R/datasets.R
In SamCH93/ReplicationSuccess: Design and Analysis of Replication Studies
#' Data from the Social Sciences Replication Project
#'
#' @description Data from the \emph{Social Sciences Replication Project} (SSRP)
#' including the details of the interim analysis. The variables are as follows:
#' \describe{
#' \item{\code{study}}{Study identifier, usually names of authors
#' from original study}
#' \item{\code{ro}}{Effect estimate of original study on correlation scale}
#' \item{\code{ri}}{Effect estimate of replication study at the interim analysis
#' on correlation scale}
#' \item{\code{rr}}{Effect estimate of replication study at the final analysis
#' on correlation scale}
#' \item{\code{fiso}}{Effect estimate of original study transformed to
#' Fisher-z scale}
#' \item{\code{fisi}}{Effect estimate of replication study at
#' the interim analysis transformed to Fisher-z scale}
#' \item{\code{fisr}}{Effect estimate of replication study at the final analysis
#' transformed to Fisher-z scale}
#' \item{\code{se_fiso}}{Standard error of Fisher-z transformed effect estimate
#' of original study}
#' \item{\code{se_fisi}}{Standard error of Fisher-z transformed effect estimate
#' of replication study at the interim analysis}
#' \item{\code{se_fisr}}{Standard error of Fisher-z transformed effect estimate
#' of replication study at the final analysis}
#' \item{\code{no}}{ Sample size in original study}
#' \item{\code{ni}}{Sample size in replication study at the interim analysis}
#' \item{\code{nr}}{Sample size in replication study at the final analysis}
#' \item{\code{po}}{Two-sided p-value from significance test of effect estimate
#' from original study}
#' \item{\code{pi}}{Two-sided p-value from significance test of effect
#' estimate from replication study at the interim analysis}
#' \item{\code{pr}}{Two-sided p-value from significance test of effect estimate
#' from replication study at the final analysis}
#' \item{\code{n75}}{Sample size calculated to have 90\% power in replication study
#' to detect 75\% of the original effect size (expressed as the correlation
#' coefficient r)}
#' \item{\code{n50}}{Sample size calculated to have 90\% power in replication
#' study to detect 50\% of the original effect size (expressed as the correlation
#' coefficient r)}
#' }
#'
#' @details Two-sided p-values were calculated assuming normality of Fisher-z
#' transformed effect estimates.A two-stage procedure was used for the
#' replications. In stage 1, the authors had 90\% power to detect 75\% of
#' the original effect size at the 5\% significance level in a two-sided
#' test. If the original result replicated in stage 1 (two-sided P-value <
#' 0.05 and effect in the same direction as in the original study), the data
#' collection was stopped. If not, a second data collection was carried out
#' in stage 2 to have 90\% power to detect 50\% of the original effect size
#' for the first and the second data collections pooled. \code{n75} and
#' \code{n50} are the planned sample sizes calculated to reach 90\% power in
#' stage 1 and 2, respectively. They sometimes differ from the sample sizes
#' that were actually collected (\code{ni} and \code{nr}, respectively). See
#' supplementary information of Camerer et al. (2018) for details.
#' @name SSRP
#' @docType data
#' @usage data(SSRP)
#' @format A data frame with 21 rows and 18 variables
#' @source \url{https://osf.io/abu7k}
#' @references Camerer, C. F., Dreber, A., Holzmeister, F., Ho, T.-H., Huber,
#' J., Johannesson, M., ... Wu, H. (2018). Evaluating the replicability of
#' social science experiments in Nature and Science between 2010 and 2015.
#' \emph{Nature Human Behaviour}, \bold{2}, 637-644.
