diff --git a/docs/source/models/concept_models/vivarium_nutrition_optimization_extension/concept_model.rst b/docs/source/models/concept_models/vivarium_nutrition_optimization_extension/concept_model.rst index f85a69f6e9..de38c46fab 100644 --- a/docs/source/models/concept_models/vivarium_nutrition_optimization_extension/concept_model.rst +++ b/docs/source/models/concept_models/vivarium_nutrition_optimization_extension/concept_model.rst @@ -47,7 +47,6 @@ Artifact-only updates (data updates to come): Components that need to be altered to support new wasting state (more details to come): - :ref:`Child underweight risk exposure <2020_risk_exposure_child_underweight>`: exposure lookup table needs to support additional wasting state (apply existing cat1 values to both cat1_complicated and cat1_uncomplicated) -- :ref:`Effect of birthweight on wasting (see initialization section) <2021_risk_exposure_wasting_state_exposure>`: needs to support additional wasting state - :ref:`CGF risk effects <2019_risk_effect_wasting>`: EMRs for all SAM states set to zero Components with substantial updates (links/updates to come) @@ -58,8 +57,8 @@ Components with substantial updates (links/updates to come) - Transition rates, see `relevant changes to modeling strategy in this PR `__. Data values for transition rates still to come as of 4/15/2026 - SAM treatment for complicated SAM -- Protein energy malnutrition/mortality attributable to child wasting -- Mortality due to other causes +- :ref:`Child wasting state-specific mortality and morbidity <2021_pem_inpatient_sam_extension>` +- Mortality due to other causes: set to zero for this simulation (all mortality will be captured in the :ref:`Child wasting state-specific mortality and morbidity <2021_pem_inpatient_sam_extension>` modeling strategy) .. _nutrition_optimization_extension2.2: diff --git a/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021/index.rst b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021/index.rst new file mode 100644 index 0000000000..d2a273ad48 --- /dev/null +++ b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021/index.rst @@ -0,0 +1,470 @@ +.. role:: underline + :class: underline + + + +.. + Section title decorators for this document: + + ============== + Document Title + ============== + + Section Level 1 (#.0) + +++++++++++++++++++++ + + Section Level 2 (#.#) + --------------------- + + Section Level 3 (#.#.#) + ~~~~~~~~~~~~~~~~~~~~~~~ + + Section Level 4 + ^^^^^^^^^^^^^^^ + + Section Level 5 + ''''''''''''''' + + The depth of each section level is determined by the order in which each + decorator is encountered below. If you need an even deeper section level, just + choose a new decorator symbol from the list here: + https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#sections + And then add it to the list of decorators above. + + + +.. _2021_pem: + +=============================================================== +2021 Protein energy malnutrition risk-attributable cause model +=============================================================== + +.. contents:: + :local: + +Overview +++++++++ + +This page contains information pertaining to the 2021 protein energy malnutrition (PEM) +risk-attributable cause model. The PEM cause model is 100% attributable to the +child wasting risk factor. The child wasting risk exposure document for the +:ref:`nutrition optimization simulation <2021_concept_model_vivarium_nutrition_optimization>` +can be :ref:`found here<2021_risk_exposure_wasting_state_exposure>`. + +.. note:: + + For information on the background of PEM and child wasting, see the + :ref:`2020 joint risk-cause model for wasting and PEM <2020_risk_exposure_wasting_state_exposure>`. + ++-------------------------------------------------+ +| List of abbreviations | ++=======+=========================================+ +| AM | Acute malnutrition | ++-------+-----------------------------------------+ +| MAM | Moderate acute malnutrtion | ++-------+-----------------------------------------+ +| SAM | Severe acute malnutrition | ++-------+-----------------------------------------+ +| TMREL | Theoretical minimum risk exposure level | ++-------+-----------------------------------------+ +| CGF | Child growth failure composed of wasting| +| | stunging and underweight | ++-------+-----------------------------------------+ +| PEM | Protein energy malnutrition | ++-------+-----------------------------------------+ + +Protein Energy Malnutrition in GBD 2019/2021 +++++++++++++++++++++++++++++++++++++++++++++ + +PEM is responsible for both fatal and nonfatal outcomes within the GBD +framework. GBD maintains a cause of death model called "Nutritional +deficiencies" that is split into *PEM* and *Other Nutritional Deficiencies* that +estimates PEM mortality. Nonfatal PEM cases are modelled