diff --git a/DESCRIPTION b/DESCRIPTION
index 42eb8642..4d90845e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,58 +1,43 @@
 Package: devMSMs
 Type: Package
 Title: Implementing Marginal Structural Models with Longitudinal Data
-Version: 0.0.0.9000
-Authors@R: c(person("Isabella", "Stallworthy",
-            email = "istall@seas.upenn.edu",
-            role = c("aut", "cre")),
-            person("Noah", "Greifer",
-            email = "ngreifer@iq.harvard.edu",
-            role = c("aut", "ctb")),
-	    person("Kyle", "Butts",
-	    email = "buttskyle96@gmail.com",
-	    role = ("ctb")),
-            person("Meriah", "DeJoseph",
-            email = "meriahd@stanford.edu",
-            role = c("aut")),
-            person("Emily", "Padrutt",
-            email = "padru004@umn.edu",
-            role = c("aut")),
-            person("Daniel", "Berry",
-            email = "dberry@umn.edu",
-            role = c("aut")))
+Version: 0.0.0.9001
+Authors@R: c(person("Isabella", "Stallworthy", email = "istall@seas.upenn.edu", role = c("aut", "cre")),
+            person("Noah", "Greifer", email = "noah.greifer@gmail.com", role = c("aut", "ctb"),
+	                 comment=c(ORCID="0000-0003-3067-7154")),
+	          person("Kyle", "Butts", email = "buttskyle96@gmail.com", role = ("ctb")),
+            person("Meriah", "DeJoseph", email = "meriahd@stanford.edu", role = c("aut")),
+            person("Emily", "Padrutt", email = "padru004@umn.edu", role = c("aut")),
+            person("Daniel", "Berry", email = "dberry@umn.edu", role = c("aut")))
 Description: Functions for implementing MSMS with longitudinal data.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports:
-    cobalt,
-    dreamerr,
-    ggplot2,
-    marginaleffects,
-    markdown,
+    cobalt (>= 4.5.0),
+    dreamerr (>= 1.4.0),
+    fs (>= 1.6.4),
+    ggplot2 (>= 3.5.1),
+    lmtest (>= 0.9-40),
+    marginaleffects (>= 0.21.0),
     modelsummary,
     rlang,
     stats,
-    survey,
     tinytable,
-    WeightIt,
-    utils,
-    fs
+    WeightIt (>= 1.2.0),
+    utils
 Suggests: 
-    CBPS,
     dbarts,
     gbm,
     knitr,
     mice,
-    mitml,
     rmarkdown,
     SuperLearner,
-    webshot2,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 URL: https://istallworthy.github.io/devMSMs/, https://github.com/istallworthy/devMSMs
 VignetteBuilder: knitr
 Depends: 
-    R (>= 2.10)
+    R (>= 4.0.0)
diff --git a/NAMESPACE b/NAMESPACE
index 99a526c1..8702cc84 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,7 @@ S3method(print,devMSM_models)
 S3method(print,devMSM_weights)
 S3method(summary,devMSM_bal_stats)
 S3method(summary,devMSM_comparisons)
+S3method(summary,devMSM_weights)
 export(assessBalance)
 export(compareHistories)
 export(createFormulas)
@@ -18,7 +19,6 @@ export(createWeights)
 export(fitModel)
 export(initMSM)
 export(trimWeights)
-import(ggplot2)
 import(stats)
 import(utils)
-importFrom(survey,svyglm)
+importFrom(ggplot2,.data)
diff --git a/man/assessBalance.Rd b/man/assessBalance.Rd
index ac4dda49..9725fc9f 100644
--- a/man/assessBalance.Rd
+++ b/man/assessBalance.Rd
@@ -19,7 +19,7 @@ assessBalance(
 
 \method{print}{devMSM_bal_stats}(x, i = NA, t = TRUE, save.out = FALSE, ...)
 
-\method{summary}{devMSM_bal_stats}(object, i = NA, t = TRUE, save.out = FALSE, ...)
+\method{summary}{devMSM_bal_stats}(object, i = NA, save.out = FALSE, ...)
 
