The data is obtained from IADB with a restricted access. After obtaining the access, you may read the following documentation describing standard IADB variables.
Most of the works in this repository, especially the R
scripts, should
be directly reproducible. You’ll need
git
,
R
,
quarto
, and more conveniently
RStudio IDE installed and running well in
your system. You simply need to fork/clone this repository using RStudio
by following this tutorial, start right away from
Step 2
.
Using terminal in linux/MacOS, you can issue the following command:
quarto tools install tinytex
This command will install tinytex
in your path, which is required to
compile quarto documents as latex/pdf. Afterwards, in your RStudio
command line, you can copy paste the following code to setup your
working directory:
install.packages("renv") # Only need to run this step if `renv` is not installed
This step will install renv
package, which will help you set up the
R
environment. Please note that renv
helps tracking, versioning, and
updating packages I used throughout the analysis.
renv::restore()
This step will read renv.lock
file and install required packages to
your local machine. When all packages loaded properly (make sure there’s
no error at all), you have to restart your R session. Then, you should
be able to proceed with:
targets::tar_make()
This step will read _targets.R
file, where I systematically draft all
of the analysis steps. Once it’s done running, you will find the
rendered document (either in html
or pdf
) inside the draft
directory.
This is the analysis pipeline for conducting analysis in an umbrella
review. The complete flow can be viewed in the following mermaid
diagram:
graph LR
style Legend fill:#FFFFFF00,stroke:#000000;
style Graph fill:#FFFFFF00,stroke:#000000;
subgraph Legend
direction LR
x7420bd9270f8d27d([""Up to date""]):::uptodate --- x5b3426b4c7fa7dbc([""Started""]):::started
x5b3426b4c7fa7dbc([""Started""]):::started --- x0a52b03877696646([""Outdated""]):::outdated
x0a52b03877696646([""Outdated""]):::outdated --- xbf4603d6c2c2ad6b([""Stem""]):::none
xbf4603d6c2c2ad6b([""Stem""]):::none --- x70a5fa6bea6f298d[""Pattern""]:::none
x70a5fa6bea6f298d[""Pattern""]:::none --- xf0bce276fe2b9d3e>""Function""]:::none
xf0bce276fe2b9d3e>""Function""]:::none --- x5bffbffeae195fc9{{""Object""}}:::none
end
subgraph Graph
direction LR
x82e62d618bc88e7e>"getLabel"]:::uptodate --> x55e2af9f684b7032>"vizReconSsa"]:::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> xa117c043e8f9b503>"vizMonth"]:::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> xfc9293f408401e5e>"vizAutocor"]:::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> xab29c0af1a4e1af0>"vizArima"]:::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> x203d559dcf99559c>"vizDot"]:::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> x098757b4b84b914a>"vizPeriod"]:::uptodate
xd22f295990a4c67c>"tsReconSsa"]:::uptodate --> x5509cc22a0bc4e12>"tidyReconSsa"]:::uptodate
x5509cc22a0bc4e12>"tidyReconSsa"]:::uptodate --> x530163c6df184499>"reconSsa"]:::uptodate
x97c70e20651b3e03>"genColor"]:::uptodate --> x1e87c6f89e191de7>"setStripColor"]:::uptodate
x97c70e20651b3e03>"genColor"]:::uptodate --> x55e2af9f684b7032>"vizReconSsa"]:::uptodate
x97c70e20651b3e03>"genColor"]:::uptodate --> xfc9293f408401e5e>"vizAutocor"]:::uptodate
x97c70e20651b3e03>"genColor"]:::uptodate --> x203d559dcf99559c>"vizDot"]:::uptodate
