update readme

docs/_build/html/_sources/index.rst.txt

@@ -15,6 +15,9 @@ Welcome to Adjustin's documentation!
    src/user_guide.rst
    src/developer_guide.rst
 
+The Adjustin package is a julia package for model simulation, parameters estimation and sensitivity_analysis.
+The Adjustin applications repository contains example of how to use this package and with which folder organisation.
+
 
 .. topic:: Installation guide
    

docs/_build/html/index.html

@@ -161,6 +161,8 @@
 <h1>Welcome to Adjustin’s documentation!<a class="headerlink" href="#welcome-to-adjustin-s-documentation" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
 </div>
+<p>The Adjustin package is a julia package for model simulation, parameters estimation and sensitivity_analysis.
+The Adjustin applications repository contains example of how to use this package and with which folder organisation.</p>
 <div class="topic">
 <p class="topic-title first">Installation guide</p>
 <p><a class="reference internal" href="src/installation_guide.html#installation-guide"><span class="std std-ref">To installation_guide</span></a></p>

docs/_build/html/searchindex.js

-Search.setIndex({docnames:["index","src/developer_guide","src/installation_guide","src/user_guide"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":3,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["index.rst","src\\developer_guide.rst","src\\installation_guide.rst","src\\user_guide.rst"],objects:{},objnames:{},objtypes:{},terms:{"1":3,"2":3,"2009viaudg":[1,2],"3":2,"default":2,"do":[1,2,3],"final":[1,3],"import":[2,3],"int":3,"new":[1,3],"return":3,"true":3,"try":1,A:3,And:1,As:3,For:3,If:[1,2,3],In:[2,3],It:[1,2,3],OR:3,One:3,The:[1,2,3],Then:3,There:3,To:[0,3],__dir__:3,abc_pop_mc:3,abc_simpl:3,abc_smc:3,abc_subsim:3,abl:[2,3],abov:3,access:2,account:3,activ:[2,3],actual:3,ad:[1,2],add:[2,3],addit:3,adjustin:1,adjustin_path_databas:3,adjustin_path_result:3,adjustinappl:[2,3],adjustincor:[],after:3,afterward:1,again:1,algo_:3,all:3,allow:1,alpha:3,alreadi:[2,3],also:[2,3],alt:2,amwg:3,an:[2,3],analys:3,ani:[1,2],anoth:[2,3],anyth:3,ar:[1,2,3],arabidopsi:3,argument:3,arrai:3,associ:2,atom:[1,2],attribut:3,automata:3,automaticali:2,automt:3,avoid:1,back:1,bash:[1,2],bayesian:3,becaus:[1,3],becom:3,befor:1,begin:3,being:3,belief:3,below:[2,3],best:3,beta:3,better:3,between:3,big:3,block:[],branch:[1,2],bug:3,c:2,call:3,can:[1,2,3],carlo:3,cd:2,centralesupelec:[1,2],cf:[2,3],cfg:3,chain:3,chang:[1,2,3],check:2,checkout:[1,2],choic:3,chose:2,client:2,clone:2,close:1,code:[2,3],come:3,command:[1,2],commit:1,compil:1,comput:[2,3],confid:3,configur:[2,3],configurationtc_algo_estim:3,configurationtc_algo_sensitivity_analysi:3,consid:3,contain:[1,3],continu:2,control:3,core:3,correct:2,could:1,cours:2,cpf:3,creat:[1,3],create_observation_funct:3,create_observer_funct:3,create_results_diretcori:3,ctrl:3,current:[2,3],data:3,databas:3,decrib:3,defin:3,degre:3,delet:3,depend:2,depositori:2,desir:3,det:3,determinist:3,dev:[1,2],develop:0,deviat:3,dictionari:3,differ:[2,3],directli:1,directori:[1,2],distribut:3,doesn:3,done:[1,2],download:[1,2],dure:2,e:[2,3],each:3,editor:[2,3],either:3,end:[1,2,3],enkf:3,enter:3,env:3,environ:[1,2,3],error:3,estim:3,etc:3,eval:3,everi:3,everyth:[1,2,3],everytim:1,exactli:2,exampl:2,exclud:3,execut:[2,3],exist:3,experiment:3,explicitli:3,extern:3,f:3,famili:3,faster:1,fetch:[1,2],few:[1,3],field:3,file:[1,2,3],filter:3,find:3,first:[2,3],fit:3,fix:3,flag_plot:3,flag_writ:3,folder:[1,3],follow:[2,3],form:3,fr:[1,2],free:1,frequenc:3,frequenti:3,frequentist:3,from:[2,3],g:3,galiota_branch:2,gener:3,get:1,get_observation_funct:3,git:[1,2],gitlab:[1,2],gl:3,gls_vector:3,go:[1,2,3],gr:2,greenlab:3,gsobol:3,handl:3,have:[2,3],helper:3,here:3,hidden:3,how:3,howev:[1,2],http:[1,2],i:[2,3],imperfect:3,implement:[1,3],includ:2,incorpor:3,indic:[1,2,3],influenc:3,inform:3,input:3,input_output:3,insid:3,instal:1,installation_guid:0,instead:3,interpret:3,interv:3,ip:3,itselft:3,jl:3,julia:[1,2],julia_vers:[1,2],juno:2,just:[1,3],keep:3,kei:2,kf:3,kind:3,knowledg:3,known:3,label:3,labellist:3,last:[],later:3,launch:3,layout:2,let:[1,3],lign:3,like:[1,2,3],limit:3,line:[1,2,3],list:3,ll_det:3,ll_sto:3,lna:3,load:3,load_control:3,load_from_ob:3,load_local_model:3,load_model:3,load_paramet:3,load_stat:3,local:[1,2],locat:[2,3],lognorm:3,m:1,macro:3,mail:[],main:3,make:1,manual:3,markov:3,master:2,math:3,mcmc:3,mcmc_abc:3,mcmc_simplifi:3,mean:3,measur:3,memori:3,messag:1,meta:3,method:3,mic:2,might:2,mn:3,mn_:3,modelis:3,modellingnois:3,modifi:1,mont:3,more:[1,3],multiindex:3,multipl:[2,3],must:[2,3],mutabl:3,n:3,name:[1,3],natur:3,nbr_arg:3,necessari:3,need:[1,2,3],next:[2,3],nois:3,noisi:3,normal:3,notat:3,note:[2,3],noth:3,now:[1,2,3],number:3,o:3,ob:3,object:3,obs_tc_field_name_observ:3,obs_tc_field_name_observed1:3,obs_tc_field_name_observed2:3,observ:3,observation_funct:3,observation_nois:3,observationnois:3,observationtuplelist:3,observermodel:3,ofl:3,ol:3,om1:3,om2:3,om3:3,om:3,oml:3,on_:3,onc:3,one:[2,3],ones:3,onli:[1,3],open:[1,2,3],option:[2,3],optionn:3,order:3,origin:[1,2],other:3,otherwis:3,otll:3,our:3,own:3,p:3,packag:[1,2,3],parallel_abc:3,paramet:3,pars:3,part:3,particl:3,pass:3,past:2,path:2,path_to_adjustin:2,path_to_julia:2,phenomenon:3,pkg:[1,2],plot:3,pmmh:3,possibl:[1,3],preexist:3,press:[2,3],previou:1,print:3,prior:3,probability_density_funct:3,probabl:3,problem:2,process:3,project:[1,2],properli:2,push:1,put:3,pygmalion:3,quickli:1,random:3,readm:3,recognis:1,recov:[2,3],rememb:2,repl:2,replac:1,repres:3,research:[1,2],result:3,retriev:3,revis:1,right:1,rn:3,root:1,s:[1,2,3],same:[1,2,3],sampl:3,save:3,save_to_ob:3,saw:3,section:[1,3],see:[1,2,3],seen:[1,3],select:3,sens:3,sensitivity_analysi:3,sequenti:3,set:[2,3],should:[2,3],simpli:1,simul:3,sir:3,slightli:2,smc:3,smc_abc:3,smoothli:1,so:[1,2,3],so_:3,so_exp:3,sobol:3,sobol_gl:3,specif:[2,3],src:3,stand:3,standard:3,start:3,state:3,statist:3,statu:2,step:[1,2,3],sto:3,stochast:3,store:[2,3],str_c:3,str_