small form changes

analyses/Script_figure_1.Rmd

@@ -310,7 +310,7 @@ D <- ggplot2::ggplot(data=p1, ggplot2::aes(x=X, y=Y, z=Perf)) +
   ggplot2::labs(x="x", y = "y")
 
 Fig_1 <- ggpubr::ggarrange(A, D, B, C,
-                           labels=c("A", "C", "B", "D"),
+                           labels=c("a", "c", "b", "d"),
                            widths = c(1,1.3),
                            hjust=c(-3, -3, -3, -3),
                            vjust=c(2, 2, 2, 2))

analyses/clonal_analysis/clonal_analysis.Rmd

@@ -10,7 +10,7 @@ output:
     toc_float: true
     number_sections: true
 bibliography: "`r here::here('References.bib')`"
-csl: "`r here::here('ecology-letters.csl')`"
+csl: "`r here::here('bib_style.csl')`"
 header-includes:
   - \usepackage{booktabs}
   - \usepackage{longtable}
@@ -132,7 +132,7 @@ The dataset included `r nrow(Data)` growth estimates corresponding to `r length(
 
 ```{r PlotsGrowthLight, fig.cap="The original data without negative growth values (A) and the log-transformed growth (B).", message=FALSE, warning=FALSE}
 
-g <- ggpubr::ggarrange(plot1,plot2,ncol=2,nrow=1,labels=c("A", "B"))
+g <- ggpubr::ggarrange(plot1,plot2,ncol=2,nrow=1,labels=c("a", "b"))
 ggplot2::ggsave(filename = "Histograms_Raw_Data.png", plot = g, path=here::here("outputs", "clonal_analysis", "figures"), device = "png", width = 7, height = 5)
 knitr::include_graphics(here::here("outputs", "clonal_analysis", "figures", "Histograms_Raw_Data.png"))
 
@@ -418,7 +418,7 @@ Sum_EUCFLUX <- summary(brms_mod)
 ```
 
 ```{r PlotsRanef, fig.cap="Mean values and 95% confidence interval of the temporal, genetic and spatial and random effects."}
-g <- ggpubr::ggarrange(g1, g2, g3, ncol=1, nrow=3, labels = c("A", "B", "C"))
+g <- ggpubr::ggarrange(g1, g2, g3, ncol=1, nrow=3, labels = c("a", "b", "c"))
 ggplot2::ggsave(filename = "Ranef_values.png", plot = g, path=here::here("outputs", "clonal_analysis", "figures"), device = "png", width = 7, height = 10 )
 knitr::include_graphics(here::here("outputs", "clonal_analysis", "figures", "Ranef_values.png"))
 ```

analyses/full_supplementary.Rmd

@@ -5,7 +5,7 @@ output:
     toc_float: true
     number_sections: true
 bibliography: "`r here::here('References.bib')`"
-csl: "`r here::here('ecology-letters.csl')`"
+csl: "`r here::here('bib_style.csl')`"
 always_allow_html: true
 ---
 ```{r setup, include=FALSE}
@@ -892,7 +892,7 @@ The dataset included `r nrow(Data)` growth estimates corresponding to `r length(
 
 ```{r PlotsGrowthLight, fig.cap="The original data without negative growth values (A) and the log-transformed growth (B).", message=FALSE, warning=FALSE}
 
-g <- ggpubr::ggarrange(plot1,plot2,ncol=2,nrow=1,labels=c("A", "B"))
+g <- ggpubr::ggarrange(plot1,plot2,ncol=2,nrow=1,labels=c("a", "b"))
 ggplot2::ggsave(filename = "Histograms_Raw_Data.png", plot = g, path=here::here("outputs", "clonal_analysis", "figures"), device = "png", width = 7, height = 5)
 knitr::include_graphics(here::here("outputs", "clonal_analysis", "figures", "Histograms_Raw_Data.png"))
 
