This data describes the long-term population dynamics of seasonal, laboratory populations of Drosophila melanogaster (the common fruit fly) experiencing chronic, multi-generation reductions in habitat. Populations were exposed to habitat loss in either the breeding or non-breeding period (seasonT), and were subject to one of two rates of loss: 10% or 20% per generation (lossT).The data set includes time series of two vital rates and two other intrinsic metrics for each replicate population (repID). Vital rates: log per capita reproductive output (repr), log per capita non-breeding survival (surv). Intrinsic metrics: coefficient of variation (coefvar), lag-1 autocorrelation (autocorr). These values were calculated separately for each replicate using a sliding window of three generations. We also derived a composite of these variable (pc1) using a principal component analysis. presented values are standardized and centred within generation to account for expected divergence of metrics through time. We tested the effect of the season of treatment and generation on reproduction, survival, and reproduction, using separate models for each rate of habitat loss.

This data set contains estimated teen birth rates for age group 15–19 (expressed per 1,000 females aged 15–19) by county and year.

DEFINITIONS

Estimated teen birth rate: Model-based estimates of teen birth rates for age group 15–19 (expressed per 1,000 females aged 15–19) for a specific county and year. Estimated county teen birth rates were obtained using the methods described elsewhere (1,2,3,4). These annual county-level teen birth estimates “borrow strength” across counties and years to generate accurate estimates where data are sparse due to small population size (1,2,3,4). The inferential method uses information—including the estimated teen birth rates from neighboring counties across years and the associated explanatory variables—to provide a stable estimate of the county teen birth rate.
Median teen birth rate: The middle value of the estimated teen birth rates for the age group 15–19 for counties in a state.
Bayesian credible intervals: A range of values within which there is a 95% probability that the actual teen birth rate will fall, based on the observed teen births data and the model.

NOTES

Data on the number of live births for women aged 15–19 years were extracted from the National Center for Health Statistics’ (NCHS) National Vital Statistics System birth data files for 2003–2015 (5).

Population estimates were extracted from the files containing intercensal and postcensal bridged-race population estimates provided by NCHS. For each year, the July population estimates were used, with the exception of the year of the decennial census, 2010, for which the April estimates were used.

Hierarchical Bayesian space–time models were used to generate hierarchical Bayesian estimates of county teen birth rates for each year during 2003–2015 (1,2,3,4).

The Bayesian analogue of the frequentist confidence interval is defined as the Bayesian credible interval. A 100*(1-α)% Bayesian credible interval for an unknown parameter vector θ and observed data vector y is a subset C of parameter space Ф such that
1-α≤P({C│y})=∫p{θ │y}dθ,
where integration is performed over the set and is replaced by summation for discrete components of θ. The probability that θ lies in C given the observed data y is at least (1- α) (6).

County borders in Alaska changed, and new counties were formed and others were merged, during 2003–2015. These changes were reflected in the population files but not in the natality files. For this reason, two counties in Alaska were collapsed so that the birth and population counts were comparable. Additionally, Kalawao County, a remote island county in Hawaii, recorded no births, and census estimates indicated a denominator of 0 (i.e., no females between the ages of 15 and 19 years residing in the county from 2003 through 2015). For this reason, Kalawao County was removed from the analysis. Also , Bedford City, Virginia, was added to Bedford County in 2015 and no longer appears in the mortality file in 2015. For consistency, Bedford City was merged with Bedford County, Virginia, for the entire 2003–2015 period. Final analysis was conducted on 3,137 counties for each year from 2003 through 2015. County boundaries are consistent with the vintage 2005–2007 bridged-race population file geographies (7).

SOURCES

National Center for Health Statistics. Vital statistics data available online, Natality all-county files. Hyattsville, MD. Published annually.

For details about file release and access policy, see NCHS data release and access policy for micro-data and compressed vital statistics files, available from: http://www.cdc.gov/nchs/nvss/dvs_data_release.htm.

For natality public-use files, see vital statistics data available online, available from: https://www.cdc.gov/nchs/data_access/vitalstatsonline.htm.

National Center for Health Statistics. U.S. Census populations with bridged race categories. Estimated population data available. Postcensal and intercensal files. Hyattsville, MD. Released annually.

For population files, see U.S. Census populations with bridged race categories, available from: https://www.cdc.gov/nchs/nvss/bridged_race.htm.

REFERENCES

1. Khan D, Rossen LM, Hamilton B, Dienes E, He Y, Wei R. Spatiotemporal trends in teen birth rates in the USA, 2003–2012. J R Stat Soc A 181(1):35–58. 2017. Available from: http://onlinelibrary.wiley.com/doi/10.1111/rssa.12266/abstract.

2. Khan D, Rossen LM, Hamilton BE, He Y, Wei R, Dienes E. Hot spots, cluster detection and spatial outlier analysis of teen birth rates in the U.S., 2003–2012. Spat Spatiotemporal Epidemiol 21:67–75. 2017. Available from: http://www.sciencedirect.com/science/article/pii/S1877584516300442.

3. Rue H, Martino S, Lindgren F. INLA: Functions which allow to perform a full Bayesian analysis of structured additive models using Integrated Nested Laplace Approximation. R package, version 0.0. 2009.

