Source code for geosnap.data.data

"""Tools for creating and manipulating neighborhood datasets."""

import os
import zipfile
from warnings import warn
from appdirs import user_data_dir
import pandas as pd
import quilt3
import geopandas as gpd
import numpy as np
import sys
import pathlib
from requests.exceptions import Timeout

sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))

from analyze import cluster as _cluster, cluster_spatial as _cluster_spatial
from harmonize import harmonize as _harmonize
from .util import adjust_inflation, convert_gdf, get_lehd
from analyze import transition as _transition, sequence as _sequence

_fipstable = pd.read_csv(
    os.path.join(os.path.dirname(os.path.abspath(__file__)), "stfipstable.csv"),
    converters={"FIPS Code": str},
)

appname = "geosnap"
appauthor = "geosnap"
data_dir = user_data_dir(appname, appauthor)
if not os.path.exists(data_dir):
    pathlib.Path(data_dir).mkdir(parents=True, exist_ok=True)

# look for local storage and create if missing
try:
    from quilt3.data.geosnap_data import storage
except ImportError:
    storage = quilt3.Package()


[docs]class DataStore(object): """Storage for geosnap data. Currently supports US Census data."""
[docs] def __init__(self): """Instantiate a new DataStore object.""" try: # if any of these aren't found, stream them insteead from quilt3.data.census import tracts_cartographic, administrative except ImportError: warn( "Unable to locate local census data. Streaming instead.\n" "If you plan to use census data repeatedly you can store it locally " "with the data.store_census function for better performance" ) try: tracts_cartographic = quilt3.Package.browse( "census/tracts_cartographic", "s3://quilt-cgs" ) administrative = quilt3.Package.browse( "census/administrative", "s3://quilt-cgs" ) except Timeout: warn( "Unable to locate local census data and unable to reach s3 bucket." "You will be unable to use built-in data during this session. " "If you need these data, please try downloading a local copy " "with the data.store_census function, then restart your " "python kernel and try again." ) self.tracts_cartographic = tracts_cartographic self.administrative = administrative
def __dir__(self): atts = [ "blocks_2000", "blocks_2010", "codebook", "counties", "ltdb", "msa_definitions", "msas", "ncdb", "states", "tracts_1990", "tracts_2000", "tracts_2010", ] return atts
[docs] def blocks_2000(self, states=None, convert=True): """Census blocks for 2000. Parameters ---------- states : list-like list of state fips codes to return as a datafrrame. convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- type pandas.DataFrame or geopandas.GeoDataFrame. 2000 blocks as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ try: # if any of these aren't found, stream them insteead from quilt3.data.census import blocks_2000 except ImportError: warn( "Unable to locate local census 2000 block data. Streaming instead.\n" "If you plan to use census data repeatedly you can store it locally " "with the data.store_blocks_2000 function for better performance" ) try: blocks_2000 = quilt3.Package.browse( "census/blocks_2000", "s3://quilt-cgs" ) except Timeout: warn( "Unable to locate local census data and unable to reach s3 bucket." "You will be unable to use built-in data during this session. " "Try downloading a local copy with the data.store_blocks_2000 function," "then restart your python kernel and try again." ) if isinstance(states, (str,)): states = [states] if isinstance(states, (int,)): states = [states] blks = {} for state in states: blks[state] = blocks_2000["{state}.parquet".format(state=state)]() blks[state]["year"] = 2000 blocks = list(blks.values()) blocks = pd.concat(blocks, sort=True) if convert: return convert_gdf(blocks) return blocks
[docs] def blocks_2010(self, states=None, convert=True): """Census blocks for 2010. Parameters ---------- states : list-like list of state fips codes to return as a datafrrame. convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- type pandas.DataFrame or geopandas.GeoDataFrame. 2010 blocks as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ try: # if any of these aren't found, stream them insteead from quilt3.data.census import blocks_2010 except ImportError: warn( "Unable to locate local census 2010 block data. Streaming instead.\n" "If you plan to use census data repeatedly you can store it locally " "with the data.store_blocks_2010 function for better performance" ) try: blocks_2010 = quilt3.Package.browse( "census/blocks_2010", "s3://quilt-cgs" ) except Timeout: warn( "Unable to locate local census data and unable to reach s3 bucket." "You will be unable to use built-in data during this session. " "If you need these data, please try downloading a local copy " "with the data.store_blocks_2010 function, then restart your " "python kernel and try again." ) if isinstance(states, (str, int)): states = [states] blks = {} for state in states: blks[state] = blocks_2010["{state}.parquet".format(state=state)]() blks[state]["year"] = 2010 blocks = list(blks.values()) blocks = pd.concat(blocks, sort=True) if convert: return convert_gdf(blocks) return blocks