independently, using +the case definition moderate and severe acute malnutrition, defined in terms of +weight-for-height Z-scores (WHZ). All PEM cases are attributed to the +:ref:`GBD Child Growth Failure risk factor `. +We include specifics on +the PEM cause models below. [GBD-2019-Capstone-Appendix-Wasting]_, p789. + +PEM Fatal Model +--------------- + +GBD runs a parent CODEm model to estimate deaths attributable to nutritional +deficiency, using vital registration and verbal autopsy data as inputs. The +applicable ICD codes are as follows: [GBD-2019-Capstone-Appendix-Wasting]_ + +.. list-table:: PEM CoD ICD-10 Codes + :widths: 10 20 + :header-rows: 1 + + * - GBD Cause + - ICD-10 Code + * - Protein-energy malnutrition + - E40-E46.9 (Kwashiorkor, marasmus, specified and unspecified proteincalorie malnutrition) + * - Other nutritional deficiencies + - D51-D52.0 (vitamin B12 deficiency anaemia and folate deficiency anaemia) + * - Other nutritional deficiencies + - D52.8-D53.9 (other nutritional anaemias) + * - Other nutritional deficiencies + - D64.3 (other sideroblastic anaemias) + * - Other nutritional deficiencies + - E51-E61.9 (thiamine, niacin, other B group vitamins, ascorbic acid, vitamin D, other vitamin, dietary calcium, dietary selenium, dietary zinc, and other nutrient element deficiencies) + * - Other nutritional deficiencies + - E63-E64.0 (other nutritional deficiencies and sequelae of protein-calorie malnutrition) + * - Other nutritional deficiencies + - E64.2-E64.9 (sequelae of vitamin C deficiency, rickets, other nutritional deficiencies, and unspecified nutritional deficiencies) + * - Other nutritional deficiencies + - M12.1-M12.19 (Kashin-Beck disease) + * - Garbage code + - D50, D50.0 and D50.9 (unspecified anaemia) + +They then run (1) an under-5 PEM model, (2) a 5-and-over PEM model, and (3) an +other nutritional deficiencies model. These models are scaled using CODCorrect +to fit the parent nutritional deficiency model. [GBD-2019-Capstone-Appendix-Wasting]_ + +Note that as PEM is defined as "a lack of dietary protein and/or energy", it +includes famines and severe droughts. These result in discontinuities in PEM +estimation, which the GBD team accounts for. The appendix specifically mentions +using the Tombstone report to estimate deaths due to the famine during the Great +Leap Forward in the 1960s in China. [GBD-2019-Capstone-Appendix-Wasting]_ + +PEM Nonfatal Model +------------------ +GBD's nonfatal PEM model takes as its case definition "moderate and severe acute +malnutrition", defined in terms of distance from the mean WHZ score given by the +WHO 2006 growth standard for children. The relevant ICD 10 codes are E40-E46.9, +E64.0, and ICD 9 codes are 260-263.9. PEM is partitioned into the following four +sequelae: [GBD-2019-Capstone-Appendix-Wasting]_ + +.. list-table:: Nonfatal PEM Sequelae 2019/2021 + :widths: 10 15 15 15 + :header-rows: 1 + + * - Sequela Name + - WHZ range + - Clinical description + - Disability weights + * - Moderate wasting without oedema + - {WHZ_i | -3SD < WHZ_i < -2SD} + - Asymptomatic + - NA + * - Moderate wasting with oedema + - {WHZ_i | -3SD < WHZ_i < -2SD} + - Is very tired and irritable and has diarrhoea + - 0.051 (0.031–0.079) + * - Severe wasting without oedema + - {WHZ_i | WHZ_i < -3SD} + - Is extremely skinny and has no energy. + - 0.128 (0.082–0.183) + * - Severe wasting with oedema + - {WHZ_i | WHZ_i < -3SD} + - Is very tired and irritable and has diarrhoea. Is extremely skinny and has no energy. + - 0.051 (0.031–0.079); 0.128 (0.082–0.183). Applied multiplicatively. + +These are mapped onto clinically-defined wasting states as follows: + +.. list-table:: Clinical definitions 2019/2021 + :widths: 5 10 + :header-rows: 1 + + * - Condition + - Estimated by GBD sequelae + * - Kwashiorkor + - {Moderate wasting with oedema} + {Severe wasting with oedema} + * - Marasmus + - {Severe wasting without oedema} + {Severe wasting with oedema} + +The above table represents GBD definitions. In the literature these definitions +are highly debated, often defining marasmus as strictly "severe wasting without +oedema". + +The nonfatal estimation pipeline comprises five models: + +.. list-table:: Nonfatal PEM sub-models 2019/2021 + :widths: 15 5 5 + :header-rows: 1 + + * - Modeled entity + - Age + - Modeling software + * - Prevalence of WHZ <-2SD + - under-5 + - STGPR + * - Prevalence of WHZ <-3SD + - under-5 + - STGPR + * - Proportion of WHZ <-2SD with oedema + - under-5 + - DisMod + * - Proportion of WHZ <-3SD with oedema + - under-5 + - DisMod + * - All WHZ <-2SD (PEM) + - All ages + - DisMod + +For the all-age model, they set the duration of PEM to 9 months after consulting +with nutrition experts. The current modelers (as of June 2021 no longer have +documentation of these conversations, which