 \method{plot}{devMSM_bal_stats}(x, i = NA, t = TRUE, save.out = FALSE, ...)
 }
@@ -49,11 +49,11 @@ default is FALSE.}
 
 \item{x}{devMSM_bal_stats object from \code{assessBalance}}
 
-\item{i}{For multiply imputed datset, \code{i} selects which imputation to print results for.
-Default is \code{i = 1}. With \code{i = TRUE}, all imputed datasets will be looped over. With \code{i = NULL}, will average over all imputed datasets and summarize that.}
+\item{i}{For multiply imputed datasets, \code{i} selects which imputation to print results for.
+Default is \code{i = 1}. With \code{i = TRUE}, all imputed datasets will be looped over. With \code{i = NULL}, will average over all imputed datasets and summarize that. Ignored for non-imputed data.}
 
-\item{t}{Which exposure variable to use. Can either be an index from 1, ..., num exposures or
-a string containing the exposure varaible name (e.g. \code{"A.3"}). With \code{t = TRUE}, all exposure
+\item{t}{Which exposure variable to use. Can either be an index from 1 to the number of exposures or
+a string containing the exposure variable name (e.g. \code{"A.3"}). With \code{t = TRUE}, all exposure
 variables will be looped over.}
 
 \item{...}{ignored}
@@ -102,8 +102,8 @@ plot(b, t = 3)
 
 # Weighted
 f <- createFormulas(obj, type = "short")
-w <- createWeights(data = data, obj = obj, formulas = f)
-bw <- assessBalance(data = data, obj = obj, weights = w)
+w <- createWeights(data = data, formulas = f)
+bw <- assessBalance(data = data, weights = w)
 print(bw)
 plot(bw)
 
diff --git a/man/calc_bal_stats.Rd b/man/calc_bal_stats.Rd
deleted file mode 100644
index 0c969318..00000000
--- a/man/calc_bal_stats.Rd
+++ /dev/null
@@ -1,39 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/calc_bal_stats.R
-\name{calc_bal_stats}
-\alias{calc_bal_stats}
-\title{Calculate balance stats based on Jackson paper}
-\usage{
-calc_bal_stats(
-  data,
-  obj,
-  weights = NULL,
-  balance_thresh = NULL,
-  imp_conf = NULL
-)
-}
-\arguments{
-\item{data}{data in wide format as: a data frame, path to folder of imputed
-.csv files, or mids object}
-
-\item{obj}{initialized MSM object from \code{initMSM}}
-
-\item{weights}{(optional) list of IPTW weights output from createWeights}
-
-\item{balance_thresh}{(optional) one or two numbers between 0 and 1
-indicating a single balancingn threshold or thresholds for more and less
-important confounders, respectively}
-
-\item{imp_conf}{(optional) list of variable names reflecting important
-confounders (required if two balance thresholds are provided)}
-}
-\value{
-data frame of balance statistics
-}
-\description{
-Calculate weighted or unweighted standardized balance statistics for a given
-exposure time point, using all relevant confounders. Draws on Jackson, 2016
-approaches to assessing balance for time-varying exposures by weighting
-statistics based on sample distribution in exposure histories.
-}
-\keyword{internal}
diff --git a/man/compareHistories.Rd b/man/compareHistories.Rd
index 7de9d44d..91a1d41c 100644
--- a/man/compareHistories.Rd
+++ b/man/compareHistories.Rd
@@ -8,13 +8,12 @@
 \title{Estimate, compare, and visualize exposure histories}
 \usage{
 compareHistories(
-  obj,
   fit,
   hi_lo_cut = c(0.4, 0.6),
-  dose_level = c("h", "l"),
+  dose_level = "h",
   reference = NULL,
   comparison = NULL,
-  mc_comp_method = stats::p.adjust.methods,
+  mc_comp_method = "BH",
   verbose = FALSE,
   save.out = FALSE
 )
@@ -30,11 +29,9 @@ compareHistories(
   ...
 )
 
-\method{summary}{devMSM_comparisons}(object, type = c("preds", "comps"), ...)
+\method{summary}{devMSM_comparisons}(object, type = "comps", ...)
 }
 \arguments{
-\item{obj}{initialized MSM object from \code{\link[=initMSM]{initMSM()}}}
-
 \item{fit}{list of model outputs from \code{\link[=fitModel]{fitModel()}}}
 
 \item{hi_lo_cut}{list of two numbers indicating quantile values
@@ -82,7 +79,7 @@ colors (n(epochs)+1) for plotting (default is "Dark2" palette)}
 
