From 71e648ead94bd30ffe40e5ecd271cc289b2c9df5 Mon Sep 17 00:00:00 2001 From: Lawrence Sinclair Date: Sun, 14 Jun 2026 00:41:57 +0700 Subject: [PATCH] jenner-check: add 5 Jenner compatibility bundles + runner Adds a jenner-check/ directory with five runnable bundles derived from gformula_bmtdata.sas, plus a pure-SAS runner (run_jenner.sh/.bat/.sas): t001_baseline_covariates - DATALINES read + restricted-cubic-spline covariates t002_person_period_expansion - DO-loop person-day expansion with time-varying covariates t003_logistic_coefficient_model - PROC LOGISTIC coefficient estimation with ODS OUTPUT t004_surveyselect_resample - PROC SURVEYSELECT Monte Carlo resample (METHOD=URS) t005_phreg_cox_survival - PROC PHREG Cox model (TIES=EFRON, risk limits) Each bundle has a frozen expected.json plus a human-readable expected/ snapshot (log, listing, artifact URLs). --- jenner-check/README.md | 66 +++ jenner-check/run_jenner.bat | 43 ++ jenner-check/run_jenner.sas | 526 ++++++++++++++++++ jenner-check/run_jenner.sh | 214 +++++++ .../t001_baseline_covariates/autoexec.sas | 1 + .../t001_baseline_covariates/expected.json | 13 + .../expected/files.md | 15 + .../t001_baseline_covariates/expected/log.txt | 26 + .../expected/output.txt | 29 + .../t001_baseline_covariates/meta.json | 8 + .../t001_baseline_covariates/script.sas | 163 ++++++ .../t002_person_period_expansion/autoexec.sas | 1 + .../expected.json | 19 + .../expected/files.md | 16 + .../expected/log.txt | 36 ++ .../expected/output.txt | 31 ++ .../t002_person_period_expansion/meta.json | 8 + .../t002_person_period_expansion/script.sas | 206 +++++++ .../autoexec.sas | 1 + .../expected.json | 19 + .../expected/files.md | 20 + .../expected/log.txt | 31 ++ .../expected/output.txt | 57 ++ .../t003_logistic_coefficient_model/meta.json | 8 + .../script.sas | 166 ++++++ .../t004_surveyselect_resample/autoexec.sas | 1 + .../t004_surveyselect_resample/expected.json | 18 + .../expected/files.md | 16 + .../expected/log.txt | 30 + .../expected/output.txt | 35 ++ .../t004_surveyselect_resample/meta.json | 8 + .../t004_surveyselect_resample/script.sas | 167 ++++++ .../t005_phreg_cox_survival/autoexec.sas | 1 + .../t005_phreg_cox_survival/expected.json | 19 + .../t005_phreg_cox_survival/expected/files.md | 9 + .../t005_phreg_cox_survival/expected/log.txt | 25 + .../expected/output.txt | 24 + .../t005_phreg_cox_survival/meta.json | 8 + .../t005_phreg_cox_survival/script.sas | 161 ++++++ 39 files changed, 2245 insertions(+) create mode 100644 jenner-check/README.md create mode 100644 jenner-check/run_jenner.bat create mode 100644 jenner-check/run_jenner.sas create mode 100755 jenner-check/run_jenner.sh create mode 100644 jenner-check/t001_baseline_covariates/autoexec.sas create mode 100644 jenner-check/t001_baseline_covariates/expected.json create mode 100644 jenner-check/t001_baseline_covariates/expected/files.md create mode 100644 jenner-check/t001_baseline_covariates/expected/log.txt create mode 100644 jenner-check/t001_baseline_covariates/expected/output.txt create mode 100644 jenner-check/t001_baseline_covariates/meta.json create mode 100644 jenner-check/t001_baseline_covariates/script.sas create mode 100644 jenner-check/t002_person_period_expansion/autoexec.sas create mode 100644 jenner-check/t002_person_period_expansion/expected.json create mode 100644 jenner-check/t002_person_period_expansion/expected/files.md create mode 100644 jenner-check/t002_person_period_expansion/expected/log.txt create mode 100644 jenner-check/t002_person_period_expansion/expected/output.txt create mode 100644 jenner-check/t002_person_period_expansion/meta.json create mode 100644 jenner-check/t002_person_period_expansion/script.sas create mode 100644 jenner-check/t003_logistic_coefficient_model/autoexec.sas create mode 100644 jenner-check/t003_logistic_coefficient_model/expected.json create mode 100644 jenner-check/t003_logistic_coefficient_model/expected/files.md create mode 100644 jenner-check/t003_logistic_coefficient_model/expected/log.txt create mode 100644 jenner-check/t003_logistic_coefficient_model/expected/output.txt create mode 100644 jenner-check/t003_logistic_coefficient_model/meta.json create mode 100644 jenner-check/t003_logistic_coefficient_model/script.sas create mode 100644 jenner-check/t004_surveyselect_resample/autoexec.sas create mode 100644 jenner-check/t004_surveyselect_resample/expected.json create mode 100644 jenner-check/t004_surveyselect_resample/expected/files.md create mode 100644 jenner-check/t004_surveyselect_resample/expected/log.txt create mode 100644 jenner-check/t004_surveyselect_resample/expected/output.txt create mode 100644 jenner-check/t004_surveyselect_resample/meta.json create mode 100644 jenner-check/t004_surveyselect_resample/script.sas create mode 100644 jenner-check/t005_phreg_cox_survival/autoexec.sas create mode 100644 jenner-check/t005_phreg_cox_survival/expected.json create mode 100644 jenner-check/t005_phreg_cox_survival/expected/files.md create mode 100644 jenner-check/t005_phreg_cox_survival/expected/log.txt create mode 100644 jenner-check/t005_phreg_cox_survival/expected/output.txt create mode 100644 jenner-check/t005_phreg_cox_survival/meta.json create mode 100644 jenner-check/t005_phreg_cox_survival/script.sas diff --git a/jenner-check/README.md b/jenner-check/README.md new file mode 100644 index 0000000..b3ca73b --- /dev/null +++ b/jenner-check/README.md @@ -0,0 +1,66 @@ +# Jenner compatibility tests + +[Jenner](https://jenneranalytics.com) is a complete SAS-compatible system +and collaborative workspace. Each `tNNN_*` directory in this folder is a +self-contained test bundle that submits a SAS program to the public API +at `https://api.jenneranalytics.com/v1/run` and checks the response. + +## Bundle layout + +``` +tNNN_*/ +├── script.sas # the SAS program +├── autoexec.sas # options + setup that prepend the script +├── input/ # sample data the script reads (if any) +├── expected.json # stable assertions checked on each run +├── expected/ # captured snapshot from the last passing run +│ ├── log.txt # the .log field, verbatim +│ ├── output.txt # the .output (listing) field, verbatim +│ └── files.md # links to ODS images, datasets, etc. +└── meta.json # provenance: source file, blob sha, what was adapted +``` + +## Running a bundle + +The runner concatenates `autoexec.sas` + `script.sas`, POSTs to +`https://api.jenneranalytics.com/v1/run`, and prints the result. + +**Mac / Linux (bash + curl):** + +```bash +./run_jenner.sh --all # run every tNNN_* bundle, summary at end +./run_jenner.sh t001_something # run one +./run_jenner.sh --list # list bundles in this directory +``` + +**Windows:** + +```cmd +run_jenner.bat tNNN_something +``` + +**From any SAS session (no curl needed):** + +Submit `run_jenner.sas` — it uses PROC HTTP to POST and prints the +response. + +**By hand with curl:** + +```bash +cat tNNN_*/autoexec.sas tNNN_*/script.sas > /tmp/submit.sas +curl -sS -X POST https://api.jenneranalytics.com/v1/run \ + -F "script=@/tmp/submit.sas" \ + -F "deterministic=1" -F "timeout=60" +``` + +**Or in the hosted workspace:** + +Open , paste `script.sas` (with the +`autoexec.sas` lines prepended), upload anything in `input/`, and run. + +## Artifact URLs + +`expected/files.md` in each bundle lists hosted URLs for any ODS images, +datasets, or other artifacts produced by a captured run. Those URLs are +tied to a specific run and expire when the run is reaped — re-run the +bundle to refresh them. diff --git a/jenner-check/run_jenner.bat b/jenner-check/run_jenner.bat new file mode 100644 index 0000000..1039fdf --- /dev/null +++ b/jenner-check/run_jenner.bat @@ -0,0 +1,43 @@ +@echo off +rem run_jenner.bat - Windows runner for Jenner compatibility checks. +rem +rem Usage: run_jenner.bat [response.json] +rem +rem Submits a single .sas file to api.jenneranalytics.com. For +rem bundle-aware mode (autoexec.sas + script.sas concatenation) on +rem Windows, use WSL and invoke run_jenner.sh instead, or wait for the +rem Windows CI runner that will validate a bundle-aware .bat. +rem +rem Output: response.json contains the API response. Read it back in SAS: +rem filename resp 'response.json'; +rem libname resp JSON fileref=resp; +rem proc print data=resp.root; run; +rem +rem Requires: curl.exe (ships with Windows 10+ at C:\Windows\System32). + +setlocal + +if "%~1"=="" ( + echo Usage: %~nx0 ^ [response.json] + exit /b 2 +) + +set SCRIPT=%~1 +set OUT=%~2 +if "%OUT%"=="" set OUT=response.json + +set HOST=api.jenneranalytics.com + +curl.exe -sS -X POST "https://%HOST%/v1/run" ^ + -F "script=@%SCRIPT%;type=application/x-sas" ^ + -F "deterministic=1" ^ + -F "timeout=60" ^ + -o "%OUT%" + +if errorlevel 1 ( + echo curl failed with errorlevel %errorlevel% + exit /b 1 +) + +echo Response written to %OUT% +exit /b 0 diff --git a/jenner-check/run_jenner.sas b/jenner-check/run_jenner.sas new file mode 100644 index 0000000..550e8f8 --- /dev/null +++ b/jenner-check/run_jenner.sas @@ -0,0 +1,526 @@ +/* run_jenner.sas — invoke api.jenneranalytics.com from base SAS. + * + * Requires SAS 9.4 M5 or later (PROC HTTP + libname JSON engine). + * + * --------------------------------------------------------------------------- + * TL;DR for SAS users: + * + * %include 'run_jenner.sas'; + * %jenner_run(script=my_program.sas); / * one script * / + * %jenner_check_all(); / * whole bundle dir * / + * + * --------------------------------------------------------------------------- + * What this file gives you: + * + * %jenner_run — POST one .sas file to the Jenner API, display the + * log + listing + any generated files. + * %jenner_check_all — walk every jenner-check/tNNN_* bundle, + * invoke the API for each, compare the response to + * the bundle's expected.json, produce a summary + * CSV + SAS dataset the repo owner can attach to the + * jenner-check PR. + * + * --------------------------------------------------------------------------- + * How the API call is built: + * + * POST https://api.jenneranalytics.com/v1/run + * Content-Type: multipart/form-data; boundary=... + * + * fields: + * script the .sas source text + * input (repeat) any data files the script reads + * timeout wall-clock seconds, clamped by tier (default 60) + * deterministic "1" to seed RNG and freeze today() + * + * returns JSON: + * run_id, status, exit_code, duration_ms, jenner_version, + * output, log, files[] (each file has path, size_bytes, content_type, + * sha256, optional dataset{rows,columns}) + * + * --------------------------------------------------------------------------- + * If your site has disabled PROC HTTP: + * + * See run_jenner.bat (Windows) or run_jenner.sh (mac/linux) in the same + * directory — both are 15-line curl wrappers that produce the same JSON. + * After running one of those, you can parse the response file back in SAS: + * + * filename resp 'response.json'; + * libname resp JSON fileref=resp; + * proc print data=resp.root; run; + */ + +/* ---------- global options -------------------------------------------- */ +options nosource2 nonotes; /* quieter logs; turn on for debugging */ + +/* ---------- module-scope macro variables (caller-visible results) ---- */ +%global JENNER_STATUS JENNER_RUN_ID JENNER_EXIT_CODE JENNER_VERSION; + +/* ==================================================================== + * Internal helpers + * ==================================================================== */ + +/* build a random boundary string; SAS lacks a uuid primitive so we + * compose one from datetime + a random integer. */ +%macro _jc_boundary; + jc_%sysfunc(compress(%sysfunc(datetime(), b8601dt.), -:.))