[docs] def tracts_1990(self, states=None, convert=True): """Nationwide Census Tracts as drawn in 1990 (cartographic 500k). Parameters ---------- states : list-like list of state fips to subset the national dataframe convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- pandas.DataFrame or geopandas.GeoDataFrame. 1990 tracts as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ t = self.tracts_cartographic["tracts_1990_500k.parquet"]() if states: t = t[t.geoid.str[:2].isin(states)] t["year"] = 1990 if convert: return convert_gdf(t) else: return t
[docs] def tracts_2000(self, states=None, convert=True): """Nationwide Census Tracts as drawn in 2000 (cartographic 500k). Parameters ---------- states : list-like list of state fips to subset the national dataframe convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- pandas.DataFrame. 2000 tracts as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ t = self.tracts_cartographic["tracts_2000_500k.parquet"]() if states: t = t[t.geoid.str[:2].isin(states)] t["year"] = 2000 if convert: return convert_gdf(t) else: return t
[docs] def tracts_2010(self, states=None, convert=True): """Nationwide Census Tracts as drawn in 2010 (cartographic 500k). Parameters ---------- states : list-like list of state fips to subset the national dataframe convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- pandas.DataFrame. 2010 tracts as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ t = self.tracts_cartographic["tracts_2010_500k.parquet"]() if states: t = t[t.geoid.str[:2].isin(states)] t["year"] = 2010 if convert: return convert_gdf(t) else: return t
[docs] def msas(self, convert=True): """Metropolitan Statistical Areas as drawn in 2010. Parameters ---------- convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- geopandas.GeoDataFrame. 2010 MSAs as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ if convert: return convert_gdf( self.administrative["msas.parquet"]().sort_values(by="name") ) else: return self.administrative["msas.parquet"]().sort_values(by="name")
[docs] def states(self, convert=True): """States. Parameters ---------- convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- geopandas.GeoDataFrame. US States as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ if convert: return convert_gdf(self.administrative["states.parquet"]()) else: return self.administrative["states.parquet"]()
[docs] def counties(self, convert=True): """Nationwide counties as drawn in 2010. Parameters ---------- convert : bool if True, return geodataframe, else return dataframe (the default is True). Returns ------- geopandas.GeoDataFrame. 2010 counties as a geodataframe or as a dataframe with geometry stored as well-known binary on the 'wkb' column. """ return convert_gdf(self.administrative["counties.parquet"]())
@property def msa_definitions(self): """2010 Metropolitan Statistical Area definitions. Parameters ---------- None Returns ------- pandas.DataFrame. dataframe that stores state/county --> MSA crosswalk definitions. """ return self.administrative["msa_definitions.parquet"]() @property def ltdb(self): """Longitudinal Tract Database (LTDB). Parameters ---------- None Returns ------- pandas.DataFrame or geopandas.GeoDataFrame LTDB as a long-form geo/dataframe """ try: return storage["ltdb"]() except KeyError: print( "Unable to locate LTDB data. Try saving the data again " "using the `store_ltdb` function" ) @property def ncdb(self): """Geolytics Neighborhood Change Database (NCDB). Parameters ---------- None Returns ------- pandas.DataFrarme NCDB as a long-form dataframe """ try: return storage["ncdb"]() except KeyError: print( "Unable to locate NCDB data. Try saving the data again " "using the `store_ncdb` function" ) @property def codebook(self): """Codebook. Parameters ---------- None Returns ------- pandas.DataFrame. codebook that stores variable names, definitions, and formulas. """ return pd.read_csv( os.path.join(os.path.dirname(os.path.abspath(__file__)), "variables.csv") )
data_store = DataStore()
[docs]def store_census(): """Save census data to the local quilt package storage. Parameters ---------- None Returns ------- None Data will be available in the geosnap.data.data_store and will be used in place of streaming data for all census queries. The raster package is 3.05 GB. """ quilt3.Package.install("census/tracts_cartographic", "s3://quilt-cgs") quilt3.Package.install("census/administrative", "s3://quilt-cgs")
