Merge pull request #11 from Big-Life-Lab/dev

Hotfix update

NEWS.md

@@ -1,4 +1,13 @@
-# cchsflow 0.2.1 (Latest build)
+# cchsflow 0.2.2 (Latest build)
+
+## Features:
+
+- Updated ref branch of bllflow to match latest version of `RecWTable()`
+- Minor formatting changes in data, function, and derived variable documentation to improve 
+  readability
+- Minor corrections to derived variables article
+
+# cchsflow 0.2.1 
 
 ## Features:
 

R/alcohol.R

@@ -2,12 +2,15 @@
 #'
 #' @description \strong{NOTE:} this is not a function.
 #'  
-#'  This is a continuous variable derived by Statistics Canada that quantifies the amount of alcohol that is consumed in a week.
-#'  This is calculated by adding the number of drinks consumed during each day in the past week.
-#'  Respondents of each CCHS cycle are asked how much alcohol they have consumed each day in the past week (ie. how much alcohol did you consume on Sunday,
-#'  how much did you consume on Monday etc.). Each day in considered an individual variable and ALWDWKY takes the sum of all daily variables.
+#'  This is a continuous variable derived by Statistics Canada that quantifies the amount of alcohol 
+#'  that is consumed in a week. This is calculated by adding the number of drinks consumed during 
+#'  each day in the past week. Respondents of each CCHS cycle are asked how much alcohol they have 
+#'  consumed each day in the past week (ie. how much alcohol did you consume on Sunday,
+#'  how much did you consume on Monday etc.). Each day in considered an individual variable and 
+#'  ALWDWKY takes the sum of all daily variables.
 #'
-#' @details This variable is used in all CCHS cycles in cchsflow and how it was derived remains consistent from 2001 to 2014.
+#' @details This variable is used in all CCHS cycles in cchsflow and how it was derived remains 
+#'  consistent from 2001 to 2014.
 #'
 #' @param ALWDWKY cchsflow variable name for number of drinks consumed in the past week
 #'
@@ -20,10 +23,11 @@ ALWDWKY <- function(ALWDWKY) {
 #'
 #' @description \strong{NOTE:} this is not a function. 
 #'  
-#'  This is a continuous variable derived by Statistics Canada that quantifies the mean daily consumption of alcohol. 
-#'  This takes the value of ALWDWKY and divides it by 7.
+#'  This is a continuous variable derived by Statistics Canada that quantifies the mean daily 
+#'  consumption of alcohol. This takes the value of ALWDWKY and divides it by 7.
 #'
-#' @details This variable is used in all CCHS cycles in cchsflow and how it was derived remains consistent from 2001 to 2014.
+#' @details This variable is used in all CCHS cycles in cchsflow and how it was derived remains 
+#' consistent from 2001 to 2014.
 #'
 #' @param ALWDDLY cchsflow variable name for average daily alcohol consumption
 #'
@@ -36,19 +40,21 @@ ALWDDLY <- function(ALWDDLY) {
 #'
 #' @description \strong{NOTE:} this is not a function. 
 #'  
-#'  This is a categorical variable derived by Statistics Canada that uses various intermediate alcohol variables to 
-#'  categorize individuals into 4 distinct groups:
+#'  This is a categorical variable derived by Statistics Canada that uses various intermediate 
+#'  alcohol variables to categorize individuals into 4 distinct groups:
 #'
 #'  1. Regular Drinker
 #'  2. Occasional Drinker
 #'  3. Former Drinker
 #'  4. Never Drinker
 #'
-#' @details This variable is used in CCHS cycles from 2001 to 2007. How it was derived remained consistent during these years.
+#' @details This variable is used in CCHS cycles from 2001 to 2007. How it was derived remained 
+#'  consistent during these years.
 #'
-#'  Starting in 2007, Statistics Canada created a derived variable that looked at drinking type in the last 12 months.
-#'  This new derived variable did not distinguish between former and never drinkers. If your research requires you
-#'  to differentiate between former and never drinkers, we recommend using earlier cycles fo the CCHS.
+#'  Starting in 2007, Statistics Canada created a derived variable that looked at drinking type in 
+#'  the last 12 months. This new derived variable did not distinguish between former and never 
+#'  drinkers. If your research requires you to differentiate between former and never drinkers, 
+#'  we recommend using earlier cycles of the CCHS.
 #'
 #' @param ALCDTYP cchsflow variable name for type of drinker
 #'
@@ -61,16 +67,16 @@ ALCDTYP <- function(ALCDTYP) {
 #'
 #' @description \strong{NOTE:} this is not a function. 
 #'  
-#'  This is a categorical variable derived by Statistics Canada that uses various intermediate alcohol variables to 
-#'  categorize individuals into 3 distinct groups:
+#'  This is a categorical variable derived by Statistics Canada that uses various intermediate 
+#'  alcohol variables to categorize individuals into 3 distinct groups:
 #'
 #'  1. Regular Drinker
 #'  2. Occasional Drinker
 #'  3. No drink in the last 12 months.
 #'
-#' @details This variable was introuced in the 2007-2008 cycle of the CCHS, and became the sole derived variable that categorized
-#'  people into various drinker types from 2009 onwards. Unlike `ALCDTYP`, this variable does not distinguish between
-#'  former and never drinkers.
+#' @details This variable was introuced in the 2007-2008 cycle of the CCHS, and became the sole 
+#'  derived variable that categorized people into various drinker types from 2009 onwards. 
+#'  Unlike ALCDTYP, this variable does not distinguish between former and never drinkers.
 #'
 #' @param ALCDTTM cchsflow variable name for type of drinker (12 months)
 #'

