-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
0 parents
commit ae7598d
Showing
89 changed files
with
12,387 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| Package: popEpi | ||
| Title: Functions for Epidemiological Analysis using Population Data | ||
| Version: 0.2.1 | ||
| Date: 2015-09-28 | ||
| Author: J Miettinen, M Rantanen, K Seppa, J Pitkaniemi | ||
| Maintainer: Joonas Miettinen <joonas.miettinen@cancer.fi> | ||
| Description: | ||
| Enables computation of various epidemiological statistics where the use of population data such as population counts and hazards is required. Relatively high computation speed achieved by using data.table. | ||
| Depends: R (>= 3.2.0), data.table (>= 1.9.6) | ||
| Imports: Epi | ||
| Suggests: reshape2, methods, testthat, knitr, survival, relsurv, | ||
| ggplot2, mstate, date, splines | ||
| Encoding: UTF-8 | ||
| License: GPL-3 | ||
| LazyData: true | ||
| ByteCompile: true | ||
| VignetteBuilder: knitr | ||
| URL: https://github.com/WetRobot/popEpi | ||
| BugReports: https://github.com/WetRobot/popEpi/issues | ||
| NeedsCompilation: no | ||
| Packaged: 2015-09-29 09:07:04 UTC; joonas.miettinen | ||
| Repository: CRAN | ||
| Date/Publication: 2015-09-29 17:33:23 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| e02a45a7d4abdbf4ef60d864011d6bff *DESCRIPTION | ||
| fb1bbafca31d64a433905682082b5bef *NAMESPACE | ||
| 6a3a30fdb8c5ed218389c979a49a1c98 *NEWS | ||
| d9a4209761357c2c691fed2d1398caab *R/S3_definitions.R | ||
| a8a9c870cd9b8aba7cfe6ec39ee6ceb1 *R/data_document.R | ||
| 8f7ac5cf3463e3db9b9bb9da76f98bb5 *R/lexpand.R | ||
| 2d4193e72b02e7ad9863a041020b0821 *R/ltable.R | ||
| 26d68090a651c4c28011c77d6fa41e21 *R/mean_survival.R | ||
| 32789284f39e55e57a8efbc341041a5b *R/popEpi_package.r | ||
| f010cbd367a0ef22bc30145385097044 *R/relative_poisson.R | ||
| b2030dcc4f4d10161438279d7857c4cf *R/relative_poisson_net_survival.R | ||
| 7535f77cf8db5e9408505efea3f1e79a *R/sir_devaus.R | ||
| 32d980c566c8daddaed8a2c16d93d9e5 *R/splitLexisDT.R | ||
| d2ab1dc64cb48c92b8dea9d1bbf64183 *R/splitMulti.R | ||
| 1a9b2c90a65e35324dde782c30d680dc *R/splitting_utility_functions.R | ||
| 15b1ccf2a975e635657664c4bde73b43 *R/startup_message.R | ||
| d321ef98ac18a42a7ec99bf090dbe765 *R/survival.R | ||
| 8b9544ddb298a1ffecfcda374db8b8ef *R/survival_utility_functions.R | ||
| 8ed4a946d88c1838826bee626e8429fa *R/utility_functions.R | ||
| b5db1606a2ec672ac5fff1cbf75eb552 *README.md | ||
| 3534062550217af539a1421e2f5e24d5 *build/vignette.rds | ||
| e8027dd145a86037f0fdf9b27b6b5f32 *data/ICSS.rdata | ||
| 05088fc20f12cae9637924c134357c08 *data/popmort.rdata | ||
| 240db5fe45bc081c42987c8779724716 *data/sibr.rdata | ||
| f8b6b03a59279d571a94cb823869c395 *data/sire.rdata | ||
| f56f8703273f46cb7dbc041164b5cede *inst/doc/sir.R | ||
| 5522d218ce000974e3417a5e9e29a658 *inst/doc/sir.Rmd | ||
| c444c541fdd08220fb165770ec948c67 *inst/doc/sir.html | ||
