Merge pull request #295 from pbs-assess/Lewis-Barnett-NOAA-patch-3

text edits to standardize reference formats

R/fit.R

@@ -295,7 +295,7 @@ NULL
 #'
 #' *Reference for local trends:*
 #'
-#' Barnett, L.A.K., E.J. Ward, S.C. Anderson. Improving estimates of species
+#' Barnett, L.A.K., E.J. Ward, S.C. Anderson. 2021. Improving estimates of species
 #' distribution change by incorporating local trends. Ecography. 44(3):427-439.
 #' \doi{10.1111/ecog.05176}.
 #'
@@ -311,14 +311,14 @@ NULL
 #' *Discussion of and illustration of some decision points when fitting these
 #' models:*
 #'
-#' Commander, C.J.C., Barnett, L.A.K., Ward, E.J., Anderson, S.C., and
-#' Essington, T.E. 2022. The shadow model: how and why small choices in
+#' Commander, C.J.C., L.A.K. Barnett, E.J. Ward, S.C. Anderson, T.E.
+#' Essington. 2022. The shadow model: how and why small choices in
 #' spatially explicit species distribution models affect predictions. PeerJ 10:
 #' e12783. \doi{10.7717/peerj.12783}.
 #'
 #' *Application and description of threshold/break-point models:*
 #'
-#' Essington, T.E. S.C. Anderson, L.A.K. Barnett, H.M. Berger, S.A. Siedlecki,
+#' Essington, T.E., S.C. Anderson, L.A.K. Barnett, H.M. Berger, S.A. Siedlecki,
 #' E.J. Ward. 2022. Advancing statistical models to reveal the effect of
 #' dissolved oxygen on the spatial distribution of marine taxa using thresholds
 #' and a physiologically based index. Ecography. 2022: e06249
@@ -333,7 +333,7 @@ NULL
 #' *Several sections of the original TMB model code were adapted from the
 #' VAST R package:*
 #'
-#' Thorson, J.T., 2019. Guidance for decisions using the Vector Autoregressive
+#' Thorson, J.T. 2019. Guidance for decisions using the Vector Autoregressive
 #' Spatio-Temporal (VAST) package in stock, ecosystem, habitat and climate
 #' assessments. Fish. Res. 210:143–161.
 #' \doi{10.1016/j.fishres.2018.10.013}.
@@ -343,16 +343,16 @@ NULL
 #' idea behind the TMB prediction approach were adapted from the glmmTMB R
 #' package:*
 #'
-#' Mollie E. Brooks, Kasper Kristensen, Koen J. van Benthem, Arni Magnusson,
-#' Casper W. Berg, Anders Nielsen, Hans J. Skaug, Martin Maechler and Benjamin
-#' M. Bolker (2017). glmmTMB Balances Speed and Flexibility Among Packages for
+#' Brooks, M.E., K. Kristensen, K.J. van Benthem, A. Magnusson,
+#' C.W. Berg, A. Nielsen, H.J. Skaug, M. Maechler, B.M. Bolker.
+#'  2017. glmmTMB Balances Speed and Flexibility Among Packages for
 #' Zero-inflated Generalized Linear Mixed Modeling. The R Journal, 9(2):378-400.
 #' \doi{10.32614/rj-2017-066}.
 #'
 #' *Implementation of geometric anisotropy with the SPDE and use of random
 #' field GLMMs for index standardization*:
 #'
-#' Thorson, J.T., Shelton, A.O., Ward, E.J., and Skaug, H.J. 2015.
+#' Thorson, J.T., A.O. Shelton, E.J. Ward, H.J. Skaug. 2015.
 #' Geostatistical delta-generalized linear mixed models improve precision for
 #' estimated abundance indices for West Coast groundfishes. ICES J. Mar. Sci.
 #' 72(5): 1297–1310. \doi{10.1093/icesjms/fsu243}.