diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt index de5c5351..f42bfb43 100644 --- a/docs/_sources/index.rst.txt +++ b/docs/_sources/index.rst.txt @@ -10,8 +10,14 @@ TIGRAMITE Tigramite is a causal time series analysis python package. It allows to efficiently reconstruct causal graphs from high-dimensional time series datasets and model the obtained causal dependencies for causal mediation and prediction analyses. Causal discovery is based on linear as well as non-parametric conditional independence tests applicable to discrete or continuously-valued time series. Also includes functions for high-quality plots of the results. Please cite the following papers depending on which method you use: -1. J. Runge et al. (2018): Detecting Causal Associations in Large Nonlinear Time Series Datasets. - https://arxiv.org/abs/1702.07007v2 + +0. J. Runge et al. (2019): Inferring causation from time series in Earth system sciences. + Nature Communications, 10(1):2553. + https://www.nature.com/articles/s41467-019-10105-3 + +1. J. Runge, P. Nowack, M. Kretschmer, S. Flaxman, D. Sejdinovic (2019): Detecting and quantifying causal associations in large nonlinear time series datasets. + Sci. Adv. 5, eaau4996. + https://advances.sciencemag.org/content/5/11/eaau4996 2. J. Runge et al. (2015): Identifying causal gateways and mediators in complex spatio-temporal systems. Nature Communications, 6, 8502. diff --git a/docs/index.html b/docs/index.html index 5f49f5d6..74c1f362 100644 --- a/docs/index.html +++ b/docs/index.html @@ -69,9 +69,13 @@

Quick search

TIGRAMITEΒΆ

Github repo

Tigramite is a causal time series analysis python package. It allows to efficiently reconstruct causal graphs from high-dimensional time series datasets and model the obtained causal dependencies for causal mediation and prediction analyses. Causal discovery is based on linear as well as non-parametric conditional independence tests applicable to discrete or continuously-valued time series. Also includes functions for high-quality plots of the results. Please cite the following papers depending on which method you use:

-
    -

  1. J. Runge et al. (2018): Detecting Causal Associations in Large Nonlinear Time Series Datasets. -https://arxiv.org/abs/1702.07007v2

    2. +
      +

    1. J. Runge et al. (2019): Inferring causation from time series in Earth system sciences. +Nature Communications, 10(1):2553. +https://www.nature.com/articles/s41467-019-10105-3

      2. +

    2. J. Runge, P. Nowack, M. Kretschmer, S. Flaxman, D. Sejdinovic (2019): Detecting and quantifying causal associations in large nonlinear time series datasets. +Sci. Adv. 5, eaau4996. +https://advances.sciencemag.org/content/5/11/eaau4996

    3. J. Runge et al. (2015): Identifying causal gateways and mediators in complex spatio-temporal systems. Nature Communications, 6, 8502. http://doi.org/10.1038/ncomms9502

      4. diff --git a/docs/searchindex.js b/docs/searchindex.js index 53af83e6..1fe65b25 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({docnames:["index"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["index.rst"],objects:{"tigramite.data_processing":{DataFrame:[0,1,1,""],lowhighpass_filter:[0,4,1,""],ordinal_patt_array:[0,4,1,""],quantile_bin_array:[0,4,1,""],smooth:[0,4,1,""],time_bin_with_mask:[0,4,1,""],var_process:[0,4,1,""],weighted_avg_and_std:[0,4,1,""]},"tigramite.data_processing.DataFrame":{construct_array:[0,2,1,""],data:[0,3,1,""],datatime:[0,3,1,""],mask:[0,3,1,""],missing_flag:[0,3,1,""],print_array_info:[0,2,1,""],var_names:[0,3,1,""]},"tigramite.independence_tests":{CMIknn:[0,1,1,""],CMIsymb:[0,1,1,""],CondIndTest:[0,1,1,""],GPDC:[0,1,1,""],ParCorr:[0,1,1,""],RCOT:[0,1,1,""]},"tigramite.independence_tests.CMIknn":{get_dependence_measure:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.CMIsymb":{get_dependence_measure:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.CondIndTest":{get_analytic_confidence:[0,2,1,""],get_analytic_significance:[0,2,1,""],get_bootstrap_confidence:[0,2,1,""],get_confidence:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_fixed_thres_significance:[0,2,1,""],get_measure:[0,2,1,""],get_model_selection_criterion:[0,2,1,""],get_shuffle_significance:[0,2,1,""],get_significance:[0,2,1,""],measure:[0,2,1,""],print_info:[0,2,1,""],run_test:[0,2,1,""],run_test_raw:[0,2,1,""],set_dataframe:[0,2,1,""],set_mask_type:[0,2,1,""]},"tigramite.independence_tests.GPDC":{generate_and_save_nulldists:[0,2,1,""],generate_nulldist:[0,2,1,""],get_analytic_significance:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_model_selection_criterion:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.ParCorr":{get_analytic_confidence:[0,2,1,""],get_analytic_significance:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_model_selection_criterion:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.RCOT":{get_analytic_significance:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.models":{LinearMediation:[0,1,1,""],Models:[0,1,1,""],Prediction:[0,1,1,""]},"tigramite.models.LinearMediation":{fit_model:[0,2,1,""],get_ace:[0,2,1,""],get_acs:[0,2,1,""],get_all_ace:[0,2,1,""],get_all_acs:[0,2,1,""],get_all_amce:[0,2,1,""],get_amce:[0,2,1,""],get_ce:[0,2,1,""],get_ce_max:[0,2,1,""],get_coeff:[0,2,1,""],get_mce:[0,2,1,""],get_mediation_graph_data:[0,2,1,""],get_tsg:[0,2,1,""],get_val_matrix:[0,2,1,""],net_to_tsg:[0,2,1,""],tsg_to_net:[0,2,1,""]},"tigramite.models.Models":{get_coefs:[0,2,1,""],get_fit:[0,2,1,""]},"tigramite.models.Prediction":{fit:[0,2,1,""],get_predictors:[0,2,1,""],get_test_array:[0,2,1,""],get_train_array:[0,2,1,""],predict:[0,2,1,""]},"tigramite.pcmci":{PCMCI:[0,1,1,""]},"tigramite.pcmci.PCMCI":{N:[0,3,1,""],T:[0,3,1,""],all_parents:[0,3,1,""],get_corrected_pvalues:[0,2,1,""],get_lagged_dependencies:[0,2,1,""],iterations:[0,3,1,""],p_max:[0,3,1,""],print_results:[0,2,1,""],print_significant_links:[0,2,1,""],return_significant_parents:[0,2,1,""],run_bivci:[0,2,1,""],run_fullci:[0,2,1,""],run_mci:[0,2,1,""],run_pc_stable:[0,2,1,""],run_pcmci:[0,2,1,""],val_min:[0,3,1,""]},"tigramite.plotting":{plot_graph:[0,4,1,""],plot_lagfuncs:[0,4,1,""],plot_mediation_graph:[0,4,1,""],plot_mediation_time_series_graph:[0,4,1,""],plot_time_series_graph:[0,4,1,""],plot_timeseries:[0,4,1,""],setup_matrix:[0,1,1,""]},"tigramite.plotting.setup_matrix":{add_lagfuncs:[0,2,1,""],savefig:[0,2,1,""]},tigramite:{data_processing:[0,0,0,"-"],plotting:[0,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:attribute","4":"py:function"},terms:{"07007v2":0,"21st":0,"2xtau_max":0,"abstract":0,"boolean":0,"case":0,"class":0,"default":0,"float":0,"import":0,"int":0,"new":0,"null":0,"return":0,"true":0,"var":0,"while":0,ACE:0,ACS:0,But:0,For:0,Its:0,OLS:0,One:0,The:0,Then:0,There:0,These:0,Used:0,Useful:0,Uses:0,With:0,_get_single_residu:0,_print_significant_link:0,about:0,abs:0,absmax:0,absolut:0,accord:0,accur:0,ace:0,across:0,acs:0,act:0,adapt:0,add:0,add_lagfunc:0,add_lagfunc_arg:0,add_to_null_dist:0,adding:0,addit:0,adjust:0,adv:0,advanc:0,affect:0,after:0,ahead:0,aip:0,akaik:0,algorithm:0,all:0,all_lag:0,all_par:0,alloc:0,allow:0,along:0,alpha:0,alpha_level:0,also:0,altern:0,although:0,alwai:0,amc:0,among:0,analys:0,analysi:0,analyt:0,analyz:0,ani:0,appli:0,applic:0,appropri:0,approx:0,approxim:0,arang:0,arg:0,argument:0,around:0,arrai:0,array_lik:0,array_mask:0,arrow:0,arrow_linewidth:0,arrowhead_s:0,articl:0,artifici:0,arxiv:0,assign:0,associ:0,assum:0,assumpt:0,attribut:0,auto:0,autocovari:0,automat:0,autoregress:0,avail:0,averag:0,avoid:0,axes:0,axi:0,backward:0,bakirov:0,bandwidth:0,basak:0,base:0,basemap:0,becaus:0,been:0,befor:0,beforehand:0,begin:0,below:0,benjamini:0,beta:0,beta_i:0,beta_x:0,better:0,between:0,bia:0,bias:0,bin:0,bincount:0,bindata:0,bivci:0,black:0,block:0,blue:0,bool:0,bootstrap:0,both:0,bottom:0,bound:0,box:0,briefli:0,bucklei:0,butterworth:0,call:0,callabl:0,can:0,cardin:0,care:0,caus:0,causal:0