R/bmi.R

@@ -31,29 +31,34 @@ ifelse2 <- function(x, a, b) {
 
 #' @title Body Mass Index (BMI) derived variable
 #' 
-#' @description This function creates a harmonized BMI variable. The BMI variable provided by the CCHS calculates BMI using methods
-#'  that vary across cycles, leading to measurement error when using multiple CCHS cycles. In certain CCHS cycles (2001-2003, 2007+),
-#'  there are age restrictions in which respondents under the age of 20 and over the age of 64 were not included. Across all CCHS cycles,
-#'  female respondents who identifed as being pregnant were excluded; and in certain CCHS cycles (2003-2007, 2013-2014), females who did not
-#'  answer the pregnancy question were coded as NS (not stated) for HWTGBMI. As well, in certain CCHS cycles (2001-2003, 2009-2014),
-#'  respondents outside certain height and weight ranges (0.914-2.108m for height, 0-260kg for weight) were excluded from HWTGBMI. 
-#' 
-#'  BMI_fun() creates a derived variable (HWTGBMI_der) that is harmonized across all CCHS cycles. This function divides weight by the
-#'  square of height.
+#' @description This function creates a harmonized BMI variable. The BMI variable provided by the 
+#'  CCHS calculates BMI using methods that vary across cycles, leading to measurement error when 
+#'  using multiple CCHS cycles. In certain CCHS cycles (2001-2003, 2007+), there are age 
+#'  restrictions in which respondents under the age of 20 and over the age of 64 were not included. 
+#'  Across all CCHS cycles, female respondents who identifed as being pregnant were excluded; and 
+#'  in certain CCHS cycles (2003-2007, 2013-2014), females who did not answer the pregnancy 
+#'  question were coded as NS (not stated) for HWTGBMI. As well, in certain CCHS cycles (2001-2003, 
+#'  2009-2014), respondents outside certain height and weight ranges (0.914-2.108m for height, 
+#'  0-260kg for weight) were excluded from HWTGBMI. 
+#' 
+#'  BMI_fun() creates a derived variable (HWTGBMI_der) that is harmonized across all CCHS cycles. 
+#'  This function divides weight by the square of height.
 #'  
-#' @details For HWTGBMI_der, there are no restrictions to age, height, weight, or pregnancy status. While pregnancy was consistent across 
-#'  all CCHS cycles, its variable (MAM_037) was not available in the PUMF CCHS datasets so it could not be harmonized and included into 
-#'  the function.
+#' @details For HWTGBMI_der, there are no restrictions to age, height, weight, or pregnancy status. 
+#'  While pregnancy was consistent across all CCHS cycles, its variable (MAM_037) was not available 
+#'  in the PUMF CCHS datasets so it could not be harmonized and included into the function.
 #' 
-#'  For any single CCHS survey year, it is appropriate to use the CCHS BMI variable (HWTGBMI) that is also available on cchsflow.
-#'  HWTGBMI_der is recommended when using multiple survey cycles.  
+#'  For any single CCHS survey year, it is appropriate to use the CCHS BMI variable (HWTGBMI) that 
+#'  is also available on cchsflow. HWTGBMI_der is recommended when using multiple survey cycles.  
 #' 
-#'  HWTGBMI_der uses the CCHS variables for height and weight that have been transformed by cchsflow. In order to 
-#'  generate a value for BMI across CCHS cycles, height and weight must be transformed and harmonized.
