customize issue templates for GH (#70)

insightsengineering · Mar 11, 2024 · 3fa9c60 · 3fa9c60
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -22,3 +22,4 @@ init.sh
 workflows.md
 images
 ^data-raw$
+^\.gitleaksignore$
diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml
@@ -0,0 +1,50 @@
+---
+name: 🐞 Bug Report
+description: File a bug report
+title: "[Bug]: <title>"
+labels: ["bug"]
+assignees:
+  - danielinteractive
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us, what did you expect to happen?
+      placeholder: Tell us what you see!
+      value: "A bug happened!"
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+  - type: checkboxes
+    id: code-of-conduct
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://github.com/insightsengineering/.github/blob/main/CODE_OF_CONDUCT.md)
+      options:
+        - label: I agree to follow this project's Code of Conduct.
+          required: true
+  - type: checkboxes
+    id: contributor-guidelines
+    attributes:
+      label: Contribution Guidelines
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://github.com/insightsengineering/.github/blob/main/CONTRIBUTING.md)
+      options:
+        - label: I agree to follow this project's Contribution Guidelines.
+          required: true
+  - type: checkboxes
+    id: security-policy
+    attributes:
+      label: Security Policy
+      description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/insightsengineering/.github/security/policy)
+      options:
+        - label: I agree to follow this project's Security Policy.
+          required: true
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,10 @@
+---
+blank_issues_enabled: true
+
+contact_links:
+  - name: We are hiring!
+    url: https://careers.gene.com/
+    about: Genentech and Roche are hiring!
+  - name: openstatsware
+    url: https://openstatsware.org/
+    about: Software Engineering in Biostatistics
diff --git a/.github/ISSUE_TEMPLATE/feature.yml b/.github/ISSUE_TEMPLATE/feature.yml
@@ -0,0 +1,37 @@
+---
+name: ✨ Feature Request
+description: Request or propose a new feature
+title: "[Feature Request]: <title>"
+labels: ["enhancement"]
+assignees:
+  - danielinteractive
+body:
+  - type: textarea
+    attributes:
+      label: Feature description
+    validations:
+      required: true
+  - type: checkboxes
+    id: code-of-conduct
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://github.com/insightsengineering/.github/blob/main/CODE_OF_CONDUCT.md)
+      options:
+        - label: I agree to follow this project's Code of Conduct.
+          required: true
+  - type: checkboxes
+    id: contributor-guidelines
+    attributes:
+      label: Contribution Guidelines
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://github.com/insightsengineering/.github/blob/main/CONTRIBUTING.md)
+      options:
+        - label: I agree to follow this project's Contribution Guidelines.
+          required: true
+  - type: checkboxes
+    id: security-policy
+    attributes:
+      label: Security Policy
+      description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/insightsengineering/.github/security/policy)
+      options:
+        - label: I agree to follow this project's Security Policy.
+          required: true
diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml
@@ -0,0 +1,37 @@
+---
+name: ❓ Question
+description: Question about usage or documentation
+title: "[Question]: <title>"
+labels: ["question"]
+assignees:
+  - danielinteractive
+body:
+  - type: textarea
+    attributes:
+      label: What is your question?
+    validations:
+      required: true
+  - type: checkboxes
+    id: code-of-conduct
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct.](https://github.com/insightsengineering/.github/blob/main/CODE_OF_CONDUCT.md)
+      options:
+        - label: I agree to follow this project's Code of Conduct.
+          required: true
+  - type: checkboxes
+    id: contributor-guidelines
+    attributes:
+      label: Contribution Guidelines
+      description: By submitting this issue, you agree to follow our [Contribution Guidelines.](https://github.com/insightsengineering/.github/blob/main/CONTRIBUTING.md)
+      options:
+        - label: I agree to follow this project's Contribution Guidelines.
+          required: true
+  - type: checkboxes
+    id: security-policy
+    attributes:
+      label: Security Policy
+      description: By submitting this issue, you agree to follow our [Security Policy.](https://github.com/insightsengineering/.github/security/policy)
+      options:
+        - label: I agree to follow this project's Security Policy.