 \item{type}{Either "preds" or "comps" corresponding to the
 results of \code{\link[marginaleffects:predictions]{marginaleffects::avg_predictions()}} at low and high dosages or
-\code{\link[marginaleffects:comparisons]{marginaleffects::comparisons()}} respectively}
+\code{\link[marginaleffects:comparisons]{marginaleffects::avg_comparisons()}} respectively}
 }
 \value{
 list containing two dataframes: \code{preds} with predictions from
@@ -116,14 +113,13 @@ obj <- initMSM(
   tv_conf = c("B.1", "B.2", "B.3", "D.3")
 )
 f <- createFormulas(obj, type = "short")
-w <- createWeights(data = data, obj = obj, formulas = f)
+w <- createWeights(data = data, formulas = f)
 fit <- fitModel(
-  data = data, obj = obj, weights = w,
+  data = data, weights = w,
   outcome = "D.3", model = "m0"
 )
 
 comp <- compareHistories(
-  obj,
   fit = fit,
   hi_lo_cut = c(0.3, 0.6)
 )
@@ -133,7 +129,6 @@ summary(comp, "preds")
 summary(comp, "comps")
 
 comp2 <- compareHistories(
-  obj,
   fit = fit,
   reference = "l-l-l",
   comparison = c("h-h-h", "h-h-l")
diff --git a/man/createFormulas.Rd b/man/createFormulas.Rd
index 3b5cf810..a8f8ac3d 100644
--- a/man/createFormulas.Rd
+++ b/man/createFormulas.Rd
@@ -83,8 +83,8 @@ f <- createFormulas(obj, type = "short")
 print(f)
 
 # Update Formulas
-w <- createWeights(data = data, obj = obj, formulas = f)
-b <- assessBalance(data = data, obj = obj, weights = w)
+w <- createWeights(data = data, formulas = f)
+b <- assessBalance(data = data, weights = w)
 f <- createFormulas(obj, type = "update", bal_stats = b)
 print(f)
 
diff --git a/man/createWeights.Rd b/man/createWeights.Rd
index 88a12576..a15a3ead 100644
--- a/man/createWeights.Rd
+++ b/man/createWeights.Rd
@@ -4,13 +4,13 @@
 \alias{createWeights}
 \alias{print.devMSM_weights}
 \alias{plot.devMSM_weights}
+\alias{summary.devMSM_weights}
 \title{Creates IPTW balancing weights}
 \usage{
 createWeights(
   data,
-  obj,
   formulas,
-  method = c("glm", "gbm", "bart", "super", "cbps", "ipt"),
+  method = "glm",
   verbose = FALSE,
   save.out = FALSE,
   ...
@@ -19,13 +19,13 @@ createWeights(
 \method{print}{devMSM_weights}(x, i = 1, ...)
 
 \method{plot}{devMSM_weights}(x, i = 1, save.out = FALSE, ...)
+
+\method{summary}{devMSM_weights}(object, i = 1, ...)
 }
 \arguments{
 \item{data}{data in wide format as: a data frame, list of imputed data
 frames, or \code{mids} object from the \code{mice} package}
 
-\item{obj}{initialized MSM object from \code{\link[=initMSM]{initMSM()}}}
-
 \item{formulas}{list of balancing formulas at each time point output from \code{\link[=createFormulas]{createFormulas()}}}
 
 \item{method}{(optional) character string of weightitMSM() balancing method
@@ -40,12 +40,12 @@ To use a non-default file name, specify a character string with the file name. I
 There might be naming conflicts where two objects get saved to the same file. In these cases, users should specify a custom name.
 default is FALSE.}
 
-\item{...}{ignored}
+\item{\dots}{arguments passed to \code{\link[WeightIt:weightitMSM]{WeightIt::weightitMSM()}} or \code{\link[=summary.weightitMSM]{summary.weightitMSM()}}}
 
-\item{x}{devMSM_weights object from \code{\link[=createWeights]{createWeights()}}}
+\item{x, object}{devMSM_weights object from \code{createWeights()}}
 
-\item{i}{For multiply imputed datset, \code{i} selects which imputation to print results for.
-Default is \code{i = 1}. With \code{i = TRUE}, all imputed datasets will be looped over. With \code{i = NULL}, will average over all imputed datasets and summarize that.}
+\item{i}{For multiply imputed datasets, \code{i} selects which imputation to print results for.
+Default is \code{i = 1}. With \code{i = TRUE}, all imputed datasets will be looped over. With \code{i = NULL}, will average over all imputed datasets and summarize that. Ignored for non-imputed data.}
 }
 \value{
 a list containing \code{\link[WeightIt:weightitMSM]{WeightIt::weightitMSM()}} output. It is the length
@@ -77,25 +77,29 @@ obj <- initMSM(
 )
 f <- createFormulas(obj, type = "short")
 
