diff --git a/.gitignore b/.gitignore
index 03984b8..3fbbeaa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,7 +12,6 @@ src/*.dll
 *.desc
 gfiles
 Gac
-man
 gemino_*.tgz
 *.pdf
 methods
diff --git a/man/add_mutations.Rd b/man/add_mutations.Rd
new file mode 100644
index 0000000..64ef3ed
--- /dev/null
+++ b/man/add_mutations.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RcppExports.R
+\name{add_mutations}
+\alias{add_mutations}
+\alias{add_substitution}
+\alias{add_insertion}
+\alias{add_deletion}
+\title{Add mutations manually from R.}
+\usage{
+add_substitution(vs_, var_ind, seq_ind, nucleo_, new_pos_)
+
+add_insertion(vs_, var_ind, seq_ind, nucleos_, new_pos_)
+
+add_deletion(vs_, var_ind, seq_ind, size_, new_pos_)
+}
+\arguments{
+\item{vs_}{External pointer to a C++ \code{VarSet} object}
+
+\item{var_ind}{Integer index to the desired variant. Uses 0-based indexing!}
+
+\item{seq_ind}{Integer index to the desired sequence. Uses 0-based indexing!}
+
+\item{nucleo_}{Character to substitute for existing one.}
+
+\item{new_pos_}{Integer index to the desired subsitution location.
+Uses 0-based indexing!}
+
+\item{nucleos_}{Nucleotides to insert at the desired location.}
+
+\item{size_}{Size of deletion.}
+}
+\description{
+Note that all indices are in 0-based C++ indexing. This means that the first
+item is indexed by \code{0}, and so forth.
+}
+\section{Functions}{
+\itemize{
+\item \code{add_substitution}: Add a substitution.
+
+\item \code{add_insertion}: Add an insertion.
+
+\item \code{add_deletion}: Add a deletion.
+}}
+
diff --git a/man/binding_sites.Rd b/man/binding_sites.Rd
new file mode 100644
index 0000000..6e94bf9
--- /dev/null
+++ b/man/binding_sites.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{binding_sites}
+\alias{binding_sites}
+\title{Binding sites for selected restriction enzymes.}
+\format{A list of length 11. For each element in the list...
+\describe{
+\item{name}{The element's name is the restriction enzyme's name.
+The enzymes present in this list are
+\emph{AclI}, \emph{ApeKI}, \emph{AscI}, \emph{BspEI}, \emph{BstBI},
+\emph{EcoT22I}, \emph{FspI}, \emph{MluI-HF}, \emph{NruI-HF}, \emph{PstI},
+and \emph{SbfI}.}
+\item{sites}{Enzyme binding site sequences. This vector is of the binding sites,
+5' then 3', for each unique site that the enzyme can bind to.}
+}}
+\source{
+\url{http://www.neb.com}
+}
+\usage{
+binding_sites
+}
+\description{
+Binding sites for selected restriction enzymes.
+}
+\keyword{datasets}
diff --git a/man/create_genome.Rd b/man/create_genome.Rd
new file mode 100644
index 0000000..b99a49e
--- /dev/null
+++ b/man/create_genome.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RcppExports.R
+\name{create_genome}
+\alias{create_genome}
+\alias{rando_seqs}
+\title{Create \code{RefGenome} pointer based on nucleotide equilibrium frequencies.}
+\usage{
+create_genome(n_seqs, len_mean, len_sd = 0, equil_freqs = numeric(0),
+  n_cores = 1L)
+
+rando_seqs(n_seqs, len_mean, len_sd = 0, equil_freqs = numeric(0),
+  n_cores = 1L)
+}
+\arguments{
+\item{n_seqs}{Number of sequences.}
+
+\item{len_mean}{Mean for the gamma distribution for sequence sizes.}
+
+\item{len_sd}{Standard deviation for the gamma distribution for sequence sizes.
+If set to \code{<= 0}, all sequences will be the same length. Defaults to \code{0}.}
+
+\item{equil_freqs}{Vector of nucleotide equilibrium frequencies for
+"T", "C", "A", and "G", respectively. Defaults to \code{rep(0.25, 4)}.}
+
+\item{n_cores}{Number of cores to use via OpenMP.}
+}
+\value{
+External pointer to a \code{RefGenome} C++ object.
+
+Character vector of sequence strings.
+}
+\description{
+Function to create random sequences for a new reference genome object.
+}
+\details{
+Note that this function will never return empty sequences.
+}
+\section{Functions}{
+\itemize{
+\item \code{rando_seqs}: create random sequences as a character vector.
+}}
+
+\examples{
+
+\dontrun{
+genome <- create_genome(10, 100e6, 10e6, equil_freqs = c(0.1, 0.2, 0.3, 0.4))
+}
+
+\dontrun{
+randos <- rando_seqs(10, 1000, 10)
+}
+
+}
diff --git a/man/digest.Rd b/man/digest.Rd
new file mode 100644
index 0000000..729aa2e
--- /dev/null
+++ b/man/digest.Rd
@@ -0,0 +1,62 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/digest.R
+\name{digest}
+\alias{digest}
+\title{Digest genome(s).}
+\usage{
+digest(object, enzyme_names, n_cores = 1, chunk_size = 1000,
+  enz_list = binding_sites, in_place = FALSE)
+}
+\arguments{
+\item{object}{Either a \code{dna_set} or \code{variants} object.}
+
+\item{enzyme_names}{Name of enzyme(s).}
+
+\item{n_cores}{Number of cores to use for parallel processing. This argument is
+ignored if OpenMP is not enabled. Defaults to \code{1}.}
+
+\item{chunk_size}{The size of chunks to break up scaffolds into when digesting
+a \code{variants} object.
+(This argument is ignored if digesting a \code{dna_set}.)
+Changing this might affect performance, for better or worse.
+The default worked best on my computer. Defaults to \code{1000}.}
+
+\item{enz_list}{List of enzymes with binding sites. Default is the internal
+\code{binding_sites} list (see \code{\link{binding_sites}}).}
+
+\item{in_place}{Boolean for whether to edit the object in place without
+making a new copy. Defaults to \code{FALSE}.}
+}
+\value{
+If \code{in_place == FALSE}, a \code{variants} or \code{dna_set} object
+with the \code{digests} field filled in.
+If \code{in_place == TRUE}, it returns \code{NULL}, but it changes the input
+object in place.
+}
+\description{
+\emph{Note:} This will override any digestions currently in place in the
+object. If you want to add a new digestion, re-run this function with the names
+of all enzymes you're interested in included in the \code{enzyme_names} argument.
+}
+\examples{
+
+\dontrun{
+
+ref_genome <- dna_set$new(rando_seqs(100, mean_len = 1e3, sd_len = 1e2))
+digest(ref_genome, 'ApeKI', n_cores = 1, in_place = TRUE)
+ref_genome
+
+variants_obj <- make_variants(ref_genome, n_vars = 10)
+variants_obj
+
+# Returns a new variants object
+digest(variants_obj, 'ApeKI')
+
+# Returns nothing, but changes variants_obj object
+digest(variants_obj, 'AscI', in_place = TRUE)
+# To see the changes...
+variants_obj
+
+}
+
+}
diff --git a/man/evo_rates.Rd b/man/evo_rates.Rd
new file mode 100644
index 0000000..2709401
--- /dev/null
+++ b/man/evo_rates.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{evo_rates}
+\alias{evo_rates}
+\title{Table of evolutionary rates.}
+\format{A data frame with 15 rows and 4 variables:
+\describe{
+\item{domain}{Either \code{Bacteria} or \code{Eukarya} for what type of organism
+the species is.}
+\item{species}{Species name.}
+\item{indels}{Rate of insertions and deletions (events per site per generation).}
+\item{subs}{Base-substitution mutation rate (events per site per generation).}
+}}
+\source{
+\url{http://dx.doi.org/10.1534/g3.116.030890}
+}
+\usage{
+evo_rates
+}
+\description{
+From Table 1 in Sung et al. (2016).
