Merge branch 'release/v0.0.1'

.Rbuildignore

@@ -1,2 +1,9 @@
 ^multinma\.Rproj$
 ^\.Rproj\.user$
+^inst/.*\.bib\.bak$
+^inst/.*\.bib\.sav$
+^README\.Rmd$
+^data-raw/.*$
+^man-roxygen/.*$
+^data-raw$
+^\.travis\.yml$

.gitignore

@@ -1,3 +1,19 @@
 .Rproj.user
 .Rhistory
 .RData
+src/*.o
+src/*.cc
+src/*.cpp
+src/*.hpp
+src/*.h
+src/multinma.so
+src/multinma.dll
+src/init.o
+man/*.Rd
+vignettes/*.R
+!vignettes/*.Rmd
+vignettes/*.html
+vignettes/*_files
+inst/*.bib.bak
+inst/*.bib.sav
+inst/doc

DESCRIPTION

@@ -1,28 +1,60 @@
 Package: multinma
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
+Title: Network Meta-Analysis of Individual and Aggregate Data in Stan
+Version: 0.0.1
 Authors@R: 
-    person(given = "First",
-           family = "Last",
+    person(given = "David",
+           family = "Phillippo",
            role = c("aut", "cre"),
-           email = "first.last@example.com",
-           comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
-License: What license it uses
+           email = "david.phillippo@bristol.ac.uk",
+           comment = c(ORCID = "0000-0003-2672-7841"))
+Description: Network meta-analysis (NMA) and network meta-regression (NMR) models for 
+    aggregate data (AgD), individual patient data (IPD), and mixtures of both IPD and AgD
+    using multilevel NMR (ML-NMR). Models are estimated in a Bayesian framework using 
+    Stan.
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Biarch: true
 Depends: 
     R (>= 3.4.0)
 Imports: 
     methods,
+    stats,
+    graphics,
     Rcpp (>= 0.12.0),
     rstan (>= 2.18.1),
-    rstantools (>= 2.0.0.9000)
+    rstantools (>= 2.0.0),
+    loo (>= 2.0.0),
+    Rdpack (>= 0.7),
+    tibble,
+    dplyr (>= 0.8.1),
+    rlang,
+    purrr,
+    forcats,
+    glue,
+    crayon,
+    randtoolbox,
+    copula,
+    tidyr (>= 0.8.3),
+    stringr,
+    logitnorm,
+    Matrix
 LinkingTo: 
     BH (>= 1.66.0),
     Rcpp (>= 0.12.0),
     RcppEigen (>= 0.3.3.3.0),
     rstan (>= 2.18.1),
     StanHeaders (>= 2.18.0)
 SystemRequirements: GNU make
+RoxygenNote: 6.1.1
+Roxygen: list(markdown = TRUE)
+Suggests: 
+    testthat (>= 2.1.0),
+    knitr,
+    rmarkdown,
+    parallel,
+    bayesplot
+RdMacros: Rdpack
+URL: http://github.com/dmphillippo/multinma
+BugReports: http://github.com/dmphillippo/multinma/issues
+VignetteBuilder: knitr

NAMESPACE

@@ -1,6 +1,67 @@
-# Generated by roxygen2: fake comment so roxygen2 overwrites silently.
-exportPattern("^[^\\.]")
+# Generated by roxygen2: do not edit by hand
+
+S3method(as.array,stan_nma)
+S3method(as.data.frame,stan_nma)
+S3method(as.matrix,stan_nma)
+S3method(as.stanfit,default)
+S3method(as.stanfit,stan_nma)
+S3method(loo,stan_nma)
+S3method(pairs,stan_nma)
+S3method(print,mlnmr_data)
+S3method(print,nma_data)
+S3method(print,nma_dic)
+S3method(print,nma_prior)
+S3method(print,stan_nma)
+S3method(waic,stan_nma)
+export(RE_cor)
+export(add_integration)
+export(as.stanfit)
+export(cauchy)
+export(combine_network)
+export(dbern)
+export(dgamma)
+export(dic)
+export(distr)
+export(dlogitnorm)
+export(exponential)
+export(half_cauchy)
+export(half_normal)
+export(half_student_t)
+export(nma)
+export(nma.fit)
+export(normal)
+export(pbern)
+export(pgamma)
+export(plogitnorm)
+export(qbern)
+export(qgamma)
+export(qlogitnorm)
+export(set_agd_arm)
+export(set_agd_contrast)
+export(set_ipd)
+export(student_t)
+export(which_RE)
 import(Rcpp)
 import(methods)
-importFrom(rstan, sampling)
+importFrom(Rdpack,reprompt)
+importFrom(dplyr,"%>%")
+importFrom(graphics,pairs)
+importFrom(loo,loo)
+importFrom(loo,waic)
+importFrom(rlang,.data)
+importFrom(rlang,abort)
+importFrom(rlang,enquo)
+importFrom(rlang,inform)
+importFrom(rlang,warn)
+importFrom(rstan,sampling)
+importFrom(stats,complete.cases)
+importFrom(stats,dbinom)
+importFrom(stats,median)
+importFrom(stats,model.frame)
+importFrom(stats,model.matrix)
+importFrom(stats,optim)
+importFrom(stats,pbinom)
+importFrom(stats,qbinom)
+importFrom(stats,update.formula)
+importFrom(stats,weighted.mean)
 useDynLib(multinma, .registration = TRUE)

NEWS.md

@@ -0,0 +1,3 @@
+# multinma 0.0.1
+
+* Initial release.