@@ -1178,7 +1178,7 @@ Sum_EUCFLUX <- summary(brms_mod)
 ```
 
 ```{r PlotsRanef, fig.cap="Mean values and 95% confidence interval of the temporal, genetic and spatial and random effects."}
-g <- ggpubr::ggarrange(g1, g2, g3, ncol=1, nrow=3, labels = c("A", "B", "C"))
+g <- ggpubr::ggarrange(g1, g2, g3, ncol=1, nrow=3, labels = c("a", "b", "c"))
 ggplot2::ggsave(filename = "Ranef_values.png", plot = g, path=here::here("outputs", "clonal_analysis", "figures"), device = "png", width = 7, height = 10 )
 knitr::include_graphics(here::here("outputs", "clonal_analysis", "figures", "Ranef_values.png"))
 ```
@@ -1591,15 +1591,15 @@ ggplot2::ggsave(filename = "Map_growth.png", plot=A, path=here::here("outputs",
 
 ```{r HistogramsGrowth, fig.cap="Histogram of raw and log-transformed Y with and without genetic IV"}
 
-g <- ggpubr::ggarrange(histo1, histo2, histo3, histo4, ncol=2, nrow=2, labels=c("A", "B", "C", "D"))
+g <- ggpubr::ggarrange(histo1, histo2, histo3, histo4, ncol=2, nrow=2, labels=c("a", "b", "c", "d"))
 ggplot2::ggsave(filename="arranged_histograms_theoretical.png",path=here::here("outputs", "theoretical_model", "figures"),plot=g, device = "png", width = 7, height = 5, dpi = 300)
 knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "arranged_histograms_theoretical.png"))
 
 ```
 
 ```{r PlotsXY, fig.cap="Raw and log-transformed Y versus X1 plots with and without genetic IV"}
 
-g <- ggpubr::ggarrange(scatterplot1, scatterplot2, scatterplot3, scatterplot4, ncol=2, nrow=2, labels=c("A", "B", "C", "D"))
+g <- ggpubr::ggarrange(scatterplot1, scatterplot2, scatterplot3, scatterplot4, ncol=2, nrow=2, labels=c("a", "b", "c", "d"))
 ggplot2::ggsave(filename="arranged_plots_theoretical.png",path=here::here("outputs", "theoretical_model", "figures"),plot=g, device = "png", width = 7, height = 5, dpi = 300)
 knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "arranged_plots_theoretical.png"))
 ```
@@ -1990,7 +1990,7 @@ knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "P
 
 ```{r TwoPanelsFigure, fig.cap="Response to an environmental variable and inferred intraspecific variability. (A) Positions of a sample of I=600 individuals from J=2 species in a landscape defined by a square grid of C x C cells (C=500). The background color indicates the value of the environmental variable X1 (e.g., light) on each cell at date t. The response (e.g., growth) of each individual, which depends on the environment within each cell (Eq. I), is also indicated by a color scale. (B) Response as a function of the observed environmental variable X1 for the two species. Points represent the data {Yijt, X1ijt}. Thick lines represent the predictive posterior means for the two species. The envelopes delimited by two thin lines represent the 95% credible intervals of the predictive posterior marginalized over individuals (taking into account Vbj). The envelopes thus represent the intraspecific variability which is due to the N-1 unobserved environmental variables. "}
 
-g <- ggpubr::ggarrange(A, B, ncol = 2, labels = c("A", "B"))
+g <- ggpubr::ggarrange(A, B, ncol = 2, labels = c("a", "b"))
 ggplot2::ggsave(filename = "landscape_relationship.png",plot=g, path=here::here("outputs", "theoretical_model", "figures"), device = "png", width = 10, height = 5, bg="white", dpi = 300)
 
 knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "landscape_relationship.png"))
@@ -2438,7 +2438,7 @@ D <- ggplot2::ggplot(data=p1, ggplot2::aes(x=X, y=Y, z=Perf)) +
   ggplot2::labs(x="x", y = "y")
 
 Fig_1 <- ggpubr::ggarrange(A, D, B, C,
-                           labels=c("A", "C", "B", "D"),
+                           labels=c("a", "c", "b", "d"),
                            widths = c(1,1.3),
                            hjust=c(-3, -3, -3, -3),
                            vjust=c(2, 2, 2, 2))