+#'  HWTGBMI_der uses the CCHS variables for height and weight that have been transformed by 
+#'  cchsflow. In order to generate a value for BMI across CCHS cycles, height and weight must be 
+#'  transformed and harmonized.
 #' 
-#' @note In earlier CCHS cycles (2001 and 2003), height was collected in inches; while in later CCHS cycles (2005+) 
-#'  it was collected in meters. To harmonize values across cycles, height was converted to meters (to 3 decimal points). 
-#'  Weight was collected in kilograms across all CCHS cycles, so no transformations were required in the harmonization process.
+#' @note In earlier CCHS cycles (2001 and 2003), height was collected in inches; while in later CCHS
+#'  cycles (2005+) it was collected in meters. To harmonize values across cycles, height was 
+#'  converted to meters (to 3 decimal points). Weight was collected in kilograms across all CCHS 
+#'  cycles, so no transformations were required in the harmonization process.
 #' 
 #' @param HWTGHTM CCHS variable for height (in meters)
 #' 
@@ -63,29 +68,30 @@ ifelse2 <- function(x, a, b) {
 #' 
 #' @examples 
 #' # Using BMI_fun() to create BMI values across cycles
-#' # BMI_fun() is specified in variableDetails.csv along with the CCHS variables and cycles included. 
+#' # BMI_fun() is specified in variableDetails.csv along with the CCHS variables and cycles 
+#' # included. 
 #' 
-#' # To transform the derived BMI variable, use RecWTable() for each CCHS cycle and specify HWTGBMI_der, 
-#' # along with height (HWTGHTM) and weight (HWTGWTK). Then by using bind_rows(), you can combined HWTGBMI_der
-#' # across cycles.
+#' # To transform the derived BMI variable, use RecWTable() for each CCHS cycle and specify 
+#' # HWTGBMI_der, along with height (HWTGHTM) and weight (HWTGWTK). Then by using bind_rows(), you 
+#' # can combined HWTGBMI_der across cycles.
 #' 
 #' suppressMessages(library(bllflow))
 #' library(cchsflow)
-#' bmi2010 <- RecWTable(dataSource = cchs2010, variableDetails = variableDetails, datasetName = "cchs2010", 
-#' variables = c("HWTGHTM", "HWTGWTK", "HWTGBMI_der"))
+#' bmi2010 <- RecWTable(dataSource = cchs2010, variableDetails = variableDetails, 
+#' datasetName = "cchs2010", variables = c("HWTGHTM", "HWTGWTK", "HWTGBMI_der"))
 #' head(bmi2010)
 #' 
-#' bmi2012 <- RecWTable(dataSource = cchs2012, variableDetails = variableDetails, datasetName = "cchs2012", 
-#' variables = c("HWTGHTM", "HWTGWTK", "HWTGBMI_der"))
+#' bmi2012 <- RecWTable(dataSource = cchs2012, variableDetails = variableDetails, datasetName = 
+#' "cchs2012", variables = c("HWTGHTM", "HWTGWTK", "HWTGBMI_der"))
 #' tail(bmi2012)
 #' 
 #' combined_bmi <- bind_rows(bmi2010, bmi2012)
 #' head(combined_bmi)
 #' tail(combined_bmi)
 #' 
 #' # Using BMI_fun() to generate a BMI value with user inputted height and weight values
-#' # BMI_fun() can also generate a value for BMI if you input a value for height and weight. Let's say your height is
-#' # 170cm (1.7m) and your weight is 50kg, your BMI can be calculated as followed:
+#' # BMI_fun() can also generate a value for BMI if you input a value for height and weight. Let's 
+#' # say your height is 170cm (1.7m) and your weight is 50kg, your BMI can be calculated as follows:
 #' 
 #' library(cchsflow)
 #' BMI <- BMI_fun(HWTGHTM = 1.7, HWTGWTK = 50)

