PennChopMicrobiomeProgram · Ulthran · Sep 1, 2023 · Aug 31, 2023 · Aug 31, 2023 · Aug 31, 2023
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,6 @@
+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^codecov\.yml$
diff --git a/.Rprofile b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,6 +7,12 @@ Author: Eric Zhang Chen
 Maintainer: Eric Zhang Chen <chvlyl@gmail.com>
 Description: A zero-inflated beta random effect model for longitudinal
     microbiome data.
-License: GPL-2
+License: file LICENSE
 LazyData: TRUE
-RoxygenNote: 5.0.1
+RoxygenNote: 7.2.3
+Encoding: UTF-8
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+Depends: 
+    R (>= 2.10)
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,3 +2,8 @@
 
 export(simulate_zero_inflated_beta_random_effect_data)
 export(zibr)
+importFrom(stats,nlminb)
+importFrom(stats,pchisq)
+importFrom(stats,rbeta)
+importFrom(stats,rbinom)
+importFrom(stats,rnorm)
diff --git a/R/data.R b/R/data.R
@@ -4,7 +4,6 @@
 #' a longitudinal human microbiome study
 #'
 #' @docType data
-#' @usage data(ibd.data)
 #' @keywords datasets
 #'
 #' @format A data frame with 236 rows and 5 variables:
@@ -17,4 +16,4 @@
 #'   ...
 #' }
 #' @references Lewis and Chen et al. (2016) Cell Host & Microbe 18 (4), 489-500
-"ibd.data"
+"ibd"
diff --git a/R/fit_beta_regression_random_effect.R b/R/fit_beta_regression_random_effect.R
@@ -39,6 +39,7 @@ cal_beta_loglik = function(para,Z.aug,Y,subject.n,time.n,
 
 
 #######################################
+#' @importFrom stats nlminb pchisq
 fit_beta_random_effect = function(Z=Z,Y=Y,
                                       subject.ind=subject.ind,time.ind=time.ind,
                                       quad.n=30,verbose=FALSE){

diff --git a/R/fit_logistic_regression_random_effect.R b/R/fit_logistic_regression_random_effect.R
@@ -32,6 +32,7 @@ cal_logistic_loglik = function(para,X.aug,Y,subject.n,time.n,
 ### system.time(rs4 <- colSums(aperm(b, c(2,1,3))))
 
 #######################################
+#' @importFrom stats nlminb pchisq
 fit_logistic_random_effect = function(X=X,Y=Y,
                                 subject.ind=subject.ind,time.ind=time.ind,
                                 quad.n=30,verbose=FALSE){

diff --git a/R/fit_zero_inflated_beta_regression_random_effect.R b/R/fit_zero_inflated_beta_regression_random_effect.R
@@ -34,6 +34,7 @@ cal_zibeta_loglik = function(para,
 #######################################
 
 #######################################
+#' @importFrom stats nlminb pchisq
 fit_zero_inflated_beta_random_effect = function(X=X,Z=Z,Y=Y,
                                                 subject.ind=subject.ind,time.ind=time.ind,
                                                 component.wise.test = TRUE,

diff --git a/R/generate_gaussian_quad_points.R b/R/generate_gaussian_quad_points.R
diff --git a/R/simulate_beta_data.R b/R/simulate_beta_data.R
@@ -1,3 +1,4 @@
+#' @importFrom stats rnorm rbeta
 simulate_beta_random_effect_data = function(subject.n=50, time.n=5, v=2,
                               beta=as.matrix(c(-0.5,-0.5,0.5)),
                               Z=NA, s2=1, sim.seed=100){
@@ -13,7 +14,7 @@ simulate_beta_random_effect_data = function(subject.n=50, time.n=5, v=2,
     Z <- as.matrix(Z)
     colnames(Z) <- paste('var',seq(1,ncol(Z)),sep='')
   }
-  
+
   set.seed(sim.seed*5000+1)
   c <- as.matrix(rnorm(subject.n,mean=0,sd=s2))
   c.rep <- as.matrix(as.vector(matrix(c,nrow=time.n,ncol=length(c),byrow=TRUE)))
@@ -32,7 +33,7 @@ simulate_beta_random_effect_data = function(subject.n=50, time.n=5, v=2,
   set.seed(sim.seed*5000+4)
   Y <- rbeta(subject.n*time.n, shape1 = u*v, shape2=(1-u)*v)
   if(any(Y>1-10^(-6))){Y[Y>1-10^(-6)] <- 1-10^(-6)}
-  
+
   #### For test purpose
   #### betareg can not fit random effect model
   #### so set the s2 to a small value (small random effect)
@@ -48,7 +49,7 @@ simulate_beta_random_effect_data = function(subject.n=50, time.n=5, v=2,
   #
   #fit_beta_random_effect(Z=Z,Y=Y,subject.ind=subject.ind,time.ind=time.ind,
   #                      quad.n=30,verbose=FALSE)
-  
+
   return(list(Y=Y,Z=Z,c=c,u=u,v=v,beta=beta,s2=s2,
               subject.ind=subject.ind,time.ind=time.ind))
 }
diff --git a/R/simulate_logistic_data.R b/R/simulate_logistic_data.R
@@ -1,3 +1,4 @@
+#' @importFrom stats rnorm rbinom
 simulate_logistic_data = function(){
 #########################
 #########################

