updating scripts and readme, deleting unnecessary files

README.md

@@ -1,34 +1,55 @@
-## **Paleoecological Analysis in R**
+# **Paleoecological Analysis in R**
 
-
-
-|Open the Gitbook to get started: [johannabosch/Paleoecological Analysis in R](https://johannabosch.github.io/Paleolimnological_Analysis_in_R/)|
-|--|
-|This is a tutorial-based review of the analysis from Bosch et al. 2024 (see below), hosted by Github pages. It includes a total of 5 chapters, each pertaining to a specific analysis conducted in R using the data found in this repository|
-
-### Study overview
+## Study overview
 
 This is a public repo that can be used to learn how to conduct a paleoecological analysis in R. The project methods described here are formally reviewed and cited in the following paper. Please use this citation to cite this repository:
 
     Bosch J, Álvarez-Manzaneda I, Smol J, Michelutti N, Robertson GJ, Wilhelm SI, Montevecchi WA. 2024 Blending census and paleolimnological data allows for tracking the establishment and growth of a major gannet colony over several centuries. Proceedings of the Royal Society B [in review].
+
 
-### Accessing the data
+## Accessing the data
 
 A list of each of the data files from the `/data` folder and their contents:
 
-* `FileS1_ColonialSeabirdDatabase_WilhelmSI.csv` : Historical population reports collected for seabird species nesting in Cape St. Mary’s Ecological Reserve from 1883-2018. A blank cell indicates that population counts were not collected for that year.
+
+| File name | Descriptions |
+|----|---|
+|`FileS1_ColonialSeabirdDatabase_WilhelmSI.csv`| Historical population reports collected for seabird species nesting in Cape St. Mary’s Ecological Reserve from 1883-2018. A blank cell indicates that population counts were not collected for that year. |
+|`FileS2_MonitoringData.csv`|Raw monitoring data from File S1 used to align population data to the proxies.|
+|`FileS3_Dating_CSM-IMP.csv` and `File S4_Dating_CSM-REF.csv`| Table containing 210Pb dating profiles over the depth of the impact core (CSM-IMP) and reference core (CSM-REF).|
+|`FileS5_ProxyData_CSM-IMP.csv` and `FileS6_ProxyData_CSM-REF.csv`| Table containing the isotope, metal(loid), chlorophyll a, and diatom count data for the depths of the sediment core collected from the reference pond.|
+|`File S7_Metalloids_CSM-IMP.csv` and `File S8_Metalloids_CSM-REF.csv`|Table of all metal(loid)s analyzed for the impact core and reference core.|
+|`FileS9_ZScores_CSM-IMP.csv` | Z-score data for the isotope, metal(loid)s, chlorophyll a, and diatom count for the depths of the sediment core collected from the impact pond.|
 
 
-* `FileS2_MonitoringData.csv` : Raw monitoring data from File S1 used to align population data to the proxies.
+## Scripts and Figures
 
+Here is a description of all the scripts used in this analysis (see `/scripts`) and the final figures produced by each script.
 
-* `FileS3_Dating_CSM-IMP.csv` and `File S4_Dating_CSM-REF.csv` : Table containing 210Pb dating profiles over the depth of the impact core (CSM-IMP) and reference core (CSM-REF).
+### **Proxy Alignment with Population Data**
+- **Script:** See `scripts/Z_score_analysis.R`
+![Proxy Alignment with Population Data](figs/proxy_alignment_populations.png)
 
+### **Broken Stick Analysis for Metals**
+- **Script:** See `scripts/breakpoint_analysis_metals.R`
+![Broken Stick Analysis for Metals](figs/broken_stick_metals.png)
 
-* `FileS5_ProxyData_CSM-IMP.csv` and `FileS6_ProxyData_CSM-REF.csv` : Table containing the isotope, metal(loid), chlorophyll a, and diatom count data for the depths of the sediment core collected from the reference pond.
+### **Core Activity**
+- **Script:** See `scripts/dating_profiles.R`
+![Core Activity](figs/core_activity.png)
 