R/data.R

@@ -1,8 +1,10 @@
 #' 2001 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2001 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2001 cycle of the Canadian Community Health Survey 
+#' (CCHS) Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics 
+#' Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' Long name: cchs-82M0013-E-2001-c1-1-general-file
 #' 
@@ -25,9 +27,11 @@ NULL
 
 #' 2003 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2003 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2003 cycle of the Canadian Community 
+#' Health Survey (CCHS) Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by 
+#' Statistics Canada. 
+#' 
+#' See the open license\href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' 
 #' Long name: cchs-82M0013-E-2003-c2-1-General File
@@ -51,9 +55,11 @@ NULL
 
 #' 2005 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2005 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2005 cycle of the Canadian Community Health Survey 
+#' (CCHS) Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by 
+#' Statistics Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' 
 #' Long name: cchs-82M0013-E-2005-c3-1-main-file
@@ -77,9 +83,11 @@ NULL
 
 #' 2007-2008 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2007-2008 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2007-2008 cycle of the Canadian Community Health 
+#' Survey (CCHS) Public Use Microdata file (PUMF) dataset. 
+#' The CCHS survey is conducted by Statistics Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' Long name: cchs-E-2007-2008-AnnualComponent
 #' 
@@ -102,10 +110,11 @@ NULL
 
 #' 2009-2010 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2009-2010 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
+#' This is a subset of 200 observations from the 2009-2010 cycle of the Canadian Community 
+#' Health Survey (CCHS) Public Use Microdata file (PUMF) dataset. 
+#' The CCHS survey is conducted by Statistics Canada. 
 #' 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' Long name: CCHS-82M0013-E-2009-2010-Annualcomponent
 #' 
@@ -128,9 +137,11 @@ NULL
 
 #' 2010 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2010 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2010 cycle of the Canadian Community Health Survey 
+#' (CCHS) Public Use Microdata file (PUMF) dataset. 
+#' The CCHS survey is conducted by Statistics Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' Long name: CCHS-82M0013-E-2010-AnnualComponent
 #' 
@@ -153,9 +164,11 @@ NULL
 
 #' 2011-2012 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2011-2012 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2011-2012 cycle of the Canadian Community Health 
+#' Survey (CCHS) Public Use Microdata file (PUMF) dataset. 
+#' The CCHS survey is conducted by Statistics Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' 
 #' Long name: cchs-82M0013-E-2011-2012-Annual-component
@@ -179,9 +192,11 @@ NULL
 
 #' 2012 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2012 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2012 cycle of the Canadian Community Health Survey 
+#' (CCHS) Public Use Microdata file (PUMF) dataset. 
+#' The CCHS survey is conducted by Statistics Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' Long name: cchs-82M0013-E-2012-Annual-component
 #' 
@@ -204,9 +219,11 @@ NULL
 
 #' 2013-2014 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2013-2014 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2013-2014 cycle of the Canadian Community Health 
+#' Survey (CCHS) Public Use Microdata file (PUMF) dataset. 
+#' The CCHS survey is conducted by Statistics Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' Long name: cchs-82M0013-E-2013-2014-Annual-component
 #' 
@@ -229,9 +246,11 @@ NULL
 
 #' 2014 CCHS data
 #' 
-#' This is a subset of 200 observations from the 2014 cycle of the Canadian Community Health Survey (CCHS) 
-#' Public Use Microdata file (PUMF) dataset. The CCHS survey is conducted by Statistics Canada. 
-#' See the Statistics Canada Open License \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
+#' This is a subset of 200 observations from the 2014 cycle of the Canadian Community Health Survey 
+#' (CCHS) Public Use Microdata file (PUMF) dataset. 
+#' The CCHS survey is conducted by Statistics Canada. 
+#' 
+#' See the open license \href{https://www.statcan.gc.ca/eng/reference/licence}{here}.
 #' 
 #' Long name: cchs-82M0013-E-2014-Annual-component
 #'