[docs]def store_blocks_2000(): """Save census 2000 census block data to the local quilt package storage. Parameters ---------- None Returns ------- None Data will be available in the geosnap.data.data_store and will be used in place of streaming data for all census queries. """ quilt3.Package.install("census/blocks_2000", "s3://quilt-cgs")
[docs]def store_blocks_2010(): """Save census 2010 census block data to the local quilt package storage. Parameters ---------- None Returns ------- None Data will be available in the geosnap.data.data_store and will be used in place of streaming data for all census queries. """ quilt3.Package.install("census/blocks_2010", "s3://quilt-cgs")
[docs]def store_ltdb(sample, fullcount): """ Read & store data from Brown's Longitudinal Tract Database (LTDB). Parameters ---------- sample : str file path of the zip file containing the standard Sample CSV files downloaded from https://s4.ad.brown.edu/projects/diversity/Researcher/LTBDDload/Default.aspx fullcount: str file path of the zip file containing the standard Fullcount CSV files downloaded from https://s4.ad.brown.edu/projects/diversity/Researcher/LTBDDload/Default.aspx Returns ------- pandas.DataFrame """ sample_zip = zipfile.ZipFile(sample) fullcount_zip = zipfile.ZipFile(fullcount) def _ltdb_reader(path, file, year, dropcols=None): df = pd.read_csv( path.open(file), na_values=["", " ", 99999, -999], converters={0: str, "placefp10": str}, low_memory=False, encoding="latin1", ) if dropcols: df.drop(dropcols, axis=1, inplace=True) df.columns = df.columns.str.lower() names = df.columns.values.tolist() names[0] = "geoid" newlist = [] # ignoring the first 4 columns, remove year suffix from column names for name in names[4:]: newlist.append(name[:-2]) colnames = names[:4] + newlist df.columns = colnames # prepend a 0 when FIPS is too short df["geoid"] = df["geoid"].str.rjust(11, "0") df.set_index("geoid", inplace=True) df["year"] = year inflate_cols = [ "mhmval", "mrent", "incpc", "hinc", "hincw", "hincb", "hinch", "hinca", ] inflate_available = list(set(df.columns).intersection(set(inflate_cols))) if len(inflate_available): df = adjust_inflation(df, inflate_available, year) return df # read in Brown's LTDB data, both the sample and fullcount files for each # year population, housing units & occupied housing units appear in both # "sample" and "fullcount" files-- currently drop sample and keep fullcount sample70 = _ltdb_reader( sample_zip, "ltdb_std_all_sample/ltdb_std_1970_sample.csv", dropcols=["POP70SP1", "HU70SP", "OHU70SP"], year=1970, ) fullcount70 = _ltdb_reader(fullcount_zip, "LTDB_Std_1970_fullcount.csv", year=1970) sample80 = _ltdb_reader( sample_zip, "ltdb_std_all_sample/ltdb_std_1980_sample.csv", dropcols=["pop80sf3", "pop80sf4", "hu80sp", "ohu80sp"], year=1980, ) fullcount80 = _ltdb_reader(fullcount_zip, "LTDB_Std_1980_fullcount.csv", year=1980) sample90 = _ltdb_reader( sample_zip, "ltdb_std_all_sample/ltdb_std_1990_sample.csv", dropcols=["POP90SF3", "POP90SF4", "HU90SP", "OHU90SP"], year=1990, ) fullcount90 = _ltdb_reader(fullcount_zip, "LTDB_Std_1990_fullcount.csv", year=1990) sample00 = _ltdb_reader( sample_zip, "ltdb_std_all_sample/ltdb_std_2000_sample.csv", dropcols=["POP00SF3", "HU00SP", "OHU00SP"], year=2000, ) fullcount00 = _ltdb_reader(fullcount_zip, "LTDB_Std_2000_fullcount.csv", year=2000) sample10 = _ltdb_reader( sample_zip, "ltdb_std_all_sample/ltdb_std_2010_sample.csv", year=2010 ) # join the sample and fullcount variables into a single df for the year ltdb_1970 = sample70.drop(columns=["year"]).join( fullcount70.iloc[:, 7:], how="left" ) ltdb_1980 = sample80.drop(columns=["year"]).join( fullcount80.iloc[:, 7:], how="left" ) ltdb_1990 = sample90.drop(columns=["year"]).join( fullcount90.iloc[:, 7:], how="left" ) ltdb_2000 = sample00.drop(columns=["year"]).join( fullcount00.iloc[:, 7:], how="left" ) ltdb_2010 = sample10 df = pd.concat([ltdb_1970, ltdb_1980, ltdb_1990, ltdb_2000, ltdb_2010], sort=True) renamer = dict( zip( data_store.codebook["ltdb"].tolist(), data_store.codebook["variable"].tolist(), ) ) df.rename(renamer, axis="columns", inplace=True) # compute additional variables from lookup table for row in data_store.codebook["formula"].dropna().tolist(): df.eval(row, inplace=True) keeps = df.columns[ df.columns.isin(data_store.codebook["variable"].tolist() + ["year"]) ] df = df[keeps] df.to_parquet(os.path.join(data_dir, "ltdb.parquet"), compression="brotli") storage.set("ltdb", os.path.join(data_dir, "ltdb.parquet")) storage.build("geosnap_data/storage")