-w <- createWeights(data = data, obj = obj, formulas = f)
+w <- createWeights(data = data, formulas = f)
 print(w)
 plot(w)
 
 # Methods from `WeightIt::weightitMSM`
-\dontshow{if (requireNamespace("CBPS", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-w <- createWeights(data = data, obj = obj, formulas = f, method = "cbps")
-\dontshow{\}) # examplesIf}
+w <- createWeights(data = data, formulas = f,
+                   method = "glm")
+
+w <- createWeights(data = data, formulas = f,
+                   method = "cbps")
 \dontshow{if (requireNamespace("gbm", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-w <- createWeights(data = data, obj = obj, formulas = f, method = "gbm")
+w <- createWeights(data = data, formulas = f,
+                   method = "gbm")
 \dontshow{\}) # examplesIf}
 \dontshow{if (requireNamespace("dbarts", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-w <- createWeights(data = data, obj = obj, formulas = f, method = "bart")
+w <- createWeights(data = data, formulas = f,
+                   method = "bart")
 \dontshow{\}) # examplesIf}
 \dontshow{if (requireNamespace("SuperLearner", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
-w <- createWeights(data = data, obj = obj, formulas = f, method = "super")
+w <- createWeights(data = data, formulas = f,
+                   method = "super")
 \dontshow{\}) # examplesIf}
 }
 \seealso{
-\code{\link[WeightIt:weightitMSM]{WeightIt::weightitMSM()}},
-\url{https://ngreifer.github.io/WeightIt/reference/weightitMSM.html};
+\code{\link[WeightIt:weightitMSM]{WeightIt::weightitMSM()}}
 }
diff --git a/man/devMSM_common_docs.Rd b/man/devMSM_common_docs.Rd
deleted file mode 100644
index 64ae9a2e..00000000
--- a/man/devMSM_common_docs.Rd
+++ /dev/null
@@ -1,54 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/devMSMs-package.R
-\name{devMSM_common_docs}
-\alias{devMSM_common_docs}
-\title{Common documentation for devMSMs functions}
-\usage{
-devMSM_common_docs(
-  data,
-  obj,
-  formulas,
-  weights,
-  fit,
-  bal_stats,
-  verbose,
-  save.out,
-  home_dir,
-  i,
-  t
-)
-}
-\arguments{
-\item{data}{data in wide format as: a data frame, list of imputed data
-frames, or \code{mids} object from the \code{mice} package}
-
-\item{obj}{initialized MSM object from \code{\link[=initMSM]{initMSM()}}}
-
-\item{formulas}{list of balancing formulas at each time point output from \code{\link[=createFormulas]{createFormulas()}}}
-
-\item{weights}{list of IPTW weights output from \code{\link[=createWeights]{createWeights()}}}
-
-\item{fit}{list of model outputs from \code{\link[=fitModel]{fitModel()}}}
-
-\item{bal_stats}{list of balance statistics from \code{\link[=assessBalance]{assessBalance()}}}
-
-\item{verbose}{(optional) TRUE or FALSE indicator for printing output to console.
-default is FALSE.}
-
-\item{save.out}{(optional) Either logical or a character string. If \code{TRUE},
-it will output the result to a default file name within \code{home_dir} set in \code{initMSM()}. You can load the data with \code{x <- readRDS(file)}.
-To use a non-default file name, specify a character string with the file name. It will save relative to \code{home_dir}.
-There might be naming conflicts where two objects get saved to the same file. In these cases, users should specify a custom name.
-default is FALSE.}
-
-\item{i}{For multiply imputed datset, \code{i} selects which imputation to print results for.
-Default is \code{i = 1}. With \code{i = TRUE}, all imputed datasets will be looped over. With \code{i = NULL}, will average over all imputed datasets and summarize that.}
-
-\item{t}{Which exposure variable to use. Can either be an index from 1, ..., num exposures or
-a string containing the exposure varaible name (e.g. \code{"A.3"}). With \code{t = TRUE}, all exposure
-variables will be looped over.}
-}
-\description{
-Common documentation for devMSMs functions
-}
-\keyword{internal}
diff --git a/man/dot-add_histories.Rd b/man/dot-add_histories.Rd
deleted file mode 100644
index f5b36961..00000000
--- a/man/dot-add_histories.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.add_histories}
-\alias{.add_histories}
-\title{Add history labels and dose to table based on \code{epoch_vars}}
-\usage{
-.add_histories(p, epoch_vars)
-}
-\arguments{
-\item{p}{table output from marginaleffects::avg_predictions() or hypotheses()}
-
-\item{epoch_vars}{variable names of exposure epoch (in time order)}
-}
-\value{
-table with histories labeled
-}
-\description{
