EcoSimR-package |
EcoSimR EcoSimR is a collection of functions for calculating community metrics and algorithms for randomizing community data for null model analysis. Current modules are included for the analysis of niche overlap, body size overlap, and species co-occurrence. EcoSimR also allows users to define their own functions and algorithms to develop new null models. |
checker |
Checker Co-occurrence Metric |
cooc_null_model |
Co-Occurrence Null model |
czekanowski |
Czekanowski Niche Overlap Metric |
czekanowski_skew |
CzekanowskiSkew Niche Overlap Metric |
czekanowski_var |
CzekanowskiVariance Niche Overlap Metric |
c_score |
CScore Co-occurrence Metric |
c_score_skew |
CScoreSkew Co-occurrence Metric |
c_score_var |
CScoreVariance Co-occurrence Metric |
dataMacWarb |
MacArthur's (1958) warbler data This data matrix is from MacArthur's classic (1958) paper on the coexistence of 5 species of New England warbler. Each row of the data matrix is a different species of warbler, and each column is one of 16 different subregions of a coniferous tree. Each entry is the percentage of time that each species was observed foraging in a different subregion of the tree (see Figures 2-4 in MacArthur 1958). Zeroes indicate subregions of the tree in which a species was not recorded foraging. |
dataRodents |
Desert rodent data set This data vector is from Brown's (1975) study of the coexistence of desert rodent species. Each entry is the average adult body mass in grams of six co-occurring species of Sonoran Desert rodents. |
dataWiFinches |
West Indian Finches data This data frame is a binary presence-absence matrix for West Indies finches (Fringillidae). Each row is a different species of finch and each column is one of the 19 major islands in the West Indies. Entries indicate the presence (1) or absence (0) of a species on an island. Data from Gotelli and Abele (1982). |
EcoSimR |
EcoSimR EcoSimR is a collection of functions for calculating community metrics and algorithms for randomizing community data for null model analysis. Current modules are included for the analysis of niche overlap, body size overlap, and species co-occurrence. EcoSimR also allows users to define their own functions and algorithms to develop new null models. |
min_diff |
MinDiff Size Overlap Metric |
min_ratio |
MinRatio Size Overlap Ratio Metric |
niche_null_model |
Niche overlap null models |
null_model_engine |
Run null model |
pianka |
Pianka Niche Overlap Metric |
pianka_skew |
PiankaSkew Niche Overlap Metric |
pianka_var |
PiankaVariance Niche Overlap Metric |
plot.coocnullmod |
Co-Occurrence Model Plot Function |
plot.nichenullmod |
Niche Null Model Plot function |
plot.nullmod |
plot a histogram null model |
plot.sizenullmod |
Size Ratio Plot Function |
ra1 |
RA1 Niche Overlap Randomization Algorithm |
ra2 |
RA2 Niche Overlap Randomization Algorithm |
ra3 |
RA3 Niche Overlap Randomization Algorithm |
ra4 |
RA4 Niche Overlap Randomization Algorithm |
ranMatGen |
Random Matrix Generator |
reproduce_model |
Reproduce a result |
sim1 |
Sim1 Co-occurrence Randomization Algorithm |
sim10 |
Sim10 Co-occurrence Randomization Algorithm |
sim2 |
Sim2 Co-occurrence Randomization Algorithm |
sim3 |
Sim3 Co-occurrence Randomization Algorithm |
sim4 |
Sim4 Co-occurrence Randomization Algorithm |
sim5 |
Sim5 Co-occurrence Randomization Algorithm |
sim6 |
Sim6 Co-occurrence Randomization Algorithm |
sim7 |
Sim7 Co-occurrence Randomization Algorithm |
sim8 |
Sim8 Co-occurrence Randomization Algorithm |
sim9 |
Sim9 Co-occurrence Randomization Algorithm |
sim9_single |
sim9_single |
size_gamma |
SizeGamma Size Overlap Randomization Algorithm |
size_null_model |
Size Ratio |
size_source_pool |
SizeSourcePoolDraw Size Overlap Randomization Algorithm |
size_uniform |
SizeUniform Size Overlap Randomization Algorithm |
size_uniform_user |
SizeUser Size Overlap Randomization Algorithm |
species_combo |
SpeciesCombo Co-occurrence Metric |
summary.coocnullmod |
Generic function for calculating null model summary statistics. |
summary.nichenullmod |
Generic function for calculating null model summary statistics |
summary.nullmod |
Generic function for calculating null model summary statistics |
summary.sizenullmod |
Generic function for calculating null model summary statistics |
var_diff |
VarDiff Size Overlap Ratio Metric |
var_ratio |
VarRatio Size Overlap Ratio Metric |
vector_sample |
Vector Sample Function |
v_ratio |
SchlutersVRatio Co-occurrence Metric |