From 1098a3546cd14088576cd86e2994858e076e68e2 Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Tue, 12 Jul 2022 09:21:08 +0000
Subject: [PATCH 01/18] Cleared Some notes and warnings of PEcAn.MA package.

---
 modules/meta.analysis/DESCRIPTION               | 12 ++++++------
 modules/meta.analysis/R/meta.analysis.R         |  1 +
 modules/meta.analysis/R/meta.analysis.summary.R |  2 +-
 modules/meta.analysis/R/run.meta.analysis.R     |  5 +----
 modules/meta.analysis/R/single.MA.R             |  2 +-
 modules/meta.analysis/man/p.point.in.prior.Rd   |  2 +-
 modules/meta.analysis/man/pecan.ma.Rd           |  2 ++
 modules/meta.analysis/man/single.MA.Rd          |  2 ++
 8 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index db0f7f145a0..0e08faff6ec 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -25,19 +25,19 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation. The PEcAn.MA package contains
     the functions used in the Bayesian meta-analysis of trait data.
-Depends:
+Imports:
+    coda (>= 0.18),
     XML,
+    R2WinBUGS,
     lattice,
-    MASS,
     PEcAn.utils,
-    PEcAn.DB
-Imports:
-    coda (>= 0.18),
+    PEcAn.DB,
     PEcAn.logger,
+    MASS,
     PEcAn.settings,
     rjags
 Suggests:
-    testthat (>= 1.0.2)
+    testthat (>= 1.0.2),
 SystemRequirements: JAGS
 License: BSD_3_clause + file LICENSE
 Copyright: Authors
diff --git a/modules/meta.analysis/R/meta.analysis.R b/modules/meta.analysis/R/meta.analysis.R
index 6a55f5d35b1..7bf9da9876a 100644
--- a/modules/meta.analysis/R/meta.analysis.R
+++ b/modules/meta.analysis/R/meta.analysis.R
@@ -27,6 +27,7 @@
 ##' @param prior.distns `data.frame` of prior distributions generated
 ##'   by call to [PEcAn.DB::query.priors()]
 ##' @param taupriors priors on variance parameters, can be scaled as needed with data mean
+##' @param data data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic.
 ##' @param j.iter number of MCMC samples
 ##' @param outdir output directory
 ##' @param random use random effects, `FALSE` by default
diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index 1004c7fa686..f6ed14cd275 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -36,7 +36,7 @@ pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FAL
   for (trait in names(mcmc.object)) {
     
     if (gg) {
-      gg <- require(ggmcmc)
+      gg <- requireNamespace(ggmcmc)
     }
     ## new diagnostic plots. But very slow & !any(grepl('^gg', dir(outdir)))){
     if (gg) {
diff --git a/modules/meta.analysis/R/run.meta.analysis.R b/modules/meta.analysis/R/run.meta.analysis.R
index 308d668d8ad..6a4079860e9 100644
--- a/modules/meta.analysis/R/run.meta.analysis.R
+++ b/modules/meta.analysis/R/run.meta.analysis.R
@@ -235,15 +235,12 @@ runModule.run.meta.analysis <- function(settings) {
 ##'
 ##' used to compare data to prior, meta analysis posterior to prior
 ##' @title find quantile of point within prior distribution
-##' @param point 
+##' @param point quantile of given prior to return
 ##' @param prior list of distn, parama, paramb
 ##' @return result of p<distn>(point, parama, paramb)
 ##' @export p.point.in.prior
 ##' @author David LeBauer
 p.point.in.prior <- function(point, prior) {
-  # Why is this (below) called, and then never used?
-  prior.median <- do.call(paste0("q", prior$distn),
-                          list(0.5, prior$parama, prior$paramb))
   out <- do.call(paste0("p", prior$distn), 
                  list(point, prior$parama, prior$paramb))
   return(out)
diff --git a/modules/meta.analysis/R/single.MA.R b/modules/meta.analysis/R/single.MA.R
index 5e5aeb035e8..d53f0aeca5a 100644
--- a/modules/meta.analysis/R/single.MA.R
+++ b/modules/meta.analysis/R/single.MA.R
@@ -13,8 +13,8 @@
 ##' single.MA. This will allow power analysis  to run repeated MA outside of the
 ##' full loop over traits and PFTs.
 ##' @title Single MA
-##' @param data
 ##' @param j.chains number of chains in meta-analysis
+##' @param data data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic
 ##' @param j.iter  number of mcmc samples
 ##' @param tauA prior on variance parameters
 ##' @param tauB  prior on variance parameters
diff --git a/modules/meta.analysis/man/p.point.in.prior.Rd b/modules/meta.analysis/man/p.point.in.prior.Rd
index a03b211c5eb..39e2528441a 100644
--- a/modules/meta.analysis/man/p.point.in.prior.Rd
+++ b/modules/meta.analysis/man/p.point.in.prior.Rd
@@ -7,7 +7,7 @@
 p.point.in.prior(point, prior)
 }
 \arguments{
-\item{point}{}
+\item{point}{quantile of given prior to return}
 
 \item{prior}{list of distn, parama, paramb}
 }
diff --git a/modules/meta.analysis/man/pecan.ma.Rd b/modules/meta.analysis/man/pecan.ma.Rd
index d97a3146386..886a32a5e76 100644
--- a/modules/meta.analysis/man/pecan.ma.Rd
+++ b/modules/meta.analysis/man/pecan.ma.Rd
@@ -38,6 +38,8 @@ by call to \code{\link[PEcAn.DB:query.priors]{PEcAn.DB::query.priors()}}}
 \code{NULL}, only print output to console.}
 
 \item{verbose}{Logical. If \code{TRUE} (default), print progress messages.}
+
+\item{data}{data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic.}
 }
 \value{
 four chains with 5000 total samples from posterior
diff --git a/modules/meta.analysis/man/single.MA.Rd b/modules/meta.analysis/man/single.MA.Rd
index 7b729767110..3ce23ada584 100644
--- a/modules/meta.analysis/man/single.MA.Rd
+++ b/modules/meta.analysis/man/single.MA.Rd
@@ -16,6 +16,8 @@ single.MA(
 )
 }
 \arguments{
+\item{data}{data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic}
+
 \item{j.chains}{number of chains in meta-analysis}
 
 \item{j.iter}{number of mcmc samples}

From 20e49b06fddd62be915367386ff71bc87bf33f28 Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Tue, 12 Jul 2022 10:28:37 +0000
Subject: [PATCH 02/18] some changes in global variables.