,caveat:0,cdot:0,chain:0,chao:0,check:0,chi2:0,chi:0,child:0,choic:0,chosen:0,cite:0,ckdtree:0,clash:0,clean:0,cmap_edg:0,cmap_nod:0,cmi:0,cmiknn:0,cmisymb:0,code:0,coef1:0,coef2:0,coeff:0,coeffici:0,color:0,colorbar:0,colormap:0,column:0,com:0,combin:0,come:0,commun:0,compar:0,comparison:0,complex:0,comprehens:0,comput:0,concret:0,cond_ind_test:0,condindtest:0,condition:0,conduct:0,conf_blocklength:0,conf_lev:0,conf_low:0,conf_matrix:0,conf_sampl:0,conf_upp:0,confer:0,confid:0,consid:0,consider:0,constant:0,construct:0,construct_arrai:0,contain:0,contemporan:0,content:0,context:0,continu:0,control:0,convert:0,coordin:0,copi:0,copyright:0,correct:0,correl:0,correspond:0,cost:0,could:0,coupl:0,covari:0,creat:0,criteria:0,criterion:0,cross:0,cube:0,current:0,curv:0,curvatur:0,curved_radiu:0,cut_off:0,cutoff:0,cutperiod:0,cython:0,d_z:0,dash:0,data_linewidth:0,data_transform:0,datafram:0,dataset:0,datatim:0,debug:0,decai:0,defin:0,degre:0,delai:0,denot:0,densiti:0,depend:0,dependence_measur:0,deriv:0,describ:0,detect:0,determin:0,deviat:0,dict:0,dictionari:0,differ:0,digamma:0,dim:0,dimens:0,dimension:0,directli:0,disabl:0,discoveri:0,discret:0,discuss:0,disk:0,dismiss:0,dist:0,distanc:0,distribut:0,do_check:0,doc:0,document:0,doe:0,doi:0,draw:0,drawn:0,driver:0,due:0,duplic:0,dure:0,eaau4996:0,each:0,eagleson:0,easi:0,edg:0,edge_tick:0,effect:0,effici:0,either:0,els:0,eman:0,embed:0,empti:0,ensur:0,entri:0,enumer:0,epsilon_:0,equal:0,equival:0,eric:0,ericstrobl:0,estim:0,eta:0,etc:0,everi:0,exampl:0,exclud:0,exclude_contemporan:0,exclude_i:0,exclude_j:0,exclude_k:0,exclude_self_effect:0,exist:0,expect:0,explain:0,extern:0,f_x:0,f_y:0,faculti:0,fals:0,fancyarrowpatch:0,fast:0,faster:0,fdr_bh:0,fdr_method:0,featur:0,ffinkernagel:0,fig:0,fig_ax:0,figsiz:0,figur:0,file:0,fill:0,filter:0,finkernagel:0,first:0,fit:0,fit_model:0,fit_result:0,fix:0,fixed_thr:0,flag:0,flaxman:0,flexibl:0,florian:0,follow:0,fontsiz:0,form:0,format:0,forward:0,fourier:0,frac:0,fraction:0,framework:0,free:0,freedom:0,frenzel:0,friendli:0,from:0,full:0,fullci:0,fulli:0,further:0,gabor:0,gamma:0,gatewai:0,gauss_pr:0,gaussian:0,gaussianprocessregressor:0,gaussprocreg:0,gener:0,generate_and_save_nulldist:0,generate_nulldist:0,get:0,get_ac:0,get_all_ac:0,get_all_amc:0,get_amc:0,get_analytic_confid:0,get_analytic_signific:0,get_bootstrap_confid:0,get_c:0,get_ce_max:0,get_coef:0,get_coeff:0,get_confid:0,get_corrected_pvalu:0,get_dependence_measur:0,get_fit:0,get_fixed_thres_signific:0,get_lagged_depend:0,get_mc:0,get_measur:0,get_mediation_graph_data:0,get_model_selection_criterion:0,get_predictor:0,get_shuffle_signific:0,get_signific:0,get_test_arrai:0,get_train_arrai:0,get_tsg:0,get_val_matrix:0,gist:0,github:0,given:0,going:0,gp_param:0,gp_version:0,gpace:0,gpdc:0,graph:0,graph_data:0,greater:0,grei:0,grey_masked_sampl:0,grid:0,guarante:0,hall:0,handl:0,has:0,have:0,hbe:0,head:0,heavisid:0,helper:0,henc:0,here:0,high:0,highli:0,histogram:0,hochberg:0,horizont:0,how:0,html:0,http:0,hyper:0,hyperparamet:0,hypothesi:0,identifi:0,iint:0,implement:0,impli:0,improv:0,includ:0,include_lagzero_par:0,include_neighbor:0,incom:0,index:0,info:0,inform:0,inherit:0,initi:0,initial_valu:0,inno_cov:0,innov:0,input:0,instal:0,instanc:0,instanti:0,instead:0,integ:0,intellig:0,interdisciplinari:0,intern:0,interv:0,introduc:0,inv_inno_cov:0,invers:0,irrelev:0,iter:0,its:0,itself:0,j_t:0,job:0,joint:0,journal:0,just:0,kcit:0,kei:0,kernel:0,kind:0,knn:0,kretschmer:0,kun:0,kwarg:0,label:0,label_fonts:0,label_space_left:0,label_space_top:0,lag1:0,lag2:0,lag:0,lag_arrai:0,lag_mod:0,lag_unit:0,lagfunct:0,larg:0,larger:0,last:0,later:0,lead:0,learn:0,least:0,left:0,legend:0,legend_fonts:0,legend_width:0,length:0,less:0,let:0,lett:0,level:0,levelof:0,like:0,likelihood:0,limit:0,lindsai:0,line:0,linear:0,linear_model:0,linearli:0,linearmedi:0,linearregress:0,linewidth:0,link:0,link_attribut:0,link_colorbar_label:0,link_label_fonts:0,link_matrix:0,link_width:0,links