https://china.befdata.biow.uni-leipzig.de/datasets/144
CSPs: Diversity measures based on tree and shrub species of the CSPs
Karin
Nadrowski
nadrowski@uni-leipzig.de
2011-11-14
en_US
Updated 2011-11-14: Different diversity measures, including richness, Shannon, Simpson, Eveness, rarefaction and phylogenetic diversity based on the tree and shrub species in the CSPs. Comparative Study Plots (CSP) of the Biodiversity - Ecosystem Functioning Experiment (BEF-China) were selected according to gradients in successive age and woody species diversity. Diversity indices are based on the dataset "Abundance of Tree and Shrub species in the Comparative Study Plots (CSP)" from Z1, SP3
biodiversity
CSP
diversity
eveness
phylogenetic diversity
rarefied diversity
shannon diversity
shrub species
simpson diversity
species richness
tree species
Find the list of keywords here: https://china.befdata.biow.uni-leipzig.de/keywords
CSP
rarefy_100
rarefy_150
rar_se_150
shannon
simpson
rich
even_shan
gen_fam_div
List of headers of the data columns in this dataset
BEF-China intern
https://china.befdata.biow.uni-leipzig.de/datasets/144/download.csv?separate_category_columns=true
The Gutianshan National Nature Reserve (NNR) is located in the western part of Zhejiang Province (29º8'18" – 29º17'29" N, 118º2'14" – 118º11'12" E, Fig. 1). The Gutianshan NNR has an area of approximately 81 km2 and was initially established as a National Forest Reserve in 1975 and became a National Nature Reserve in 2001. The NNR comprises a large portion of broad-leaved forests of advanced successional stages (Hu & Yu 2008), which have not been managed since the beginning of the 1990ies, as well as young successional stages and conifer plantations, mainly of Cunninghamia lanceolata and Pinus massoniana. --- The vegetation is composed of different types of subtropical evergreen and mixed broad-leaved forests (Yu et al. 2001). Most of the stands are secondary forests, evidenced by maximum tree ages of 180 years, by agricultural terraces in almost all plots and by the presence of charcoal in almost all soil profiles. Around the Gutianshan NRR extensive deforestation has occurred during the Great Leap Forward in the 1950s, as in most parts of Southeast China. However, due to prevailing steep slopes, the Gutianshan area was only marginally usable for agricultural activities, and thus an exceptionally intact forest cover has been preserved. --- The climate at Gutianshan NNR is warm and temperate with a short dry season in November and December and with warm summers (Fig. 2). The climatic conditions are characteristic for the subtropics with an annual average temperature of 15.1°C, January minimum temperatures of -6.8°C, July maximum temperatures of 38.1°C and an accumulated temperature sum (≥ 5°C) of 5221.5 degree days.
117.89978
118.148346
29.285201
29.101777
2007-12-31
2009-12-30
nadrowski
CSPs: Diversity measures based on tree and shrub species of the CSPs
Updated 2011-11-14: Different diversity measures, including richness, Shannon, Simpson, Eveness, rarefaction and phylogenetic diversity based on the tree and shrub species in the CSPs. Comparative Study Plots (CSP) of the Biodiversity - Ecosystem Functioning Experiment (BEF-China) were selected according to gradients in successive age and woody species diversity. Diversity indices are based on the dataset "Abundance of Tree and Shrub species in the Comparative Study Plots (CSP)" from Z1, SP3
2007-12-31 00:00:00 UTC - 2009-12-30 00:00:00 UTC
2007-2009
The Gutianshan National Nature Reserve (NNR) is located in the western part of Zhejiang Province (29º8'18" – 29º17'29" N, 118º2'14" – 118º11'12" E, Fig. 1). The Gutianshan NNR has an area of approximately 81 km2 and was initially established as a National Forest Reserve in 1975 and became a National Nature Reserve in 2001. The NNR comprises a large portion of broad-leaved forests of advanced successional stages (Hu & Yu 2008), which have not been managed since the beginning of the 1990ies, as well as young successional stages and conifer plantations, mainly of Cunninghamia lanceolata and Pinus massoniana. --- The vegetation is composed of different types of subtropical evergreen and mixed broad-leaved forests (Yu et al. 2001). Most of the stands are secondary forests, evidenced by maximum tree ages of 180 years, by agricultural terraces in almost all plots and by the presence of charcoal in almost all soil profiles. Around the Gutianshan NRR extensive deforestation has occurred during the Great Leap Forward in the 1950s, as in most parts of Southeast China. However, due to prevailing steep slopes, the Gutianshan area was only marginally usable for agricultural activities, and thus an exceptionally intact forest cover has been preserved. --- The climate at Gutianshan NNR is warm and temperate with a short dry season in November and December and with warm summers (Fig. 2). The climatic conditions are characteristic for the subtropics with an annual average temperature of 15.1°C, January minimum temperatures of -6.8°C, July maximum temperatures of 38.1°C and an accumulated temperature sum (≥ 5°C) of 5221.5 degree days.
