class Patch:
'''
An object representing an empirical census.
Parameters
----------
data_path : str
Path to csv file containing census data.
subset : dict or str
Dictionary of permanent subset to data, {'column_name': 'condition'},
which will limit all analysis to records in which column_name meets the
condition, ie, {'year': ('==', 2005), 'x': [('>', 20), ('<', 40)]}
restricts analysis to year 2005 and x values between 20 and 40. These
conditions can also be passed to the individual methods, but subsetting
the data table up front may save analysis time. Subsetting on a string
would look something like {'name' : [('==', 'John'), ('==', 'Harry')]}.
In addition, subset can be a query string for a SQL database.
Attributes
----------
data_table : object of class DataTable
Object containing patch data and metadata.
'''
def __init__(self, datapath, subset = {}):
'''Initialize object of class Patch. See class documentation.'''
# Handle csv
self.data_table = DataTable(datapath, subset=subset)
# If datapath is sql or db the subsetting is already done.
if type(subset) == type({}):
self.data_table.table = self.data_table.get_subtable(subset)
def sad(self, criteria, clean=False):
'''
Calculates an empirical species abundance distribution given criteria.
Parameters
----------
criteria : dict
Dictionary of form {column_name: value}. Must contain a key with a
value of 'species' indicating the column with species identifiers
(this column must be type categorical in metadata). If a column
giving the counts of species found at a point is also in the data,
a key with the value 'count' should also be given.
Value has a different meaning depending on column type:
- metric - number of divisions of data along this axis, int/float
- categorical - 'split' calculates each category separately,
'whole' takes the entire column.
clean : bool
If True, all the zeros are removed from the sads. If False, sads
are left as is.
Returns
-------
result : list
List of tuples containing results, where the first element is a
dictionary of criteria for this calculation and second element is a
1D ndarray of length species containing the abundance for each
species. The third element is 1D array listing identifiers for
species in the same order as they appear in the second element of
result.
'''
spp_list, spp_col, count_col, engy_col, mass, combinations = \
self.parse_criteria(criteria)
if spp_col == None:
raise TypeError('No species column specified in "criteria" ' +
'parameter')
result = []
for comb in combinations:
subtable = self.data_table.get_subtable(comb)
sad_list = []
for species in spp_list:
spp_subtable = subtable[subtable[spp_col] == species]
if count_col:
count = np.sum(spp_subtable[count_col])
else:
count = len(spp_subtable)
sad_list.append(count)
sad_list = np.array(sad_list)
if clean:
ind = np.where(sad_list != 0)[0]
sad_list = sad_list[ind]
temp_spp_list = spp_list[ind]
else:
temp_spp_list = spp_list
result.append((comb, sad_list, temp_spp_list))
return result
def ssad(self, criteria):
'''
Calculates empirical species-level spatial abundance distributions
given criteria.
Parameters
----------
criteria : dict
See Patch.sad docstring
Returns
-------
: tuple
Returns a tuple with two objects. The first object is an array of
dicts that correspond to the criteria used to generate each cell.
The length of the first object in equal to the number of divisions
specified. The second object is a dictionary that has length
species and each keyword is a species. Each species keyword looks
up an array with the ssad for the given species. The array that
each keyword looks up is the same length as criteria.
'''
sad_return = self.sad(criteria, clean=False)
spp_list = sad_return[0][2]
combs, array_res = flatten_sad(sad_return)
ssad = {}
for i, spp in enumerate(spp_list):
ssad[spp] = array_res[i,:]
return combs, ssad
def parse_criteria(self, criteria):
'''
Parses criteria list to get all possible column combinations.
Parameters
----------
criteria : dict
(See docstring for Patch.sad)
energy : bool
If False, does not return an energy column, if True, returns an
energy column.
Returns
-------
spp_list : ndarray
1D array listing identifiers for species in the same order as they
appear in arrays found in result.
spp_col : str
Name of column containing species identifiers.
count_col : str
Name of column containing counts, if any.
combinations : list of dicts
List of dictionaries giving all possible combinations of criteria.