_coeff:0,list:0,load:0,log:0,low:0,lower:0,lowhighpass_filt:0,lpd4:0,made:0,magnitud:0,mai:0,main:0,make:0,mani:0,map:0,margin:0,maria:0,mark:0,marker:0,markers:0,mask:0,mask_typ:0,match:0,mathcal:0,matplotlib:0,matric:0,matrix:0,max:0,max_combin:0,max_conds_dim:0,max_conds_pi:0,max_conds_px:0,max_delai:0,max_lag:0,max_lag_or_tau_max:0,maxim:0,maximum:0,mce:0,mci:0,mean:0,measur:0,med:0,memori:0,method:0,minimum:0,minu:0,miss:0,missing_flag:0,mlr:0,mode:0,model_param:0,modul:0,modulo:0,momentari:0,more:0,most:0,much:0,multi:0,multipl:0,multivari:0,must:0,mutual:0,n_job:0,n_symb:0,nail:0,name:0,nan:0,natur:0,ncomms9502:0,nearest:0,necessari:0,need:0,neg:0,neighbor:0,net_to_tsg:0,network:0,network_lower_bound:0,new_data:0,newer:0,niehgbor:0,no_nois:0,node:0,node_colorbar_label:0,node_label_s:0,node_po:0,node_s:0,node_tick:0,nois:0,non:0,none:0,nonlinear:0,nonzero:0,normal:0,note:0,nowack:0,npz:0,null_dist:0,null_dist_filenam:0,nulldist:0,num_f:0,number:0,numer:0,numpi:0,object:0,observ:0,obtain:0,occur:0,old:0,older:0,onc:0,one:0,onli:0,opac:0,optim:0,optimz:0,option:0,order:0,ordin:0,ordinal_patt_arrai:0,ordinari:0,org:0,origin:0,orrd:0,other:0,otherwis:0,otion:0,out:0,output:0,over:0,overlaid:0,overrid:0,overwrit:0,p_matrix:0,p_max:0,packag:0,page:0,pair:0,pairwis:0,panda:0,panel:0,paper:0,parallel:0,paramet:0,parametr:0,parcorr:0,parent:0,parent_node_id:0,parents_neighbors_coeff:0,partial:0,particular:0,pass:0,pass_period:0,past:0,path:0,path_node_arrai:0,path_val_matrix:0,pathwai:0,patt:0,patt_mask:0,patt_tim:0,pattern:0,pc1:0,pc_1:0,pc_alpha:0,peak:0,pearson:0,perform:0,period:0,perm:0,permut:0,perp:0,phase:0,phi:0,phy:0,physrev:0,pilla:0,plai:0,pleas:0,plot_graph:0,plot_gridlin:0,plot_lagfunc:0,plot_mediation_graph:0,plot_mediation_time_series_graph:0,plot_time_series_graph:0,plot_timeseri:0,point:0,pomp:0,pos:0,posit:0,possibl:0,power:0,pq_matrix:0,practic:0,pre:0,precis:0,precomput:0,pred_param:0,prediction_model:0,predictor:0,preprocess:0,present:0,preserv:0,press:0,previou:0,print:0,print_array_info:0,print_info:0,print_result:0,print_significant_link:0,prior:0,prl:0,problemat:0,procedur:0,proceed:0,processor:0,properti:0,provid:0,psi:0,pval:0,pyplot:0,python:0,q_matrix:0,qualiti:0,quantifi:0,quantil:0,quantile_bin_arrai:0,quantiti:0,r_x:0,r_y:0,random:0,rang:0,rank:0,rate:0,rather:0,rcit:0,rcot:0,rdbu_r:0,recommend:0,reconstruct:0,recycle_residu:0,red:0,reduc:0,refer:0,regard:0,regress:0,regular:0,rel:0,remov:0,repeat:0,repo:0,repres:0,reproduc:0,requir:0,residu:0,respect:0,restrict:0,result:0,return_cleaned_xyz:0,return_confid:0,return_data:0,return_dict:0,return_null_dist:0,return_significant_par:0,rev:0,rho:0,right:0,rizzo:0,role:0,row:0,rpy:0,rtype:0,run:0,run_bivci:0,run_fullci:0,run_mci:0,run_pc_stabl:0,run_pcmci:0,run_test:0,run_test_raw:0,rung:0,runge18a:0,runtim:0,same:0,sampl:0,sample_s:0,saniti:0,satterthwait:0,save:0,save_iter:0,save_nam:0,savefig:0,scale:0,schedul:0,sci:0,scienc:0,sciencemag:0,scikit:0,scipi:0,scitat:0,score:0,search:0,section:0,see:0,seed:0,seen:0,sejdinov:0,select:0,selected_link:0,selected_target:0,selected_vari:0,self:0,set:0,set_datafram:0,set_mask_typ:0,setter:0,setup:0,setup_arg:0,setup_matrix:0,shape:0,shorter:0,should:0,show:0,show_colorbar:0,shown:0,shuffl:0,shuffle_neighbor:0,shuffle_test:0,shyam:0,side:0,sig_blocklength:0,sig_overrid:0,sig_sampl:0,sig_thr:0,sigma:0,signatur:0,signfic:0,signficic:0,signific:0,sim:0,simpl:0,simul:0,sinc:0,size:0,skip:0,skip_ticks_data_i:0,skip_ticks_data_x:0,sklearn:0,slice:0,slightli:0,slow:0,small:0,smaller:0,smooth:0,smooth_width:0,sourc:0,space:0,spatial:0,spatio:0,specif:0,specifi:0,squar:0,stack:0,standard:0,standardscal:0,stationar:0,statist:0,std:0,step:0,steps_ahead:0,still:0,store:0,str:0,straight:0,string:0,strobl:0,structur:0,student:0,style:0,subplot:0,subspac:0,suggest:0,suitabl:0,sum:0,sum_:0,summar:0,superset:0,supplement:0,suppli:0,sure:0,surrog:0,suscept:0,symb_arrai:0,symbol:0,symbolifi:0,system:0,szeke