def plot_r2_comp(name_site_combo, dat_dir='./out_files/', out_fig_dir='./out_figs/'): """Plot r2 of the three patterns separately for each community.""" models = ['asne', 'agsne', 'ssnt_0', 'ssnt_1'] model_names = ['ASNE', 'AGSNE', 'SSNT_N', 'SSNT_M'] patterns = ['rad', 'isd', 'sdr'] pattern_names = ['SAD', 'ISD', 'SDR'] col_list = ['b', '#787878', 'r'] symbol_list = ['o', 's', '*'] fig = plt.figure(figsize=(10.5, 3.5)) for i, pattern in enumerate(patterns): r2_dic = {'asne': [], 'agsne': [], 'ssnt_0': [], 'ssnt_1': []} r2_list = [] for j, model in enumerate(models): for dat_name, site in name_site_combo: pred_obs_model_pattern = wk.import_obs_pred_data(dat_dir + dat_name + '_obs_pred_' + pattern + '_' + model + '.csv') pred_obs_site = pred_obs_model_pattern[ pred_obs_model_pattern['site'] == site] r2 = mtools.obs_pred_rsquare(np.log10(pred_obs_site['obs']), np.log10(pred_obs_site['pred'])) r2_dic[model].append(r2) r2_list.append(r2) ax = plt.subplot(1, 3, i + 1) for j in range(1, 4): model = models[j] plt.scatter(r2_dic['asne'], r2_dic[model], s=20, marker=symbol_list[j - 1], facecolors=col_list[j - 1], edgecolors='none', label=model_names[j]) min_val, max_val = min(r2_list), max(r2_list) if min_val < 0: axis_min = 1.1 * min_val else: axis_min = 0.9 * min_val if max_val < 0: axis_max = 0.9 * max_val else: axis_max = 1.1 * max_val plt.plot([axis_min, axis_max], [axis_min, axis_max], 'k-') plt.xlim(axis_min, axis_max) plt.ylim(axis_min, axis_max) ax.tick_params(axis='both', which='major', labelsize=6) ax.set_xlabel(r'$R^2$ of ASNE', labelpad=4, size=10) ax.set_ylabel(r'$R^2$ of the other models', labelpad=4, size=10) ax.set_title(pattern_names[i], size=16) if i == 0: ax.legend(loc=2, prop={'size': 10}) plt.subplots_adjust(left=0.08, wspace=0.3) plt.tight_layout() plt.savefig(out_fig_dir + 'r2_comp.png', dpi=400)
def bootstrap_SDR(name_site_combo, model, in_dir = './data/', out_dir = './out_files/', Niter = 200): """A general function of bootstrapping for ISD applying to all four models. Inputs: name_site_combo: a list with dat_name and site model - takes one of four values 'ssnt_0', 'ssnt_1', 'asne', or 'agsne' in_dir - directory of raw data out_dir - directory used both in input (obs_pred.csv file) and output Niter - number of bootstrap samples Output: Writes to one file on disk for R^2. """ dat_name, site = name_site_combo dat = wk.import_raw_data(in_dir + dat_name + '.csv') dat_site = dat[dat['site'] == site] dat_clean = clean_data_agsne(dat_site) G, S, N, E = get_GSNE(dat_clean) lambda1, beta, lambda3 = agsne.get_agsne_lambdas(G, S, N, E) par_list = [] for sp in np.unique(dat_clean['sp']): dat_sp = dat_clean[dat_clean['sp'] == sp] n = len(dat_sp) genus_sp = dat_sp['genus'][0] m = len(np.unique(dat_clean[dat_clean['genus'] == genus_sp]['sp'])) par_list.append([m, n]) pred_obs = wk.import_obs_pred_data(out_dir + dat_name + '_obs_pred_sdr_' + model + '.csv') pred = pred_obs[pred_obs['site'] == site]['pred'] obs = pred_obs[pred_obs['site'] == site]['obs'] out_list_rsquare = [dat_name, site, str(mtools.obs_pred_rsquare(np.log10(obs), np.log10(pred)))] iisd_agsne = mete_distributions.theta_agsne([G, S, N, E], [lambda1, beta, lambda3, agsne.agsne_lambda3_z(lambda1, beta, S) / lambda3]) iisd_asne = mete_distributions.theta_epsilon(S, N, E) dbh_scaled = np.array(dat_clean['dbh'] / min(dat_clean['dbh'])) iisd_ssnt_0 = ssnt_isd_bounded(1, N / (sum(dbh_scaled ** 1) - N)) iisd_ssnt_1 = ssnt_isd_bounded(2/3, N / (sum(dbh_scaled ** (2/3)) - N)) dist_for_model = {'ssnt_0': iisd_ssnt_0, 'ssnt_1': iisd_ssnt_1, 'asne': iisd_asne, 'agsne': iisd_agsne} dist = dist_for_model[model] for i in range(Niter): if model in ['ssnt_0', 'ssnt_1']: obs_boot = np.array([np.mean((dist.rvs(par[1])) ** 2) for par in par_list]) # Here par[1] is n for each species elif model == 'asne': obs_boot = np.array([np.mean(np.array(dist.rvs(par[1], par[1]))) for par in par_list]) else: obs_boot = np.array([np.mean(np.array(dist.rvs(par[1], par[1], par[0]))) for par in par_list]) out_list_rsquare.append(str(mtools.obs_pred_rsquare(np.log10(obs_boot), np.log10(pred)))) wk.write_to_file(out_dir + 'SDR_bootstrap_' + model + '_rsquare.txt', ",".join(str(x) for x in out_list_rsquare))
def bootstrap_SAD(name_site_combo, model, in_dir = './data/', out_dir = './out_files/', Niter = 200): """A general function of bootstrapping for SAD applying to all four models. Inputs: name_site_combo: a list with dat_name and site model - takes one of four values 'ssnt_0', 'ssnt_1', 'asne', or 'agsne' in_dir - directory of raw data out_dir - directory used both in input (obs_pred.csv file) and output Niter - number of bootstrap samples Output: Writes to disk, with one file for R^2 and one for KS statistic. """ dat_name, site = name_site_combo dat = wk.import_raw_data(in_dir + dat_name + '.csv') dat_site = dat[dat['site'] == site] dat_clean = clean_data_agsne(dat_site) G, S, N, E = get_GSNE(dat_clean) beta_ssnt = mete.get_beta(S, N, version = 'untruncated') beta_asne = mete.get_beta(S, N) lambda1, beta, lambda3 = agsne.get_agsne_lambdas(G, S, N, E) sad_agsne = mete_distributions.sad_agsne([G, S, N, E], [lambda1, beta, lambda3, agsne.agsne_lambda3_z(lambda1, beta, S) / lambda3]) dist_for_model = {'ssnt_0': stats.logser(np.exp(-beta_ssnt)), 'ssnt_1': stats.logser(np.exp(-beta_ssnt)), 'asne': md.trunc_logser(np.exp(-beta_asne), N), 'agsne': sad_agsne} dist = dist_for_model[model] pred_obs = wk.import_obs_pred_data(out_dir + dat_name + '_obs_pred_rad_' + model + '.csv') pred = pred_obs[pred_obs['site'] == site]['pred'][::-1] obs = pred_obs[pred_obs['site'] == site]['obs'][::-1] out_list_rsquare = [dat_name, site, str(mtools.obs_pred_rsquare(np.log10(obs), np.log10(pred)))] emp_cdf = mtools.get_emp_cdf(obs) out_list_ks = [dat_name, site, str(max(abs(emp_cdf - np.array([dist.cdf(x) for x in obs]))))] for i in range(Niter): obs_boot = np.array(sorted(dist.rvs(S))) cdf_boot = np.array([dist.cdf(x) for x in obs_boot]) emp_cdf_boot = mtools.get_emp_cdf(obs_boot) out_list_rsquare.append(str(mtools.obs_pred_rsquare(np.log10(obs_boot), np.log10(pred)))) out_list_ks.append(str(max(abs(emp_cdf_boot - np.array(cdf_boot))))) wk.write_to_file(out_dir + 'SAD_bootstrap_' + model + '_rsquare.txt', ",".join(str(x) for x in out_list_rsquare)) wk.write_to_file(out_dir + 'SAD_bootstrap_' + model + '_ks.txt', ",".join(str(x) for x in out_list_ks))