+          required: true
diff --git a/.gitleaksignore b/.gitleaksignore
@@ -0,0 +1,2 @@
+R/RcppExports.R:generic-api-key:2
+src/RcppExports.cpp:generic-api-key:2
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,13 @@
 Type: Package
 Package: shrinkforest
-Title: Shrinkage based Forest Plots
+Title: Shrinkage Based Forest Plots
 Version: 0.0.0.9033
-Date: 2023-02-28
+Date: 2024-03-07
 Authors@R:
-    person("Mar", "Vazquez Rabunal", , "mar.vazquez_rabunal@roche.com", role = c("aut", "cre"))
+    c(
+      person("Mar", "Vazquez Rabunal", , "mar.vazquez_rabunal@roche.com", role = c("aut", "cre")),
+      person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@roche.com", role = "aut")
+    )
 Description: Subgroup analyses are routinely performed in clinical trial
     analyses.  From a methodological perspective, two key issues of
     subgroup analyses are multiplicity (even if only predefined subgroups
@@ -49,4 +52,4 @@ Language: en-US
 LazyData: true
 LazyDataCompression: xz
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/R/generate_stacked_data.R b/R/generate_stacked_data.R
@@ -37,18 +37,24 @@ generate_stacked_data <- function(base_model, subgroup_model, data,
   }
   tmp <- lapply(data[, subgroup_vars], function(x) levels(factor(x)))
   subgroup_names <- paste(rep(names(tmp), lapply(tmp, length)),
-                          unlist(tmp), sep = ".")
+    unlist(tmp),
+    sep = "."
+  )
   data <- data[, c(arm_var, resp_var, status_var, subgroup_vars)]
   data[, subgroup_vars] <- lapply(data[, subgroup_vars], as.character)
-  d <- tidyr::gather(data, "subgroup_var", "subgroup_value",
-                     -arm_var, -resp_var, -status_var)
+  d <- tidyr::gather(
+    data, "subgroup_var", "subgroup_value",
+    -arm_var, -resp_var, -status_var
+  )
   subgroup <- paste(d$subgroup_var, d$subgroup_value, sep = ".")
   subgroup <- factor(subgroup, levels = subgroup_names)
   d <- cbind(d, subgroup)
   d <- dplyr::arrange(d, subgroup)
   d <- if (resptype == "survival") {
-    dplyr::rename_at(d, dplyr::vars(c(arm_var, resp_var, status_var)),
-                     ~ c("arm", "time", "status"))
+    dplyr::rename_at(
+      d, dplyr::vars(c(arm_var, resp_var, status_var)),
+      ~ c("arm", "time", "status")
+    )
   } else if (resptype == "binary") {
     dplyr::rename_at(d, dplyr::vars(c(arm_var, resp_var)), ~ c("arm", "y"))
   }

diff --git a/R/horseshoe.R b/R/horseshoe.R
@@ -29,7 +29,8 @@
 #' @examples
 #' horseshoe("ev_pfs", "arm", c("x_1", "x_2"), c("x_1", "x_2", "x_3"),
 #'   example_data, "binary",
-#'   chains = 1, seed = 0, control = list(adapt_delta = 0.95)
+#'   chains = 1, seed = 0, control = list(adapt_delta = 0.95),
+#'   iter = 50 # In practice, you need to omit this or set it much higher!
 #' )
 horseshoe <- function(resp, trt, subgr, covars, data,
                       resptype = c("survival", "binary"), status = NULL,
@@ -75,9 +76,12 @@ horseshoe <- function(resp, trt, subgr, covars, data,
     design_main <- prep_data$design_main[, -1]
     design_matrix <- cbind(design_main, prep_data$design_ia)
     form <- stats::as.formula(paste(resp, " ~ a + b"))
-    form_a <- stats::as.formula(paste("a ~ 1 +", paste0(colnames(design_main),
-      collapse = " + "
-    )))
+    form_a <- stats::as.formula(
+      paste(
+        "a ~ 1 +",
+        paste0(colnames(design_main), collapse = " + ")
+      )
+    )
     y <- as.data.frame(data[[resp]])
     colnames(y) <- resp
     data_model <- cbind(design_matrix, y)
@@ -90,11 +94,8 @@ horseshoe <- function(resp, trt, subgr, covars, data,
         brms::lf(form_b),
       data = data_model,
       family = family,
-      brms::prior(normal(0, 5), class = "b", nlpar = "a") +
-        brms::prior(horseshoe(1),
-          class = "b",
-          nlpar = "b"
-        ),
+      brms::prior_string("normal(0, 5)", class = "b", nlpar = "a") +
+        brms::prior_string("horseshoe(1)", class = "b", nlpar = "b"),
       ...
