Merge pull request #69 from getwilds/test

more linting
getwilds · Mar 8, 2024 · d9bf492 · d9bf492
2 parents 4f72e87 + 069c53e
commit d9bf492
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Showing 13 changed files with 173 additions and 57 deletions.
diff --git a/R/process-incidence.R b/R/process-incidence.R
@@ -1,6 +1,7 @@
 #' Process Cancer Incidence Response Data
 #'
-#' This function processes the Cancer Incidence response data from State Cancer Profiles
+#' This function processes the Cancer Incidence response data
+#' from State Cancer Profiles
 #'
 #' @param resp A response object
 #'
@@ -21,7 +22,7 @@
 process_incidence <- function(resp) {
   nenv <- new.env()
   data("state", envir = nenv)
-  state.name <- nenv$state.name
+  state_name <- nenv$state.name
 
   resp_lines <- resp %>%
     resp_body_string() %>%
@@ -31,12 +32,29 @@ process_incidence <- function(resp) {
   index_first_line_break <- which(resp_lines == "")[4]
   index_second_line_break <- which(resp_lines == "")[5]
 
-  resp <- resp_lines[(index_first_line_break + 1):(index_second_line_break - 1)] %>%
+  resp <- resp_lines[
+    (index_first_line_break + 1):
+      (index_second_line_break - 1)
+  ] %>%
     paste(collapse = "\n") %>%
-    (\(x) read.csv(textConnection(x), header = TRUE, colClasses = "character"))()
+    (
+      \(x) {
+        read.csv(textConnection(x),
+          header = TRUE,
+          colClasses = "character"
+        )
+      }
+    )()
 
-
-  column <- c("County", "Health.Service.Area", "State")[c("County", "Health.Service.Area", "State") %in% colnames(resp)]
+  column <- c(
+    "County",
+    "Health.Service.Area",
+    "State"
+  )[c(
+    "County",
+    "Health.Service.Area",
+    "State"
+  ) %in% colnames(resp)]
 
   resp <- resp %>%
     filter(!!sym(column) != "US (SEER+NPCR)(1)") %>%
@@ -45,7 +63,7 @@ process_incidence <- function(resp) {
 
   if (column %in% c("Health.Service.Area", "County")) {
     resp <- resp %>%
-      filter(!(!!sym(column) %in% state.name))
+      filter(!(!!sym(column) %in% state_name))
   }
   resp
 }
diff --git a/R/process-mortality.R b/R/process-mortality.R
@@ -1,6 +1,7 @@
 #' Process Cancer Mortality Response Data
 #'
-#' This function processes the Cancer Mortality response data from State Cancer Profiles
+#' This function processes the Cancer Mortality response data
+#' from State Cancer Profiles
 #'
 #' @param resp A response object
 #'
@@ -20,7 +21,7 @@
 process_mortality <- function(resp) {
   nenv <- new.env()
   data("state", envir = nenv)
-  state.name <- nenv$state.name
+  state_name <- nenv$state.name
 
   resp_lines <- resp %>%
     resp_body_string() %>%
@@ -30,19 +31,36 @@ process_mortality <- function(resp) {
   index_first_line_break <- which(resp_lines == "")[4]
   index_second_line_break <- which(resp_lines == "")[5]
 
-  resp <- resp_lines[(index_first_line_break + 1):(index_second_line_break - 1)] %>%
+  resp <- resp_lines[
+    (index_first_line_break + 1):
+      (index_second_line_break - 1)
+  ] %>%
     paste(collapse = "\n") %>%
-    (\(x) read.csv(textConnection(x), header = TRUE, colClasses = "character"))()
+    (
+      \(x) {
+        read.csv(textConnection(x),
+          header = TRUE,
+          colClasses = "character"
+        )
+      }
+    )()
 