| a1705f6ae97dc82a0ec295ba404ff42f *inst/doc/survtab_examples.R | ||
| 08062ec00a4eab7375617141d78977b6 *inst/doc/survtab_examples.Rmd | ||
| ad0a9c5afa59418a53ae38de907f7b3a *inst/doc/survtab_examples.html | ||
| a1d4353f336517ef59e8ea692c5910bc *man/ICSS.Rd | ||
| 6144fcc15ce446dc8bccdea998f4bfd0 *man/RPL.Rd | ||
| fcb19fe4d5bd1be40956f538ba280823 *man/all_names_present.Rd | ||
| 52ab70e115094b5e494a2dc2c6994285 *man/as.data.frame.ratetable.Rd | ||
| 8de48d846b407308b3e15f90641d28dc *man/as.data.table.ratetable.Rd | ||
| c8a040a38e1d7fd0446b3adc20b490bc *man/as.pe.Lexis.Rd | ||
| 847e12de6918163def65b9fe3d1d2582 *man/as.pe.data.table.Rd | ||
| d663dc3743e0418cb70951ad6abfb0d1 *man/as.pe.list.Rd | ||
| 5e9f341f94cd04dd120708a5009218ae *man/cast_simple.Rd | ||
| 42829d16c9f3f03f91ab38c5f5cf6548 *man/cut_bound.Rd | ||
| 63ba72aca0a89f52d9b244ed6ffadfb0 *man/expr.by.cj.Rd | ||
| df810e93be4849fee8da2de2746eebd3 *man/fac2num.Rd | ||
| f3fb56af2d74dbe407fa8aaecad5f4b4 *man/get.yrs.Rd | ||
| 6415eda98b4db9e7f34893c29d191744 *man/is.Date.Rd | ||
| c5f5208842242a05aabd4ade2c7e246e *man/is_leap_year.Rd | ||
| 97a04016dd33f9c5e155d1b47b42dcac *man/lexpand.Rd | ||
| 0e02b914a5702fef2782f27ea2d544d3 *man/lines.survtab.Rd | ||
| 0bd775367dee1ddb45334d8a9745cddd *man/longDF2ratetable.Rd | ||
| 652eff7d52f681aef8e9d6a6377c81cd *man/lower_bound.Rd | ||
| b91d9b7aa8c2465b889ea2f6f1d00427 *man/ltable.Rd | ||
| 7a08c971156f16959d7367c8c2c1d774 *man/na2zero.Rd | ||
| 6b4a22f989434411402a760001b9e5f7 *man/plot.pe.Rd | ||
| ba53fa6494d3e7904fa2d6e5bc34f4ea *man/plot.sir.Rd | ||
| 65434a87353b69f9a5efae9e2d26eccf *man/plot.sirspline.Rd | ||
| 38ada74dfe5545a8ecee153af7752084 *man/plot.survtab.Rd | ||
| df6d6427fb66d5460b354a8e54affaef *man/poisson.ci.Rd | ||
| 74a8ef92e8861a18e54c05e39ac71173 *man/popEpi.Rd | ||
| b6da0257021ef94c8c8d2a79605eb243 *man/popmort.Rd | ||
| 08a542331859972f66304e14dab5d373 *man/print.sir.Rd | ||
| 0da6d437ae44da66ced5af4e5c57fa05 *man/print.sirspline.Rd | ||
| fed55882647f0a6f827d830789c0ce00 *man/relpois.Rd | ||
| f8e4a5a80f04b8fdb2a7caadbd78279a *man/robust_values.Rd | ||
| 0cf79c1c185e50cd06a22c51bfa152b2 *man/rpcurve.Rd | ||
| 3d08b5259262ca9e04e38c1e2b8e66f9 *man/setclass.Rd | ||
| 78df5ea3e388fbf5ea7af581f73136a9 *man/setcolsnull.Rd | ||
| f4c0ba017bfcffdd70c904ee38811b37 *man/shift.var.Rd | ||
| aa2eb48b53a043b1749f4030b22509b8 *man/sibr.Rd | ||
| 9ddfb55ba600f268c553834bb6a19585 *man/sir.Rd | ||
| 69cde2f705d67e9e49973134c3aad050 *man/sire.Rd | ||
| 580e54ea5132b0620928cc90e63c2f8d *man/sirspline.Rd | ||
| 03da80643ec9ad948542ac0da16a0556 *man/splitLexisDT.Rd | ||
| 5d8d9b3305dc3a462dc367ce12a8862c *man/splitMulti.Rd | ||
| 242611e03a2bf5b3e00ed68440558636 *man/survmean.Rd | ||
| 9330aadc1725277ba9aa97328899dfb0 *man/survtab.Rd | ||
| dcf976d0d27bb029070eb0424c469665 *man/try2int.Rd | ||
| 37587c989150e75f7826c248bd58f57e *tests/testthat.R | ||