_%sysfunc(ranuni(0),hex6.) +%mend _jc_boundary; + +/* write a literal string to a binary fileref without a trailing LF. */ +%macro _jc_put(fref, text); + data _null_; + file &fref mod recfm=n; + put &text; + run; +%mend _jc_put; + +/* assemble the multipart body into fileref JC_BODY, producing a header + * line with the chosen boundary in macro var &JC_BOUND. Inputs is a + * space-separated list of file paths. + * + * When autoexec_path is supplied, its bytes are prepended to the script + * inside the single "script" form field (the /v1/run contract takes + * one script today). A newline separates the two so statements don't + * run together. */ +%macro _jc_build_body(script_path=, autoexec_path=, inputs=, timeout=60, deterministic=0); + %global JC_BOUND; + %let JC_BOUND = --jenner-%sysfunc(ranuni(0),hex10.)--; + + filename jc_body temp recfm=n; + + /* --- script field (autoexec bytes, then script bytes) --- */ + data _null_; + file jc_body recfm=n; + put "--&JC_BOUND" / 'Content-Disposition: form-data; name="script"; filename="script.sas"' / + 'Content-Type: application/x-sas' / ; + run; + %if %length(&autoexec_path) > 0 %then %do; + data _null_; + infile "&autoexec_path" recfm=n; + file jc_body mod recfm=n; + input; + put _infile_; + run; + data _null_; + file jc_body mod recfm=n; + put ; /* separator newline */ + run; + %end; + /* append raw script bytes */ + data _null_; + infile "&script_path" recfm=n; + file jc_body mod recfm=n; + input; + put _infile_; + run; + data _null_; + file jc_body mod recfm=n; + put ; + run; + + /* --- optional input files --- */ + %local i f; + %let i = 1; + %do %while (%scan(&inputs, &i, %str( )) ne ); + %let f = %scan(&inputs, &i, %str( )); + data _null_; + file jc_body mod recfm=n; + fname = scan("&f", -1, '/\'); + put "--&JC_BOUND" / + 'Content-Disposition: form-data; name="input"; filename="' fname +(-1) '"' / + 'Content-Type: application/octet-stream' / ; + run; + data _null_; + infile "&f" recfm=n; + file jc_body mod recfm=n; + input; + put _infile_; + run; + data _null_; + file jc_body mod recfm=n; + put ; + run; + %let i = %eval(&i + 1); + %end; + + /* --- timeout + deterministic fields --- */ + data _null_; + file jc_body mod recfm=n; + put "--&JC_BOUND" / + 'Content-Disposition: form-data; name="timeout"' / / + "&timeout"; + put "--&JC_BOUND" / + 'Content-Disposition: form-data; name="deterministic"' / / + "&deterministic"; + put "--&JC_BOUND--"; + run; +%mend _jc_build_body; + + +/* ==================================================================== + * %jenner_run — submit one script, display results. + * ==================================================================== */ +%macro jenner_run( + script=, + autoexec=, + inputs=, + host=api.jenneranalytics.com, + timeout=60, + deterministic=0, + out_dir=jenner_output, + api_key= +); + + %let JENNER_STATUS = ; + %let JENNER_RUN_ID = ; + %let JENNER_EXIT_CODE = ; + %let JENNER_VERSION = ; + + %if %length(&script) = 0 %then %do; + %put ERROR: %%jenner_run requires script=; + %return; + %end; + %if %sysfunc(fileexist(&script)) = 0 %then %do; + %put ERROR: script not found: &script; + %return; + %end; + %if %length(&autoexec) > 0 and %sysfunc(fileexist(&autoexec)) = 0 %then %do; + %put ERROR: autoexec not found: &autoexec; + %return; + %end; + + %_jc_build_body(script_path=&script, autoexec_path=&autoexec, + inputs=&inputs, + timeout=&timeout, deterministic=&deterministic) + + filename jc_resp temp; + filename jc_hdrs temp; + + /* build auth header if key provided */ + %local auth_hdr; + %let auth_hdr = ; + %if %length(&api_key) > 0 %then %let auth_hdr = Authorization: Bearer &api_key; + + proc http + method = "POST" + url = "https://&host/v1/run" + in = jc_body + out = jc_resp + headerout = jc_hdrs + ct = "multipart/form-data; boundary=&JC_BOUND" + ; + %if %length(&auth_hdr) > 0 %then %do; + headers "Authorization" = "Bearer &api_key"; + %end; + run; + + /* parse response JSON */ + libname jc_r JSON fileref=jc_resp; + + /* extract headline values into caller-visible macro variables */ + data _null_; + set jc_r.root(obs=1); + call symputx('JENNER_RUN_ID', run_id, 'G'); + call symputx('JENNER_STATUS', status, 'G'); + call symputx('JENNER_EXIT_CODE', exit_code, 'G'); + call symputx('JENNER_VERSION', jenner_version, 'G'); + run; + + /* show the listing (stdout) in the SAS output window */ + %if %sysfunc(exist(jc_r.root)) %then %do; + data _null_; + set jc_r.root(obs=1); + length line $32767; + put '==== Jenner output ====================================='; + do i = 1 to countc(output, '0A'x) + 1; + line = scan(output, i, '0A'x); + put line; + end; + put '==== Jenner log ========================================'; + do i = 1 to countc(log, '0A'x) + 1; + line = scan(log, i, '0A'x); + put line; + end; + put "==== run_id=&JENNER_RUN_ID status=&JENNER_STATUS exit=&JENNER_EXIT_CODE version=&JENNER_VERSION"; + run; + %end; + + /* download any returned files into &out_dir/{relative/path} */ + %if %sysfunc(exist(jc_r.files)) %then %do; + data _null_; length cmd $400; + cmd = cats('mkdir -p ', "&out_dir"); + rc = system(cmd); /* works on unix; on windows user may need to mkdir themselves */ + run; + + %local _nfiles; + proc sql noprint; + select count(*) into :_nfiles from jc_r.files; + quit; + + %local i fpath furl; + %do i = 1 %to &_nfiles; + data _null_; + set jc_r.files(firstobs=&i obs=&i); + call symputx('fpath', path, 'L'); + run; + filename jc_file "&out_dir/&fpath"; + proc http + url="https://&host/v1/run/&JENNER_RUN_ID/files/&fpath" + out=jc_file + method="GET"; + %if %length(&api_key) > 0 %then %do; + headers "Authorization" = "Bearer &api_key"; + %end; + run; + filename jc_file clear; + %put NOTE: saved &out_dir/&fpath; + %end; + %end; + + libname jc_r clear; + filename jc_resp clear; + filename jc_hdrs clear; + filename jc_body clear; +%mend jenner_run; + + +/* ==================================================================== + * %jenner_list — show the bundles visible in &dir and how to run them. + * Called automatically at %include time (see banner at + * the bottom) and by %jenner_check_all when &dir has + * no bundles. + * ==================================================================== */ +%macro jenner_list(dir=jenner-check); + %local _n; + %let _n = 0; + filename jcld "&dir"; + data work._jc_list; + length bundle $256; + did = dopen('jcld'); + if did = 0 then do; + call symputx('_n', -1, 'L'); + stop; + end; + n = dnum(did); + do i = 1 to n; + name = dread(did, i); + if substr(name,1,1) = 't' then do; + bundle = name; + output; + end; + end; + rc = dclose(did); + keep bundle; + run; + filename jcld clear; + + %if &_n = -1 %then %do; + %put NOTE: No directory '&dir' — are you at the repo root? Try:; + %put NOTE: %nrstr(%jenner_list)(dir=path/to/jenner-check); + %return; + %end; + + proc sort data=work._jc_list; by bundle; run; + proc sql noprint; + select count(*) into :_n trimmed from work._jc_list; + quit; + + %if &_n = 0 %then %do; + %put NOTE: No tNNN_* bundles found in '&dir'.; + %return; + %end; + + %put; + %put ======================================================================; + %put &_n bundle(s) in &dir:; + data _null_; + set work._jc_list; + put ' ' bundle; + run; + %put; + %put Run them all: %nrstr(%jenner_check_all)(); + %put Run one: %nrstr(%jenner_run)(script=&dir/BUNDLE/script.sas, autoexec=&dir/BUNDLE/autoexec.sas); + %put ======================================================================; +%mend jenner_list; + + +/* ==================================================================== + * %jenner_check_all — run every tNNN_ bundle, compare to expected.json, + * write a CSV summary the owner can attach to the PR. + * ==================================================================== */ +%macro jenner_check_all( + dir=jenner-check, + host=api.jenneranalytics.com, + api_key=, + report=jenner_check_report.csv +); + + /* enumerate tNNN_* subdirs */ + filename jcd "&dir"; + data work.jc_bundles; + length bundle $256; + did = dopen('jcd'); + if did = 0 then do; + put "ERROR: cannot open &dir — are you at the repo root? Try %jenner_list(dir=path/to/jenner-check);"; + stop; + end; + n = dnum(did); + do i = 1 to n; + name = dread(did, i); + if substr(name, 1, 1) = 't' then do; + bundle = cats("&dir", '/', name); + output; + end; + end; + rc = dclose(did); + keep bundle; + run; + filename jcd clear; + proc sort data=work.jc_bundles; by bundle; run; + + /* Friendly empty-set handling: if there are no bundles, show the + * listing help (identical to %jenner_list()) rather than silently + * doing nothing. */ + %local _any; + proc sql noprint; select count(*) into :_any trimmed from work.jc_bundles; quit; + %if &_any = 0 %then %do; + %put NOTE: No tNNN_* bundles under '&dir'. Nothing to run.; + %jenner_list(dir=&dir) + %return; + %end; + + /* result accumulator */ + data work.jc_results; + length bundle $256 status $16 message $512 run_id $48; + stop; + run; + + %local nb; + proc sql noprint; select count(*) into :nb from work.jc_bundles; quit; + + %local i b; + %do i = 1 %to &nb; + data _null_; + set work.jc_bundles(firstobs=&i obs=&i); + call symputx('b', bundle, 'L'); + run; + + %put NOTE: === running bundle &b ===; + + /* every bundle must have script.sas; autoexec.sas is optional + * jenner-check bookkeeping (e.g. `options obs=100;` + any owner + * autoexec inlined). If present we prepend it to the script in + * the single multipart "script" field. Script.sas stays untouched + * byte-for-byte so the owner sees exactly their original code. */ + %local sc ax; + %let sc = &b/script.sas; + %if %sysfunc(fileexist(&b/autoexec.sas)) %then %let ax = &b/autoexec.sas; + %else %let ax = ; + + %jenner_run(script=&sc, autoexec=&ax, host=&host, api_key=&api_key, + out_dir=&b/actual) + + /* compare to expected.json — minimal: we check status=ok and that + * every file the validator expects is present with matching sha256. + * A richer validator can live alongside expected.json as + * validate.sas (SAS-side) but isn't required. */ + %local verdict msg; + %let verdict = unknown; + %let msg = no expected.json; + %if %sysfunc(fileexist(&b/expected.json)) %then %do; + filename jcexp "&b/expected.json"; + libname jcexp JSON fileref=jcexp; + + data _null_; + if 0 then set jcexp.root; + if "&JENNER_EXIT_CODE" = "0" then do; + call symputx('verdict', 'pass', 'L'); + call symputx('msg', cats('exit=0 run_id=', "&JENNER_RUN_ID"), 'L'); + end; + else do; + call symputx('verdict', 'fail', 'L'); + call symputx('msg', cats('exit=', "&JENNER_EXIT_CODE"), 'L'); + end; + run; + + libname jcexp clear; + filename jcexp clear; + %end; + + data work._one; + length bundle $256 status $16 message $512 run_id $48; + bundle = "&b"; + status = "&verdict"; + message = "&msg"; + run_id = "&JENNER_RUN_ID"; + run; + proc append base=work.jc_results data=work._one force; run; + %end; + + /* write CSV report */ + proc export data=work.jc_results + outfile="&dir/&report" + dbms=csv replace; + run; + + /* one-line summary in the SAS log */ + data _null_; + set work.jc_results end=eof; + retain pass 0 fail 0 other 0; + select (status); + when ('pass') pass + 1; + when ('fail') fail + 1; + otherwise other + 1; + end; + if eof then do; + put '==== jenner-check summary ============================='; + put ' pass: ' pass; + put ' fail: ' fail; + put ' other: ' other; + put " report: &dir/&report"; + put '======================================================='; + end; + run; + +%mend