---
 modules/meta.analysis/R/meta.analysis.summary.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index f6ed14cd275..022a07b4169 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -26,6 +26,7 @@
 ##'  settings$meta.analysis$threshold)
 ##' }
 ##' @author David LeBauer, Shawn Serbin
+globalVariables(c("ggmcmc","is.mcmc.list","theme_set","theme_bw","ggs","pdf","box","dev.off"))
 pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FALSE) {
   
   fail <- rep(FALSE, length(mcmc.object))

From 7a8962243dd8de1249484409b0bfdf96055817a9 Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Tue, 12 Jul 2022 10:28:37 +0000
Subject: [PATCH 03/18] Binding variables locally to the function
 "pecan.ma.summary"

---
 modules/meta.analysis/R/meta.analysis.summary.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index f6ed14cd275..d457008bf5b 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -27,7 +27,7 @@
 ##' }
 ##' @author David LeBauer, Shawn Serbin
 pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FALSE) {
-  
+  ggmcmc <- is.mcmc.list <- theme_set <- theme_bw <- ggs <- pdf<- box <- dev.off <- NULL
   fail <- rep(FALSE, length(mcmc.object))
   names(fail) <- names(mcmc.object)
   not.converged <- data.frame()

From c874c0cb5e0829793341f593a6c2c2813da028ff Mon Sep 17 00:00:00 2001
From: nanu1605 <83662210+nanu1605@users.noreply.github.com>
Date: Wed, 13 Jul 2022 01:46:53 +0530
Subject: [PATCH 04/18] Update modules/meta.analysis/R/meta.analysis.summary.R

Co-authored-by: Chris Black <chris@ckblack.org>
---
 modules/meta.analysis/R/meta.analysis.summary.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index d457008bf5b..a582843c65e 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -36,7 +36,12 @@ pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FAL
   for (trait in names(mcmc.object)) {
     
     if (gg) {
-      gg <- requireNamespace(ggmcmc)
+      if (!requireNamespace(ggmcmc, quietly = TRUE)) {
+        PEcAn.logger::logger.severe(
+          "Can't find package 'ggmcmc',",
+          "needed by `PEcAn.MA::meta.analysis.summary()` when `gg = TRUE`.",
+          "Please install it and try again.")
+      }
     }
     ## new diagnostic plots. But very slow & !any(grepl('^gg', dir(outdir)))){
     if (gg) {

From c88521506f48bab1a264dd3a640354362a346824 Mon Sep 17 00:00:00 2001
From: nanu1605 <83662210+nanu1605@users.noreply.github.com>
Date: Wed, 13 Jul 2022 01:47:42 +0530
Subject: [PATCH 05/18] Update modules/meta.analysis/DESCRIPTION

Co-authored-by: Chris Black <chris@ckblack.org>
---
 modules/meta.analysis/DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index 0e08faff6ec..c21dd138f59 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -37,7 +37,8 @@ Imports:
     PEcAn.settings,
     rjags
 Suggests:
-    testthat (>= 1.0.2),
+    ggmcmc,
+    testthat (>= 1.0.2)
 SystemRequirements: JAGS
 License: BSD_3_clause + file LICENSE
 Copyright: Authors

From df5c7a14bb89c803bb0ccd149448bdec6aadfa17 Mon Sep 17 00:00:00 2001
From: nanu1605 <83662210+nanu1605@users.noreply.github.com>
Date: Wed, 13 Jul 2022 01:47:58 +0530
Subject: [PATCH 06/18] Update modules/meta.analysis/R/meta.analysis.R

Co-authored-by: Chris Black <chris@ckblack.org>
---
 modules/meta.analysis/R/meta.analysis.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/meta.analysis/R/meta.analysis.R b/modules/meta.analysis/R/meta.analysis.R
index 7bf9da9876a..3cc3edad9a3 100644
--- a/modules/meta.analysis/R/meta.analysis.R
+++ b/modules/meta.analysis/R/meta.analysis.R
@@ -27,7 +27,9 @@
 ##' @param prior.distns `data.frame` of prior distributions generated
 ##'   by call to [PEcAn.DB::query.priors()]
 ##' @param taupriors priors on variance parameters, can be scaled as needed with data mean
-##' @param data data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic.
+##' @param data data frame generated by jagify function
+##'   with indexed values for greenhouse, treatment, and site (ghs, trt, site)
+##'   as well as Y, SE, and n for each observation or summary statistic.
 ##' @param j.iter number of MCMC samples
 ##' @param outdir output directory
 ##' @param random use random effects, `FALSE` by default

From 4a37f075d73ea5e75668c64cbffb52500ac48238 Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Wed, 13 Jul 2022 13:11:37 +0000
Subject: [PATCH 07/18] Fixed undefined global function.

---
 modules/meta.analysis/R/approx.posterior.R    | 28 +++++++++----------
 modules/meta.analysis/R/meta.analysis.R       |  6 ++--
 .../meta.analysis/R/meta.analysis.summary.R   | 17 ++++++-----
 modules/meta.analysis/R/run.meta.analysis.R   | 10 +++----
 modules/meta.analysis/R/single.MA.R           |  4 ++-
 5 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/modules/meta.analysis/R/approx.posterior.R b/modules/meta.analysis/R/approx.posterior.R
index 2864e7f648d..f988a2959f8 100644
--- a/modules/meta.analysis/R/approx.posterior.R
+++ b/modules/meta.analysis/R/approx.posterior.R
@@ -34,7 +34,7 @@ approx.posterior <- function(trait.mcmc, priors, trait.data = NULL, outdir = NUL
   posteriors <- priors
   do.plot <- !is.null(outdir)
   if (do.plot == TRUE) {
-    pdf(file.path(outdir, paste("posteriors", filename.flag, ".pdf", sep = "")))
+    grDevices::pdf(file.path(outdir, paste("posteriors", filename.flag, ".pdf", sep = "")))
   }
   
   ## loop over traits
@@ -55,7 +55,7 @@ approx.posterior <- function(trait.mcmc, priors, trait.data = NULL, outdir = NUL
     zerobound <- c("exp", "gamma", "lnorm", "weibull")
     if (pdist %in% "beta") {
       m   <- mean(dat)
-      v   <- var(dat)
+      v   <- stats::var(dat)
       k   <- (1 - m)/m
       a   <- (k / ((1 + k) ^ 2 * v) - 1) / (1 + k)
       b   <- a * k
@@ -63,13 +63,13 @@ approx.posterior <- function(trait.mcmc, priors, trait.data = NULL, outdir = NUL
       
       if (do.plot) {
         x <- seq(0, 1, length = 1000)
-        plot(density(dat), col = 2, lwd = 2, main = trait)
+        plot(stats::density(dat), col = 2, lwd = 2, main = trait)
         if (!is.null(trait.data)) {
-          rug(trait.data[[trait]]$Y, lwd = 2, col = "purple")
+          graphics::rug(trait.data[[trait]]$Y, lwd = 2, col = "purple")
         }
-        lines(x, dbeta(x, fit$estimate[1], fit$estimate[2]), lwd = 2, type = "l")
-        lines(x, dbeta(x, pparm[1], pparm[2]), lwd = 3, type = "l", col = 3)
-        legend("topleft", 
+        graphics::lines(x, dbeta(x, fit$estimate[1], fit$estimate[2]), lwd = 2, type = "l")
+        graphics::lines(x, dbeta(x, pparm[1], pparm[2]), lwd = 3, type = "l", col = 3)
+        graphics::legend("topleft", 
                legend = c("data", "prior", "post", "approx"), 
                col = c("purple", 3, 2, 1), lwd = 2)
       }
@@ -111,7 +111,7 @@ approx.posterior <- function(trait.mcmc, priors, trait.data = NULL, outdir = NUL
       ## default: NORMAL
       posteriors[trait, "distn"] <- "norm"
       posteriors[trait, "parama"] <- mean(dat)
-      posteriors[trait, "paramb"] <- sd(dat)
+      posteriors[trait, "paramb"] <- stats::sd(dat)
       if (do.plot) {
         .dens_plot(posteriors, priors, ptrait, dat, trait, trait.data)
       }
@@ -119,7 +119,7 @@ approx.posterior <- function(trait.mcmc, priors, trait.data = NULL, outdir = NUL
   }  ## end trait loop
   