Columns not mentioned in criteria are ignored and will be averaged
over in later analyses.
'''
spp_list = None
spp_col = None
count_col = None
engy_col = None
mass_col = None
combinations = []
# Calculate all possible combinations of columns based on criteria
# TODO: Add error checking
for key, value in criteria.items():
# Look for two special values indicating species and count cols
if value == 'species':
spp_list = np.unique(self.data_table.table[key])
spp_col = key
continue
if value == 'count':
count_col = key
continue
if value == 'energy':
engy_col = key
continue
if value == 'mass':
mass_col = key
continue
# Get levels of categorial or metric data
if value == 'split': # Categorial
levels = np.unique(self.data_table.table[key])
levels_str = [('==' , x.astype(levels.dtype)) for x in levels]
elif value == 'whole':
# Random string to minimize chance of overlap?
levels_str = [('==','whole')]
else: # Metric
# TODO: Throw a warning if the data is not divisible by the
# divisions specified.
try:
dmin = self.data_table.meta[(key, 'minimum')]
dmax = self.data_table.meta[(key, 'maximum')]
dprec = self.data_table.meta[(key, 'precision')]
# TODO: Error if step < prec
step = (dmax + dprec - dmin) / value
starts = np.arange(dmin, dmax + dprec, step)
ends = starts + step
except TypeError:
raise TypeError('Unable to proceed to with values ' +
'obtained from metadata. Please check ' +
'the metadata file and/or parameters file')
starts_str = [('>=', x) for x in starts]
ends_str = [('<', x) for x in ends]
levels_str = [list(lvl) for lvl in zip(starts_str, ends_str)]
# Add these levels to combinations dictionary
if len(combinations) == 0: # If first criteria
for i, level in enumerate(levels_str):
combinations.append({key: level})
else:
temp_comb = []
for i, level in enumerate(levels_str):
exist_recs = deepcopy(combinations)
for rec in exist_recs:
rec[key] = level
temp_comb += exist_recs
combinations = temp_comb
if len(combinations) == 0:
combinations.append({})
return spp_list, spp_col, count_col, engy_col, mass_col, combinations
def sar(self, div_cols, div_list, criteria, form='sar'):
'''
Calulate an empirical species-area relationship given criteria.
Parameters
----------
div_cols : tuple
Column names to divide, eg, ('x', 'y'). Must be metric.
div_list : list of tuples
List of division pairs in same order as div_cols, eg, [(2,2),
(2,4), (4,4)]. Values are number of divisions of div_col.
criteria : dict
See docstring for EPatch.sad. Here, criteria SHOULD NOT include
items referring to div_cols (if there are any, they are ignored).
form : string
'sar' or 'ear' for species or endemics area relationship. EAR is
relative to the subtable selected after criteria is applied.
Returns
-------
rec_sar: structured array
Returns a structured array with fields 'items' and 'area' that
contains the average items/species for each given area specified by
critieria.
full_result : list of ndarrays
List of same length as areas containing arrays with element for
count of species or endemics in each subpatch at corresponding
area.
'''
# If any element in div_cols in criteria, remove from criteria
criteria = {k: v for k, v in criteria.items() if k not in div_cols}
# Loop through div combinations (ie, areas), calc sad, and summarize
areas = []
mean_result = []
full_result = []
for div in div_list:
# Add divs to criteria dict
this_criteria = deepcopy(criteria)
for i, col in enumerate(div_cols):
this_criteria[col] = div[i]
# Get flattened sad for all criteria and this div
sad_return = self.sad(this_criteria)
flat_sad = flatten_sad(sad_return)[1]
# Store results
if form == 'sar':
this_full = np.sum((flat_sad > 0), axis=0)
this_mean = np.mean(this_full)
elif form == 'ear':
totcnt = np.sum(flat_sad, axis=1)
totcnt_arr = \
np.array([list(totcnt),]*np.shape(flat_sad)[1]).transpose()
this_full = np.sum(np.equal(flat_sad, totcnt_arr), axis=0)
this_mean = np.mean(this_full)
else:
raise NotImplementedError('No SAR of form %s available' % form)
full_result.append(this_full)
mean_result.append(this_mean)
# Store area
area = 1
for i, col in enumerate(div_cols):
dmin = self.data_table.meta[(col, 'minimum')]
dmax = self.data_table.meta[(col, 'maximum')]
dprec = self.data_table.meta[(col, 'precision')]
length = (dmax + dprec - dmin)
area *= length / div[i]
areas.append(area)
# Return
rec_sar = np.array(zip(mean_result, areas), dtype=[('items', np.float),
('area', np.float)])
return rec_sar, full_result
def ied(self, criteria, normalize=True, exponent=0.75):
'''
Calculates the individual energy distribution for the entire community
given the criteria
Parameters
----------
criteria : dict
Dictionary must have contain a key with the value 'energy'. See
sad method for further requirements.
