R/datasets.R

In MBNMAdose: Dose-Response MBNMA Models

#' Studies of triptans for headache pain relief
#'
#' A dataset from a systematic review of interventions for pain relief in migraine \insertCite{thorlund2014}{MBNMAdose}.
#' The outcome is binary, and represents (as aggregate data) the proportion of participants who were
#' headache-free at 2 hours. Data are from patients who had had at least one migraine attack, who were
#' not lost to follow-up, and who did not violate the trial protocol. The dataset includes 70 Randomised-Controlled
#' Trials (RCTs), comparing 7 triptans with placebo. Doses are standardised as relative to a "common" dose,
#' and in total there are 23 different treatments (combination of dose and agent).
#'
#' @format A data frame in long format (one row per arm and study), with with 181 rows and 6 variables:
#' * `studyID` Study identifiers
#' * `AuthorYear` The author and year published of the study
#' * `n` Numeric data indicating the number of participants in a study arm
#' * `r` Numeric data indicating the number of responders (headache free at 2 hours) in a study arm
#' * `dose` Numeric data indicating the standardised dose received
#' * `agent` Factor data indicating the agent to which participants were randomised
#'
#' @source
#' \insertAllCited{}
"triptans"




#' Studies of treatments for Serum Uric Acid reduction in patients with gout
#'
#' A dataset from a systematic review of interventions for lowering Serum Uric Acid (SUA) concentration in
#' patients with gout **(not published previously)**. The outcome is continuous, and aggregate data responses
#' correspond to the mean change from baseline in SUA in mg/dL at 2 weeks follow-up. The dataset includes 10
#' Randomised-Controlled Trials (RCTs), comparing 5 different agents, and placebo. Data for one agent (RDEA)
#' arises from an RCT that is not placebo-controlled, and so is not connected to the network directly. In total
#' there were 19 different treatments (combination of dose and agent).
#'
#' @format A data frame in long format (one row per arm and study), with 27 rows and 5 variables:
#' * `studyID` Study identifiers
#' * `y` Numeric data indicating the mean change from baseline in SUA in a study arm
#' * `se` Numeric data indicating the standard error for the mean change from baseline in SUA in a study arm
#' * `agent` Character data indicating the agent to which participants were randomised
#' * `dose` Numeric data indicating the standardised dose received
#'
#' @source Pfizer Ltd.
"gout"




#' Studies of treatments for pain relief in patients with osteoarthritis
#'
#' A dataset from a systematic review of interventions for pain relief in osteoarthritis, used previously
#' in \insertCite{pedder2019;textual}{MBNMAdose}. The outcome is continuous, and aggregate data responses correspond to
#' the mean WOMAC pain score at 2 weeks follow-up. The dataset includes 18 Randomised-Controlled Trials (RCTs),
#' comparing 8 different agents with placebo. In total there were 26 different treatments (combination of dose and
#' agent). The active treatments can also be grouped into 3 different classes, within which they have similar
#' mechanisms of action.
#'
#'
#' @format A data frame in long format (one row per arm and study), with 74 rows and 7 variables:
#' * `studyID` Study identifiers
#' * `agent` Character data indicating the agent to which participants were randomised
#' * `dose` Numeric data indicating the standardised dose received
#' * `class` Character data indicating the drug class to which the agent belongs to
#' * `y` Numeric data indicating the mean pain score on the WOMAC scale in a study arm
#' * `se` Numeric data indicating the standard error for the mean pain score on the WOMAC scale in a study arm
#' * `n` Numeric data indicating the number of participants randomised
#'
#' @references
#' \insertAllCited{}
#'
#' @source Pfizer Ltd.
"osteopain"






#' Studies of alogliptin for lowering blood glucose concentration in patients with type II diabetes
#'
#' A dataset from a systematic review of Randomised-Controlled Trials (RCTs) comparing different doses of
#' alogliptin with placebo \insertCite{langford2016}{MBNMAdose}. The systematic review was simply performed and was intended to
#' provide data to illustrate a statistical methodology rather than for clinical inference. Alogliptin is
#' a treatment aimed at reducing blood glucose concentration in type II diabetes. The outcome is continuous,
#' and aggregate data responses correspond to the mean change in HbA1c from baseline to follow-up in studies
#' of at least 12 weeks follow-up. The dataset includes 14 Randomised-Controlled Trials (RCTs), comparing 5
#' different doses of alogliptin with placebo, leading to 6 different treatments (combination of dose and agent)
#' within the network.
#'
#' `alog_pcfb` is a data frame in long format (one row per arm and study), with the variables `studyID`, `agent`, `dose`, `y`, `se`, and `N`.
#'
#' @format A data frame in long format (one row per arm and study), with 46 rows and 6 variables:
#' * `studyID` Study identifiers
#' * `agent` Character data indicating the agent to which participants were randomised
#' * `dose` Numeric data indicating the standardised dose received
#' * `y` Numeric data indicating the mean change from baseline in blood glucose concentration (mg/dL) in a study arm
#' * `se` Numeric data indicating the standard error for the mean change from baseline in blood glucose concentration (mg/dL) in a study arm
#' * `n` Numeric data indicating the number of participants randomised
#'
#' @references
#' \insertAllCited{}
#'
"alog_pcfb"