def plot_r2_comp(name_site_combo, dat_dir = './out_files/', out_fig_dir = './out_figs/'): """Plot r2 of the three patterns separately for each community.""" models = ['asne', 'agsne', 'ssnt_0', 'ssnt_1'] model_names = ['ASNE', 'AGSNE', 'SSNT_N', 'SSNT_M'] patterns = ['rad', 'isd', 'sdr'] pattern_names = ['SAD', 'ISD', 'SDR'] col_list = ['b', '#787878', 'r'] symbol_list = ['o', 's', '*'] fig = plt.figure(figsize = (10.5, 3.5)) for i, pattern in enumerate(patterns): r2_dic = {'asne':[], 'agsne':[], 'ssnt_0':[], 'ssnt_1':[]} r2_list = [] for j, model in enumerate(models): for dat_name, site in name_site_combo: pred_obs_model_pattern = wk.import_obs_pred_data(dat_dir + dat_name + '_obs_pred_' + pattern + '_' + model + '.csv') pred_obs_site = pred_obs_model_pattern[pred_obs_model_pattern['site'] == site] r2 = mtools.obs_pred_rsquare(np.log10(pred_obs_site['obs']), np.log10(pred_obs_site['pred'])) r2_dic[model].append(r2) r2_list.append(r2) ax = plt.subplot(1, 3, i + 1) for j in range(1, 4): model = models[j] plt.scatter(r2_dic['asne'], r2_dic[model], s = 20, marker = symbol_list[j - 1], facecolors = col_list[j - 1], edgecolors = 'none', label = model_names[j]) min_val, max_val = min(r2_list), max(r2_list) if min_val < 0: axis_min = 1.1 * min_val else: axis_min = 0.9 * min_val if max_val < 0: axis_max = 0.9 * max_val else: axis_max= 1.1 * max_val plt.plot([axis_min, axis_max], [axis_min, axis_max], 'k-') plt.xlim(axis_min, axis_max) plt.ylim(axis_min, axis_max) ax.tick_params(axis = 'both', which = 'major', labelsize = 6) ax.set_xlabel(r'$R^2$ of ASNE', labelpad = 4, size = 10) ax.set_ylabel(r'$R^2$ of the other models', labelpad = 4, size = 10) ax.set_title(pattern_names[i], size = 16) if i == 0: ax.legend(loc = 2, prop = {'size': 10}) plt.subplots_adjust(left = 0.08, wspace = 0.3) plt.tight_layout() plt.savefig(out_fig_dir + 'r2_comp.png', dpi = 400)
def bootstrap_ISD(name_site_combo, model, in_dir = './data/', out_dir = './out_files/', Niter = 200): """A general function of bootstrapping for ISD applying to all four models. Inputs: name_site_combo: a list with dat_name and site model - takes one of four values 'ssnt_0', 'ssnt_1', 'asne', or 'agsne' in_dir - directory of raw data out_dir - directory used both in input (obs_pred.csv file) and output Niter - number of bootstrap samples Output: Writes to disk, with one file for R^2 and one for KS statistic. """ dat_name, site = name_site_combo dat = wk.import_raw_data(in_dir + dat_name + '.csv') dat_site = dat[dat['site'] == site] dat_clean = clean_data_agsne(dat_site) G, S, N, E = get_GSNE(dat_clean) lambda1, beta, lambda3 = agsne.get_agsne_lambdas(G, S, N, E) isd_agsne = mete_distributions.psi_agsne([G, S, N, E], [lambda1, beta, lambda3, agsne.agsne_lambda3_z(lambda1, beta, S) / lambda3]) isd_asne = mete_distributions.psi_epsilon_approx(S, N, E) dbh_scaled = np.array(dat_clean['dbh'] / min(dat_clean['dbh'])) isd_ssnt_0 = ssnt_isd_bounded(1, N / (sum(dbh_scaled ** 1) - N)) isd_ssnt_1 = ssnt_isd_bounded(2/3, N / (sum(dbh_scaled ** (2/3)) - N)) dist_for_model = {'ssnt_0': isd_ssnt_0, 'ssnt_1': isd_ssnt_1, 