| fe249f0df8a97e2d888471cd68a649cf *tests/testthat/test_lexpand.R | ||
| a6050860a2f9184fa04211d17a46d426 *tests/testthat/test_mean_survival.R | ||
| 8ab51cf0385a2077ef8559e3ffc57761 *tests/testthat/test_relpois_mean_curve.R | ||
| 9bb60bf501dfcde2bbb3f4bd344e5802 *tests/testthat/test_sir.R | ||
| 8af57488f8f3bcfe7bcb86becfc0c4c6 *tests/testthat/test_splitLexisDT.R | ||
| 34390dee1de98698c07778d325557c20 *tests/testthat/test_splitMulti.R | ||
| a836509f606f6e1ea9650faeeb55807d *tests/testthat/test_survtab_bad_surv_ints.R | ||
| 2007419a061f70ca5f893a48b72b8b24 *tests/testthat/test_survtab_observed.R | ||
| cf4f8640da9af1a0e1d35e9cd2c529be *tests/testthat/test_survtab_relative.R | ||
| 5522d218ce000974e3417a5e9e29a658 *vignettes/sir.Rmd | ||
| 08062ec00a4eab7375617141d78977b6 *vignettes/survtab_examples.Rmd |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| # Generated by roxygen2 (4.1.1): do not edit by hand | ||
|
|
||
| S3method(as.data.frame,ratetable) | ||
| S3method(as.data.table,ratetable) | ||
| S3method(as.pe,Lexis) | ||
| S3method(as.pe,data.table) | ||
| S3method(as.pe,list) | ||
| S3method(lines,survtab) | ||
| S3method(plot,pe) | ||
| S3method(plot,sir) | ||
| S3method(plot,sirspline) | ||
| S3method(plot,survtab) | ||
| S3method(print,sir) | ||
| S3method(print,sirspline) | ||
| export(RPL) | ||
| export(all_names_present) | ||
| export(as.data.frame.ratetable) | ||
| export(as.data.table.ratetable) | ||
| export(as.pe.Lexis) | ||
| export(as.pe.data.table) | ||
| export(as.pe.list) | ||
| export(cast_simple) | ||
| export(cut_bound) | ||
| export(expr.by.cj) | ||
| export(fac2num) | ||
| export(get.yrs) | ||
| export(is.Date) | ||
| export(is_leap_year) | ||
| export(lexpand) | ||
| export(lines.survtab) | ||
| export(lower_bound) | ||
| export(ltable) | ||
| export(na2zero) | ||
| export(plot.pe) | ||
| export(plot.sir) | ||
| export(plot.sirspline) | ||
| export(plot.survtab) | ||
| export(poisson.ci) | ||
| export(print.sir) | ||
| export(print.sirspline) | ||
| export(relpois) | ||
| export(robust_values) | ||
| export(rpcurve) | ||
| export(setcolsnull) | ||
| export(shift.var) | ||
| export(sir) | ||
| export(sirspline) | ||
| export(splitLexisDT) | ||
| export(splitMulti) | ||
| export(survmean) | ||
| export(survtab) | ||
| export(try2int) | ||
| import(Epi) | ||
| import(data.table) | ||
| import(grDevices) | ||
| import(graphics) | ||
| import(splines) | ||
| import(stats) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| popEpi 0.2.1 | ||
| ====== | ||
| * fixes various issues detected in R CMD CHECK at CRAN end | ||
| * all examples should only use data.frame syntax now (not data.table) | ||
|
|
||
| popEpi 0.2.0 | ||
| ====== | ||
| * uses data.table 1.9.6 | ||
| * first CRAN upload | ||
| * documentation improved | ||
|
|
||
| popEpi 0.1.17 | ||
| ====== | ||
| * various bug fixes towards CRAN upload | ||
| * survtab: pp.int renamed to pp, only TRUE/FALSE for public use | ||
