force detectseparation v0.2 (corncob bug)

statdivlab/corncob#141

R/corncob.R

@@ -52,7 +52,8 @@
 #' 
 #' ## Define step with default parameters and prep
 #' rec <- 
-#'   step_corncob(rec) # %>% prep(parallel = TRUE)
+#'   step_corncob(rec) %>% 
+#'   prep(parallel = TRUE)
 #'   
 #' rec
 #' 
@@ -206,6 +207,26 @@ run_corncob <- function(rec,
                         log2FC,
                         rarefy) {
 
+
+  ## Temporal solution to https://github.com/bryandmartin/corncob/issues/141
+  ver <- utils::packageVersion("detectseparation")
+  if (ver != "0.2") {
+    rlang::abort(c(
+      glue::glue(
+        "Temporarily the version of the package ", 
+        "{crayon::bgMagenta(pkg)} must be {crayon::blue(paste0('v', v))}, but ", 
+        "you have the version {crayon::blue(ver)} installed."
+      ), 
+      "*" = glue::glue(
+        "Please first run {crayon::blue('remove.packages(\"detectseparation\")')}.",
+      ), 
+      "*" = glue::glue(
+        "Finally install the necessary version with ", 
+        "{crayon::blue('devtools::install_version(\"detectseparation\", version = 0.2)')}."
+      )
+    ), use_cli_format = TRUE)
+  }
+
   phy <- get_phy(rec)
   vars <- get_var(rec)
   tax_level <- get_tax(rec)

R/filter_taxa.R

@@ -79,7 +79,7 @@ run_filter_taxa <- function(rec, .f) {
 
   val <- 
     zero_otu(rec) %>% 
-    dplyr::filter(pct == 0) %>% 
+    dplyr::filter(.data$pct == 0) %>% 
     nrow()
 
   if (val > 0 & rm_zeros == 0 & is_metagenomeseq) {
@@ -132,16 +132,16 @@ methods::setMethod(
     otu_table(obj) %>% 
       tidyr::pivot_longer(-1, names_to = "sample_id") %>% 
       dplyr::left_join(sample_data(obj), by = "sample_id") %>% 
-      dplyr::mutate(no_zero = ifelse(value == 0, 0, 1)) %>% 
+      dplyr::mutate(no_zero = ifelse(.data$value == 0, 0, 1)) %>% 
       dplyr::group_by(taxa_id, !!dplyr::sym(var)) %>%
       dplyr::summarise(
-        no_zero = sum(no_zero), 
+        no_zero = sum(.data$no_zero), 
         total = dplyr::n(), 
-        pct = no_zero / total,
+        pct = .data$no_zero / .data$total,
         .groups = "drop"
       ) %>%
-      dplyr::arrange(pct) %>% 
-      dplyr::filter(pct >= pct_cutoff)
+      dplyr::arrange(.data$pct) %>% 
+      dplyr::filter(.data$pct >= pct_cutoff)
   }
 )
 
@@ -160,15 +160,15 @@ methods::setMethod(
           dplyr::select(1, !!var),
         by = "sample_id"
       ) %>%
-      dplyr::mutate(no_zero = ifelse(value == 0, 0, 1)) %>% 
+      dplyr::mutate(no_zero = ifelse(.data$value == 0, 0, 1)) %>% 
       dplyr::group_by(taxa_id, !!dplyr::sym(var)) %>%
       dplyr::summarise(
-        no_zero = sum(no_zero), 
+        no_zero = sum(.data$no_zero), 
         total = dplyr::n(), 
-        pct = no_zero / total,
+        pct = .data$no_zero / .data$total,
         .groups = "drop"
       ) %>%
-      dplyr::arrange(pct) %>% 
-      dplyr::filter(pct >= pct_cutoff)
+      dplyr::arrange(.data$pct) %>% 
+      dplyr::filter(.data$pct >= pct_cutoff)
   }
 )

R/metagenomeseq.R

@@ -202,7 +202,7 @@ run_metagenomeseq <- function(rec,
 
           vct_var <- phyloseq::sample_data(phy2)[[var]]
           norm_factor <- metagenomeSeq::normFactors(mr_obj)
-          norm_factor <- log2(norm_factor / median(norm_factor) + 1)
+          norm_factor <- log2(norm_factor / stats::median(norm_factor) + 1)
 
           model <- stats::model.matrix( ~ 1 + vct_var + norm_factor)
 
@@ -221,7 +221,7 @@ run_metagenomeseq <- function(rec,
             metagenomeSeq::MRfulltable(number = Inf, by = 2) %>%
             tibble::as_tibble(rownames = "taxa_id") %>%
             dplyr::left_join(tax_table(rec), by = "taxa_id") %>%
-            dplyr::rename(pvalue = pvalues, padj = adjPvalues) %>%
+            dplyr::rename(pvalue = .data$pvalues, padj = .data$adjPvalues) %>%
             dplyr::mutate(
               comparison = stringr::str_c(comparison, collapse = "_"),
               var = var

R/pkg_check.R

@@ -80,3 +80,16 @@ methods::setMethod(
     invisible()
   }
 )
+
+check_version <- function(pkg, v) {
+
+  check <- utils::packageVersion(pkg) == v
+  if (!check) {
+    rlang::warn(c(
+     "i" = glue::glue(
+       "Temporarily the version of the package ", 
+       "{crayon::blue(pkg)} must be {crayon::blue(paste0('v', v))}, but you ")
+    ), use_cli_format = TRUE)
+  }
+}
+