normalize : bool
If True, this distribution is normalized by dividing by the lowest
energy value within each element of criteria. If False, returns raw
energy values.
exponent : float
The exponent of the allometric scaling relationship if energy is
calculated from mass.
Returns
-------
result : list
List of tuples containing results, where first element is
dictionary of criteria for this calculation and second element is a
1D ndarray containing the energy measurement of each individual in
the subset. The third element is the full (not unique) species
list for the given criteria.
Notes
-----
If count_col is None or is all ones, the entire energy column for each
subtable is returned. Else, the average energy per individual,
repeated for each individual is returned. This is equivalent to the psi
distribution from Harte (2011).
'''
spp_list, spp_col, count_col, engy_col, mass_col, combinations = \
self.parse_criteria(criteria)
if engy_col == None and mass_col == None:
raise ValueError("No energy or mass column given")
elif engy_col == None and mass_col != None:
mass = True
this_engy = mass_col
else:
mass = False
this_engy = engy_col
result = []
for comb in combinations:
subtable = self.data_table.get_subtable(comb)
# If all counts are not 1
if count_col and (not np.all(subtable[count_col] == 1)):
# Remove any zero counts
subtable = subtable[subtable[count_col] != 0]
# Convert counts to ints
temp_counts = subtable[count_col].astype(int)
energy = np.repeat((subtable[this_engy] /
subtable[count_col]), temp_counts)
species = np.repeat(subtable[spp_col], temp_counts)
else:
energy = subtable[this_engy]
species = subtable[spp_col]
# Convert mass to energy if mass is True
if mass:
energy = (energy ** exponent)
# Normalizing energy
if normalize:
energy = energy / np.min(energy)
result.append((comb, energy, species))
return result
def sed(self, criteria, normalize=True, exponent=0.75, clean=False):
'''
Calculates the species-level energy distribution for each given species
in the community.
Parameters
----------
criteria : dict
Dictionary must have contain a key with the value 'energy' or
'mass'. See sad method for further requirements.
normalize : bool
If True, this distribution is normalized by dividing by the lowest
energy value within each element of criteria. If False, returns raw
energy values.
exponent : float
The exponent of the allometric scaling relationship if energy is
calculated from mass
clean : bool
If False, sed dictionary contains all species. If True, species
with no individuals are removed. This is useful when subsetting.
Returns
-------
result : list of tuples
Each tuple contains two objects. The first object is a dict with
the division specifications that generated the given species energy
distributions. The second object is a dict with a keyword
corresponding to each species in the spp_list. Each species
keyword looks up a np.array that contains the given species
energy distribution.
Note
----
The theta distribution from Harte (2011) is a an sed.
'''
spp_list, spp_col, count_col, engy_col, mass_col, combinations = \
self.parse_criteria(criteria)
ied = self.ied(criteria, normalize=normalize, exponent=exponent)
result = []
for this_ied in ied:
this_criteria_sed = {}
for spp in spp_list:
spp_ind = (spp == this_ied[2])
this_spp_sed = this_ied[1][spp_ind]
if clean: # If True, don't add empty species lists
if len(this_spp_sed) > 0:
this_criteria_sed[spp] = this_spp_sed
else:
this_criteria_sed[spp] = this_spp_sed
result.append((this_ied[0], this_criteria_sed))
return result
def ased(self, criteria, normalize=True, exponent=0.75):
'''
Calculates the average species energy distribution for each given
species in a subset.
