NEWS.md

In mrc-ide/threemc: (Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa

threemc 0.1.45

• Update data/datapack_psnu_area_level.RData so that SWZ is modelled at the Tinkundla (level 2), rather than Region (level 1) area level.
• Update data/datapack_psnu_area_level.RData so that MOZ is modelled at area level 3, rather than area level 2.

threemc 0.1.44

• Fill future as well as historical populations in and threemc_fill_downup_populations, to allow for forecasts past 2021.

threemc 0.1.43

• Add on.Load.R function to set spdep::set.ZeroPolicyOption(TRUE). This avoids error whereby shapefiles with areas with no neighbours (e.g. islands) do not result in errors.

threemc 0.1.42

• Add threemc_ppc2 function to implement method from Matt's paper for posterior predictive checks, gives better results than threemc_ppc, particularly for MC coverage. The function code itself still requires tidying up.

threemc 0.1.41

• Use tmb.ad.framework = "TMBad", rather than the default "CppAD". This framework performs sparse hessian compression, which leads to significantly lower memory usage (particularly in the "spike" experienced at the "optimising tape..." optimisation stage) during model fit.

threemc 0.1.40

• Remove dependencies on non-CRAN packages (i.e. naomi), by adding necessary R and C functions from naomi and TMB to the package.

threemc 0.1.39

• Add extensive developer notes to README.md (mostly just as a reminder to myself!)

threemc 0.1.38

• Fix bug in threemc_ppc. Weighted mean is calculated using circ_status and indweight. However, this ignores circ_type. For type %in% c("MMC", "TMC"), need to have circ_status == 0 for all circ_type == "Missing". This does not apply to type == "MC", as we do not need to know circ_type to still count it amongst MC circumcisions.

threec 0.1.37

• In create_shell_dataset, replace missing populations for less granular areas with their respective child areas' populations.

threemc 0.1.36

• Add optional penalised time spline, by specifying a non-null value for the k_dt_time argument of threemc_prepare_model_data.

threemc 0.1.35

• Adds models ("Surv_SpaceAgeTime_ByType_withUnknownType_RW_MMC2" and "Surv_SpaceAgeTime_ByType_withUnknownType_Const_Paed_MMC_RW_MMC2") which use a random walk temporal prior for MMC, but an AR 1 temporal prior for TMC.

threemc 0.1.34

• Version 0.1.27 introduced filling in missing population data in create_shell_dataset; this update decouples this behaviour from this function into a separate internal function fill_downup_populations, and this functionality has been added to threemc_aggregate as well.

threemc 0.1.33

• threemc_ppc rewritten in data.table for significant speed and memory efficicency increase.

threemc 0.1.32

• Add initial introductory vignette.

threemc 0.1.31

• Add TMB model for every iteration of:
• Including a time effect for TMC or not,
• Including a constant peadiatric MMC rate or not, and
• Using a random walk, rather than AR 1 prior Urgent need to functionalise all of this to greatly decrease code complexity and package compilation time.

threemc 0.1.30

• Have verbose output on function progress from threemc_fit_model as default.

threemc 0.1.29

• Can have threemc_fit_model choose mod itself based on parameters in either parameters (for new fits) or fit$par (for re-sampling from fits). Like 0.1.28, this update abstracts model specification from the end user, which involves generally involves setting a global variable mod to a quite "esoteric" model name, such as "Surv_SpaceAgeTime_ByType_withUnknownType_RW2". Instead, the user can simply specify the much more intuitive parameters rw_order and include_tmc to threemc_prepare_model_data, simplifying their experience.

threemc 0.1.28

• new function threemc_initial_pars to abstract initial hyperparameter specification from the end user. In scripts, this section is quite long and ugly and in general can often go wrong due to parameter order etc, so it is best to abstract this functionality. Defaults can still be overridden (e.g. when we want to fit a model with "mapped"/fixed hyperparameters) by specifying the custom_init argument using a named list of parameter values.

threemc 0.1.27

• In prepare_survey_data, fill NA populations for earlier years than we have data for with the earliest known value for each age and area_id.

threemc 0.1.26

• Fix bug in prepare_survey_data whereby surveys not at maximum area level have their area_id columns coerced to NA, when reassiging survey area_level to the specified argument area_level.

threemc 0.1.25

• Add models which include a random effect for time for traditional male circumcision.
• Add inc_time_tmc argument to threemc_prepare_model_data to produce X_time_tmc so we can use these non-constant TMC models.

threemc 0.1.24

• Add function (threemc_oos_pcc) to perform posterior predictive checks with OOS survey estimates, for model validation and comparison.

threemc 0.1.23

• Add function (survey_points_dmmpt2_convert_convention) which can be used to change the age group, circumcision type and column naming conventions used in DMMPT2 and empirical survey circumcision estimates to match those used in threemc aggregations.

threemc 0.1.22

• Add rw_order argument to threemc_prepare_model_data, which allows one to specify a Random Walk temporal process for our temporal prior. Leaving rw_order = NULL uses the default AR 1 temporal prior.

threemc 0.1.21

• Replace loop in aggregate_sample_age_group with method which uses left_join, ~4x faster for SWZ, likely scales much better for larger countries.

threemc 0.1.2

• Conditionals added to produce design matrices when modelling at the country level, where the adjacency matrix will just be a 1x1 matrix with entry 0.

threemc 0.1.1

• Added a NEWS.md file to track changes to the package.
• Change title: (Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa
• Remove wildcard matching (dplyr::any_of(), dplyr::contains()) from survey data set construction.
• Don't reference the space index in the survey data set; only add when merging survey data to the model frame.

mrc-ide/threemc documentation built on Feb. 9, 2024, 5:16 p.m.