#' \doi{10.1038/s41562-018-0399-z}
#' @seealso \code{\link{RProjects}}
#' @examples
#' # plot of the sample sizes
#' plot(ni ~ no, data = SSRP, ylim = c(0, 2500), xlim = c(0, 400),
#' xlab = expression(n[o]), ylab = expression(n[i]))
#' abline(a = 0, b = 1, col = "grey")
#'
#'
#' plot(nr ~ no, data = SSRP, ylim = c(0, 2500), xlim = c(0, 400),
#' xlab = expression(n[o]), ylab = expression(n[r]))
#' abline(a = 0, b = 1, col = "grey")
#'
#'
#' @keywords data
"SSRP"
#' Data from four large-scale replication projects
#'
#' @description Data from \emph{Reproduciblity Project Psychology} (RPP),
#' \emph{Experimental Economics Replication Project} (EERP), \emph{Social
#' Sciences Replication Project} (SSRP), \emph{Experimental Philosophy
#' Replicability Project} (EPRP). The variables are as follows:
#' \describe{
#' \item{\code{study}}{Study identifier, usually names of authors
#' from original study}
#' \item{\code{project}}{Name of replication project}
#' \item{\code{ro}}{Effect estimate of original study on correlation scale}
#' \item{\code{rr}}{Effect estimate of replication study on correlation scale}
#' \item{\code{fiso}}{Effect estimate of original study transformed to
#' Fisher-z scale}
#' \item{\code{fisr}}{Effect estimate of replication study transformed
#' to Fisher-z scale}
#' \item{\code{se_fiso}}{Standard error of Fisher-z transformed effect estimate
#' of original study}
#' \item{\code{se_fisr}}{Standard error of Fisher-z transformed effect estimate
#' of replication study}
#' \item{\code{po}}{Two-sided p-value from significance test of effect estimate
#' from original study}
#' \item{\code{pr}}{Two-sided p-value from significance test of effect estimate
#' from replication study}
#' \item{\code{po1}}{One-sided p-value from significance test of effect estimate
#' from original study (in the direction of the original effect estimate)}
#' \item{\code{pr1}}{One-sided p-value from significance test of effect estimate
#' from replication study (in the direction of the original effect estimate)}
#' \item{\code{pm_belief}}{Peer belief about whether replication effect estimate
#' will achieve statistical significance elicited through prediction market (only
#' available for EERP and SSRP)}
#' \item{\code{no}}{Sample size in original study}
#' \item{\code{nr}}{Sample size in replication study}
#' }
#'
#' @details Two-sided p-values were calculated assuming normality of Fisher-z
#' transformed effect estimates. From the RPP only the \emph{meta-analytic
#' subset} is included, which consists of 73 out of 100 study pairs for
#' which the standard error of the z-transformed correlation coefficient can
#' be computed. For the RPP sample sizes were recalculated from the reported
#' standard errors of Fisher z-transformed correlation coefficients. From
#' the EPRP only 31 out of 40 study pairs are included where effective
#' sample size for original and replication study are available
#' simultaneously. For more details about how the the data was preprocessed
#' see source below and supplement S1 of Pawel and Held (2020).
#' @name RProjects
#' @docType data
#' @usage data(RProjects)
#' @format A data frame with 143 rows and 15 variables
#' @source RPP: The source files were downloaded from
#' \url{https://github.com/CenterForOpenScience/rpp/}. The "masterscript.R"
#' file was executed and the relevant variables were extracted from the
#' generated "final" object (standard errors of Fisher-z transformed
#' correlations) and "MASTER" object (everything else). The data set is
#' licensed under a CC0 1.0 Universal license, see
#' \url{https://creativecommons.org/publicdomain/zero/1.0/} for the terms of
#' reuse.
#'
#' EERP: The source files were downloaded from \url{https://osf.io/pnwuz/}. The
#' required data were then manually extracted from the code in the files
#' "effectdata.py" (sample sizes) and "create_studydetails.do" (everything
#' else). Data regarding the prediction market and survey beliefs were manually
#' extracted from table S3 of the supplementary materials of the EERP. The
#' authors of this R package have been granted permission to share this data set
#' by the coordinators of the EERP.
#'
#' SSRP: The relevant variables were extracted from the file
#' "D3 - ReplicationResults.csv" downloaded from \url{https://osf.io/abu7k}. For
#' replications which underwent only the first stage, the data from the first
#' stage were taken as the data for the replication study. For the replications
#' which reached the second stage, the pooled data from both stages were taken
#' as the data for the replication study. Data regarding survey and prediction
#' market beliefs were extracted from the "D6 - MeanPeerBeliefs.csv" file, which
#' was downloaded from \url{https://osf.io/vr6p8/}. The data set is licensed
#' under a CC0 1.0 Universal license, see
#' \url{https://creativecommons.org/publicdomain/zero/1.0/} for the terms of
#' reuse.