diff --git a/R/simulate_zero_inflated_beta_data.R b/R/simulate_zero_inflated_beta_data.R
@@ -19,6 +19,7 @@
 #' @return s2 the stardard deviation of random effect in beta component
 #' @return subject.ind the IDs for each subject
 #' @return time.ind time points
+#' @importFrom stats rnorm rbinom rbeta
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/R/zibr.R b/R/zibr.R
@@ -59,7 +59,7 @@ zibr = function(logistic.cov=logistic.cov,
   #### if the colnames are the same, jointly test the two component
   if (identical(colnames(logistic.cov),colnames(beta.cov))){
     joint.test <- TRUE
-  } 
+  }
   else{
     joint.test <- FALSE
   }

diff --git a/README.md b/README.md
@@ -1,5 +1,10 @@
 # ZIBR (Zero-Inflated Beta Random Effect model)
 
+<!-- badges: start -->
+  [![R-CMD-check](https://github.com/PennChopMicrobiomeProgram/ZIBR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/PennChopMicrobiomeProgram/ZIBR/actions/workflows/R-CMD-check.yaml)
+  [![codecov](https://codecov.io/gh/PennChopMicrobiomeProgram/ZIBR/graph/badge.svg?token=6A7MIF2IPE)](https://codecov.io/gh/PennChopMicrobiomeProgram/ZIBR)
+  <!-- badges: end -->
+
 ## Introduction
 The longitudinal microbiome compositional data are highly skewed, bounded in [0,1), and often sparse with many zeros. In addition, the observations from repeated measures are correlated. We propose a two-part zero-inflated Beta regression model with random effects (ZIBR) for testing the association between microbial abundance and clinical covariates for longitudinal microbiome data. The model includes a logistic component to model presence/absence of the microbe in samples and a Beta component to model non-zero microbial abundance and each component includes a random effect to take into account the correlation among repeated measurements on the same subject.
 
@@ -81,7 +86,7 @@ zibr.fit
 #### Real data  
 Let's try anohter example on the real data. I will use a dataset from a longitudinal human microbiome study containing the bacterial abundance and clinical information from [Lewis and Chen et al.](http://www.cell.com/cell-host-microbe/references/S1931-3128(15)00377-7). I only include the abundance from one genus.   
 
-Type ```ibd.data```.
+Type ```ibd```.
 ```r
      Sample Subject Time Treatment    Abundance
 1   5001-01    5001    1         0 0.000000e+00
@@ -116,10 +121,10 @@ The current model can not handle missing data. That is, each subject must have t
 We can run the zibr function to the real data. Here, I'm interested in comparing the two treatments and use treatment as the only covariate in both logistic and beta component. Depending on the scientific questions you are interested in, you can also include time and treament-time interaction in the covariates. 
 
 ```r
-zibr.fit <- zibr(logistic.cov = data.frame(Treatment=ibd.data$Treatment), 
-    beta.cov = data.frame(Treatment=ibd.data$Treatment), 
-    Y = ibd.data$Abundance, subject.ind = ibd.data$Subject,
-    time.ind = ibd.data$Time)
+zibr.fit <- zibr(logistic.cov = data.frame(Treatment=ibd$Treatment), 
+    beta.cov = data.frame(Treatment=ibd$Treatment), 
+    Y = ibd$Abundance, subject.ind = ibd$Subject,
+    time.ind = ibd$Time)
 zibr.fit
 ```
 

diff --git a/ZIBR.Rproj b/ZIBR.Rproj
@@ -1,21 +1,22 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: knitr
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette
diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
diff --git a/data/ibd.rda b/data/ibd.rda
diff --git a/data/realdata.RData b/data/realdata.RData
diff --git a/man/ibd.data.Rd → man/ibd.Rd b/man/ibd.data.Rd → man/ibd.Rd
diff --git a/man/simulate_zero_inflated_beta_random_effect_data.Rd b/man/simulate_zero_inflated_beta_random_effect_data.Rd