xaba6069a563b12e8>"getNeuroMeds"]:::uptodate --> x1e87c6f89e191de7>"setStripColor"]:::uptodate
xaba6069a563b12e8>"getNeuroMeds"]:::uptodate --> xc04d85957c4a84d0>"setGroupFactor"]:::uptodate
xaba6069a563b12e8>"getNeuroMeds"]:::uptodate --> x6c212354357aadc8>"mergeTS"]:::uptodate
x1e87c6f89e191de7>"setStripColor"]:::uptodate --> xfc9293f408401e5e>"vizAutocor"]:::uptodate
x1e87c6f89e191de7>"setStripColor"]:::uptodate --> x203d559dcf99559c>"vizDot"]:::uptodate
x1e87c6f89e191de7>"setStripColor"]:::uptodate --> x098757b4b84b914a>"vizPeriod"]:::uptodate
xc366d1d8806979f6>"genLabel"]:::uptodate --> x970b27788a81a7b0>"mkMatrix"]:::uptodate
xeb859985bc1ac4aa>"aggregateTS"]:::uptodate --> x6c212354357aadc8>"mergeTS"]:::uptodate
xc04d85957c4a84d0>"setGroupFactor"]:::uptodate --> x6c212354357aadc8>"mergeTS"]:::uptodate
xa117c043e8f9b503>"vizMonth"]:::uptodate --> xb9f54242cee3597e>"vizPolar"]:::uptodate
xb9f54242cee3597e>"vizPolar"]:::uptodate --> x2a89da525d1cc153>"describe"]:::uptodate
x59afdd7893d2ce9b>"describeMean"]:::uptodate --> x2a89da525d1cc153>"describe"]:::uptodate
x970b27788a81a7b0>"mkMatrix"]:::uptodate --> x9ca1aa7607080a7b>"mkGraph"]:::uptodate
x4e58fb85b5f553b2>"groupAtc"]:::uptodate --> x7514d3a2992ccd63>"splitAtc"]:::uptodate
x530163c6df184499>"reconSsa"]:::uptodate --> x7932dde01bed8634>"fitSsa"]:::uptodate
xb5a1412177d32e97>"vizPair"]:::uptodate --> x2a89da525d1cc153>"describe"]:::uptodate
xec523c05a7988872>"pairByRow"]:::uptodate --> x970b27788a81a7b0>"mkMatrix"]:::uptodate
x0f6bf75cdbde6203>"getSsaGroup"]:::uptodate --> x530163c6df184499>"reconSsa"]:::uptodate
x3e87573bd30d006b>"evalUnitRoot"]:::uptodate --> xd4fc6dffefb838f3["ts_diff2_uroot_week"]:::uptodate
xa81f3ac85c3ab6fc(["ts_diff2_week"]):::uptodate --> xd4fc6dffefb838f3["ts_diff2_uroot_week"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> xd4fc6dffefb838f3["ts_diff2_uroot_week"]:::uptodate
x3455a1c44fd0ba64(["decom_ts_month_1.year_loess_eigen"]):::uptodate --> x4801de0cb1b805de(["plt_decom_ts_month_1.year_loess_eigen"]):::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> x4801de0cb1b805de(["plt_decom_ts_month_1.year_loess_eigen"]):::uptodate
x203d559dcf99559c>"vizDot"]:::uptodate --> x4801de0cb1b805de(["plt_decom_ts_month_1.year_loess_eigen"]):::uptodate
x31faa9d48477f81b(["ts_diff_week"]):::uptodate --> x37afaee2bd3e651d["plt_pacf_diff_week"]:::uptodate
xfc9293f408401e5e>"vizAutocor"]:::uptodate --> x37afaee2bd3e651d["plt_pacf_diff_week"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> x37afaee2bd3e651d["plt_pacf_diff_week"]:::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> x721b6cba1628c845(["decom_ts_week_1.month_classic_strength"]):::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> x721b6cba1628c845(["decom_ts_week_1.month_classic_strength"]):::uptodate
xcd136c75f6948bfd(["med_groups"]):::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x4f2d2e559519efe1["mod_arima_claim2patient"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x79fa432b43dcafaf["mod_arima_eigen"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x11abd7770785b634["mod_arima_eval_claim2patient"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x91a77d5b4dfa50f4["mod_arima_eval_eigen"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