#'
#' EPRP: Data were taken from the "XPhiReplicability_CompleteData.csv" file,
#' which was downloaded from \url{https://osf.io/4ewkh/}. The authors of this R
#' package have been granted permission to share this data set by the
#' coordinators of the EPRP.
#'
#' @references Camerer, C. F., Dreber, A., Forsell, E., Ho, T.-H., Huber, J.,
#' Johannesson, M., ... Hang, W. (2016). Evaluating replicability of
#' laboratory experiments in economics. \emph{Science}, \bold{351}, 1433-1436.
#' \doi{10.1126/science.aaf0918}
#'
#' Camerer, C. F., Dreber, A., Holzmeister, F., Ho, T.-H., Huber, J.,
#' Johannesson, M., ... Wu, H. (2018). Evaluating the replicability of
#' social science experiments in Nature and Science between 2010 and 2015.
#' \emph{Nature Human Behaviour}, \bold{2}, 637-644.
#' \doi{10.1038/s41562-018-0399-z}
#'
#' Cova, F., Strickland, B., Abatista, A., Allard, A., Andow, J., Attie, M., ...
#' Zhou, X. (2018). Estimating the reproducibility of experimental philosophy.
#' \emph{Review of Philosophy and Psychology}. \doi{10.1007/s13164-018-0400-9}
#'
#' Open Science Collaboration. (2015). Estimating the reproducibility of
#' psychological science. \emph{Science}, \bold{349}, aac4716.
#' \doi{10.1126/science.aac4716}
#'
#' Pawel, S., Held, L. (2020). Probabilistic forecasting of replication studies.
#' \emph{PLOS ONE}. \bold{15}, e0231416. \doi{10.1371/journal.pone.0231416}
#'
#' @seealso \code{\link{SSRP}}
#' @examples
#' data("RProjects", package = "ReplicationSuccess")
#'
#' ## Computing key quantities
#' RProjects$zo <- RProjects$fiso/RProjects$se_fiso
#' RProjects$zr <- RProjects$fisr/RProjects$se_fisr
#' RProjects$c <- RProjects$se_fiso^2/RProjects$se_fisr^2
#'
#' ## Computing one-sided p-values for alternative = "greater"
#' RProjects$po1 <- z2p(z = RProjects$zo, alternative = "greater")
#' RProjects$pr1 <- z2p(z = RProjects$zr, alternative = "greater")
#'
#' ## Plots of effect estimates
#' parOld <- par(mfrow = c(2, 2))
#' for (p in unique(RProjects$project)) {
#' data_project <- subset(RProjects, project == p)
#' plot(rr ~ ro, data = data_project, ylim = c(-0.5, 1),
#' xlim = c(-0.5, 1), main = p, xlab = expression(italic(r)[o]),
#' ylab = expression(italic(r)[r]))
#' abline(h = 0, lty = 2)
#' abline(a = 0, b = 1, col = "grey")
#' }
#' par(parOld)
#'
#' ## Plots of peer beliefs
#' RProjects$significant <- factor(RProjects$pr < 0.05,
#' levels = c(FALSE, TRUE),
#' labels = c("no", "yes"))
#' parOld <- par(mfrow = c(1, 2))
#' for (p in c("Experimental Economics", "Social Sciences")) {
#' data_project <- subset(RProjects, project == p)
#' boxplot(pm_belief ~ significant, data = data_project, ylim = c(0, 1),
#' main = p, xlab = "Replication effect significant", ylab = "Peer belief")
#' stripchart(pm_belief ~ significant, data = data_project, vertical = TRUE,
#' add = TRUE, pch = 1, method = "jitter")
#' }
#' par(parOld)
#'
#' ## Computing the sceptical p-value
#' ps <- with(RProjects, pSceptical(zo = fiso/se_fiso,
#' zr = fisr/se_fisr,
#' c = se_fiso^2/se_fisr^2))
#' @keywords data
"RProjects"
#' Data from Protzko et al. (2020)
#'
#' @description Data from "High Replicability of Newly-Discovered Social-behavioral
#' Findings is Achievable" by Protzko et al. (2020). The variables are as follows:
#' \describe{
#' \item{\code{experiment}}{Experiment name}
#' \item{\code{type}}{Type of study, either "original", "self-replication", or
#' "external-replication"}