[docs]def store_ncdb(filepath): """ Read & store data from Geolytics's Neighborhood Change Database. Parameters ---------- filepath : str location of the input CSV file extracted from your Geolytics DVD """ ncdb_vars = data_store.codebook["ncdb"].dropna()[1:].values names = [] for name in ncdb_vars: for suffix in ["7", "8", "9", "0", "1", "2"]: names.append(name + suffix) names.append("GEO2010") c = pd.read_csv(filepath, nrows=1).columns c = pd.Series(c.values) keep = [] for i, col in c.items(): for name in names: if col.startswith(name): keep.append(col) df = pd.read_csv( filepath, usecols=keep, engine="c", na_values=["", " ", 99999, -999], converters={ "GEO2010": str, "COUNTY": str, "COUSUB": str, "DIVISION": str, "REGION": str, "STATE": str, }, ) cols = df.columns fixed = [] for col in cols: if col.endswith("D"): fixed.append("D" + col[:-1]) elif col.endswith("N"): fixed.append("N" + col[:-1]) elif col.endswith("1A"): fixed.append(col[:-2] + "2") orig = [] for col in cols: if col.endswith("D"): orig.append(col) elif col.endswith("N"): orig.append(col) elif col.endswith("1A"): orig.append(col) renamer = dict(zip(orig, fixed)) df.rename(renamer, axis="columns", inplace=True) df = df[df.columns[df.columns.isin(names)]] df = pd.wide_to_long( df, stubnames=ncdb_vars, i="GEO2010", j="year", suffix="(7|8|9|0|1|2)" ).reset_index() df["year"] = df["year"].replace( {7: 1970, 8: 1980, 9: 1990, 0: 2000, 1: 2010, 2: 2010} ) df = df.groupby(["GEO2010", "year"]).first() mapper = dict(zip(data_store.codebook.ncdb, data_store.codebook.variable)) df.reset_index(inplace=True) df = df.rename(mapper, axis="columns") df = df.set_index("geoid") for row in data_store.codebook["formula"].dropna().tolist(): try: df.eval(row, inplace=True) except: warn("Unable to compute " + str(row)) keeps = df.columns[ df.columns.isin(data_store.codebook["variable"].tolist() + ["year"]) ] df = df[keeps] df = df.loc[df.n_total_pop != 0] df.to_parquet(os.path.join(data_dir, "ncdb.parquet"), compression="brotli") storage.set("ncdb", os.path.join(data_dir, "ncdb.parquet")) storage.build("geosnap_data/storage")
def _fips_filter( state_fips=None, county_fips=None, msa_fips=None, fips=None, data=None ): if isinstance(state_fips, (str,)): state_fips = [state_fips] if isinstance(county_fips, (str,)): county_fips = [county_fips] if isinstance(fips, (str,)): fips = [fips] # if counties already present in states, ignore them if county_fips: for i in county_fips: if state_fips and i[:2] in county_fips: county_fips.remove(i) # if any fips present in state or counties, ignore them too if fips: for i in fips: if state_fips and i[:2] in state_fips: fips.remove(i) if county_fips and i[:5] in county_fips: fips.remove(i) fips_list = [] if fips: fips_list += fips if county_fips: fips_list += county_fips if state_fips: fips_list += state_fips if msa_fips: fips_list += data_store.msa_definitions[ data_store.msa_definitions["CBSA Code"] == msa_fips ]["stcofips"].tolist() dfs = [] for index in fips_list: dfs.append(data[data.geoid.str.startswith(index)]) return pd.concat(dfs) def _from_db( data, state_fips=None, county_fips=None, msa_fips=None, fips=None, years=None ): data = data[data.year.isin(years)] data = data.reset_index() df = _fips_filter( state_fips=state_fips, county_fips=county_fips, msa_fips=msa_fips, fips=fips, data=data, ) # we know we're using 2010, need to drop the year column so no conficts tracts = data_store.tracts_2010(convert=False) tracts = tracts[["geoid", "wkb"]] tracts = tracts[tracts.geoid.isin(df.geoid)] tracts = convert_gdf(tracts) gdf = df.merge(tracts, on="geoid", how="left").set_index("geoid") gdf = gpd.GeoDataFrame(gdf) return gdf
[docs]class Community(object): """Spatial and tabular data for a collection of "neighborhoods". A community is a collection of "neighborhoods" represented by spatial boundaries (e.g. census tracts, or blocks in the US), and tabular data which describe the composition of each neighborhood (e.g. data from surveys, sensors, or geocoded misc.). A Community can be large (e.g. a metropolitan region), or small (e.g. a handfull of census tracts) and may have data pertaining to multiple discrete points in time. Parameters ---------- gdf : geopandas.GeoDataFrame long-form geodataframe that holds spatial and tabular data. harmonized : bool Whether neighborhood boundaries have been harmonized into a set of time-consistent units **kwargs Attributes ---------- gdf : geopandas.GeoDataFrame long-form geodataframe that stores neighborhood-level attributes and geometries for one or more time periods harmonized : bool Whether neighborhood boundaries have been harmonized into consistent units over time """
[docs] def __init__(self, gdf=None, harmonized=None, **kwargs): """Initialize a new Community. Parameters ---------- gdf : geopandas.GeoDataFrame long-form geodataframe that stores neighborhood-level attributes and geometries for one or more time periods harmonized : bool Whether neighborhood boundaries have been harmonized into consistent units over time **kwargs : kwargs extra keyword arguments `**kwargs`. """ self.gdf = gdf self.harmonized = harmonized