:0,take:0,target:0,target_predictor:0,tau:0,tau_:0,tau_max:0,tau_min:0,techniqu:0,tempor:0,test_indic:0,than:0,thei:0,them:0,themselv:0,theoret:0,thi:0,those:0,threshold:0,through:0,tick:0,tickmark:0,tild:0,time_bin_length:0,time_bin_with_mask:0,time_label:0,time_lag:0,timelabel:0,too:0,top:0,toward:0,train:0,train_indic:0,transfer:0,transform:0,translat:0,true_par:0,true_parent_neighbor:0,tsg:0,tsg_path_val_matrix:0,tsg_to_net:0,tupl:0,twice:0,two:0,two_sided_thr:0,type:0,typic:0,under:0,underli:0,undirect:0,undirected_styl:0,uniform:0,uniqu:0,unit:0,unlik:0,unrestrict:0,unshuffl:0,upper:0,use:0,use_mask:0,used:0,useful:0,user:0,uses:0,using:0,util:0,v84:0,val:0,val_matrix:0,val_min:0,valu:0,var1:0,var2:0,var_nam:0,var_network:0,var_process:0,var_unit:0,vari:0,variabl:0,varianc:0,variant:0,varx:0,vector:0,verbos:0,veri:0,version:0,vertic:0,via:0,view:0,visual:0,visweswaran:0,vmax_edg:0,vmax_nod:0,vmin_edg:0,vmin_nod:0,warn:0,weight:0,weighted_avg_and_std:0,welch:0,well:0,when:0,where:0,whether:0,which:0,whichev:0,whole:0,wide:0,widehat:0,width:0,window:0,with_mean:0,with_std:0,within:0,won:0,wrapper:0,x_base:0,x_i:0,x_j:0,x_t:0,xyz:0,y_base:0,y_t:0,yield:0,you:0,z_i:0,z_j:0,z_t:0,zero:0,zhang:0},titles:["TIGRAMITE"],titleterms:{"function":0,condit:0,data:0,data_process:0,independ:0,independence_test:0,indic:0,mediat:0,model:0,pcmci:0,plot:0,predict:0,process:0,seri:0,tabl:0,test:0,tigramit:0,time:0}}) \ No newline at end of file +Search.setIndex({docnames:["index"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["index.rst"],objects:{"tigramite.data_processing":{DataFrame:[0,1,1,""],lowhighpass_filter:[0,4,1,""],ordinal_patt_array:[0,4,1,""],quantile_bin_array:[0,4,1,""],smooth:[0,4,1,""],time_bin_with_mask:[0,4,1,""],var_process:[0,4,1,""],weighted_avg_and_std:[0,4,1,""]},"tigramite.data_processing.DataFrame":{construct_array:[0,2,1,""],data:[0,3,1,""],datatime:[0,3,1,""],mask:[0,3,1,""],missing_flag:[0,3,1,""],print_array_info:[0,2,1,""],var_names:[0,3,1,""]},"tigramite.independence_tests":{CMIknn:[0,1,1,""],CMIsymb:[0,1,1,""],CondIndTest:[0,1,1,""],GPDC:[0,1,1,""],ParCorr:[0,1,1,""],RCOT:[0,1,1,""]},"tigramite.independence_tests.CMIknn":{get_dependence_measure:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.CMIsymb":{get_dependence_measure:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.CondIndTest":{get_analytic_confidence:[0,2,1,""],get_analytic_significance:[0,2,1,""],get_bootstrap_confidence:[0,2,1,""],get_confidence:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_fixed_thres_significance:[0,2,1,""],get_measure:[0,2,1,""],get_model_selection_criterion:[0,2,1,""],get_shuffle_significance:[0,2,1,""],get_significance:[0,2,1,""],measure:[0,2,1,""],print_info:[0,2,1,""],run_test:[0,2,1,""],run_test_raw:[0,2,1,""],set_dataframe:[0,2,1,""],set_mask_type:[0,2,1,""]},"tigramite.independence_tests.GPDC":{generate_and_save_nulldists:[0,2,1,""],generate_nulldist:[0,2,1,""],get_analytic_significance:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_model_selection_criterion:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.ParCorr":{get_analytic_confidence:[0,2,1,""],get_analytic_significance:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_model_selection_criterion:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.independence_tests.RCOT":{get_analytic_significance:[0,2,1,""],get_dependence_measure:[0,2,1,""],get_shuffle_significance:[0,2,1,""],measure:[0,2,1,""]},"tigramite.models":{LinearMediation:[0,1,1,""],Models:[0,1,1,""],Prediction:[0,1,1,""]},"tigramite.models.LinearMediation":{fit_model:[0,2,1,""],get_ace:[0,2,1,""],get_acs:[0,2,1,""],get_all_ace:[0,2,1,""],get_all_acs:[0,2,1,""],get_all_amce:[0,2,1,""],get_amce:[0,2,1,""],get_ce:[0,2,1,""],get_ce_max:[0,2,1,""],get_coeff:[0,2,1,""],get_mce:[0,2,1,""],get_mediation_graph_data:[0,2,1,""],get_tsg:[0,2,1,""],get_val_matrix:[0,2,1,""],net_to_tsg:[0,2,1,""],tsg_to_net:[0,2,1,""]},"tigramite.models.Models":{get_coefs:[0,2,1,""],get_fit:[0,2,1,""]},"tigramite.models.Prediction":{fit:[0,2,1,""],get_predictors:[0,2,1,""],get_test_array:[0,2,1,""],get_train_array:[0,2,1,""],predict:[0,2,1,""]},"tigramite.pcmci":{PCMCI:[0,1,1,""]},"tigramite.pcmci.PCMCI":{N:[0,3,1,""],T:[0,3,1,""],all_parents:[0,3,1,""],get_corrected_pvalues:[0,2,1,""],get_lagged_dependencies:[0,2,1,""],iterations:[0,3,1,""],p_max:[0,3,1,""],print_results:[0,2,1,""],print_significant_links:[0,2,1,""],return_significant_parents:[0,2,1,""],run_bivci:[0,2,1,""],run_fullci:[0,2,1,""],run_mci:[0,2,1,""],run_pc_stable:[0,2,1,""],run_pcmci:[0,2,1,""],val_min:[0,3,1,""]},"tigramite.plotting":{plot_graph:[0,4,1,""],plot_lagfuncs:[0,4,1,""],plot_mediation_graph:[0,4,1,""],plot_mediation_time_series_graph:[0,4,1,""],plot_time_series_graph:[0,4,1,""],plot_timeseries:[0,4,1,""],setup_matrix:[0,1,1,""]},"tigramite.plotting.setup_matrix":{add_lagfuncs:[0,2,1,""],savefig:[0,2,1,""]},tigramite:{data_processing:[0,0,0,"-"],plotting:[0,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:attribute","4":"py:function"},terms:{"07007v2":[],"21st":0,"2xtau_max":0,"abstract":0,"boolean":0,"case":0,"class":0,"default":0,"float":0,"import":0,"int":0,"new":0,"null":0,"return":0,"true":0,"var":0,"while":0,ACE:0,ACS:0,But:0,For:0,Its:0,OLS:0,One:0,The:0,Then:0,There:0,These:0,Used:0,Useful:0,Uses:0,With:0,_get_single_residu:0,_print_significant_link:0,about:0,abs:0,absmax:0,absolut:0,accord:0,accur:0,ace:0,across:0,acs:0,act:0,adapt:0,add:0,add_lagfunc:0,add_lagfunc_arg:0,add_to_null_dist:0,adding:0,addit:0,adjust:0,adv:0,advanc:0,affect:0,after:0,ahead:0,aip:0,akaik:0,algorithm:0,all:0,all_lag:0,all_par:0,alloc:0,allow:0,along:0,alpha:0,alpha_level:0,also:0,altern:0,although:0,alwai:0,amc:0,among:0,analys:0,analysi:0,analyt:0,analyz:0,ani:0,appli:0,applic:0,appropri:0,approx:0,approxim:0,arang:0,arg:0,argument:0,around:0,arrai:0,array_lik:0,array_mask:0,arrow:0,arrow_linewidth:0,arrowhead_s:0,articl:0,artifici:0,arxiv:0,assign:0,associ:0,assum:0,assumpt:0,attribut:0,auto:0,autocovari:0,automat:0,autoregress:0,avail:0,averag:0,avoid:0,axes:0,axi:0,backward:0,bakirov:0,bandwidth:0,basak:0,base:0,basemap:0,becaus:0,been:0,befor:0,beforehand:0,begin:0,below:0,benjamini:0,beta:0,beta_i:0,beta_x:0,better:0,between:0,bia:0,bias:0,bin:0,bincount:0,bindata:0,bivci:0,black:0,block:0,blue:0,bool:0,bootstrap:0,both:0,bottom:0,bound:0,box:0,briefli:0,bucklei:0,butterworth:0,call:0,callabl:0,can:0,cardin:0,care:0,caus:0,causal:0,causat:0,caveat:0,cdot:0,chain:0,chao:0,check:0,chi2:0,chi:0,child:0,choic:0,chosen:0,cite:0,ckdtree:0,clash:0,clean:0,cmap_edg:0,cmap_nod:0,cmi:0,cmiknn:0,cmisymb:0,code:0,coef1:0,coef2:0,coeff:0,coeffici:0,color:0,colorbar:0,colormap:0,column:0,com:0,combin:0,come:0,commun:0,compar:0,comparison:0,complex:0,comprehens:0,comput:0,concret:0,cond_ind_test:0,condindtest:0,condition:0,conduct:0,conf_blocklength:0,conf_lev:0,conf_low:0,conf_matrix:0,conf_sampl:0,conf_upp:0,confer:0,confid:0,consid:0,consider:0,constant:0,construct:0,construct_arrai:0,contain:0,contemporan:0,content:0,context:0,continu:0,control:0,convert:0,coordin:0,copi:0,copyright:0,correct:0,correl:0,correspond:0,cost:0,could:0,coupl:0,covari:0,creat:0,criteria:0,criterion:0,cross:0,cube:0,current:0,curv:0,curvatur:0,curved_radiu:0,cut_off:0,cutoff:0,cutperiod:0,cython:0,d_z:0,dash:0,data_linewidth:0,data_transform:0,datafram:0,dataset:0,datatim:0,debug:0,decai:0,defin:0,degre:0,delai:0,denot:0,densiti:0,depend:0,dependence_measur:0,deriv:0,describ:0,detect:0,determin:0,deviat:0,dict:0,dictionari:0,differ:0,digamma:0,dim:0,dimens:0,dimension:0,directli:0,disabl:0,discoveri:0,discret:0,discuss:0,disk:0,dismiss:0,dist:0,distanc:0,distribut:0,do_check:0,doc:0,document:0,doe:0,doi:0,draw:0,drawn:0,driver:0,due:0,duplic:0,dure:0,eaau4996:0,each:0,eagleson:0,earth:0,easi:0,edg:0,edge_tick:0,effect:0,effici:0,either:0,els:0,eman:0,embed:0,empti:0,ensur:0,entri:0,enumer:0,epsilon_:0,equal:0,equival:0,eric:0,ericstrobl:0,estim:0,eta:0,etc:0,everi:0,exampl:0,exclud:0,exclude_contemporan:0,exclude_i:0,exclude_j:0,exclude_k:0,exclude_self_effect:0,exist:0,expect:0,explain:0,extern:0,f_x:0,f_y:0,faculti:0,fals:0,fancyarrowpatch:0,fast:0,faster:0,fdr_bh:0,fdr_method:0,featur:0,ffinkernagel:0,fig:0,fig_ax:0,figsiz:0,figur:0,file:0,fill:0,filter:0,finkernagel:0,first:0,fit:0,fit_model:0,fit_result:0,fix:0,fixed_thr:0,flag:0,flaxman:0,flexibl:0,florian:0,follow:0,fontsiz:0,form:0,format:0,forward:0,fourier:0,frac:0,fraction:0,framework:0,free:0,freedom:0,frenzel:0,friendli:0,from:0,full:0,fullci:0,fulli:0,further:0,gabor:0,gamma:0,gatewai:0,gauss_pr:0,gaussian:0,gaussianprocessregressor:0,gaussprocreg:0,gener:0,generate_and_save_nulldist:0,generate_nulldist:0,get:0,get_ac:0,get_all_ac:0,get_all_amc:0,get_amc:0,get_analytic_confid:0,get_analytic_signific:0,get_bootstrap_confid:0,get_c:0,get_ce_max:0,get_coef:0,get_coeff:0,get_confid:0,get_corrected_pvalu:0,get_dependence_measur:0,get_fit:0,get_fixed_thres_signific:0,get_lagged_depend:0,get_mc:0,get_measur:0,get_mediation_graph_data:0,get_model_selection_criterion:0,get_predictor:0,get_shuffle_signific:0,get_signific:0,get_test_arrai:0,get_train_arrai:0,get_tsg:0,get_val_matrix:0,gist:0,github:0,given:0,going:0,gp_param:0,gp_version:0,gpace:0,gpdc:0,graph:0,graph_data:0,greater:0,grei:0,grey_masked_sampl:0,grid:0,guarante:0,hall:0,handl:0,has:0,have:0,hbe:0,head:0,heavisid:0,helper:0,henc:0,here:0,high:0,highli:0,histogram:0,hochberg:0,horizont:0,how:0,html:0,http:0,hyper:0,hyperparamet:0,hypothesi:0,identifi:0,iint:0,implement:0,impli:0,improv:0,includ:0,include_lagzero_par:0,include_neighbor:0,incom:0,index:0,infer:0,info:0,inform:0,inherit:0,initi:0,initial_valu:0,inno_cov:0,innov:0,input:0,instal:0,instanc:0,instanti:0,instead:0,integ:0,intellig:0,interdisciplinari:0,intern:0,interv:0,introduc:0,inv_inno_cov:0,invers:0,irrelev:0,iter:0,its:0,itself:0,j_t:0,job:0,joint:0,journal:0,just:0,kcit:0,kei:0,kernel:0,kind:0,knn:0,kretschmer:0,kun:0,kwarg:0,label:0,label_fonts:0,label_space_left:0,label_space_top:0,lag1:0,lag2:0,lag:0,lag_arrai:0,lag_mod:0,lag_unit:0,lagfunct:0,larg:0,larger:0,last:0,later:0,lead:0,learn:0,least:0,left:0,legend:0,legend_fonts:0,legend_width:0,length:0,less:0,let:0,lett:0,level:0,levelof:0,like:0,likelihood:0,limit:0,lindsai:0,line:0,linear:0,linear_model:0,linearli:0,linearmedi:0,linearregress:0,linewidth:0,link:0,link_attribut:0,link_colorbar_label:0,link_label_fonts:0,link_matrix:0,link_width:0,links_coeff:0,list:0,load:0,log:0,low:0,lower:0,lowhighpass_filt:0,lpd4:0,made:0,magnitud:0,mai:0,main:0,make:0,mani:0,map:0,margin:0,maria:0,mark:0,marker:0,markers:0,mask:0,mask_typ:0,match:0,mathcal:0,matplotlib:0,matric:0,matrix:0,max:0,max_combin:0,max_conds_dim:0,max_conds_pi:0,max_conds_px:0,max_delai:0,max_lag:0,max_lag_or_tau_max:0,maxim:0,maximum:0,mce:0,mci:0,mean:0,measur:0,med:0,memori:0,method:0,minimum:0,minu:0,miss:0,missing_flag:0,mlr:0,mode:0,model_param:0,modul:0,modulo:0,momentari:0,more:0,most:0,much:0,multi:0,multipl:0,multivari:0,must:0,mutual:0,n_job:0,n_symb:0,nail:0,name:0,nan:0,natur:0,ncomms9502:0,nearest:0,necessari:0,need:0,neg:0,neighbor:0,net_to_tsg:0,network:0,network_lower_bound:0,new_data:0,newer:0,niehgbor:0,no_nois:0,node:0,node_colorbar_label:0,node_label_s:0,node_po:0,node_s:0,node_tick:0,nois:0,non:0,none:0,nonlinear:0,nonzero:0,normal:0,note:0,nowack:0,npz:0,null_dist:0,null_dist_filenam:0,nulldist:0,num_f:0,number:0,numer:0,numpi:0,object:0,observ:0,obtain:0,occur:0,old:0,older:0,onc:0,one:0,onli:0,opac:0,optim:0,optimz:0,option:0,order:0,ordin:0,ordinal_patt_arrai:0,ordinari:0,org:0,origin:0,orrd:0,other:0,otherwis:0,otion:0,out:0,output:0,over:0,overlaid:0,overrid:0,overwrit:0,p_matrix:0,p_max:0,packag:0,page:0,pair:0,pairwis:0,panda:0,panel:0,paper:0,parallel:0,paramet:0,parametr:0,parcorr:0,parent:0,parent_node_id:0,parents_neighbors_coeff:0,partial:0,particular:0,pass:0,pass_period:0,past:0,path:0,path_