xa43e6b5b1b499bca["mod_arima_eval_n_claim"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x7e1814e57b0b1be4["mod_arima_n_claim"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x8ae03bd67401026c["plt_arima_forecast_claim2patient"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x6eb2cd606ce0984c["plt_arima_forecast_eigen"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x55a0e476a043137e["plt_arima_forecast_n_claim"]:::uptodate --> x7dbb58def017efbe(["report_arima"]):::outdated
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> x4a5cabf4ebd7accb(["decom_ts_day_1.week_loess_strength"]):::uptodate
x7ffe35eee48c2674(["ts_day"]):::uptodate --> x4a5cabf4ebd7accb(["decom_ts_day_1.week_loess_strength"]):::uptodate
xf2831b13ede46eac(["iadb_metrics"]):::uptodate --> x14bcf0b7ef5959f1(["ts_month"]):::uptodate
x6bbf38eac08a1fe8(["iadb_stats"]):::uptodate --> x14bcf0b7ef5959f1(["ts_month"]):::uptodate
x6c212354357aadc8>"mergeTS"]:::uptodate --> x14bcf0b7ef5959f1(["ts_month"]):::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> xc058910fe0c21157(["decom_ts_day_1.week_loess_eigen"]):::uptodate
x7ffe35eee48c2674(["ts_day"]):::uptodate --> xc058910fe0c21157(["decom_ts_day_1.week_loess_eigen"]):::uptodate
x9ca1aa7607080a7b>"mkGraph"]:::uptodate --> x278d817c06f60e98["iadb_graph"]:::uptodate
xf7e9b577faef0a3a["tbl_iadb_split_atc"]:::uptodate --> x278d817c06f60e98["iadb_graph"]:::uptodate
xc6e289d90e4f347f>"fitArima"]:::uptodate --> x4f2d2e559519efe1["mod_arima_claim2patient"]:::uptodate
x6c570eed1079677b>"fitModel"]:::uptodate --> x4f2d2e559519efe1["mod_arima_claim2patient"]:::uptodate
xcd136c75f6948bfd(["med_groups"]):::uptodate --> x4f2d2e559519efe1["mod_arima_claim2patient"]:::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> x4f2d2e559519efe1["mod_arima_claim2patient"]:::uptodate
x897e8856e62b7088(["decom_ts_day_1.week_classic_n_claim"]):::uptodate --> xc91cfe6f7292e4b4(["plt_decom_ts_day_1.week_classic_n_claim"]):::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> xc91cfe6f7292e4b4(["plt_decom_ts_day_1.week_classic_n_claim"]):::uptodate
x203d559dcf99559c>"vizDot"]:::uptodate --> xc91cfe6f7292e4b4(["plt_decom_ts_day_1.week_classic_n_claim"]):::uptodate
x14e721e34c9c8b1b(["decom_ts_week_1.month_loess_n_claim"]):::uptodate --> xc396e37111805a84(["plt_decom_ts_week_1.month_loess_n_claim"]):::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> xc396e37111805a84(["plt_decom_ts_week_1.month_loess_n_claim"]):::uptodate
x203d559dcf99559c>"vizDot"]:::uptodate --> xc396e37111805a84(["plt_decom_ts_week_1.month_loess_n_claim"]):::uptodate
x6c48091042266f38["plt_acf_day"]:::uptodate --> x7142295daf13496f["fig_acf_day"]:::uptodate
x0e2a1e9ee6890aa6>"saveFig"]:::uptodate --> x7142295daf13496f["fig_acf_day"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> x7142295daf13496f["fig_acf_day"]:::uptodate
x3f3f5a0c614e32c5["mod_ssa_claim2patient"]:::uptodate --> x5a026dafb9f9840e["mod_ssa_recon_claim2patient"]:::uptodate
x530163c6df184499>"reconSsa"]:::uptodate --> x5a026dafb9f9840e["mod_ssa_recon_claim2patient"]:::uptodate
xfff40f8096285418["mod_ssa_n_claim"]:::uptodate --> xcd2ea74d422880aa["mod_ssa_recon_n_claim"]:::uptodate
x530163c6df184499>"reconSsa"]:::uptodate --> xcd2ea74d422880aa["mod_ssa_recon_n_claim"]:::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> x2eab2a0f6af8a669(["decom_ts_week_1.month_loess_eigen"]):::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> x2eab2a0f6af8a669(["decom_ts_week_1.month_loess_eigen"]):::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> xee05927e7b88ad5d["plt_pacf_week"]:::uptodate