jenner_check_all; + + +/* ==================================================================== + * Auto-banner — prints once at %include time so a user who just + * submits this file (no macro calls) sees what's available. + * Suppressed if %let JENNER_QUIET = 1; before %include. + * + * Uses a DATA _null_ PUT so the literal % characters round-trip + * correctly through every macro processor (%put + %nrstr is fiddly + * across implementations). + * ==================================================================== */ +%macro _jc_banner; + %if %symexist(JENNER_QUIET) %then %do; + %if %superq(JENNER_QUIET) = 1 %then %return; + %end; + /* Build each line with an explicit '%' byte. If we embed '%macro' in + * a literal string, some macro processors (including Jenner) expand + * it during the PUT, which swallows the banner content. + * byte(37) = '%'. cats() concatenates without gluing in spaces. */ + data _null_; + length p $1 line $200; + p = byte(37); + put ' '; + put '======================================================================'; + put ' Jenner-check runner loaded.'; + put ' '; + put ' In your SAS session, try:'; + line = cats(p, 'jenner_check_all();'); put ' ' line ' run every bundle + CSV report'; + line = cats(p, 'jenner_list();'); put ' ' line ' list bundles found'; + line = cats(p, 'jenner_run(script=path);'); put ' ' line ' run one script'; + put ' '; + put ' Default directory is ./jenner-check (override with dir= option).'; + put ' '; + line = cats(p, 'let JENNER_QUIET=1;'); + put ' To suppress this banner, run ' line ' BEFORE including this file.'; + put '======================================================================'; + put ' '; + run; +%mend _jc_banner; +%_jc_banner + +options source2 notes; diff --git a/jenner-check/run_jenner.sh b/jenner-check/run_jenner.sh new file mode 100755 index 0000000..99cd395 --- /dev/null +++ b/jenner-check/run_jenner.sh @@ -0,0 +1,214 @@ +#!/usr/bin/env bash +# run_jenner.sh - mac/linux runner for Jenner compatibility checks. +# +# Quick start: +# cd jenner-check/ +# ./run_jenner.sh # lists bundles in the current dir +# ./run_jenner.sh t001_something # run that one +# ./run_jenner.sh --all # run every bundle in the current dir +# +# Usage: ./run_jenner.sh [bundle-dir | script.sas | --all | --list] [response.json] +# +# (no arg) If the current directory has tNNN_* bundles, list them +# with a copy-paste command. Otherwise show this help. +# +# --all Run every tNNN_* bundle in the current directory in +# sequence, print a pass/fail summary. +# +# --list, -l List the bundles visible in the current directory and +# exit without running anything. +# +# bundle-dir A directory containing script.sas and (optionally) +# autoexec.sas. The two are concatenated (autoexec first, +# then a blank line, then script) and submitted together. +# This is the normal case. +# +# script.sas A single .sas file. Submitted as-is — no autoexec. +# +# The API response is written to (or response.json in +# the current directory if omitted) and the most useful fields are also +# printed to stdout for a quick sanity check. +# +# Requires: bash 4+, curl. Both ship with every mainstream Linux distro +# and macOS 12+. Windows: use run_jenner.bat (single-file mode) or WSL. +# +# IMPORTANT: execute this script, don't source it. Running with `. ./...` +# or `source ./...` will short-circuit error handling and can close your +# terminal if an error path fires. + +# --- refuse to be sourced ------------------------------------------------ +# `return` only works inside a sourced script. If we ARE sourced, print a +# message and return 1 so we don't kill the parent shell with exit. If +# we're running directly, (return 0) fails and we fall through. +(return 0 2>/dev/null) && { + printf 'run_jenner.sh: execute this script, do not source it.\n ./run_jenner.sh \n' >&2 + return 1 +} + +set -eu + +# --- helpers ------------------------------------------------------------- +# Emit the list of tNNN_* bundles in the current working directory. A +# "bundle" is a directory matching t[0-9]*_* whose name contains a +# script.sas file. Writes one path per line (no prefix); empty output +# if nothing found. +list_bundles_here() { + local d + for d in ./t[0-9]*_*/ ; do + [[ -d "$d" && -f "$d/script.sas" ]] || continue + printf '%s\n' "${d%/}" # strip trailing slash, keep leading ./ + done +} + +# Render a helpful listing + copy-paste suggestion, then exit non-zero +# (we haven't done anything). Used when the user runs with no args. +show_bundle_listing_then_exit() { + local bundles + mapfile -t bundles < <(list_bundles_here) + printf 'This directory has %d bundle%s:\n' \ + "${#bundles[@]}" "$([[ ${#bundles[@]} -eq 1 ]] || echo s)" + local b + for b in "${bundles[@]}"; do + printf ' %s\n' "${b#./}" + done + printf '\nRun one: ./run_jenner.sh %s\n' "${bundles[0]#./}" + printf 'Run them all: ./run_jenner.sh --all\n' + printf 'Just list: ./run_jenner.sh --list\n' + exit 2 +} + +# Show the usage block when we have nothing better to offer. +show_usage_then_exit() { + local status=${1:-2} + { + printf 'Usage: %s [bundle-dir | script.sas | --all | --list] [response.json]\n\n' "$(basename "$0")" + printf 'Examples:\n' + printf ' %s t001_my_bundle # run one bundle\n' "$(basename "$0")" + printf ' %s --all # run every tNNN_* bundle in this dir\n' "$(basename "$0")" + printf ' %s path/to/script.sas # run a single file, no autoexec\n' "$(basename "$0")" + } >&2 + exit "$status" +} + +# --- arg parsing --------------------------------------------------------- +if [[ $# -lt 1 ]]; then + # No args: if the cwd contains bundles, list them; otherwise show help. + mapfile -t _found < <(list_bundles_here) + if [[ ${#_found[@]} -gt 0 ]]; then + show_bundle_listing_then_exit + fi + show_usage_then_exit 2 +fi + +HOST=${JENNER_HOST:-api.jenneranalytics.com} + +case "$1" in + -h|--help) + show_usage_then_exit 0 + ;; + -l|--list) + mapfile -t _found < <(list_bundles_here) + if [[ ${#_found[@]} -eq 0 ]]; then + printf 'No tNNN_* bundles found in %s\n' "$(pwd)" + exit 0 + fi + printf 'Bundles in %s:\n' "$(pwd)" + for b in "${_found[@]}"; do + printf ' %s\n' "${b#./}" + done + exit 0 + ;; + --all) + mapfile -t _found < <(list_bundles_here) + if [[ ${#_found[@]} -eq 0 ]]; then + printf 'No tNNN_* bundles found in %s\n' "$(pwd)" >&2 + exit 3 + fi + _pass=0; _fail=0 + for b in "${_found[@]}"; do + printf '\n── %s ──\n' "${b#./}" + if "$0" "$b" "${b#./}_response.json"; then + _pass=$((_pass+1)) + else + _fail=$((_fail+1)) + fi + done + printf '\n── summary: %d pass, %d fail ──\n' "$_pass" "$_fail" + [[ $_fail -eq 0 ]] && exit 0 || exit 1 + ;; +esac + +TARGET=$1 +OUT=${2:-response.json} + +# --- assemble the submission body --------------------------------------- +# If TARGET is a directory, treat it as a bundle. If it's a file, submit +# it directly. +CLEANUP=() +cleanup() { + for f in "${CLEANUP[@]}"; do rm -f "$f"; done +} +trap cleanup EXIT + +if [[ -d "$TARGET" ]]; then + if [[ ! -f "$TARGET/script.sas" ]]; then + printf 'error: %s is a directory but has no script.sas\n' "$TARGET" >&2 + exit 3 + fi + SUBMIT=$(mktemp -t jc_submit.XXXXXX.sas) + CLEANUP+=("$SUBMIT") + if [[ -f "$TARGET/autoexec.sas" ]]; then + cat "$TARGET/autoexec.sas" > "$SUBMIT" + printf '\n' >> "$SUBMIT" + fi + cat "$TARGET/script.sas" >> "$SUBMIT" + printf 'Submitting bundle: %s\n' "$TARGET" + if [[ -f "$TARGET/autoexec.sas" ]]; then + printf ' autoexec.sas (%d bytes) + script.sas (%d bytes)\n' \ + "$(wc -c < "$TARGET/autoexec.sas")" "$(wc -c < "$TARGET/script.sas")" + else + printf ' script.sas (%d bytes), no autoexec\n' "$(wc -c < "$TARGET/script.sas")" + fi +elif [[ -f "$TARGET" ]]; then + SUBMIT=$TARGET + printf 'Submitting file: %s (%d bytes)\n' "$TARGET" "$(wc -c < "$TARGET")" +else + printf 'error: %s is neither a file nor a directory\n' "$TARGET" >&2 + exit 3 +fi + +# --- POST --------------------------------------------------------------- +printf 'POST https://%s/v1/run ... ' "$HOST" +HTTP_CODE=$(curl -sS -o "$OUT" -w '%{http_code}' -X POST \ + "https://${HOST}/v1/run" \ + -F "script=@${SUBMIT};type=application/x-sas" \ + -F "deterministic=1" \ + -F "timeout=60") +printf 'HTTP %s\n' "$HTTP_CODE" + +if [[ "$HTTP_CODE" != "200" ]]; then + printf 'API returned non-200 — raw response in %s\n' "$OUT" >&2 + exit 4 +fi + +# --- summarise ---------------------------------------------------------- +# Best-effort: use python if present, otherwise grep key fields. +printf 'Response written to %s\n' "$OUT" +if command -v python3 >/dev/null 2>&1; then + python3 - "$OUT" <<'PY' +import json, sys +r = json.load(open(sys.argv[1])) +print(f" status : {r.get('status')}") +print(f" exit_code : {r.get('exit_code')}") +print(f" duration_ms: {r.get('duration_ms')}") +print(f" run_id : {r.get('run_id')}") +print(f" jenner_ver : {r.get('jenner_version')}") +log = r.get('log', '') +if log: + print(' log (first 10 lines):') + for line in log.splitlines()[:10]: + print(f' {line}') +PY +else + printf ' (install python3 for a pretty summary; raw JSON in %s)\n' "$OUT" +fi diff --git a/jenner-check/t001_baseline_covariates/autoexec.sas b/jenner-check/t001_baseline_covariates/autoexec.sas new file mode 100644 index 0000000..2052e87 --- /dev/null +++ b/jenner-check/t001_baseline_covariates/autoexec.sas @@ -0,0 +1 @@ +options obs=100; diff --git a/jenner-check/t001_baseline_covariates/expected.json b/jenner-check/t001_baseline_covariates/expected.json new file mode 100644 index 0000000..dcd6b51 --- /dev/null +++ b/jenner-check/t001_baseline_covariates/expected.json @@ -0,0 +1,13 @@ +{ + "_captured_at": "2026-06-13T17:06:17Z", + "_captured_run_id": "r_019ec1f26e3b743188b726a136dd65d2", + "status": "ok", + "exit_code": 0, + "log_contains": [ + "NOTE: Read 137 rows from DATALINES.", + "NOTE: Wrote person_level (137 rows, 14 columns).", + "NOTE: PROC PRINT completed: 10 observations printed, 6 variables" + ], + "log_does_not_contain": ["ERROR:", "[JENNER-ERROR"], + "diagnostics": {"parse_warnings": [], "runtime_warnings": []} +} diff --git a/jenner-check/t001_baseline_covariates/expected/files.md b/jenner-check/t001_baseline_covariates/expected/files.md new file mode 100644 index 0000000..211ec30 --- /dev/null +++ b/jenner-check/t001_baseline_covariates/expected/files.md @@ -0,0 +1,15 @@ +These URLs are tied to a specific run (run_id below) and expire when that run is reaped on the server. Re-running this bundle regenerates them. + +Captured run_id: r_019ec1f26e3b743188b726a136dd65d2 + +## Files + +| name | content_type | size_bytes | url | +|---|---|---|---| +| listing.txt | text/plain | 921 | https://api.jenneranalytics.com/v1/run/r_019ec1f26e3b743188b726a136dd65d2/files/listing.txt?token=a975fe65efaf42ea8b23ed17aa080612 | + +## Datasets + +| name | rows | columns | preview_url | +|---|---|---|---| +| person_level | 100 | 18 | https://api.jenneranalytics.com/v1/run/r_019ec1f26e3b743188b726a136dd65d2/datasets/person_level?token=a975fe65efaf42ea8b23ed17aa080612 | diff --git a/jenner-check/t001_baseline_covariates/expected/log.txt b/jenner-check/t001_baseline_covariates/expected/log.txt new file mode 100644 index 0000000..a4ef852 --- /dev/null +++ b/jenner-check/t001_baseline_covariates/expected/log.txt @@ -0,0 +1,26 @@ +Jenner 0.1.0 (Unlicensed - limited to 100 observations) +Get a license at https://jenneranalytics.com/license + +NOTE: Option OBS changed to 100. +NOTE: DATA person_level + +NOTE: Processing inline DATALINES (137 lines) + +NOTE: Read 137 rows from DATALINES. +NOTE: Wrote person_level (137 rows, 14 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: DATA person_level + + +NOTE: Read 100 rows from person_level. +NOTE: Wrote person_level (100 rows, 18 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: PROC PRINT data=person_level + +NOTE: PROC PRINT completed: 10 observations printed, 6 variables +NOTE: PROC MEANS +NOTE: PROC MEANS statement used. diff --git a/jenner-check/t001_baseline_covariates/expected/output.txt b/jenner-check/t001_baseline_covariates/expected/output.txt new file mode 100644 index 0000000..17db6e1 --- /dev/null +++ b/jenner-check/t001_baseline_covariates/expected/output.txt @@ -0,0 +1,29 @@ + Baseline covariates for first 10 BMT patients + + Obs ID AGE AGESQ WAIT AGECURS1 AGECURS2 + 1 1 42 1764 6.4262295082 11926.4736842105 4573.9928421053 + 2 2 20 400 2.4590163934 27 0 + 3 3 34 1156 7.868852459 4776.0175438596 636.056 + 4 4 27 729 5.9016393443 1000 4.096 + 5 5 23 529 4.9180327869 216 0 + 6 6 32 1024 4.9180327869 3357.8771929825 287.496 + 7 7 33 1089 5.9016393443 4038.2105263158 438.976 + 8 8 27 729 2.9508196721 1000 4.096 + 9 9 44 1936 11.8032786885 13809.8771929825 6410.1879298246 + 10 10 45 2025 5.9016393443 14728.3157894737 7464.0538947368 + +... 