监测、队列与结局分析
Surveillance, cohorts & outcomes analysis
Enter case data, select clinical cohorts from health-record tables against stated criteria, compute rates and survival or outcome statistics, and map clusters.
20 条本项目编写的提案 · 分类 v1.1 · 新增基准运行 0 次。下方验证方式与部分得分规则是设计，不是执行结果。
- 典型应用
- Epi Info · R · QGIS
- 小类 GUI 需求标签
HY· 混合
任务提案 · 20
展开查看完整原文与建议检查方式；两种界面均保留提案英文原文。
R09.04.01.01-T01 Build an outbreak form with check code and compute attack-rate RR in Epi Info
原始指令
In Epi Info 7 Form Designer create project output/picnic.prj with form 'Case' (ID, age, sex, onset datetime, ate_potato_salad, ate_chicken, ill) and check code restricting age to 0-120 and requiring onset if ill=Yes. Enter the 20 synthetic questionnaires in input/questionnaires.pdf, then in Classic Analysis run TABLES for each food by ill and write the risk ratios to output/rr.json.
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
G2· GUI 必要- 交互原语
click· 指向与点击type· 文字与表单drag· 拖放- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Checker opens the .prj/.mdb: 7 fields with types; check code rules present and enforced (inserting age 130 fails); 20 records exact; rr.json values within 0.01 of gold for both foods. The VM has no shell, R, Python or Access, so the project and results can only be produced in Epi Info; file writes by any other process are caught by file-access auditing.
建议部分得分
20% form fields; 20% check code; 35% records; 25% risk ratios
R09.04.01.01-T02 Map county case rates as a choropleth in Epi Info Maps
原始指令
In Epi Info Maps, load the county boundary shapefile input/counties.shp and the case line list input/cases.csv (synthetic, 1,240 cases), compute cases per 100,000 using the population column, display a 5-class quantile choropleth with a legend titled 'Cases per 100k', and save the map file output/rate_map.map7 and output/rate_map.png.
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
G3· 仅 GUI- 交互原语
click· 指向与点击type· 文字与表单vis· 视觉判断- 工作产物
WP04· 三维 / 空间模型- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Saved map XML: data join key correct, rate expression, quantile classification with 5 breaks equal to gold; PNG legend title OCR exact; sampled county fill colors correspond to the right class for 10 counties. The VM has no shell, R, Python or Access, so the project and results can only be produced in Epi Info; file writes by any other process are caught by file-access auditing.
建议部分得分
25% join; 25% rate field; 30% class breaks; 20% legend and export
R09.04.01.01-T03 Compute age-adjusted incidence rates by county with confidence intervals
原始指令
Using R, compute directly age-standardized incidence rates (2000 US standard population, 18 age groups) of the reportable disease in input/linelist.csv by county with gamma (Fay-Feuer) 95% CIs, using county-age populations from input/pop.csv. Write output/adj_rates.csv.
- 平台
mac· macOSwin· Windowslin· Linux- 应用
- R
- 交互表面
term· 终端- GUI 需求 · 任务设定
CL· CLI 足够- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
code· 代码与命令- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Rates within 0.01 per 100k and CI bounds within 0.05 of reference computed with epitools ageadjust.direct; all 24 counties present.
建议部分得分
20% case counts by county and age; 50% adjusted rates; 30% CIs
R09.04.01.01-T04 Join case counts to counties and lay out a printable rate map in QGIS
原始指令
In QGIS join input/case_counts.csv to input/counties.gpkg, compute rate per 100k in a new field, style with 5 Jenks classes (YlOrRd), and build an A4 landscape print layout with map, legend, scale bar, north arrow, title 'Pertussis rate per 100k, 2025' and data source note. Save output/pertussis.qgz and export output/pertussis.pdf.
- 平台
mac· macOSwin· Windows- 应用
- QGIS
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
click· 指向与点击drag· 拖放vis· 视觉判断- 工作产物
WP03· 视觉排版- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Parsed .qgz: join and rate expression correct; renderer graduated Jenks 5 classes with breaks equal to gold; layout items (map, legend, scalebar, north arrow, title text, note) present on A4 landscape; PDF text contains title. QGIS Interface Customization hides the Python Console and Processing script tools, and the VM has no shell for qgis_process, so the work must be done through QGIS dialogs.