-Add history labels and dose to table based on \code{epoch_vars}
-}
-\keyword{internal}
diff --git a/man/dot-avg_imp_bal_stats.Rd b/man/dot-avg_imp_bal_stats.Rd
deleted file mode 100644
index 2e0769c0..00000000
--- a/man/dot-avg_imp_bal_stats.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.avg_imp_bal_stats}
-\alias{.avg_imp_bal_stats}
-\title{Added by IS: averages balance stats across time points and recalculates balance:
-returns one bal stat per covar}
-\usage{
-.avg_imp_bal_stats(bal_stats)
-}
-\description{
-Added by IS: averages balance stats across time points and recalculates balance:
-returns one bal stat per covar
-}
-\keyword{internal}
diff --git a/man/dot-avg_imp_bal_stats_time.Rd b/man/dot-avg_imp_bal_stats_time.Rd
deleted file mode 100644
index 433a93f1..00000000
--- a/man/dot-avg_imp_bal_stats_time.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.avg_imp_bal_stats_time}
-\alias{.avg_imp_bal_stats_time}
-\title{Added by IS: Averages balance stats across imputed datasets: list by time}
-\usage{
-.avg_imp_bal_stats_time(bal_stats)
-}
-\description{
-Added by IS: Averages balance stats across imputed datasets: list by time
-}
-\keyword{internal}
diff --git a/man/dot-characterize_exposure.Rd b/man/dot-characterize_exposure.Rd
deleted file mode 100644
index 58fb4e1e..00000000
--- a/man/dot-characterize_exposure.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.characterize_exposure}
-\alias{.characterize_exposure}
-\title{Used in \code{assessBalance} to define history}
-\usage{
-.characterize_exposure(mat, exposure_type)
-}
-\description{
-Used in \code{assessBalance} to define history
-}
-\keyword{internal}
diff --git a/man/dot-create_hypotheses_mat.Rd b/man/dot-create_hypotheses_mat.Rd
deleted file mode 100644
index e0a6ffa9..00000000
--- a/man/dot-create_hypotheses_mat.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.create_hypotheses_mat}
-\alias{.create_hypotheses_mat}
-\title{Create contrast map using comparison and reference}
-\usage{
-.create_hypotheses_mat(histories, reference, comparison)
-}
-\arguments{
-\item{histories}{character vector (from preds$term corresponding to average predictions)}
-
-\item{reference}{character vector of exposure histories}
-
-\item{comparison}{character vector of exposure histories}
-}
-\description{
-Create contrast map using comparison and reference
-}
-\keyword{internal}
diff --git a/man/dot-dose_from_history.Rd b/man/dot-dose_from_history.Rd
deleted file mode 100644
index be859779..00000000
--- a/man/dot-dose_from_history.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.dose_from_history}
-\alias{.dose_from_history}
-\title{Calculate number of doses from history string (e.g. "l-l-l")}
-\usage{
-.dose_from_history(history, dose_level = "h")
-}
-\description{
-Calculate number of doses from history string (e.g. "l-l-l")
-}
-\examples{
-library(devMSMs)
-devMSMs:::.dose_from_history(c("l-l-l-h", "l-l-l-l"), dose_level = "h")
-devMSMs:::.dose_from_history(c("l-l-l-h", "l-l-l-l"), dose_level = "l")
-
-}
-\keyword{internal}
diff --git a/man/dot-dose_from_history_contrast.Rd b/man/dot-dose_from_history_contrast.Rd
deleted file mode 100644
index f9f5d6b7..00000000
--- a/man/dot-dose_from_history_contrast.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.dose_from_history_contrast}
-\alias{.dose_from_history_contrast}
-\title{Calculate number of doses from history string (e.g. "l-l-l")}
-\usage{
-.dose_from_history_contrast(history, dose_level = "h")
-}
-\description{
-Calculate number of doses from history string (e.g. "l-l-l")
-}
-\examples{
-library(devMSMs)
-devMSMs:::.dose_from_history_contrast(c("(h-h-h) - (l-l-l)"), dose_level = "h")
-devMSMs:::.dose_from_history_contrast(c("(h-h-h) - (l-l-l)"), dose_level = "l")
-
-}
-\keyword{internal}
diff --git a/man/dot-extract_time_pts_from_vars.Rd b/man/dot-extract_time_pts_from_vars.Rd
deleted file mode 100644
index a1ec25f2..00000000
--- a/man/dot-extract_time_pts_from_vars.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.extract_time_pts_from_vars}
-\alias{.extract_time_pts_from_vars}
-\title{Grabs trailing numbers after the last occurance of \code{sep} in \code{vars}}
-\usage{
-.extract_time_pts_from_vars(vars, sep = "[\\\\._]")
-}
-\description{
-Grabs trailing numbers after the last occurance of \code{sep} in \code{vars}
-}
-\keyword{internal}
diff --git a/man/dot-generate_epoch_exposures.Rd b/man/dot-generate_epoch_exposures.Rd
deleted file mode 100644
index 7c6edbd9..00000000
--- a/man/dot-generate_epoch_exposures.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.generate_epoch_exposures}