https://china.befdata.biow.uni-leipzig.de/datasets/144
CSPs: Diversity measures based on tree and shrub species of the CSPs
/datasets/144
ASCII
1
column
,
https://china.befdata.biow.uni-leipzig.de/datasets/144/download.csv?separate_category_columns=true
BEF research plot name (CSP), id
CSP
Reasearch plots of the Biodiversity - Ecosystem functioning experiment (BEF-China). There are three main sites for research plots in the BEF Experiment: Comparative Study Plots (CSP) in the Gutianshan Nature Reserve (29º8'18" – 29º17'29" N, 118º2'14" – 118º11'12" E, Zhejiang Province Southeast China), having a size of 30x30m^2, measured on the ground. Main Experiment plots have a size of 1 mu, which is about 25x25m^2 in horizontal projection. Pilot Study Plots have a size of 1x1 m^2.
Research plots on the main experiment have a "p" in front of their IDs and then a 6 digit code: Plots in the main sites A (29°07'28.2"N 117°54'27.5"E) and B (29°05'06.8"N 117°55'44.4"E) are named according to their position in the original spreadsheet, in which they were designed. They consist of 6 digits: _1st digit_: Site (1:A, 2:B), _digit 2and3_: southwards row: as in spreadsheets the rows are named from the top to the bottom; _digit 4 and 5_: westward column: as in the original spreadsheet, but the letters are converted to numbers (A=01, B=02); _6th digit_: indicator, if the plot has been shifted a quarter mu. Example: "p205260": "p" means that this is a plot that is specified. "2" means, that we are at site B. Now the coordinates of the south - west corner: "0526". Since "e" is the fifth letter of the alphabet, this is Plot E26. The last digit "0" means that this plot was not moved by a quarter of a Mu, as some sites in Site A. The 6th digit can also indicate the subplot within the plot. "5", "6", "7", "8" indicate the northwest, northeast, southeast, and southwest quarter plot respectively.
Morover, Plots from the main experiment may be labelled in the more ambiguous form of e.g. A32. This indicates a plat either on Site A (29°07'28.2"N 117°54'27.5"E) or Site B (29°05'06.8"N 117°55'44.4"E) of the main experiment. This value only becomes a unique identifier if supported with the "site" information from another cell.
Plots labelled in the form of "1_AO1" or "g1_AO1" or "pilot1_AO1" belong to the "Pilot Experiment" (approx location: 29°06'20.2"N 117°55'12.1"E, Jiangxi Province) (CSP: name of the CSP in the Nature ReserveBEF research plot nameReasearch plots of the Biodiversity - Ecosystem functioning experiment (BEF-China). There are three main sites for research plots in the BEF Experiment: Comparative Study Plots (CSP) in the Gutianshan Nature Reserve, having a size of 30x30m^2, measured on the ground.)
Reasearch plots of the Biodiversity - Ecosystem functioning experiment (BEF-China). There are three main sites for research plots in the BEF Experiment: Comparative Study Plots (CSP) in the Gutianshan Nature Reserve (29º8'18" – 29º17'29" N, 118º2'14" – 118º11'12" E, Zhejiang Province Southeast China), having a size of 30x30m^2, measured on the ground. Main Experiment plots have a size of 1 mu, which is about 25x25m^2 in horizontal projection. Pilot Study Plots have a size of 1x1 m^2.
Research plots on the main experiment have a "p" in front of their IDs and then a 6 digit code: Plots in the main sites A (29°07'28.2"N 117°54'27.5"E) and B (29°05'06.8"N 117°55'44.4"E) are named according to their position in the original spreadsheet, in which they were designed. They consist of 6 digits: _1st digit_: Site (1:A, 2:B), _digit 2and3_: southwards row: as in spreadsheets the rows are named from the top to the bottom; _digit 4 and 5_: westward column: as in the original spreadsheet, but the letters are converted to numbers (A=01, B=02); _6th digit_: indicator, if the plot has been shifted a quarter mu. Example: "p205260": "p" means that this is a plot that is specified. "2" means, that we are at site B. Now the coordinates of the south - west corner: "0526". Since "e" is the fifth letter of the alphabet, this is Plot E26. The last digit "0" means that this plot was not moved by a quarter of a Mu, as some sites in Site A. The 6th digit can also indicate the subplot within the plot. "5", "6", "7", "8" indicate the northwest, northeast, southeast, and southwest quarter plot respectively.
Morover, Plots from the main experiment may be labelled in the more ambiguous form of e.g. A32. This indicates a plat either on Site A (29°07'28.2"N 117°54'27.5"E) or Site B (29°05'06.8"N 117°55'44.4"E) of the main experiment. This value only becomes a unique identifier if supported with the "site" information from another cell.
