Set the parameters for FPsim, specifically for Senegal.
- data2interp(data, ages, normalize=False)¶
Convert unevenly spaced data into an even spline interpolation
Data files for use with calibration, etc – not needed for running a sim
Starting age bin, male population, female population
Age-dependent mortality rates, Senegal specific from 1990-1995 – see age_dependent_mortality.py in the fp_analyses repository Mortality rate trend from crude mortality rate per 1000 people: https://data.worldbank.org/indicator/SP.DYN.CDRT.IN?locations=SN
Risk of maternal death assessed at each pregnancy. Data from Huchon et al. (2013) prospective study on risk of maternal death in Senegal and Mali. Maternal deaths: The annual number of female deaths from any cause related to or aggravated by pregnancy or its management (excluding accidental or incidental causes) during pregnancy and childbirth or within 42 days of termination of pregnancy, irrespective of the duration and site of the pregnancy, expressed per 100,000 live births, for a specified time period.
From World Bank indicators for infant morality (< 1 year) for Senegal, per 1000 live births From API_SP.DYN.IMRT.IN_DS2_en_excel_v2_1495452.numbers Adolescent increased risk of infant mortality gradient taken from Noori et al for Sub-Saharan African from 2014-2018. Odds ratios with age 23-25 as reference group: https://www.medrxiv.org/content/10.1101/2021.06.10.21258227v1
Returns a linear interpolation of the likelihood of a miscarriage by age, taken from data from Magnus et al BMJ 2019: https://pubmed.ncbi.nlm.nih.gov/30894356/ Data to be fed into likelihood of continuing a pregnancy once initialized in model Age 0 and 5 set at 100% likelihood. Age 10 imputed to be symmetrical with probability at age 45 for a parabolic curve
From Report of the UN Inter-agency Group for Child Mortality Estimation, 2020 https://childmortality.org/wp-content/uploads/2020/10/UN-IGME-2020-Stillbirth-Report.pdf
Age adjustments come from an extension of Noori et al., which were conducted June 2022.
Use fecundity rates from PRESTO study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712257/ Fecundity rate assumed to be approximately linear from onset of fecundity around age 10 (average age of menses 12.5) to first data point at age 20 45-50 age bin estimated at 0.10 of fecundity of 25-27 yr olds, based on fertility rates from Senegal
Returns an array of fecundity ratios for a nulliparous woman vs a gravid woman from PRESTO study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712257/ Approximates primary infertility and its increasing likelihood if a woman has never conceived by age
Returns an array of the percent of breastfeeding women by month postpartum 0-11 months who meet criteria for LAM: Exclusively breastfeeding (bf + water alone), menses have not returned. Extended out 5-11 months to better match data as those women continue to be postpartum insusceptible. From DHS Senegal calendar data
Returns a linear interpolation of rates of female sexual activity, defined as percentage women who have had sex within the last four weeks. From STAT Compiler DHS https://www.statcompiler.com/en/ Using indicator “Timing of sexual intercourse” Includes women who have had sex “within the last four weeks” Excludes women who answer “never had sex”, probabilities are only applied to agents who have sexually debuted Data taken from 2018 DHS, no trend over years for now Onset of sexual activity probabilities assumed to be linear from age 10 to first data point at age 15
Returns an array of monthly likelihood of having resumed sexual activity within 0-35 months postpartum Uses DHS Senegal 2018 individual recode (postpartum (v222), months since last birth, and sexual activity within 30 days. Limited to 35 months postpartum (can use any limit you want 0-35 max) Postpartum month 0 refers to the first month after delivery
Returns an array of weighted probabilities of sexual debut by a certain age 10-45. Data taken from DHS variable v531 (imputed age of sexual debut, imputed with data from age at first union) Use sexual_debut_age_probs.py under fp_analyses/data to output for other DHS countries
Returns an array of experimental factors to be applied to account for residual exposure to either pregnancy or live birth by age. Exposure to pregnancy will increase factor number and residual likelihood of avoiding live birth (mostly abortion, also miscarriage), will decrease factor number
Returns an array of experimental factors to be applied to account for residual exposure to either pregnancy or live birth by parity.
Returns an array of birth spacing preferences by closest postpartum month. Applied to postpartum pregnancy likelihoods.
NOTE: spacing bins must be uniform!
Names, indices, modern/traditional flag, and efficacies of contraceptive methods – see also parameters.py Efficacy from Guttmacher, fp_prerelease/docs/gates_review/contraceptive-failure-rates-in-developing-world_1.pdf BTL failure rate from general published data Pooled efficacy rates for all women in this study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4970461/
Define “raw” (un-normalized, un-trended) matrices to give transitional probabilities from 2018 DHS Senegal contraceptive calendar data.
Probabilities in this function are annual probabilities of initiating (top row), discontinuing (first column), continuing (diagonal), or switching methods (all other entries).
Probabilities at postpartum month 1 are 1 month transitional probabilities for starting a method after delivery.
Probabilities at postpartum month 6 are 5 month transitional probabilities for starting or changing methods over the first 6 months postpartum.
Data from Senegal DHS contraceptive calendars, 2017 and 2018 combined
Reasons for nonuse – taken from DHS
Take all parameters and construct into a dictionary