-
-  column <- c("County", "Health.Service.Area", "State")[c("County", "Health.Service.Area", "State") %in% colnames(resp)]
+  column <- c(
+    "County",
+    "Health.Service.Area",
+    "State"
+  )[c(
+    "County",
+    "Health.Service.Area",
+    "State"
+  ) %in% colnames(resp)]
 
   resp <- resp %>%
     filter(!!sym(column) != "United States")
 
   if (column %in% c("Health.Service.Area", "County")) {
     resp <- resp %>%
-      filter(!(!!sym(column) %in% state.name))
+      filter(!(!!sym(column) %in% state_name))
   }
 
   resp %>%

diff --git a/R/process-response.R b/R/process-response.R
@@ -20,7 +20,7 @@
 process_response <- function(resp) {
   nenv <- new.env()
   data("state", envir = nenv)
-  state.name <- nenv$state.name
+  state_name <- nenv$state.name
 
   resp_lines <- resp %>%
     resp_body_string() %>%
@@ -30,21 +30,36 @@ process_response <- function(resp) {
   index_first_line_break <- which(resp_lines == "")[1]
   index_second_line_break <- which(resp_lines == "")[2]
 
-  resp <- resp_lines[(index_first_line_break + 1):(index_second_line_break - 1)] %>%
+  resp <- resp_lines[
+    (index_first_line_break + 1):
+      (index_second_line_break - 1)
+  ] %>%
     paste(collapse = "\n") %>%
-    (\(x) read.csv(textConnection(x), header = TRUE, colClasses = "character"))()
+    (
+      \(x) {
+        read.csv(textConnection(x),
+          header = TRUE,
+          colClasses = "character"
+        )
+      }
+    )()
 
-  # resp <- resp %>%
-  #   read.csv(text=.)
-
-  column <- c("Health.Service.Area", "County", "State")[c("Health.Service.Area", "County", "State") %in% colnames(resp)]
+  column <- c(
+    "Health.Service.Area",
+    "County",
+    "State"
+  )[c(
+    "Health.Service.Area",
+    "County",
+    "State"
+  ) %in% colnames(resp)]
 
   resp <- resp %>%
     filter(!!sym(column) != "United States")
 
   if (column %in% c("Health.Service.Area", "County")) {
     resp <- resp %>%
-      filter(!(!!sym(column) %in% state.name))
+      filter(!(!!sym(column) %in% state_name))
   }
   resp %>%
     mutate_all(\(x) na_if(x, "N/A")) %>%

diff --git a/R/process-screening.R b/R/process-screening.R
@@ -18,10 +18,6 @@
 #' process_screening(resp)
 #' }
 process_screening <- function(resp) {
-  nenv <- new.env()
-  data("state", envir = nenv)
-  state.name <- nenv$state.name
-
   resp_lines <- resp %>%
     resp_body_string() %>%
     strsplit("\\n") %>%
@@ -30,9 +26,19 @@ process_screening <- function(resp) {
   index_first_line_break <- which(resp_lines == "")[3]
   index_second_line_break <- which(resp_lines == "")[4]
 
-  resp <- resp_lines[(index_first_line_break + 1):(index_second_line_break - 1)] %>%
+  resp <- resp_lines[
+    (index_first_line_break + 1):
+      (index_second_line_break - 1)
+  ] %>%
     paste(collapse = "\n") %>%
-    (\(x) read.csv(textConnection(x), header = TRUE, colClasses = "character"))()
+    (
+      \(x) {
+        read.csv(textConnection(x),
+          header = TRUE,
+          colClasses = "character"
+        )
+      }
+    )()
 
   column <- c("County", "State")[c("County", "State") %in% colnames(resp)]
 

diff --git a/R/risk-alcohol.R b/R/risk-alcohol.R
@@ -4,7 +4,8 @@
 #' from State Cancer Profiles.
 #'
 #' @param alcohol The only permissible value is
-#' `"binge drinking (4+ drinks on one occasion for women, 5+ drinks for one occasion for men), ages 21+"`.
+#' `paste("binge drinking (4+ drinks on one occasion for women,",
+#'        "5+ drinks for one occasion for men), ages 21+")
 #' @param race One of the following values:
 #' - `"All Races (includes Hispanic)"`
 #' - `"White (non-Hispanic)"`

