Merge pull request #7 from dynverse/devel

dynfeature 1.0.0

.Rbuildignore

@@ -2,4 +2,6 @@
 ^\.Rproj\.user$
 ^\.travis
 ^README\.Rmd$
-^\.git$
+^\.git$
+^\.github$
+^cran-comments\.md$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yml

@@ -0,0 +1,83 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+  pull_request:
+    branches:
+      - master
+  schedule:
+    - cron: "0 0 * * 1"
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          #- {os: windows-latest, r: 'release'}
+          #- {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+

.github/workflows/test_coverage.yml

@@ -0,0 +1,54 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'ci skip')"
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ubuntu-r-release-${{ hashFiles('depends.Rds') }}
+          restore-keys: ubuntu-r-release-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
+

DESCRIPTION

@@ -1,14 +1,22 @@
 Package: dynfeature
 Type: Package
-Title: Dynamic feature importance
-Version: 1.0.0.9000
-Authors@R: c(
-  person("Robrecht", "Cannoodt", email = "[email protected]", role = c("aut")),
-  person("Wouter", "Saelens", email = "[email protected]", role = c("aut", "cre")))
-Description: Calculating feature importance scores from trajectories
+Title: Feature Importance for Dynamic Processes
+Version: 1.0.0
+Authors@R: 
+    c(person(given = "Robrecht",
+             family = "Cannoodt",
+             role = c("aut", "cre"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),
+      person(given = "Wouter",
+             family = "Saelens",
+             role = "aut",
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0002-7114-6248", github = "zouter")))
+Description: Calculating feature importance scores from trajectories using the random forests algorithm and more. Saelens and Cannoodt et
+    al. (2019) <doi:10.1038/s41587-019-0071-9>.
 License: GPL-3
 Encoding: UTF-8
-LazyData: true
 Imports:
   dplyr,
   dynutils (>= 1.0.2),
@@ -22,19 +30,7 @@ Imports:
   tidyr,
   tibble
 Suggests:
-  caret
-RoxygenNote: 6.1.1
+  caret,
+  covr
+RoxygenNote: 7.1.1
 Roxygen: list(markdown = TRUE)
-Remotes: 
-    dynverse/dynutils@devel,
-    dynverse/dynwrap@devel
-Collate: 
-    'calculate_feature_importances.R'
-    'calculate_branch_feature_importance.R'
-    'calculate_branching_point_feature_importance.R'
-    'calculate_cell_feature_importance.R'
-    'calculate_milestone_feature_importance.R'
-    'calculate_overall_feature_importance.R'
-    'calculate_waypoint_feature_importance.R'
-    'fi_methods.R'
-    'package.R'

NAMESPACE

@@ -9,11 +9,11 @@ export(calculate_waypoint_feature_importance)
 export(fi_caret)
 export(fi_ranger_rf)
 export(fi_ranger_rf_lite)
+export(fi_ranger_rf_tiny)
 import(dplyr)
 import(dynutils)
 import(dynwrap)
 import(methods)
-import(tibble)
 import(tidyr)
 importFrom(purrr,"%>%")
 importFrom(purrr,invoke)
@@ -28,3 +28,6 @@ importFrom(purrr,map_lgl)
 importFrom(purrr,set_names)
 importFrom(ranger,ranger)
 importFrom(reshape2,acast)
+importFrom(tibble,as_tibble)
+importFrom(tibble,tibble)
+importFrom(tibble,tribble)

inst/NEWS.md → NEWS.md

@@ -1,8 +1,12 @@
-# dynfeature 1.0.0 (28-03-2019)
+# dynfeature 1.0.0
+
+Initial release of dynfeature on CRAN.
 
 * MINOR CHANGE: Use only one core by default.
 
-* MINOR CHANGE: Support sparse matrices
+* MINOR CHANGE: Support sparse matrices.
+
+* DOCUMENTATION: Add examples and returns.
 
 # dynfeature 0.2.0 (25-10-2018)
 

R/calculate_branch_feature_importance.R

@@ -1,52 +1,46 @@
 #' @rdname calculate_overall_feature_importance
 #'
 #' @export
-#'
-#' @include calculate_feature_importances.R
-calculate_branch_feature_importance <- inherit_default_params(
-  super_functions = list(calculate_feature_importances),
-  fun = function(
-    trajectory,
-    expression_source = "expression",
-    fi_method,
-    verbose
-  ) {
-    # assign name to each edge
-    milestone_network <-
-      trajectory$milestone_network %>%
-      mutate(edge_id = as.character(row_number())) %>%
-      select(from, to, edge_id)
+calculate_branch_feature_importance <- function(
+  trajectory,
+  expression_source = "expression",
+  fi_method = fi_ranger_rf_lite(),
+  verbose = FALSE
+) {
+  # assign name to each edge
+  milestone_network <-
+    trajectory$milestone_network %>%
+    mutate(edge_id = as.character(row_number())) %>%
+    select(.data$from, .data$to, .data$edge_id)
 
-    # determine which cell is part of which edge
-    edge_membership <-
-      trajectory$progressions %>%
-      group_by(cell_id) %>%
-      top_n(1, percentage) %>%
-      ungroup() %>%
-      left_join(milestone_network, c("from", "to")) %>%
-      reshape2::acast(cell_id ~ edge_id, value.var = "percentage") %>%
-      {!is.na(.)}
+  # determine which cell is part of which edge
+  edge_membership <-
+    trajectory$progressions %>%
+    group_by(.data$cell_id) %>%
+    top_n(1, .data$percentage) %>%
+    ungroup() %>%
+    left_join(milestone_network, c("from", "to")) %>%
+    mutate(contains = TRUE) %>%
+    reshape2::acast(cell_id ~ edge_id, value.var = "contains", fill = FALSE)
 
-    expression <- get_expression(trajectory, expression_source)
+  expression <- get_expression(trajectory, expression_source)
 
+  out <- calculate_feature_importances(
+    X = expression,
+    Y = edge_membership,
+    fi_method = fi_method,
+    verbose = verbose
+  )
+  suppressWarnings({
+    out <- out %>%
+      left_join(milestone_network, c("predictor_id" = "edge_id"))
+  })
 
-    out <- calculate_feature_importances(
-      X = expression,
-      Y = edge_membership,
-      fi_method = fi_method,
-      verbose = verbose
+  out %>%
+    transmute(
+      .data$feature_id,
+      from = factor(.data$from, trajectory$milestone_ids),
+      to = factor(.data$to, trajectory$milestone_ids),
+      .data$importance
     )
-    suppressWarnings({
-      out <- out %>%
-        left_join(milestone_network, c("predictor_id" = "edge_id"))
-    })
-
-    out %>%
-      transmute(
-        feature_id,
-        from = factor(from, trajectory$milestone_ids),
-        to = factor(to, trajectory$milestone_ids),
-        importance
-      )
-  }
-)
+}