+### **Core Age Model**
+- **Script:** See `scripts/dating_profiles.R`
+![Core Age Model](figs/core_age.png)
 
-* `File S7_Metalloids_CSM-IMP.csv` and `File S8_Metalloids_CSM-REF.csv` : Table of all metal(loid)s analyzed for the impact core and reference core.
+### **GAM Depth Plot**
+- **Script:** See `scripts/GAM_depth.R`
+![GAM Depth Plot](figs/GAM_depth.png)
 
+### **Nested Metals Plot**
+- **Script:** See `scripts/breakpoint_analysis_metals.R`
+![Nested Metals Plot](figs/nested_metals.png)
 
-* `FileS9_ZScores_CSM-IMP.csv` : Z-score data for the isotope, metal(loid)s, chlorophyll a, and diatom count for the depths of the sediment core collected from the impact pond.
+### **Paleostratigraphies**
+- **Script:** See `scripts/paleostratigraphies.R`
+![Paleostratigraphies](figs/paleostratigraphies.png)

data/FileS4_Dating_CSM-REF.csv

@@ -1,4 +1,4 @@
-midpoint,Total 210Pb_activity (Bq/kg),Error Total 210Pb_activity (Bq/kg),Sed. Rate (cm/y),Error Sed. Rate (cm/y),Year (CRS),Age (CRS),Error (CRS)
+depth,Total 210Pb_activity (Bq/kg),Error Total 210Pb_activity (Bq/kg),Sed. Rate (cm/y),Error Sed. Rate (cm/y),Year (CRS),Age (CRS),Error (CRS)
 0,,,,,2021.68,0,0
 0.25,572.38,39.95,0.0359,0.003,2015.39,6.3,0.68
 0.75,644.69,39.98,0.019,0.0016,1996.48,25.21,1.89

