New data set dat.barone2019, added data tests, added concepts to documentation, fixed typos

.gitignore

@@ -3,3 +3,4 @@
 .Rapp.history
 .Rproj.user
 *.Rproj
+.RData

.travis.yml

@@ -1,13 +1,31 @@
 language: r
-r:
-  - oldrel
-  - release
-  - devel
 cache: packages
-r_packages: covr
+r: release
+dist: xenial
+warnings_are_errors: true
+r_check_args: --no-tests --as-cran --no-manual
+sudo: required
+
+env:
+  - NOT_CRAN=true
+
+r_packages:
+  - ape
+  - covr
+  - devtools
+  - BiasedUrn
+  - digest
+  - lme4
+  - gsl
+  - R.rsp
+  - metafor
+
+apt_packages:
+  - libgsl-dev
+
+
 after_success:
-  - Rscript -e 'covr::codecov()'
-notifications:
-  email:
-    on_success: never
-    on_failure: never
+  - Rscript -e 'library(covr);codecov()'
+
+
+

DESCRIPTION

@@ -5,7 +5,7 @@ Title: Meta-Analysis Datasets
 Authors@R: c(person(given = "Thomas", family="White", role="aut", email = ""), person(given = "Daniel", family="Noble", role="aut", email = ""), person(given = "Alistair", family="Senior", role="aut", email = ""), person(given = "Wolfgang", family = "Viechtbauer", role = c("aut","cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3463-4063")))
 Depends: R (>= 3.2.0)
 Imports: utils, tools
-Suggests: metafor, ape, multcomp
+Suggests: metafor, ape, multcomp, testthat
 Description: A collection of meta-analytic datasets.
 License: GPL (>=2)
 ByteCompile: TRUE

data-raw/.rfiles.txt

@@ -1,4 +1,5 @@
 "dat.bangertdrowns2004.r"
+"dat.barone2019.r"
 "dat.begg1989.r"
 "dat.berkey1998.r"
 "dat.besson2016.r"
@@ -14,15 +15,18 @@
 "dat.english2016.r"
 "dat.fine1993.r"
 "dat.gibson2002.r"
+"dat.griffith2006.r"
 "dat.hackshaw1998.r"
 "dat.hart1999.r"
 "dat.hasselblad1998.r"
 "dat.hine1989.r"
+"dat.ho2012.r"
 "dat.ishak2007.r"
 "dat.konstantopoulos2011.r"
 "dat.laopaiboon2015.r"
 "dat.lee2004.r"
 "dat.li2007.r"
+"dat.lim2014.r"
 "dat.linde2005.r"
 "dat.maire2019.r"
 "dat.mcdaniel1994.r"
@@ -36,6 +40,7 @@
 "dat.pignon2000.r"
 "dat.pritz1997.r"
 "dat.raudenbush1985.r"
+"dat.reed2001.r"
 "dat.riley2003.r"
 "dat.senn2013.r"
 "dat.tamim2011.r"