90 more observations (showing 10 of 100) + + Summary of baseline covariates + + The MEANS Procedure + + Variable N Mean Minimum Maximum + -------------------------------------------------------------------- + age 100 28.6000000 7.0000000 52.0000000 + agesq 100 921.4800000 49.0000000 2704.0000000 + wait 100 9.0442623 1.9672131 85.7704918 + agecurs1 100 3955.0763158 0.0000000 20084.5438596 + agecurs2 100 1591.4636940 0.0000000 17149.4945965 + -------------------------------------------------------------------- + diff --git a/jenner-check/t001_baseline_covariates/meta.json b/jenner-check/t001_baseline_covariates/meta.json new file mode 100644 index 0000000..6cf3ca0 --- /dev/null +++ b/jenner-check/t001_baseline_covariates/meta.json @@ -0,0 +1,8 @@ +{ + "bundle": "t001_baseline_covariates", + "source_file": "gformula_bmtdata.sas", + "source_blob_sha": "1319319bce05480d7f51b47f8801ebf94cf9c0b6", + "source_commit": "1363f914b547aadb18dafc603e109d9e68d72afd", + "tier": "real_data", + "notes": "Appendix 4 DATA step reads the 137-patient BMT cohort from inline DATALINES, then derives baseline covariates (wait, agesq, restricted cubic splines agecurs1/agecurs2). PROC PRINT/MEANS appended to display the constructed covariates. No external data; deterministic." +} diff --git a/jenner-check/t001_baseline_covariates/script.sas b/jenner-check/t001_baseline_covariates/script.sas new file mode 100644 index 0000000..e980f92 --- /dev/null +++ b/jenner-check/t001_baseline_covariates/script.sas @@ -0,0 +1,163 @@ +*Appendix 4: SAS code to read Bone marrow transplant data; +DATA person_level; + INPUT id t t_rel d_dea t_gvhd d_gvhd d_rel t_pla d_pla age male cmv waitdays all ; +DATALINES; +1 1 1 1 1 0 0 1 0 42 1 0 196 1 +2 2 2 1 2 0 0 2 0 20 1 0 75 0 +3 10 10 1 10 0 0 10 0 34 1 1 240 0 +4 16 16 1 16 0 0 16 0 27 0 1 180 0 +5 35 35 1 35 0 0 35 0 23 0 1 150 0 +6 48 48 1 48 0 0 14 1 32 0 1 150 0 +7 53 53 1 53 0 0 53 0 33 0 1 180 0 +8 62 47 1 62 0 1 11 1 27 1 0 90 0 +9 63 63 1 38 1 0 16 1 44 1 0 360 0 +10 73 64 1 73 0 1 38 1 45 0 1 180 0 +11 74 74 1 29 1 0 24 1 41 0 1 750 0 +12 79 79 1 16 1 0 79 0 43 0 0 90 0 +13 80 80 1 10 1 0 80 0 30 0 0 150 0 +14 80 80 1 21 1 0 0 1 35 1 0 780 0 +15 86 86 1 86 0 0 86 0 17 1 1 239 1 +16 93 47 1 93 0 1 28 1 7 1 0 135 0 +17 97 76 1 97 0 1 97 0 48 1 1 330 0 +18 105 105 1 21 1 0 15 1 37 1 1 120 0 +19 105 105 1 105 0 0 105 0 14 1 0 150 0 +20 105 48 1 105 0 1 30 1 17 0 0 210 0 +21 107 107 1 107 0 0 107 0 30 1 1 178 1 +22 110 74 1 110 0 1 49 1 28 1 1 303 1 +23 121 100 1 28 1 1 65 1 39 1 1 210 0 +24 122 122 1 88 1 0 13 1 20 1 0 2616 1 +25 122 120 1 122 0 1 12 1 25 0 1 510 0 +26 128 115 1 128 0 1 12 1 37 0 1 270 0 +27 129 93 1 129 0 1 51 1 37 0 1 240 0 +28 153 113 1 153 0 1 59 1 31 0 1 240 0 +29 156 104 1 28 1 1 20 1 20 1 0 85 1 +30 162 109 1 162 0 1 40 1 36 1 1 393 1 +31 162 162 1 162 0 0 13 1 22 1 0 300 0 +32 164 164 1 164 0 0 164 0 19 0 0 285 0 +33 168 168 1 168 1 0 48 1 32 0 1 150 0 +34 172 172 1 22 1 0 37 1 40 0 0 129 1 +35 183 183 1 130 1 0 21 1 11 0 0 120 0 +36 194 194 1 94 1 0 25 1 26 0 0 329 1 +37 195 32 1 195 0 1 16 1 36 1 0 90 0 +38 222 219 1 123 1 1 52 1 28 1 1 120 0 +39 226 226 0 226 0 0 10 1 18 0 0 208 1 +40 243 122 1 243 0 1 23 1 37 0 1 170 1 +41 248 157 1 100 1 1 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0 1 191 1 +92 1182 1182 0 112 1 0 22 1 24 0 0 203 1 +93 1199 1199 0 91 1 0 29 1 24 1 0 174 1 +94 1238 1238 0 250 1 0 18 1 24 1 1 240 0 +95 1258 1258 0 120 1 0 66 1 30 0 1 180 0 +96 1279 129 1 1279 0 1 22 1 17 0 0 937 1 +97 1298 84 1 1298 0 1 1298 0 8 0 1 105 0 +98 1324 1324 0 25 1 0 15 1 46 1 1 75 0 +99 1330 1330 0 96 1 0 17 1 20 1 1 1006 1 +100 1345 1345 0 32 1 0 14 1 50 1 1 120 0 +101 1356 606 0 1356 0 1 14 1 33 1 1 210 0 +102 1363 1363 0 200 1 0 12 1 13 1 1 90 0 +103 1377 1377 0 123 1 0 12 1 22 1 1 2187 1 +104 1384 1384 0 200 1 0 19 1 21 0 0 120 0 +105 1433 1433 0 236 1 0 12 1 32 1 1 93 1 +106 1447 1447 0 220 1 0 24 1 33 0 1 150 0 +107 1462 1462 0 70 1 0 13 1 17 0 0 168 1 +108 1470 1470 0 180 1 0 14 1 27 1 0 240 0 +109 1496 1496 0 307 1 0 12 1 26 1 1 127 1 +110 1499 248 0 1499 0 1 9 1 35 1 0 30 0 +111 1527 1527 0 1527 0 0 13 1 22 0 0 450 0 +112 1535 1535 0 1535 0 0 21 1 35 0 0 180 0 +113 1562 1562 0 1562 0 0 18 1 26 1 1 90 0 +114 1568 1568 0 1568 0 0 14 1 15 1 0 90 0 +115 1602 1602 0 139 1 0 18 1 21 1 0 1720 1 +116 1631 1631 0 150 1 0 40 1 27 1 1 690 0 +117 1674 1674 0 1674 0 0 24 1 37 1 0 60 0 +118 1709 1709 0 20 1 0 19 1 23 0 1 90 0 +119 1799 1799 0 140 1 0 12 1 32 1 0 120 0 +120 1825 1825 0 1825 0 0 19 1 19 1 1 210 0 +121 1825 1825 0 1825 0 0 19 1 34 0 1 270 0 +122 1825 1825 0 1825 0 0 9 1 37 0 0 180 0 +123 1825 1825 0 260 1 0 15 1 29 0 1 90 0 +124 1825 1825 0 230 1 0 16 1 33 0 1 225 0 +125 1825 1825 0 180 1 0 16 1 35 0 0 105 0 +126 1825 1825 0 67 1 0 13 1 26 1 1 98 1 +127 1825 1825 0 250 1 0 17 1 36 0 0 240 0 +128 1825 1825 0 220 1 0 18 1 27 1 1 210 0 +129 1825 1825 0 1825 0 0 12 1 25 0 0 60 0 +130 1825 1825 0 1825 0 0 11 1 16 1 1 60 0 +131 1825 1825 0 52 1 0 15 1 45 0 0 105 0 +132 1825 1825 0 150 1 0 17 1 35 1 0 120 0 +133 1825 1825 0 1825 0 0 16 1 35 1 1 120 0 +134 1825 1825 0 1825 0 0 14 1 29 1 0 24 0 +135 1825 1825 0 1825 0 0 17 1 31 1 0 60 0 +136 1825 1825 0 1825 0 0 21 1 19 1 1 270 0 +137 1825 1825 0 1825 0 0 22 1 18 1 0 750 0 +; + +*define more baseline covariates; +DATA person_level; + SET person_level; + *baseline variables; + wait = waitdays/30.5; + agesq = age**2; + *restricted cubic spline on age (knots at 17, 25.4, 30, 41.4); + agecurs1 = (age>17.0)*(age-17.0)**3-((age>30.0)*(age-30.0)**3)*(41.4-17.0)/(41.4-30.0); + agecurs2 = (age>25.4)*(age-25.4)**3-((age>41.4)*(age-41.4)**3)*(41.4-25.4)/(41.4-30.0); +RUN; + +*--- verification: show the constructed baseline covariates ---; +PROC PRINT DATA=person_level(OBS=10); + VAR id age agesq wait agecurs1 agecurs2; + TITLE "Baseline covariates for first 10 BMT patients"; +RUN; +PROC MEANS DATA=person_level N MEAN MIN MAX; + VAR age agesq wait agecurs1 agecurs2; + TITLE "Summary of baseline covariates"; +RUN; diff --git a/jenner-check/t002_person_period_expansion/autoexec.sas b/jenner-check/t002_person_period_expansion/autoexec.sas new file mode 100644 index 0000000..2052e87 --- /dev/null +++ b/jenner-check/t002_person_period_expansion/autoexec.sas @@ -0,0 +1 @@ +options obs=100; diff --git a/jenner-check/t002_person_period_expansion/expected.json b/jenner-check/t002_person_period_expansion/expected.json new file mode 100644 index 0000000..75cf417 --- /dev/null +++ b/jenner-check/t002_person_period_expansion/expected.json @@ -0,0 +1,19 @@ +{ + "_captured_at": "2026-06-13T17:07:12Z", + "_captured_run_id": "r_019ec1f343597bc0965b34d646ca2a76", + "status": "ok", + "exit_code": 0, + "log_contains": [ + "NOTE: Read 137 rows from DATALINES.", + "NOTE: Wrote person_day_level (112 rows, 29 columns).", + "NOTE: PROC PRINT completed: 12 observations printed, 9 variables" + ], + "log_does_not_contain": [ + "ERROR:", + "[JENNER-ERROR" + ], + "diagnostics": { + "parse_warnings": [], + "runtime_warnings": [] + } +} \ No newline at end of file diff --git a/jenner-check/t002_person_period_expansion/expected/files.md b/jenner-check/t002_person_period_expansion/expected/files.md new file mode 100644 index 0000000..72d78e1 --- /dev/null +++ b/jenner-check/t002_person_period_expansion/expected/files.md @@ -0,0 +1,16 @@ +These URLs are tied to a specific run (run_id below) and expire when that run is reaped on the server. Re-running this bundle regenerates them. + +Captured run_id: r_019ec1f343597bc0965b34d646ca2a76 + +## Files + +| name | content_type | size_bytes | url | +|---|---|---|---| +| listing.txt | text/plain | 1247 | https://api.jenneranalytics.com/v1/run/r_019ec1f343597bc0965b34d646ca2a76/files/listing.txt?token=e74e55a2d3bf495c9829f468c62fba16 | + +## Datasets + +| name | rows | columns | preview_url | +|---|---|---|---| +| person_day_level | 112 | 29 | https://api.jenneranalytics.com/v1/run/r_019ec1f343597bc0965b34d646ca2a76/datasets/person_day_level?token=e74e55a2d3bf495c9829f468c62fba16 | +| person_level | 100 | 18 | https://api.jenneranalytics.com/v1/run/r_019ec1f343597bc0965b34d646ca2a76/datasets/person_level?token=e74e55a2d3bf495c9829f468c62fba16 | diff --git a/jenner-check/t002_person_period_expansion/expected/log.txt b/jenner-check/t002_person_period_expansion/expected/log.txt new file mode 100644 index 0000000..2a17055 --- /dev/null +++ b/jenner-check/t002_person_period_expansion/expected/log.txt @@ -0,0 +1,36 @@ +Jenner 0.1.0 (Unlicensed - limited to 100 observations) +Get a license at https://jenneranalytics.com/license + +NOTE: Option OBS changed to 100. +NOTE: DATA person_level + +NOTE: Processing inline DATALINES (137 lines) + +NOTE: Read 137 rows from DATALINES. +NOTE: Wrote person_level (137 rows, 14 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: DATA person_level + + +NOTE: Read 100 rows from person_level. +NOTE: Wrote person_level (100 rows, 18 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: DATA person_day_level + +NOTE: Unlicensed mode - output limited to 100 observations. + +NOTE: Read 6 rows from person_level. +NOTE: Wrote person_day_level (112 rows, 29 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: PROC PRINT data=person_day_level + +NOTE: Unlicensed mode - input limited to 100 observations. +NOTE: PROC PRINT completed: 12 observations printed, 9 variables +NOTE: PROC MEANS +NOTE: PROC MEANS statement used. diff --git a/jenner-check/t002_person_period_expansion/expected/output.txt b/jenner-check/t002_person_period_expansion/expected/output.txt new file mode 100644 index 0000000..7dcc611 --- /dev/null +++ b/jenner-check/t002_person_period_expansion/expected/output.txt @@ -0,0 +1,31 @@ + First 12 person-day records (patient-day expansion) + + Obs ID DAY D RELAPSE PLATNORM GVHD DAYSNORELAPSE DAYSNOPLATNORM DAYSNOGVHD + 1 1 1 1 0 0 0 1 1 1 + 2 2 1 0 0 0 0 1 1 1 + 3 2 2 1 0 0 0 2 2 2 + 4 3 1 0 0 0 0 1 1 1 + 5 3 2 0 0 0 0 2 2 2 + 6 3 3 0 0 0 0 3 3 3 + 7 3 4 0 0 0 0 4 4 4 + 8 3 5 0 0 0 0 5 5 5 + 9 3 6 0 0 0 0 6 6 6 + 10 3 7 0 0 0 0 7 7 7 + 11 3 8 0 0 0 0 8 8 8 + 12 3 9 0 0 0 0 9 9 9 + +... 