CRAN doi changes

tbates · Jan 24, 2021 · 5113946 · 5113946
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diff --git a/R/TRHG_code.R b/R/TRHG_code.R
@@ -7,7 +7,7 @@
 #' @seealso - [umx()]
 #' @references - Bates, T. C., Neale, M. C., & Maes, H. H. (2019). 
 #' umx: A library for Structural Equation and Twin Modelling in R. 
-#' *Twin Research and Human Genetics*, **22**, 27-41. DOI: [https://doi.org/10.1017/thg.2019.2](https://doi.org/10.1017/thg.2019.2)
+#' *Twin Research and Human Genetics*, **22**, 27-41. \doi{10.1017/thg.2019.2}.
 #' @md
 #' @aliases umxExampleCode_TRHGpaper
 #' @examples

diff --git a/R/build_run_modify.R b/R/build_run_modify.R
@@ -1604,7 +1604,7 @@ umxACE <- function(name = "ACE", selDVs, selCovs = NULL, dzData= NULL, mzData= N
 #' @seealso [umxGxE_window()], [umxReduce()], [umxSummary()]
 #' @family Twin Modeling Functions
 #' @references - Purcell, S. (2002). Variance components models for gene-environment interaction in twin analysis. *Twin Research*,
-#'  **6**, 554-571. DOI: [10.1375/twin.5.6.554](https://doi.org/10.1375/twin.5.6.554)
+#'  **6**, 554-571. DOI: \doi{10.1375/twin.5.6.554}
 #' @md
 #' @examples
 #' require(umx)
@@ -2117,11 +2117,11 @@ umxGxE_window <- function(selDVs = NULL, moderator = NULL, mzData = mzData, dzDa
 #' @references 
 #' Neale, M. C., & Martin, N. G. (1989). The effects of age, sex, 
 #' and genotype on self-report drunkenness following a challenge dose of alcohol. 
-#' *Behavior Genetics*, **19**, 63-78. doi:<https://doi.org/10.1007/BF01065884>.
+#' *Behavior Genetics*, **19**, 63-78. doi:\doi{10.1007/BF01065884}.
 #' 
 #' Schwabe, I., Boomsma, D. I., Zeeuw, E. L., & Berg, S. M. (2015). A New Approach
 #' to Handle Missing Covariate Data in Twin Research : With an Application to
-#' Educational Achievement Data. *Behavior Genetics*, **46**, 583-95. doi:<https://doi.org/10.1007/s10519-015-9771-1>.
+#' Educational Achievement Data. *Behavior Genetics*, **46**, 583-95. doi:\doi{10.1007/s10519-015-9771-1}.
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/datasets.R b/R/datasets.R
@@ -294,7 +294,7 @@ NULL
 #' @family datasets
 #' @name Fischbein_wt
 #' @references Fischbein, S. (1977). Intra-pair similarity in physical growth of monozygotic and of dizygotic twins during puberty. 
-#' *Annals of Human Biology*, **4**. 417-430. <https://doi.org/10.1080/03014467700002401>
+#' *Annals of Human Biology*, **4**. 417-430. \doi{10.1080/03014467700002401}
 #' @usage data(Fischbein_wt)
 #' @format A 6*6 correlation matrix based on n = 66 female subjects.
 #' @md

diff --git a/R/fit_and_reporting.R b/R/fit_and_reporting.R
@@ -144,7 +144,7 @@ umxWeightedAIC <- function(models, digits= 2) {
 #' @family Reporting Functions
 #' @family Twin Modeling Functions
 #' @seealso [umxReduceGxE()], [umxReduceACE()]
-#' @references - Wagenmakers, E.J., & Farrell, S. (2004). AIC model selection using Akaike weights. *Psychonomic Bulletin and Review*, **11**, 192-196. [doi:](https://doi.org/10.3758/BF03206482)
+#' @references - Wagenmakers, E.J., & Farrell, S. (2004). AIC model selection using Akaike weights. *Psychonomic Bulletin and Review*, **11**, 192-196. \doi{10.3758/BF03206482}
 #' @export
 #' @md
 umxReduce <- function(model, report = c("markdown", "inline", "html"), baseFileName = "tmp", ...){
@@ -179,7 +179,7 @@ umxReduce.default <- function(model, ...){
 #' @family Twin Modeling Functions
 #' @seealso [umxReduceACE()], [umxReduce()]
 #' @references - Wagenmakers, E.J., & Farrell, S. (2004). AIC model selection using Akaike weights.
-#' *Psychonomic Bulletin and Review*, **11**, 192-196. [doi:](https://doi.org/10.3758/BF03206482).
+#' *Psychonomic Bulletin and Review*, **11**, 192-196. \doi{10.3758/BF03206482}.
 #' @md
 #' @examples
 #' \dontrun{
@@ -266,7 +266,7 @@ umxReduce.MxModelGxE <- umxReduceGxE
 #' @export
 #' @family Twin Modeling Functions
 #' @seealso [umxReduceGxE()], [umxReduce()]
-#' @references - Wagenmakers, E.J., & Farrell, S. (2004). AIC model selection using Akaike weights. *Psychonomic Bulletin and Review*, **11**, 192-196. [doi:](https://doi.org/10.3758/BF03206482)
+#' @references - Wagenmakers, E.J., & Farrell, S. (2004). AIC model selection using Akaike weights. *Psychonomic Bulletin and Review*, **11**, 192-196. \doi{10.3758/BF03206482}
 #' @md
 #' @examples
 #' \dontrun{