-\alias{.generate_epoch_exposures}
-\title{Takes row means of eposure variables in the same epoch}
-\usage{
-.generate_epoch_exposures(data, exposure, epoch, sep)
-}
-\description{
-Takes row means of eposure variables in the same epoch
-}
-\keyword{internal}
diff --git a/man/dot-get_avg_predictions_variables.Rd b/man/dot-get_avg_predictions_variables.Rd
deleted file mode 100644
index b7322d4c..00000000
--- a/man/dot-get_avg_predictions_variables.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.get_avg_predictions_variables}
-\alias{.get_avg_predictions_variables}
-\title{Grab values of epoch variables to evaluate in \code{marginaleffects::predictions}}
-\usage{
-.get_avg_predictions_variables(
-  data,
-  epoch_vars,
-  exposure_type,
-  hi_lo_cut = NULL
-)
-}
-\description{
-For continuous variables, grab quantiles of the epoch variables based on hi_lo_cut
-For binary variables, use 0 and 1.
-}
-\keyword{internal}
diff --git a/man/dot-get_epoch_var_names.Rd b/man/dot-get_epoch_var_names.Rd
deleted file mode 100644
index aa4580ce..00000000
--- a/man/dot-get_epoch_var_names.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.get_epoch_var_names}
-\alias{.get_epoch_var_names}
-\title{Simple function to get the variable names associated with epochs}
-\usage{
-.get_epoch_var_names(exposure, epoch, sep)
-}
-\description{
-Simple function to get the variable names associated with epochs
-}
-\keyword{internal}
diff --git a/man/dot-get_history_values.Rd b/man/dot-get_history_values.Rd
deleted file mode 100644
index 0c0f9010..00000000
--- a/man/dot-get_history_values.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.get_history_values}
-\alias{.get_history_values}
-\title{Finds custom reference values (currently unused)}
-\usage{
-.get_history_values(epoch_d, exp_history)
-}
-\arguments{
-\item{epoch_d}{data frame of high and low values per exposure main effect}
-
-\item{exp_history}{sequence of "h" and/or "l" (e.g., "h-h-h")}
-}
-\value{
-exposure history values
-}
-\description{
-Finds custom reference values (currently unused)
-}
-\examples{
-epoch_d <- data.frame(
-  e = c("A.1", "A.2", "A.3"),
-  l = c(0, 0, 0),
-  h = c(1, 1, 1)
-)
-r <- devMSMs:::.get_history_values(
-  epoch_d = epoch_d,
-  exp_history = "l-l-l"
-)
-r <- devMSMs:::.get_history_values(
-  epoch_d = epoch_d,
-  exp_history = "h-h-h"
-)
-
-}
-\keyword{internal}
diff --git a/man/dot-get_interaction_terms.Rd b/man/dot-get_interaction_terms.Rd
deleted file mode 100644
index 6386ad4a..00000000
--- a/man/dot-get_interaction_terms.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.get_interaction_terms}
-\alias{.get_interaction_terms}
-\title{Return interactions up to order n of variables in \code{x}}
-\usage{
-.get_interaction_terms(x, n = 2)
-}
-\arguments{
-\item{x}{character vector of variable names}
-
-\item{n}{order of interaction}
-}
-\description{
-Return interactions up to order n of variables in \code{x}
-}
-\keyword{internal}
diff --git a/man/dot-remove_time_pts_from_vars.Rd b/man/dot-remove_time_pts_from_vars.Rd
deleted file mode 100644
index 237f4a12..00000000
--- a/man/dot-remove_time_pts_from_vars.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.remove_time_pts_from_vars}
-\alias{.remove_time_pts_from_vars}
-\title{Gets prefix of variable by numbers after last occurance of \code{sep} and optionally deleting \code{sep}}
-\usage{
-.remove_time_pts_from_vars(vars, sep = "[\\\\._]", keep_sep = FALSE)
-}
-\description{
-Gets prefix of variable by numbers after last occurance of \code{sep} and optionally deleting \code{sep}
-}
-\keyword{internal}
diff --git a/man/dot-string_count.Rd b/man/dot-string_count.Rd
deleted file mode 100644
index f33ad06f..00000000
--- a/man/dot-string_count.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{.string_count}
-\alias{.string_count}
-\title{Base R rewrite of stringr::str_count(); pattern can only be length 1}
-\usage{
-.string_count(string, pattern = "")
-}
-\description{
-Base R rewrite of stringr::str_count(); pattern can only be length 1
-}
-\keyword{internal}
diff --git a/man/fitModel.Rd b/man/fitModel.Rd
index aa1f9824..c102e193 100644
--- a/man/fitModel.Rd
+++ b/man/fitModel.Rd
@@ -8,18 +8,17 @@
 fitModel(
   data,
   obj,
-  weights,
+  weights = NULL,
   outcome,
-  model = c("m0", "m1", "m2", "m3"),
+  model = "m0",
   int_order = NA,
   covariates = NULL,
-  family = NULL,
-  link = NA,
+  family = gaussian(),
   verbose = FALSE,
   save.out = FALSE
 )
 