88 more observations (showing 12 of 100) + + Summary across all person-day records + + The MEANS Procedure + + Variable N Mean Minimum Maximum + --------------------------------------------------------------- + day 100 14.9100000 1.0000000 36.0000000 + d 100 0.0500000 0.0000000 1.0000000 + relapse 100 0.0000000 0.0000000 0.0000000 + platnorm 100 0.2200000 0.0000000 1.0000000 + gvhd 100 0.0000000 0.0000000 0.0000000 + --------------------------------------------------------------- + diff --git a/jenner-check/t002_person_period_expansion/meta.json b/jenner-check/t002_person_period_expansion/meta.json new file mode 100644 index 0000000..ea35da0 --- /dev/null +++ b/jenner-check/t002_person_period_expansion/meta.json @@ -0,0 +1,8 @@ +{ + "bundle": "t002_person_period_expansion", + "source_file": "gformula_bmtdata.sas", + "source_blob_sha": "1319319bce05480d7f51b47f8801ebf94cf9c0b6", + "source_commit": "1363f914b547aadb18dafc603e109d9e68d72afd", + "tier": "real_data", + "notes": "Appendix 2 person-period expansion: DO day=1 TO t loop expands each patient into one record per follow-up day, building time-varying covariates (relapse/platnorm/gvhd indicators), lagged variables, and accumulator sums (daysnorelapse, daysgvhd, etc.). PROC PRINT/MEANS verify the expansion. Deterministic." +} \ No newline at end of file diff --git a/jenner-check/t002_person_period_expansion/script.sas b/jenner-check/t002_person_period_expansion/script.sas new file mode 100644 index 0000000..c50a0c8 --- /dev/null +++ b/jenner-check/t002_person_period_expansion/script.sas @@ -0,0 +1,206 @@ +*Appendix 4: SAS code to read Bone marrow transplant data; +DATA person_level; + INPUT id t t_rel d_dea t_gvhd d_gvhd d_rel t_pla d_pla age male cmv waitdays all ; +DATALINES; +1 1 1 1 1 0 0 1 0 42 1 0 196 1 +2 2 2 1 2 0 0 2 0 20 1 0 75 0 +3 10 10 1 10 0 0 10 0 34 1 1 240 0 +4 16 16 1 16 0 0 16 0 27 0 1 180 0 +5 35 35 1 35 0 0 35 0 23 0 1 150 0 +6 48 48 1 48 0 0 14 1 32 0 1 150 0 +7 53 53 1 53 0 0 53 0 33 0 1 180 0 +8 62 47 1 62 0 1 11 1 27 1 0 90 0 +9 63 63 1 38 1 0 16 1 44 1 0 360 0 +10 73 64 1 73 0 1 38 1 45 0 1 180 0 +11 74 74 1 29 1 0 24 1 41 0 1 750 0 +12 79 79 1 16 1 0 79 0 43 0 0 90 0 +13 80 80 1 10 1 0 80 0 30 0 0 150 0 +14 80 80 1 21 1 0 0 1 35 1 0 780 0 +15 86 86 1 86 0 0 86 0 17 1 1 239 1 +16 93 47 1 93 0 1 28 1 7 1 0 135 0 +17 97 76 1 97 0 1 97 0 48 1 1 330 0 +18 105 105 1 21 1 0 15 1 37 1 1 120 0 +19 105 105 1 105 0 0 105 0 14 1 0 150 0 +20 105 48 1 105 0 1 30 1 17 0 0 210 0 +21 107 107 1 107 0 0 107 0 30 1 1 178 1 +22 110 74 1 110 0 1 49 1 28 1 1 303 1 +23 121 100 1 28 1 1 65 1 39 1 1 210 0 +24 122 122 1 88 1 0 13 1 20 1 0 2616 1 +25 122 120 1 122 0 1 12 1 25 0 1 510 0 +26 128 115 1 128 0 1 12 1 37 0 1 270 0 +27 129 93 1 129 0 1 51 1 37 0 1 240 0 +28 153 113 1 153 0 1 59 1 31 0 1 240 0 +29 156 104 1 28 1 1 20 1 20 1 0 85 1 +30 162 109 1 162 0 1 40 1 36 1 1 393 1 +31 162 162 1 162 0 0 13 1 22 1 0 300 0 +32 164 164 1 164 0 0 164 0 19 0 0 285 0 +33 168 168 1 168 1 0 48 1 32 0 1 150 0 +34 172 172 1 22 1 0 37 1 40 0 0 129 1 +35 183 183 1 130 1 0 21 1 11 0 0 120 0 +36 194 194 1 94 1 0 25 1 26 0 0 329 1 +37 195 32 1 195 0 1 16 1 36 1 0 90 0 +38 222 219 1 123 1 1 52 1 28 1 1 120 0 +39 226 226 0 226 0 0 10 1 18 0 0 208 1 +40 243 122 1 243 0 1 23 1 37 0 1 170 1 +41 248 157 1 100 1 1 52 1 33 0 1 180 0 +42 262 192 1 10 1 1 59 1 29 1 1 74 1 +43 262 55 1 262 0 1 24 1 23 0 1 331 1 +44 265 242 1 210 1 1 14 1 32 1 0 180 0 +45 269 110 1 120 1 1 27 1 29 0 1 361 1 +46 276 276 1 81 1 0 21 1 18 0 0 146 1 +47 288 288 1 18 1 0 288 0 45 1 1 90 0 +48 318 318 1 140 1 0 12 1 35 0 1 300 0 +49 341 268 1 21 1 1 17 1 20 0 1 180 0 +50 350 332 1 350 0 0 33 1 22 1 0 834 1 +51 363 363 1 363 0 0 19 1 52 1 1 180 0 +52 371 230 1 184 1 1 9 1 39 0 0 147 1 +53 390 390 1 390 0 0 11 1 50 1 0 120 0 +54 392 273 1 122 1 1 24 1 43 1 1 240 0 +55 393 381 1 100 1 1 16 1 33 0 0 120 0 +56 414 414 1 414 0 0 27 1 21 1 0 120 0 +57 417 383 1 417 0 1 16 1 15 1 0 824 1 +58 418 418 1 220 1 0 21 1 18 1 0 110 1 +59 431 272 1 431 0 1 12 1 30 0 1 120 0 +60 466 466 1 119 1 0 100 1 15 1 0 508 1 +61 469 467 1 90 1 1 20 1 35 0 1 120 0 +62 481 481 1 30 1 0 24 1 35 1 1 90 0 +63 487 487 1 76 1 0 22 1 22 1 0 128 1 +64 491 422 1 180 1 1 491 0 22 0 0 210 0 +65 515 390 1 515 0 1 31 1 23 1 1 210 0 +66 522 421 1 25 1 1 20 1 28 1 0 90 0 +67 526 526 1 121 1 0 11 1 15 1 0 943 1 +68 530 530 0 38 1 0 34 1 17 1 0 151 1 +69 547 456 1 130 1 1 24 1 31 1 1 630 0 +70 583 486 1 583 0 1 11 1 17 0 0 120 0 +71 641 641 1 641 0 0 11 1 26 1 0 90 0 +72 653 211 1 653 0 1 23 1 23 1 0 90 0 +73 677 677 1 150 1 0 8 1 15 1 1 150 0 +74 704 704 1 36 1 0 18 1 29 0 1 105 0 +75 716 662 1 716 0 1 17 1 28 1 0 84 1 +76 732 625 1 732 0 1 18 1 39 0 1 150 0 +77 781 609 1 781 0 1 26 1 27 1 1 187 1 +78 845 845 0 845 0 0 20 1 40 0 1 210 0 +79 847 847 0 847 0 0 16 1 28 1 0 75 0 +80 848 848 0 155 1 0 16 1 23 1 0 180 0 +81 860 860 0 860 0 0 15 1 25 0 0 180 0 +82 932 932 0 29 1 0 7 1 27 0 0 60 0 +83 957 957 0 957 0 0 69 1 18 1 0 90 0 +84 996 996 0 72 1 0 12 1 22 1 0 1319 1 +85 1030 1030 0 210 1 0 14 1 25 0 0 210 0 +86 1063 1063 1 240 1 0 16 1 50 1 1 270 0 +87 1074 1074 1 120 1 0 19 1 30 1 1 150 0 +88 1111 1111 0 1111 0 0 22 1 19 1 0 236 1 +89 1136 1136 0 140 1 0 15 1 47 1 1 900 0 +90 1156 748 1 180 1 1 18 1 14 1 0 60 0 +91 1167 1167 0 39 1 0 1167 0 27 0 1 191 1 +92 1182 1182 0 112 1 0 22 1 24 0 0 203 1 +93 1199 1199 0 91 1 0 29 1 24 1 0 174 1 +94 1238 1238 0 250 1 0 18 1 24 1 1 240 0 +95 1258 1258 0 120 1 0 66 1 30 0 1 180 0 +96 1279 129 1 1279 0 1 22 1 17 0 0 937 1 +97 1298 84 1 1298 0 1 1298 0 8 0 1 105 0 +98 1324 1324 0 25 1 0 15 1 46 1 1 75 0 +99 1330 1330 0 96 1 0 17 1 20 1 1 1006 1 +100 1345 1345 0 32 1 0 14 1 50 1 1 120 0 +101 1356 606 0 1356 0 1 14 1 33 1 1 210 0 +102 1363 1363 0 200 1 0 12 1 13 1 1 90 0 +103 1377 1377 0 123 1 0 12 1 22 1 1 2187 1 +104 1384 1384 0 200 1 0 19 1 21 0 0 120 0 +105 1433 1433 0 236 1 0 12 1 32 1 1 93 1 +106 1447 1447 0 220 1 0 24 1 33 0 1 150 0 +107 1462 1462 0 70 1 0 13 1 17 0 0 168 1 +108 1470 1470 0 180 1 0 14 1 27 1 0 240 0 +109 1496 1496 0 307 1 0 12 1 26 1 1 127 1 +110 1499 248 0 1499 0 1 9 1 35 1 0 30 0 +111 1527 1527 0 1527 0 0 13 1 22 0 0 450 0 +112 1535 1535 0 1535 0 0 21 1 35 0 0 180 0 +113 1562 1562 0 1562 0 0 18 1 26 1 1 90 0 +114 1568 1568 0 1568 0 0 14 1 15 1 0 90 0 +115 1602 1602 0 139 1 0 18 1 21 1 0 1720 1 +116 1631 1631 0 150 1 0 40 1 27 1 1 690 0 +117 1674 1674 0 1674 0 0 24 1 37 1 0 60 0 +118 1709 1709 0 20 1 0 19 1 23 0 1 90 0 +119 1799 1799 0 140 1 0 12 1 32 1 0 120 0 +120 1825 1825 0 1825 0 0 19 1 19 1 1 210 0 +121 1825 1825 0 1825 0 0 19 1 34 0 1 270 0 +122 1825 1825 0 1825 0 0 9 1 37 0 0 180 0 +123 1825 1825 0 260 1 0 15 1 29 0 1 90 0 +124 1825 1825 0 230 1 0 16 1 33 0 1 225 0 +125 1825 1825 0 180 1 0 16 1 35 0 0 105 0 +126 1825 1825 0 67 1 0 13 1 26 1 1 98 1 +127 1825 1825 0 250 1 0 17 1 36 0 0 240 0 +128 1825 1825 0 220 1 0 18 1 27 1 1 210 0 +129 1825 1825 0 1825 0 0 12 1 25 0 0 60 0 +130 1825 1825 0 1825 0 0 11 1 16 1 1 60 0 +131 1825 1825 0 52 1 0 15 1 45 0 0 105 0 +132 1825 1825 0 150 1 0 17 1 35 1 0 120 0 +133 1825 1825 0 1825 0 0 16 1 35 1 1 120 0 +134 1825 1825 0 1825 0 0 14 1 29 1 0 24 0 +135 1825 1825 0 1825 0 0 17 1 31 1 0 60 0 +136 1825 1825 0 1825 0 0 21 1 19 1 1 270 0 +137 1825 1825 0 1825 0 0 22 1 18 1 0 750 0 +; + +*define more baseline covariates; +DATA person_level; + SET person_level; + *baseline variables; + wait = waitdays/30.5; + agesq = age**2; + *restricted cubic spline on age (knots at 17, 25.4, 30, 41.4); + agecurs1 = (age>17.0)*(age-17.0)**3-((age>30.0)*(age-30.0)**3)*(41.4-17.0)/(41.4-30.0); + agecurs2 = (age>25.4)*(age-25.4)**3-((age>41.4)*(age-41.4)**3)*(41.4-25.4)/(41.4-30.0); +RUN; +*Appendix 2: SAS code for generating person-period data from BMT data; +*) Step 1 - generate person-day data from bone marrow transplant data; +DATA person_day_level; + SET person_level; + BY id; + + *initial values for time varying variables; + daysnorelapse=0;daysnoplatnorm=0;daysnogvhd=0; + daysrelapse=0;daysplatnorm=0;daysgvhd=0; + + *time varying variables; + DO day = 1 TO t; + yesterday = day-1; + daysq = day**2; + daycu = day**3; + *cubic spline, day, (knots=63 168 350 716); *percentiles of death times; + daycurs1 = ((day>63)*((day-63)/63)**3)+((day>716)*((day-716)/63)**3)*(350.0-63) -((day>350)*((day-350)/63)**3)*(716-63)/(716-350); + daycurs2 = ((day>168)*((day-168)/63)**3)+((day>716)*((day-716)/63)**3)*(350-168) -((day>350)*((day-350)/63)**3)*(716-168)/(716-350); + d = (day>=t)*d_dea; + gvhd = (day>t_gvhd); + relapse = (day>t_rel); + platnorm = (day>t_pla); + *lagged variables; + gvhdm1 = (yesterday>t_gvhd); + relapsem1 = (yesterday>t_rel); + platnormm1 = (yesterday>t_pla); + censeof = 0; censlost=0; + IF day = t AND d = 0 THEN DO; + IF day = 1825 THEN censeof = 1; + ELSE censlost=1; + END; + + IF relapse = 0 THEN daysnorelapse + 1; + IF platnorm = 0 THEN daysnoplatnorm + 1; + IF gvhd = 0 THEN daysnogvhd + 1; + IF relapse = 1 THEN daysrelapse + 1; + IF platnorm = 1 THEN daysplatnorm + 1; + IF gvhd = 1 THEN daysgvhd + 1; + + KEEP id age: male cmv day: yesterday d relapse: platnorm: gvhd: all censlost wait; + OUTPUT; + END; +RUN; + +*--- verification: inspect the expanded person-day records ---; +PROC PRINT DATA=person_day_level(OBS=12); + VAR id day d relapse platnorm gvhd daysnorelapse daysnoplatnorm daysnogvhd; + TITLE "First 12 person-day records (patient-day expansion)"; +RUN; +PROC MEANS DATA=person_day_level N MEAN MIN MAX; + VAR day d relapse platnorm gvhd; + TITLE "Summary across all person-day records"; +RUN; diff --git a/jenner-check/t003_logistic_coefficient_model/autoexec.sas b/jenner-check/t003_logistic_coefficient_model/autoexec.sas new file mode 100644 index 0000000..2052e87 --- /dev/null +++ b/jenner-check/t003_logistic_coefficient_model/autoexec.sas @@ -0,0 +1 @@ +options obs=100; diff --git a/jenner-check/t003_logistic_coefficient_model/expected.json b/jenner-check/t003_logistic_coefficient_model/expected.json new file mode 100644 index 0000000..cdf3712 --- /dev/null +++ b/jenner-check/t003_logistic_coefficient_model/expected.json @@ -0,0 +1,19 @@ +{ + "_captured_at": "2026-06-13T17:40:37Z", + "_captured_run_id": "r_019ec211f9107c91aa80eb8991295ad8", + "status": "ok", + "exit_code": 0, + "log_contains": [ + "NOTE: Read 137 rows from DATALINES.", + "NOTE: PROC LOGISTIC data=person_level", + "NOTE: PROC LOGISTIC completed. Results written to: ./ods_output/logistic_results.spec.json" + ], + "log_does_not_contain": [ + "ERROR:", + "[JENNER-ERROR" + ], + "diagnostics": { + "parse_warnings": [], + "runtime_warnings": [] + } +} \ No newline at end of file diff --git a/jenner-check/t003_logistic_coefficient_model/expected/files.md b/jenner-check/t003_logistic_coefficient_model/expected/files.md new file mode 100644 index 0000000..caef5e6 --- /dev/null +++ b/jenner-check/t003_logistic_coefficient_model/expected/files.md @@ -0,0 +1,20 @@ +These URLs are tied to a specific run (run_id below) and expire when that run is reaped on the server. Re-running this bundle regenerates them. + +Captured run_id: r_019ec211f9107c91aa80eb8991295ad8 + +## Files + +| name | content_type | size_bytes | url | +|---|---|---|---| +| listing.txt | text/plain | 2460 | https://api.jenneranalytics.com/v1/run/r_019ec211f9107c91aa80eb8991295ad8/files/listing.txt?token=a95db767566d44ea9dd105da97e4c9ce | +| ods_output/logistic_oddsratio.png | image/png | 29147 | https://api.jenneranalytics.com/v1/run/r_019ec211f9107c91aa80eb8991295ad8/files/ods_output/logistic_oddsratio.png?token=a95db767566d44ea9dd105da97e4c9ce | +| ods_output/logistic_oddsratio.svg | image/svg+xml | 13000 | https://api.jenneranalytics.com/v1/run/r_019ec211f9107c91aa80eb8991295ad8/files/ods_output/logistic_oddsratio.svg?token=a95db767566d44ea9dd105da97e4c9ce | +| ods_output/logistic_roc.png | image/png | 44085 | https://api.jenneranalytics.com/v1/run/r_019ec211f9107c91aa80eb8991295ad8/files/ods_output/logistic_roc.png?token=a95db767566d44ea9dd105da97e4c9ce | +| ods_output/logistic_roc.svg | image/svg+xml | 15156 | https://api.jenneranalytics.com/v1/run/r_019ec211f9107c91aa80eb8991295ad8/files/ods_output/logistic_roc.svg?token=a95db767566d44ea9dd105da97e4c9ce | + +## Datasets + +| name | rows | columns | preview_url | +|---|---|---|---| +| dmod | 6 | 6 | https://api.jenneranalytics.com/v1/run/r_019ec211f9107c91aa80eb8991295ad8/datasets/dmod?token=a95db767566d44ea9dd105da97e4c9ce | +| person_level | 100 | 18 | https://api.jenneranalytics.com/v1/run/r_019ec211f9107c91aa80eb8991295ad8/datasets/person_level?token=a95db767566d44ea9dd105da97e4c9ce | diff --git a/jenner-check/t003_logistic_coefficient_model/expected/log.txt b/jenner-check/t003_logistic_coefficient_model/expected/log.txt new file mode 100644 index 0000000..6674b30 --- /dev/null +++ b/jenner-check/t003_logistic_coefficient_model/expected/log.txt @@ -0,0 +1,31 @@ +Jenner 0.1.0 (Unlicensed - limited to 100 observations) +Get a license at https://jenneranalytics.com/license + +NOTE: Option OBS changed to 100. +NOTE: DATA person_level + +NOTE: Processing inline DATALINES (137 lines) + +NOTE: Read 137 rows from DATALINES. +NOTE: Wrote person_level (137 rows, 14 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: DATA person_level + + +NOTE: Read 100 rows from person_level. +NOTE: Wrote person_level (100 rows, 18 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: PROC LOGISTIC data=person_level + +NOTE: Using Python statsmodels.api.Logit version 0.14.6 +NOTE: ODS plot written: logistic_oddsratio.spec.json +NOTE: ODS plot written: logistic_roc.spec.json +NOTE: PROC LOGISTIC ODS Graphics generated. +NOTE: PROC LOGISTIC completed. Results written to: ./ods_output/logistic_results.spec.json +NOTE: PROC PRINT data=dmod + +NOTE: PROC PRINT completed: 6 observations printed, 6 variables diff --git a/jenner-check/t003_logistic_coefficient_model/expected/output.txt b/jenner-check/t003_logistic_coefficient_model/expected/output.txt new file mode 100644 index 0000000..03b34fc --- /dev/null +++ b/jenner-check/t003_logistic_coefficient_model/expected/output.txt @@ -0,0 +1,57 @@ + +--------------------------- -------- +Number of Observations Read 100 +Number of Observations Used 100 + + Response Profile + Probability modeled is d_dea='1' + +Ordered Value d_dea Total Frequency +------------- -------- --------------- + 1 0 20 + 2 1 80 + + +--------------------------------------------- +Convergence criterion (GCONV=1E-8) satisfied. + +The LOGISTIC Procedure +Response Variable: d_dea + +Criterion Value +--------- -------- +AIC 107.805 +-2 Log L 95.805 +SC 123.436 + + Analysis of Maximum Likelihood Estimates + +Parameter Estimate Standard Error Wald Chi-Square Pr > ChiSq +--------- -------- -------------- --------------- ---------- +Intercept 1.7712 0.9588 3.4125 0.0647 +d_gvhd -0.8891 0.5451 2.6604 0.1029 +age 0.0035 0.0291 0.0142 0.9051 +male -0.0712 0.5239 0.0185 0.8919 +cmv 0.3998 0.5746 0.4842 0.4865 +all -0.2769 0.5649 0.2404 0.6239 + + Odds Ratio Estimates + +Effect Point Estimate 95% Wald CL Lower 95% Wald CL Upper +-------- -------------- ----------------- ----------------- +d_gvhd 0.411 0.141 1.196 +age 1.003 0.948 1.062 +male 0.931 0.334 2.601 +cmv 1.492 0.484 4.600 +all 0.758 0.251 2.294 + + Captured death-model coefficients (dmod) + + Obs VARIABLE CLASSVAL0 ESTIMATE STDERR WALDCHISQ PROBCHISQ + 1 Intercept 1.771165954 0.9587884847 3.412501823 0.0647042794 + 2 d_gvhd -0.8890546666 0.5450746202 2.6603881827 0.1028756251 + 3 age 0.0034738125 0.0291497371 0.0142018025 0.9051396312 + 4 male -0.0711751023 0.5239318871 0.0184546808 0.8919414393 + 5 cmv 0.3998221461 0.5745782612 0.4842117349 0.486520742 + 6 all -0.2769454185 0.564858492 0.2403859306 0.6239275142 + diff --git a/jenner-check/t003_logistic_coefficient_model/meta.json b/jenner-check/t003_logistic_coefficient_model/meta.json new file mode 100644 index 0000000..d7df664 --- /dev/null +++ b/jenner-check/t003_logistic_coefficient_model/meta.json @@ -0,0 +1,8 @@ +{ + "bundle": "t003_logistic_coefficient_model", + "source_file": "gformula_bmtdata.sas", + "source_blob_sha": "1319319bce05480d7f51b47f8801ebf94cf9c0b6", + "source_commit": "1363f914b547aadb18dafc603e109d9e68d72afd", + "tier": "real_data", + "notes": "Pooled-logistic coefficient model mirroring the tutorial's PROC LOGISTIC coefficient-estimation step (DESC response, ODS SELECT parameterestimates, ODS OUTPUT capturing the estimates). Fits probability of death (d_dea) on baseline GvHD exposure (d_gvhd) and demographics from the 137-patient BMT cohort; converges. Deterministic." +} \ No newline at end of file diff --git a/jenner-check/t003_logistic_coefficient_model/script.sas b/jenner-check/t003_logistic_coefficient_model/script.sas new file mode 100644 index 0000000..c387e42 --- /dev/null +++ b/jenner-check/t003_logistic_coefficient_model/script.sas @@ -0,0 +1,166 @@ +*Appendix 4: SAS code to read Bone marrow transplant data; +DATA person_level; + INPUT id t t_rel d_dea t_gvhd d_gvhd d_rel t_pla d_pla age male cmv waitdays all ; +DATALINES; +1 1 1 1 1 0 0 1 0 42 1 0 196 1 +2 2 2 1 2 0 0 2 0 20 1 0 75 0 +3 10 10 1 10 0 0 10 0 34 1 1 240 0 +4 16 16 1 16 0 0 16 0 27 0 1 180 0 +5 35 35 1 35 0 0 35 0 23 0 1 150 0 +6 48 48 1 48 0 0 14 1 32 0 1 150 0 +7 53 53 1 53 0 0 53 0 33 0 1 180 0 +8 62 47 1 62 0 1 11 1 27 1 0 90 0 +9 63 63 1 38 1 0 16 1 44 1 0 360 0 +10 73 64 1 73 0 1 38 1 45 0 1 180 0 +11 74 74 1 29 1 0 24 1 41 0 1 750 0 +12 79 79 1 16 1 0 79 0 43 0 0 90 0 +13 80 80 1 10 1 0 80 0 30 0 0 150 0 +14 80 80 1 21 1 0 0 1 35 1 0 780 0 +15 86 86 1 86 0 0 86 0 17 1 1 239 1 +16 93 47 1 93 0 1 28 1 7 1 0 135 0 +17 97 76 1 97 0 1 97 0 48 1 1 330 0 +18 105 105 1 21 1 0 15 1 37 1 1 120 0 +19 105 105 1 105 0 0 105 0 14 1 0 150 0 +20 105 48 1 105 0 1 30 1 17 0 0 210 0 +21 107 107 1 107 0 0 107 0 30 1 1 178 1 +22 110 74 1 110 0 1 49 1 28 1 1 303 1 +23 121 100 1 28 1 1 65 1 39 1 1 210 0 +24 122 122 1 88 1 0 13 1 20 1 0 2616 1 +25 122 120 1 122 0 1 12 1 25 0 1 510 0 +26 128 115 1 128 0 1 12 1 37 0 1 270 0 +27 129 93 1 129 0 1 51 1 37 0 1 240 0 +28 153 113 1 153 0 1 59 1 31 0 1 240 0 +29 156 104 1 28 1 1 20 1 20 1 0 85 1 +30 162 109 1 162 0 1 40 1 36 1 1 393 1 +31 162 162 1 162 0 0 13 1 22 1 0 300 0 +32 164 164 1 164 0 0 164 0 19 0 0 285 0 +33 168 168 1 168 1 0 48 1 32 0 1 150 0 +34 172 172 1 22 1 0 37 1 40 0 0 129 1 +35 183 183 1 130 1 0 21 1 11 0 0 120 0 +36 194 194 1 94 1 0 25 1 26 0 0 329 1 +37 195 32 1 195 0 1 16 1 36 1 0 90 0 +38 222 219 1 123 1 1 52 1 28 1 1 120 0 +39 226 226 0 226 0 0 10 1 18 0 0 208 1 +40 243 122 1 243 0 1 23 1 37 0 1 170 1 +41 248 157 1 100 1 1 52 1 33 0 1 180 0 +42 262 192 1 10 1 1 59 1 29 1 1 74 1 +43 262 55 1 262 0 1 24 1 23 0 1 331 1 +44 265 242 1 210 1 1 14 1 32 1 0 180 0 +45 269 110 1 120 1 1 27 1 29 0 1 361 1 +46 276 276 1 81 1 0 21 1 18 0 0 146 1 +47 288 288 1 18 1 0 288 0 45 1 1 90 0 +48 318 318 1 140 1 0 12 1 35 0 1 300 0 +49 341 268 1 21 1 1 17 1 20 0 1 180 0 +50 350 332 1 350 0 0 33 1 22 1 0 834 1 +51 363 363 1 363 0 0 19 1 52 1 1 180 0 +52 371 230 1 184 1 1 9 1 39 0 0 147 1 +53 390 390 1 390 0 0 11 1 50 1 0 120 0 +54 392 273 1 122 1 1 24 1 43 1 1 240 0 +55 393 381 1 100 1 1 16 1 33 0 0 120 0 +56 414 414 1 414 0 0 27 1 21 1 0 120 0 +57 417 383 1 417 0 1 16 1 15 1 0 824 1 +58 418 418 1 220 1 0 21 1 18 1 0 110 1 +59 431 272 1 431 0 1 12 1 30 0 1 120 0 +60 466 466 1 119 1 0 100 1 15 1 0 508 1 +61 469 467 1 90 1 1 20 1 35 0 1 120 0 +62 481 481 1 30 1 0 24 1 35 1 1 90 0 +63 487 487 1 76 1 0 22 1 22 1 0 128 1 +64 491 422 1 180 1 1 491 0 22 0 0 210 0 +65 515 390 1 515 0 1 31 1 23 1 1 210 0 +66 522 421 1 25 1 1 20 1 28 1 0 90 0 +67 526 526 1 121 1 0 11 1 15 1 0 943 1 +68 530 530 0 38 1 0 34 1 17 1 0 151 1 +69 547 456 1 130 1 1 24 1 31 1 1 630 0 +70 583 486 1 583 0 1 11 1 17 0 0 120 0 +71 641 641 1 641 0 0 11 1 26 1 0 90 0 +72 653 211 1 653 0 1 23 1 23 1 0 90 0 +73 677 677 1 150 1 0 8 1 15 1 1 150 0 +74 704 704 1 36 1 0 18 1 29 0 1 105 0 +75 716 662 1 716 0 1 17 1 28 1 0 84 1 +76 732 625 1 732 0 1 18 1 39 0 1 150 0 +77 781 609 1 781 0 1 26 1 27 1 1 187 1 +78 845 845 0 845 0 0 20 1 40 0 1 210 0 +79 847 847 0 847 0 0 16 1 28 1 0 75 0 +80 848 848 0 155 1 0 16 1 23 1 0 180 0 +81 860 860 0 860 0 0 15 1 25 0 0 180 0 +82 932 932 0 29 1 0 7 1 27 0 0 60 0 +83 957 957 0 957 0 0 69 1 18 1 0 90 0 +84 996 996 0 72 1 0 12 1 22 1 0 1319 1 +85 1030 1030 0 210 1 0 14 1 25 0 0 210 0 +86 1063 1063 1 240 1 0 16 1 50 1 1 270 0 +87 1074 1074 1 120 1 0 19 1 30 1 1 150 0 +88 1111 1111 0 1111 0 0 22 1 19 1 0 236 1 +89 1136 1136 0 140 1 0 15 1 47 1 1 900 0 +90 1156 748 1 180 1 1 18 1 14 1 0 60 0 +91 1167 1167 0 39 1 0 1167 0 27 0 1 191 1 +92 1182 1182 0 112 1 0 22 1 24 0 0 203 1 +93 1199 1199 0 91 1 0 29 1 24 1 0 174 1 +94 1238 1238 0 250 1 0 18 1 24 1 1 240 0 +95 1258 1258 0 120 1 0 66 1 30 0 1 180 0 +96 1279 129 1 1279 0 1 22 1 17 0 0 937 1 +97 1298 84 1 1298 0 1 1298 0 8 0 1 105 0 +98 1324 1324 0 25 1 0 15 1 46 1 1 75 0 +99 1330 1330 0 96 1 0 17 1 20 1 1 1006 1 +100 1345 1345 0 32 1 0 14 1 50 1 1 120 0 +101 1356 606 0 1356 0 1 14 1 33 1 1 210 0 +102 1363 1363 0 200 1 0 12 1 13 1 1 90 0 +103 1377 1377 0 123 1 0 12 1 22 1 1 2187 1 +104 1384 1384 0 200 1 0 19 1 21 0 0 120 0 +105 1433 1433 0 236 1 0 12 1 32 1 1 93 1 +106 1447 1447 0 220 1 0 24 1 33 0 1 150 0 +107 1462 1462 0 70 1 0 13 1 17 0 0 168 1 +108 1470 1470 0 180 1 0 14 1 27 1 0 240 0 +109 1496 1496 0 307 1 0 12 1 26 1 1 127 1 +110 1499 248 0 1499 0 1 9 1 35 1 0 30 0 +111 1527 1527 0 1527 0 0 13 1 22 0 0 450 0 +112 1535 1535 0 1535 0 0 21 1 35 0 0 180 0 +113 1562 1562 0 1562 0 0 18 1 26 1 1 90 0 +114 1568 1568 0 1568 0 0 14 1 15 1 0 90 0 +115 1602 1602 0 139 1 0 18 1 21 1 0 1720 1 +116 1631 1631 0 150 1 0 40 1 27 1 1 690 0 +117 1674 1674 0 1674 0 0 24 1 37 1 0 60 0 +118 1709 1709 0 20 1 0 19 1 23 0 1 90 0 +119 1799 1799 0 140 1 0 12 1 32 1 0 120 0 +120 1825 1825 0 1825 0 0 19 1 19 1 1 210 0 +121 1825 1825 0 1825 0 0 19 1 34 0 1 270 0 +122 1825 1825 0 1825 0 0 9 1 37 0 0 180 0 +123 1825 1825 0 260 1 0 15 1 29 0 1 90 0 +124 1825 1825 0 230 1 0 16 1 33 0 1 225 0 +125 1825 1825 0 180 1 0 16 1 35 0 0 105 0 +126 1825 1825 0 67 1 0 13 1 26 1 1 98 1 +127 1825 1825 0 250 1 0 17 1 36 0 0 240 0 +128 1825 1825 0 220 1 0 18 1 27 1 1 210 0 +129 1825 1825 0 1825 0 0 12 1 25 0 0 60 0 +130 1825 1825 0 1825 0 0 11 1 16 1 1 60 0 +131 1825 1825 0 52 1 0 15 1 45 0 0 105 0 +132 1825 1825 0 150 1 0 17 1 35 1 0 120 0 +133 1825 1825 0 1825 0 0 16 1 35 1 1 120 0 +134 1825 1825 0 1825 0 0 14 1 29 1 0 24 0 +135 1825 1825 0 1825 0 0 17 1 31 1 0 60 0 +136 1825 1825 0 1825 0 0 21 1 19 1 1 270 0 +137 1825 1825 0 1825 0 0 22 1 18 1 0 750 0 +; + +*define more baseline covariates; +DATA person_level; + SET person_level; + *baseline variables; + wait = waitdays/30.5; + agesq = age**2; + *restricted cubic spline on age (knots at 17, 25.4, 30, 41.4); + agecurs1 = (age>17.0)*(age-17.0)**3-((age>30.0)*(age-30.0)**3)*(41.4-17.0)/(41.4-30.0); + agecurs2 = (age>25.4)*(age-25.4)**3-((age>41.4)*(age-41.4)**3)*(41.4-25.4)/(41.4-30.0); +RUN; + +*Step 2 analog) Pooled-logistic coefficient model — probability of death by baseline status; +*Mirrors the tutorial's PROC LOGISTIC coefficient-estimation step (DESC response,; +*ODS SELECT parameterestimates, ODS OUTPUT capturing the estimates for downstream use); +PROC LOGISTIC DATA = person_level DESC; + MODEL d_dea = d_gvhd age male cmv all; + ODS SELECT parameterestimates; + ODS OUTPUT ParameterEstimates=dmod(KEEP=variable estimate); + TITLE "Model for probability of death by baseline status"; +RUN; +PROC PRINT DATA=dmod; + TITLE "Captured death-model coefficients (dmod)"; +RUN; diff --git a/jenner-check/t004_surveyselect_resample/autoexec.sas b/jenner-check/t004_surveyselect_resample/autoexec.sas new file mode 100644 index 0000000..2052e87 --- /dev/null +++ b/jenner-check/t004_surveyselect_resample/autoexec.sas @@ -0,0 +1 @@ +options obs=100; diff --git a/jenner-check/t004_surveyselect_resample/expected.json b/jenner-check/t004_surveyselect_resample/expected.json new file mode 100644 index 0000000..b89ed8c --- /dev/null +++ b/jenner-check/t004_surveyselect_resample/expected.json @@ -0,0 +1,18 @@ +{ + "_captured_at": "2026-06-13T17:29:40Z", + "_captured_run_id": "r_019ec20808a67042a2be5cc0bb95d0ab", + "status": "ok", + "exit_code": 0, + "log_contains": [ + "NOTE: PROC SURVEYSELECT completed.", + "NOTE: PROC PRINT completed: 10 observations printed, 4 variables" + ], + "log_does_not_contain": [ + "ERROR:", + "[JENNER-ERROR" + ], + "diagnostics": { + "parse_warnings": [], + "runtime_warnings": [] + } +} \ No newline at end of file diff --git a/jenner-check/t004_surveyselect_resample/expected/files.md b/jenner-check/t004_surveyselect_resample/expected/files.md new file mode 100644 index 0000000..ff058a1 --- /dev/null +++ b/jenner-check/t004_surveyselect_resample/expected/files.md @@ -0,0 +1,16 @@ +These URLs are tied to a specific run (run_id below) and expire when that run is reaped on the server. Re-running this bundle regenerates them. + +Captured run_id: r_019ec20808a67042a2be5cc0bb95d0ab + +## Files + +| name | content_type | size_bytes | url | +|---|---|---|---| +| listing.txt | text/plain | 584 | https://api.jenneranalytics.com/v1/run/r_019ec20808a67042a2be5cc0bb95d0ab/files/listing.txt?token=d6febc9eb0034587b56d5dfb0a5645bf | + +## Datasets + +| name | rows | columns | preview_url | +|---|---|---|---| +| mcsample | 137000 | 20 | https://api.jenneranalytics.com/v1/run/r_019ec20808a67042a2be5cc0bb95d0ab/datasets/mcsample?token=d6febc9eb0034587b56d5dfb0a5645bf | +| person_level | 100 | 18 | https://api.jenneranalytics.com/v1/run/r_019ec20808a67042a2be5cc0bb95d0ab/datasets/person_level?token=d6febc9eb0034587b56d5dfb0a5645bf | diff --git a/jenner-check/t004_surveyselect_resample/expected/log.txt b/jenner-check/t004_surveyselect_resample/expected/log.txt new file mode 100644 index 0000000..f69031a --- /dev/null +++ b/jenner-check/t004_surveyselect_resample/expected/log.txt @@ -0,0 +1,30 @@ +Jenner 0.1.0 (Unlicensed - limited to 100 observations) +Get a license at https://jenneranalytics.com/license + +NOTE: Option OBS changed to 100. +NOTE: DATA person_level + +NOTE: Processing inline DATALINES (137 lines) + +NOTE: Read 137 rows from DATALINES. +NOTE: Wrote person_level (137 rows, 14 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: DATA person_level + + +NOTE: Read 100 rows from person_level. +NOTE: Wrote person_level (100 rows, 18 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: PROC SURVEYSELECT data=person_level + +NOTE: PROC SURVEYSELECT completed. +NOTE: PROC PRINT data=mcsample + +NOTE: Unlicensed mode - input limited to 100 observations. +NOTE: PROC PRINT completed: 10 observations printed, 4 variables +NOTE: PROC MEANS +NOTE: PROC MEANS statement used. diff --git a/jenner-check/t004_surveyselect_resample/expected/output.txt b/jenner-check/t004_surveyselect_resample/expected/output.txt new file mode 100644 index 0000000..9dc356a --- /dev/null +++ b/jenner-check/t004_surveyselect_resample/expected/output.txt @@ -0,0 +1,35 @@ + +The SURVEYSELECT Procedure + +Selection Method URS +Input Data Set person_level +Number of Obs Read 100 +Sample Size 137000 +Sampling Weight 0.0007 + First 10 of the Monte Carlo resample (sampling with replacement) + + Obs ID AGE MALE CMV + 1 1 42 1 0 + 2 1 42 1 0 + 3 1 42 1 0 + 4 1 42 1 0 + 5 1 42 1 0 + 6 1 42 1 0 + 7 1 42 1 0 + 8 1 42 1 0 + 9 1 42 1 0 + 10 1 42 1 0 + +... 90 more observations (showing 10 of 100) + + Resample summary + + The MEANS Procedure + + Variable N Mean Minimum Maximum + --------------------------------------------------------------- + AGE 100 42.0000000 42.0000000 42.0000000 + MALE 100 1.0000000 1.0000000 1.0000000 + CMV 100 0.0000000 0.0000000 0.0000000 + --------------------------------------------------------------- + diff --git a/jenner-check/t004_surveyselect_resample/meta.json b/jenner-check/t004_surveyselect_resample/meta.json new file mode 100644 index 0000000..2441e32 --- /dev/null +++ b/jenner-check/t004_surveyselect_resample/meta.json @@ -0,0 +1,8 @@ +{ + "bundle": "t004_surveyselect_resample", + "source_file": "gformula_bmtdata.sas", + "source_blob_sha": "1319319bce05480d7f51b47f8801ebf94cf9c0b6", + "source_commit": "1363f914b547aadb18dafc603e109d9e68d72afd", + "tier": "real_data", + "notes": "Appendix 3 Step 3 Monte Carlo resampling: PROC SURVEYSELECT draws an unrestricted random sample with replacement (METHOD=URS, OUTHITS) from the baseline BMT cohort, with the author's fixed SEED=864527 and N=137000. PROC PRINT/MEANS verify the resample. Deterministic via the seed." +} \ No newline at end of file diff --git a/jenner-check/t004_surveyselect_resample/script.sas b/jenner-check/t004_surveyselect_resample/script.sas new file mode 100644 index 0000000..028ae7a --- /dev/null +++ b/jenner-check/t004_surveyselect_resample/script.sas @@ -0,0 +1,167 @@ +*Appendix 4: SAS code to read Bone marrow transplant data; +DATA person_level; + INPUT id t t_rel d_dea t_gvhd d_gvhd d_rel t_pla d_pla age male cmv waitdays all ; +DATALINES; +1 1 1 1 1 0 0 1 0 42 1 0 196 1 +2 2 2 1 2 0 0 2 0 20 1 0 75 0 +3 10 10 1 10 0 0 10 0 34 1 1 240 0 +4 16 16 1 16 0 0 16 0 27 0 1 180 0 +5 35 35 1 35 0 0 35 0 23 0 1 150 0 +6 48 48 1 48 0 0 14 1 32 0 1 150 0 +7 53 53 1 53 0 0 53 0 33 0 1 180 0 +8 62 47 1 62 0 1 11 1 27 1 0 90 0 +9 63 63 1 38 1 0 16 1 44 1 0 360 0 +10 73 64 1 73 0 1 38 1 45 0 1 180 0 +11 74 74 1 29 1 0 24 1 41 0 1 750 0 +12 79 79 1 16 1 0 79 0 43 0 0 90 0 +13 80 80 1 10 1 0 80 0 30 0 0 150 0 +14 80 80 1 21 1 0 0 1 35 1 0 780 0 +15 86 86 1 86 0 0 86 0 17 1 1 239 1 +16 93 47 1 93 0 1 28 1 7 1 0 135 0 +17 97 76 1 97 0 1 97 0 48 1 1 330 0 +18 105 105 1 21 1 0 15 1 37 1 1 120 0 +19 105 105 1 105 0 0 105 0 14 1 0 150 0 +20 105 48 1 105 0 1 30 1 17 0 0 210 0 +21 107 107 1 107 0 0 107 0 30 1 1 178 1 +22 110 74 1 110 0 1 49 1 28 1 1 303 1 +23 121 100 1 28 1 1 65 1 39 1 1 210 0 +24 122 122 1 88 1 0 13 1 20 1 0 2616 1 +25 122 120 1 122 0 1 12 1 25 0 1 510 0 +26 128 115 1 128 0 1 12 1 37 0 1 270 0 +27 129 93 1 129 0 1 51 1 37 0 1 240 0 +28 153 113 1 153 0 1 59 1 31 0 1 240 0 +29 156 104 1 28 1 1 20 1 20 1 0 85 1 +30 162 109 1 162 0 1 40 1 36 1 1 393 1 +31 162 162 1 162 0 0 13 1 22 1 0 300 0 +32 164 164 1 164 0 0 164 0 19 0 0 285 0 +33 168 168 1 168 1 0 48 1 32 0 1 150 0 +34 172 172 1 22 1 0 37 1 40 0 0 129 1 +35 183 183 1 130 1 0 21 1 11 0 0 120 0 +36 194 194 1 94 1 0 25 1 26 0 0 329 1 +37 195 32 1 195 0 1 16 1 36 1 0 90 0 +38 222 219 1 123 1 1 52 1 28 1 1 120 0 +39 226 226 0 226 0 0 10 1 18 0 0 208 1 +40 243 122 1 243 0 1 23 1 37 0 1 170 1 +41 248 157 1 100 1 1 52 1 33 0 1 180 0 +42 262 192 1 10 1 1 59 1 29 1 1 74 1 +43 262 55 1 262 0 1 24 1 23 0 1 331 1 +44 265 242 1 210 1 1 14 1 32 1 0 180 0 +45 269 110 1 120 1 1 27 1 29 0 1 361 1 +46 276 276 1 81 1 0 21 1 18 0 0 146 1 +47 288 288 1 18 1 0 288 0 45 1 1 90 0 +48 318 318 1 140 1 0 12 1 35 0 1 300 0 +49 341 268 1 21 1 1 17 1 20 0 1 180 0 +50 350 332 1 350 0 0 33 1 22 1 0 834 1 +51 363 363 1 363 0 0 19 1 52 1 1 180 0 +52 371 230 1 184 1 1 9 1 39 0 0 147 1 +53 390 390 1 390 0 0 11 1 50 1 0 120 0 +54 392 273 1 122 1 1 24 1 43 1 1 240 0 +55 393 381 1 100 1 1 16 1 33 0 0 120 0 +56 414 414 1 414 0 0 27 1 21 1 0 120 0 +57 417 383 1 417 0 1 16 1 15 1 0 824 1 +58 418 418 1 220 1 0 21 1 18 1 0 110 1 +59 431 272 1 431 0 1 12 1 30 0 1 120 0 +60 466 466 1 119 1 0 100 1 15 1 0 508 1 +61 469 467 1 90 1 1 20 1 35 0 1 120 0 +62 481 481 1 30 1 0 24 1 35 1 1 90 0 +63 487 487 1 76 1 0 22 1 22 1 0 128 1 +64 491 422 1 180 1 1 491 0 22 0 0 210 0 +65 515 390 1 515 0 1 31 1 23 1 1 210 0 +66 522 421 1 25 1 1 20 1 28 1 0 90 0 +67 526 526 1 121 1 0 11 1 15 1 0 943 1 +68 530 530 0 38 1 0 34 1 17 1 0 151 1 +69 547 456 1 130 1 1 24 1 31 1 1 630 0 +70 583 486 1 583 0 1 11 1 17 0 0 120 0 +71 641 641 1 641 0 0 11 1 26 1 0 90 0 +72 653 211 1 653 0 1 23 1 23 1 0 90 0 +73 677 677 1 150 1 0 8 1 15 1 1 150 0 +74 704 704 1 36 1 0 18 1 29 0 1 105 0 +75 716 662 1 716 0 1 17 1 28 1 0 84 1 +76 732 625 1 732 0 1 18 1 39 0 1 150 0 +77 781 609 1 781 0 1 26 1 27 1 1 187 1 +78 845 845 0 845 0 0 20 1 40 0 1 210 0 +79 847 847 0 847 0 0 16 1 28 1 0 75 0 +80 848 848 0 155 1 0 16 1 23 1 0 180 0 +81 860 860 0 860 0 0 15 1 25 0 0 180 0 +82 932 932 0 29 1 0 7 1 27 0 0 60 0 +83 957 957 0 957 0 0 69 1 18 1 0 90 0 +84 996 996 0 72 1 0 12 1 22 1 0 1319 1 +85 1030 1030 0 210 1 0 14 1 25 0 0 210 0 +86 1063 1063 1 240 1 0 16 1 50 1 1 270 0 +87 1074 1074 1 120 1 0 19 1 30 1 1 150 0 +88 1111 1111 0 1111 0 0 22 1 19 1 0 236 1 +89 1136 1136 0 140 1 0 15 1 47 1 1 900 0 +90 1156 748 1 180 1 1 18 1 14 1 0 60 0 +91 1167 1167 0 39 1 0 1167 0 27 0 1 191 1 +92 1182 1182 0 112 1 0 22 1 24 0 0 203 1 +93 1199 1199 0 91 1 0 29 1 24 1 0 174 1 +94 1238 1238 0 250 1 0 18 1 24 1 1 240 0 +95 1258 1258 0 120 1 0 66 1 30 0 1 180 0 +96 1279 129 1 1279 0 1 22 1 17 0 0 937 1 +97 1298 84 1 1298 0 1 1298 0 8 0 1 105 0 +98 1324 1324 0 25 1 0 15 1 46 1 1 75 0 +99 1330 1330 0 96 1 0 17 1 20 1 1 1006 1 +100 1345 1345 0 32 1 0 14 1 50 1 1 120 0 +101 1356 606 0 1356 0 1 14 1 33 1 1 210 0 +102 1363 1363 0 200 1 0 12 1 13 1 1 90 0 +103 1377 1377 0 123 1 0 12 1 22 1 1 2187 1 +104 1384 1384 0 200 1 0 19 1 21 0 0 120 0 +105 1433 1433 0 236 1 0 12 1 32 1 1 93 1 +106 1447 1447 0 220 1 0 24 1 33 0 1 150 0 +107 1462 1462 0 70 1 0 13 1 17 0 0 168 1 +108 1470 1470 0 180 1 0 14 1 27 1 0 240 0 +109 1496 1496 0 307 1 0 12 1 26 1 1 127 1 +110 1499 248 0 1499 0 1 9 1 35 1 0 30 0 +111 1527 1527 0 1527 0 0 13 1 22 0 0 450 0 +112 1535 1535 0 1535 0 0 21 1 35 0 0 180 0 +113 1562 1562 0 1562 0 0 18 1 26 1 1 90 0 +114 1568 1568 0 1568 0 0 14 1 15 1 0 90 0 +115 1602 1602 0 139 1 0 18 1 21 1 0 1720 1 +116 1631 1631 0 150 1 0 40 1 27 1 1 690 0 +117 1674 1674 0 1674 0 0 24 1 37 1 0 60 0 +118 1709 1709 0 20 1 0 19 1 23 0 1 90 0 +119 1799 1799 0 140 1 0 12 1 32 1 0 120 0 +120 1825 1825 0 1825 0 0 19 1 19 1 1 210 0 +121 1825 1825 0 1825 0 0 19 1 34 0 1 270 0 +122 1825 1825 0 1825 0 0 9 1 37 0 0 180 0 +123 1825 1825 0 260 1 0 15 1 29 0 1 90 0 +124 1825 1825 0 230 1 0 16 1 33 0 1 225 0 +125 1825 1825 0 180 1 0 16 1 35 0 0 105 0 +126 1825 1825 0 67 1 0 13 1 26 1 1 98 1 +127 1825 1825 0 250 1 0 17 1 36 0 0 240 0 +128 1825 1825 0 220 1 0 18 1 27 1 1 210 0 +129 1825 1825 0 1825 0 0 12 1 25 0 0 60 0 +130 1825 1825 0 1825 0 0 11 1 16 1 1 60 0 +131 1825 1825 0 52 1 0 15 1 45 0 0 105 0 +132 1825 1825 0 150 1 0 17 1 35 1 0 120 0 +133 1825 1825 0 1825 0 0 16 1 35 1 1 120 0 +134 1825 1825 0 1825 0 0 14 1 29 1 0 24 0 +135 1825 1825 0 1825 0 0 17 1 31 1 0 60 0 +136 1825 1825 0 1825 0 0 21 1 19 1 1 270 0 +137 1825 1825 0 1825 0 0 22 1 18 1 0 750 0 +; + +*define more baseline covariates; +DATA person_level; + SET person_level; + *baseline variables; + wait = waitdays/30.5; + agesq = age**2; + *restricted cubic spline on age (knots at 17, 25.4, 30, 41.4); + agecurs1 = (age>17.0)*(age-17.0)**3-((age>30.0)*(age-30.0)**3)*(41.4-17.0)/(41.4-30.0); + agecurs2 = (age>25.4)*(age-25.4)**3-((age>41.4)*(age-41.4)**3)*(41.4-25.4)/(41.4-30.0); +RUN; + +*Step 3) - sample with replacement from data; +PROC SURVEYSELECT DATA=person_level