   if (do.plot) {
-    dev.off()
+    imguR::dev.off()
   }
   
   return(posteriors)
@@ -159,13 +159,13 @@ approx.posterior <- function(trait.mcmc, priors, trait.data = NULL, outdir = NUL
     rng <- range(trait.data[[trait]]$Y)
   }
 
-  plot(density(dat), col = 2, lwd = 2, main = trait, xlim = rng)
+  plot(stats::density(dat), col = 2, lwd = 2, main = trait, xlim = rng)
   if (!is.null(trait.data)) {
-    rug(trait.data[[trait]]$Y, lwd = 2, col = "purple")
+    graphics::rug(trait.data[[trait]]$Y, lwd = 2, col = "purple")
   }
-  lines(x, f(x), lwd = 2, type = "l")
-  lines(x, fp(x), lwd = 3, type = "l", col = 3)
-  legend("topleft", 
+  graphics::lines(x, f(x), lwd = 2, type = "l")
+  graphics::lines(x, fp(x), lwd = 3, type = "l", col = 3)
+  graphics::legend("topleft", 
          legend = c("data", "prior", "post", "approx"), 
          col = c("purple", 3, 2, 1), lwd = 2)
 }
diff --git a/modules/meta.analysis/R/meta.analysis.R b/modules/meta.analysis/R/meta.analysis.R
index 3cc3edad9a3..290ef2391d7 100644
--- a/modules/meta.analysis/R/meta.analysis.R
+++ b/modules/meta.analysis/R/meta.analysis.R
@@ -127,10 +127,10 @@ pecan.ma <- function(trait.data, prior.distns,
                        "\nmean:", signif(mean(data$Y, na.rm = TRUE), 3),
                        "\nn:", length(data$Y)))
       writeLines("stem plot of data points")
-      writeLines(paste(stem(data$Y)))
+      writeLines(paste(graphics::stem(data$Y)))
       if (any(!is.na(data$obs.prec)) && all(!is.infinite(data$obs.prec))) {
         writeLines("stem plot of obs.prec:")
-        writeLines(paste(stem(data[["obs.prec"]] ^ 2)))
+        writeLines(paste(graphics::stem(data[["obs.prec"]] ^ 2)))
       } else {
         writeLines(paste("no estimates of SD for", trait.name))
       }
@@ -155,7 +155,7 @@ pecan.ma <- function(trait.data, prior.distns,
       print(summary(jags.out))
     }
     
-    jags.out.trunc <- window(jags.out, start = j.iter / 2)
+    jags.out.trunc <- stats::window(jags.out, start = j.iter / 2)
 
     mcmc.object[[trait.name]] <- jags.out.trunc
   }
diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index a582843c65e..4e29597d163 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -27,7 +27,6 @@
 ##' }
 ##' @author David LeBauer, Shawn Serbin
 pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FALSE) {
-  ggmcmc <- is.mcmc.list <- theme_set <- theme_bw <- ggs <- pdf<- box <- dev.off <- NULL
   fail <- rep(FALSE, length(mcmc.object))
   names(fail) <- names(mcmc.object)
   not.converged <- data.frame()
@@ -45,9 +44,9 @@ pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FAL
     }
     ## new diagnostic plots. But very slow & !any(grepl('^gg', dir(outdir)))){
     if (gg) {
-      if (is.mcmc.list(mcmc.object[[trait]])) {
-        theme_set(theme_bw())
-        ggmcmc(ggs(mcmc.object[[trait]]), 
+      if (coda::is.mcmc.list(mcmc.object[[trait]])) {
+        ggplot2::theme_set(ggplot2::theme_bw())
+        ggmcmc::ggmcmc(ggmcmc::ggs(mcmc.object[[trait]]), 
                plot = c("ggs_density", "ggs_traceplot", "ggs_autocorrelation", "ggs_Rhat", "ggs_geweke"), 
                file.path(outdir, paste0("gg.ma.summaryplots.", trait, ".pdf")))
       }
@@ -59,23 +58,23 @@ pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FAL
     maparms  <- .maparms[c(which(.maparms %in% .parms), which(!.maparms %in% .parms))]
     
     ## plots for mcmc diagnosis
-    pdf(file.path(outdir, paste0("ma.summaryplots.", trait, ".pdf")))
+    grDevices::pdf(file.path(outdir, paste0("ma.summaryplots.", trait, ".pdf")))
 
     for (i in maparms) {
       plot(mcmc.object[[trait]][, i],
            trace = FALSE,
            density = TRUE,
            main = paste("summary plots of", i, "for", pft, trait))
-      box(lwd = 2)
+      graphics::box(lwd = 2)
       plot(mcmc.object[[trait]][, i], density = FALSE)
-      box(lwd = 2)
+      graphics::box(lwd = 2)
       coda::autocorr.plot(mcmc.object[[trait]][, i][1], xlim = c(1, 50))
-      box(lwd = 2)
+      graphics::box(lwd = 2)
     }
     lattice::xyplot(mcmc.object[[trait]])
     lattice::densityplot(mcmc.object[[trait]])
     coda::acfplot(mcmc.object[[trait]])
-    dev.off()
+    imguR::dev.off()
 
     ## G-R diagnostics to ensure convergence
     gd            <- coda::gelman.diag(mcmc.object[[trait]])
diff --git a/modules/meta.analysis/R/run.meta.analysis.R b/modules/meta.analysis/R/run.meta.analysis.R
index 6a4079860e9..ab474a966eb 100644
--- a/modules/meta.analysis/R/run.meta.analysis.R
+++ b/modules/meta.analysis/R/run.meta.analysis.R
@@ -94,7 +94,7 @@ run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.
   
   ## Check that data is consistent with prior
   for (trait in names(jagged.data)) {
-    data.median <- median(jagged.data[[trait]]$Y)
+    data.median <- stats::median(jagged.data[[trait]]$Y)
     prior       <- prior.distns[trait, ]
     check       <- check_consistent(data.median, prior, trait, "data")
     if (is.na(check)) {
@@ -123,7 +123,7 @@ run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.
   