-\method{print}{devMSM_models}(x, i = 1, save.out = FALSE, ...)
+\method{print}{devMSM_models}(x, i = NA, save.out = FALSE, ...)
 }
 \arguments{
 \item{data}{data in wide format as: a data frame, list of imputed data
@@ -46,9 +45,7 @@ interaction, required for interaction models ("m2", "m3")}
 \item{covariates}{list of characters reflecting variable names of covariates,
 required for covariate models ("m1", "m3")}
 
-\item{family}{(optional) family function specification for \code{\link[WeightIt:glm_weightit]{WeightIt::glm_weightit()}} model}
-
-\item{link}{(optional) character link function specification for \code{\link[WeightIt:glm_weightit]{WeightIt::glm_weightit()}} model}
+\item{family}{(optional) family function specification for \code{\link[WeightIt:glm_weightit]{WeightIt::glm_weightit()}} model.}
 
 \item{verbose}{(optional) TRUE or FALSE indicator for printing output to console.
 default is FALSE.}
@@ -61,8 +58,8 @@ default is FALSE.}
 
 \item{x}{devMSM_models object from \code{fitModel}}
 
-\item{i}{For multiply imputed datset, \code{i} selects which imputation to print results for.
-Default is \code{i = 1}. With \code{i = TRUE}, all imputed datasets will be looped over. With \code{i = NULL}, will average over all imputed datasets and summarize that.}
+\item{i}{For multiply imputed datasets, \code{i} selects which imputation to print results for.
+Default is \code{i = 1}. With \code{i = TRUE}, all imputed datasets will be looped over. With \code{i = NULL}, will average over all imputed datasets and summarize that. Ignored for non-imputed data.}
 
 \item{...}{ignored}
 }
@@ -95,30 +92,30 @@ obj <- initMSM(
   tv_conf = c("B.1", "B.2", "B.3", "D.3")
 )
 f <- createFormulas(obj, type = "short")
-w <- createWeights(data = data, obj = obj, formulas = f)
+w <- createWeights(data = data, formulas = f)
 
 fit_m0 <- fitModel(
-  data = data, obj = obj, weights = w, 
+  data = data, weights = w, 
   outcome = "D.3", model = "m0"
 )
 print(fit_m0)
 
 fit_m1 <- fitModel(
-  data = data, obj = obj, weights = w, 
+  data = data, weights = w, 
   outcome = "D.3", model = "m1", 
   covariates = c("C")
 )
 print(fit_m1)
 
 fit_m2 <- fitModel(
-  data = data, obj = obj, weights = w, 
+  data = data, weights = w, 
   outcome = "D.3", model = "m2", 
   int_order = 2
 )
 print(fit_m2)
 