took place sometime before 2015). +They used a remission rate of 0.25 - 1.25 remitted cases of PEM per person-year +of illness. Note this is a rather wide interval that allowed DisMod to choose a +remission rate within the given bounds based on other input data. +[GBD-2019-Capstone-Appendix-Wasting]_ + +From the all-age model, they then derived (1) a prevalence:incidence ratio that +was applied across all categories of non-fatal PEM, and (2) a moderate:severe +wasting ratio for both under and over 5. [GBD-2019-Capstone-Appendix-Wasting]_ + +The modelers then assumed that there is zero prevalence of oedema in anyone over +5. [GBD-2019-Capstone-Appendix-Wasting]_ + +Additionally, they calculated the fraction of wasting attributable to severe +worm infestation and subtracted this out of all wasting, attributing the +remainder to PEM. They assumed no oedema due to worms, and the +prevalence:incidence ratio derived from the all-age PEM model. [GBD-2019-Capstone-Appendix-Wasting]_ + +The modelers used child anthropometry data from health surveys, literature, +and national reports, from which they estimate the WHZ SDs that correspond with +the case definitions. They additionally used SMART datasets to estimate the +proportion under 5 with oedema. In the GBD 2019 Appendix, they note, "Future +work in systematically evaluating longitudinal datasets on nutrition and growth +failure will allow us to improve the empirical basis for PEM incidence +estimates, including improved resolution for the component +categories." [GBD-2019-Capstone-Appendix-Wasting]_ + +Cause Hierarchy +--------------- + +.. image:: pem_cause_hierarchy.svg + +Vivarium Modeling Strategy +++++++++++++++++++++++++++ + +.. list-table:: PEM parameters + :widths: 5 10 10 20 + :header-rows: 1 + + * - State + - Measure + - Value + - Notes + * - Wasting exposure cat2 (MAM) + - disability weight + - :math:`\frac{{\sum_{sequelae\in \text{MAM}}} \scriptstyle{\text{disability_weight}_s \times\ \text{prevalence}_s}}{{\sum_{sequelae\in xt{MAM}} \scriptstyle{\text{prevalence}_s}}}` + - disability weight for MAM + * - Wasting exposure cat1 (SAM) + - disability weight + - :math:`\frac{{\sum_{sequelae\in \text{SAM}}} \scriptstyle{\text{disability_weight}_s \times\ \text{prevalence}_s}}{{\sum_{sequelae\in \text{SAM}} \scriptstyle{\text{prevalence}_s}}}` + - disability weight for SAM + * - Wasting exposure cat3 and cat4 + - disability weight + - 0 + - No disability in wasting cat3 or cat4 + * - Wasting exposure cat1 and cat2 (SAM and MAM) + - excess mortality + - :math:`\frac{\text{deaths_c387}}{\text{population} \times \text{prevalence_c387}}` + - death counts come from codcorrect + * - wasting exposure cat3 and cat4 + - excess mortality rate + - 0 + - No PEM deaths in wasting cat3 or cat4 + * - All + - cause specific mortality + - :math:`\frac{\text{deaths_c387}}{\text{population}}` + - death counts come from codcorrect + +.. todo:: + + Determine the status of GBD 2021 PEM model and decide how to proceed. Remember that CIFF implementation used 2019 version. + +.. note:: + + The 2020 Codcorrect model for PEM is not yet completed. Check here on central machinary to see latest codcorrect modeling. + https://hub.ihme.washington.edu/pages/viewpage.action?spaceKey=GBD2020&title=GBD+2020+CodCorrect+Tracking + + and here for scheduled finishing time (currently scheduled to complete on july 30th- 12July2021) + https://hub.ihme.washington.edu/pages/viewpage.action?spaceKey=GBD2020&title=GBD+2020+Release+1+Computation + + +The following code can be used to access draw-level deaths for PEM + +.. code-block:: python + + # GBD 2019 (this is the version we will use for PEM for now) + + get_draws(gbd_id_type = 'cause_id', + gbd_id = [387], #pem + source = "codcorrect", + metric_id = 1, #counts + measure_id = 1, #deaths + location_id = [179], + sex_id = [1,2], + age_group_id = [4,5], + gbd_round_id = 6, + year_id =2019, + decomp_step = 'step5') + + + # GBD 2020 (not fully formed) + + get_draws(gbd_id_type = 'cause_id', + gbd_id = [387], #pem + source = "codcorrect", + metric_id = 1, #counts + measure_id = 1, #deaths + location_id = [179], + sex_id = [1,2], + age_group_id = [388,389,238,34], + gbd_round_id = 7, + year_id = 2020, + decomp_step = 'step3', #this is the latest decomp step, will get updated + version_id = 260) #this is the latest version, will get updated + + +.. list-table:: PEM Data Sources and Definitions + :widths: 10 10 20 20 + :header-rows: 1 + + * - Variable + - Source + - Description + - Notes + * - MAM sequelae + - + - {s198, s2033} + - Moderate wasting with eodema, moderate wasting without oedema + * - SAM sequelae + - + - {s2036, s199} + - Severe wasting with eodema, severe wasting without oedema + +.. note:: + + The 2020 Como model for PEM is not yet completed, with only 100 