Species Parameters - UVAFME/UVAFME_model GitHub Wiki

The UVAFME2018_specieslist.csv contains the species-level parameters for each species to be simulated. Most parameters can be determined from a literature review (see Burns & Honkala 1990, for example).

The species_id column must match those set up in the rangelist file.

The current parameters are as follows:

Column Number	Parameter Name	Description	Units
1	group	genus group number	integer
2	genus	genus of tree (scientific)	character
3	individual	individual species number within genus	integer
4	scientific_name	scientific name of species	character
5	english_name	common name of species	character
6	age_max	average maximum age	years
7	dbh_max	average maximum diameter at breast height	centimetres
8	ht_max	average maximum height	meters
9	s	initial height-DBH relationship	m/cm
10	g	growth parameter
11	bulk	bulk density of wood	tonnes/m3
12	D_L	scalar parameter for leaf area ~ Dcbb2 relationship
13	LMA	leaf mass per area	tonnes C/ha
14	gdd_min	minimum degree-day threshold	degree-days
15	gdd_opt	optimum degree-days	degree-days
16	gdd_max	maximum degree-days threshold	degree-days
17	shade	relative shade tolerance	1-5; 5 = least tolerant
18	drought	relative drought tolerance	1-6; 6 = least tolerant
19	flood	relative flood tolerance	1-6; 6 = least tolerant
20	permf	relative permafrost tolerance	1-3; 3 = least tolerant
21	nutrient	relative low nutrient tolerance	1-3; 3 = least tolerant
22	back_thick	bark thickness per cm DBH	cm bark/cm DBH
23	fire_regen	relative ability of plant to resprout or reproduce seed following fire	1-6; 1 = high reproduction post fire; 6 = low reproduction post fire
24	stress	relative tolerance to surviving low growth periods	1-5; 5 = least tolerant
25	death	relative ability to live to age_max	1-3; 3 = least likely
26	evergreen	evergreen or deciduous	1 = evergreen; 0 = deciduous
27	litter_class	litter class type	integer
28	invader	probability of inseeding from outside plot	0 to 1
29	seed	seeding from within plot	seeds/m2
30	sprout	average sprouts produced per individual
31	layering	ability of species to reproduce by layering	0 = no; 1 = yes
32	org_resp	relative ability of species to reproduce on deep organic/moss layers	1-3; 3 = least tolerant
33	recr_age	age at which species can start reproducing	years
34	NDE	proportion of seedbank lost annually	0 to 1
35	NDS	proportion of seedlings lost annually	0 to 1
36	species_id	unique eight character code consisting of first four letters of genus and first four letters of species	character

Note that these columns must be in the correct order as shown above as UVAFME does not use column names to read in parameters, only column order. This also means that you can rename the columns as you see fit.

See the How To Guide for more information about these parameters.

The UVAFME2018_rangelist.csv file determines which species are eligible for colonization and growth at each site. The column names are the 8-character ids set up in the specieslist file (see above), and the rows are each site. If a species is present at a site, then the column/row will have a 1. If a species is absent, the column/row will be 0. The presence/absence of a species is generally derived from species range maps (see Little 1971, for example) or site descriptions.

VERY IMPORTANT: This is the only file where the column names are actually explicitly read by UVAFME. They must match the species_id column from the specieslist file.

The file is set up as follows:

Column Number	Parameter Name	Description	Units
1	site	unique site ID	integer
2	latitude	latitude of site	decimal degrees
3	longitude	longitude of site	decimal degrees
4...nspecies	unique species ID	presence or absence of species at site	0: absent; 1: present