Parameters
----------
criteria : dict
Dictionary must have contain a key with the value 'energy' or
'mass'. See sad method for further requirements.
Returns
-------
result : list
List of tuples containing results, where the first element is a
dictionary of criteria for this calculation and second element is a
1D ndarray of length species containing the average energy for each
species. The third element is 1D array listing identifiers for
species in the same order as they appear in the second element of
result.
Notes
-----
This is equivalent to the nu distribution from Harte 2011
'''
sed = self.sed(criteria, normalize=normalize, exponent=exponent)
result = []
for this_sed in sed:
spp_list = list(this_sed[1].viewkeys())
spp_list.sort()
# Take the mean energy for each species
nu = [np.mean(this_sed[1][spp]) for spp in spp_list if
len(this_sed[1][spp]) != 0]
# Truncated spp_list if necessary
spp_list = [spp for spp in spp_list if len(this_sed[1][spp]) != 0]
result.append((this_sed[0], np.array(nu), np.array(spp_list)))
return result
class Patch:
'''
An object representing an empirical census.
Parameters
----------
data_path : str
Path to csv file containing census data.
subset : dict or str
Dictionary of permanent subset to data, {'column_name': 'condition'},
which will limit all analysis to records in which column_name meets the
condition, ie, {'year': ('==', 2005), 'x': [('>', 20), ('<', 40)]}
restricts analysis to year 2005 and x values between 20 and 40. These
conditions can also be passed to the individual methods, but subsetting
the data table up front may save analysis time. Subsetting on a string
would look something like {'name' : [('==', 'John'), ('==', 'Harry')]}.
In addition, subset can be a query string for a SQL database.
Attributes
----------
data_table : object of class DataTable
Object containing patch data and metadata.
'''
def __init__(self, datapath, subset = {}):
'''Initialize object of class Patch. See class documentation.'''
# Handle csv
self.data_table = DataTable(datapath, subset=subset)
# If datapath is sql or db the subsetting is already done.
if type(subset) == type({}):
self.data_table.table = self.data_table.get_subtable(subset)
def sad(self, criteria, clean=False):
'''
Calculates an empirical species abundance distribution given criteria.
Parameters
----------
criteria : dict
Dictionary of form {column_name: value}. Must contain a key with a
value of 'species' indicating the column with species identifiers
(this column must be type categorical in metadata). If a column
giving the counts of species found at a point is also in the data,
a key with the value 'count' should also be given.
Value has a different meaning depending on column type:
- metric - number of divisions of data along this axis, int/float
- categorical - 'split' calculates each category separately,
'whole' takes the entire column.
clean : bool
If True, all the zeros are removed from the sads. If False, sads
are left as is.
Returns
-------
result : list
List of tuples containing results, where the first element is a
dictionary of criteria for this calculation and second element is a
1D ndarray of length species containing the abundance for each
species. The third element is 1D array listing identifiers for
species in the same order as they appear in the second element of
result.
'''
spp_list, spp_col, count_col, engy_col, mass, combinations = \
self.parse_criteria(criteria)
if spp_col == None:
raise TypeError('No species column specified in "criteria" ' +
'parameter')
result = []
for comb in combinations:
subtable = self.data_table.get_subtable(comb)
sad_list = []
for species in spp_list:
spp_subtable = subtable[subtable[spp_col] == species]
if count_col:
count = np.sum(spp_subtable[count_col])
else:
count = len(spp_subtable)
sad_list.append(count)
sad_list = np.array(sad_list)
if clean:
ind = np.where(sad_list != 0)[0]
sad_list = sad_list[ind]
temp_spp_list = spp_list[ind]
else:
temp_spp_list = spp_list
result.append((comb, sad_list, temp_spp_list))
return result
def ssad(self, criteria):
'''
Calculates empirical species-level spatial abundance distributions
given criteria.
Parameters
----------
criteria : dict
See Patch.sad docstring
Returns
-------
: tuple
Returns a tuple with two objects. The first object is an array of
dicts that correspond to the criteria used to generate each cell.