#' \item{\code{lab}}{The lab which conducted the study, either 1, 2, 3, or 4.}
#' \item{\code{smd}}{Standardized mean difference effect estimate}
#' \item{\code{se}}{Standard error of standardized mean difference effect estimate}
#' \item{\code{n}}{Total sample size of the study}
#' }
#'
#' @details This data set originates from a prospective replication project
#' involving four laboratories. Each of them conducted four original studies
#' and for each original study a replication study was carried out within
#' the same lab (self-replication) and by the other three labs
#' (external-replication). Most studies used simple between-subject designs
#' with two groups and a continuous outcome so that for each study, an
#' estimate of the standardized mean difference (SMD) could be computed from
#' the group means, group standard deviations, and group sample sizes. For
#' studies with covariate adjustment and/or binary outcomes, effect size
#' transformations as described in the supplementary material of Protzko
#' (2020) were used to obtain effect estimates and standard errors on SMD
#' scale. The data set is licensed under a CC-By Attribution 4.0
#' International license, see
#' \url{https://creativecommons.org/licenses/by/4.0/} for the terms of
#' reuse.
#'
#' @name protzko2020
#' @docType data
#' @usage data("protzko2020")
#' @format A data frame with 80 rows and 6 variables
#' @source The relevant files were downloaded from \url{https://osf.io/42ef9/}
#' on January 24, 2022. The R markdown script
#' "Decline effects main analysis.Rmd" was executed and the relevant
#' variables from the objects "ES_experiments" and "decline_effects" were
#' saved.
#' @references Protzko, J., Krosnick, J., Nelson, L. D., Nosek, B. A., Axt, J.,
#' Berent, M., ... Schooler, J. (2020, September 10). High Replicability of
#' Newly-Discovered Social-behavioral Findings is Achievable.
#' \doi{10.31234/osf.io/n2a9x}
#'
#' Protzko, J., Berent, M., Buttrick, N., DeBell, M., Roeder, S. S., Walleczek,
#' J., ... Nosek, B. A. (2021, January 5). Results & Data. Retrieved from
#' \url{https://osf.io/42ef9/}
#'
#' @examples
#' data("protzko2020", package = "ReplicationSuccess")
#'
#' ## forestplots of effect estimates
#' graphics.off()
#' parOld <- par(mar = c(5, 8, 4, 2), mfrow = c(4, 4))
#' experiments <- unique(protzko2020$experiment)
#' for (ex in experiments) {
#' ## compute CIs
#' dat <- subset(protzko2020, experiment == ex)
#' za <- qnorm(p = 0.975)
#' plotDF <- data.frame(lower = dat$smd - za*dat$se,
#' est = dat$smd,
#' upper = dat$smd + za*dat$se)
#' colpalette <- c("#000000", "#1B9E77", "#D95F02")
#' cols <- colpalette[dat$type]
#' yseq <- seq(1, nrow(dat))
#'
#' ## forestplot
#' plot(x = plotDF$est, y = yseq, xlim = c(-0.15, 0.8),
#' ylim = c(0.8*min(yseq), 1.05*max(yseq)), type = "n",
#' yaxt = "n", xlab = "Effect estimate (SMD)", ylab = "")
#' abline(v = 0, col = "#0000004D")
#' arrows(x0 = plotDF$lower, x1 = plotDF$upper, y0 = yseq, angle = 90,
#' code = 3, length = 0.05, col = cols)
#' points(y = yseq, x = plotDF$est, pch = 20, lwd = 2, col = cols)
#' axis(side = 2, at = yseq, las = 1, labels = dat$type, cex.axis = 0.85)
#' title(main = ex)
#' }
#' par(parOld)
#' @keywords data
"protzko2020"
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#' Data from the Social Sciences Replication Project
#'
#' @description Data from the \emph{Social Sciences Replication Project} (SSRP)