draw. Check here on central machinary to see latest como modeling. + https://hub.ihme.washington.edu/display/GBD2020/COMO+tracking + + +To pull PEM sequelae prevalence, use the following code + +.. code-block:: python + + #GBD 2019 + + get_draws(gbd_id_type = 'sequela_id', + gbd_id = [198,2033,2036,199], + source = "como", + location_id = [179], + sex_id = [1,2], + age_group_id = [2,3,4,5], + gbd_round_id = 6, + decomp_step = 'step5') + + + #GBD 2020 (currently only 100 draws) + + get_draws(gbd_id_type = 'sequela_id', + gbd_id = [198,2033,2036,199], + source = "como", + location_id = [179], + sex_id = [1,2], + age_group_id = [2,3,388,389,238,34], + gbd_round_id = 7, + decomp_step = 'iterative') + + + #as well as from db_queries + + from db_queries import get_sequela_metadata + + hierarchy_2019 = get_sequela_metadata(sequela_set_id=2, gbd_round_id=6, decomp_step="step4") + hierarchy_2019.loc[(hierarchy_2019.cause_id==387)] #2019 + +.. list-table:: PEM Restrictions 2019 + :widths: 10 10 20 + :header-rows: 1 + + * - Restriction type + - Value + - Notes + * - Male only + - False + - + * - Female only + - False + - + * - YLL only + - False + - + * - YLD only + - False + - + * - YLL age group start + - Post Neonatal + - age_group_id = 4 + * - YLL age group end + - 95 plus + - age_group_id = 235 + * - YLD age group start + - Early Neonatal + - age_group_id = 2 + * - YLD age group end + - 95 Plus + - age_group_id = 235 + +.. list-table:: PEM Restrictions 2021 + :widths: 10 10 20 + :header-rows: 1 + + * - Restriction type + - Value + - Notes + * - Male only + - False + - + * - Female only + - False + - + * - YLL only + - False + - + * - YLD only + - False + - + * - YLL age group start + - 1-5 months + - age_group_id = 388 + * - YLL age group end + - 95 plus + - age_group_id = 235 + * - YLD age group start + - Early Neonatal + - age_group_id = 2 + * - YLD age group end + - 95 Plus + - age_group_id = 235 + +.. code-block:: python + + #age group id differences between 2019 and 2021 + + #2021 age ids + early nn = 2 + late nn = 3 + 1m-5m = 388 #2019 it was 4 = postneonatal + 6m-11m = 389 #2019 it was 4 = postneonatal + 12m-23m = 238 #2019 it was 5 = 1-5 + 2y-4y = 34 #2019 it was 5 = 1-5 + +Validation +++++++++++ + +All of the following should match expected values for the PEM model: + + - prevalence + - ylds + - csmr + - emr + +References +++++++++++ + diff --git a/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/pem_cause_hierarchy.svg b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021/pem_cause_hierarchy.svg similarity index 100% rename from docs/source/models/risk_attributable_causes/protein_energy_malnutrition/pem_cause_hierarchy.svg rename to docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021/pem_cause_hierarchy.svg diff --git a/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021_inpatient_sam_extension/index.rst b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021_inpatient_sam_extension/index.rst new file mode 100644 index 0000000000..2d41ed4ce0 --- /dev/null +++ b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021_inpatient_sam_extension/index.rst @@ -0,0 +1,134 @@ +.. role:: underline + :class: underline + + + +.. + Section title decorators for this document: + + ============== + Document Title + ============== + + Section Level 1 (#.0) + +++++++++++++++++++++ + + Section Level 2 (#.#) + --------------------- + + Section Level 3 (#.#.#) + ~~~~~~~~~~~~~~~~~~~~~~~ + + Section Level 4 + ^^^^^^^^^^^^^^^ + + Section Level 5 + ''''''''''''''' + + The depth of each section level is determined by the order in which each + decorator is encountered below. If you need an even deeper section level, just + choose a new decorator symbol from the list here: + https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#sections + And then add it to the list of decorators above. + + + +.. _2021_pem_inpatient_sam_extension: + +========================================================================================================== +2021 Wasting risk-attributable cause model: Extended for modeling Inpatient Treatment of Complicated SAM +========================================================================================================== + +.. contents:: + :local: + +Overview +++++++++ + +This page contains information pertaining to morbidity and mortality directly attributable to the child wasting risk factor. Note that this risk-attributable model has been extended beyond the scope of the :ref:`protein energy malnutrition risk-attributable cause <2021_pem>` used in the :ref:`original nutrition optimization child simulation model <2021_concept_model_vivarium_nutrition_optimization_children>` to support the modeling strategy of inpatient SAM treatment in the :ref:`nutrition optimization inpatient SAM extension simulation