建议部分得分
25% join and rate field; 25% classification; 35% layout items; 15% PDF
R09.04.01.01-T05 Draw an epidemic curve and identify the likely exposure date in Epi Info
原始指令
In Epi Info Visual Dashboard, load the synthetic norovirus line list input/noro.csv and create an epidemic curve histogram of onset date-time in 6-hour bins. Given a 12-48 h incubation period (median 33 h), write the most likely common exposure window to output/exposure.json and save the canvas output/epicurve.cvs7.
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
G2· GUI 必要- 交互原语
click· 指向与点击vis· 视觉判断- 工作产物
WP12· 答案 / 决策- 条件
- 未声明
- 提案难度
- 2 / 5
建议验证方式
Canvas file has a histogram gadget on onset with 6-hour interval; exposure window within 6 h of gold (point-source back-calculation from first case, median and last case). The VM has no shell, R, Python or Access, so the project and results can only be produced in Epi Info; file writes by any other process are caught by file-access auditing.
建议部分得分
40% epi curve configured; 60% exposure window
R09.04.01.01-T06 Create a kernel density hotspot map of cases in QGIS
原始指令
In QGIS, load geocoded synthetic case points input/cases_geo.gpkg (EPSG:4326), reproject to EPSG:32615, run the Heatmap (kernel density) tool with 1,000 m radius and 50 m pixels, style it, and identify the centroid of the densest cluster. Save output/kde.tif, output/hotspot.qgz and write the centroid (lat, lon) to output/hotspot.json.
- 平台
mac· macOSwin· Windows- 应用
- QGIS
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
click· 指向与点击type· 文字与表单vis· 视觉判断- 工作产物
WP04· 三维 / 空间模型- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
kde.tif CRS 32615, 50 m resolution, values correlate r>=0.99 with reference KDE; reported centroid within 200 m of the gold peak. QGIS Interface Customization hides the Python Console and Processing script tools, and the VM has no shell for qgis_process, so the work must be done through QGIS dialogs.
建议部分得分
25% reprojection; 35% KDE parameters/output; 40% hotspot centroid
R09.04.01.01-T07 Detect aberrations in syndromic surveillance counts with EARS methods
原始指令
input/ed_visits_ili.csv has daily ILI-like ED visit counts for 3 regions over 2 years. In R, apply EARS C1, C2 and C3 (surveillance package or equivalent, 7-day baseline, 2-day guard band for C2/C3) and write output/alerts.csv listing region, date and method for each alarm.
- 平台
mac· macOSwin· Windowslin· Linux- 应用
- R
- 交互表面
term· 终端- GUI 需求 · 任务设定
CL· CLI 足够- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
code· 代码与命令- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 4 / 5
建议验证方式
Alert set per method equals reference computed with surveillance::earsC under the same parameters (F1>=0.98); dates exact.
建议部分得分
30% C1; 35% C2; 35% C3
R09.04.01.01-T08 Enter thirty paper case report forms into an Epi Info form
原始指令
Open Epi Info project input/salmonella.prj and enter the 30 scanned case report forms in input/crf_scans.pdf (handwritten, synthetic) via Enter Data, following the form's skip logic. Leave illegible fields blank and list them in output/queries.csv (record, field).
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
G2· GUI 必要- 交互原语
type· 文字与表单vis· 视觉判断key· 快捷键- 工作产物
WP02· 记录 / 表格- 条件
long· 长流程- 提案难度
- 4 / 5
建议验证方式
Field-level accuracy >=98% vs double-entered gold (normalized dates and codes); skip-logic fields empty where required; illegible-field query list exact (5 planted). The VM has no shell, R, Python or Access, so the project and results can only be produced in Epi Info; file writes by any other process are caught by file-access auditing.