   ### Check that meta-analysis posteriors are consistent with priors
   for (trait in names(trait.mcmc)) {
-    post.median <- median(as.matrix(trait.mcmc[[trait]][, "beta.o"]))
+    post.median <- stats::median(as.matrix(trait.mcmc[[trait]][, "beta.o"]))
     prior       <- prior.distns[trait, ]
     check <- check_consistent(post.median, prior, trait, "data")
     if (is.na(check)) {
@@ -157,7 +157,7 @@ run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.
     }
     filename <- file.path(pathname, file)
     file.copy(file.path(pft$outdir, file), filename)
-    dbfile.insert(pathname, file, "Posterior", pft$posteriorid, dbcon)
+    PEcAn.DB::dbfile.insert(pathname, file, "Posterior", pft$posteriorid, dbcon)
   }
 } # run.meta.analysis.pft
 
@@ -185,8 +185,8 @@ run.meta.analysis.pft <- function(pft, iterations, random = TRUE, threshold = 1.
 ##' @author Shawn Serbin, David LeBauer
 run.meta.analysis <- function(pfts, iterations, random = TRUE, threshold = 1.2, dbfiles, database, use_ghs = TRUE) {
   # process all pfts
-  dbcon <- db.open(database)
-  on.exit(db.close(dbcon), add = TRUE)
+  dbcon <- PEcAn.DB::db.open(database)
+  on.exit(PEcAn.DB::db.close(dbcon), add = TRUE)
 
   result <- lapply(pfts, run.meta.analysis.pft, iterations = iterations, random = random, 
                    threshold = threshold, dbfiles = dbfiles, dbcon = dbcon, use_ghs = use_ghs)
diff --git a/modules/meta.analysis/R/single.MA.R b/modules/meta.analysis/R/single.MA.R
index d53f0aeca5a..2f38b0456cd 100644
--- a/modules/meta.analysis/R/single.MA.R
+++ b/modules/meta.analysis/R/single.MA.R
@@ -14,7 +14,9 @@
 ##' full loop over traits and PFTs.
 ##' @title Single MA
 ##' @param j.chains number of chains in meta-analysis
-##' @param data data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic
+##' @param data data frame generated by jagify function
+##'   with indexed values for greenhouse, treatment, and site (ghs, trt, site)
+##'   as well as Y, SE, and n for each observation or summary statistic.
 ##' @param j.iter  number of mcmc samples
 ##' @param tauA prior on variance parameters
 ##' @param tauB  prior on variance parameters

From 8304559e73c42ef46ca1f48926dfba58b71421aa Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Wed, 13 Jul 2022 13:18:31 +0000
Subject: [PATCH 08/18] Resolved R2WinBUGS dependency.

---
 modules/meta.analysis/DESCRIPTION                   | 1 -
 modules/meta.analysis/R/meta.analysis.write.model.R | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index c21dd138f59..1b01186344d 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -28,7 +28,6 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
 Imports:
     coda (>= 0.18),
     XML,
-    R2WinBUGS,
     lattice,
     PEcAn.utils,
     PEcAn.DB,
diff --git a/modules/meta.analysis/R/meta.analysis.write.model.R b/modules/meta.analysis/R/meta.analysis.write.model.R
index 7ddfc693ab9..304cae315b1 100644
--- a/modules/meta.analysis/R/meta.analysis.write.model.R
+++ b/modules/meta.analysis/R/meta.analysis.write.model.R
@@ -9,7 +9,7 @@
 
 ##' Convert template ma.model.template.R to a JAGS model.
 ##'
-##'  Writes a meta-analysis model based on available data and prior specification. Adapted from \code{\link[R2WinBUGS]{write.model}}
+##'  Writes a meta-analysis model based on available data and prior specification. Adapted from \code{R2WinBUGS::write.model}
 ##' @name write.ma.model
 ##' @title write.ma.model
 ##' @param modelfile model template file (ma.model.template.R)

From aca2329a2e674f440c7932b012d1397e1e2e9e9f Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Wed, 13 Jul 2022 13:44:23 +0000
Subject: [PATCH 09/18] Changed Documentation.

---
 modules/meta.analysis/man/pecan.ma.Rd       | 4 +++-
 modules/meta.analysis/man/single.MA.Rd      | 4 +++-
 modules/meta.analysis/man/write.ma.model.Rd | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/modules/meta.analysis/man/pecan.ma.Rd b/modules/meta.analysis/man/pecan.ma.Rd
index 886a32a5e76..0ed7a41f4ff 100644
--- a/modules/meta.analysis/man/pecan.ma.Rd
+++ b/modules/meta.analysis/man/pecan.ma.Rd
@@ -39,7 +39,9 @@ by call to \code{\link[PEcAn.DB:query.priors]{PEcAn.DB::query.priors()}}}
 
 \item{verbose}{Logical. If \code{TRUE} (default), print progress messages.}
 
-\item{data}{data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic.}
+\item{data}{data frame generated by jagify function
+with indexed values for greenhouse, treatment, and site (ghs, trt, site)
+as well as Y, SE, and n for each observation or summary statistic.}
 }
 \value{
 four chains with 5000 total samples from posterior
diff --git a/modules/meta.analysis/man/single.MA.Rd b/modules/meta.analysis/man/single.MA.Rd
index 3ce23ada584..9956175aa04 100644
--- a/modules/meta.analysis/man/single.MA.Rd
+++ b/modules/meta.analysis/man/single.MA.Rd
@@ -16,7 +16,9 @@ single.MA(
 )
 }
 \arguments{
-\item{data}{data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic}
+\item{data}{data frame generated by jagify function
+with indexed values for greenhouse, treatment, and site (ghs, trt, site)
+as well as Y, SE, and n for each observation or summary statistic.}
 
 \item{j.chains}{number of chains in meta-analysis}
 
diff --git a/modules/meta.analysis/man/write.ma.model.Rd b/modules/meta.analysis/man/write.ma.model.Rd
index dec1ec1ee23..8766b63b58d 100644
--- a/modules/meta.analysis/man/write.ma.model.Rd
+++ b/modules/meta.analysis/man/write.ma.model.Rd
@@ -51,7 +51,7 @@ Nothing, but as a side effect, the model is written
 Convert template ma.model.template.R to a JAGS model.
 }
 \details{
-Writes a meta-analysis model based on available data and prior specification. Adapted from \code{\link[R2WinBUGS]{write.model}}
+Writes a meta-analysis model based on available data and prior specification. Adapted from \code{R2WinBUGS::write.model}
 }
 \author{
 David LeBauer and Mike Dietze, based on original work on the \code{write.model} function in the \code{R2WinBUGS} package by Jouni Kerman and Uwe Ligges.

From 9bcf367ccf53c7915b3fd0951b43dbcd8af9ee8a Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Wed, 13 Jul 2022 13:44:23 +0000
Subject: [PATCH 10/18] Changed Documentation.