model `. This modeling strategy was designed for the specific application in the N.O. inpatient SAM extension model and will not generalize to other use cases. + +Modeling strategy ++++++++++++++++++ + +The following disability weights and excess mortality weights should apply to each wasting exposure state as detailed on the :ref:`wasting risk exposure with complicated SAM model document <2021_risk_exposure_wasting_with_complicated_sam>`. We have suggested cause nomenclature in the table below for consistency with prior implementation, but the choice is arbitrary and we can deviate from it if desired. + +.. list-table:: State data + :header-rows: 1 + + * - Wasting state + - Cause name + - Disability weight + - Excess mortality rate + - Note + * - cat4 (susceptible to child wasting), cat3 (mild childwasting), cat2_better (better MAM), cat2_worse (worse MAM) + - other_protein_energy_malnutrition + - 0 + - daily_probability_to_annual_rate(other_causes_mortality_daily_probability) + - + * - cat1_uncomplicated + - uncomplicated_severe_protein_energy_malnutrition + - DW_uncomplicated_sam + - daily_probability_to_annual_rate(d1_uncomplicated) + - + * - cat1_complicated + - complicated_severe_protein_energy_malnutrition + - DW_severe_wasting_and_oedema + - daily_probability_to_annual_rate(d1_complicated) + - For simplicity, assumed all complicated SAM cases have DW corresponding with severe wasting and oedema + +.. list-table:: Parameter values + :header-rows: 1 + + * - Parameter + - Definition + - Value + - Note + * - DW_severe_wasting + - Disability weight of severe wasting + - 0.128 (0.082–0.183) + - + * - DW_oedema + - Disability weight of oedema + - 0.051 (0.031–0.079) + - + * - prev_s199 + - Prevalence of severe wasting without oedema + - ``get_draws(release_id=9, year_id=2021, gbd_id_type='sequela_id', gbd_id=199, measure_id=5, source='como')`` + - + * - prev_s198 + - Prevalence of moderate wasting with oedema + - ``get_draws(release_id=9, year_id=2021, gbd_id_type='sequela_id', gbd_id=198, measure_id=5, source='como')`` + - + * - DW_uncomplicated_sam + - Overall disability weight of uncomplicated SAM + - DW_severe_wasting * prev_s199 / (prev_s199 + prev_s198) + DW_oedema * prev_s198 / (prev_s199 + prev_s198) + - We make the simplifying assumption that uncomplicated SAM has no cases with concurrent severe wasting and oedema (these cases are assumed to be complicated SAM) and that the ratio of cases with moderate wasting and oedema to cases of severe wasting without oedema within uncomplicated SAM is equal to the ratio of these two sequelae in GBD. + * - DW_severe_wasting_and_oedema + - Disability weight of concurrent severe wasting and oedema + - 1 - (1 - DW_severe_wasting) * (1 - DW_oedema) + - + * - d1_complicated + - Daily probability of mortality in the complicated SAM state + - `See placeholder values here `__ (parameter == 'd1_complicated') + - Represents mortality due to all causes + * - d1_uncomplicated + - Daily probability of mortality in the uncomplicated SAM state + - `See placeholder values here `__ (parameter == 'd1_complicated') + - Represents mortality due to all causes + * - other_causes_mortality_daily_probability + - Daily probability of mortality due to causes other than diarrheal diseases, lower respiratory infections, malaria, or measles + - `See placeholder values here `__ (parameter == 'other_causes_mortality_daily_probability') + - Represents mortality due to causes other than modeled infectious diseases in non-SAM states and mortality experienced in SAM states + +Validation +++++++++++ + +As a validation, YLDs due to the wasting-attributable cause model should be similar in magnitude to YLDs due to PEM. + +As a verification, EMRs of for the wasting-attributable cause model should match input data + +As a verification, ACMR at the population level should match GBD expectation. + +References +++++++++++ + diff --git a/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021_inpatient_sam_extension/pem_cause_hierarchy.svg b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021_inpatient_sam_extension/pem_cause_hierarchy.svg new file mode 100644 index 0000000000..8e464a4039 --- /dev/null +++ b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/gbd_2021_inpatient_sam_extension/pem_cause_hierarchy.svg @@ -0,0 +1,3 @@ + + +
All causes
(c_294)
All causes...
Communicable, maternal, neonatal, and nutritional diseases
(c_295)
Communicable, matern...
Nutritional deficiencies
(c_386)
Nutritional deficien...
Protein-energy malnutrition
(c_387)
Protein-energy malnu...
Other
Other
Moderate wasting with edema
(s_198)
Moderate wasting wit...
Moderate wasting without edema
(s_2033)
Moderate wasting witho...
Severe wasting with edema
(s_2036)
Severe wasting with...
Severe wasting without edema
(s_199)
Severe wasting witho...