d:3,str_dir:3,str_m:3,str_p:3,str_x:3,string:3,struct:3,studi:3,system:3,system_observ:3,systemobserv:3,t1:3,t2:3,t:[1,3],take:3,tc_:3,tc_algo_estim:3,tc_algo_sensitivity_analysi:3,tc_controle_file_nam:3,tc_field_name_det:3,tc_field_name_observ:3,tc_field_name_observed1:3,tc_field_name_observed2:3,tc_field_name_sto:3,tc_fieldc1:3,tc_fieldc2:3,tc_fieldm1:3,tc_fieldm2:3,tc_fieldp1:3,tc_fieldp2:3,tc_fields1:3,tc_int:3,tc_int_param_noise_1:3,tc_int_param_noise_2:3,tc_kind:3,tc_model_nam:3,tc_model_name_vers:3,tc_observation_file_nam:3,tc_parameters_file_nam:3,tc_results_part_of_file_nam:3,tc_state_file_nam:3,tc_string_kind:3,tc_type_field_name_observ:3,tc_type_field_name_sto:3,tc_type_fieldc1:3,tc_type_fieldc2:3,tc_type_fieldm1:3,tc_type_fieldm2:3,tc_type_fieldp1:3,tc_type_fieldp2:3,tc_type_fields1:3,tc_what_you_want_to_sav:3,term:3,termin:2,than:3,thank:3,thei:[2,3],them:[2,3],theta:3,theta_:3,thi:[1,2,3],those:3,thrown:3,thu:[2,3],time:[2,3],timelin:3,timestep:3,tip:1,titl:3,tmax:3,tml:3,tn:3,toml:2,transit:3,tupl:3,two:3,type:3,u:3,u_:3,uber:2,ui:2,ukf:3,uniform:3,until:1,up:[1,2],us:[1,3],user:2,usual:3,v1:2,valu:3,variabl:3,variou:3,vector:3,version:2,vl:3,wa:2,wai:3,want:[1,2,3],we:3,were:[1,3],what:[2,3],when:[1,2,3],where:[2,3],which:[2,3],whole:[1,3],witch:3,wl:3,word:3,work:[1,2],workaround:1,would:2,writ:2,write:[2,3],x0:3,x:3,x_:3,x_t1_om1:3,x_t1_om2:3,x_t1_om3:3,x_t2_om1:3,x_t2_om2:3,x_t2_om3:3,x_tn_om1:3,x_tn_om2:3,x_tn_om3:3,xn:3,xnplus1:3,y:3,y_:3,you:[1,2,3],your:[1,2],your_app_her:3,your_branch_nam:1,your_model:3},titles:["Welcome to Adjustin\u2019s documentation!","Developper guide","Installation guide","User guide"],titleterms:{"function":3,"try":3,ad:3,add:1,adjustin:[0,2,3],algorithm:[1,3],applic:[2,3],detail:3,develop:2,developp:[0,1],document:0,exampl:3,framework:3,fucntion:1,guid:[0,1,2,3],instal:[0,2],mathemat:3,model:[1,3],nois:1,onli:2,out:3,probabl:1,s:0,simul:1,structur:3,templat:3,test:3,understand:3,us:2,user:[0,3],welcom:0,work:3,workflow:1,your:3}})
\ No newline at end of file
+Search.setIndex({docnames:["index","src/developer_guide","src/installation_guide","src/user_guide"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":3,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["index.rst","src\\developer_guide.rst","src\\installation_guide.rst","src\\user_guide.rst"],objects:{},objnames:{},objtypes:{},terms:{"1":3,"2":3,"2009viaudg":[1,2],"3":2,"default":2,"do":[1,2,3],"final":[1,3],"import":[2,3],"int":3,"new":[1,3],"return":3,"true":3,"try":1,A:3,And:1,As:3,For:3,If:[1,2,3],In:[2,3],It:[1,2,3],OR:3,One:3,The:[0,1,2,3],Then:3,There:3,To:[0,3],__dir__:3,abc_pop_mc:3,abc_simpl:3,abc_smc:3,abc_subsim:3,abl:[2,3],abov:3,access:2,account:3,activ:[2,3],actual:3,ad:[1,2],add:[2,3],addit:3,adjustin:1,adjustin_path_databas:3,adjustin_path_result:3,adjustinappl:[2,3],adjustincor:[],after:3,afterward:1,again:1,algo_:3,all:3,allow:1,alpha:3,alreadi:[2,3],also:[2,3],alt:2,amwg:3,an:[2,3],analys:3,ani:[1,2],anoth:[2,3],anyth:3,applic:0,ar:[