data/FileS5_ProxyData_CSM-IMP.csv

@@ -1,83 +1,83 @@
-midpoint,chla,Al,P,Zn,Cd,d15N,d13C,S.cons,S.exi
-0.125,0.145270351,,,,,,,99.36170213,0
-0.375,0.137215245,9700,8700,100,2,,,,
-0.625,0.114581613,,,,,10.91,-27.05,,
-0.875,0.125933135,,,,,,,,
-1.125,0.10597335,,,,,,,98.9626556,0.829875519
-1.375,0.095384889,12000,8600,140,2.6,,,,
-1.625,0.098482268,,,,,10.52,-27.24,,
-1.875,0.101783636,,,,,,,,
-2.125,0.11823101,,,,,,,98.43400447,1.342281879
-2.375,0.113150233,11000,9100,140,2.6,,,,
-2.625,0.127812676,,,,,10.97,-26.65,,
-2.875,0.122760865,,,,,,,,
-3.125,0.10051457,,,,,,,99.5584989,0
-3.375,0.110048778,12000,9400,140,2.5,,,,
-3.625,0.095809123,,,,,10.81,-26.68,,
-3.875,0.078333919,,,,,,,,
-4.125,0.089725407,,,,,,,96.98681733,1.506591337
-4.375,0.092749386,12000,9300,140,2.4,,,,
-4.625,0.063825771,,,,,9.88,-26.87,,
-4.875,0.066423368,,,,,,,,
-5.125,0.057837761,,,,,,,99.19224556,0
-5.375,0.038124295,7600,1900,70,0.69,,,,
-5.625,0.021130601,,,,,6.6,-27.14,,
-5.875,0.018618849,,,,,,,,
-6.125,0.019621569,,,,,,,91.92825112,7.623318386
-6.375,0.012173345,7500,1900,57,0.61,,,,
-6.625,0.011422115,,,,,2.03,-26.84,,
-6.875,0.012290873,,,,,,,,
-7.125,0.009889201,,,,,,,67.32673267,30.44554455
-7.375,0.010313611,8300,1900,46,0.55,,,,
-7.625,0.008518601,,,,,1.56,-26.63,,
-7.875,0.008423684,,,,,,,,
-8.125,0.008307514,,,,,,,48.26789838,45.72748268
-8.375,0.008086348,7700,1500,28,0.39,,,,
-8.625,0.007920309,,,,,1.31,-26.66,,
-8.875,0.008470573,,,,,,,,
-9.125,0.009500857,,,,,1.1,-26.57,63.57466063,34.61538462
-9.375,0.008822984,8200,1500,27,0.42,,,,
-9.625,0.008322194,,,,,,,,
-9.875,0.007737618,,,,,,,,
-10.125,0.009139681,,,,,1.19,-26.66,38.18181818,60.77922078
-10.375,0.008866411,7300,1000,22,0.36,,,,
-10.625,0.009233503,,,,,,,,
-10.875,0.009553048,,,,,,,,
-11.125,0.008989856,,,,,0.63,-26.51,48.8700565,51.1299435
-11.375,0.00830988,6500,970,17,0.34,,,,
-11.625,0.007843139,,,,,,,,
-11.875,0.008911591,,,,,,,,
-12.125,0.006402951,,,,,0.59,-26.53,36.99059561,62.69592476
-12.375,0.007844279,4500,700,11,0.25,,,,
-12.625,0.006342522,,,,,,,,
-12.875,0.00582727,,,,,,,,
-13.125,0.004688441,,,,,1.02,-26.76,38.56041131,59.89717224
-13.375,0.005974773,3900,590,8.8,0.23,,,,
-13.625,0.006078542,,,,,,,,
-13.875,0.005798085,,,,,,,,
-14.125,0.005294491,,,,,0.88,-26.9,26.83615819,71.18644068
-14.375,0.006329112,3800,560,7.4,0.16,,,,
-14.625,0.005333492,,,,,,,,
-14.875,0.005979681,,,,,,,,
-15.25,0.00732149,,,,,0.16,-26.75,26.39296188,71.5542522
-15.75,0.005624772,,,,,,,,
-16.25,0.005426568,,,,,0.79,-26.85,93.33333333,4.761904762
-16.75,0.004616399,,,,,,,,
-17.25,0.005131782,,,,,1.46,-27.29,,
-17.75,0.006898658,,,,,,,,
-18.25,0.006522627,,,,,1.36,-26.71,,
-18.75,0.005801503,,,,,,,,
-19.25,0.006620656,,,,,1.81,-27.27,,
-19.75,0.004970344,,,,,,,,
-20.25,0.005253386,,,,,1.49,-26.56,,
-20.75,0.005709259,,,,,,,,
-21.25,0.005876788,,,,,1.81,-27.24,,
-21.75,0.005570214,,,,,,,,
-22.25,0.005648216,,,,,0.2,-26.37,,
-22.75,0.005321178,,,,,,,,
-23.25,0.005717279,,,,,1.15,-27.29,,
-23.75,0.004890984,,,,,,,,
-24.25,0.004610089,,,,,1.05,-27.25,,
-24.75,0.004503866,,,,,,,,
-25.25,0.004808118,,,,,1.22,-27.28,,
-25.75,0.004901238,,,,,,,,
+midpoint,year,chla,Al,P,Zn,Cd,d15N,d13C,S.cons,S.exi
+0.125,2021.04,0.145270351,,,,,,,99.36170213,0
+0.375,2019.42,0.137215245,9700,8700,100,2,,,,
+0.625,2017.8,0.114581613,,,,,10.91,-27.05,,
+0.875,2016.17,0.125933135,,,,,,,,