#' including the details of the interim analysis. The variables are as follows:
#' \describe{
#' \item{\code{study}}{Study identifier, usually names of authors
#' from original study}
#' \item{\code{ro}}{Effect estimate of original study on correlation scale}
#' \item{\code{ri}}{Effect estimate of replication study at the interim analysis
#' on correlation scale}
#' \item{\code{rr}}{Effect estimate of replication study at the final analysis
#' on correlation scale}
#' \item{\code{fiso}}{Effect estimate of original study transformed to
#' Fisher-z scale}
#' \item{\code{fisi}}{Effect estimate of replication study at
#' the interim analysis transformed to Fisher-z scale}
#' \item{\code{fisr}}{Effect estimate of replication study at the final analysis
#' transformed to Fisher-z scale}
#' \item{\code{se_fiso}}{Standard error of Fisher-z transformed effect estimate
#' of original study}
#' \item{\code{se_fisi}}{Standard error of Fisher-z transformed effect estimate
#' of replication study at the interim analysis}
#' \item{\code{se_fisr}}{Standard error of Fisher-z transformed effect estimate
#' of replication study at the final analysis}
#' \item{\code{no}}{ Sample size in original study}
#' \item{\code{ni}}{Sample size in replication study at the interim analysis}
#' \item{\code{nr}}{Sample size in replication study at the final analysis}
#' \item{\code{po}}{Two-sided p-value from significance test of effect estimate
#' from original study}
#' \item{\code{pi}}{Two-sided p-value from significance test of effect
#' estimate from replication study at the interim analysis}
#' \item{\code{pr}}{Two-sided p-value from significance test of effect estimate
#' from replication study at the final analysis}
#' \item{\code{n75}}{Sample size calculated to have 90\% power in replication study
#' to detect 75\% of the original effect size (expressed as the correlation
#' coefficient r)}
#' \item{\code{n50}}{Sample size calculated to have 90\% power in replication
#' study to detect 50\% of the original effect size (expressed as the correlation
#' coefficient r)}
#' }
#'
#' @details Two-sided p-values were calculated assuming normality of Fisher-z
#' transformed effect estimates.A two-stage procedure was used for the
#' replications. In stage 1, the authors had 90\% power to detect 75\% of
#' the original effect size at the 5\% significance level in a two-sided
#' test. If the original result replicated in stage 1 (two-sided P-value <
#' 0.05 and effect in the same direction as in the original study), the data
#' collection was stopped. If not, a second data collection was carried out
#' in stage 2 to have 90\% power to detect 50\% of the original effect size
#' for the first and the second data collections pooled. \code{n75} and
#' \code{n50} are the planned sample sizes calculated to reach 90\% power in
#' stage 1 and 2, respectively. They sometimes differ from the sample sizes
#' that were actually collected (\code{ni} and \code{nr}, respectively). See
#' supplementary information of Camerer et al. (2018) for details.
#' @name SSRP
#' @docType data
#' @usage data(SSRP)
#' @format A data frame with 21 rows and 18 variables
#' @source \url{https://osf.io/abu7k}
#' @references Camerer, C. F., Dreber, A., Holzmeister, F., Ho, T.-H., Huber,
#' J., Johannesson, M., ... Wu, H. (2018). Evaluating the replicability of
#' social science experiments in Nature and Science between 2010 and 2015.
#' \emph{Nature Human Behaviour}, \bold{2}, 637-644.