Plots labelled in the form of "1_AO1" or "g1_AO1" or "pilot1_AO1" belong to the "Pilot Experiment" (approx location: 29°06'20.2"N 117°55'12.1"E, Jiangxi Province)
BEF research plot name
Reasearch plots of the Biodiversity - Ecosystem functioning experiment (BEF-China). There are three main sites for research plots in the BEF Experiment: Comparative Study Plots (CSP) in the Gutianshan Nature Reserve (29º8'18" – 29º17'29" N, 118º2'14" – 118º11'12" E, Zhejiang Province Southeast China), having a size of 30x30m^2, measured on the ground. Main Experiment plots have a size of 1 mu, which is about 25x25m^2 in horizontal projection. Pilot Study Plots have a size of 1x1 m^2.
Research plots on the main experiment have a "p" in front of their IDs and then a 6 digit code: Plots in the main sites A (29°07'28.2"N 117°54'27.5"E) and B (29°05'06.8"N 117°55'44.4"E) are named according to their position in the original spreadsheet, in which they were designed. They consist of 6 digits: _1st digit_: Site (1:A, 2:B), _digit 2and3_: southwards row: as in spreadsheets the rows are named from the top to the bottom; _digit 4 and 5_: westward column: as in the original spreadsheet, but the letters are converted to numbers (A=01, B=02); _6th digit_: indicator, if the plot has been shifted a quarter mu. Example: "p205260": "p" means that this is a plot that is specified. "2" means, that we are at site B. Now the coordinates of the south - west corner: "0526". Since "e" is the fifth letter of the alphabet, this is Plot E26. The last digit "0" means that this plot was not moved by a quarter of a Mu, as some sites in Site A. The 6th digit can also indicate the subplot within the plot. "5", "6", "7", "8" indicate the northwest, northeast, southeast, and southwest quarter plot respectively.
Morover, Plots from the main experiment may be labelled in the more ambiguous form of e.g. A32. This indicates a plat either on Site A (29°07'28.2"N 117°54'27.5"E) or Site B (29°05'06.8"N 117°55'44.4"E) of the main experiment. This value only becomes a unique identifier if supported with the "site" information from another cell.
Plots labelled in the form of "1_AO1" or "g1_AO1" or "pilot1_AO1" belong to the "Pilot Experiment" (approx location: 29°06'20.2"N 117°55'12.1"E, Jiangxi Province)
name of the CSP in the Nature ReserveBEF research plot nameReasearch plots of the Biodiversity - Ecosystem functioning experiment (BEF-China). There are three main sites for research plots in the BEF Experiment: Comparative Study Plots (CSP) in the Gutianshan Nature Reserve, having a size of 30x30m^2, measured on the ground.
Taxonomic biodiversity (rarefy_100), count
rarefy_100
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (rarefy_100: estimate of species number by randomly drawing 100 individuals (rarefaction) Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals.)
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
estimate of species number by randomly drawing 100 individuals (rarefaction) Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals.
Taxonomic biodiversity (rarefy_150), count
rarefy_150
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (rarefy_150: estimate of species number by randomly drawing 150 individuals (rarefaction) Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals.)
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
estimate of species number by randomly drawing 150 individuals (rarefaction) Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals.
Taxonomic biodiversity (rar_se_150), count
rar_se_150
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (rar_se_150: standard error of the rarefaction estimate of species number given 150 , individuals, Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. This is done by randomly drawing individuals from the specified set of individuals. Since this is done several times, a standard error of the estimate can be given.)
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
standard error of the rarefaction estimate of species number given 150 , individuals, Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. This is done by randomly drawing individuals from the specified set of individuals. Since this is done several times, a standard error of the estimate can be given.
Taxonomic biodiversity (shannon), dimensionless
shannon
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (shannon: Shannon diversity, The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). )
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
Shannon diversity, The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x).
Taxonomic biodiversity (simpson), dimensionless
simpson
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (simpson: Simpson diversity, The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson"))
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
Simpson diversity, The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson")
Taxonomic biodiversity (rich), count
rich
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (rich: Species richness of trees and shrubs, Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber())
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
Species richness of trees and shrubs, Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber()
Taxonomic biodiversity (even_shan), dimensionless
even_shan
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (even_shan: Evenness based on Shannon diversity and species richness, Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich))
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
Evenness based on Shannon diversity and species richness, Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich)
Taxonomic biodiversity (gen_fam_div), dimensionless
gen_fam_div
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc() (gen_fam_div: Phylogenetic diversity based on genus and familiy, Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc())
dimensionless
real
Taxonomic biodiversity
Taxon diversity can be given as species richness, or other diversity indices. We also use rarefied species richness, shannon diversity index, and phylogenetic diversity indices. Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals. -- The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x). -- The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson") -- Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber() -- Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich) -- Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
Phylogenetic diversity based on genus and familiy, Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
yes
27