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fix age15plus indexing #5

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fix age15plus indexing #5

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jeffeaton
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@jeffeaton
implemented likelihood for age-specific prevalence and mortality
24590d6 
this is somewhat incomplete
@jeffeaton
more efficient version of ageprev() function
baab1e1 
Only calculates the age-specific prevalence for specified array indices.

Should extend to allow specification of age/sex/year indices instead.
@jeffeaton
estimate age-specific incidence rate ratios
b1093c0
@jeffeaton
add fitmod() and specfit method for simfit()
3f6ec38
@jeffeaton
add fastmatch dependency, bump version number
75badae
@jeffeaton
fixed error in fitmod()
b39487c
@jeffeaton
corrected default prior and likelihood functions to this package
cf355d3
@jeffeaton
added projection start year to state-space definition
3a206e1
@jeffeaton
update ageprev() to accept age/sex/time arguments
1e33885
@jeffeaton
add plot functions to package, bump version number to 0.0.4
0f08549
@jeffeaton
updated read_hivproj_X() to extract from PJNZ file, bump version numb…
814e1c9 
…er 0.0.5

Extracts DP file directly from zipped .PJNZ file. Note: not backward
compatible.

Bump version to 0.0.5
@jeffeaton
add methods for generics to calculate outputs from species
a197aca
@jeffeaton
implemented binomial likelihood for age-specific prevalence
04f5c34
@jeffeaton
fixed bug in deff approximation data preparation
5ad6fc1
@jeffeaton
fixed bug in control flow statement for choosing age-prevalence likel…
25c4c3c 
…ihood
@jeffeaton
bug fixes to reading Spectrum results
bd5aa3d 
- add DP$ to avoid reading DPP files
- fix total pop size parsing to handle Spectrum files with Urban/Rural
populations
- add function for calculating AIDS death rate
@jeffeaton
added default parameters for subfertility by stage
4c8e9a6
@jeffeaton
added piecewise linear incidence rate ratio
7fdfea8
@jeffeaton
corrected to use control-flow version of logical operator (&&)
c7fb5ad
@jeffeaton
implement shifted lognormal age-IRR
b467618
@jeffeaton
add an optional third model fit to plot_agefit()
5a4b186
@jeffeaton
add prepare_national_fit() to package
99fae62
@jeffeaton
Merge branch 'linear-incrr' into dev
c53d097
@jeffeaton
add some mortality calculation functions
bab029b
@jeffeaton
Merge branch 'master' into dev
01fa686 
# Conflicts:
#	DESCRIPTION
#	R/fit-model.R
#	R/read-spectrum-files.R
@jeffeaton
Merge branch 'incid' into dev
c2351ae 
# Conflicts:
#	DESCRIPTION
#	R/fit-model.R
#	R/read-spectrum-files.R
@jeffeaton
Merge branch 'master' into dev
4c31af1
@jeffeaton
Merge branch 'dev' into allcausemx
4cf6911
@jeffeaton
Merge branch 'master' into dev
a4772b5
@jeffeaton
Merge branch 'master' into allcausemx
684e217
jeffeaton added 30 commits October 6, 2017 11:30
@jeffeaton
Add optimization option to fitmod()
44844d2
@jeffeaton
fit model without and site-level ANC data
3275dc3
@jeffeaton
Merge branch 'no-anc' into dev
5010805
@jeffeaton
Merge branch 'dev' into r-hybrid
0737921 
# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/fit-model.R
#	R/likelihood.R
@jeffeaton
modularize code for calculating new infections
5ed566f
@jeffeaton
implement sex-specific transmission rate
662f545
@jeffeaton
implement effect of CD4 stage on contact rate
482faf1
@jeffeaton
implement model fitting for simpletransm model
0323701
@jeffeaton
bug fix to create_spectrum_fixpar()
50b3c03
@jeffeaton
Merge branch 'r-hybrid' into transmission
72c8a00 
# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/spectrum.R
#	src/spectrum.cpp
@jeffeaton
bug fix in extend_projection() if no prior_args specified
0a4b703
@jeffeaton
Implement age 15 entrant prevalence and ART coverage inputs.
a5a945c
@jeffeaton
update r-hybrid model to use classic r-spline (not log o-spline)
66f35dd
@jeffeaton
update plot functions to plot age-standardized prevalence
f3e5b79
@jeffeaton
add age-specific incidence function
269c633
@jeffeaton
logit transformation of logiota parameter uniform prior.
589000d 
To map to range (-Inf, Inf), should help optimization failures.  Have
moved code to functions in rt-models.R
@jeffeaton
preliminary implementation of age-specific exposure model
de78f52
@jeffeaton
bug fix to create_spectrum_fixpar()
65e3c94
@jeffeaton
Merge branch 'r-hybrid' into sexbehav
6381b5b 
# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/likelihood.R
#	R/rt-models.R
@jeffeaton
all M:F transmission rate to change over time
8d2b486
@jeffeaton
implement piecewise constant time-varying IRRs
f6a9cb8
@jeffeaton
add cubic-spline interpolation of log age IRRs
5e57cdd 
This is not very good and needs more work…
@jeffeaton
add functions to calculate age-specific number of new infections and …
0201f13 
…ART coverage
@jeffeaton
add new summary output functions and plot functions
64dd5d5 
Note: plot functions and estci2() are duplicative and need to be tidied.
@jeffeaton
bug fix: prior for piecewise-linear varying IRRs (commit f6a9cb8)
5f15d50
@jeffeaton
Updated default IRR priors to informative priors based on fits to cou…
c5bd7ab 
…ntries with 3+ surveys.
@jeffeaton
Merge branch 'sexbehav' into r-hybrid
1126188
@jeffeaton
Merge branch 'r-hybrid' into dev
2daff80
@jeffeaton
bug fix: indexing for age 15 plus population
629eeda
@jeffeaton
implement annual incidence input option
3afabcb
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@jeffeaton