The length of the first object in equal to the number of divisions
specified. The second object is a dictionary that has length
species and each keyword is a species. Each species keyword looks
up an array with the ssad for the given species. The array that
each keyword looks up is the same length as criteria.
'''
sad_return = self.sad(criteria, clean=False)
spp_list = sad_return[0][2]
combs, array_res = flatten_sad(sad_return)
ssad = {}
for i, spp in enumerate(spp_list):
ssad[spp] = array_res[i,:]
return combs, ssad
def parse_criteria(self, criteria):
'''
Parses criteria list to get all possible column combinations.
Parameters
----------
criteria : dict
(See docstring for Patch.sad)
energy : bool
If False, does not return an energy column, if True, returns an
energy column.
Returns
-------
spp_list : ndarray
1D array listing identifiers for species in the same order as they
appear in arrays found in result.
spp_col : str
Name of column containing species identifiers.
count_col : str
Name of column containing counts, if any.
combinations : list of dicts
List of dictionaries giving all possible combinations of criteria.
Columns not mentioned in criteria are ignored and will be averaged
over in later analyses.
'''
spp_list = None
spp_col = None
count_col = None
engy_col = None
mass_col = None
combinations = []
# Calculate all possible combinations of columns based on criteria
# TODO: Add error checking
for key, value in criteria.items():
# Look for two special values indicating species and count cols
if value == 'species':
spp_list = np.unique(self.data_table.table[key])
spp_col = key
continue
if value == 'count':
count_col = key
continue
if value == 'energy':
engy_col = key
continue
if value == 'mass':
mass_col = key
continue
# Get levels of categorial or metric data
if value == 'split': # Categorial
levels = np.unique(self.data_table.table[key])
levels_str = [('==' , x.astype(levels.dtype)) for x in levels]
elif value == 'whole':
# Random string to minimize chance of overlap?
levels_str = [('==','whole')]
else: # Metric
# TODO: Throw a warning if the data is not divisible by the
# divisions specified.
try:
dmin = self.data_table.meta[(key, 'minimum')]
dmax = self.data_table.meta[(key, 'maximum')]
dprec = self.data_table.meta[(key, 'precision')]
# TODO: Error if step < prec
step = (dmax + dprec - dmin) / value
starts = np.arange(dmin, dmax + dprec, step)
ends = starts + step
except TypeError:
raise TypeError('Unable to proceed to with values ' +
'obtained from metadata. Please check ' +
'the metadata file and/or parameters file')
starts_str = [('>=', x) for x in starts]
ends_str = [('<', x) for x in ends]
levels_str = [list(lvl) for lvl in zip(starts_str, ends_str)]
# Add these levels to combinations dictionary
if len(combinations) == 0: # If first criteria
for i, level in enumerate(levels_str):
combinations.append({key: level})
else:
temp_comb = []
for i, level in enumerate(levels_str):
exist_recs = deepcopy(combinations)
for rec in exist_recs:
rec[key] = level
temp_comb += exist_recs
combinations = temp_comb
if len(combinations) == 0:
combinations.append({})
return spp_list, spp_col, count_col, engy_col, mass_col, combinations
def sar(self, div_cols, div_list, criteria, form='sar', output_N=False):
'''
Calculate an empirical species-area relationship given criteria.
Parameters
----------
div_cols : tuple
Column names to divide, eg, ('x', 'y'). Must be metric.
div_list : list of tuples
List of division pairs in same order as div_cols, eg, [(2,2),
(2,4), (4,4)]. Values are number of divisions of div_col.
criteria : dict
See docstring for EPatch.sad. Here, criteria SHOULD NOT include
items referring to div_cols (if there are any, they are ignored).
form : string
'sar' or 'ear' for species or endemics area relationship. EAR is
relative to the subtable selected after criteria is applied.
output_N : bool
Adds the column N to the output rec array which contains the
average N for a given area.