[docs] def harmonize( self, target_year=None, weights_method="area", extensive_variables=None, intensive_variables=None, allocate_total=True, raster="nlcd_2011", codes=[21, 22, 23, 24], force_crs_match=True, ): """Short summary. Parameters ---------- target_year: int Polygons from this year will become the target boundaries for spatial interpolation. weights_method : string The method that the harmonization will be conducted. This can be set to: "area" : harmonization according to area weights. "land_type_area" : harmonization according to the Land Types considered 'populated' areas. "land_type_Poisson_regression" : NOT YET INTRODUCED. "land_type_Gaussian_regression" : NOT YET INTRODUCED. extensive_variables : list extensive variables to be used in interpolation. intensive_variables : type intensive variables to be used in interpolation. allocate_total : boolean True if total value of source area should be allocated. False if denominator is area of i. Note that the two cases would be identical when the area of the source polygon is exhausted by intersections. See (3) in Notes for more details raster_path : str path to the raster image that has the types of each pixel in the spatial context. Only taken into consideration for harmonization raster based. codes : list pixel values that should be included in the regression (the default is [21, 22, 23, 24]). force_crs_match : bool whether source and target dataframes should be reprojected to match (the default is True). Returns ------- None New data are added to the input Community """ # convert the long-form into a list of dataframes # data = [x[1] for x in self.gdf.groupby("year")] gdf = _harmonize( self.gdf, target_year=target_year, weights_method=weights_method, extensive_variables=extensive_variables, intensive_variables=intensive_variables, allocate_total=allocate_total, raster=raster, codes=codes, force_crs_match=force_crs_match, ) return Community(gdf, harmonized=True)
[docs] def cluster( self, n_clusters=6, method=None, best_model=False, columns=None, verbose=False, return_model=False, scaler=None, **kwargs, ): """Create a geodemographic typology by running a cluster analysis on the study area's neighborhood attributes Parameters ---------- gdf : pandas.DataFrame long-form (geo)DataFrame containing neighborhood attributes n_clusters : int the number of clusters to model. The default is 6). method : str the clustering algorithm used to identify neighborhood types best_model : bool if using a gaussian mixture model, use BIC to choose the best n_clusters. (the default is False). columns : list-like subset of columns on which to apply the clustering verbose : bool whether to print warning messages (the default is False). return_model : bool whether to return the underlying cluster model instance for further analysis scaler: str or sklearn.preprocessing.Scaler a scikit-learn preprocessing class that will be used to rescale the data. Defaults to StandardScaler Returns ------- pandas.DataFrame with a column of neighborhood cluster labels appended as a new column. Will overwrite columns of the same name. """ harmonized = self.harmonized if return_model: gdf, model = _cluster( gdf=self.gdf.copy(), n_clusters=n_clusters, method=method, best_model=best_model, columns=columns, verbose=verbose, return_model=return_model, **kwargs, ) return Community(gdf, harmonized=harmonized), model else: gdf = _cluster( gdf=self.gdf.copy(), n_clusters=n_clusters, method=method, best_model=best_model, columns=columns, verbose=verbose, return_model=return_model, **kwargs, ) return Community(gdf, harmonized=harmonized)
[docs] def cluster_spatial( self, n_clusters=6, spatial_weights="rook", method=None, best_model=False, columns=None, threshold_variable="count", threshold=10, return_model=False, scaler=None, **kwargs, ): """Create a *spatial* geodemographic typology by running a cluster analysis on the metro area's neighborhood attributes and including a contiguity constraint. Parameters ---------- gdf : geopandas.GeoDataFrame long-form geodataframe holding neighborhood attribute and geometry data. n_clusters : int the number of clusters to model. The default is 6). weights_type : str 'queen' or 'rook' spatial weights matrix specification` (the default is "rook"). method : str the clustering algorithm used to identify neighborhood types best_model : type Description of parameter `best_model` (the default is False). columns : list-like subset of columns on which to apply the clustering threshold_variable : str for max-p, which variable should define `p`. The default is "count", which will grow regions until the threshold number of polygons have been aggregated threshold : numeric threshold to use for max-p clustering (the default is 10). return_model : bool whether to return the underlying cluster model instance for further analysis scaler: str or sklearn.preprocessing.Scaler a scikit-learn preprocessing class that will be used to rescale the data. Defaults to StandardScaler Returns ------- geopandas.GeoDataFrame with a column of neighborhood cluster labels appended as a new column. Will overwrite columns of the same name. """ harmonized = self.harmonized if return_model: gdf, model = _cluster_spatial( gdf=self.gdf.copy(), n_clusters=n_clusters, spatial_weights=spatial_weights, method=method, best_model=best_model, columns=columns, threshold_variable=threshold_variable, threshold=threshold, return_model=return_model, **kwargs, ) return Community(gdf, harmonized=True), model else: gdf = _cluster_spatial( gdf=self.gdf.copy(), n_clusters=n_clusters, spatial_weights=spatial_weights, method=method, best_model=best_model, columns=columns, threshold_variable=threshold_variable, threshold=threshold, return_model=return_model, **kwargs, ) return Community(gdf, harmonized=harmonized)