+}
+\references{
+Sung, W., M. S. Ackerman, M. M. Dillon, T. G. Platt, C. Fuqua, V. S. Cooper, and
+M. Lynch. 2016. Evolution of the insertion-deletion mutation rate across the
+tree of life. \emph{G3: Genes | Genomes | Genetics} \strong{6}:2583–2591.
+}
+\keyword{datasets}
diff --git a/man/gemino.Rd b/man/gemino.Rd
new file mode 100644
index 0000000..cbeb207
--- /dev/null
+++ b/man/gemino.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gemino.R
+\docType{package}
+\name{gemino}
+\alias{gemino}
+\alias{gemino-package}
+\title{gemino: An efficient, flexible molecular evolution and sequencing simulator.}
+\description{
+\code{gemino} efficiently (i) reads and simulates reference genomes;
+(ii) generates variants using summary statistics, phylogenies, Variant
+Call Format (VCF) files, and coalescent simulations—the latter of which can include
+selection, recombination, and demographic fluctuations;
+(iii) simulates sequencing error, mapping qualities, restriction-enzyme digestion,
+and variance in coverage among sites; and
+(iv) writes outputs to standard file formats.
+\code{gemino} can simulate single or paired-ended reads for WGS on the Illumina platform,
+and can be extended to simulate different methods (e.g., original RADseq,
+double-digest RADseq, and genotyping-by-sequencing), and sequencing technologies
+(e.g., Pacific BioSciences, Oxford Nanopore Technologies).
+}
+\section{gemino functions}{
+
+}
+
diff --git a/man/random_variants.Rd b/man/random_variants.Rd
new file mode 100644
index 0000000..f094bec
--- /dev/null
+++ b/man/random_variants.Rd
@@ -0,0 +1,72 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/random_variants.R
+\name{random_variants}
+\alias{random_variants}
+\title{Construct a \code{VarSet} object from a reference genome and summary statistics.}
+\usage{
+random_variants(dna_set_in, n_vars, theta_w, theta_pi,
+  indel_probs = exp(-1:-10), snp_probs = rep(0.25, 4),
+  snp_proportion = NULL, n_cores = 1, n2N = 50, alpha = 0.8)
+}
+\arguments{
+\item{dna_set_in}{A \code{dna_set} object of sequences representing the reference
+genome.}
+
+\item{n_vars}{The number of variants to create.}
+
+\item{theta_w}{Watterson's estimator for the focal population.}
+
+\item{theta_pi}{Average nucleotide diversity for the focal population.}
+
+\item{indel_probs}{Relative probabilities of indel types and sizes.
+If insertions and deletions have the same probabilities, this is simply
+a numeric vector where the value in location \code{i} indicates the relative
+probability of an indel of size \code{i}.
+If insertions and deletions do not have the same probabilities, then
+this argument should be a list where the \code{insertion} and \code{deletion} fields are
+numeric vectors specifying relative probabilities for insertions and deletions,
+respectively.
+Note that if specifying a list, the proportion of insertions to deletions will
+be \code{sum(indel_probs$insertions) / sum(indel_probs$deletions)}.
+Defaults to \code{exp(-1:-10)}.}
+
+\item{snp_probs}{Relative probabilities of substitution types:
+"A", "C", "G", and "T" respectively. Defaults to \code{rep(0.25, 4)}.}
+
+\item{snp_proportion}{The proportion of mutations (not sites) that are SNPs.
+Defaults to the proportion calculated using the average ratio of indels
+to substitutions in eukaryotes from Sung et al. (2016).}
+
+\item{n_cores}{Number of cores to use. Defaults to 1.}
+
+\item{n2N}{A numeric threshold placed on the algorithm used to find new locations.