Other
Other
Other
OtherViewer does not support full SVG 1.1 \ No newline at end of file diff --git a/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/index.rst b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/index.rst index d2a273ad48..b631ed39c7 100644 --- a/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/index.rst +++ b/docs/source/models/risk_attributable_causes/protein_energy_malnutrition/index.rst @@ -1,470 +1,11 @@ -.. role:: underline - :class: underline +.. _pem_landing_page: +=========================================================== +Wasting-attributable mortality: Protein energy malnutrition +=========================================================== +.. toctree:: + :maxdepth: 1 + :glob: -.. - Section title decorators for this document: - - ============== - Document Title - ============== - - Section Level 1 (#.0) - +++++++++++++++++++++ - - Section Level 2 (#.#) - --------------------- - - Section Level 3 (#.#.#) - ~~~~~~~~~~~~~~~~~~~~~~~ - - Section Level 4 - ^^^^^^^^^^^^^^^ - - Section Level 5 - ''''''''''''''' - - The depth of each section level is determined by the order in which each - decorator is encountered below. If you need an even deeper section level, just - choose a new decorator symbol from the list here: - https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#sections - And then add it to the list of decorators above. - - - -.. _2021_pem: - -=============================================================== -2021 Protein energy malnutrition risk-attributable cause model -=============================================================== - -.. contents:: - :local: - -Overview -++++++++ - -This page contains information pertaining to the 2021 protein energy malnutrition (PEM) -risk-attributable cause model. The PEM cause model is 100% attributable to the -child wasting risk factor. The child wasting risk exposure document for the -:ref:`nutrition optimization simulation <2021_concept_model_vivarium_nutrition_optimization>` -can be :ref:`found here<2021_risk_exposure_wasting_state_exposure>`. - -.. note:: - - For information on the background of PEM and child wasting, see the - :ref:`2020 joint risk-cause model for wasting and PEM <2020_risk_exposure_wasting_state_exposure>`. - -+-------------------------------------------------+ -| List of abbreviations | -+=======+=========================================+ -| AM | Acute malnutrition | -+-------+-----------------------------------------+ -| MAM | Moderate acute malnutrtion | -+-------+-----------------------------------------+ -| SAM | Severe acute malnutrition | -+-------+-----------------------------------------+ -| TMREL | Theoretical minimum risk exposure level | -+-------+-----------------------------------------+ -| CGF | Child growth failure composed of wasting| -| | stunging and underweight | -+-------+-----------------------------------------+ -| PEM | Protein energy malnutrition | -+-------+-----------------------------------------+ - -Protein Energy Malnutrition in GBD 2019/2021 -++++++++++++++++++++++++++++++++++++++++++++ - -PEM is responsible for both fatal and nonfatal outcomes within the GBD -framework. GBD maintains a cause of death model called "Nutritional -deficiencies" that is split into *PEM* and *Other Nutritional Deficiencies* that -estimates PEM mortality. Nonfatal PEM cases are modelled independently, using -the case definition moderate and severe acute malnutrition, defined in terms of -weight-for-height Z-scores (WHZ). All PEM cases are attributed to the -:ref:`GBD Child Growth Failure risk factor `. -We include specifics on -the PEM cause models below. [GBD-2019-Capstone-Appendix-Wasting]_, p789. - -PEM Fatal Model ---------------- - -GBD runs a parent CODEm model to estimate deaths attributable to nutritional -deficiency, using vital registration and verbal autopsy data as inputs. The -applicable ICD codes are as follows: [GBD-2019-Capstone-Appendix-Wasting]_ - -.. list-table:: PEM CoD ICD-10 Codes - :widths: 10 20 - :header-rows: 1 - - * - GBD Cause - - ICD-10 Code - * - Protein-energy malnutrition - - E40-E46.9 (Kwashiorkor, marasmus, specified and unspecified proteincalorie malnutrition) - * - Other nutritional deficiencies - - D51-D52.0 (vitamin B12 deficiency anaemia and folate deficiency anaemia) - * - Other nutritional deficiencies - - D52.8-D53.9 (other nutritional anaemias) - * - Other nutritional deficiencies - - D64.3 (other sideroblastic anaemias) - * - Other nutritional deficiencies - - E51-E61.9 (thiamine, niacin, other B group vitamins, ascorbic acid, vitamin D, other vitamin, dietary calcium, dietary selenium, dietary zinc, and other nutrient element deficiencies) - * - Other nutritional deficiencies - - E63-E64.0 (other nutritional deficiencies and sequelae of protein-calorie malnutrition) - * - Other nutritional deficiencies - - E64.2-E64.9 (sequelae of vitamin C deficiency, rickets, other nutritional deficiencies, and unspecified nutritional deficiencies) - * - Other nutritional deficiencies - - M12.1-M12.19 (Kashin-Beck disease) - * - Garbage code - - D50, D50.0 and D50.9 (unspecified anaemia) - -They