[docs] def transition( self, cluster_col, time_var="year", id_var="geoid", w_type=None, permutations=0 ): """ (Spatial) Markov approach to transitional dynamics of neighborhoods. The transitional dynamics approach should be adopted after neighborhood segmentation since the column name of neighborhood labels is a required input. Parameters ---------- cluster_col : string or int Column name for the neighborhood segmentation, such as "ward", "kmeans", etc. time_var : string, optional Column defining time and or sequencing of the long-form data. Default is "year". id_var : string, optional Column identifying the unique id of spatial units. Default is "geoid". w_type : string, optional Type of spatial weights type ("rook", "queen", "knn" or "kernel") to be used for spatial structure. Default is None, if non-spatial Markov transition rates are desired. permutations : int, optional number of permutations for use in randomization based inference (the default is 0). Return ------ mar : object if w_type=None, return a giddy.markov.Markov instance; if w_type is given, return a giddy.markov.Spatial_Markov instance. """ mar = _transition( self.gdf, cluster_col, time_var=time_var, id_var=id_var, w_type=w_type, permutations=permutations, ) return mar
[docs] def sequence( self, cluster_col, seq_clusters=5, subs_mat=None, dist_type=None, indel=None, time_var="year", id_var="geoid", ): """ Pairwise sequence analysis to evaluate the distance/dissimilarity between every two neighborhood sequences. The sequence approach should be adopted after neighborhood segmentation since the column name of neighborhood labels is a required input. Parameters ---------- cluster_col : string or int Column name for the neighborhood segmentation, such as "ward", "kmeans", etc. seq_clusters : int, optional Number of neighborhood sequence clusters. Agglomerative Clustering with Ward linkage is now used for clustering the sequences. Default is 5. subs_mat : array (k,k), substitution cost matrix. Should be hollow ( 0 cost between the same type), symmetric and non-negative. dist_type : string "hamming": hamming distance (substitution only and its cost is constant 1) from sklearn.metrics; "markov": utilize empirical transition probabilities to define substitution costs; "interval": differences between states are used to define substitution costs, and indel=k-1; "arbitrary": arbitrary distance if there is not a strong theory guidance: substitution=0.5, indel=1. "tran": transition-oriented optimal matching. Sequence of transitions. Based on :cite:`Biemann:2011`. indel : float, optional insertion/deletion cost. time_var : string, optional Column defining time and or sequencing of the long-form data. Default is "year". id_var : string, optional Column identifying the unique id of spatial units. Default is "geoid". Return ------ gdf_new : Community instance New Community instance with attribute "gdf" having a new column for sequence labels. df_wide : pandas.DataFrame Wide-form DataFrame with k (k is the number of periods) columns of neighborhood types and 1 column of sequence labels. seq_dis_mat : array (n,n), distance/dissimilarity matrix for each pair of sequences """ gdf_temp, df_wide, seq_dis_mat = _sequence( self.gdf, cluster_col, seq_clusters=seq_clusters, subs_mat=subs_mat, dist_type=dist_type, indel=indel, time_var=time_var, id_var=id_var, ) gdf_new = Community(gdf_temp) return gdf_new, df_wide, seq_dis_mat
[docs] @classmethod def from_ltdb( cls, state_fips=None, county_fips=None, msa_fips=None, fips=None, boundary=None, years=[1970, 1980, 1990, 2000, 2010], ): """Create a new Community from LTDB data. Instiantiate a new Community from pre-harmonized LTDB data. To use you must first download and register LTDB data with geosnap using the `store_ltdb` function. Pass lists of states, counties, or any arbitrary FIPS codes to create a community. All fips code arguments are additive, so geosnap will include the largest unique set. Alternatively, you may provide a boundary to use as a clipping feature. Parameters ---------- state_fips : list or str string or list of strings of two-digit fips codes defining states to include in the study area. county_fips : list or str string or list of strings