+This is not recommended to be changed. Defaults to 50.}
+
+\item{alpha}{A numeric threshold placed on the algorithm used to find new locations.
+This is not recommended to be changed. Defaults to 0.8.}
+}
+\value{
+A \code{VarSet} object.
+}
+\description{
+This function creates a \code{VarSet} object, which is designed to be a
+low-memory way to store variants.
+(The variants class also prevents what might otherwise be an annoyingly long list
+from ever printing in the console.)
+}
+\examples{
+\dontrun{
+n_vars <- 10
+dna_set_in <- dna_set$new(rando_seqs(100, 100))
+set.seed(1)
+varseq_out <- random_variants(dna_set_in, n_vars,
+                              theta_w = 0.0045, theta_pi = 0.005)
+}
+
+}
+\references{
+Sung, W., M. S. Ackerman, M. M. Dillon, T. G. Platt, C. Fuqua, V. S. Cooper, and M.
+Lynch. 2016.
+Evolution of the insertion-deletion mutation rate across the tree of life.
+\emph{G3: Genes|Genomes|Genetics} \strong{6}:2583-2591.
+}
diff --git a/man/read_fasta.Rd b/man/read_fasta.Rd
new file mode 100644
index 0000000..7fbf27c
--- /dev/null
+++ b/man/read_fasta.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_write.R
+\name{read_fasta}
+\alias{read_fasta}
+\title{Read a fasta file to an external pointer object.}
+\usage{
+read_fasta(fasta_file, fai_file = NULL, cut_names = TRUE,
+  rm_soft_mask = TRUE)
+}
+\arguments{
+\item{fasta_file}{File name of the fasta file.}
+
+\item{fai_file}{File name of the fasta file.
+Providing this argument speeds up the reading process significantly.
+Defaults to \code{NULL}, which indicates the fasta file is not indexed.}
+
+\item{cut_names}{Boolean for whether to cut sequence names at the first space.
+Defaults to \code{TRUE}.}
+
+\item{rm_soft_mask}{Boolean for whether to remove soft-masking by making
+sequences all uppercase. Defaults to \code{TRUE}.}
+}
+\value{
+An external pointer to a \code{RefGenome} object in C++.
+}
+\description{
+Accepts uncompressed and gzipped fasta files.
+}
diff --git a/man/table_gammas.Rd b/man/table_gammas.Rd
new file mode 100644
index 0000000..b8ae4b2
--- /dev/null
+++ b/man/table_gammas.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RcppExports.R
+\name{table_gammas}
+\alias{table_gammas}
+\title{Faster version of table function to count the number of mutations in Gamma regions.}
+\usage{
+table_gammas(gamma_ends, positions)
+}
+\arguments{
+\item{gamma_ends}{Vector of endpoints for gamma regions}
+
+\item{positions}{Vector of positions that you want to bin into gamma regions.}
+}
+\description{
+Faster version of table function to count the number of mutations in Gamma regions.
+}
diff --git a/man/write_fasta.Rd b/man/write_fasta.Rd
new file mode 100644
index 0000000..1a91855
--- /dev/null
+++ b/man/write_fasta.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_write.R
+\name{write_fasta}
+\alias{write_fasta}
+\title{Write to FASTA file.}
+\usage{
+write_fasta(file_name, ptr, text_width = 80, compression = "none")
+}
+\arguments{
+\item{file_name}{File name of the output fasta file.}
+
+\item{ptr}{External pointer to a \code{RefGenome} C++ object.}
+
+\item{text_width}{The number of characters per line in the output fasta file.
+Defaults to 80.}
+
+\item{compression}{Type of compression. Takes either \code{"none"} or \code{"gzip"}.
+Defaults to \code{"none"}.}
+}
+\value{
+Nothing.
+}
+\description{
+Write to FASTA file.
+}