then run (1) an under-5 PEM model, (2) a 5-and-over PEM model, and (3) an -other nutritional deficiencies model. These models are scaled using CODCorrect -to fit the parent nutritional deficiency model. [GBD-2019-Capstone-Appendix-Wasting]_ - -Note that as PEM is defined as "a lack of dietary protein and/or energy", it -includes famines and severe droughts. These result in discontinuities in PEM -estimation, which the GBD team accounts for. The appendix specifically mentions -using the Tombstone report to estimate deaths due to the famine during the Great -Leap Forward in the 1960s in China. [GBD-2019-Capstone-Appendix-Wasting]_ - -PEM Nonfatal Model ------------------- -GBD's nonfatal PEM model takes as its case definition "moderate and severe acute -malnutrition", defined in terms of distance from the mean WHZ score given by the -WHO 2006 growth standard for children. The relevant ICD 10 codes are E40-E46.9, -E64.0, and ICD 9 codes are 260-263.9. PEM is partitioned into the following four -sequelae: [GBD-2019-Capstone-Appendix-Wasting]_ - -.. list-table:: Nonfatal PEM Sequelae 2019/2021 - :widths: 10 15 15 15 - :header-rows: 1 - - * - Sequela Name - - WHZ range - - Clinical description - - Disability weights - * - Moderate wasting without oedema - - {WHZ_i | -3SD < WHZ_i < -2SD} - - Asymptomatic - - NA - * - Moderate wasting with oedema - - {WHZ_i | -3SD < WHZ_i < -2SD} - - Is very tired and irritable and has diarrhoea - - 0.051 (0.031–0.079) - * - Severe wasting without oedema - - {WHZ_i | WHZ_i < -3SD} - - Is extremely skinny and has no energy. - - 0.128 (0.082–0.183) - * - Severe wasting with oedema - - {WHZ_i | WHZ_i < -3SD} - - Is very tired and irritable and has diarrhoea. Is extremely skinny and has no energy. - - 0.051 (0.031–0.079); 0.128 (0.082–0.183). Applied multiplicatively. - -These are mapped onto clinically-defined wasting states as follows: - -.. list-table:: Clinical definitions 2019/2021 - :widths: 5 10 - :header-rows: 1 - - * - Condition - - Estimated by GBD sequelae - * - Kwashiorkor - - {Moderate wasting with oedema} + {Severe wasting with oedema} - * - Marasmus - - {Severe wasting without oedema} + {Severe wasting with oedema} - -The above table represents GBD definitions. In the literature these definitions -are highly debated, often defining marasmus as strictly "severe wasting without -oedema". - -The nonfatal estimation pipeline comprises five models: - -.. list-table:: Nonfatal PEM sub-models 2019/2021 - :widths: 15 5 5 - :header-rows: 1 - - * - Modeled entity - - Age - - Modeling software - * - Prevalence of WHZ <-2SD - - under-5 - - STGPR - * - Prevalence of WHZ <-3SD - - under-5 - - STGPR - * - Proportion of WHZ <-2SD with oedema - - under-5 - - DisMod - * - Proportion of WHZ <-3SD with oedema - - under-5 - - DisMod - * - All WHZ <-2SD (PEM) - - All ages - - DisMod - -For the all-age model, they set the duration of PEM to 9 months after consulting -with nutrition experts. The current modelers (as of June 2021 no longer have -documentation of these conversations, which took place sometime before 2015). -They used a remission rate of 0.25 - 1.25 remitted cases of PEM per person-year -of illness. Note this is a rather wide interval that allowed DisMod to choose a -remission rate within the given bounds based on other input data. -[GBD-2019-Capstone-Appendix-Wasting]_ - -From the all-age model, they then derived (1) a prevalence:incidence ratio that -was applied across all categories of non-fatal PEM, and (2) a moderate:severe -wasting ratio for both under and over 5. [GBD-2019-Capstone-Appendix-Wasting]_ - -The modelers then assumed that there is zero prevalence of oedema in anyone over -5. [GBD-2019-Capstone-Appendix-Wasting]_ - -Additionally, they calculated the fraction of wasting attributable to severe -worm infestation and subtracted this out of all wasting, attributing the -remainder to PEM. They assumed no oedema due to worms, and the -prevalence:incidence ratio derived from the all-age PEM model. [GBD-2019-Capstone-Appendix-Wasting]_ - -The modelers used child anthropometry data from health surveys, literature, -and national reports, from which they estimate the WHZ SDs that correspond with -the case definitions. They additionally used SMART datasets to estimate the -proportion under 5 with oedema. In the GBD 2019 Appendix, they note, "Future -work in systematically evaluating longitudinal datasets on nutrition and growth -failure will allow us to improve the empirical basis for PEM incidence -estimates, including improved resolution for the component -categories." [GBD-2019-Capstone-Appendix-Wasting]_ - -Cause Hierarchy ---------------- - -.. image:: pem_cause_hierarchy.svg - -Vivarium Modeling Strategy -++++++++++++++++++++++++++ - -.. list-table:: PEM parameters - :widths: 5 10 10 20 - :header-rows: 1 - - * - State - - Measure - - Value - - Notes - * - Wasting exposure cat2 (MAM) - - disability weight - - :math:`\frac{{\sum_{sequelae\in \text{MAM}}} \scriptstyle{\text{disability_weight}_s \times\ \text{prevalence}_s}}{{\sum_{sequelae\in xt{MAM}} \scriptstyle{\text{prevalence}_s}}}` - - disability