 fit_m3 <- fitModel(
-  data = data, obj = obj, weights = w, 
+  data = data, weights = w, 
   outcome = "D.3", model = "m3",
   int_order = 2, covariates = c("C")
 )
diff --git a/man/make_love_plot.Rd b/man/make_love_plot.Rd
deleted file mode 100644
index e9f51b12..00000000
--- a/man/make_love_plot.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/make_love_plot.R
-\name{make_love_plot}
-\alias{make_love_plot}
-\title{Create love plots showing balancing statistics}
-\usage{
-make_love_plot(
-  obj,
-  balance_stats,
-  exposure_type = c("continuous", "binary"),
-  k = 0,
-  weight_method = NULL
-)
-}
-\arguments{
-\item{balance_stats}{data frame of balance statistics}
-
-\item{exposure_type}{String either "continuous" or "binary"}
-
-\item{k}{imputation number}
-
-\item{weight_method}{name of weighting method (NULL for unweighted)}
-}
-\value{
-ggplot2 object
-}
-\description{
-Create love plots showing balancing statistics
-}
-\examples{
-print("tbd")
-
-}
-\keyword{internal}
diff --git a/man/perm2.Rd b/man/perm2.Rd
deleted file mode 100644
index f4e5deec..00000000
--- a/man/perm2.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{perm2}
-\alias{perm2}
-\title{Adaptation of gtools::permutations(2, repeats.allowed = TRUE)}
-\usage{
-perm2(r, v)
-}
-\description{
-Adaptation of gtools::permutations(2, repeats.allowed = TRUE)
-}
-\keyword{internal}
diff --git a/man/print_eval_hist.Rd b/man/print_eval_hist.Rd
deleted file mode 100644
index 0b6d3cc5..00000000
--- a/man/print_eval_hist.Rd
+++ /dev/null
@@ -1,40 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/print_eval_hist.R
-\name{print_eval_hist}
-\alias{print_eval_hist}
-\title{Visualize distribution of sample across exposure histories}
-\usage{
-print_eval_hist(
-  epoch_history,
-  epoch,
-  hi_lo_cut,
-  reference = NULL,
-  comparison = NULL
-)
-}
-\arguments{
-\item{epoch_history}{character vector of length \code{nrow(data)} containing epochi histories for
-each unit}
-
-\item{epoch}{character vector of epoch values}
-
-\item{hi_lo_cut}{list of two numbers indicating quantile values
-that reflect high and low values, respectively, for continuous exposure
-(default is median split)}
-
-\item{reference}{lists of one or more strings of "-"-separated "l"
-and "h" values indicative of a reference exposure history to which to
-compare comparison, required if comparison is supplied}
-
-\item{comparison}{(optional) list of one or more strings of "-"-separated "l"
-and "h" values indicative of comparison history/histories to compare to
-reference, required if reference is supplied}
-}
-\value{
-invisibly NULL
-}
-\description{
-Create customized, user-specified exposure histories and tables displaying
-sample distribution across them for user inspection.
-}
-\keyword{internal}
diff --git a/man/trimWeights.Rd b/man/trimWeights.Rd
index 0079b7f9..9a7241ef 100644
--- a/man/trimWeights.Rd
+++ b/man/trimWeights.Rd
@@ -4,18 +4,9 @@
 \alias{trimWeights}
 \title{Trim IPTW balancing weights, if needed}
 \usage{
-trimWeights(
-  obj,
-  weights,
-  at = 0,
-  lower = FALSE,
-  verbose = FALSE,
-  save.out = FALSE
-)
+trimWeights(weights, at = 0, lower = FALSE, verbose = FALSE, save.out = FALSE)
 }
 \arguments{
-\item{obj}{initialized MSM object from \code{\link[=initMSM]{initMSM()}}}
-
 \item{weights}{list of IPTW weights output from \code{\link[=createWeights]{createWeights()}}}
 
 \item{at}{\code{numeric}; either the quantile of the weights above which
@@ -65,12 +56,12 @@ obj <- initMSM(
 )
 f <- createFormulas(obj, type = "short")
 
-w <- createWeights(data = data, obj = obj, formulas = f)
-tw <- trimWeights(obj, w)
+w <- createWeights(data = data, formulas = f)
+tw <- trimWeights(w, at = 0.975)
 print(tw)
 plot(tw)
 
-trimWeights(obj, w, at = 0.975, lower = TRUE)
+trimWeights(w, at = 0.975, lower = TRUE)
 
 }
 \seealso{