data-raw/dat.barone2019.csv

@@ -0,0 +1,57 @@
+id;Author;Year;Paradigm;Measure;Age_months;n;Dropped_participants;Dropped_participants_corrected;Familiarization;Belief;Agent;Target_object_Presence;Object_movements;Motive_transformation;Salience_of_agents_MS;Interaction;Design;Test_trials;logit.p.;vlogit.p.;sei
+voe1;Onishi & Baillargeon;2005;VOE;VOE;15.23;14;14;7;2;L;real present person;real, present;1;other reason;absence;no;BS;1;2.3398012;1.1514538;1.073058153
+voe2;Onishi & Baillargeon;2005;VOE;VOE;15.23;14;NA;7;2;L;real present person;real, present;1;other reason;absence;no;BS;1;3.0834589;1.2830486;1.132717352
+al1;Southgate et al.;2007;AL;AL;25.13;10;16;8;2;L;videotaped person;absent;1;other reason;back turned;no;BS;1;2.197225;1.111111;1.054092501
+al2;Southgate et al.;2007;AL;AL;25.2;10;NA;8;2;L;videotaped person;absent;2;other reason;back turned;no;BS;1;1.386294;0.625;0.790569415
+voe3;Surian et al. ;2007;VOE;VOE;13.13;28;8;8;5;L;virtual agent;real, present;1;other reason;absence;no;BS;1;0.9250377;0.4934802;0.702481459
+voe4;Surian et al. ;2007;VOE;VOE;13.1;26;7;7;5;L;virtual agent;real, present;1;other reason;absence;no;BS;1;0.4897258;0.5263789;0.725519745
+voe5;Song et al.;2008;VOE;VOE;18.6;14;9;9;3;L;real present person;real, present;1;other reason;absence;no;BS;1;2.5574571;1.1843525;1.088279606
+voe6;Song et al.;2008;VOE;VOE;18.57;16;13;13;3;L;real present person;real, present;1;other reason;absence;no;BS;1;2.6481471;1.0527578;1.026039863
+int1;Buttelmann et al.;2009;Interactive;Help;18;25;119;60;0;L;real present person;real, present;1;trick;absence;yes;BS;1;0.9444616;0.1984127;0.445435405
+int2;Buttelmann et al.;2009;Interactive;Help;16.3;25;NA;59;0;L;real present person;real, present;1;trick;absence;yes;BS;1;1.386294;0.25;0.5
+voe7;Scott & Baillargeon;2009;VOE;VOE;17.73;14;19;19;4;I;real present person;real, present;0;other reason;absence;no;WS;2;1.126369;0.2802925;0.529426577
+voe8;Scott & Baillargeon;2009;VOE;VOE;17.8;14;10;10;4;I;real present person;real, present;0;other reason;absence;no;WS;2;1.822959;0.3536756;0.594706314
+int3;Southgate et al.;2010;Interactive;Pointing;17.73;12;3;3;0;L;real present person;real, present;1;trick;absence;yes;BS;1;1.098612;0.4444444;0.666666633
+int4;Southgate et al.;2010;Interactive;Pointing;17.83;12;11;11;0;L;real present person;real, present;1;trick;absence;yes;BS;1;1.609438;0.6;0.774596669
+int5;Southgate et al.;2010;Interactive;Pointing;17.97;12;6;6;0;L;real present person;real, present;1;trick;absence;yes;BS;1;1.098612;0.4444444;0.666666633
+voe9;Scott et al.;2010;VOE;VOE;18.67;18;10;10;1;NP;real present person;real, present;0;other reason;absence;no;BS;1;2.3216632;0.8882644;0.942477798
+voe10;Scott et al.;2010;VOE;VOE;18.8;16;3;3;2;NP;real present person;real, present;0;other reason;absence;no;BS;1;1.7956614;0.9211631;0.959772421
+al3;Senju et al.;2011;AL;AL;18;18;12;12;4;L;videotaped person;absent;1;other reason;first-person experience;no;BS;1;1.252763;0.3214286;0.566946735