     )
   }

diff --git a/R/lOR_estimation.R b/R/lOR_estimation.R
@@ -18,18 +18,22 @@ lor_estimation <- function(x_subg, dummy_subg, est_coef) {
   assert_matrix(dummy_subg)
   assert_matrix(est_coef)
   x_arm <- list()
-  for (i in 0:1){
-    x_arm[[i + 1]] <- cbind(rep(1, nrow(x_subg)), rep(i, nrow(x_subg)),
-               x_subg[, 2:(ncol(x_subg) - ncol(dummy_subg))], i * dummy_subg)
+  for (i in 0:1) {
+    x_arm[[i + 1]] <- cbind(
+      rep(1, nrow(x_subg)), rep(i, nrow(x_subg)),
+      x_subg[, 2:(ncol(x_subg) - ncol(dummy_subg))], i * dummy_subg
+    )
   }
   prob <- function(x, est_coef) {
-    k <- as.matrix(x) %*%  as.matrix(est_coef)
+    k <- as.matrix(x) %*% as.matrix(est_coef)
     p <- exp(k) / (1 + exp(k))
     y <- apply(p, 2, mean)
     y
   }
   y_arm <- lapply(x_arm, prob, est_coef = est_coef)
-  phi <- as.numeric(log(y_arm[[2]] / (1 - y_arm[[2]])) -
-                      log(y_arm[[1]] / (1 - y_arm[[1]])))
+  phi <- as.numeric(
+    log(y_arm[[2]] / (1 - y_arm[[2]])) -
+      log(y_arm[[1]] / (1 - y_arm[[1]]))
+  )
   phi
 }
diff --git a/R/plot.R b/R/plot.R
@@ -16,12 +16,24 @@ plot.summary.naive <- function(x, ...) {
   data$subgroup <- as.factor(data$subgroup)
   forestplot <- ggplot(
     data = data,
-    aes(x = trt.estimate, y = model, xmin = trt.low, xmax = trt.high)
+    aes(
+      x = .data$trt.estimate,
+      y = .data$model,
+      xmin = .data$trt.low,
+      xmax = .data$trt.high
+    )
   ) +
     ggtitle("Forest plot Naive") +
-    geom_pointrange(aes(col = model)) +
+    geom_pointrange(aes(col = .data$model)) +
     ylab("Subgroup") +
-    geom_errorbar(aes(xmin = trt.low, xmax = trt.high, col = model), width = 0.5, cex = 1) +
+    geom_errorbar(
+      aes(
+        xmin = .data$trt.low,
+        xmax = .data$trt.high,
+        col = .data$model
+      ),
+      width = 0.5, cex = 1
+    ) +
     facet_wrap(~ forcats::fct_inorder(subgroup),
       strip.position = "left",
       nrow = nrow(data), scales = "free_y"
@@ -70,10 +82,10 @@ plot.summary.elastic_net <- function(x, ...) {
   data$subgroup <- as.factor(data$subgroup)
   forestplot <- ggplot(
     data = data,
-    aes(x = trt.estimate, y = model)
+    aes(x = .data$trt.estimate, y = .data$model)
   ) +
     ggtitle("Forest plot Elastic Net") +
-    geom_point(aes(col = model)) +
+    geom_point(aes(col = .data$model)) +
     ylab("Subgroup") +
     facet_wrap(~ forcats::fct_inorder(subgroup),
       strip.position = "left",
@@ -117,12 +129,25 @@ plot.summary.horseshoe <- function(x, ...) {
   data$subgroup <- as.factor(data$subgroup)
   forestplot <- ggplot(
     data = data,
-    aes(x = trt.estimate, y = model, xmin = trt.low, xmax = trt.high)
+    aes(
+      x = .data$trt.estimate,
+      y = .data$model,
+      xmin = .data$trt.low,
+      xmax = .data$trt.high
+    )
   ) +
     ggtitle("Forest plot Horseshoe") +
-    geom_pointrange(aes(col = model)) +
