--------------------------------------- lines 6-291 of file: xrst/glossary.xrst --------------------------------------- {xrst_begin glossary} {xrst_spell avgint dage dtime init meas mtall mtexcess mtother mtspecific mtstandard nslist pini sincidence smoothings tprevalence } Glossary ######## chi *** The model rate for excess mortality as a function of age and time. This is also denoted by :math:`\chi(a, t)`. child jobs ********** #. If :ref:`option_all_table@refit_split` is false, there is one child job for each child node of the current :ref:`glossary@fit_node` . #. If :ref:`option_all_table@refit_split` is true, and the current fit_node is **not** in the :ref:`node_split_table-name` , there is one child job for each child node of the current :ref:`glossary@fit_node` . #. If :ref:`option_all_table@refit_split` is true, and the current fit_node is in the :ref:`node_split_table-name` , the child jobs have the same fit_node and there is one job for each :ref:`split_reference_table@split_reference_value` that is not equal to the current job's split_reference value. dage **** The abbreviation *dage* is used for differences of a function value with rest to age values. These are differences and not derivative approximations. dtime ***** The abbreviation *dtime* is used for finite differences of a function value with rest to time values. These are differences and not derivative approximations. eta *** This is an offset in a log transformation; i.e., a mapping of the form :math:`x \rightarrow \log(x + \eta )`. Note that this transformation is finite valued at :math:`x` equal to zero. fit_goal_set ************ This is the set of nodes that we need a fit for. It must be a subset (which could be all) of the :ref:`fit_goal_table-name` . fit_node ******** For a dismod_at database, *fit_node* is the parent node in the dismod_at option table. fit_node_set ************ This is the set of nodes that need to be fit in order to fit the :ref:`glossary@fit_goal_set`. This includes all the nodes between the root node and the goal nodes (including the root node and he goal nodes). fit_database ************ This is a dismod_at database with the following properties: Constant Tables =============== see :ref:`module@at_cascade.constant_table_list`. Option Table ============ The *fit_database* option table is the same as in the *root_database* except for the value of *parent_node_name*. This node is called the fit_node for the database. The value of *parent_node_id* does not appear in the option table. Covariate Table =============== For each :ref:`glossary@Relative Covariate`, the covariate table reference value is the average returned by :ref:`com_cov_reference-name` for this node and split_reference_id. The split covariate reference value is one of the :ref:`split_reference_table@split_reference_value` in the split_reference table. The other columns in the covariate table are the same as in the root_database. Fixed Effects Smoothings ======================== The age and time points corresponding to the smoothing for the parent rates (except omega) and the covariate multipliers are the same as in the *root_database*. In addition, the age and time difference prior corresponding to each age and time point is the same as in the *root_database*. Random Effects Smoothing ======================== The smoothing for the child rate effects (except omega) are the same as in the *root_database*. Rate Table ========== The rate table smoothing for pini must be null or the corresponding smooth_grid entries must use the age_id corresponding to the smallest age in the age table. Integrand Table =============== For the list of rates [ pini, iota, rho, chi ] the corresponding integrand names are [ prevalence, Sincidence, remission, mtexcess ]. If the parent_smooth_id in the rate table for one of these rates is not null, the corresponding integrand name must be in the integrand table. For each value covariate multiplier index *mulcov_id*, the integrand name ``mulcov_``\ *mulcov_id* must be in the integrand table. input_node_database ******************* This is a fit_database with the following extra properties: Input Tables ============ Only the dismod_at input tables are significant in a fit_databases; e.g., an init command should be executed before any other dismod_at commands (except possibly a set command). nslist Table ============ The nslist and nslist_pair tables must be empty. avgint Table ============ The avgint table must be empty. Rate Table ========== The rate table must have null entries for the omega parent and child smoothings. iota **** The model rate for incidence, relative to the susceptible population, as a function of age and time. This is also denoted by :math:`\iota(a, t)`. job *** A job corresponds to one row of the :ref:`create_job_table@job_table`; i.e., one fit node and split_reference_id. The results for a job is its fit and the value priors for its :ref:`glossary@child jobs` ; see :ref:`create_job_table@job_table@start_child_job_id` and *end_child_job_id*\ . meas_noise ********** The abbreviation used for measurement noise covariate multiplier. mtall ***** The abbreviation used for all cause mortality data. mtexcess ******** The abbreviation used for excess mortality data. mtother ******* The abbreviation used for other cause mortality data. mtspecific ********** The abbreviation used for cause specific mortality data. node_name ********* Is the *node_name* for a node in the *root_database* node table. node_split_set ************** This is the set of nodes at which the cascade is split by the value of the splitting covariate. No node in this set can be a descendant (or ancestor) of another node in this set. (Because the splitting can only occur once in the path from the *root_node* to any other node.) ode_integrand ************* The following integrands requires solving the dismod_at ode to model and hence each of them is called an *ode_integrand*: susceptible, withC, prevalence, Tprevalence, mtspecific, mtall, mtstandard. omega ***** The model rate for other cause mortality as a function of age and time. This is also denoted by :math:`\omega(a, t)`. Note that omega a a special rate because it is know ahead of time; see :ref:`omega_all-name` . omega_grid ********** A single age-time grid used for the *omega* constraints. pini **** The initial prevalence as a function of time. If the initial age is zero, time is *t* , and prevalence is *p*, then pini is the function :math:`p(0,t)` . This often referred to as a rate because it can be estimated and is an input to the dismod_at ordinary differential equation, like the other rates in the dismod_at model. prevalence ********** This is the ratio the number of people with the condition divided by the number of people currently alive. rate_value ********** The abbreviation used for rate value covariate multiplier. Relative Covariate ****************** A relative covariate is any covariate that is not an :ref:`absolute covariate` and is not the splitting covariate (which is specified by the :ref:`option_all_table@split_covariate_name`). The reference value for a relative covariate can depend on the node and the value of the splitting covariate. remission ********* The abbreviation used for the remission integrand. This corresponds to a directly measurement of *rho* rho *** The mode rate for remission as a function of age an time. This is also denoted by :math:`\rho(a, t)`. root_node ********* The top level node for this cascade; see :ref:`option_all_table@root_node_name`. root_database ************* This is a dismod_at database where the *root_node* is the parent node in the dismod_at option table. It must satisfy all the conditions for an :ref:`glossary@input_node_database` plus the following: #. The subgroup table must have one row; i.e., there is one subgroup, one group and they correspond to all the nodes. #. The option table must not have an *other_database* or *other_input_table* entry. Sincidence ********** The abbreviation used for the susceptible incidence integrand. This corresponds to a directly measurement of :ref:`glossary@iota`. top_directory ************* Directory where the input data is located. {xrst_end glossary}