diff --git a/R/umxPower.R b/R/umxPower.R
@@ -41,10 +41,10 @@
 #' @seealso - [OpenMx::mxPower()]
 #' @references * Visscher, P.M., Gordon, S., Neale, M.C. (2008). Power of the classical twin design
 #' revisited: II detection of common environmental variance. *Twin Res Hum Genet*, **11**: 48-54.
-#' doi: [10.1375/twin.11.1.48](https://doi.org/10.1375/twin.11.1.48)
+#' \doi{10.1375/twin.11.1.48}.
 #' * Button, K. S., Ioannidis, J. P., Mokrysz, C., Nosek, B. A., Flint, J., Robinson, E. S., and Munafo, M. R. (2013).
 #' Power failure: why small sample size undermines the reliability of neuroscience. 
-#' *Nature Reviews Neuroscience*, **14**, 365-376. doi: [10.1038/nrn3475](https://doi.org/10.1038/nrn3475)
+#' *Nature Reviews Neuroscience*, **14**, 365-376. \doi{10.1038/nrn3475}
 #' @export
 #' @md
 #' @examples

diff --git a/R/umx_build_high_level_models.R b/R/umx_build_high_level_models.R
@@ -85,9 +85,9 @@
 #' @seealso - [factanal()], [mxFactorScores()]
 #' @references - <https://github.com/tbates/umx>,
 #' 
-#' Hendrickson, A. E. and White, P. O. (1964). Promax: a quick method for rotation to orthogonal oblique structure. *British Journal of Statistical Psychology*, **17**, 65–70. doi: [10.1111/j.2044-8317.1964.tb00244.x](https://doi.org/10.1111/j.2044-8317.1964.tb00244.x).
+#' Hendrickson, A. E. and White, P. O. (1964). Promax: a quick method for rotation to orthogonal oblique structure. *British Journal of Statistical Psychology*, **17**, 65–70. \doi{10.1111/j.2044-8317.1964.tb00244.x}.
 #' 
-#' Kaiser, H. F. (1958). The varimax criterion for analytic rotation in factor analysis. *Psychometrika*, **23**, 187–200. doi: [10.1007/BF02289233](https://doi.org/10.1007/BF02289233).
+#' Kaiser, H. F. (1958). The varimax criterion for analytic rotation in factor analysis. *Psychometrika*, **23**, 187–200. \doi{10.1007/BF02289233}.
 #' 
 #'
 #' @examples

diff --git a/R/umx_build_polychoricMatrix3.R b/R/umx_build_polychoricMatrix3.R
@@ -8,7 +8,7 @@
 #' @return - list of output and diagnostics. matrix of correlations = $polychorics
 #' @export
 #' @family Data Functions
-#' @references - \url{https://doi.org/10.3389/fpsyg.2016.00528}
+#' @references - \doi{10.3389/fpsyg.2016.00528}
 #' @examples
 #' tmp = mtcars
 #' tmp$am = umxFactor(mtcars$am)
@@ -213,7 +213,7 @@ umx_polychoric <- function(data, useDeviations = TRUE, tryHard = c("no", "yes",
 #' @return - matrix of correlations
 #' @export
 #' @family Data Functions
-#' @references - \url{https://doi.org/10.3389/fpsyg.2016.00528}
+#' @references - \doi{10.3389/fpsyg.2016.00528}
 #' @examples
 #' umx_set_optimizer("SLSQP")
 #' tmp = mtcars
@@ -286,7 +286,7 @@ umx_polypairwise <- function (data, useDeviations= TRUE, printFit= FALSE, use= "
 #' @return - matrix of correlations
 #' @export
 #' @family Data Functions
-#' @references - \url{https://doi.org/10.3389/fpsyg.2016.00528}
+#' @references - \doi{10.3389/fpsyg.2016.00528}
 #' @examples
 #' tmp = mtcars
 #' tmp$am = umxFactor(mtcars$am)

