Merge pull request #168 from svteichman/fix_latex

replace "bryandmartin/corncob" with "statdivlab/corncob" in a few places to make sure all urls are valid

Author: svteichman

Dockerfile

@@ -15,4 +15,4 @@ RUN R -e "install.packages('tidyverse', repos = 'http://cran.us.r-project.org');
 RUN R -e "install.packages('vroom', repos = 'http://cran.us.r-project.org'); library(vroom)"
 
 # Install corncob
-RUN R -e "library(devtools); devtools::install_github('bryandmartin/corncob')"
+RUN R -e "library(devtools); devtools::install_github('statdivlab/corncob')"

R/contrastsTest.R

@@ -29,7 +29,7 @@
 #'                                                  "DayAmdmt22 - DayAmdmt21"),
 #'                              data = soil_phylum_small_contrasts,
 #'                              fdr_cutoff = 0.05,
-#'                              try_only = 5)
+#'                              try_only = 1:5)
 #' @export
 contrastsTest <- function(formula, phi.formula,
                           contrasts_DA = NULL,
@@ -102,14 +102,14 @@ contrastsTest <- function(formula, phi.formula,
   }
 
   if (is.null(try_only)) {
-    try_only <- length(taxanames)
+    try_only <- 1:length(taxanames)
   }
 
   if (is.character(try_only)) {
     try_only <- which(taxanames %in% try_only)
   }
   # Loop through OTU/taxa
-  for (i in 1:try_only) {
+  for (i in try_only) {
 
     # Subset data to only select that taxa
     data_i <- convert_phylo(data, select = taxanames[i])

R/corncob.R

@@ -9,5 +9,5 @@
 #' @details
 #' For details on the model implemented in this package, see Martin et al. (2020) <doi:10.1214/19-AOAS1283>.
 #'
-#' The development version of the package will be maintained on \url{https://github.com/bryandmartin/corncob}.
+#' The development version of the package will be maintained on \url{https://github.com/statdivlab/corncob}.
 NULL

R/differentialTest.R

@@ -37,7 +37,8 @@
 #'                                 phi.formula_null = ~ DayAmdmt,
 #'                                 test = "Wald", boot = FALSE,
 #'                                 data = soil_phylum_small,
-#'                                 fdr_cutoff = 0.05)
+#'                                 fdr_cutoff = 0.05,
+#'                                 try_only = 1:5)
 #' @export
 differentialTest <- function(formula, phi.formula,
                              formula_null, phi.formula_null,

R/plot_differentialTest.R

@@ -17,7 +17,8 @@
 #'                                 phi.formula_null = ~ DayAmdmt,
 #'                                 test = "Wald", boot = FALSE,
 #'                                 data = soil_phylum_small,
-#'                                 fdr_cutoff = 0.05)
+#'                                 fdr_cutoff = 0.05,
+#'                                 try_only = 1:5)
 #' plot(da_analysis, level = "Phylum")
 #'
 #' @export