+voe11;Luo;2011;VOE;VOE;10.1;12;7;7;3;L;real present person;real, present;0;other reason;absence;no;WS;2;1.0128669;0.31690148;0.562940032
+al4;Surian & Geraci;2012;AL;AL;17.13;24;2;2;2;L;virtual agent;real, present;1;other reason;absence;no;WS;1;0.8873032;0.2016807;0.449088744
+al5;Surian & Geraci;2012;AL;AL;11.5;16;3;3;2;L;virtual agent;real, present;1;other reason;absence;no;WS;1;-0.2513144;0.2539683;0.503952676
+al6;Meristo et al.;2012;AL;AL;23;10;4;4;2;L;virtual agent;real, present;1;other reason;absence;no;WS;1;3.044522;2.095238;1.447493696
+al7;Thoermer et al.;2012;AL;AL;18.07;44;10;10;2;L;videotaped person;absent;2;other reason;back turned;no;BS;1;0.1823216;0.09166667;0.302765041
+int6;Knudsen & Liszkowski (a);2012;Interactive;Pointing;18.4;19;5;5;0;L;real present person;absent;2;other reason;absence;yes;BS;4;0.5389965;0.2261905;0.475594891
+int7;Knudsen & Liszkowski (a);2012;Interactive;Pointing;18.67;19;5;5;0;L;real present person;absent;2;other reason;absence;yes;BS;4;-0.1053605;0.2111111;0.45946828
+int8;Knudsen & Liszkowski (b);2012;Interactive;Pointing;18.33;16;7;7;0;L;real present person;real, present;1;other reason;absence;yes;BS;2;-0.2513144;0.2539683;0.503952676
+int9;Knudsen & Liszkowski (b);2012;Interactive;Pointing;24.47;16;NA;6;0;L;real present person;real, present;1;other reason;absence;yes;WS;2;0.7884574;0.2909091;0.539359898
+voe12;Yott & Poulin-Dubois;2012;VOE;VOE;18.77;34;34;34;3;L;real present person;real, present;1;other reason;absence;no;BS;1;1.5780054;0.4276829;0.653974694
+voe13;Poulin-Dubois et al.;2013;VOE;VOE;16.13;51;17;17;3;L;real present person;real, present;1;other reason;used a blindfold;no;BS;1;-0.33;0.2631895;0.51301998
+int10;Buttelmann et al.;2014;Interactive;Help;18.3;18;21;21;0;C;real present person;real, present;0;other reason;absence;yes;BS;1;0.6931472;0.25;0.5
+al8;Zmyj et al.;2015;AL;AL;18.07;22;15;15;2;L;videotaped person;absent;2;other reason;back turned;no;BS;1;-0.7621401;0.2095238;0.457737698
+int11;Buttelmann et al.;2015;Interactive;Help;18.17;31;10;10;0;I;real present person;real, present;0;other reason;absence;yes;BS;4;0.06453852;0.1291667;0.359397691
+voe14;Scott et al.;2015;VOE;VOE;17.47;18;3;3;6;I;real present person;absent;0;trick;absence;no;BS;1;2.5393191;0.9211631;0.959772421
+voe15;Scott et al.;2015;VOE;VOE;17.53;18;7;7;6;I;real present person;absent;0;trick;absence;no;BS;1;2.1221453;0.8553657;0.924859827
+voe16;Scott et al.;2015;VOE;VOE;17.4;18;5;5;6;I;real present person;absent;0;trick;absence;no;BS;1;2.1221453;0.8553657;0.924859827
+voe17;Yott & Poulin-Dubois;2016;VOE;VOE;16;72;25;25;3;L;real present person;real, present;1;other reason;absence;no;WS;2;0.4471367;0.04708104;0.216981658
+int12;Fizke et al.;2017;Interactive;Help;26;23;25;23;0;L;real present person;real, present;1;trick;absence;yes;BS;2;-0.8266786;0.2053571;0.453163436