of five-digit fips codes defining counties to include in the study area. msa_fips : type string or list of strings of fips codes defining MSAs to include in the study area. fips : type string or list of strings of five-digit fips codes defining counties to include in the study area. boundary: geopandas.GeoDataFrame geodataframe that defines the total extent of the study area. This will be used to clip tracts lazily by selecting all `GeoDataFrame.representative_point()`s that intersect the boundary gdf years : list list of years (decades) to include in the study data (the default is [1970, 1980, 1990, 2000, 2010]). Returns ------- Community Community with LTDB data """ if isinstance(boundary, gpd.GeoDataFrame): tracts = data_store.tracts_2010()[["geoid", "geometry"]] ltdb = data_store.ltdb.reset_index() if boundary.crs != tracts.crs: warn( "Unable to determine whether boundary CRS is WGS84 " "if this produces unexpected results, try reprojecting" ) tracts = tracts[ tracts.representative_point().intersects(boundary.unary_union) ] gdf = ltdb[ltdb["geoid"].isin(tracts["geoid"])] gdf = gpd.GeoDataFrame(gdf.merge(tracts, on="geoid", how="left")) else: gdf = _from_db( data=data_store.ltdb, state_fips=state_fips, county_fips=county_fips, msa_fips=msa_fips, fips=fips, years=years, ) return cls(gdf=gdf.reset_index(), harmonized=True)
[docs] @classmethod def from_ncdb( cls, state_fips=None, county_fips=None, msa_fips=None, fips=None, boundary=None, years=[1970, 1980, 1990, 2000, 2010], ): """Create a new Community from NCDB data. Instiantiate a new Community from pre-harmonized NCDB data. To use you must first download and register LTDB data with geosnap using the `store_ncdb` function. Pass lists of states, counties, or any arbitrary FIPS codes to create a community. All fips code arguments are additive, so geosnap will include the largest unique set. Alternatively, you may provide a boundary to use as a clipping feature. Parameters ---------- state_fips : list or str string or list of strings of two-digit fips codes defining states to include in the study area. county_fips : list or str string or list of strings of five-digit fips codes defining counties to include in the study area. msa_fips : type string or list of strings of fips codes defining MSAs to include in the study area. fips : type string or list of strings of five-digit fips codes defining counties to include in the study area. boundary: geopandas.GeoDataFrame geodataframe that defines the total extent of the study area. This will be used to clip tracts lazily by selecting all `GeoDataFrame.representative_point()`s that intersect the boundary gdf years : list list of years (decades) to include in the study data (the default is [1970, 1980, 1990, 2000, 2010]). Returns ------- Community Community with NCDB data """ if isinstance(boundary, gpd.GeoDataFrame): tracts = data_store.tracts_2010()[["geoid", "geometry"]] ncdb = data_store.ncdb.reset_index() if boundary.crs != tracts.crs: warn( "Unable to determine whether boundary CRS is WGS84 " "if this produces unexpected results, try reprojecting" ) tracts = tracts[ tracts.representative_point().intersects(boundary.unary_union) ] gdf = ncdb[ncdb["geoid"].isin(tracts["geoid"])] gdf = gpd.GeoDataFrame(gdf.merge(tracts, on="geoid", how="left")) else: gdf = _from_db( data=data_store.ncdb, state_fips=state_fips, county_fips=county_fips, msa_fips=msa_fips, fips=fips, years=years, ) return cls(gdf=gdf.reset_index(), harmonized=True)
[docs] @classmethod def from_census( cls, state_fips=None, county_fips=None, msa_fips=None, fips=None, boundary=None, years=[1990, 2000, 2010], ): """Create a new Community from original vintage US Census data. Instiantiate a new Community from . To use you must first download and register census data with geosnap using the `store_census` function. Pass lists of states, counties, or any arbitrary FIPS codes to create a community. All fips code arguments are additive, so geosnap will include the largest unique set. Alternatively, you may provide a boundary to use as a clipping feature. Parameters ---------- state_fips : list or str string or list of strings of two-digit fips codes defining states to include in the study area. county_fips : list or str string or list of strings of five-digit fips codes defining counties to include in the study area. msa_fips : type string or list of strings of fips codes defining MSAs to include in the study area. fips : type string or list of strings of five-digit fips codes defining counties to include in the study area. boundary: geopandas.GeoDataFrame geodataframe that defines the total extent of the study area. This will be used to clip tracts lazily by selecting all `GeoDataFrame.representative_point()`s that intersect the boundary gdf years : list list of years to include in the study data (the default is [1990, 2000, 2010]). Returns ------- Community Community with unharmonized census data """ if isinstance(years, (str, int)): years = [years] msa_states = [] if msa_fips: msa_states += data_store.msa_definitions[ data_store.msa_definitions["CBSA Code"] == msa_fips ]["stcofips"].tolist() msa_states = [i[:2] for i in msa_states] # build a list of states in the dataset allfips = [] for i in [state_fips, county_fips, fips, msa_states]: if i: allfips.append(i[:2]) states = np.unique(allfips) # if using a boundary there will be no fips, so reset states to None if len(states) == 0: states = None df_dict = { 1990: data_store.tracts_1990(states=states), 2000: data_store.tracts_2000(states=states), 2010: data_store.tracts_2010(states=states), } tracts = [] for year in years: tracts.append(df_dict[year]) tracts = pd.concat(tracts, sort=False) if isinstance(boundary, gpd.GeoDataFrame): if boundary.crs != tracts.crs: warn( "Unable to determine whether boundary CRS is WGS84 " "if this produces unexpected results, try reprojecting" ) tracts = tracts[ tracts.representative_point().intersects(boundary.unary_union) ] else: gdf = _fips_filter( state_fips=state_fips, county_fips=county_fips, msa_fips=msa_fips, fips=fips, data=tracts, ) return cls(gdf=gdf, harmonized=False)
[docs] @classmethod def from_lodes( cls, state_fips=None, county_fips=None, msa_fips=None, fips=None, boundary=None, years=2015, dataset="wac", ): """Create a new Community from Census LEHD/LODES data. Instiantiate a new Community from LODES data. Pass lists of states, counties, or any arbitrary FIPS codes to create a community. All fips code arguments are additive, so geosnap will include the largest unique set. Alternatively, you may provide a boundary to use as a clipping feature. Parameters ---------- state_fips : list or str string or list of strings of two-digit fips codes defining states to include in the study area. county_fips : list or str string or list of strings of five-digit fips codes defining counties to include in the study area. msa_fips : type string or list of strings of fips codes defining MSAs to include in the study area. fips : type string or list of strings of five-digit fips codes defining counties to include in the study area. boundary: geopandas.GeoDataFrame geodataframe that defines the total extent of the study area. This will be used to clip tracts lazily by selecting all `GeoDataFrame.representative_point()`s that intersect the boundary gdf years : list list of years to include in the study data (the default is [1990, 2000, 2010]). dataset: str which LODES dataset should be used to create the Community. Options are 'wac' for workplace area characteristics or 'rac' for residence area characteristics. Returns ------- Community Community with LODES data """ if isinstance(years, (str, int)): years = [years] msa_states = [] if msa_fips: msa_states += data_store.msa_definitions[ data_store.msa_definitions["CBSA Code"] == msa_fips ]["stcofips"].tolist() msa_states = [i[:2] for i in msa_states] # build a list of states in the dataset allfips = [] for i in [state_fips, county_fips, fips, msa_states]: if i: allfips.append(i[:2]) states = np.unique(allfips) # states = np.unique([i[:2] for i in allfips]) if any(years) < 2010: gdf00 = data_store.blocks_2000(states=states) gdf00 = gdf00.drop(columns=["year"]) gdf = data_store.blocks_2010(states=states) gdf = gdf.drop(columns=["year"]) # grab state abbreviations names = ( _fipstable[_fipstable["FIPS Code"].isin(states)]["State Abbreviation"] .str.lower() .tolist() ) dfs = [] if isinstance(names, str): names = [names] for name in names: for year in years: df = get_lehd(dataset=dataset, year=year, state=name) if year < 2010: df = gdf00.merge(df, on="geoid", how="left") else: df = gdf.merge(df, on="geoid", how="left") df["year"] = year dfs.append(df) gdf = pd.concat(dfs) if isinstance(boundary, gpd.GeoDataFrame): if boundary.crs != gdf.crs: warn( "Unable to determine whether boundary CRS is WGS84 " "if this produces unexpected results, try reprojecting" ) gdf = gdf[gdf.representative_point().intersects(boundary.unary_union)] else: gdf = _fips_filter( state_fips=state_fips, county_fips=county_fips, msa_fips=msa_fips, fips=fips, data=gdf, ) return cls(gdf=gdf, harmonized=False)
[docs] @classmethod def from_geodataframes(cls, gdfs=None): """Create a new Community from a list of geodataframes. Parameters ---------- gdfs : list-like list of geodataframes that hold attribute and geometry data for a study area. Each geodataframe must have neighborhood attribute data, geometry data, and a time column that defines how the geodataframes are sequenced. The geometries may be stable over time (in which case the dataset is harmonized) or may be unique for each time. If the data are harmonized, the dataframes must also have an ID variable that indexes neighborhood units over time. """ gdf = pd.concat(gdfs, sort=True) return cls(gdf=gdf)