R/data.R

@@ -0,0 +1,98 @@
+#' Smoking cessation data
+#'
+#' Data frame containing the results of 24 trials of 4 smoking cessation
+#' treatments \insertCite{Hasselblad1998,TSD4}{multinma}.
+#'
+#' @format A data frame with 50 rows and 5 variables:
+#' \describe{
+#'   \item{studyn}{numeric study ID}
+#'   \item{trtn}{numeric treatment code}
+#'   \item{trtc}{treatment name}
+#'   \item{r}{total number of events}
+#'   \item{n}{total number of individuals}
+#' }
+#'
+#' @references
+#'   \insertAllCited{}
+#'
+
+"smoking"
+
+#' Plaque psoriasis data
+#'
+#' Two data frames, `psoriasis_ipd` and `psoriasis_agd`, containing (simulated)
+#' individual patient data from three studies (UNCOVER-1, -2, and -3)
+#' \insertCite{Griffiths2015,Gordon2016}{multinma} and aggregate data from one
+#' study (FIXTURE) \insertCite{Langley2014}{multinma}, respectively. Outcomes
+#' are binary success/failure to achieve 75\% reduction in symptoms on the
+#' Psoriasis Area and Severity Index (PASI) scale.
+#'
+#' @format The individual patient data are contained in a data frame
+#'   `psoriasis_ipd` with 3858 rows, one per individual, and 11 variables:
+#'   \describe{
+#'     \item{studyc}{study name}
+#'     \item{studyn}{numeric study ID}
+#'     \item{trtc_long}{treatment name (long format)}
+#'     \item{trtc}{treatment name}
+#'     \item{trtn}{numeric treatment code}
+#'     \item{bsa}{body surface area (percent)}
+#'     \item{weight}{weight (kilograms)}
+#'     \item{durnpso}{duration of psoriasis (years)}
+#'     \item{prevsys}{previous systemic treatmet (yes = 1, no = 0)}
+#'     \item{psa}{psoriatic arthritis (yes = 1, no = 0)}
+#'     \item{pasi75}{binary PASI 75 outcome (success = 1, failure = 0)}
+#'   }
+#'
+#'  The aggregate data are contained in a data frame `psoriasis_agd` with 4
+#'  rows, one per study arm, and 16 variables:
+#'   \describe{
+#'     \item{studyc}{study name}
+#'     \item{studyn}{numeric study ID}
+#'     \item{trtc_long}{treatment name (long format)}
+#'     \item{trtc}{treatment name}
+#'     \item{trtn}{numeric treatment code}
+#'     \item{sample_size_w0}{sample size at week zero}
+#'     \item{bsa_mean}{mean body surface area (percent)}
+#'     \item{bsa_sd}{standard deviation of body surface area (percent)}
+#'     \item{weight_mean}{mean weight (kilograms)}
+#'     \item{weight_sd}{standard deviation of weight (kilograms)}
+#'     \item{durnpso_mean}{mean duration of psoriasis (years)}
+#'     \item{durnpso_sd}{standard deviation of duration of psoriasis (years)}
+#'     \item{prevsys}{percentage of individuals with previous systemic treatment}
+#'     \item{psa}{percentage of individuals with psoriatic arthritis}
+#'     \item{pasi75_n}{PASI 75 outcome denominator}
+#'     \item{pasi75_r}{PASI 75 outcome numerator}
+#'   }
+#'
+#' @references \insertAllCited{}
+#'
+#' @rdname psoriasis
+#' @aliases psoriasis psoriasis_agd
+#'
+
+"psoriasis_ipd"
+
+#' Thrombolytic treatments data
+#'
+#' Data frame containing the results of 50 trials of 8 thrombolytic drugs
+#' (streptokinase, SK; alteplase, t-PA; accelerated alteplase, Acc t-PA;
+#' streptokinase plus alteplase, SK+tPA; reteplase, r-PA; tenocteplase, TNK;
+#' urokinase, UK; anistreptilase, ASPAC) plus per-cutaneous transluminal
+#' coronary angioplasty (PTCA)
+#' \insertCite{Boland2003,Lu2006,TSD4}{multinma}. The number of
+#' deaths in 30 or 35 days following accute myocardial infarction are recorded.
+#'
+#' @format A data frame with 50 rows and 5 variables:
+#' \describe{
+#'   \item{studyn}{numeric study ID}
+#'   \item{trtn}{numeric treatment code}
+#'   \item{trtc}{treatment name}
+#'   \item{r}{total number of events}
+#'   \item{n}{total number of individuals}
+#' }
+#'
+#' @references
+#'   \insertAllCited{}
+#'
+
+"thrombolytics"