---
 modules/meta.analysis/R/approx.posterior.R      | 2 +-
 modules/meta.analysis/R/meta.analysis.summary.R | 2 +-
 modules/meta.analysis/man/pecan.ma.Rd           | 4 +++-
 modules/meta.analysis/man/single.MA.Rd          | 4 +++-
 modules/meta.analysis/man/write.ma.model.Rd     | 2 +-
 5 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/modules/meta.analysis/R/approx.posterior.R b/modules/meta.analysis/R/approx.posterior.R
index f988a2959f8..451f9d29467 100644
--- a/modules/meta.analysis/R/approx.posterior.R
+++ b/modules/meta.analysis/R/approx.posterior.R
@@ -119,7 +119,7 @@ approx.posterior <- function(trait.mcmc, priors, trait.data = NULL, outdir = NUL
   }  ## end trait loop
   
   if (do.plot) {
-    imguR::dev.off()
+    grDevices::dev.off()
   }
   
   return(posteriors)
diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index 4e29597d163..e63b346bed7 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -74,7 +74,7 @@ pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FAL
     lattice::xyplot(mcmc.object[[trait]])
     lattice::densityplot(mcmc.object[[trait]])
     coda::acfplot(mcmc.object[[trait]])
-    imguR::dev.off()
+    grDevices::dev.off()
 
     ## G-R diagnostics to ensure convergence
     gd            <- coda::gelman.diag(mcmc.object[[trait]])
diff --git a/modules/meta.analysis/man/pecan.ma.Rd b/modules/meta.analysis/man/pecan.ma.Rd
index 886a32a5e76..0ed7a41f4ff 100644
--- a/modules/meta.analysis/man/pecan.ma.Rd
+++ b/modules/meta.analysis/man/pecan.ma.Rd
@@ -39,7 +39,9 @@ by call to \code{\link[PEcAn.DB:query.priors]{PEcAn.DB::query.priors()}}}
 
 \item{verbose}{Logical. If \code{TRUE} (default), print progress messages.}
 
-\item{data}{data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic.}
+\item{data}{data frame generated by jagify function
+with indexed values for greenhouse, treatment, and site (ghs, trt, site)
+as well as Y, SE, and n for each observation or summary statistic.}
 }
 \value{
 four chains with 5000 total samples from posterior
diff --git a/modules/meta.analysis/man/single.MA.Rd b/modules/meta.analysis/man/single.MA.Rd
index 3ce23ada584..9956175aa04 100644
--- a/modules/meta.analysis/man/single.MA.Rd
+++ b/modules/meta.analysis/man/single.MA.Rd
@@ -16,7 +16,9 @@ single.MA(
 )
 }
 \arguments{
-\item{data}{data frame generated by jagify function with indexed values for greenhouse, treatment, and site (ghs, trt, site) as well as Y, SE, and n for each observation or summary statistic}
+\item{data}{data frame generated by jagify function
+with indexed values for greenhouse, treatment, and site (ghs, trt, site)
+as well as Y, SE, and n for each observation or summary statistic.}
 
 \item{j.chains}{number of chains in meta-analysis}
 
diff --git a/modules/meta.analysis/man/write.ma.model.Rd b/modules/meta.analysis/man/write.ma.model.Rd
index dec1ec1ee23..8766b63b58d 100644
--- a/modules/meta.analysis/man/write.ma.model.Rd
+++ b/modules/meta.analysis/man/write.ma.model.Rd
@@ -51,7 +51,7 @@ Nothing, but as a side effect, the model is written
 Convert template ma.model.template.R to a JAGS model.
 }
 \details{
-Writes a meta-analysis model based on available data and prior specification. Adapted from \code{\link[R2WinBUGS]{write.model}}
+Writes a meta-analysis model based on available data and prior specification. Adapted from \code{R2WinBUGS::write.model}
 }
 \author{
 David LeBauer and Mike Dietze, based on original work on the \code{write.model} function in the \code{R2WinBUGS} package by Jouni Kerman and Uwe Ligges.

From 4f972ca19314b49d59b209ace14f0c7e16f45cb0 Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Wed, 13 Jul 2022 15:25:56 +0000
Subject: [PATCH 11/18] added ggplot2 to DESCRIPTION

---
 modules/meta.analysis/DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index 1b01186344d..692c423f73b 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -34,7 +34,8 @@ Imports:
     PEcAn.logger,
     MASS,
     PEcAn.settings,
-    rjags
+    rjags,
+    ggplot2
 Suggests:
     ggmcmc,
     testthat (>= 1.0.2)

From c4c7827d7ea6b7fd3f3b59a988d67a639a7450d5 Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Wed, 13 Jul 2022 15:55:15 +0000
Subject: [PATCH 12/18] Added ggplot2 in Suggests.

---
 modules/meta.analysis/DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index 692c423f73b..614da0c60a1 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -34,10 +34,10 @@ Imports:
     PEcAn.logger,
     MASS,
     PEcAn.settings,
-    rjags,
-    ggplot2
+    rjags
 Suggests:
     ggmcmc,
+    ggplot2,
     testthat (>= 1.0.2)
 SystemRequirements: JAGS
 License: BSD_3_clause + file LICENSE

From 49337865c53290f84bbd0bdfbde499f960235fdf Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Fri, 15 Jul 2022 13:34:07 +0000
Subject: [PATCH 13/18] updated pecan.depends.R

---
 Makefile.depends               | 90 +++++++++++++++++++---------------
 docker/depends/pecan.depends.R |  1 +
 2 files changed, 52 insertions(+), 39 deletions(-)