#' \doi{10.1038/s41562-018-0399-z}
#' @seealso \code{\link{RProjects}}
#' @examples
#' # plot of the sample sizes
#' plot(ni ~ no, data = SSRP, ylim = c(0, 2500), xlim = c(0, 400),
#' xlab = expression(n[o]), ylab = expression(n[i]))
#' abline(a = 0, b = 1, col = "grey")
#'
#'
#' plot(nr ~ no, data = SSRP, ylim = c(0, 2500), xlim = c(0, 400),
#' xlab = expression(n[o]), ylab = expression(n[r]))
#' abline(a = 0, b = 1, col = "grey")
#'
#'
#' @keywords data
"SSRP"
#' Data from four large-scale replication projects
#'
#' @description Data from \emph{Reproduciblity Project Psychology} (RPP),
#' \emph{Experimental Economics Replication Project} (EERP), \emph{Social
#' Sciences Replication Project} (SSRP), \emph{Experimental Philosophy
#' Replicability Project} (EPRP). The variables are as follows:
#' \describe{
#' \item{\code{study}}{Study identifier, usually names of authors
#' from original study}
#' \item{\code{project}}{Name of replication project}
#' \item{\code{ro}}{Effect estimate of original study on correlation scale}
#' \item{\code{rr}}{Effect estimate of replication study on correlation scale}
#' \item{\code{fiso}}{Effect estimate of original study transformed to
#' Fisher-z scale}
#' \item{\code{fisr}}{Effect estimate of replication study transformed
#' to Fisher-z scale}
#' \item{\code{se_fiso}}{Standard error of Fisher-z transformed effect estimate
#' of original study}
#' \item{\code{se_fisr}}{Standard error of Fisher-z transformed effect estimate
#' of replication study}
#' \item{\code{po}}{Two-sided p-value from significance test of effect estimate
#' from original study}
#' \item{\code{pr}}{Two-sided p-value from significance test of effect estimate
#' from replication study}
#' \item{\code{po1}}{One-sided p-value from significance test of effect estimate
#' from original study (in the direction of the original effect estimate)}
#' \item{\code{pr1}}{One-sided p-value from significance test of effect estimate
#' from replication study (in the direction of the original effect estimate)}
#' \item{\code{pm_belief}}{Peer belief about whether replication effect estimate
#' will achieve statistical significance elicited through prediction market (only
#' available for EERP and SSRP)}
#' \item{\code{no}}{Sample size in original study}
#' \item{\code{nr}}{Sample size in replication study}
#' }
#'
#' @details Two-sided p-values were calculated assuming normality of Fisher-z
#' transformed effect estimates. From the RPP only the \emph{meta-analytic
#' subset} is included, which consists of 73 out of 100 study pairs for
#' which the standard error of the z-transformed correlation coefficient can
#' be computed. For the RPP sample sizes were recalculated from the reported
#' standard errors of Fisher z-transformed correlation coefficients. From
#' the EPRP only 31 out of 40 study pairs are included where effective
#' sample size for original and replication study are available
#' simultaneously. For more details about how the the data was preprocessed
#' see source below and supplement S1 of Pawel and Held (2020).
#' @name RProjects
#' @docType data
#' @usage data(RProjects)
#' @format A data frame with 143 rows and 15 variables
#' @source RPP: The source files were downloaded from
#' \url{https://github.com/CenterForOpenScience/rpp/}. The "masterscript.R"
#' file was executed and the relevant variables were extracted from the
#' generated "final" object (standard errors of Fisher-z transformed
#' correlations) and "MASTER" object (everything else). The data set is
#' licensed under a CC0 1.0 Universal license, see
#' \url{https://creativecommons.org/publicdomain/zero/1.0/} for the terms of
#' reuse.
#'
#' EERP: The source files were downloaded from \url{https://osf.io/pnwuz/}. The
#' required data were then manually extracted from the code in the files
#' "effectdata.py" (sample sizes) and "create_studydetails.do" (everything
#' else). Data regarding the prediction market and survey beliefs were manually
#' extracted from table S3 of the supplementary materials of the EERP. The
#' authors of this R package have been granted permission to share this data set
#' by the coordinators of the EERP.
#'
#' SSRP: The relevant variables were extracted from the file
#' "D3 - ReplicationResults.csv" downloaded from \url{https://osf.io/abu7k}. For
#' replications which underwent only the first stage, the data from the first
#' stage were taken as the data for the replication study. For the replications
#' which reached the second stage, the pooled data from both stages were taken
#' as the data for the replication study. Data regarding survey and prediction
#' market beliefs were extracted from the "D6 - MeanPeerBeliefs.csv" file, which
#' was downloaded from \url{https://osf.io/vr6p8/}. The data set is licensed
#' under a CC0 1.0 Universal license, see
#' \url{https://creativecommons.org/publicdomain/zero/1.0/} for the terms of
#' reuse.