diff --git a/R/umx_build_umxACEv.R b/R/umx_build_umxACEv.R
@@ -94,7 +94,7 @@
 #' @family Twin Modeling Functions
 #' @references - Verhulst, B., Prom-Wormley, E., Keller, M., Medland, S., & Neale, M. C. (2019).
 #' Type I Error Rates and Parameter Bias in Multivariate Behavioral Genetic Models. *Behav Genet*, 
-#' **49**, 99-111. doi:<https://doi.org/10.1007/s10519-018-9942-y>
+#' **49**, 99-111. \doi{10.1007/s10519-018-9942-y}
 #' Eaves, L. J., Last, K. A., Young, P. A., & Martin, N. G. (1978). Model-fitting approaches 
 #' to the analysis of human behaviour. *Heredity*, **41**, 249-320. <https://www.nature.com/articles/hdy1978101.pdf>
 #' @md

diff --git a/R/umx_build_umxGxEbiv.R b/R/umx_build_umxGxEbiv.R
@@ -40,11 +40,11 @@
 #' @seealso - [plot()], [umxSummary()], [umxReduce()]
 #' @references
 #' - Purcell, S. (2002). Variance components models for gene-environment interaction in twin analysis. \emph{Twin Research}, 
-#' \strong{6}, 554-571. doi:[10.1375/twin.5.6.554](https://doi.org/10.1375/twin.5.6.554).
+#' \strong{6}, 554-571. \doi{10.1375/twin.5.6.554}.
 #' 
 #' - van der Sluis, S., Posthuma, D., & Dolan, C. V. (2012). A note on false positives and
 #' power in G x E modelling of twin data. \emph{Behavior Genetics}, 
-#' \strong{42}, 170-186. doi:[10.1007/s10519-011-9480-3](https://doi.org/10.1007/s10519-011-9480-3).
+#' \strong{42}, 170-186. \doi{10.1007/s10519-011-9480-3}.
 #'
 #' @examples
 #' require(umx)

diff --git a/cran-comments.md b/cran-comments.md
@@ -2,7 +2,7 @@
 new features
 ## Test environments
 * OS X 11.0.0, R version 4.0.3 (2020-06-22)
-* Win R Under development (unstable) (2020-12-09 r79601)
+* Win R Under development (unstable) (2021-01-21 r79854)
 * 64-bit Linux, R version 4.0.3
 
 ## R CMD check results

diff --git a/man/Fischbein_wt.Rd b/man/Fischbein_wt.Rd
diff --git a/man/power.ACE.test.Rd b/man/power.ACE.test.Rd
diff --git a/man/umxACEcov.Rd b/man/umxACEcov.Rd
diff --git a/man/umxACEv.Rd b/man/umxACEv.Rd
diff --git a/man/umxEFA.Rd b/man/umxEFA.Rd
diff --git a/man/umxExamples.Rd b/man/umxExamples.Rd
diff --git a/man/umxGxE.Rd b/man/umxGxE.Rd
diff --git a/man/umxGxEbiv.Rd b/man/umxGxEbiv.Rd
diff --git a/man/umxReduce.Rd b/man/umxReduce.Rd
diff --git a/man/umxReduceACE.Rd b/man/umxReduceACE.Rd
diff --git a/man/umxReduceGxE.Rd b/man/umxReduceGxE.Rd
diff --git a/man/umx_lower.tri.Rd b/man/umx_lower.tri.Rd
diff --git a/man/umx_polychoric.Rd b/man/umx_polychoric.Rd
diff --git a/man/umx_polypairwise.Rd b/man/umx_polypairwise.Rd
diff --git a/man/umx_polytriowise.Rd b/man/umx_polytriowise.Rd
diff --git a/man/umx_set_plot_file_suffix.Rd b/man/umx_set_plot_file_suffix.Rd
diff --git a/man/umx_set_plot_use_hrbrthemes.Rd b/man/umx_set_plot_use_hrbrthemes.Rd
diff --git a/man/umx_set_silent.Rd b/man/umx_set_silent.Rd