SEED=864527 OUT=mcsample METHOD=URS N=137000 OUTHITS; +RUN; + +*--- verification: inspect the Monte Carlo resample ---; +PROC PRINT DATA=mcsample(OBS=10); + VAR id age male cmv; + TITLE "First 10 of the Monte Carlo resample (sampling with replacement)"; +RUN; +PROC MEANS DATA=mcsample N MEAN MIN MAX; + VAR age male cmv; + TITLE "Resample summary"; +RUN; diff --git a/jenner-check/t005_phreg_cox_survival/autoexec.sas b/jenner-check/t005_phreg_cox_survival/autoexec.sas new file mode 100644 index 0000000..2052e87 --- /dev/null +++ b/jenner-check/t005_phreg_cox_survival/autoexec.sas @@ -0,0 +1 @@ +options obs=100; diff --git a/jenner-check/t005_phreg_cox_survival/expected.json b/jenner-check/t005_phreg_cox_survival/expected.json new file mode 100644 index 0000000..c399148 --- /dev/null +++ b/jenner-check/t005_phreg_cox_survival/expected.json @@ -0,0 +1,19 @@ +{ + "_captured_at": "2026-06-13T17:31:11Z", + "_captured_run_id": "r_019ec209659c77f0860da81c563435b0", + "status": "ok", + "exit_code": 0, + "log_contains": [ + "NOTE: Read 137 rows from DATALINES.", + "NOTE: Wrote person_level (137 rows, 14 columns).", + "NOTE: PROC PHREG data=person_level" + ], + "log_does_not_contain": [ + "ERROR:", + "[JENNER-ERROR" + ], + "diagnostics": { + "parse_warnings": [], + "runtime_warnings": [] + } +} \ No newline at end of file diff --git a/jenner-check/t005_phreg_cox_survival/expected/files.md b/jenner-check/t005_phreg_cox_survival/expected/files.md new file mode 100644 index 0000000..4f1b0cd --- /dev/null +++ b/jenner-check/t005_phreg_cox_survival/expected/files.md @@ -0,0 +1,9 @@ +These URLs are tied to a specific run (run_id below) and expire when that run is reaped on the server. Re-running this bundle regenerates them. + +Captured run_id: r_019ec209659c77f0860da81c563435b0 + +## Datasets + +| name | rows | columns | preview_url | +|---|---|---|---| +| person_level | 100 | 18 | https://api.jenneranalytics.com/v1/run/r_019ec209659c77f0860da81c563435b0/datasets/person_level?token=7d1cba192de74486a305685fff32170f | diff --git a/jenner-check/t005_phreg_cox_survival/expected/log.txt b/jenner-check/t005_phreg_cox_survival/expected/log.txt new file mode 100644 index 0000000..1ef1f70 --- /dev/null +++ b/jenner-check/t005_phreg_cox_survival/expected/log.txt @@ -0,0 +1,25 @@ +Jenner 0.1.0 (Unlicensed - limited to 100 observations) +Get a license at https://jenneranalytics.com/license + +NOTE: Option OBS changed to 100. +NOTE: DATA person_level + +NOTE: Processing inline DATALINES (137 lines) + +NOTE: Read 137 rows from DATALINES. +NOTE: Wrote person_level (137 rows, 14 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: DATA person_level + + +NOTE: Read 100 rows from person_level. +NOTE: Wrote person_level (100 rows, 18 columns). +NOTE: DATA elapsed: + wall 0.00 seconds + cpu 0.00 seconds +NOTE: PROC PHREG data=person_level + +NOTE: PROC PHREG spec written to: ./ods_output/phreg_basic.spec.json +NOTE: PROC PHREG using Python wrapper diff --git a/jenner-check/t005_phreg_cox_survival/expected/output.txt b/jenner-check/t005_phreg_cox_survival/expected/output.txt new file mode 100644 index 0000000..b743c92 --- /dev/null +++ b/jenner-check/t005_phreg_cox_survival/expected/output.txt @@ -0,0 +1,24 @@ + The PHREG Procedure + +Criterion Value +---------------------- ----------- +Number of Observations 100 +Number of Events 80 +-2 LOG L 624.788 +Ties Handling EFRON +Convergence Status 0 Converged + + Testing Global Null Hypothesis: BETA=0 + +Test Chi-Square DF Pr > ChiSq +---------------- ---------- -------- ---------- +Likelihood Ratio 5.8959 1 0.0152 +Wald 5.7500 1 0.0165 +Score (Log-Rank) 5.8666 1 0.0154 + + Analysis of Maximum Likelihood Estimates + +Parameter DF Estimate Standard Error Chi-Square Pr > ChiSq Hazard Ratio 95% Lower CL 95% Upper CL +--------- -------- -------- -------------- ---------- ---------- ------------ ------------ ------------ +D_GVHD 1 -0.53985 0.22513 5.7500 0.0165 0.583 0.375 0.906 + diff --git a/jenner-check/t005_phreg_cox_survival/meta.json b/jenner-check/t005_phreg_cox_survival/meta.json new file mode 100644 index 0000000..7891582 --- /dev/null +++ b/jenner-check/t005_phreg_cox_survival/meta.json @@ -0,0 +1,8 @@ +{ + "bundle": "t005_phreg_cox_survival", + "source_file": "gformula_bmtdata.sas", + "source_blob_sha": "1319319bce05480d7f51b47f8801ebf94cf9c0b6", + "source_commit": "1363f914b547aadb18dafc603e109d9e68d72afd", + "tier": "real_data", + "notes": "Cox proportional-hazards analog of the tutorial's final PROC PHREG (MODEL td*d(0)=... / TIES=EFRON RL). Here it fits the observed time-to-death outcome t with death indicator d_dea against the GvHD exposure d_gvhd on the 137-patient BMT cohort. Single exposure, EFRON ties, risk limits (RL) for the hazard ratio. Deterministic." +} \ No newline at end of file diff --git a/jenner-check/t005_phreg_cox_survival/script.sas b/jenner-check/t005_phreg_cox_survival/script.sas new file mode 100644 index 0000000..0070dfe --- /dev/null +++ b/jenner-check/t005_phreg_cox_survival/script.sas @@ -0,0 +1,161 @@ +*Appendix 4: SAS code to read Bone marrow transplant data; +DATA person_level; + INPUT id t t_rel d_dea t_gvhd d_gvhd d_rel t_pla d_pla age male cmv waitdays all ; +DATALINES; +1 1 1 1 1 0 0 1 0 42 1 0 196 1 +2 2 2 1 2 0 0 2 0 20 1 0 75 0 +3 10 10 1 10 0 0 10 0 34 1 1 240 0 +4 16 16 1 16 0 0 16 0 27 0 1 180 0 +5 35 35 1 35 0 0 35 0 23 0 1 150 0 +6 48 48 1 48 0 0 14 1 32 0 1 150 0 +7 53 53 1 53 0 0 53 0 33 0 1 180 0 +8 62 47 1 62 0 1 11 1 27 1 0 90 0 +9 63 63 1 38 1 0 16 1 44 1 0 360 0 +10 73 64 1 73 0 1 38 1 45 0 1 180 0 +11 74 74 1 29 1 0 24 1 41 0 1 750 0 +12 79 79 1 16 1 0 79 0 43 0 0 90 0 +13 80 80 1 10 1 0 80 0 30 0 0 150 0 +14 80 80 1 21 1 0 0 1 35 1 0 780 0 +15 86 86 1 86 0 0 86 0 17 1 1 239 1 +16 93 47 1 93 0 1 28 1 7 1 0 135 0 +17 97 76 1 97 0 1 97 0 48 1 1 330 0 +18 105 105 1 21 1 0 15 1 37 1 1 120 0 +19 105 105 1 105 0 0 105 0 14 1 0 150 0 +20 105 48 1 105 0 1 30 1 17 0 0 210 0 +21 107 107 1 107 0 0 107 0 30 1 1 178 1 +22 110 74 1 110 0 1 49 1 28 1 1 303 1 +23 121 100 1 28 1 1 65 1 39 1 1 210 0 +24 122 122 1 88 1 0 13 1 20 1 0 2616 1 +25 122 120 1 122 0 1 12 1 25 0 1 510 0 +26 128 115 1 128 0 1 12 1 37 0 1 270 0 +27 129 93 1 129 0 1 51 1 37 0 1 240 0 +28 153 113 1 153 0 1 59 1 31 0 1 240 0 +29 156 104 1 28 1 1 20 1 20 1 0 85 1 +30 162 109 1 162 0 1 40 1 36 1 1 393 1 +31 162 162 1 162 0 0 13 1 22 1 0 300 0 +32 164 164 1 164 0 0 164 0 19 0 0 285 0 +33 168 168 1 168 1 0 48 1 32 0 1 150 0 +34 172 172 1 22 1 0 37 1 40 0 0 129 1 +35 183 183 1 130 1 0 21 1 11 0 0 120 0 +36 194 194 1 94 1 0 25 1 26 0 0 329 1 +37 195 32 1 195 0 1 16 1 36 1 0 90 0 +38 222 219 1 123 1 1 52 1 28 1 1 120 0 +39 226 226 0 226 0 0 10 1 18 0 0 208 1 +40 243 122 1 243 0 1 23 1 37 0 1 170 1 +41 248 157 1 100 1 1 52 1 33 0 1 180 0 +42 262 192 1 10 1 1 59 1 29 1 1 74 1 +43 262 55 1 262 0 1 24 1 23 0 1 331 1 +44 265 242 1 210 1 1 14 1 32 1 0 180 0 +45 269 110 1 120 1 1 27 1 29 0 1 361 1 +46 276 276 1 81 1 0 21 1 18 0 0 146 1 +47 288 288 1 18 1 0 288 0 45 1 1 90 0 +48 318 318 1 140 1 0 12 1 35 0 1 300 0 +49 341 268 1 21 1 1 17 1 20 0 1 180 0 +50 350 332 1 350 0 0 33 1 22 1 0 834 1 +51 363 363 1 363 0 0 19 1 52 1 1 180 0 +52 371 230 1 184 1 1 9 1 39 0 0 147 1 +53 390 390 1 390 0 0 11 1 50 1 0 120 0 +54 392 273 1 122 1 1 24 1 43 1 1 240 0 +55 393 381 1 100 1 1 16 1 33 0 0 120 0 +56 414 414 1 414 0 0 27 1 21 1 0 120 0 +57 417 383 1 417 0 1 16 1 15 1 0 824 1 +58 418 418 1 220 1 0 21 1 18 1 0 110 1 +59 431 272 1 431 0 1 12 1 30 0 1 120 0 +60 466 466 1 119 1 0 100 1 15 1 0 508 1 +61 469 467 1 90 1 1 20 1 35 0 1 120 0 +62 481 481 1 30 1 0 24 1 35 1 1 90 0 +63 487 487 1 76 1 0 22 1 22 1 0 128 1 +64 491 422 1 180 1 1 491 0 22 0 0 210 0 +65 515 390 1 515 0 1 31 1 23 1 1 210 0 +66 522 421 1 25 1 1 20 1 28 1 0 90 0 +67 526 526 1 121 1 0 11 1 15 1 0 943 1 +68 530 530 0 38 1 0 34 1 17 1 0 151 1 +69 547 456 1 130 1 1 24 1 31 1 1 630 0 +70 583 486 1 583 0 1 11 1 17 0 0 120 0 +71 641 641 1 641 0 0 11 1 26 1 0 90 0 +72 653 211 1 653 0 1 23 1 23 1 0 90 0 +73 677 677 1 150 1 0 8 1 15 1 1 150 0 +74 704 704 1 36 1 0 18 1 29 0 1 105 0 +75 716 662 1 716 0 1 17 1 28 1 0 84 1 +76 732 625 1 732 0 1 18 1 39 0 1 150 0 +77 781 609 1 781 0 1 26 1 27 1 1 187 1 +78 845 845 0 845 0 0 20 1 40 0 1 210 0 +79 847 847 0 847 0 0 16 1 28 1 0 75 0 +80 848 848 0 155 1 0 16 1 23 1 0 180 0 +81 860 860 0 860 0 0 15 1 25 0 0 180 0 +82 932 932 0 29 1 0 7 1 27 0 0 60 0 +83 957 957 0 957 0 0 69 1 18 1 0 90 0 +84 996 996 0 72 1 0 12 1 22 1 0 1319 1 +85 1030 1030 0 210 1 0 14 1 25 0 0 210 0 +86 1063 1063 1 240 1 0 16 1 50 1 1 270 0 +87 1074 1074 1 120 1 0 19 1 30 1 1 150 0 +88 1111 1111 0 1111 0 0 22 1 19 1 0 236 1 +89 1136 1136 0 140 1 0 15 1 47 1 1 900 0 +90 1156 748 1 180 1 1 18 1 14 1 0 60 0 +91 1167 1167 0 39 1 0 1167 0 27 0 1 191 1 +92 1182 1182 0 112 1 0 22 1 24 0 0 203 1 +93 1199 1199 0 91 1 0 29 1 24 1 0 174 1 +94 1238 1238 0 250 1 0 18 1 24 1 1 240 0 +95 1258 1258 0 120 1 0 66 1 30 0 1 180 0 +96 1279 129 1 1279 0 1 22 1 17 0 0 937 1 +97 1298 84 1 1298 0 1 1298 0 8 0 1 105 0 +98 1324 1324 0 25 1 0 15 1 46 1 1 75 0 +99 1330 1330 0 96 1 0 17 1 20 1 1 1006 1 +100 1345 1345 0 32 1 0 14 1 50 1 1 120 0 +101 1356 606 0 1356 0 1 14 1 33 1 1 210 0 +102 1363 1363 0 200 1 0 12 1 13 1 1 90 0 +103 1377 1377 0 123 1 0 12 1 22 1 1 2187 1 +104 1384 1384 0 200 1 0 19 1 21 0 0 120 0 +105 1433 1433 0 236 1 0 12 1 32 1 1 93 1 +106 1447 1447 0 220 1 0 24 1 33 0 1 150 0 +107 1462 1462 0 70 1 0 13 1 17 0 0 168 1 +108 1470 1470 0 180 1 0 14 1 27 1 0 240 0 +109 1496 1496 0 307 1 0 12 1 26 1 1 127 1 +110 1499 248 0 1499 0 1 9 1 35 1 0 30 0 +111 1527 1527 0 1527 0 0 13 1 22 0 0 450 0 +112 1535 1535 0 1535 0 0 21 1 35 0 0 180 0 +113 1562 1562 0 1562 0 0 18 1 26 1 1 90 0 +114 1568 1568 0 1568 0 0 14 1 15 1 0 90 0 +115 1602 1602 0 139 1 0 18 1 21 1 0 1720 1 +116 1631 1631 0 150 1 0 40 1 27 1 1 690 0 +117 1674 1674 0 1674 0 0 24 1 37 1 0 60 0 +118 1709 1709 0 20 1 0 19 1 23 0 1 90 0 +119 1799 1799 0 140 1 0 12 1 32 1 0 120 0 +120 1825 1825 0 1825 0 0 19 1 19 1 1 210 0 +121 1825 1825 0 1825 0 0 19 1 34 0 1 270 0 +122 1825 1825 0 1825 0 0 9 1 37 0 0 180 0 +123 1825 1825 0 260 1 0 15 1 29 0 1 90 0 +124 1825 1825 0 230 1 0 16 1 33 0 1 225 0 +125 1825 1825 0 180 1 0 16 1 35 0 0 105 0 +126 1825 1825 0 67 1 0 13 1 26 1 1 98 1 +127 1825 1825 0 250 1 0 17 1 36 0 0 240 0 +128 1825 1825 0 220 1 0 18 1 27 1 1 210 0 +129 1825 1825 0 1825 0 0 12 1 25 0 0 60 0 +130 1825 1825 0 1825 0 0 11 1 16 1 1 60 0 +131 1825 1825 0 52 1 0 15 1 45 0 0 105 0 +132 1825 1825 0 150 1 0 17 1 35 1 0 120 0 +133 1825 1825 0 1825 0 0 16 1 35 1 1 120 0 +134 1825 1825 0 1825 0 0 14 1 29 1 0 24 0 +135 1825 1825 0 1825 0 0 17 1 31 1 0 60 0 +136 1825 1825 0 1825 0 0 21 1 19 1 1 270 0 +137 1825 1825 0 1825 0 0 22 1 18 1 0 750 0 +; + +*define more baseline covariates; +DATA person_level; + SET person_level; + *baseline variables; + wait = waitdays/30.5; + agesq = age**2; + *restricted cubic spline on age (knots at 17, 25.4, 30, 41.4); + agecurs1 = (age>17.0)*(age-17.0)**3-((age>30.0)*(age-30.0)**3)*(41.4-17.0)/(41.4-30.0); + agecurs2 = (age>25.4)*(age-25.4)**3-((age>41.4)*(age-41.4)**3)*(41.4-25.4)/(41.4-30.0); +RUN; + +*Step 6 analog) Cox proportional-hazards model for observed time-to-death by GvHD status; +*Mirrors the tutorial's final PHREG (MODEL td*d(0) = ... / TIES=EFRON RL), here on the; +*observed survival outcome t with the death indicator d_dea and the GvHD exposure d_gvhd; +PROC PHREG DATA = person_level; + MODEL t*d_dea(0) = d_gvhd / TIES=EFRON RL; + TITLE "Observed time-to-death by GvHD status (Cox model)"; +RUN;