#'
#' EPRP: Data were taken from the "XPhiReplicability_CompleteData.csv" file,
#' which was downloaded from \url{https://osf.io/4ewkh/}. The authors of this R
#' package have been granted permission to share this data set by the
#' coordinators of the EPRP.
#'
#' @references Camerer, C. F., Dreber, A., Forsell, E., Ho, T.-H., Huber, J.,
#' Johannesson, M., ... Hang, W. (2016). Evaluating replicability of
#' laboratory experiments in economics. \emph{Science}, \bold{351}, 1433-1436.
#' \doi{10.1126/science.aaf0918}
#'
#' Camerer, C. F., Dreber, A., Holzmeister, F., Ho, T.-H., Huber, J.,
#' Johannesson, M., ... Wu, H. (2018). Evaluating the replicability of
#' social science experiments in Nature and Science between 2010 and 2015.
#' \emph{Nature Human Behaviour}, \bold{2}, 637-644.
#' \doi{10.1038/s41562-018-0399-z}
#'
#' Cova, F., Strickland, B., Abatista, A., Allard, A., Andow, J., Attie, M., ...
#' Zhou, X. (2018). Estimating the reproducibility of experimental philosophy.
#' \emph{Review of Philosophy and Psychology}. \doi{10.1007/s13164-018-0400-9}
#'
#' Open Science Collaboration. (2015). Estimating the reproducibility of
#' psychological science. \emph{Science}, \bold{349}, aac4716.
#' \doi{10.1126/science.aac4716}
#'
#' Pawel, S., Held, L. (2020). Probabilistic forecasting of replication studies.
#' \emph{PLOS ONE}. \bold{15}, e0231416. \doi{10.1371/journal.pone.0231416}
#'
#' @seealso \code{\link{SSRP}}
#' @examples
#' data("RProjects", package = "ReplicationSuccess")
#'
#' ## Computing key quantities
#' RProjects$zo <- RProjects$fiso/RProjects$se_fiso
#' RProjects$zr <- RProjects$fisr/RProjects$se_fisr
#' RProjects$c <- RProjects$se_fiso^2/RProjects$se_fisr^2
#'
#' ## Computing one-sided p-values for alternative = "greater"
#' RProjects$po1 <- z2p(z = RProjects$zo, alternative = "greater")
#' RProjects$pr1 <- z2p(z = RProjects$zr, alternative = "greater")
#'
#' ## Plots of effect estimates
#' parOld <- par(mfrow = c(2, 2))
#' for (p in unique(RProjects$project)) {
#' data_project <- subset(RProjects, project == p)
#' plot(rr ~ ro, data = data_project, ylim = c(-0.5, 1),
#' xlim = c(-0.5, 1), main = p, xlab = expression(italic(r)[o]),
#' ylab = expression(italic(r)[r]))
#' abline(h = 0, lty = 2)
#' abline(a = 0, b = 1, col = "grey")
#' }
#' par(parOld)
#'
#' ## Plots of peer beliefs
#' RProjects$significant <- factor(RProjects$pr < 0.05,
#' levels = c(FALSE, TRUE),
#' labels = c("no", "yes"))
#' parOld <- par(mfrow = c(1, 2))
#' for (p in c("Experimental Economics", "Social Sciences")) {
#' data_project <- subset(RProjects, project == p)
#' boxplot(pm_belief ~ significant, data = data_project, ylim = c(0, 1),
#' main = p, xlab = "Replication effect significant", ylab = "Peer belief")
#' stripchart(pm_belief ~ significant, data = data_project, vertical = TRUE,
#' add = TRUE, pch = 1, method = "jitter")
#' }
#' par(parOld)
#'
#' ## Computing the sceptical p-value
#' ps <- with(RProjects, pSceptical(zo = fiso/se_fiso,
#' zr = fisr/se_fisr,
#' c = se_fiso^2/se_fisr^2))
#' @keywords data
"RProjects"
#' Data from Protzko et al. (2020)
#'
#' @description Data from "High Replicability of Newly-Discovered Social-behavioral
#' Findings is Achievable" by Protzko et al. (2020). The variables are as follows:
#' \describe{
#' \item{\code{experiment}}{Experiment name}