analyses/theoretical_model/theoretical_model.Rmd

@@ -10,7 +10,7 @@ output:
     toc_float: true
     number_sections: true
 bibliography: "`r here::here('References.bib')`"
-csl: "`r here::here('ecology-letters.csl')`"
+csl: "`r here::here('bib_style.csl')`"
 header-includes:
   - \usepackage{booktabs}
   - \usepackage{longtable}
@@ -369,15 +369,15 @@ ggplot2::ggsave(filename = "Map_growth.png", plot=A, path=here::here("outputs",
 
 ```{r HistogramsGrowth, fig.cap="Histogram of raw and log-transformed Y with and without genetic IV"}
 
-g <- ggpubr::ggarrange(histo1, histo2, histo3, histo4, ncol=2, nrow=2, labels=c("A", "B", "C", "D"))
+g <- ggpubr::ggarrange(histo1, histo2, histo3, histo4, ncol=2, nrow=2, labels=c("a", "b", "c", "d"))
 ggplot2::ggsave(filename="arranged_histograms_theoretical.png",path=here::here("outputs", "theoretical_model", "figures"),plot=g, device = "png", width = 7, height = 5, dpi = 300)
 knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "arranged_histograms_theoretical.png"))
 
 ```
 
 ```{r PlotsXY, fig.cap="Raw and log-transformed Y versus X1 plots with and without genetic IV"}
 
-g <- ggpubr::ggarrange(scatterplot1, scatterplot2, scatterplot3, scatterplot4, ncol=2, nrow=2, labels=c("A", "B", "C", "D"))
+g <- ggpubr::ggarrange(scatterplot1, scatterplot2, scatterplot3, scatterplot4, ncol=2, nrow=2, labels=c("a", "b", "c", "d"))
 ggplot2::ggsave(filename="arranged_plots_theoretical.png",path=here::here("outputs", "theoretical_model", "figures"),plot=g, device = "png", width = 7, height = 5, dpi = 300)
 knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "arranged_plots_theoretical.png"))
 ```
@@ -768,7 +768,7 @@ knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "P
 
 ```{r TwoPanelsFigure, fig.cap="Response to an environmental variable and inferred intraspecific variability. (A) Positions of a sample of I=600 individuals from J=2 species in a landscape defined by a square grid of C x C cells (C=500). The background color indicates the value of the environmental variable X1 (e.g., light) on each cell at date t. The response (e.g., growth) of each individual, which depends on the environment within each cell (Eq. I), is also indicated by a color scale. (B) Response as a function of the observed environmental variable X1 for the two species. Points represent the data {Yijt, X1ijt}. Thick lines represent the predictive posterior means for the two species. The envelopes delimited by two thin lines represent the 95% credible intervals of the predictive posterior marginalized over individuals (taking into account Vbj). The envelopes thus represent the intraspecific variability which is due to the N-1 unobserved environmental variables. "}
 
-g <- ggpubr::ggarrange(A, B, ncol = 2, labels = c("A", "B"))
+g <- ggpubr::ggarrange(A, B, ncol = 2, labels = c("a", "b"))
 ggplot2::ggsave(filename = "landscape_relationship.png",plot=g, path=here::here("outputs", "theoretical_model", "figures"), device = "png", width = 10, height = 5, bg="white", dpi = 300)
 
 knitr::include_graphics(here::here("outputs", "theoretical_model", "figures", "landscape_relationship.png"))

analyses/tropical_analysis/tropical_analysis.Rmd

@@ -10,7 +10,7 @@ output:
     toc_float: true
     number_sections: true
 bibliography: "`r here::here('References.bib')`"
-csl: "`r here::here('ecology-letters.csl')`"
+csl: "`r here::here('bib_style.csl')`"
 header-includes:
   - \usepackage{booktabs}
   - \usepackage{longtable}

bib_style.csl

@@ -0,0 +1,188 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" default-locale="en-US" version="1.0" demote-non-dropping-particle="sort-only">
+  <info>
+    <title>Ecology</title>
+    <id>http://www.zotero.org/styles/ecology</id>
+    <link href="http://www.zotero.org/styles/ecology" rel="self"/>
+    <link href="http://esapubs.org/esapubs/AuthorInstructions.htm" rel="documentation"/>
+    <author>
+      <name>Rintze Zelle</name>
+      <uri>http://twitter.com/rintzezelle</uri>
+    </author>
+    <category citation-format="author-date"/>
+    <category field="biology"/>
+    <issn>0012-9658</issn>
+    <updated>2015-07-27T08:57:33+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="container-contributors">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <text term="in" suffix=" " font-style="italic"/>
+        <names variable="editor translator" delimiter=", ">
+          <name and="text" initialize-with=". " delimiter=", "/>
+          <label form="long" prefix=", " suffix="."/>
+        </names>
+      </if>
+    </choose>
+  </macro>
+  <macro name="secondary-contributors">
+    <choose>
+      <if type="chapter paper-conference" match="none">