Returns
-------
rec_sar: structured array
Returns a structured array with fields 'items' and 'area' that
contains the average items/species for each given area specified by
critieria.
full_result : list of ndarrays
List of same length as areas containing arrays with element for
count of species or endemics in each subpatch at corresponding
area.
'''
# If any element in div_cols in criteria, remove from criteria
criteria = {k: v for k, v in criteria.items() if k not in div_cols}
# Loop through div combinations (ie, areas), calc sad, and summarize
areas = []
mean_result = []
full_result = []
N_result = []
for div in div_list:
# Add divs to criteria dict
this_criteria = deepcopy(criteria)
for i, col in enumerate(div_cols):
this_criteria[col] = div[i]
# Get flattened sad for all criteria and this div
sad_return = self.sad(this_criteria)
if output_N:
N_result.append(np.mean([sum(sad[1]) for sad in sad_return]))
flat_sad = flatten_sad(sad_return)[1]
# Store results
if form == 'sar':
this_full = np.sum((flat_sad > 0), axis=0)
this_mean = np.mean(this_full)
elif form == 'ear':
totcnt = np.sum(flat_sad, axis=1)
totcnt_arr = \
np.array([list(totcnt),]*np.shape(flat_sad)[1]).transpose()
this_full = np.sum(np.equal(flat_sad, totcnt_arr), axis=0)
this_mean = np.mean(this_full)
else:
raise NotImplementedError('No SAR of form %s available' % form)
full_result.append(this_full)
mean_result.append(this_mean)
# Store area
area = 1
for i, col in enumerate(div_cols):
dmin = self.data_table.meta[(col, 'minimum')]
dmax = self.data_table.meta[(col, 'maximum')]
dprec = self.data_table.meta[(col, 'precision')]
length = (dmax + dprec - dmin)
area *= length / div[i]
areas.append(area)
# Return
if not output_N:
rec_sar = np.array(zip(mean_result, areas), dtype=[('items',
np.float), ('area', np.float)])
else:
rec_sar = np.array(zip(mean_result, N_result, areas),
dtype=[('items', np.float), ('N', np.float), ('area', np.float)])
return rec_sar, full_result
def universal_sar(self, div_cols, div_list, criteria, include_full=False):
'''
Calculates the empirical universal sar given criteria. The universal
sar calculates the slope of the SAR and the ratio of N / S at all
the areas in div_cols (where N is the total number of species and S is
the total number of species).
This function assumes that the div_list contains halvings. If they are not,
the function will still work but the results will be meaningless. An
example a of div_list with halvings is:
[(1,1), (1,2), (2,2), (2,4), (4,4)]
Parameters
----------
div_cols : tuple
Column names to divide, eg, ('x', 'y'). Must be metric.
div_list : list of tuples
List of division pairs in same order as div_cols, eg, [(2,2),
(2,4), (4,4)]. Values are number of divisions of div_col.
criteria : dict
See docstring for EPatch.sad. Here, criteria SHOULD NOT include
items referring to div_cols (if there are any, they are ignored).
include_full : bool
If include_full = True, the division (1,1) will be included if it
was now already included. Else it will not be included. (1,1) is
equivalent to the full plot
Returns
-------
z_array : a structured array
Has the columns names:
'z' : slope of the SAR at the given area
'S' : Number of species at the given division
'N' : Number of individuals at the given division
'N/S' : The ratio of N/S at the given division
Notes
-----
If you give it n divisions in div_list you will get a structured array
back that has length n - 2. Therefore, if you only have one
'''
# If (1,1) is not included, include it
if include_full:
try:
div_list.index((1,1))
except ValueError:
div_list.insert(0, (1,1))
# Run sar with the div_cols
sar = self.sar(div_cols, div_list, criteria, output_N=True)[0]
# sort by area
sar = np.sort(sar, order=['area'])[::-1]
# Calculate z's
if len(sar) >= 3: # Check the length of sar
z_list = [z(sar['items'][i - 1], sar['items'][i + 1]) for i in
np.arange(1, len(sar)) if sar['items'][i] != sar['items'][-1]]
else:
return np.empty(0, dtype=[('z', np.float), ('S', np.float), ('N',
np.float), ('N/S', np.float)])
N_over_S = sar['N'][1:len(sar) - 1] / sar['items'][1:len(sar) - 1]
z_array = np.array(zip(z_list, sar['items'][1:len(sar) - 1],
sar['N'][1:len(sar) - 1], N_over_S), dtype=[('z', np.float), ('S',
np.float), ('N', np.float), ('N/S', np.float)])
return z_array
def comm_sep(self, plot_locs, criteria, loc_unit=None):
'''
Calculates commonality (Sorensen and Jaccard) between pairs of plots.