xfc9293f408401e5e>"vizAutocor"]:::uptodate --> xee05927e7b88ad5d["plt_pacf_week"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> xee05927e7b88ad5d["plt_pacf_week"]:::uptodate
x15823228216e9e2e["plt_dot_week"]:::uptodate --> x710d593c64216c80["fig_dot_week"]:::uptodate
x0e2a1e9ee6890aa6>"saveFig"]:::uptodate --> x710d593c64216c80["fig_dot_week"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> x710d593c64216c80["fig_dot_week"]:::uptodate
x484af6f82192f2e9>"timeDiff"]:::uptodate --> xa81f3ac85c3ab6fc(["ts_diff2_week"]):::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> xa81f3ac85c3ab6fc(["ts_diff2_week"]):::uptodate
xf220e84da6d0ff6f(["tbl_iadb"]):::uptodate --> x960707f0c582886a(["tbl_iadb_by_date"]):::uptodate
x3e87573bd30d006b>"evalUnitRoot"]:::uptodate --> xf24ba0a5fa22e4ad["ts_uroot_day"]:::uptodate
x7ffe35eee48c2674(["ts_day"]):::uptodate --> xf24ba0a5fa22e4ad["ts_uroot_day"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> xf24ba0a5fa22e4ad["ts_uroot_day"]:::uptodate
x07ac0b71f920f889>"combineMetrics"]:::uptodate --> x6bbf38eac08a1fe8(["iadb_stats"]):::uptodate
xc082a51377a349bf>"fieldSummary"]:::uptodate --> x6bbf38eac08a1fe8(["iadb_stats"]):::uptodate
xf7e9b577faef0a3a["tbl_iadb_split_atc"]:::uptodate --> x6bbf38eac08a1fe8(["iadb_stats"]):::uptodate
x484af6f82192f2e9>"timeDiff"]:::uptodate --> x6da2e542198a5d93(["ts_diff_month"]):::uptodate
x14bcf0b7ef5959f1(["ts_month"]):::uptodate --> x6da2e542198a5d93(["ts_diff_month"]):::uptodate
x6da2e542198a5d93(["ts_diff_month"]):::uptodate --> x8d4989d190572307["plt_pacf_diff_month"]:::uptodate
xfc9293f408401e5e>"vizAutocor"]:::uptodate --> x8d4989d190572307["plt_pacf_diff_month"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> x8d4989d190572307["plt_pacf_diff_month"]:::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> x87f485f2ede7231a(["decom_ts_day_1.week_classic_eigen"]):::uptodate
x7ffe35eee48c2674(["ts_day"]):::uptodate --> x87f485f2ede7231a(["decom_ts_day_1.week_classic_eigen"]):::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> xf3e78b060469e6a9(["decom_ts_month_1.year_classic_claim2patient"]):::uptodate
x14bcf0b7ef5959f1(["ts_month"]):::uptodate --> xf3e78b060469e6a9(["decom_ts_month_1.year_classic_claim2patient"]):::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> x57a05589a58fabfc(["decom_ts_month_1.year_loess_strength"]):::uptodate
x14bcf0b7ef5959f1(["ts_month"]):::uptodate --> x57a05589a58fabfc(["decom_ts_month_1.year_loess_strength"]):::uptodate
x79fa432b43dcafaf["mod_arima_eigen"]:::uptodate --> x72cd3fa746b70917["mod_arima_forecast_eigen"]:::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> xcc3fd8f4d6a4b61b(["decom_ts_month_1.year_loess_n_claim"]):::uptodate
x14bcf0b7ef5959f1(["ts_month"]):::uptodate --> xcc3fd8f4d6a4b61b(["decom_ts_month_1.year_loess_n_claim"]):::uptodate
x57a05589a58fabfc(["decom_ts_month_1.year_loess_strength"]):::uptodate --> xf32dbf53c1b5a9b2(["plt_decom_ts_month_1.year_loess_strength"]):::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> xf32dbf53c1b5a9b2(["plt_decom_ts_month_1.year_loess_strength"]):::uptodate
x203d559dcf99559c>"vizDot"]:::uptodate --> xf32dbf53c1b5a9b2(["plt_decom_ts_month_1.year_loess_strength"]):::uptodate
x31faa9d48477f81b(["ts_diff_week"]):::uptodate --> x9a2a3b9d04de4370["plt_acf_diff_week"]:::uptodate
xfc9293f408401e5e>"vizAutocor"]:::uptodate --> x9a2a3b9d04de4370["plt_acf_diff_week"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> x9a2a3b9d04de4370["plt_acf_diff_week"]:::uptodate