weight for MAM - * - Wasting exposure cat1 (SAM) - - disability weight - - :math:`\frac{{\sum_{sequelae\in \text{SAM}}} \scriptstyle{\text{disability_weight}_s \times\ \text{prevalence}_s}}{{\sum_{sequelae\in \text{SAM}} \scriptstyle{\text{prevalence}_s}}}` - - disability weight for SAM - * - Wasting exposure cat3 and cat4 - - disability weight - - 0 - - No disability in wasting cat3 or cat4 - * - Wasting exposure cat1 and cat2 (SAM and MAM) - - excess mortality - - :math:`\frac{\text{deaths_c387}}{\text{population} \times \text{prevalence_c387}}` - - death counts come from codcorrect - * - wasting exposure cat3 and cat4 - - excess mortality rate - - 0 - - No PEM deaths in wasting cat3 or cat4 - * - All - - cause specific mortality - - :math:`\frac{\text{deaths_c387}}{\text{population}}` - - death counts come from codcorrect - -.. todo:: - - Determine the status of GBD 2021 PEM model and decide how to proceed. Remember that CIFF implementation used 2019 version. - -.. note:: - - The 2020 Codcorrect model for PEM is not yet completed. Check here on central machinary to see latest codcorrect modeling. - https://hub.ihme.washington.edu/pages/viewpage.action?spaceKey=GBD2020&title=GBD+2020+CodCorrect+Tracking - - and here for scheduled finishing time (currently scheduled to complete on july 30th- 12July2021) - https://hub.ihme.washington.edu/pages/viewpage.action?spaceKey=GBD2020&title=GBD+2020+Release+1+Computation - - -The following code can be used to access draw-level deaths for PEM - -.. code-block:: python - - # GBD 2019 (this is the version we will use for PEM for now) - - get_draws(gbd_id_type = 'cause_id', - gbd_id = [387], #pem - source = "codcorrect", - metric_id = 1, #counts - measure_id = 1, #deaths - location_id = [179], - sex_id = [1,2], - age_group_id = [4,5], - gbd_round_id = 6, - year_id =2019, - decomp_step = 'step5') - - - # GBD 2020 (not fully formed) - - get_draws(gbd_id_type = 'cause_id', - gbd_id = [387], #pem - source = "codcorrect", - metric_id = 1, #counts - measure_id = 1, #deaths - location_id = [179], - sex_id = [1,2], - age_group_id = [388,389,238,34], - gbd_round_id = 7, - year_id = 2020, - decomp_step = 'step3', #this is the latest decomp step, will get updated - version_id = 260) #this is the latest version, will get updated - - -.. list-table:: PEM Data Sources and Definitions - :widths: 10 10 20 20 - :header-rows: 1 - - * - Variable - - Source - - Description - - Notes - * - MAM sequelae - - - - {s198, s2033} - - Moderate wasting with eodema, moderate wasting without oedema - * - SAM sequelae - - - - {s2036, s199} - - Severe wasting with eodema, severe wasting without oedema - -.. note:: - - The 2020 Como model for PEM is not yet completed, with only 100 draw. Check here on central machinary to see latest como modeling. - https://hub.ihme.washington.edu/display/GBD2020/COMO+tracking - - -To pull PEM sequelae prevalence, use the following code - -.. code-block:: python - - #GBD 2019 - - get_draws(gbd_id_type = 'sequela_id', - gbd_id = [198,2033,2036,199], - source = "como", - location_id = [179], - sex_id = [1,2], - age_group_id = [2,3,4,5], - gbd_round_id = 6, - decomp_step = 'step5') - - - #GBD 2020 (currently only 100 draws) - - get_draws(gbd_id_type = 'sequela_id', - gbd_id = [198,2033,2036,199], - source = "como", - location_id = [179], - sex_id = [1,2], - age_group_id = [2,3,388,389,238,34], - gbd_round_id = 7, - decomp_step = 'iterative') - - - #as well as from db_queries - - from db_queries import get_sequela_metadata - - hierarchy_2019 = get_sequela_metadata(sequela_set_id=2, gbd_round_id=6, decomp_step="step4") - hierarchy_2019.loc[(hierarchy_2019.cause_id==387)] #2019 - -.. list-table:: PEM Restrictions 2019 - :widths: 10 10 20 - :header-rows: 1 - - * - Restriction type - - Value - - Notes - * - Male only - - False - - - * - Female only - - False - - - * - YLL only - - False - - - * - YLD only - - False - - - * - YLL age group start - - Post Neonatal - - age_group_id = 4 - * - YLL age group end - - 95 plus - - age_group_id = 235 - * - YLD age group start - - Early Neonatal - - age_group_id = 2 - * - YLD age group end - - 95 Plus - - age_group_id = 235 - -.. list-table:: PEM Restrictions 2021 - :widths: 10 10 20 - :header-rows: 1 - - * - Restriction type - - Value - - Notes - * - Male only - - False - - - * - Female only - - False - - - * - YLL only - - False - - - * - YLD only - - False - - - * - YLL age group start - - 1-5 months - - age_group_id = 388 - * - YLL age group end - - 95 plus - - age_group_id = 235 - * - YLD age group start - - Early Neonatal - - age_group_id = 2 - * - YLD age group end - - 95 Plus - - age_group_id = 235 - -.. code-block:: python - - #age group id differences between 2019 and 2021 - - #2021 age ids - early nn = 2 - late nn = 3 - 1m-5m = 388 #2019 it was 4 = postneonatal - 6m-11m = 389 #2019 it was 4 = postneonatal - 12m-23m = 238 #2019 it was 5 = 1-5 - 2y-4y = 34 #2019 it was 5 = 1-5 - -Validation -++++++++++ - -All of the following should match expected values for the PEM model: - - - prevalence - - ylds - - csmr - - emr - -References -++++++++++ - + */index