Parameters
----------
plot_locs : dict
Dictionary with keys equal to each plot name, which must be
represented by a column in the data table, and values equal to a
tuple of the x and y coordinate of each plot
criteria : dict
See docstring for Patch.sad.
loc_unit : str
Unit of plot locations. Special cases include 'decdeg' (decimal
degrees), returns result in km. Otherwise ignored.
Returns
-------
result: structured array
Returns a structured array with fields plot-a and plot-b (names of
two plots), dist (distance between plots), and sorensen and jaccard
(similarity indices). Has row for each unique pair of plots.
'''
# Set up sad_dict with key=plot and val=clean sad for that plot
sad_dict = {}
# Loop through all plot cols, updating criteria, and getting spp_list
for plot in plot_locs.keys():
# Find current count col and remove it from criteria
for crit_key in criteria.keys():
if criteria[crit_key] == 'count':
criteria.pop(crit_key, None)
# Add this plot as col with counts
criteria[plot] = 'count'
# Get SAD for existing criteria with this plot as count col
sad_return = self.sad(criteria, clean=True)
# Check that sad_return only has one element, or throw error
if len(sad_return) > 1:
raise NotImplementedError('Too many criteria for comm_sep')
# Get unique species list for this plot and store in sad_dict
sad_dict[plot] = sad_return[0][2]
# Set up recarray to hold Sorensen index for all pairs of plots
n_pairs = np.sum(np.arange(len(plot_locs.keys())))
result = np.recarray((n_pairs,), dtype=[('plot-a','S32'),
('plot-b', 'S32'),
('spp-a', int),
('spp-b', int),
('dist', float),
('sorensen', float),
('jaccard', float)])
# Loop through all combinations of plots and fill in result table
row = 0
for pair in itertools.combinations(plot_locs.keys(), 2):
# Names of plots
plota = pair[0]
plotb = pair[1]
result[row]['plot-a'] = plota
result[row]['plot-b'] = plotb
# Calculate inter-plot distance
if loc_unit == 'decdeg':
result[row]['dist'] = decdeg_distance(plot_locs[plota],
plot_locs[plotb])
else:
result[row]['dist'] = distance(plot_locs[plota],
plot_locs[plotb])
# Get similarity indices
spp_a = len(sad_dict[plota])
spp_b = len(sad_dict[plotb])
result[row]['spp-a'] = spp_a
result[row]['spp-b'] = spp_b
intersect = set(sad_dict[plota]).intersection(sad_dict[plotb])
union = set(sad_dict[plota]).union(sad_dict[plotb])
# Fill in zero if denom is zero
if spp_a + spp_b == 0:
result[row]['sorensen'] = 0
else:
result[row]['sorensen'] = (2*len(intersect)) / (spp_a+spp_b)
if len(union) == 0:
result[row]['jaccard'] = 0
else:
result[row]['jaccard'] = len(intersect) / len(union)
# Increment row counter
row += 1
return result
def ied(self, criteria, normalize=True, exponent=0.75):
'''
Calculates the individual energy distribution for the entire community
given the criteria
Parameters
----------
criteria : dict
Dictionary must have contain a key with the value 'energy'. See
sad method for further requirements.
normalize : bool
If True, this distribution is normalized by dividing by the lowest
energy value within each element of criteria. If False, returns raw
energy values.
exponent : float
The exponent of the allometric scaling relationship if energy is
calculated from mass.
Returns
-------
result : list
List of tuples containing results, where first element is
dictionary of criteria for this calculation and second element is a
1D ndarray containing the energy measurement of each individual in
the subset. The third element is the full (not unique) species
list for the given criteria.