x3e87573bd30d006b>"evalUnitRoot"]:::uptodate --> xc751146609196dc6["ts_uroot_month"]:::uptodate
x14bcf0b7ef5959f1(["ts_month"]):::uptodate --> xc751146609196dc6["ts_uroot_month"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> xc751146609196dc6["ts_uroot_month"]:::uptodate
x88a329c7ea7a65fe(["decom_ts_day_1.week_classic_strength"]):::uptodate --> x4da28536ad53b85f(["plt_decom_ts_day_1.week_classic_strength"]):::uptodate
x82e62d618bc88e7e>"getLabel"]:::uptodate --> x4da28536ad53b85f(["plt_decom_ts_day_1.week_classic_strength"]):::uptodate
x203d559dcf99559c>"vizDot"]:::uptodate --> x4da28536ad53b85f(["plt_decom_ts_day_1.week_classic_strength"]):::uptodate
xfbeb60eec79c1dee["mod_ssa_eigen"]:::uptodate --> x0aa0ece969fa8517["mod_ssa_recon_eigen"]:::uptodate
x530163c6df184499>"reconSsa"]:::uptodate --> x0aa0ece969fa8517["mod_ssa_recon_eigen"]:::uptodate
x6c570eed1079677b>"fitModel"]:::uptodate --> x3f3f5a0c614e32c5["mod_ssa_claim2patient"]:::uptodate
x7932dde01bed8634>"fitSsa"]:::uptodate --> x3f3f5a0c614e32c5["mod_ssa_claim2patient"]:::uptodate
xcd136c75f6948bfd(["med_groups"]):::uptodate --> x3f3f5a0c614e32c5["mod_ssa_claim2patient"]:::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> x3f3f5a0c614e32c5["mod_ssa_claim2patient"]:::uptodate
x6c570eed1079677b>"fitModel"]:::uptodate --> xfff40f8096285418["mod_ssa_n_claim"]:::uptodate
x7932dde01bed8634>"fitSsa"]:::uptodate --> xfff40f8096285418["mod_ssa_n_claim"]:::uptodate
xcd136c75f6948bfd(["med_groups"]):::uptodate --> xfff40f8096285418["mod_ssa_n_claim"]:::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> xfff40f8096285418["mod_ssa_n_claim"]:::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> x3e1db942d8fb6918(["decom_ts_day_1.week_loess_n_claim"]):::uptodate
x7ffe35eee48c2674(["ts_day"]):::uptodate --> x3e1db942d8fb6918(["decom_ts_day_1.week_loess_n_claim"]):::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> x177fd622fb419be5(["decom_ts_month_1.year_classic_n_claim"]):::uptodate
x14bcf0b7ef5959f1(["ts_month"]):::uptodate --> x177fd622fb419be5(["decom_ts_month_1.year_classic_n_claim"]):::uptodate
x6f31b4097fc37fb5>"timeDecom"]:::uptodate --> xe29768ff9b12a046(["decom_ts_week_1.month_classic_eigen"]):::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> xe29768ff9b12a046(["decom_ts_week_1.month_classic_eigen"]):::uptodate
x3e87573bd30d006b>"evalUnitRoot"]:::uptodate --> xe9d057717b7c09db["ts_uroot_week"]:::uptodate
xe654ad4c04f23a28(["ts_week"]):::uptodate --> xe9d057717b7c09db["ts_uroot_week"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> xe9d057717b7c09db["ts_uroot_week"]:::uptodate
xccc889a3af79aa2f["plt_acf_week"]:::uptodate --> xbde164b969460ca6["fig_acf_week"]:::uptodate
x0e2a1e9ee6890aa6>"saveFig"]:::uptodate --> xbde164b969460ca6["fig_acf_week"]:::uptodate
x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> xbde164b969460ca6["fig_acf_week"]:::uptodate
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xe654ad4c04f23a28(["ts_week"]):::uptodate --> xac3ca7d0385656a2(["decom_ts_week_1.month_classic_n_claim"]):::uptodate
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xe654ad4c04f23a28(["ts_week"]):::uptodate --> x7e1814e57b0b1be4["mod_arima_n_claim"]:::uptodate
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x9544603ba0a3eba6(["vizDotParams"]):::uptodate --> xe9bba18952d1eff6["plt_period_day"]:::uptodate
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