'asne': isd_asne, 'agsne': isd_agsne} dist = dist_for_model[model] pred_obs = wk.import_obs_pred_data(out_dir + dat_name + '_obs_pred_isd_' + model + '.csv') pred = pred_obs[pred_obs['site'] == site]['pred'] obs = pred_obs[pred_obs['site'] == site]['obs'] out_list_rsquare = [dat_name, site, str(mtools.obs_pred_rsquare(np.log10(obs), np.log10(pred)))] wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_rsquare.txt', ",".join(str(x) for x in out_list_rsquare), new_line = False) emp_cdf = mtools.get_emp_cdf(obs) out_list_ks = [dat_name, site, str(max(abs(emp_cdf - np.array([dist.cdf(x) for x in obs]))))] wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', ",".join(str(x) for x in out_list_ks), new_line = False) num_pools = 8 # Assuming that 8 pools are to be created for i in xrange(Niter): obs_boot = [] cdf_boot = [] while len(obs_boot) < N: pool = multiprocessing.Pool(num_pools) out_sample = pool.map(wk.generate_isd_sample, [dist for j in xrange(num_pools)]) for combo in out_sample: cdf_sublist, sample_sublist = combo obs_boot.extend(sample_sublist) cdf_boot.extend(cdf_sublist) pool.close() pool.join() if model in ['asne', 'agsne']: obs_boot = np.sort(obs_boot[:N]) ** 0.5 # Convert to diameter else: obs_boot = np.sort(obs_boot[:N]) sample_rsquare = mtools.obs_pred_rsquare(np.log10(obs_boot), np.log10(pred)) sample_ks = max(abs(emp_cdf - np.sort(cdf_boot[:N]))) wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_rsquare.txt', "".join([',', str(sample_rsquare)]), new_line = False) wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', "".join([',', str(sample_ks)]), new_line = False) wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_rsquare.txt', '\t') wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', '\t') wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', ",".join(str(x) for x in out_list_ks))
def bootstrap_SDR(name_site_combo, model, in_dir='./data/', out_dir='./out_files/', Niter=200): """A general function of bootstrapping for ISD applying to all four models. Inputs: name_site_combo: a list with dat_name and site model - takes one of four values 'ssnt_0', 'ssnt_1', 'asne', or 'agsne' in_dir - directory of raw data out_dir - directory used both in input (obs_pred.csv file) and output Niter - number of bootstrap samples Output: Writes to one file on disk for R^2. """ dat_name, site = name_site_combo dat = wk.import_raw_data(in_dir + dat_name + '.csv') dat_site = dat[dat['site'] == site] dat_clean = clean_data_agsne(dat_site) G, S, N, E = get_GSNE(dat_clean) lambda1, beta, lambda3 = agsne.get_agsne_lambdas(G, S, N, E) par_list = [] for sp in np.unique(dat_clean['sp']): dat_sp = dat_clean[dat_clean['sp'] == sp] n = len(dat_sp) genus_sp = dat_sp['genus'][0] m = len(np.unique(dat_clean[dat_clean['genus'] == genus_sp]['sp'])) par_list.append([m, n]) pred_obs = wk.import_obs_pred_data(out_dir + dat_name + '_obs_pred_sdr_' + model + '.csv') pred = pred_obs[pred_obs['site'] == site]['pred'] obs = pred_obs[pred_obs['site'] == site]['obs'] out_list_rsquare = [ dat_name, site, str(mtools.obs_pred_rsquare(np.log10(obs), np.log10(pred))) ] iisd_agsne = mete_distributions.theta_agsne([G, S, N, E], [ lambda1, beta, lambda3, agsne.agsne_lambda3_z(lambda1, beta, S) / lambda3 ]) iisd_asne = mete_distributions.theta_epsilon(S, N, E) dbh_scaled = np.array(dat_clean['dbh'] / min(dat_clean['dbh'])) iisd_ssnt_0 = ssnt_isd_bounded(1, N / (sum(dbh_scaled**1) - N)) iisd_ssnt_1 = ssnt_isd_bounded(2 / 3, N / (sum(dbh_scaled**(2 / 3)) - N)) dist_for_model = { 'ssnt_0': iisd_ssnt_0, 'ssnt_1': iisd_ssnt_1, 'asne': iisd_asne, 'agsne': iisd_agsne } dist = dist_for_model[model] for i in range(Niter): if model in ['ssnt_0', 'ssnt_1']: obs_boot = np.array([ np.mean((dist.rvs(par[1]))**2) for par in par_list ]) # Here par[1] is n for each species elif model == 'asne': obs_boot = np.array([ np.mean(np.array(dist.rvs(par[1], par[1]))) for par in par_list ]) else: obs_boot = np.array([ np.mean(np.array(dist.rvs(par[1], par[1], par[0]))) for par in par_list ]) out_list_rsquare.append( str(mtools.obs_pred_rsquare(np.log10(obs_boot), np.log10(pred)))) wk.write_to_file(out_dir + 'SDR_bootstrap_' + model + '_rsquare.txt', ",".join(str(x) for x in out_list_rsquare))
def bootstrap_ISD(name_site_combo, model, in_dir='./data/', out_dir='./out_files/', Niter=200): """A general function of bootstrapping for ISD applying to all four models. Inputs: name_site_combo: a list with dat_name and site model - takes one of four values 'ssnt_0', 'ssnt_1', 'asne', or 'agsne' in_dir - directory of raw data out_dir - directory used both in input (obs_pred.csv file) and output Niter - number of bootstrap samples Output: Writes to disk, with one file for R^2 and one for KS statistic. """ dat_name, site = name_site_combo dat = wk.import_raw_data(in_dir + dat_name + '.csv') dat_site = dat[dat['site'] == site] dat_clean = clean_data_agsne(dat_site) G, S, N, E = get_GSNE(dat_clean) lambda1, beta, lambda3 = agsne.get_agsne_lambdas(G, S, N, E) isd_agsne = mete_distributions.psi_agsne([G, S, N, E], [ lambda1, beta, lambda3, agsne.agsne_lambda3_z(lambda1, beta, S) / lambda3 ]) isd_asne = mete_distributions.psi_epsilon_approx(S, N, E) dbh_scaled = np.array(dat_clean['dbh'] / min(dat_clean['dbh'])) isd_ssnt_0 = ssnt_isd_bounded(1, N / (sum(dbh_scaled**1) - N)) isd_ssnt_1 = ssnt_isd_bounded(2 / 3, N / (sum(dbh_scaled**(2 / 3)) - N)) dist_for_model = { 'ssnt_0': isd_ssnt_0, 'ssnt_1': isd_ssnt_1, 'asne': isd_asne, 'agsne': isd_agsne } dist = dist_for_model[model] pred_obs = wk.import_obs_pred_data(out_dir + dat_name + '_obs_pred_isd_' + model + '.csv') pred = pred_obs[pred_obs['site'] == site]['pred'] obs = pred_obs[pred_obs['site'] == site]['obs'] out_list_rsquare = [ dat_name, site, str(mtools.obs_pred_rsquare(np.log10(obs), np.log10(pred))) ] wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_rsquare.txt', ",".join(str(x) for x in out_list_rsquare), new_line=False) emp_cdf = mtools.get_emp_cdf(obs) out_list_ks = [ dat_name, site, str(max(abs(emp_cdf - np.array([dist.cdf(x) for x in obs])))) ] wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', ",".join(str(x) for x in out_list_ks), new_line=False) num_pools = 8 # Assuming that 8 pools are to be created for i in xrange(Niter): obs_boot = [] cdf_boot = [] while len(obs_boot) < N: pool = multiprocessing.Pool(num_pools) out_sample = pool.map(wk.generate_isd_sample, [dist for j in xrange(num_pools)]) for combo in out_sample: cdf_sublist, sample_sublist = combo obs_boot.extend(sample_sublist) cdf_boot.extend(cdf_sublist) pool.close() pool.join() if model in ['asne', 'agsne']: obs_boot = np.sort(obs_boot[:N])**0.5 # Convert to diameter else: obs_boot = np.sort(obs_boot[:N]) sample_rsquare = mtools.obs_pred_rsquare(np.log10(obs_boot), np.log10(pred)) sample_ks = max(abs(emp_cdf - np.sort(cdf_boot[:N]))) wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_rsquare.txt', "".join([',', str(sample_rsquare)]), new_line=False) wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', "".join([',', str(sample_ks)]), new_line=False) wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_rsquare.txt', '\t') wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', '\t') wk.write_to_file(out_dir + 'ISD_bootstrap_' + model + '_ks.txt', ",".join(str(x) for x in out_list_ks))
def bootstrap_SAD(name_site_combo, model, in_dir='./data/', out_dir='./out_files/', Niter=200): """A general function of bootstrapping for SAD applying to all four models. Inputs: name_site_combo: a list with dat_name and site model - takes one of four values 'ssnt_0', 'ssnt_1', 'asne', or 'agsne' in_dir - directory of raw data out_dir - directory used both in input (obs_pred.csv file) and output Niter - number of bootstrap samples Output: Writes to disk, with one file for R^2 and one for KS statistic. """ dat_name, site = name_site_combo dat = wk.import_raw_data(in_dir + dat_name + '.csv') dat_site = dat[dat['site'] == site] dat_clean = clean_data_agsne(dat_site) G, S, N, E = get_GSNE(dat_clean) beta_ssnt = mete.get_beta(S, N, version='untruncated') beta_asne = mete.get_beta(S, N) lambda1, beta, lambda3 = agsne.get_agsne_lambdas(G, S, N, E) sad_agsne = mete_distributions.sad_agsne([G, S, N, E], [ lambda1, beta, lambda3, agsne.agsne_lambda3_z(lambda1, beta, S) / lambda3 ]) dist_for_model = { 'ssnt_0': stats.logser(np.exp(-beta_ssnt)), 'ssnt_1': stats.logser(np.exp(-beta_ssnt)), 'asne': md.trunc_logser(np.exp(-beta_asne), N), 'agsne': sad_agsne } dist = dist_for_model[model] pred_obs = wk.import_obs_pred_data(out_dir + dat_name + '_obs_pred_rad_' + model + '.csv') pred = pred_obs[pred_obs['site'] == site]['pred'][::-1] obs = pred_obs[pred_obs['site'] == site]['obs'][::-1] out_list_rsquare = [ dat_name, site, str(mtools.obs_pred_rsquare(np.log10(obs), np.log10(pred))) ] emp_cdf = mtools.get_emp_cdf(obs) out_list_ks = [ dat_name, site, str(max(abs(emp_cdf - np.array([dist.cdf(x) for x in obs])))) ] for i in range(Niter): obs_boot = np.array(sorted(dist.rvs(S))) cdf_boot = np.array([dist.cdf(x) for x in obs_boot]) emp_cdf_boot = mtools.get_emp_cdf(obs_boot) out_list_rsquare.append( str(mtools.obs_pred_rsquare(np.log10(obs_boot), np.log10(pred)))) out_list_ks.append(str(max(abs(emp_cdf_boot - np.array(cdf_boot))))) wk.write_to_file(out_dir + 'SAD_bootstrap_' + model + '_rsquare.txt', ",".join(str(x) for x in out_list_rsquare)) wk.write_to_file(out_dir + 'SAD_bootstrap_' + model + '_ks.txt', ",".join(str(x) for x in out_list_ks))