建议部分得分
70% field accuracy (scaled, full credit at 0.98); 15% skip logic respected; 15% queries
R09.04.01.01-T09 Find local clusters of tract-level rates with Local Moran's I
原始指令
Spatially join geocoded synthetic cases input/cases_geo.gpkg to census tracts input/tracts.gpkg in QGIS, compute rates per 10,000, smooth with empirical Bayes, then compute Local Moran's I (queen contiguity, 999 permutations, seed 1) in R or GeoDa and map High-High clusters in QGIS. Save output/lisa.gpkg (tract, rate, ebrate, I, p, cluster) and output/lisa.qgz.
- 平台
mac· macOSwin· Windows- 应用
- QGIS · R
- 交互表面
desk· 桌面 GUIterm· 终端- GUI 需求 · 任务设定
HY· 混合- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
click· 指向与点击code· 代码与命令multi· 跨应用- 工作产物
WP04· 三维 / 空间模型- 条件
multiapp· 多应用- 提案难度
- 5 / 5
建议验证方式
Tract counts exact; EB rates within 1%; local I within 1e-3 of reference (spdep localmoran on EB rates); cluster labels at p<0.05 F1>=0.9; QGIS style categorizes clusters.
建议部分得分
20% spatial join counts; 20% EB rates; 35% Local Moran's I and clusters; 25% map
R09.04.01.01-T10 Run a case-control logistic regression in Epi Info Classic Analysis
原始指令
In Epi Info Classic Analysis, read input/legionella_cc.csv (synthetic case-control study) and run LOGISTIC of case status on hot_tub_exposure, smoking, age_group and diabetes. Save the output HTML to output/logistic.html and write adjusted ORs with 95% CIs to output/or.json.
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
click· 指向与点击type· 文字与表单- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Program log shows LOGISTIC command; adjusted ORs within 0.01 and CI bounds within 0.02 of reference (R glm with same coding); age_group reference level as specified in input/coding.txt. The VM has no shell, R, Python or Access, so the project and results can only be produced in Epi Info; file writes by any other process are caught by file-access auditing.
建议部分得分
20% model specified; 50% ORs; 30% CIs
R09.04.01.01-T11 Deduplicate and standardize a surveillance line list
原始指令
input/linelist_raw.xlsx (2,100 rows) merges lab and provider reports with duplicates (name spelling variants, swapped DOB day/month), mixed date formats and county name variants. Produce output/linelist_clean.csv with one row per case (keep earliest report date), ISO dates and county FIPS codes, and output/dedup_log.csv.
- 平台
mac· macOSwin· Windowslin· Linux- 应用
- R · Excel
- 交互表面
term· 终端desk· 桌面 GUI- GUI 需求 · 任务设定
HY· 混合- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
code· 代码与命令vis· 视觉判断- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Unique case count equals gold (1,734); pairwise duplicate F1>=0.95; date and FIPS fields exact for 99% of rows; earliest report date kept.
建议部分得分
40% duplicate F1; 20% case count; 25% standardized fields; 15% log
R09.04.01.01-T12 Count cases within 500 m of a contaminated well in QGIS
原始指令
In QGIS, buffer the well location in input/well.gpkg by 500 m (in EPSG:26916) and count the synthetic Legionella case addresses in input/cases.gpkg that fall inside; also report how many residents of the buffer area there are from block populations (area-weighted). Write output/buffer.json and save output/buffer.gpkg.
- 平台
mac· macOSwin· Windows- 应用
- QGIS
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
click· 指向与点击type· 文字与表单- 工作产物
WP12· 答案 / 决策- 条件
- 未声明
- 提案难度
- 2 / 5
建议验证方式
Buffer computed in a metric CRS (area within 0.5% of pi*500^2); case count exact; area-weighted population within 1% of gold. QGIS Interface Customization hides the Python Console and Processing script tools, and the VM has no shell for qgis_process, so the work must be done through QGIS dialogs.