node_arrai:0,path_val_matrix:0,pathwai:0,patt:0,patt_mask:0,patt_tim:0,pattern:0,pc1:0,pc_1:0,pc_alpha:0,peak:0,pearson:0,perform:0,period:0,perm:0,permut:0,perp:0,phase:0,phi:0,phy:0,physrev:0,pilla:0,plai:0,pleas:0,plot_graph:0,plot_gridlin:0,plot_lagfunc:0,plot_mediation_graph:0,plot_mediation_time_series_graph:0,plot_time_series_graph:0,plot_timeseri:0,point:0,pomp:0,pos:0,posit:0,possibl:0,power:0,pq_matrix:0,practic:0,pre:0,precis:0,precomput:0,pred_param:0,prediction_model:0,predictor:0,preprocess:0,present:0,preserv:0,press:0,previou:0,print:0,print_array_info:0,print_info:0,print_result:0,print_significant_link:0,prior:0,prl:0,problemat:0,procedur:0,proceed:0,processor:0,properti:0,provid:0,psi:0,pval:0,pyplot:0,python:0,q_matrix:0,qualiti:0,quantifi:0,quantil:0,quantile_bin_arrai:0,quantiti:0,r_x:0,r_y:0,random:0,rang:0,rank:0,rate:0,rather:0,rcit:0,rcot:0,rdbu_r:0,recommend:0,reconstruct:0,recycle_residu:0,red:0,reduc:0,refer:0,regard:0,regress:0,regular:0,rel:0,remov:0,repeat:0,repo:0,repres:0,reproduc:0,requir:0,residu:0,respect:0,restrict:0,result:0,return_cleaned_xyz:0,return_confid:0,return_data:0,return_dict:0,return_null_dist:0,return_significant_par:0,rev:0,rho:0,right:0,rizzo:0,role:0,row:0,rpy:0,rtype:0,run:0,run_bivci:0,run_fullci:0,run_mci:0,run_pc_stabl:0,run_pcmci:0,run_test:0,run_test_raw:0,rung:0,runge18a:0,runtim:0,s41467:0,same:0,sampl:0,sample_s:0,saniti:0,satterthwait:0,save:0,save_iter:0,save_nam:0,savefig:0,scale:0,schedul:0,sci:0,scienc:0,sciencemag:0,scikit:0,scipi:0,scitat:0,score:0,search:0,section:0,see:0,seed:0,seen:0,sejdinov:0,select:0,selected_link:0,selected_target:0,selected_vari:0,self:0,set:0,set_datafram:0,set_mask_typ:0,setter:0,setup:0,setup_arg:0,setup_matrix:0,shape:0,shorter:0,should:0,show:0,show_colorbar:0,shown:0,shuffl:0,shuffle_neighbor:0,shuffle_test:0,shyam:0,side:0,sig_blocklength:0,sig_overrid:0,sig_sampl:0,sig_thr:0,sigma:0,signatur:0,signfic:0,signficic:0,signific:0,sim:0,simpl:0,simul:0,sinc:0,size:0,skip:0,skip_ticks_data_i:0,skip_ticks_data_x:0,sklearn:0,slice:0,slightli:0,slow:0,small:0,smaller:0,smooth:0,smooth_width:0,sourc:0,space:0,spatial:0,spatio:0,specif:0,specifi:0,squar:0,stack:0,standard:0,standardscal:0,stationar:0,statist:0,std:0,step:0,steps_ahead:0,still:0,store:0,str:0,straight:0,string:0,strobl:0,structur:0,student:0,style:0,subplot:0,subspac:0,suggest:0,suitabl:0,sum:0,sum_:0,summar:0,superset:0,supplement:0,suppli:0,sure:0,surrog:0,suscept:0,symb_arrai:0,symbol:0,symbolifi:0,system:0,szeke:0,take:0,target:0,target_predictor:0,tau:0,tau_:0,tau_max:0,tau_min:0,techniqu:0,tempor:0,test_indic:0,than:0,thei:0,them:0,themselv:0,theoret:0,thi:0,those:0,threshold:0,through:0,tick:0,tickmark:0,tild:0,time_bin_length:0,time_bin_with_mask:0,time_label:0,time_lag:0,timelabel:0,too:0,top:0,toward:0,train:0,train_indic:0,transfer:0,transform:0,translat:0,true_par:0,true_parent_neighbor:0,tsg:0,tsg_path_val_matrix:0,tsg_to_net:0,tupl:0,twice:0,two:0,two_sided_thr:0,type:0,typic:0,under:0,underli:0,undirect:0,undirected_styl:0,uniform:0,uniqu:0,unit:0,unlik:0,unrestrict:0,unshuffl:0,upper:0,use:0,use_mask:0,used:0,useful:0,user:0,uses:0,using:0,util:0,v84:0,val:0,val_matrix:0,val_min:0,valu:0,var1:0,var2:0,var_nam:0,var_network:0,var_process:0,var_unit:0,vari:0,variabl:0,varianc:0,variant:0,varx:0,vector:0,verbos:0,veri:0,version:0,vertic:0,via:0,view:0,visual:0,visweswaran:0,vmax_edg:0,vmax_nod:0,vmin_edg:0,vmin_nod:0,warn:0,weight:0,weighted_avg_and_std:0,welch:0,well:0,when:0,where:0,whether:0,which:0,whichev:0,whole:0,wide:0,widehat:0,width:0,window:0,with_mean:0,with_std:0,within:0,won:0,wrapper:0,www:0,x_base:0,x_i:0,x_j:0,x_t:0,xyz:0,y_base:0,y_t:0,yield:0,you:0,z_i:0,z_j:0,z_t:0,zero:0,zhang:0},titles:["TIGRAMITE"],titleterms:{"function":0,condit:0,data:0,data_process:0,independ:0,independence_test:0,indic:0,mediat:0,model:0,pcmci:0,plot:0,predict:0,process:0,seri:0,tabl:0,test:0,tigramit:0,time:0}}) \ No newline at end of file