diff --git a/R/test-dput-resp-incd.R b/R/test-dput-resp-incd.R
@@ -1,6 +1,7 @@
 #' Test dput-resp-incidence
 #'
-#' This function creates a response object from the Incidence section of State Cancer Profiles for
+#' This function creates a response object from the Incidence section of
+#' State Cancer Profiles to be used in testing
 #'
 #'
 #' @returns A httr2 response object
@@ -13,12 +14,20 @@
 #' }
 dput_resp_incd <- function() {
   resp <- structure(list(
-    method = "GET", url = "https://statecancerprofiles.cancer.gov/incidencerates/index.php?stateFIPS=10&areatype=county&cancer=001&race=00&age=157&stage=999&year=0&type=incd&sortVariableName=rate&sortOrder=default&output=1&sex=0",
+    method = "GET",
+    url = paste0(
+      "https://statecancerprofiles.cancer.gov/incidencerates/",
+      "index.php?stateFIPS=10&areatype=county&cancer=001",
+      "&race=00&age=157&stage=999&year=0&type=incd&",
+      "sortVariableName=rate&sortOrder=default&output=1&sex=0"
+    ),
     status_code = 200L, headers = structure(list(
       date = "Wed, 21 Feb 2024 19:21:05 GMT",
-      server = "Apache", `content-disposition` = "attachment; filename=\"incd.csv\"",
+      server = "Apache",
+      `content-disposition` = "attachment; filename=\"incd.csv\"",
       `x-frame-options` = "SAMEORIGIN", `cache-control` = "public, max-age=300",
-      `content-type` = "text/csv; charset=iso-8859-1", `strict-transport-security` = "max-age=31536000;preload",
+      `content-type` = "text/csv; charset=iso-8859-1",
+      `strict-transport-security` = "max-age=31536000;preload",
       `set-cookie` = "TKTID=web-dmzst-03; path=/; HttpOnly; Secure",
       `cache-control` = "private"
     ), class = "httr2_headers"),
@@ -455,10 +464,16 @@ dput_resp_incd <- function() {
       0x65, 0x20, 0x50, 0x75, 0x65, 0x72, 0x74, 0x6f, 0x20, 0x52,
       0x69, 0x63, 0x6f, 0x2e, 0x0a
     )), request = structure(list(
-      url = "https://statecancerprofiles.cancer.gov/incidencerates/index.php?stateFIPS=10&areatype=county&cancer=001&race=00&age=157&stage=999&year=0&type=incd&sortVariableName=rate&sortOrder=default&output=1&sex=0",
+      url = paste0(
+        "https://statecancerprofiles.cancer.gov/incidencerates/",
+        "index.php?stateFIPS=10&areatype=county&cancer=001",
+        "&race=00&age=157&stage=999&year=0&type=incd&",
+        "sortVariableName=rate&sortOrder=default&output=1&sex=0"
+      ),
       method = NULL, headers = list(), body = NULL, fields = list(),
       options = list(), policies = list()
     ), class = "httr2_request"),
     cache = new.env()
   ), class = "httr2_response")
+  return(resp)
 }
diff --git a/R/test-dput-resp-mortality.R b/R/test-dput-resp-mortality.R
@@ -1,6 +1,7 @@
 #' Test dput-resp-mortality
 #'
-#' This function creates a response object from the Mortality section of State Cancer Profiles for
+#' This function creates a response object from the Mortality section of
+#' State Cancer Profiles to be used in testing
 #'
 #'
 #' @returns A httr2 response object
@@ -13,12 +14,20 @@
 #' }
 dput_resp_mortality <- function() {
   resp <- structure(list(
-    method = "GET", url = "https://statecancerprofiles.cancer.gov/deathrates/index.php?stateFIPS=10&areatype=county&cancer=001&race=00&age=157&year=0&type=death&sortVariableName=rate&sortOrder=default&output=1&sex=0",
+    method = "GET",
+    url = paste0(
+      "https://statecancerprofiles.cancer.gov/deathrates/",
+      "index.php?stateFIPS=10&areatype=county&cancer=001",
+      "&race=00&age=157&year=0&type=death&",
+      "sortVariableName=rate&sortOrder=default&output=1&sex=0"
+    ),
     status_code = 200L, headers = structure(list(
       date = "Wed, 21 Feb 2024 19:51:18 GMT",
-      server = "Apache", `content-disposition` = "attachment; filename=\"death.csv\"",
+      server = "Apache",
+      `content-disposition` = "attachment; filename=\"death.csv\"",