+        <names variable="editor translator" delimiter=", " prefix=" (" suffix=")">
+          <name and="text" initialize-with=". " delimiter=", "/>
+          <label form="short" prefix=", " text-case="capitalize-first"/>
+        </names>
+      </if>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name name-as-sort-order="first" and="text" sort-separator=", " initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
+      <label prefix=", "/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <text variable="title"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="author-short">
+    <names variable="author">
+      <name form="short" and="text" delimiter=", " initialize-with=". "/>
+      <substitute>
+        <names variable="editor"/>
+        <names variable="translator"/>
+        <choose>
+          <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+            <text variable="title" form="short" font-style="italic"/>
+          </if>
+          <else>
+            <text variable="title" form="short" quotes="true"/>
+          </else>
+        </choose>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if type="webpage">
+        <text variable="URL"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="publisher">
+    <group delimiter=", ">
+      <choose>
+        <if type="article-journal article-magazine" match="none">
+          <text variable="genre"/>
+          <text variable="publisher"/>
+          <text variable="publisher-place"/>
+        </if>
+      </choose>
+    </group>
+  </macro>
+  <macro name="issued">
+    <choose>
+      <if variable="issued">
+        <group prefix=" " suffix=".">
+          <date variable="issued">
+            <date-part name="year"/>
+          </date>
+          <choose>
+            <if type="article-journal bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="none">
+              <date variable="issued">
+                <date-part prefix=", " name="month"/>
+                <date-part prefix=" " name="day"/>
+              </date>
+            </if>
+          </choose>
+        </group>
+      </if>
+      <else>
+        <text prefix=" (" term="no date" suffix=")." form="short"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="issued-year">
+    <choose>
+      <if variable="issued">
+        <date variable="issued">
+          <date-part name="year"/>
+        </date>
+      </if>
+      <else>
+        <text term="no date" form="short"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
+        <choose>
+          <if is-numeric="edition">
+            <number variable="edition" form="long-ordinal" text-case="capitalize-first"/>
+            <text term="edition" form="long" prefix=" " suffix="."/>
+          </if>
+          <else>
+            <text variable="edition" suffix="."/>
+          </else>
+        </choose>
+      </if>
+    </choose>
+  </macro>
+  <macro name="locators">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper" match="any">
+        <text variable="container-title" prefix=". "/>
+        <text variable="volume" prefix=" "/>
+        <text variable="page" prefix=":"/>
+      </if>
+      <else-if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
+        <group prefix=". " delimiter=" ">
+          <label variable="page" form="long" text-case="capitalize-first"/>
+          <text variable="page"/>
+          <text macro="container-contributors"/>
+          <text macro="secondary-contributors"/>
+          <text variable="container-title"/>
+        </group>
+      </else-if>
+    </choose>
+  </macro>
+  <macro name="citation-locator">
+    <group>
+      <label variable="locator" form="short"/>
+      <text variable="locator" prefix=" "/>
+    </group>
+  </macro>
+  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" collapse="year">
+    <sort>
+      <key variable="issued"/>
+      <key macro="author"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter=", ">
+      <group delimiter=" ">
+        <text macro="author-short"/>
+        <text macro="issued-year"/>
+        <text macro="citation-locator"/>
+      </group>
+    </layout>
+  </citation>
+  <bibliography hanging-indent="true" entry-spacing="0" line-spacing="2">
+    <sort>
+      <key macro="author"/>
+      <key variable="issued"/>
+    </sort>
+    <layout suffix=".">
+      <text macro="author" suffix="."/>
+      <text macro="issued" suffix=" "/>
+      <text variable="title"/>
+      <text macro="locators"/>
+      <group delimiter=". " prefix=". ">
+        <text macro="edition"/>
+        <text macro="publisher"/>
+        <text macro="access"/>
+      </group>
+    </layout>
+  </bibliography>
+</style>