+int13;Fizke et al.;2017;Interactive;Help;26;23;NA;23;0;I;real present person;real, present;0;trick;absence;yes;BS;2;-0.4418328;0.1825397;0.42724665
+voe19;Moriguchi et al.;2017;VOE;VOE;18.5;37;1;1;2;L;real present person;real, present;1;other reason;absence;no;WS;1;1.18949;0.1079077;0.328493075
+al9;Kulke et al.;2018;AL;AL;24.5;11;0;0;4;L;videotaped person;absent;1;other reason;back turned;no;BS;1;-0.9808293;0.4583333;0.677003176
+al10;Kulke et al.;2018;AL;AL;24.5;9;0;0;4;L;videotaped person;absent;2;other reason;back turned;no;BS;1;0.2231436;0.45;0.670820393
+al11;Grosse Wiesmann et al.;2018;AL;AL;25.2;25;7;4;2;L;videotaped person;absent;1;other reason;back turned;no;BS;1;0.08004271;0.1602564;0.400320372
+al12;Grosse Wiesmann et al.;2018;AL;AL;25.2;25;NA;3;2;L;videotaped person;absent;2;other reason;back turned;no;BS;1;-0.08004271;0.1602564;0.400320372
+al13;Dorrenberg et al.;2018;AL;AL;24.53;50;16;8;2;L;videotaped person;absent;1;other reason;back turned;no;WS;2;0.4895482;0.08488964;0.291358267
+al14;Dorrenberg et al.;2018;AL;AL;24.53;49;NA;8;2;L;videotaped person;absent;2;other reason;back turned;no;WS;NA;-1.126011;0.1103604;0.332205358
+al15;Schuwerk et al.;2018;AL;AL;25.5;58;20;20;2;L;videotaped person;absent;2;other reason;back turned;no;BS;1;-0.06899287;0.06904762;0.262769138
+int14;Poulin-Dubois & Yott;2018;Interactive;Help;18;53;19;19;0;L;real present person;real, present;1;trick;absence;yes;WS;1;-0.5819215;0.08204334;0.286432086
+int15;Powell et al.;2018;Interactive;Help;18.6;94;34;17;0;L;real present person;real, present;1;trick;absence;yes;BS;1;0.5221894;0.04552058;0.213355525
+int16;Powell et al.;2018;Interactive;Pointing;25.5;16;NA;17;0;L;real present person;real, present;1;other reason;absence;yes;WS;2;0.7884574;0.2909091;0.539359898
+int17;Priewasser et al.;2018;Interactive;Help;25.64;14;17;17;0;L;real present person;real, present;1;trick;absence;yes;BS;1;2.564949;1.076923;1.037749006
+int18;Crivello & Poulin-Dubois;2018;Interactive;Help;18.4;41;15;15;0;L;real present person;real, present;1;trick;absence;yes;BS;1;-0.5500463;0.1051282;0.324234791
+int19;Crivello & Poulin-Dubois;2018;Interactive;Help;18.47;97;9;9;0;L;real present person;real, present;1;trick;absence;yes;BS;1;0.3117796;0.04224739;0.205541699
+int20;Dorrenberg et al.;2018;Interactive;Pointing;24.53;32;3;3;0;L;real present person;real, present;1;trick;absence;yes;BS;3;0.5108256;0.1333333;0.365148326
+voe18;Dorrenberg et al.;2018;VOE;VOE;24.53;26;9;9;2;L;videotaped person;real, present;1;other reason;absence;no;WS;2;0.3225528;0.12853416;0.35851661
+int21;Kiraly et al.;2018;Interactive;Pointing;18.1;15;12;12;0;L;real present person;real, present;1;trick;first-person experience (belief-revision);yes;BS;1;-1.011601;0.3409091;0.583874216
+int22;Kiraly et al.;2018;Interactive;Pointing;18;15;6;6;0;L;real present person;real, present;1;trick;first-person experience;yes;BS;1;0.6931472;0.3;0.547722558