1,2,3],arabidopsi:3,argument:3,arrai:3,associ:2,atom:[1,2],attribut:3,automata:3,automaticali:2,automt:3,avoid:1,back:1,bash:[1,2],bayesian:3,becaus:[1,3],becom:3,befor:1,begin:3,being:3,belief:3,below:[2,3],best:3,beta:3,better:3,between:3,big:3,block:[],branch:[1,2],bug:3,c:2,call:3,can:[1,2,3],carlo:3,cd:2,centralesupelec:[1,2],cf:[2,3],cfg:3,chain:3,chang:[1,2,3],check:2,checkout:[1,2],choic:3,chose:2,client:2,clone:2,close:1,code:[2,3],come:3,command:[1,2],commit:1,compil:1,comput:[2,3],confid:3,configur:[2,3],configurationtc_algo_estim:3,configurationtc_algo_sensitivity_analysi:3,consid:3,contain:[0,1,3],continu:2,control:3,core:3,correct:2,could:1,cours:2,cpf:3,creat:[1,3],create_observation_funct:3,create_observer_funct:3,create_results_diretcori:3,ctrl:3,current:[2,3],data:3,databas:3,decrib:3,defin:3,degre:3,delet:3,depend:2,depositori:2,desir:3,det:3,determinist:3,dev:[1,2],develop:0,deviat:3,dictionari:3,differ:[2,3],directli:1,directori:[1,2],distribut:3,doesn:3,done:[1,2],download:[1,2],dure:2,e:[2,3],each:3,editor:[2,3],either:3,end:[1,2,3],enkf:3,enter:3,env:3,environ:[1,2,3],error:3,estim:[0,3],etc:3,eval:3,everi:3,everyth:[1,2,3],everytim:1,exactli:2,exampl:[0,2],exclud:3,execut:[2,3],exist:3,experiment:3,explicitli:3,extern:3,f:3,famili:3,faster:1,fetch:[1,2],few:[1,3],field:3,file:[1,2,3],filter:3,find:3,first:[2,3],fit:3,fix:3,flag_plot:3,flag_writ:3,folder:[0,1,3],follow:[2,3],form:3,fr:[1,2],free:1,frequenc:3,frequenti:3,frequentist:3,from:[2,3],g:3,galiota_branch:2,gener:3,get:1,get_observation_funct:3,git:[1,2],gitlab:[1,2],gl:3,gls_vector:3,go:[1,2,3],gr:2,greenlab:3,gsobol:3,handl:3,have:[2,3],helper:3,here:3,hidden:3,how:[0,3],howev:[1,2],http:[1,2],i:[2,3],imperfect:3,implement:[1,3],includ:2,incorpor:3,indic:[1,2,3],influenc:3,inform:3,input:3,input_output:3,insid:3,instal:1,installation_guid:0,instead:3,interpret:3,interv:3,ip:3,itselft:3,jl:3,julia:[0,1,2],julia_vers:[1,2],juno:2,just:[1,3],keep:3,kei:2,kf:3,kind:3,knowledg:3,known:3,label:3,labellist:3,last:[],later:3,launch:3,layout:2,let:[1,3],lign:3,like:[1,2,3],limit:3,line:[1,2,3],list:3,ll_det:3,ll_sto:3,lna:3,load:3,load_control:3,load_from_ob:3,load_local_model:3,load_model:3,load_paramet:3,load_stat:3,local:[1,2],locat:[2,3],lognorm:3,m:1,macro:3,mail:[],main:3,make:1,manual:3,markov:3,master:2,math:3,mcmc:3,mcmc_abc:3,mcmc_simplifi:3,mean:3,measur:3,memori:3,messag:1,meta:3,method:3,mic:2,might:2,mn:3,mn_:3,model:0,modelis:3,modellingnois:3,modifi:1,mont:3,more:[1,3],multiindex:3,multipl:[2,3],must:[2,3],mutabl:3,n:3,name:[1,3],natur:3,nbr_arg:3,necessari:3,need:[1,2,3],next:[2,3],nois:3,noisi:3,normal:3,notat:3,note:[2,3],noth:3,now:[1,2,3],number:3,o:3,ob:3,object:3,obs_tc_field_name_observ:3,obs_tc_field_name_observed1:3,obs_tc_field_name_observed2:3,observ:3,observation_funct:3,observation_nois:3,observationnois:3,observationtuplelist:3,observermodel:3,ofl:3,ol:3,om1:3,om2:3,om3:3,om:3,oml:3,on_:3,onc:3,one:[2,3],ones:3,onli:[1,3],open:[1,2,3],option:[2,3],optionn:3,order