建议部分得分
30% correct buffer; 40% case count; 30% population
R09.04.01.01-T13 Calculate a cohort study sample size in Epi Info StatCalc
原始指令
Use Epi Info StatCalc (Sample Size and Power > Cohort or Cross-Sectional) to compute the sample size for a cohort study with 95% confidence, 80% power, ratio unexposed:exposed 2:1, outcome 5% in unexposed and risk ratio 2.0. Write Kelsey, Fleiss and Fleiss-with-CC totals to output/samplesize.json.
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
type· 文字与表单click· 指向与点击- 工作产物
WP12· 答案 / 决策- 条件
- 未声明
- 提案难度
- 1 / 5
建议验证方式
Three totals exact vs StatCalc reference output for those inputs. The VM has no shell, R or Python to compute the formulas, so the totals must come from StatCalc in Epi Info; file writes by other processes are caught by file-access auditing.
建议部分得分
33% Kelsey total; 33% Fleiss total; 33% Fleiss-with-CC total; 1% valid JSON
R09.04.01.01-T14 Compute standardized mortality ratios by county with exact Poisson CIs
原始指令
Using R, compute indirectly standardized mortality ratios for opioid overdose deaths by county from input/deaths.csv and input/pop_age.csv using state age-specific rates as the standard, with exact Poisson 95% CIs, and flag counties whose CI excludes 1. Write output/smr.csv.
- 平台
mac· macOSwin· Windowslin· Linux- 应用
- R
- 交互表面
term· 终端- GUI 需求 · 任务设定
CL· CLI 足够- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
code· 代码与命令- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Expected counts within 0.01, SMRs within 0.001, CI bounds within 0.002 of reference; flagged set exact.
建议部分得分
30% expected counts; 30% SMRs; 25% CIs; 15% flags
R09.04.01.01-T15 Make a privacy-preserving dot-density case map from Epi Info data
原始指令
Export the cases form of Epi Info project input/measles.prj to CSV, aggregate by ZIP code, and in QGIS create a dot-density layer with one random dot per case placed within its ZIP polygon (no dots at real addresses), styled over a basemap-free ZIP layer. Save output/dots.gpkg and output/dotmap.qgz.
- 平台
win· Windows- 应用
- Epi Info · QGIS
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
HY· 混合- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
multi· 跨应用click· 指向与点击vis· 视觉判断- 工作产物
WP04· 三维 / 空间模型- 条件
multiapp· 多应用- 提案难度
- 4 / 5
建议验证方式
Per-ZIP dot counts equal case counts; every dot inside its ZIP polygon; no dot within 50 m of any real case address in the hidden address file; export CSV row count equals form records.
建议部分得分
20% export; 40% per-ZIP counts; 25% dots inside polygons; 15% privacy check
R09.04.01.01-T16 Design a parent-child contact tracing form with code tables in Epi Info
原始指令
In Epi Info Form Designer, build project output/tb_contacts.prj: parent form 'IndexCase' (case ID, site, diagnosis date, smear status from a code table) and related child form 'Contact' (1-to-many) with relationship (code table), exposure hours, TST result and a check-code rule that skips TST date unless result is entered. Enter the 3 index cases and 11 contacts from input/contacts.xlsx.
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
G3· 仅 GUI- 交互原语
drag· 拖放click· 指向与点击type· 文字与表单- 工作产物
WP08· 应用 / 系统状态- 条件
- 未声明
- 提案难度
- 4 / 5
建议验证方式
Project metadata: two forms with relate button and FK linkage; code tables with exact values; check-code skip present; 3 parent and 11 child records with correct parent keys and values. The VM has no shell, R, Python or Access, so the project and results can only be produced in Epi Info; file writes by any other process are caught by file-access auditing.
建议部分得分
25% forms and relation; 20% code tables; 15% check code; 40% records linked correctly
R09.04.01.01-T17 Smooth small-area rates with empirical Bayes and map them
原始指令
For synthetic lung cancer incidence in input/tracts_counts.csv (400 tracts, many small populations), compute raw rates, global and spatial (queen neighbours) empirical Bayes smoothed rates in R, and produce side-by-side QGIS maps of raw vs spatial-EB rates with identical class breaks in one print layout. Save output/eb.gpkg, output/eb.qgz and output/eb.pdf.