data-raw/dat.barone2019.r

@@ -0,0 +1,6 @@
+# Load
+# This csv file was downloaded from https://osf.io/re8uj/?view_only=d2605771dd664831a104318db9ff7aa9 on Sept 13, 2019
+dat.barone2019 <- read.csv("data-raw/dat.barone2019.csv", header=TRUE,  sep=";", stringsAsFactors=FALSE)
+
+# Output
+save(dat.barone2019, file="data/dat.barone2019.rda", ascii=FALSE)

man/dat.barone2019.Rd

@@ -0,0 +1,240 @@
+\name{dat.barone2019}
+\docType{data}
+\alias{dat.barone2019}
+\title{Studies on Spontaneous-Response False Belief Tasks in Infants}
+\description{Results from studies which use spontaneous-response false belief tasks in infants up to 2 years old.}
+\usage{dat.barone2019}
+\format{The data frame contains the following columns:
+\tabular{lll}{
+\bold{id}      \tab \code{character}    \tab study identifier \cr
+\bold{Author}      \tab \code{character}    \tab author names \cr
+\bold{Year}      \tab \code{integer}    \tab year published \cr
+\bold{Paradigm}      \tab \code{character}    \tab Experimental paradigm used in the study (VOE = violation of expectation; AL = anticipatory looking; interactive = Interactive design)  \cr
+\bold{Measure}      \tab \code{character}    \tab Measure used in the study (VOE = violation of expectation; AL = anticipatory looking; Pointing = Pointing behavior; Help = Correct helping)  \cr
+\bold{Age_months}      \tab \code{numeric}    \tab Average age in months \cr
+\bold{n}      \tab \code{integer}    \tab Sample size \cr
+\bold{Dropped_participants}      \tab \code{integer}    \tab  Number of participants excluded from each condition \cr
+\bold{Dropped_participants_corrected}      \tab \code{integer}    \tab Number of participants excluded from each condition corrected \cr
+\bold{Familiarization}      \tab \code{integer}    \tab Number of familiarization trials performed in each condition (0 = warm-up trials instead of familiarization trials) \cr
+\bold{Belief}        \tab \code{character}  \tab Type of belief attributed to the agent  (L = Object location; NP = Non-obvious property of an object; I = Identity of an object; C = Expected or unexpected contents)\cr
+\bold{Agent}        \tab \code{character}  \tab Agent used in study  (real present person; videotaped person; virtual agent)\cr
+\bold{Target_object_Presence}        \tab \code{character}  \tab Real presence of the target object: whether, at the test trial, the target object was real and present or absent (real, present = real and present; absent = absent)\cr
+\bold{Object_movements}      \tab \code{integer}    \tab  Number of displacements of the object that the agent did not see before the object arrived at its final position \cr
+\bold{Motive_transformation}      \tab \code{character}    \tab Capturing whether the key transformation was done to trick the agent or for some other reason (trick = Explicity trick the agent; other reason = Some other reason including no explicit reason at all)\cr
+\bold{Salience_of_agents_MS}      \tab \code{character}    \tab Salience of the agent’s mental state (absence = the false belief state had to be tracked from the agent’s absence during the key events; back turned = the false belief state had to be tracked due to the agent’s back turned during the key transformation; first-person experience = the false belief experience was demonstrated initially on the children themselves; blindfold = the agent used a blindfold during the transformation)\cr
+\bold{Interaction}      \tab \code{character}    \tab Interaction between the child and the agent during the test or not (yes = yes; no = no)\cr
+\bold{Design}      \tab \code{character}    \tab Study design employed in each condition (BS = between-subjects design; WS = within-subjects design)\cr
+\bold{Test_trials}      \tab \code{integer}    \tab Number of test trials that were conducted with each child \cr
+\bold{logit.p.}      \tab \code{numeric}    \tab  Logit transformed proportion (log odds)  \cr
+\bold{vlogit.p.}      \tab \code{numeric}    \tab Sampling variance \cr
+\bold{sei}      \tab \code{numeric}    \tab Standard error
+}
+}
+\details{
+   The dataset includes fifty-six effect sizes from studies which use spontaneous-response false belief tasks in infants up to 2 years old. Belief conditions using violation-of-expectation, anticipatory looking and interactive paradigms were included in this dataset, including 1469 infants. The data in this dataset were obtained from the authors reposatory on the Open Science Framework https://osf.io/re8uj/?view_only=d2605771dd664831a104318db9ff7aa9
+}
+\source{
+   Barone, P., Corradi, G., & Gomila, A. (2019, July 26). Infants’ performance in spontaneous-response false belief tasks: a review and meta-analysis. Retrieved from osf.io/re8uj