:3,organis:0,origin:[1,2],other:3,otherwis:3,otll:3,our:3,own:3,p:3,packag:[0,1,2,3],parallel_abc:3,paramet:[0,3],pars:3,part:3,particl:3,pass:3,past:2,path:2,path_to_adjustin:2,path_to_julia:2,phenomenon:3,pkg:[1,2],plot:3,pmmh:3,possibl:[1,3],preexist:3,press:[2,3],previou:1,print:3,prior:3,probability_density_funct:3,probabl:3,problem:2,process:3,project:[1,2],properli:2,push:1,put:3,pygmalion:3,quickli:1,random:3,readm:3,recognis:1,recov:[2,3],rememb:2,repl:2,replac:1,repositori:0,repres:3,research:[1,2],result:3,retriev:3,revis:1,right:1,rn:3,root:1,s:[1,2,3],same:[1,2,3],sampl:3,save:3,save_to_ob:3,saw:3,section:[1,3],see:[1,2,3],seen:[1,3],select:3,sens:3,sensitivity_analysi:[0,3],sequenti:3,set:[2,3],should:[2,3],simpli:1,simul:[0,3],sir:3,slightli:2,smc:3,smc_abc:3,smoothli:1,so:[1,2,3],so_:3,so_exp:3,sobol:3,sobol_gl:3,specif:[2,3],src:3,stand:3,standard:3,start:3,state:3,statist:3,statu:2,step:[1,2,3],sto:3,stochast:3,store:[2,3],str_c:3,str_d:3,str_dir:3,str_m:3,str_p:3,str_x:3,string:3,struct:3,studi:3,system:3,system_observ:3,systemobserv:3,t1:3,t2:3,t:[1,3],take:3,tc_:3,tc_algo_estim:3,tc_algo_sensitivity_analysi:3,tc_controle_file_nam:3,tc_field_name_det:3,tc_field_name_observ:3,tc_field_name_observed1:3,tc_field_name_observed2:3,tc_field_name_sto:3,tc_fieldc1:3,tc_fieldc2:3,tc_fieldm1:3,tc_fieldm2:3,tc_fieldp1:3,tc_fieldp2:3,tc_fields1:3,tc_int:3,tc_int_param_noise_1:3,tc_int_param_noise_2:3,tc_kind:3,tc_model_nam:3,tc_model_name_vers:3,tc_observation_file_nam:3,tc_parameters_file_nam:3,tc_results_part_of_file_nam:3,tc_state_file_nam:3,tc_string_kind:3,tc_type_field_name_observ:3,tc_type_field_name_sto:3,tc_type_fieldc1:3,tc_type_fieldc2:3,tc_type_fieldm1:3,tc_type_fieldm2:3,tc_type_fieldp1:3,tc_type_fieldp2:3,tc_type_fields1:3,tc_what_you_want_to_sav:3,term:3,termin:2,than:3,thank:3,thei:[2,3],them:[2,3],theta:3,theta_:3,thi:[0,1,2,3],those:3,thrown:3,thu:[2,3],time:[2,3],timelin:3,timestep:3,tip:1,titl:3,tmax:3,tml:3,tn:3,toml:2,transit:3,tupl:3,two:3,type:3,u:3,u_:3,uber:2,ui:2,ukf:3,uniform:3,until:1,up:[1,2],us:[0,1,3],user:2,usual:3,v1:2,valu:3,variabl:3,variou:3,vector:3,version:2,vl:3,wa:2,wai:3,want:[1,2,3],we:3,were:[1,3],what:[2,3],when:[1,2,3],where:[2,3],which:[0,2,3],whole:[1,3],witch:3,wl:3,word:3,work:[1,2],workaround:1,would:2,writ:2,write:[2,3],x0:3,x:3,x_:3,x_t1_om1:3,x_t1_om2:3,x_t1_om3:3,x_t2_om1:3,x_t2_om2:3,x_t2_om3:3,x_tn_om1:3,x_tn_om2:3,x_tn_om3:3,xn:3,xnplus1:3,y:3,y_:3,you:[1,2,3],your:[1,2],your_app_her:3,your_branch_nam:1,your_model:3},titles:["Welcome to Adjustin\u2019s documentation!","Developper guide","Installation guide","User guide"],titleterms:{"function":3,"try":3,ad:3,add:1,adjustin:[0,2,3],algorithm:[1,3],applic:[2,3],detail:3,develop:2,developp:[0,1],document:0,exampl:3,framework:3,fucntion:1,guid:[0,1,2,3],instal:[0,2],mathemat:3,model:[1,3],nois:1,onli:2,out:3,probabl:1,s:0,simul:1,structur:3,templat:3,test:3,understand:3,us:2,user:[0,3],welcom:0,work:3,workflow:1,your:3}})
\ No newline at end of file