4. Rue H, Martino S, Chopin N. Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. J R Stat Soc B 71(2):319–92. 2009.

5. Martin JA, Hamilton BE, Osterman MJK, Driscoll AK, Mathews TJ. Births: Final data for 2015. National Vital Statistics Reports; vol 66 no 1. Hyattsville, MD: National Center for Health Statistics. 2017. Available from: https://www.cdc.gov/nchs/data/nvsr/nvsr66/nvsr66_01.pdf (1.9 MB).

6. Carlin BP, Louis TA. Bayesian methods for data analysis. Boca Raton, FL: CRC Press, 2009.

7. National Center for Health Statistics. County geography changes: 1990–2012. Available from: http://www.cdc.gov/nchs/data/nvss/bridged_race/County_Geography_Changes.pdf (39 KB).

This dataset contains model-based county estimates for drug-poisoning mortality.

Deaths are classified using the International Classification of Diseases, Tenth Revision (ICD–10). Drug-poisoning deaths are defined as having ICD–10 underlying cause-of-death codes X40–X44 (unintentional), X60–X64 (suicide), X85 (homicide), or Y10–Y14 (undetermined intent).

Estimates are based on the National Vital Statistics System multiple cause-of-death mortality files (1). Age-adjusted death rates (deaths per 100,000 U.S. standard population for 2000) are calculated using the direct method. Populations used for computing death rates for 2011–2016 are postcensal estimates based on the 2010 U.S. census. Rates for census years are based on populations enumerated in the corresponding censuses. Rates for noncensus years before 2010 are revised using updated intercensal population estimates and may differ from rates previously published.

Death rates for some states and years may be low due to a high number of unresolved pending cases or misclassification of ICD–10 codes for unintentional poisoning as R99, “Other ill-defined and unspecified causes of mortality” (2). For example, this issue is known to affect New Jersey in 2009 and West Virginia in 2005 and 2009 but also may affect other years and other states. Drug poisoning death rates may be underestimated in those instances.

Smoothed county age-adjusted death rates (deaths per 100,000 population) were obtained according to methods described elsewhere (3–5). Briefly, two-stage hierarchical models were used to generate empirical Bayes estimates of county age-adjusted death rates due to drug poisoning for each year. These annual county-level estimates “borrow strength” across counties to generate stable estimates of death rates where data are sparse due to small population size (3,5). Estimates for 1999-2015 have been updated, and may differ slightly from previously published estimates. Differences are expected to be minimal, and may result from different county boundaries used in this release (see below) and from the inclusion of an additional year of data. Previously published estimates can be found here for comparison.(6) Estimates are unavailable for Broomfield County, Colorado, and Denali County, Alaska, before 2003 (7,8). Additionally, Clifton Forge County, Virginia only appears on the mortality files prior to 2003, while Bedford City, Virginia was added to Bedford County in 2015 and no longer appears in the mortality file in 2015. These counties were therefore merged with adjacent counties where necessary to create a consistent set of geographic units across the time period. County boundaries are largely consistent with the vintage 2005-2007 bridged-race population file geographies, with the modifications noted previously (7,8).

REFERENCES 1. National Center for Health Statistics. National Vital Statistics System: Mortality data. Available from: http://www.cdc.gov/nchs/deaths.htm.

1. CDC. CDC Wonder: Underlying cause of death 1999–2016. Available from: http://wonder.cdc.gov/wonder/help/ucd.html.

2. Rossen LM, Khan D, Warner M. Trends and geographic patterns in drug-poisoning death rates in the U.S., 1999–2009. Am J Prev Med 45(6):e19–25. 2013.

3. Rossen LM, Khan D, Warner M. Hot spots in mortality from drug poisoning in the United States, 2007–2009. Health Place 26:14–20. 2014.

4. Rossen LM, Khan D, Hamilton B, Warner M. Spatiotemporal variation in selected health outcomes from the National Vital Statistics System. Presented at: 2015 National Conference on Health Statistics, August 25, 2015, Bethesda, MD. Available from: http://www.cdc.gov/nchs/ppt/nchs2015/Rossen_Tuesday_WhiteOak_BB3.pdf.

5. Rossen LM, Bastian B, Warner M, and Khan D. NCHS – Drug Poisoning Mortality by County: United States, 1999-2015. Available from: https://data.cdc.gov/NCHS/NCHS-Drug-Poisoning-Mortality-by-County-United-Sta/pbkm-d27e.

6. National Center for Health Statistics. County geog

Vital rate sensitivity values for B. tectorum.

Correlation matrices for Sierra Nevada bighorn sheep population vital rates.

Bi-seasonal (breeding, b, and non-breeding, nb) abundances (count) from experimental population of Drosophila melanogaster exposed to chronic season-specific habitat loss. Populations were exposed to habitat loss in either the breeding or non-breeding period (seasonT), and were subject to one of two rates of loss: 10% or 20% per generation (lossT). In addition, a subset of individuals were measured from half of the replicate populations (rep; treat_rep). From each individual, measures of locomotion (activity; crosses) were collected using a Drosophila activity monitor, in which the movements of individual flies are autonomously recorded using infrared light beams. These individuals were then frozen, dried, and weighed (weight). See readme.txt for definitions of variables in both datasets.The abundance data has been used to determine whether populations losing breeding and non-breeding habitat decline in different ways and whether the season of decline is detectable in simple vital rates. By combining the abundance and phenotype data, we explored whether the production of trait-based early warning indicators of population collapse differs between populations losing breeding and non-breeding habitat.

Vital rates and transition probabilities used in the stage-structure model.