diff --git a/.gitignore b/.gitignore index efc128f..463fbed 100644 --- a/.gitignore +++ b/.gitignore @@ -40,10 +40,15 @@ rsconnect/ *.DS_Store # Data -/data +data/* +!data/*.md # Figures -/figures +figures/* +!figures/*.md # HTML *.html + +# Sandbox +sandbox.R diff --git a/README.md b/README.md index c790fb9..131060d 100644 --- a/README.md +++ b/README.md @@ -3,16 +3,16 @@ Geographic Patterns in U.S. Lung Cancer Mortality and Cigarette Smoking 1,2 [ORCID](https://orcid.org/0000-0002-0127-4391) -* **Ian D. Buller**3,4 [ORCID](https://orcid.org/0000-0001-9477-8582) +* **Alaina H. Shreves**1,2 - [ORCID](https://orcid.org/0000-0002-0127-4391) +* **Ian D. Buller**3,4 - [ORCID](https://orcid.org/0000-0001-9477-8582) * **Elizabeth Chase**5,6 - [ORCID](https://orcid.org/0000-0003-0452-2976) * **Hannah Creutzfeldt**3,7 -* **Jared A. Fisher**3 [ORCID](https://orcid.org/0000-0001-9203-5742) -* **Barry I. Graubard**6 [ORCID](https://orcid.org/0000-0002-6787-1105) +* **Jared A. Fisher**3 - [ORCID](https://orcid.org/0000-0001-9203-5742) +* **Barry I. Graubard**6 - [ORCID](https://orcid.org/0000-0002-6787-1105) * **Robert N. Hoover**8 * **Debra T. Silverman**3 * **Susan S. Devesa**5 - *Co-Senior Author* @@ -20,8 +20,8 @@ Geographic Patterns in U.S. Lung Cancer Mortality and Cigarette Smoking -R-Script +R Script Description @@ -107,6 +107,12 @@ Shreves AH, Buller ID, Chase E, Creutzfeld H, Fisher JA, Graubard BI, Hoover RN, The repository also includes the code to create the project hexsticker. +### Getting Started + +* Step 1: You must download the data (see Data Availability section) +* Step 2: Save the data set to the data directory in this repository. Currently specified as a CSV file, but modify the path on Line 58 of the `preparation.R` file based on data location and file name +* Step 3: Run R scripts for figures. The `preparation.R` file will source the `functions.R` file. + ### Data Availability County-level U.S. lung cancer mortality rates and smoking prevalences are downloadable from [Model-based Small Area Estimates of Cancer-Related Measures](https://sae.cancer.gov/nhis-brfss/) from the [Surveillance Research Program](https://surveillance.cancer.gov/) within the [Division of Cancer Control and Population Sciences](https://cancercontrol.cancer.gov/) of the [National Cancer Institute](https://www.cancer.gov/) and the [National Vital Statistics System](https://www.cdc.gov/nchs/nvss/index.htm) from the [National Center for Health Statistics](https://www.cdc.gov/nchs/index.htm) of the [Centers for Disease Control and Prevention](https://www.cdc.gov/). diff --git a/code/README.md b/code/README.md new file mode 100644 index 0000000..0bc6103 --- /dev/null +++ b/code/README.md @@ -0,0 +1,41 @@ +Geographic Patterns in U.S. Lung Cancer Mortality and Cigarette Smoking +=================================================== + +### R Scripts Included In This Repository + +This repository includes R scripts use to calculate the geospatial techniques and render the figures found in the following peer-reviewed manuscript: + +Shreves AH, Buller ID, Chase E, Creutzfeld H, Fisher JA, Graubard BI, Hoover RN, Silverman DT, Devesa SS, Jones RR. Geographic Patterns in U.S. Lung Cancer Mortality and Cigarette Smoking. _Cancer Epidemiology, Biomarkers & Prevention_ (Submitted) + + ++++ + + + + + + + + + + + + + + + + + + + + + + + + + + +
R ScriptDescription

functions.R

Custom functions to calculate the local Lee's L statistic with correction for multiple testing

preparation.R

Calculate the local Lee's L statistics for the four comparisons. Requires a data set to run (not included; see notes within).

figure1.R

Generate Figure 1

figure2.R

Generate Figure 2

supplemental1.R

Generate Supplemental Figure 1

supplemental2.R

Generate Supplemental Figure 2
diff --git a/data/README.md b/data/README.md new file mode 100644 index 0000000..eefebd7 --- /dev/null +++ b/data/README.md @@ -0,0 +1,10 @@ +Geographic Patterns in U.S. Lung Cancer Mortality and Cigarette Smoking +=================================================== + +Place data here (data not included). + +The `preparation.R` file calls a CSV file named "lung_cancer_mortality_and_smoking_prevalence.csv" + +### Data Availability + +County-level U.S. lung cancer mortality rates and smoking prevalences are downloadable from [Model-based Small Area Estimates of Cancer-Related Measures](https://sae.cancer.gov/nhis-brfss/) from the [Surveillance Research Program](https://surveillance.cancer.gov/) within the [Division of Cancer Control and Population Sciences](https://cancercontrol.cancer.gov/) of the [National Cancer Institute](https://www.cancer.gov/) and the [National Vital Statistics System](https://www.cdc.gov/nchs/nvss/index.htm) from the [National Center for Health Statistics](https://www.cdc.gov/nchs/index.htm) of the [Centers for Disease Control and Prevention](https://www.cdc.gov/). diff --git a/figures/README.md b/figures/README.md new file mode 100644 index 0000000..472bf87 --- /dev/null +++ b/figures/README.md @@ -0,0 +1,6 @@ +Geographic Patterns in U.S. Lung Cancer Mortality and Cigarette Smoking +=================================================== + +Save generated figures here (figures not included). See the figures in the following peer-reviewed manuscript: + +Shreves AH, Buller ID, Chase E, Creutzfeld H, Fisher JA, Graubard BI, Hoover RN, Silverman DT, Devesa SS, Jones RR. Geographic Patterns in U.S. Lung Cancer Mortality and Cigarette Smoking. _Cancer Epidemiology, Biomarkers & Prevention_ (Submitted)