version 0.3

README.md

@@ -2,33 +2,33 @@
 
 Ádám T. Kocsis, John Alroy, Carl J. Reddin and Wolfgang Kiessling
 
-version 0.4
+version 0.3
 
-*07. 01. 2019.*
+*20. 09. 2018., initial commit date: 2018-08-29*
 
 ## About
 
 This repository contains all data and additional functions used in the Phanerozoic-scale examples and vignette for the paper describing the 'divDyn' R package. You can access the most recently updated report at
 
-https://github.com/divDyn/ddPhanero/blob/master/doc/dd_phanero.pdf
+https://github.com/adamkocsis/ddPhanero/blob/master/doc/dd_phanero.pdf
 
 
 This is not the development repository of the divDyn package. You can find that at 
 
-http://github.com/divDyn/r_package
+http://github.com/adamkocsis/divDyn
 
 
 ## Structure
 
 The repository is organized in the following way:
 
-* ``doc``: The main document
+* ``doc``: The main document in version-specific folders
   - *dd_phanero.pdf*: The report .pdf file.
   - *dd_phanero.Rmd*: The source rmarkdown file.
 
 * ``data``: All relevant data objects in binary .RData format. 
   * ``PaleoDB``: Downloaded data from the Paleobiology Database (http://paleobiodb.org) with their metadata.
-  * ``Stratigraphy``: Additional data that can be used to assign occurrences to stratigraphic stages.
+  * ``Stratigraphy``: Additional data that can be used to assign occurrences to stratigraphic stages, in version-specific folders.
 
 * ``export``: Tables and figures directly output by the scripts presented in ``scripts``. 
   - *first.pdf*, *onetrial.pdf*, *many.pdf*: Curves of richness.
@@ -39,9 +39,9 @@ The repository is organized in the following way:
     - *subs.ai*, *rates.pdf*, *subs.png*: Figure 1. The Adobe Illustrator file uses *first.pdf*, *onetrial.pdf*, *many.pdf* with links.
     - *rates.ai*, *rates.pdf*, *rates.png*: Figure 2. *sumRates.pdf* with panel labels. The Adobe Illustrator file uses *sumRates.pdf* with a link.
     - *conditionalTable.xlsx*: Table 2. MS Excel table that uses *pBin.csv* and *pStage.csv* to conditionally format *valBin.csv* and *valStage.csv*.
-* ``scripts`` contains all R scripts that are used in the analysis in version-specific folders. In these:
+* ``scripts`` contains all R scripts that are used in the analysis in version-specific folders.In these:
   - *yyyy-mm-dd_marineAnimals_ddPhanero.R*: Analysis script, more-or-less the same as the code presented in the same version .pdf file in the ``doc`` folder.
   - *phanDyn.R*: Functions used in the analyses.
-  * ``strat``: Folder of stratigraphy-correction scripts.
+  * ``strat``: Version-specific folders of stratigraphy-correction scripts.
     - *cambProcess.R*: for the Cambrian period.
     - *ordProcess.R*: for the Ordovician period.

data/PaleoDB/metadata_2019-01-03.txt → data/PaleoDB/metadata_2018-09-14.txt

@@ -4,13 +4,13 @@
 "License URL","http://creativecommons.org/licenses/by/4.0/"
 "Documentation URL","http://paleobiodb.org/data1.2/occs/list_doc.html"
 "Data URL","http://paleobiodb.org/data1.2/occs/list.csv?datainfo&rowcount&interval=Ediacaran,Holocene&show=class,classext,genus,subgenus,abund,coll,coords,loc,paleoloc,strat,stratext,lith,env,ref,crmod,timebins,timecompare"
-"Access Time","Thu 2019-01-03 22:56:39 GMT"
+"Access Time","Fri 2018-09-14 17:07:56 GMT"
 "Title","PBDB Data Service"
 "Parameters:"
 "","interval","Ediacaran,Holocene"
 "","timerule","major"
 "","taxon_status","all"
 "","show","class,classext,genus,subgenus,abund,coll,coords,loc,paleoloc,strat,stratext,lith,env,ref,crmod,timebins,timecompare"
-"Elapsed Time","139"
-"Records Found","1382625"
-"Records Returned","1382625"
+"Elapsed Time","144"
+"Records Found","1369299"
+"Records Returned","1369299"

export/0.3/pBin.csv

@@ -0,0 +1,19 @@
+"rawPC_10my";"rawC3t_10my";"rawGF_10my";"raw2f3_10my";"crPC_10my";"crC3t_10my";"crGF_10my";"cr2f3_10my";"sqsPC_10my";"sqsC3t_10my";"sqsGF_10my";"sqs2f3_10my"
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export/0.3/pStage.csv

@@ -0,0 +1,19 @@
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export/0.3/valBin.csv

@@ -0,0 +1,19 @@
+"rawPC_10my";"rawC3t_10my";"rawGF_10my";"raw2f3_10my";"crPC_10my";"crC3t_10my";"crGF_10my";"cr2f3_10my";"sqsPC_10my";"sqsC3t_10my";"sqsGF_10my";"sqs2f3_10my"
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export/0.3/valStage.csv

@@ -0,0 +1,19 @@
+"rawPC_stages";"rawC3t_stages";"rawGF_stages";"raw2f3_stages";"crPC_stages";"crC3t_stages";"crGF_stages";"cr2f3_stages";"sqsPC_stages";"sqsC3t_stages";"sqsGF_stages";"sqs2f3_stages"
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