+1.125,2014.55,0.10597335,,,,,,,98.9626556,0.829875519
+1.375,2012.22,0.095384889,12000,8600,140,2.6,,,,
+1.625,2009.89,0.098482268,,,,,10.52,-27.24,,
+1.875,2007.56,0.101783636,,,,,,,,
+2.125,2005.23,0.11823101,,,,,,,98.43400447,1.342281879
+2.375,2003.23,0.113150233,11000,9100,140,2.6,,,,
+2.625,2001.22,0.127812676,,,,,10.97,-26.65,,
+2.875,1999.22,0.122760865,,,,,,,,
+3.125,1997.21,0.10051457,,,,,,,99.5584989,0
+3.375,1994.62,0.110048778,12000,9400,140,2.5,,,,
+3.625,1992.03,0.095809123,,,,,10.81,-26.68,,
+3.875,1989.43,0.078333919,,,,,,,,
+4.125,1986.84,0.089725407,,,,,,,96.98681733,1.506591337
+4.375,1981.23,0.092749386,12000,9300,140,2.4,,,,
+4.625,1975.62,0.063825771,,,,,9.88,-26.87,,
+4.875,1970,0.066423368,,,,,,,,
+5.125,1964.39,0.057837761,,,,,,,99.19224556,0
+5.375,1956.29,0.038124295,7600,1900,70,0.69,,,,
+5.625,1948.19,0.021130601,,,,,6.6,-27.14,,
+5.875,1940.08,0.018618849,,,,,,,,
+6.125,1931.98,0.019621569,,,,,,,91.92825112,7.623318386
+6.375,1928.17,0.012173345,7500,1900,57,0.61,,,,
+6.625,1924.36,0.011422115,,,,,2.03,-26.84,,
+6.875,1920.54,0.012290873,,,,,,,,
+7.125,1916.73,0.009889201,,,,,,,67.32673267,30.44554455
+7.375,1908.49,0.010313611,8300,1900,46,0.55,,,,
+7.625,1900.26,0.008518601,,,,,1.56,-26.63,,
+7.875,1892.02,0.008423684,,,,,,,,
+8.125,1883.78,0.008307514,,,,,,,48.26789838,45.72748268
+8.375,1874.78,0.008086348,7700,1500,28,0.39,,,,
+8.625,1866.37,0.007920309,,,,,1.31,-26.66,,
+8.875,1857.72,0.008470573,,,,,,,,
+9.125,1848.83,0.009500857,,,,,1.1,-26.57,63.57466063,34.61538462
+9.375,1839.7,0.008822984,8200,1500,27,0.42,,,,
+9.625,1830.33,0.008322194,,,,,,,,
+9.875,1820.73,0.007737618,,,,,,,,
+10.125,1810.89,0.009139681,,,,,1.19,-26.66,38.18181818,60.77922078
+10.375,1800.81,0.008866411,7300,1000,22,0.36,,,,
+10.625,1790.49,0.009233503,,,,,,,,
+10.875,1779.94,0.009553048,,,,,,,,
+11.125,1769.14,0.008989856,,,,,0.63,-26.51,48.8700565,51.1299435
+11.375,1758.11,0.00830988,6500,970,17,0.34,,,,
+11.625,1746.84,0.007843139,,,,,,,,
+11.875,1735.33,0.008911591,,,,,,,,
+12.125,1723.59,0.006402951,,,,,0.59,-26.53,36.99059561,62.69592476
+12.375,1711.6,0.007844279,4500,700,11,0.25,,,,
+12.625,1699.38,0.006342522,,,,,,,,
+12.875,1686.92,0.00582727,,,,,,,,
+13.125,1674.23,0.004688441,,,,,1.02,-26.76,38.56041131,59.89717224
+13.375,1661.29,0.005974773,3900,590,8.8,0.23,,,,
+13.625,1648.12,0.006078542,,,,,,,,
+13.875,1634.71,0.005798085,,,,,,,,
+14.125,1621.06,0.005294491,,,,,0.88,-26.9,26.83615819,71.18644068
+14.375,1607.17,0.006329112,3800,560,7.4,0.16,,,,
+14.625,1593.04,0.005333492,,,,,,,,
+14.875,1578.68,0.005979681,,,,,,,,
+15.25,1556.69,0.00732149,,,,,0.16,-26.75,26.39296188,71.5542522
+15.75,,0.005624772,,,,,,,,
+16.25,,0.005426568,,,,,0.79,-26.85,93.33333333,4.761904762
+16.75,,0.004616399,,,,,,,,
+17.25,,0.005131782,,,,,1.46,-27.29,,
+17.75,,0.006898658,,,,,,,,
+18.25,,0.006522627,,,,,1.36,-26.71,,
+18.75,,0.005801503,,,,,,,,
+19.25,,0.006620656,,,,,1.81,-27.27,,
+19.75,,0.004970344,,,,,,,,
+20.25,,0.005253386,,,,,1.49,-26.56,,
+20.75,,0.005709259,,,,,,,,
+21.25,,0.005876788,,,,,1.81,-27.24,,
+21.75,,0.005570214,,,,,,,,
+22.25,,0.005648216,,,,,0.2,-26.37,,
+22.75,,0.005321178,,,,,,,,
+23.25,,0.005717279,,,,,1.15,-27.29,,
+23.75,,0.004890984,,,,,,,,
+24.25,,0.004610089,,,,,1.05,-27.25,,
+24.75,,0.004503866,,,,,,,,
+25.25,,0.004808118,,,,,1.22,-27.28,,
+25.75,,0.004901238,,,,,,,,

