, and some groundbreaking technologies and tools are no longer available. The present article attempts to synthesize the current state-of-the art of geocoding and presents a “toolkit” of resources used across the literature to accomplish geocoding, with an emphasis on applications for geographic information retrieval.

Extraction, Transform and Load

A friend of mine in the program commented that about 90% of the time doing data science is obtaining and cleaning data.

This is where programming is incredibly useful.  In the second year of my Masters program, my programming skills are not yet at the level that I want them to be.

I recently started some work for my research assistantship concerning Twitter data for @DataONEorg.

I’m interested in the content of posts, and the relationships between the actors in the network.

In terms of content, I’d like to look at the hashtags and links.

To illustrate how difficult it is to accomplish tasks “by hand,” I recently tried to the twitter data from a free site.  My efforts are documented here: <https://notebooks.dataone.org/data-science/harvesting-dataoneorg-twitter-mentions-via-topsy/>.

I’ve read that employers should not hire a “data scientist” if the so-called “scientist” does not have programming skills.  For this reason, I’m disappointed that the School of Information Science does not offer a programming course within the School itself.  (I’ve heard Dr. Potnis will offer a course in Fall 2014, a semester after my graduation).

I enrolled in a programming course in the College of Engineering and Computer Science – Introduction to Programming for Scientists and Engineers.  The course focuses on C++ language.  This is unfortunate, as python is increasingly favored over C++.  This means more ready-made programs are available, and a user community is growing. Content management systems are even building up around python.

Python is used by a friend of mine who does genome science.  C++ is useful for taking advantage of parallelism, but that my friend who works on supercomputers uses python suggests to me that python works as well.

Programming language popularity.

http://venturebeat.com/2014/02/03/the-most-popular-coding-languages-for-2014-are/

Further reading:

Python Displacing R As The Programming Language For Data Science by @mjasay http://readwr.it/c1ew  

http://www.scipy.org/

 

 

Parkridge / Magnolia Corridor / Woodbine “Neighborhood Greenway”

Something I’d like to suggest for a Magnolia corridor development plan is a Woodbine Avenue “Neighborhood greenway.”  Woodbine is a low volume residential corridor connecting Caswell Park to Chilhowee Park and the Knoxville Zoo.  There are already street signs highlighting the route.
 
However, there is not a direct tie-in from the Caswell Park Greenway to Woodbine, and there one dangerous crossing at the intersection of Woodbine and Cherry Street.
 
Neighborhood Greenways are very popular in Portland, Oregon as “residential streets with low volumes of auto traffic and low speeds where bicycle and pedestrians are given priority.”
 
A neighborhood greenway would be very easy to accomplish – essentially adding markings on the pavement, traffic calming to deter motor vehicle thru-traffic, clear signage, and improved crossings.
 
Here’s a link to Portland’s page – http://www.portlandoregon.gov/transportation/50518
 
Traversing historic Parkridge and Park City, Woodbine is the ideal thoroughfare for Knoxville’s first “Neighborhood Greenway” to connect   Caswell Park and the Knoxville Zoo. The PCO has already expresssed interest in making the neighborhood more accessible to cyclists – and hopes to have the Tour de Lights visit this year.  A neighborhood greenway on Woodbine ​would be a great first step to a more bike-friendly Parkridge.