       `x-frame-options` = "SAMEORIGIN", `cache-control` = "public, max-age=300",
-      `content-type` = "text/csv; charset=iso-8859-1", `strict-transport-security` = "max-age=31536000;preload",
+      `content-type` = "text/csv; charset=iso-8859-1",
+      `strict-transport-security` = "max-age=31536000;preload",
       `set-cookie` = "TKTID=web-dmzst-02; path=/; HttpOnly; Secure",
       `cache-control` = "private"
     ), class = "httr2_headers"),
@@ -340,10 +349,16 @@ dput_resp_mortality <- function() {
       0x6c, 0x75, 0x64, 0x65, 0x20, 0x50, 0x75, 0x65, 0x72, 0x74,
       0x6f, 0x20, 0x52, 0x69, 0x63, 0x6f, 0x2e, 0x0a
     )), request = structure(list(
-      url = "https://statecancerprofiles.cancer.gov/deathrates/index.php?stateFIPS=10&areatype=county&cancer=001&race=00&age=157&year=0&type=death&sortVariableName=rate&sortOrder=default&output=1&sex=0",
+      url = paste0(
+        "https://statecancerprofiles.cancer.gov/deathrates/",
+        "index.php?stateFIPS=10&areatype=county&cancer=001",
+        "&race=00&age=157&year=0&type=death&",
+        "sortVariableName=rate&sortOrder=default&output=1&sex=0"
+      ),
       method = NULL, headers = list(), body = NULL, fields = list(),
       options = list(), policies = list()
     ), class = "httr2_request"),
     cache = new.env()
   ), class = "httr2_response")
+  return(resp)
 }
diff --git a/R/test-dput-resp-risk.R b/R/test-dput-resp-risk.R
@@ -1,6 +1,7 @@
 #' Test dput-resp-demo
 #'
-#' This function creates a response object from the Demographics section of State Cancer Profiles for
+#' This function creates a response object from the Demographics section of
+#' State Cancer Profiles to be used in testing
 #'
 #'
 #' @returns A httr2 response object
@@ -13,12 +14,20 @@
 #' }
 dput_resp_risk <- function() {
   resp <- structure(list(
-    method = "GET", url = "https://statecancerprofiles.cancer.gov/risk/index.php?topic=colorec&risk=v304&type=risk&sortVariableName=percent&sortOrder=default&output=1&race=00&stateFIPS=44",
+    method = "GET",
+    url = paste0(
+      "https://statecancerprofiles.cancer.gov/risk/",
+      "index.php?topic=colorec&risk=v304&type=risk&",
+      "sortVariableName=percent&sortOrder=default&",
+      "output=1&race=00&stateFIPS=44"
+    ),
     status_code = 200L, headers = structure(list(
       date = "Tue, 20 Feb 2024 20:40:10 GMT",
-      server = "Apache", `content-disposition` = "attachment; filename=\"screening_risk.csv\"",
+      server = "Apache",
+      `content-disposition` = "attachment; filename=\"screening_risk.csv\"",
       `x-frame-options` = "SAMEORIGIN", `cache-control` = "public, max-age=300",
-      `content-type` = "text/csv; charset=iso-8859-1", `strict-transport-security` = "max-age=31536000;preload",
+      `content-type` = "text/csv; charset=iso-8859-1",
+      `strict-transport-security` = "max-age=31536000;preload",
       `set-cookie` = "TKTID=web-dmzst-03; path=/; HttpOnly; Secure",
       `cache-control` = "private"
     ), class = "httr2_headers"),
@@ -154,10 +163,16 @@ dput_resp_risk <- function() {
       0x20, 0x50, 0x75, 0x65, 0x72, 0x74, 0x6f, 0x20, 0x52, 0x69,
       0x63, 0x6f, 0x2e, 0x0a
     )), request = structure(list(
-      url = "https://statecancerprofiles.cancer.gov/risk/index.php?topic=colorec&risk=v304&type=risk&sortVariableName=percent&sortOrder=default&output=1&race=00&stateFIPS=44",
+      url = paste0(
+        "https://statecancerprofiles.cancer.gov/risk/",
+        "index.php?topic=colorec&risk=v304&type=risk&",
+        "sortVariableName=percent&sortOrder=default&",
+        "output=1&race=00&stateFIPS=44"
+      ),
       method = NULL, headers = list(), body = NULL, fields = list(),
       options = list(), policies = list()
     ), class = "httr2_request"),
     cache = new.env()
   ), class = "httr2_response")
+  return(resp)
 }