#' \item{\code{type}}{Type of study, either "original", "self-replication", or
#' "external-replication"}
#' \item{\code{lab}}{The lab which conducted the study, either 1, 2, 3, or 4.}
#' \item{\code{smd}}{Standardized mean difference effect estimate}
#' \item{\code{se}}{Standard error of standardized mean difference effect estimate}
#' \item{\code{n}}{Total sample size of the study}
#' }
#'
#' @details This data set originates from a prospective replication project
#' involving four laboratories. Each of them conducted four original studies
#' and for each original study a replication study was carried out within
#' the same lab (self-replication) and by the other three labs
#' (external-replication). Most studies used simple between-subject designs
#' with two groups and a continuous outcome so that for each study, an
#' estimate of the standardized mean difference (SMD) could be computed from
#' the group means, group standard deviations, and group sample sizes. For
#' studies with covariate adjustment and/or binary outcomes, effect size
#' transformations as described in the supplementary material of Protzko
#' (2020) were used to obtain effect estimates and standard errors on SMD
#' scale. The data set is licensed under a CC-By Attribution 4.0
#' International license, see
#' \url{https://creativecommons.org/licenses/by/4.0/} for the terms of
#' reuse.
#'
#' @name protzko2020
#' @docType data
#' @usage data("protzko2020")
#' @format A data frame with 80 rows and 6 variables
#' @source The relevant files were downloaded from \url{https://osf.io/42ef9/}
#' on January 24, 2022. The R markdown script
#' "Decline effects main analysis.Rmd" was executed and the relevant
#' variables from the objects "ES_experiments" and "decline_effects" were
#' saved.
#' @references Protzko, J., Krosnick, J., Nelson, L. D., Nosek, B. A., Axt, J.,
#' Berent, M., ... Schooler, J. (2020, September 10). High Replicability of
#' Newly-Discovered Social-behavioral Findings is Achievable.
#' \doi{10.31234/osf.io/n2a9x}
#'
#' Protzko, J., Berent, M., Buttrick, N., DeBell, M., Roeder, S. S., Walleczek,
#' J., ... Nosek, B. A. (2021, January 5). Results & Data. Retrieved from
#' \url{https://osf.io/42ef9/}
#'
#' @examples
#' data("protzko2020", package = "ReplicationSuccess")
#'
#' ## forestplots of effect estimates
#' graphics.off()
#' parOld <- par(mar = c(5, 8, 4, 2), mfrow = c(4, 4))
#' experiments <- unique(protzko2020$experiment)
#' for (ex in experiments) {
#' ## compute CIs
#' dat <- subset(protzko2020, experiment == ex)
#' za <- qnorm(p = 0.975)
#' plotDF <- data.frame(lower = dat$smd - za*dat$se,
#' est = dat$smd,
#' upper = dat$smd + za*dat$se)
#' colpalette <- c("#000000", "#1B9E77", "#D95F02")
#' cols <- colpalette[dat$type]
#' yseq <- seq(1, nrow(dat))
#'
#' ## forestplot
#' plot(x = plotDF$est, y = yseq, xlim = c(-0.15, 0.8),
#' ylim = c(0.8*min(yseq), 1.05*max(yseq)), type = "n",
#' yaxt = "n", xlab = "Effect estimate (SMD)", ylab = "")
#' abline(v = 0, col = "#0000004D")
#' arrows(x0 = plotDF$lower, x1 = plotDF$upper, y0 = yseq, angle = 90,
#' code = 3, length = 0.05, col = cols)
#' points(y = yseq, x = plotDF$est, pch = 20, lwd = 2, col = cols)
#' axis(side = 2, at = yseq, las = 1, labels = dat$type, cex.axis = 0.85)
#' title(main = ex)
#' }
#' par(parOld)
#' @keywords data
"protzko2020"
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