diff --git a/Makefile.depends b/Makefile.depends
index cc64b4f329a..b9259abf9de 100644
--- a/Makefile.depends
+++ b/Makefile.depends
@@ -1,43 +1,55 @@
 # autogenerated
-$(call depends,base/all): | .install/base/db .install/base/settings .install/modules/meta.analysis .install/base/logger .install/base/utils .install/modules/uncertainty .install/modules/data.atmosphere .install/modules/data.land .install/modules/data.remote .install/modules/assim.batch .install/modules/emulator .install/modules/priors .install/modules/benchmark .install/base/remote .install/base/workflow .install/models/ed .install/models/sipnet .install/models/biocro .install/models/dalec .install/models/linkages .install/modules/allometry .install/modules/photosynthesis
-$(call depends,base/db): | .install/base/logger .install/base/remote .install/base/utils
+$(call depends,base/all): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/settings .install/modules/PEcAn.MA.Rcheck/PEcAn.MA .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils .install/modules/uncertainty .install/modules/data.atmosphere .install/modules/data.land .install/modules/data.remote .install/modules/assim.batch .install/modules/emulator .install/modules/priors .install/modules/benchmark .install/base/remote .install/base/workflow .install/models/ed .install/models/sipnet .install/models/biocro .install/models/dalec .install/models/linkages .install/modules/allometry .install/modules/photosynthesis
+$(call depends,base/db): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
 $(call depends,base/logger): |
-$(call depends,base/qaqc): | .install/base/logger .install/models/biocro .install/models/ed .install/models/sipnet .install/base/utils
-$(call depends,base/remote): | .install/base/logger
-$(call depends,base/settings): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
-$(call depends,base/utils): | .install/base/logger .install/base/remote
-$(call depends,base/visualization): | .install/base/db .install/base/logger .install/base/utils
-$(call depends,base/workflow): | .install/modules/data.atmosphere .install/modules/data.land .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils
-$(call depends,modules/allometry): | .install/base/logger .install/base/db
-$(call depends,modules/assim.batch): | .install/modules/benchmark .install/base/db .install/modules/emulator .install/base/logger .install/modules/meta.analysis .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils .install/base/workflow
-$(call depends,modules/assim.sequential): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/workflow .install/modules/benchmark .install/modules/data.remote
-$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
-$(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
-$(call depends,modules/data.hydrology): | .install/base/logger .install/base/utils
-$(call depends,modules/data.land): | .install/modules/benchmark .install/modules/data.atmosphere .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization
-$(call depends,modules/data.remote): | .install/base/db .install/base/utils .install/base/logger .install/base/remote
-$(call depends,modules/emulator): | .install/base/logger
-$(call depends,modules/meta.analysis): | .install/base/utils .install/base/db .install/base/logger .install/base/settings
+$(call depends,base/PEcAn.DB.Rcheck/00_pkg_src/PEcAn.DB): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,base/PEcAn.DB.Rcheck/PEcAn.DB): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,base/PEcAn.logger.Rcheck/00_pkg_src/PEcAn.logger): |
+$(call depends,base/PEcAn.logger.Rcheck/PEcAn.logger): |
+$(call depends,base/PEcAn.remote.Rcheck/00_pkg_src/PEcAn.remote): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
+$(call depends,base/PEcAn.remote.Rcheck/PEcAn.remote): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
+$(call depends,base/PEcAn.utils.Rcheck/00_pkg_src/PEcAn.utils): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/PEcAn.DB.Rcheck/PEcAn.DB
+$(call depends,base/PEcAn.utils.Rcheck/PEcAn.utils): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/PEcAn.DB.Rcheck/PEcAn.DB
+$(call depends,base/qaqc): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/models/biocro .install/models/ed .install/models/sipnet .install/base/utils
+$(call depends,base/remote): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
+$(call depends,base/settings): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,base/utils): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
+$(call depends,base/visualization): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
+$(call depends,base/workflow): | .install/modules/data.atmosphere .install/modules/data.land .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils
+$(call depends,modules/allometry): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/PEcAn.DB.Rcheck/PEcAn.DB
+$(call depends,modules/assim.batch): | .install/modules/benchmark .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/modules/emulator .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/PEcAn.MA.Rcheck/PEcAn.MA .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils .install/base/workflow
+$(call depends,modules/assim.sequential): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/workflow .install/modules/benchmark .install/modules/data.remote
+$(call depends,modules/benchmark): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
+$(call depends,modules/data.atmosphere): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,modules/data.hydrology): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
+$(call depends,modules/data.land): | .install/modules/benchmark .install/modules/data.atmosphere .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization
+$(call depends,modules/data.remote): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
+$(call depends,modules/emulator): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
+$(call depends,modules/meta.analysis): | .install/base/utils .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
+$(call depends,modules/PEcAn.MA.Rcheck/00_pkg_src/PEcAn.MA): | .install/base/utils .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
+$(call depends,modules/PEcAn.MA.Rcheck/PEcAn.MA): | .install/base/utils .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
+$(call depends,modules/PEcAnRTM.Rcheck/00_pkg_src/PEcAnRTM): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/assim.batch .install/base/utils .install/models/ed
+$(call depends,modules/PEcAnRTM.Rcheck/PEcAnRTM): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/assim.batch .install/base/utils .install/models/ed
 $(call depends,modules/photosynthesis): |
-$(call depends,modules/priors): | .install/base/utils .install/base/logger .install/modules/meta.analysis .install/base/visualization
-$(call depends,modules/rtm): | .install/base/logger .install/modules/assim.batch .install/base/utils .install/models/ed
-$(call depends,modules/uncertainty): | .install/base/utils .install/modules/priors .install/base/db .install/modules/emulator .install/base/logger .install/base/settings
-$(call depends,models/basgra): | .install/base/logger .install/modules/data.atmosphere .install/base/utils
-$(call depends,models/biocro): | .install/base/logger .install/base/remote .install/base/utils .install/base/settings .install/modules/data.atmosphere .install/modules/data.land .install/base/db
-$(call depends,models/cable): | .install/base/logger .install/base/utils
-$(call depends,models/clm45): | .install/base/logger .install/base/utils
-$(call depends,models/dalec): | .install/base/logger .install/base/remote .install/base/utils
+$(call depends,modules/priors): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/PEcAn.MA.Rcheck/PEcAn.MA .install/base/visualization
+$(call depends,modules/rtm): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/assim.batch .install/base/utils .install/models/ed
+$(call depends,modules/uncertainty): | .install/base/utils .install/modules/priors .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/modules/emulator .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
+$(call depends,models/basgra): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/data.atmosphere .install/base/utils
+$(call depends,models/biocro): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils .install/base/settings .install/modules/data.atmosphere .install/modules/data.land .install/base/PEcAn.DB.Rcheck/PEcAn.DB
+$(call depends,models/cable): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
+$(call depends,models/clm45): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
+$(call depends,models/dalec): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
 $(call depends,models/dvmdostem): | .install/base/utils
-$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/logger .install/base/remote .install/base/settings .install/base/utils
-$(call depends,models/fates): | .install/base/utils .install/base/logger .install/base/remote
-$(call depends,models/gday): | .install/base/utils .install/base/logger .install/base/remote
-$(call depends,models/jules): | .install/base/utils .install/base/logger .install/base/remote
-$(call depends,models/linkages): | .install/base/utils .install/modules/data.atmosphere .install/base/logger .install/base/remote
-$(call depends,models/lpjguess): | .install/base/utils .install/base/logger .install/base/remote
-$(call depends,models/maat): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/settings .install/base/utils
-$(call depends,models/maespa): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
-$(call depends,models/preles): | .install/base/utils .install/base/logger .install/modules/data.atmosphere .install/base/utils
-$(call depends,models/sibcasa): | .install/base/logger .install/base/utils
-$(call depends,models/sipnet): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
-$(call depends,models/stics): | .install/base/settings .install/base/db .install/base/logger .install/base/utils .install/base/remote
-$(call depends,models/template): | .install/base/db .install/base/logger .install/base/utils
+$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils
+$(call depends,models/fates): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
+$(call depends,models/gday): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
+$(call depends,models/jules): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
+$(call depends,models/linkages): | .install/base/utils .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
+$(call depends,models/lpjguess): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
+$(call depends,models/maat): | .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils
+$(call depends,models/maespa): | .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,models/preles): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/data.atmosphere .install/base/utils
+$(call depends,models/sibcasa): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
+$(call depends,models/sipnet): | .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,models/stics): | .install/base/settings .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils .install/base/remote
+$(call depends,models/template): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
diff --git a/docker/depends/pecan.depends.R b/docker/depends/pecan.depends.R
index 08ea1dd9fca..db47fced010 100644
--- a/docker/depends/pecan.depends.R
+++ b/docker/depends/pecan.depends.R
@@ -45,6 +45,7 @@ wanted <- c(
 'geonames',
 'getPass',
 'ggmap',
+'ggmcmc',
 'ggplot2',
 'ggrepel',
 'glue',