+}
+\references{
+   Barone, P., Corradi, G., & Gomila, A. (2019). Infants’ performance in spontaneous-response false belief tasks: A review and meta-analysis. \emph{Infant Behavior and Development}, \bold{57}, 101350.
+}
+\author{W. Kyle Hamilton, \email{[email protected]}}
+\examples{
+if (require(metafor)) {
+# This code example is a very slightly modified version of the one provided by the authors
+# which can be found here https://osf.io/s5ajt/?view_only=d2605771dd664831a104318db9ff7aa9
+
+## Make copy of dataset
+dat <- dat.barone2019
+
+
+dat$Familiarization <- as.factor(dat$Familiarization)
+dat$Test_trials <- as.factor(dat$Test_trials)
+dat$Object_movements <- as.factor(dat$Object_movements)
+dat$Belief <- as.factor(dat$Belief)
+
+# First model
+res <-
+  rma(
+    yi = logit.p.,
+    sei = sei,
+    data = dat,
+    slab = paste(Author, Year)
+  )
+res
+
+# Funnel plot
+# Note the nonsymmetrical distribution in this funnel plot
+# this is an example of publication bias.
+funnel(res, main = "Standard Error")
+
+# Forest plot (grouped by paradigm)
+par(mar = c(4, 4, 1, 2))
+dat$Paradigm[order(dat$Paradigm)]
+rows = c(5:19, 23:44, 48:66)
+length(rows)
+table(dat$Paradigm)
+### set up forest plot (with 2x2 table counts added; rows argument is used
+### to specify exactly in which rows the outcomes will be plotted)
+forest(
+  res,
+  xlim = c(-11, 10),
+  ylim = c(-1, 70),
+  order = order(dat$Paradigm),
+  rows = rows,
+  xlab = "",
+  mlab = ""
+)
+
+### add text with Q-value, dfs, p-value, and I^2 statistic
+text(-11,-1, pos = 4, cex = 0.75, bquote(
+  paste(
+    "RE Model for All Studies (Q = ",
+    .(formatC(
+      res$QE, digits = 2, format = "f"
+    )),
+    ", df = ",
+    .(res$k - res$p),
+    ", p = ",
+    .(formatC(
+      res$QEp, digits = 2, format = "f"
+    )),
+    "; ",
+    I ^ 2,
+    " = ",
+    .(formatC(
+      res$I2, digits = 1, format = "f"
+    )),
+    "\%)"
+  )
+))
+
+### set font expansion factor (as in forest() above) and use bold italic
+### font and save original settings in object 'op'
+op <- par(cex = 0.75, font = 4)
+
+### add text for the subgroups
+text(-11, c(16, 41, 63) + 4, pos = 4, c("AL",
+                                        "Interactive",
+                                        "VOE"))
+
+### switch to bold font
+par(font = 2)
+
+### set par back to the original settings
+par(op)
+
+### fit random-effects model in the three subgroups
+res.AL <-
+  rma(
+    yi = logit.p.,
+    sei = sei ,
+    data = dat[dat$Paradigm == "AL", ],
+    slab = paste(Author, Year),
+    method = "REML"
+  )
+res.AL
+res.inter <-
+  rma(
+    yi = logit.p.,
+    sei = sei,
+    data = dat[dat$Paradigm == "Interactive", ],
+    slab = paste(Author, Year),
+    method = "REML"
+  )
+res.inter
+res.VOE <-
+  rma(
+    yi = logit.p.,
+    sei = sei,
+    data = dat[dat$Paradigm == "VOE", ],
+    slab = paste(Author, Year),
+    method = "REML"
+  )
+res.VOE
+### add summary polygons for the three subgroups
+addpoly(res.AL,
+        row = 2.5,
+        cex = 0.75,
+        mlab = "")
+addpoly(res.inter,
+        row = 21.5,
+        cex = 0.75,
+        mlab = "")
+addpoly(res.VOE,
+        row = 46.5,
+        cex = 0.75,
+        mlab = "")
+
+### add text with Q-value, dfs, p-value, and I^2 statistic for subgroups
+text(-11, 2.5, pos = 4, cex = 0.75, bquote(
+  paste(
+    "RE Model for Subgroup (Q = ",
+    .(formatC(
+      res.AL$QE, digits = 2, format = "f"
+    )),
+    ", df = ",
+    .(res.AL$k - res.AL$p),
+    ", p = ",
+    .(formatC(
+      res.AL$QEp, digits = 2, format = "f"
+    )),
+    "; ",
+    I ^ 2,
+    " = ",
+    .(formatC(
+      res.AL$I2, digits = 1, format = "f"
+    )),
+    "\%)"
+  )
+))
+text(-11, 21.5, pos = 4, cex = 0.75, bquote(
+  paste(
+    "RE Model for Subgroup (Q = ",
+    .(formatC(
+      res.inter$QE, digits = 2, format = "f"
+    )),
+    ", df = ",
+    .(res.inter$k - res.inter$p),
+    ", p = ",
+    .(formatC(
+      res.inter$QEp, digits = 2, format = "f"
+    )),
+    "; ",
+    I ^ 2,
+    " = ",
+    .(formatC(
+      res.inter$I2, digits = 1, format = "f"
+    )),
+    "\%)"
+  )
+))
+text(-11, 46.5, pos = 4, cex = 0.75, bquote(
+  paste(
+    "RE Model for Subgroup (Q = ",
+    .(formatC(
+      res.VOE$QE, digits = 2, format = "f"
+    )),
+    ", df = ",
+    .(res.VOE$k - res.VOE$p),
+    ", p = ",
+    .(formatC(
+      res.VOE$QEp, digits = 2, format = "f"
+    )),
+    "; ",
+    I ^ 2,
+    " = ",
+    .(formatC(
+      res.VOE$I2, digits = 1, format = "f"
+    )),
+    "\%)"
+  )
+))
+
+
+}
+}
+\keyword{datasets}
+\concept{infants}
+\concept{psychology}