data/FileS9_ZScores_CSM-IMP.csv

@@ -1,4 +1,4 @@
-Depth (cm),year,z_d15N,z_chla,z_P,z_Zn,Z_Cd,z_S.cons,mean
+depth,year,z_d15N,z_chla,z_P,z_Zn,Z_Cd,z_S.cons,mean
 0,2021.04,1.992103479,2.597660062,1.271586818,0.879950296,1.245704793,1.099482742,1.514414698
 1,2014.55,1.891685372,1.692550449,1.2454153,1.205447201,1.382974468,1.080630792,1.416450597
 2,2005.23,2.007552419,1.97487545,1.37627289,1.459776775,1.640943262,1.064315478,1.587289379
@@ -7,7 +7,7 @@
 5,1964.39,0.882354655,0.583865737,-0.508076402,0.616473453,-0.265623675,1.087713003,0.399451129
 6,1931.98,-0.294339573,-0.296350093,-0.508076402,0.230274953,-0.389469585,0.863554095,-0.065734434
 7,1916.73,-0.415356266,-0.520511212,-0.508076402,-0.263185703,-0.586816908,0.109522398,-0.364070682
-8,1910.092734,-0.479726848,-0.556941481,-0.612762473,-0.720190995,-0.791333939,-0.411644981,-0.595433453
-9,1879.731084,-0.533798136,-0.529455775,-0.612762473,-0.80260441,-0.783866603,-0.011418306,-0.545650951
-10,1845.706634,-0.510624727,-0.537774561,-0.743620063,-0.869503856,-0.808808869,-0.798077547,-0.711401604
-11,1808.019384,-0.654814829,-0.541225414,-0.751471519,-0.965018144,-0.769614842,-0.465192048,-0.691222799
+8,1883.78,-0.479726848,-0.556941481,-0.612762473,-0.720190995,-0.791333939,-0.411644981,-0.595433453
+9,1848.83,-0.533798136,-0.529455775,-0.612762473,-0.80260441,-0.783866603,-0.011418306,-0.545650951
+10,1810.89,-0.510624727,-0.537774561,-0.743620063,-0.869503856,-0.808808869,-0.798077547,-0.711401604
+11,1769.14,-0.654814829,-0.541225414,-0.751471519,-0.965018144,-0.769614842,-0.465192048,-0.691222799