From bc37d100c125d704e6b940849ff49a6434108192 Mon Sep 17 00:00:00 2001
From: nanu1605 <83662210+nanu1605@users.noreply.github.com>
Date: Sat, 16 Jul 2022 09:13:08 +0530
Subject: [PATCH 14/18] Update modules/meta.analysis/R/meta.analysis.summary.R

Co-authored-by: Chris Black <chris@ckblack.org>
---
 modules/meta.analysis/R/meta.analysis.summary.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/meta.analysis/R/meta.analysis.summary.R b/modules/meta.analysis/R/meta.analysis.summary.R
index e63b346bed7..62cbf6faf13 100644
--- a/modules/meta.analysis/R/meta.analysis.summary.R
+++ b/modules/meta.analysis/R/meta.analysis.summary.R
@@ -35,7 +35,7 @@ pecan.ma.summary <- function(mcmc.object, pft, outdir, threshold = 1.2, gg = FAL
   for (trait in names(mcmc.object)) {
     
     if (gg) {
-      if (!requireNamespace(ggmcmc, quietly = TRUE)) {
+      if (!requireNamespace("ggmcmc", quietly = TRUE)) {
         PEcAn.logger::logger.severe(
           "Can't find package 'ggmcmc',",
           "needed by `PEcAn.MA::meta.analysis.summary()` when `gg = TRUE`.",

From 7c3526f71bd0ef9a046a9655359b20374c75bff2 Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Sat, 16 Jul 2022 05:03:31 +0000
Subject: [PATCH 15/18] changed Makefile.depends

---
 Makefile.depends | 90 +++++++++++++++++++++---------------------------
 1 file changed, 39 insertions(+), 51 deletions(-)

diff --git a/Makefile.depends b/Makefile.depends
index b9259abf9de..cc64b4f329a 100644
--- a/Makefile.depends
+++ b/Makefile.depends
@@ -1,55 +1,43 @@
 # autogenerated
-$(call depends,base/all): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/settings .install/modules/PEcAn.MA.Rcheck/PEcAn.MA .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils .install/modules/uncertainty .install/modules/data.atmosphere .install/modules/data.land .install/modules/data.remote .install/modules/assim.batch .install/modules/emulator .install/modules/priors .install/modules/benchmark .install/base/remote .install/base/workflow .install/models/ed .install/models/sipnet .install/models/biocro .install/models/dalec .install/models/linkages .install/modules/allometry .install/modules/photosynthesis
-$(call depends,base/db): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,base/all): | .install/base/db .install/base/settings .install/modules/meta.analysis .install/base/logger .install/base/utils .install/modules/uncertainty .install/modules/data.atmosphere .install/modules/data.land .install/modules/data.remote .install/modules/assim.batch .install/modules/emulator .install/modules/priors .install/modules/benchmark .install/base/remote .install/base/workflow .install/models/ed .install/models/sipnet .install/models/biocro .install/models/dalec .install/models/linkages .install/modules/allometry .install/modules/photosynthesis
+$(call depends,base/db): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,base/logger): |
-$(call depends,base/PEcAn.DB.Rcheck/00_pkg_src/PEcAn.DB): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
-$(call depends,base/PEcAn.DB.Rcheck/PEcAn.DB): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
-$(call depends,base/PEcAn.logger.Rcheck/00_pkg_src/PEcAn.logger): |
-$(call depends,base/PEcAn.logger.Rcheck/PEcAn.logger): |
-$(call depends,base/PEcAn.remote.Rcheck/00_pkg_src/PEcAn.remote): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
-$(call depends,base/PEcAn.remote.Rcheck/PEcAn.remote): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
-$(call depends,base/PEcAn.utils.Rcheck/00_pkg_src/PEcAn.utils): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/PEcAn.DB.Rcheck/PEcAn.DB
-$(call depends,base/PEcAn.utils.Rcheck/PEcAn.utils): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/PEcAn.DB.Rcheck/PEcAn.DB
-$(call depends,base/qaqc): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/models/biocro .install/models/ed .install/models/sipnet .install/base/utils
-$(call depends,base/remote): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
-$(call depends,base/settings): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
-$(call depends,base/utils): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
-$(call depends,base/visualization): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
-$(call depends,base/workflow): | .install/modules/data.atmosphere .install/modules/data.land .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils
-$(call depends,modules/allometry): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/PEcAn.DB.Rcheck/PEcAn.DB
-$(call depends,modules/assim.batch): | .install/modules/benchmark .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/modules/emulator .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/PEcAn.MA.Rcheck/PEcAn.MA .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils .install/base/workflow
-$(call depends,modules/assim.sequential): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/workflow .install/modules/benchmark .install/modules/data.remote
-$(call depends,modules/benchmark): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
-$(call depends,modules/data.atmosphere): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
-$(call depends,modules/data.hydrology): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
-$(call depends,modules/data.land): | .install/modules/benchmark .install/modules/data.atmosphere .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization
-$(call depends,modules/data.remote): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
-$(call depends,modules/emulator): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger
-$(call depends,modules/meta.analysis): | .install/base/utils .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
-$(call depends,modules/PEcAn.MA.Rcheck/00_pkg_src/PEcAn.MA): | .install/base/utils .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
-$(call depends,modules/PEcAn.MA.Rcheck/PEcAn.MA): | .install/base/utils .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
-$(call depends,modules/PEcAnRTM.Rcheck/00_pkg_src/PEcAnRTM): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/assim.batch .install/base/utils .install/models/ed
-$(call depends,modules/PEcAnRTM.Rcheck/PEcAnRTM): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/assim.batch .install/base/utils .install/models/ed
+$(call depends,base/qaqc): | .install/base/logger .install/models/biocro .install/models/ed .install/models/sipnet .install/base/utils
+$(call depends,base/remote): | .install/base/logger
+$(call depends,base/settings): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
+$(call depends,base/utils): | .install/base/logger .install/base/remote
+$(call depends,base/visualization): | .install/base/db .install/base/logger .install/base/utils
+$(call depends,base/workflow): | .install/modules/data.atmosphere .install/modules/data.land .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils
+$(call depends,modules/allometry): | .install/base/logger .install/base/db
+$(call depends,modules/assim.batch): | .install/modules/benchmark .install/base/db .install/modules/emulator .install/base/logger .install/modules/meta.analysis .install/base/remote .install/base/settings .install/modules/uncertainty .install/base/utils .install/base/workflow
+$(call depends,modules/assim.sequential): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/workflow .install/modules/benchmark .install/modules/data.remote
+$(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.land
+$(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
+$(call depends,modules/data.hydrology): | .install/base/logger .install/base/utils
+$(call depends,modules/data.land): | .install/modules/benchmark .install/modules/data.atmosphere .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization
+$(call depends,modules/data.remote): | .install/base/db .install/base/utils .install/base/logger .install/base/remote
+$(call depends,modules/emulator): | .install/base/logger
+$(call depends,modules/meta.analysis): | .install/base/utils .install/base/db .install/base/logger .install/base/settings
 $(call depends,modules/photosynthesis): |
-$(call depends,modules/priors): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/PEcAn.MA.Rcheck/PEcAn.MA .install/base/visualization
-$(call depends,modules/rtm): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/assim.batch .install/base/utils .install/models/ed
-$(call depends,modules/uncertainty): | .install/base/utils .install/modules/priors .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/modules/emulator .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/settings
-$(call depends,models/basgra): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/data.atmosphere .install/base/utils
-$(call depends,models/biocro): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils .install/base/settings .install/modules/data.atmosphere .install/modules/data.land .install/base/PEcAn.DB.Rcheck/PEcAn.DB
-$(call depends,models/cable): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
-$(call depends,models/clm45): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
-$(call depends,models/dalec): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
+$(call depends,modules/priors): | .install/base/utils .install/base/logger .install/modules/meta.analysis .install/base/visualization
+$(call depends,modules/rtm): | .install/base/logger .install/modules/assim.batch .install/base/utils .install/models/ed
+$(call depends,modules/uncertainty): | .install/base/utils .install/modules/priors .install/base/db .install/modules/emulator .install/base/logger .install/base/settings
+$(call depends,models/basgra): | .install/base/logger .install/modules/data.atmosphere .install/base/utils
+$(call depends,models/biocro): | .install/base/logger .install/base/remote .install/base/utils .install/base/settings .install/modules/data.atmosphere .install/modules/data.land .install/base/db
+$(call depends,models/cable): | .install/base/logger .install/base/utils
+$(call depends,models/clm45): | .install/base/logger .install/base/utils
+$(call depends,models/dalec): | .install/base/logger .install/base/remote .install/base/utils
 $(call depends,models/dvmdostem): | .install/base/utils
-$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils
-$(call depends,models/fates): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
-$(call depends,models/gday): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
-$(call depends,models/jules): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
-$(call depends,models/linkages): | .install/base/utils .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
-$(call depends,models/lpjguess): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote
-$(call depends,models/maat): | .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/settings .install/base/utils
-$(call depends,models/maespa): | .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
-$(call depends,models/preles): | .install/base/utils .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/modules/data.atmosphere .install/base/utils
-$(call depends,models/sibcasa): | .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
-$(call depends,models/sipnet): | .install/modules/data.atmosphere .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/remote .install/base/utils
-$(call depends,models/stics): | .install/base/settings .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils .install/base/remote
-$(call depends,models/template): | .install/base/PEcAn.DB.Rcheck/PEcAn.DB .install/base/PEcAn.logger.Rcheck/PEcAn.logger .install/base/utils
+$(call depends,models/ed): | .install/modules/data.atmosphere .install/modules/data.land .install/base/logger .install/base/remote .install/base/settings .install/base/utils
+$(call depends,models/fates): | .install/base/utils .install/base/logger .install/base/remote
+$(call depends,models/gday): | .install/base/utils .install/base/logger .install/base/remote
+$(call depends,models/jules): | .install/base/utils .install/base/logger .install/base/remote
+$(call depends,models/linkages): | .install/base/utils .install/modules/data.atmosphere .install/base/logger .install/base/remote
+$(call depends,models/lpjguess): | .install/base/utils .install/base/logger .install/base/remote
+$(call depends,models/maat): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/settings .install/base/utils
+$(call depends,models/maespa): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
+$(call depends,models/preles): | .install/base/utils .install/base/logger .install/modules/data.atmosphere .install/base/utils
+$(call depends,models/sibcasa): | .install/base/logger .install/base/utils
+$(call depends,models/sipnet): | .install/modules/data.atmosphere .install/base/logger .install/base/remote .install/base/utils
+$(call depends,models/stics): | .install/base/settings .install/base/db .install/base/logger .install/base/utils .install/base/remote
+$(call depends,models/template): | .install/base/db .install/base/logger .install/base/utils