| * lexpand: new argument aggre.type: aggregate either to only existing levels or all possible combinations of known levels, with some possibly being empty; the former by default | ||
|
|
||
| popEpi 0.1.16 | ||
| ====== | ||
| * global option popEpi.datatable for when the user prefers data.frame output instead of data.table | ||
| * lexpand: aggregated PYRS / observations now zero instead of NA | ||
| * lexpand: now supports "event" argument for when event not at the end of follow-up | ||
| * lexpand: overlapping argument | ||
| * sir: added global data.frame option | ||
| * sir: print argument accepts also a list, e.g. print = list(gender = 2-sex) | ||
| * sir: the order of print argument matters | ||
| * sirspline: print accepts list + additions to print method | ||
|
|
||
| popEpi 0.1.15 | ||
| ====== | ||
| * interchange lex and lexpand | ||
| * add multistate option to sir | ||
| * add vignette (sir) | ||
|
|
||
| popEpi 0.1.14 | ||
| ====== | ||
| * relpois rewritten | ||
| * sir re-arranged | ||
|
|
||
| popEpi 0.1.13 | ||
| ====== | ||
| * lexpand now supports at least simple multi-state data and is slightly faster | ||
| * plot.sir & lines.sir are now methods for base::plot & base::lines | ||
| * sir: small fixes | ||
|
|
||
| popEpi 0.1.11 | ||
| ====== | ||
| * fixes and clean-ups towards CRAN implementation | ||
| * moved to R 3.2.0 | ||
|
|
||
| popEpi 0.1.10 | ||
| ====== | ||
| * fixes and clean-ups towards CRAN implementation | ||
| * added testthat tests | ||
|
|
||
| popEpi 0.1.9 | ||
| ====== | ||
| * ltable bugfix | ||
| * survtab: lifetable survival now works when all persons in an interval are censored (produces Nas) | ||
|
|
||
| popEpi 0.1.8 | ||
| ====== | ||
| * survtab: fixed event.values usage; if NULL, uses non-zero lex.Xst values | ||
| * cleaned up some help files | ||
|
|
||
| popEpi 0.1.7 | ||
| ====== | ||
| * survtab: now explicitly supports cause-specific survival estimation | ||
| * new function: relpois for excess hazard poisson modeling | ||
|
|
||
| popEpi 0.1.6 | ||
| ====== | ||
| * Bugfix: SIR multivariate output order | ||
| * survtab: now supports CIF estimation | ||
|
|
||
| popEpi 0.1.5 | ||
| ====== | ||
| * Survival: pophaz is now merged via lex() for flexibility | ||
| * SIR: accepts aggre-objects (coh and ref), improve plot.sir (remove plot_sir()) | ||
|
|
||
| popEpi 0.1.4 | ||
| ====== | ||
| * survtab now supports age-standardization w/ confidence intervals | ||
| * improved documentation | ||
|
|
||
| popEpi 0.1.3 | ||
| ======= | ||
| * survival works with confidence intervals | ||
| * DESCRIPTION: add imports ggplot2, splines and RColorBrewer | ||
| * Add plot.be -method. | ||
| * Improve sir & aggre: S3-definitions for print & plot | ||
|
|
||
| popEpi 0.1.2 | ||
| ======= | ||
| * survival kinda works | ||
|
|
||
| popEpi 0.1.1 | ||
| ======= | ||
| * import functions from internal package |
Oops, something went wrong.