- 平台
mac· macOSwin· Windows- 应用
- R · QGIS
- 交互表面
desk· 桌面 GUIterm· 终端- GUI 需求 · 任务设定
HY· 混合- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
code· 代码与命令click· 指向与点击multi· 跨应用- 工作产物
WP04· 三维 / 空间模型- 条件
multiapp· 多应用- 提案难度
- 5 / 5
建议验证方式
EB rates within 1% of reference (spdep EBest and EBlocal); layout contains two maps with identical renderer breaks; PDF exported.
建议部分得分
15% raw rates; 25% global EB; 30% spatial EB; 30% layout with shared breaks
R09.04.01.01-T18 Animate weekly cases with the QGIS Temporal Controller
原始指令
In QGIS load input/weekly_cases.gpkg (county polygons x 26 weeks, field week_start), configure the layer's temporal properties, style by weekly rate, and use the Temporal Controller to export 26 frames (1 week step) to output/frames/ at 1280x720, with the week shown in a title label.
- 平台
mac· macOSwin· Windows- 应用
- QGIS
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
click· 指向与点击type· 文字与表单vis· 视觉判断- 工作产物
WP05· 时序媒体- 条件
- 未声明
- 提案难度
- 4 / 5
建议验证方式
26 PNG frames 1280x720; .qgz temporal settings (field-based, 1-week step); OCR of title label in frames 1, 13, 26 gives correct weeks; sampled county colors match the week's rate class. QGIS Interface Customization hides the Python Console and Processing script tools, and the VM has no shell for qgis_process, so the work must be done through QGIS dialogs.
建议部分得分
25% temporal config; 30% 26 frames correct size; 25% week labels; 20% colors per week
R09.04.01.01-T19 Analyse a matched case-control study in Epi Info
原始指令
In Epi Info Classic Analysis, read input/matched_cc.csv (1:1 matched pairs, synthetic hepatitis A outbreak) and run MATCH analysis for exposure to restaurant B, reporting the matched odds ratio, McNemar chi-square and exact 95% CI to output/matched.json; also save the program as output/matched.pgm7.
- 平台
win· Windows- 应用
- Epi Info
- 交互表面
desk· 桌面 GUI- GUI 需求 · 任务设定
G2· GUI 必要- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
click· 指向与点击type· 文字与表单- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 3 / 5
建议验证方式
Discordant pair counts exact; matched OR exact; McNemar statistic within 0.01; CI within 0.02; .pgm7 contains the MATCH command. The VM has no shell, R, Python or Access, so the project and results can only be produced in Epi Info; file writes by any other process are caught by file-access auditing.
建议部分得分
30% discordant pairs; 30% OR; 20% McNemar; 20% CI
R09.04.01.01-T20 Produce an MMWR-style weekly notifiable disease table
原始指令
From the 5-year synthetic line list input/notifiable_2021_2026.csv, produce for MMWR week 40 of 2026 a table of 15 conditions with: current week count, cumulative YTD 2026, YTD 2025, 5-year weekly median for weeks 39-41, and max of the previous 52 weeks. Write output/table_wk40.csv and a formatted output/table_wk40.pdf.
- 平台
mac· macOSwin· Windowslin· Linux- 应用
- R · Python
- 交互表面
term· 终端- GUI 需求 · 任务设定
CL· CLI 足够- GUI 需求 · 普通权限
CL· CLI 足够- 交互原语
code· 代码与命令- 工作产物
WP02· 记录 / 表格- 条件
- 未声明
- 提案难度
- 5 / 5
建议验证方式
MMWR week assignment per CDC rules (weeks start Sunday; week 1 is the first week with >=4 days in the year); all 75 cells exact vs reference; PDF table text equals CSV.
建议部分得分
20% MMWR week logic; 20% current week; 25% YTD columns; 35% 5-yr median/max and PDF (5:2)
已有研究映射
以下沿用研究目录中的基准与小类映射，不是逐题标注、执行记录或产品背书。