Notes
-----
If count_col is None or is all ones, the entire energy column for each
subtable is returned. Else, the average energy per individual,
repeated for each individual is returned. This is equivalent to the psi
distribution from Harte (2011).
'''
spp_list, spp_col, count_col, engy_col, mass_col, combinations = \
self.parse_criteria(criteria)
if engy_col == None and mass_col == None:
raise ValueError("No energy or mass column given")
elif engy_col == None and mass_col != None:
mass = True
this_engy = mass_col
else:
mass = False
this_engy = engy_col
result = []
for comb in combinations:
subtable = self.data_table.get_subtable(comb)
# If all counts are not 1
if count_col and (not np.all(subtable[count_col] == 1)):
# Remove any zero counts
subtable = subtable[subtable[count_col] != 0]
# Convert counts to ints
temp_counts = subtable[count_col].astype(int)
energy = np.repeat((subtable[this_engy] /
subtable[count_col]), temp_counts)
species = np.repeat(subtable[spp_col], temp_counts)
else:
energy = subtable[this_engy]
species = subtable[spp_col]
# Convert mass to energy if mass is True
if mass:
energy = (energy ** exponent)
# Normalizing energy
if normalize:
energy = energy / np.min(energy)
result.append((comb, energy, species))
return result
def sed(self, criteria, normalize=True, exponent=0.75, clean=False):
'''
Calculates the species-level energy distribution for each given species
in the community.
Parameters
----------
criteria : dict
Dictionary must have contain a key with the value 'energy' or
'mass'. See sad method for further requirements.
normalize : bool
If True, this distribution is normalized by dividing by the lowest
energy value within each element of criteria. If False, returns raw
energy values.
exponent : float
The exponent of the allometric scaling relationship if energy is
calculated from mass
clean : bool
If False, sed dictionary contains all species. If True, species
with no individuals are removed. This is useful when subsetting.
Returns
-------
result : list of tuples
Each tuple contains two objects. The first object is a dict with
the division specifications that generated the given species energy
distributions. The second object is a dict with a keyword
corresponding to each species in the spp_list. Each species
keyword looks up a np.array that contains the given species
energy distribution.
Note
----
The theta distribution from Harte (2011) is a an sed.
'''
spp_list, spp_col, count_col, engy_col, mass_col, combinations = \
self.parse_criteria(criteria)
ied = self.ied(criteria, normalize=normalize, exponent=exponent)
result = []
for this_ied in ied:
this_criteria_sed = {}
for spp in spp_list:
spp_ind = (spp == this_ied[2])
this_spp_sed = this_ied[1][spp_ind]
if clean: # If True, don't add empty species lists
if len(this_spp_sed) > 0:
this_criteria_sed[spp] = this_spp_sed
else:
this_criteria_sed[spp] = this_spp_sed
result.append((this_ied[0], this_criteria_sed))
return result
def ased(self, criteria, normalize=True, exponent=0.75):
'''
Calculates the average species energy distribution for each given
species in a subset.
Parameters
----------
criteria : dict
Dictionary must have contain a key with the value 'energy' or
'mass'. See sad method for further requirements.
Returns
-------
result : list
List of tuples containing results, where the first element is a
dictionary of criteria for this calculation and second element is a
1D ndarray of length species containing the average energy for each
species. The third element is 1D array listing identifiers for
species in the same order as they appear in the second element of
result.
Notes
-----
This is equivalent to the nu distribution from Harte 2011
'''
sed = self.sed(criteria, normalize=normalize, exponent=exponent)
result = []
for this_sed in sed:
spp_list = list(this_sed[1].viewkeys())
spp_list.sort()
# Take the mean energy for each species
nu = [np.mean(this_sed[1][spp]) for spp in spp_list if
len(this_sed[1][spp]) != 0]
# Truncated spp_list if necessary
spp_list = [spp for spp in spp_list if len(this_sed[1][spp]) != 0]
result.append((this_sed[0], np.array(nu), np.array(spp_list)))
return result