+    geom_pointrange(aes(col = .data$model)) +
     ylab("Subgroup") +
-    geom_errorbar(aes(xmin = trt.low, xmax = trt.high, col = model), width = 0.5, cex = 1) +
+    geom_errorbar(
+      aes(
+        xmin = .data$trt.low,
+        xmax = .data$trt.high,
+        col = .data$model
+      ),
+      width = 0.5,
+      cex = 1
+    ) +
     facet_wrap(~ forcats::fct_inorder(subgroup),
       strip.position = "left",
       nrow = nrow(data), scales = "free_y"
@@ -170,16 +195,19 @@ plot.compare.data <- function(x, ...) {
   forestplot <- ggplot(
     data = data,
     aes(
-      x = trt.estimate, y = forcats::fct_rev(forcats::fct_inorder(model)), xmin = trt.low,
-      xmax = trt.high
+      x = .data$trt.estimate,
+      y = forcats::fct_rev(forcats::fct_inorder(.data$model)),
+      xmin = .data$trt.low,
+      xmax = .data$trt.high
     )
   ) +
     ggtitle("Forest plot") +
-    geom_pointrange(aes(col = forcats::fct_inorder(model))) +
+    geom_pointrange(aes(col = forcats::fct_inorder(.data$model))) +
     ylab("Subgroup") +
     geom_errorbar(aes(
-      xmin = trt.low, xmax = trt.high,
-      col = forcats::fct_inorder(model)
+      xmin = .data$trt.low,
+      xmax = .data$trt.high,
+      col = forcats::fct_inorder(.data$model)
     ), width = 0.5, cex = 1) +
     facet_wrap(~ forcats::fct_inorder(subgroup),
       strip.position = "left",

diff --git a/R/trt_horseshoe.R b/R/trt_horseshoe.R
@@ -19,7 +19,7 @@
 #' @export
 #'
 #' @examples
-#' trt_horseshoe(horseshoe_fit_surv)
+#' trt_horseshoe(horseshoe_fit_surv, m = 5)
 trt_horseshoe <- function(object, gamma = 1, l = NULL, m = 50) {
   assert_class(object, c("shrinkforest", "horseshoe"))
   assert_int(m)

diff --git a/data-raw/elastic_net_fit_surv.R b/data-raw/elastic_net_fit_surv.R
@@ -1,7 +1,13 @@
-elastic_net_fit_surv <- elastic_net("tt_pfs", "arm", c("x_1", "x_2", "x_3",
-                                                       "x_4", "x_5", "x_6", "x_7",
-                                                       "x_8", "x_9", "x_10"),
-                                    c("x_1", "x_2", "x_3", "x_4", "x_5", "x_6",
-                                      "x_7", "x_8", "x_9", "x_10"),
-                                    example_data, "survival", 1, "ev_pfs")
+elastic_net_fit_surv <- elastic_net(
+  "tt_pfs", "arm", c(
+    "x_1", "x_2", "x_3",
+    "x_4", "x_5", "x_6", "x_7",
+    "x_8", "x_9", "x_10"
+  ),
+  c(
+    "x_1", "x_2", "x_3", "x_4", "x_5", "x_6",
+    "x_7", "x_8", "x_9", "x_10"
+  ),
+  example_data, "survival", 1, "ev_pfs"
+)
 usethis::use_data(elastic_net_fit_surv, compress = "xz", overwrite = TRUE)
diff --git a/data-raw/est_coef_bin1.R b/data-raw/est_coef_bin1.R
@@ -1,3 +1,4 @@
 est_coef_bin1 <- as.matrix(coef(elastic_net_fit_bin$fit,
-                                s = elastic_net_fit_bin$fit$lambda.min))
+  s = elastic_net_fit_bin$fit$lambda.min
+))
 usethis::use_data(est_coef_bin1, overwrite = TRUE)