From a4145e163175ccb80bf6b1886f7ae28de9697b8d Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Sat, 16 Jul 2022 14:42:59 +0000
Subject: [PATCH 16/18] Fixed Vignette Warning

---
 modules/meta.analysis/DESCRIPTION                  | 2 ++
 modules/meta.analysis/vignettes/single.MA_demo.Rmd | 8 ++++++++
 2 files changed, 10 insertions(+)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index 614da0c60a1..6129287e930 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -37,10 +37,12 @@ Imports:
     rjags
 Suggests:
     ggmcmc,
+    knitr,
     ggplot2,
     testthat (>= 1.0.2)
 SystemRequirements: JAGS
 License: BSD_3_clause + file LICENSE
+VignetteBuilder: knitr
 Copyright: Authors
 LazyData: FALSE
 Encoding: UTF-8
diff --git a/modules/meta.analysis/vignettes/single.MA_demo.Rmd b/modules/meta.analysis/vignettes/single.MA_demo.Rmd
index df989182936..c150f5687cf 100644
--- a/modules/meta.analysis/vignettes/single.MA_demo.Rmd
+++ b/modules/meta.analysis/vignettes/single.MA_demo.Rmd
@@ -1,3 +1,11 @@
+---
+title: "Example of Single.MA"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteIndexEntry{Example of Single.MA}
+  %\usepackage[utf8]{inputenc}
+---
 Meta-analysis: Example of Single.MA
 ========================================================
 Individual Meta-analysis

From ddb1e44c550bb7e1d1415023c78193b656c88f2e Mon Sep 17 00:00:00 2001
From: Tanishq Jain <tanishqjain010@gmail.com>
Date: Sat, 16 Jul 2022 15:03:08 +0000
Subject: [PATCH 17/18] minor changes

---
 modules/meta.analysis/DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index 6129287e930..a11c56ef89b 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -37,6 +37,7 @@ Imports:
     rjags
 Suggests:
     ggmcmc,
+    rmarkdown,
     knitr,
     ggplot2,
     testthat (>= 1.0.2)

From 8ad821e9c67a877c9e3675849fef998379a0a756 Mon Sep 17 00:00:00 2001
From: nanu1605 <83662210+nanu1605@users.noreply.github.com>
Date: Sat, 16 Jul 2022 22:10:30 +0530
Subject: [PATCH 18/18] Update modules/meta.analysis/DESCRIPTION

Co-authored-by: Chris Black <chris@ckblack.org>
---
 modules/meta.analysis/DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/meta.analysis/DESCRIPTION b/modules/meta.analysis/DESCRIPTION
index a11c56ef89b..0d59ceb71dc 100644
--- a/modules/meta.analysis/DESCRIPTION
+++ b/modules/meta.analysis/DESCRIPTION
@@ -37,9 +37,9 @@ Imports:
     rjags
 Suggests:
     ggmcmc,
-    rmarkdown,
-    knitr,
     ggplot2,
+    knitr,
+    rmarkdown,
     testthat (>= 1.0.2)
 SystemRequirements: JAGS
 License: BSD_3_clause + file LICENSE