#' Studies of biologics for treatment of moderate-to-severe psoriasis (>=75% improvement)
#'
#' A dataset from a systematic review of Randomised-Controlled Trials (RCTs) comparing biologics at different doses and placebo
#' \insertCite{warren2019}{MBNMAdose}. The outcome is the number of patients experiencing >=75% improvement on the Psoriasis
#' Area and Severity Index (PASI) measured at 12 weeks follow-up. The dataset
#' includes 28 Randomised-Controlled Trials (RCTs), comparing 9 different biologics at different doses with placebo.
#'
#' @format A data frame in long format (one row per arm and study), with 81 rows and 9 variables:
#' * `studyID` Study identifiers
#' * `agent` Character data indicating the agent to which participants were randomised
#' * `dose_mg` Numeric data indicating the dose to which participants were randomised in mg
#' * `freq` Character data indicating the frequency of the dose to which participants were randomised
#' * `dose` Numeric data indicating the dose in mg/week to which the participants were randomised
#' * `n` Numeric data indicating the number of participants randomised
#' * `r` Numeric data indicating the number of participants who achieved >=75% improvement in PASI score after 12 weeks
#'
#' @references
#' \insertAllCited{}
#'
"psoriasis75"





#' Studies of biologics for treatment of moderate-to-severe psoriasis (>=90% improvement)
#'
#' A dataset from a systematic review of Randomised-Controlled Trials (RCTs) comparing biologics at different doses and placebo
#' \insertCite{warren2019}{MBNMAdose}. The outcome is the number of patients experiencing >=90% improvement on the Psoriasis
#' Area and Severity Index (PASI) measured at 12 weeks follow-up. The dataset
#' includes 24 Randomised-Controlled Trials (RCTs), comparing 9 different biologics at different doses with placebo.
#'
#' @format A data frame in long format (one row per arm and study), with 81 rows and 9 variables:
#' * `studyID` Study identifiers
#' * `agent` Character data indicating the agent to which participants were randomised
#' * `dose_mg` Numeric data indicating the dose to which participants were randomised in mg
#' * `freq` Character data indicating the frequency of the dose to which participants were randomised
#' * `dose` Numeric data indicating the dose in mg/week to which the participants were randomised
#' * `n` Numeric data indicating the number of participants randomised
#' * `r` Numeric data indicating the number of participants who achieved >=90% improvement in PASI score after 12 weeks
#'
#' @references
#' \insertAllCited{}
#'
"psoriasis90"





#' Studies of biologics for treatment of moderate-to-severe psoriasis (100% improvement)
#'
#' A dataset from a systematic review of Randomised-Controlled Trials (RCTs) comparing biologics at different doses and placebo
#' \insertCite{warren2019}{MBNMAdose}. The outcome is the number of patients experiencing 100% improvement on the Psoriasis
#' Area and Severity Index (PASI) measured at 12 weeks follow-up. The dataset
#' includes 19 Randomised-Controlled Trials (RCTs), comparing 8 different biologics at different doses with placebo.
#'
#' @format A data frame in long format (one row per arm and study), with 81 rows and 9 variables:
#' * `studyID` Study identifiers
#' * `agent` Character data indicating the agent to which participants were randomised
#' * `dose_mg` Numeric data indicating the dose to which participants were randomised in mg
#' * `freq` Character data indicating the frequency of the dose to which participants were randomised
#' * `dose` Numeric data indicating the dose in mg/week to which the participants were randomised
#' * `n` Numeric data indicating the number of participants randomised
#' * `r` Numeric data indicating the number of participants who achieved 100% improvement in PASI score after 12 weeks
#'
#' @references
#' \insertAllCited{}
#'
"psoriasis100"






#' Studies of Selective Serotonin Reuptake Inhibitors (SSRIs) for major depression
#'
#' A dataset from a systematic review examining the efficacy of different doses of SSRI antidepressant drugs and placebo
#' \insertCite{furukawa2019}{MBNMAdose}. The response to treatment is defined as a 50% reduction in depressive symptoms after 8 weeks
#' (4-12 week range) follow-up. The dataset includes 60 RCTs comparing 5 different SSRIs with placebo.
#'
#' @format A data frame in long format (one row per arm and study), with 145 rows and 8 variables:
#' * `studyID` Study identifiers
#' * `bias` Risk of bias evaluated on 6 domains
#' * `age` Mean participant age
#' * `weeks` Duration of study follow-up
#' * `agent` Character data indicating the agent to which participants were randomised
#' * `dose` Numeric data indicating the dose to which participants were randomised in mg
#' * `n` Numeric data indicating the number of participants randomised
#' * `r` Numeric data indicating the number of participants who achieved >50% improvement in depression symptoms
#'
#' @references
#' \insertAllCited{}
#'
"ssri"





#' Studies of wound closure methods to reduce Surgical Site Infections (SSI)
#'
#' A dataset from an ongoing systematic review examining the efficacy of different wound closure methods to reduce surgical
#' site infections (SSI). The outcome is binary and represents the number of patients who experienced a SSI. The dataset
#' includes 129 RCTs comparing 16 different interventions in 6 classes. This dataset is primarily used to illustrate
#' how `MBNMAdose` can be used to perform different types of network meta-analysis without dose-response information.
#'
#' @format A data frame in long format (one row per arm and study), with 281 rows and 6 variables:
#' * `studyID` Study identifiers
#' * `Year` Year of publication
#' * `n` Numeric data indicating the number of participants randomised
#' * `r` Numeric data indicating the number of participants who achieved >50% improvement in depression symptoms
#' * `trt` Treatment names, given as character data
#' * `class` Class names, given as character data
#'
"ssi_closure"