-
{% for post in site.tags["beech"] %}
{{ post.title }} ({{ post.date | date_to_string }})
{{ post.description }} {% endfor %}
In davan690/beech-publication-wr: Small mammal dynamics in NZ beech forests
Status {#status}
TO do
Points to check
Change food avalability where approarate:
- available seed is raw data collected from seedtraps
- Seedfall $(Seed_{j,t})$ = accumulative seedfall.
- intake rate to $(S_{j,t})$ = seedfall converted to a rate conversion
Results section
- MAKE plots and figures DYNAMIC
-
[ ] This is dynamic nowish (Feb2020)
-
Wrong numbers... in anovas..
- [ ] Different numbers to wendy?? Check why?
Seed
- [x] Split this by valley because stoats dont effect seedfall so doesnt matter about control was comment.
References?
Sorting references has been much hard than I expected when there are multiple types of software to use and different ways to link them.
The core problems I have needed to solve are:
-
Storing pdfs locally and working on them.
-
Mendeley works well for looking and searching through pdfs and was the reason I switched from EndNote (that my supervisors were using at the time) to Mendeley.
-
Convert references attached to pdfs in reference manager into a bibtex file so that citr and refmanageR can read these.
-
Zotero because it has good extentions that can turn bib references into bibtex structure for R packages that use a variation on the .bib structure in R.
-
Convert stable referencing in .Rmd to other document types and structures.
-
This has now become hard to understand how this is all working so I have had to layout a software path (and maybe future Docker image) to ensure that the refences converge and the errors are solvable (or at least I can work out where they come from)
Editor??
To work with .bib files (to find errors to begin with) it is much nice to have some code snippit support (highlighting syntax). These are the options for .bib file editors:
- [ ]
> Sys.getenv()
ALLUSERSPROFILE C:\ProgramData
APPDATA C:\Users\s435389\AppData\Roaming
CLICOLOR_FORCE 1
CommonProgramFiles C:\Program Files\Common Files
CommonProgramFiles(x86) C:\Program Files (x86)\Common Files
CommonProgramW6432 C:\Program Files\Common Files
COMPUTERNAME 6MLNYY2
ComSpec C:\WINDOWS\system32\cmd.exe
DISPLAY :0
DriverData C:\Windows\System32\Drivers\DriverData
FPS_BROWSER_APP_PROFILE_STRING
Internet Explorer
FPS_BROWSER_USER_PROFILE_STRING
Default
GFORTRAN_STDERR_UNIT -1
GFORTRAN_STDOUT_UNIT -1
HOME \\Stafffiles.win.canberra.edu.au\Homes$\s435389\My Documents
HOMEDRIVE H:
HOMEPATH \
HOMESHARE \\Stafffiles.win.canberra.edu.au\Homes$\s435389
LOCALAPPDATA C:\Users\s435389\AppData\Local
LOGONSERVER \\KAYSERI
MPLENGINE tkAgg
MSYS2_ENV_CONV_EXCL R_ARCH
NUMBER_OF_PROCESSORS 8
OneDrive C:\Users\s435389\OneDrive - University of Canberra
OneDriveCommercial C:\Users\s435389\OneDrive - University of Canberra
OS Windows_NT
PATH \\Stafffiles.win.canberra.edu.au\Homes$\s435389\My
Documents\R\R-3.6.2\bin\x64;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Users\s435389\AppData\Local\Microsoft\WindowsApps;C:\Users\s435389\AppData\Local\Programs\Microsoft
VS
Code\bin;C:\Users\s435389\AppData\Local\Programs\Git\cmd;C:\Users\s435389\AppData\Local\Pandoc\
PATHEXT .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC
PROCESSOR_ARCHITECTURE AMD64
PROCESSOR_IDENTIFIER Intel64 Family 6 Model 142 Stepping 12, GenuineIntel
PROCESSOR_LEVEL 6
PROCESSOR_REVISION 8e0c
ProgramData C:\ProgramData
ProgramFiles C:\Program Files
ProgramFiles(x86) C:\Program Files (x86)
ProgramW6432 C:\Program Files
PSModulePath C:\Program
Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules
PUBLIC C:\Users\Public
QT_D3DCREATE_MULTITHREADED 1
R_ARCH /x64
R_COMPILED_BY gcc 4.9.3
R_DOC_DIR //Stafffiles.win.canberra.edu.au/Homes$/s435389/My
Documents/R/R-3.6.2/doc
R_HOME //Stafffiles.win.canberra.edu.au/Homes$/s435389/My
Documents/R/R-3.6.2
R_LIBS_USER //Stafffiles.win.canberra.edu.au/Homes$/s435389/My
Documents/R/win-library/3.6
R_USER //Stafffiles.win.canberra.edu.au/Homes$/s435389/My Documents
RMARKDOWN_MATHJAX_PATH C:/Program Files/RStudio/resources/mathjax-26
RS_LOCAL_PEER \\.\pipe\25236-rsession
RS_RPOSTBACK_PATH C:/Program Files/RStudio/bin/rpostback
RS_SHARED_SECRET 63341846741
RSTUDIO 1
RSTUDIO_CONSOLE_COLOR 256
RSTUDIO_CONSOLE_WIDTH 80
RSTUDIO_MSYS_SSH C:/Program Files/RStudio/bin/msys-ssh-1000-18
RSTUDIO_PANDOC //Stafffiles.win.canberra.edu.au/Homes$/s435389/My
Documents/rstudio-pandoc
RSTUDIO_SESSION_PORT 25236
RSTUDIO_USER_IDENTITY s435389
RSTUDIO_WINUTILS C:/Program Files/RStudio/bin/winutils
SESSIONNAME Console
SystemDrive C:
SystemRoot C:\WINDOWS
TEMP C:\Users\s435389\AppData\Local\Temp
TERM xterm-256color
TMP C:\Users\s435389\AppData\Local\Temp
UATDATA C:\WINDOWS\CCM\UATData\D9F8C395-CAB8-491d-B8AC-179A1FE1BE77
USERDNSDOMAIN UCSTAFF.WIN.CANBERRA.EDU.AU
USERDOMAIN UCSTAFF
USERDOMAIN_ROAMINGPROFILE UCSTAFF
USERNAME s435389
USERPROFILE C:\Users\s435389
windir C:\WINDOWS
if(!knitr:::is_html_output())
{
options("width"=56)
knitr::opts_chunk$set(tidy.opts=list(width.cutoff=56, indent = 2), tidy = TRUE)
knitr::opts_chunk$set(fig.pos = 'H')
}
All other data and resources to render project from raw data (copied from my private GIT repository) can be found on dropbox and online here and are currently at a draft quality as I build my phd thesis.
| GIThub Document | Overview | Status |
| ------------------------------------------------------------ | ------------------------------------------------------------ | ------------------------------------------------------------ |
| Pre-registration | not needed | NA |
| [Current draft] | As I am developing this approach to reproducible research this draft will look better and better. | Online here |
| Online link here | Dropbox is currently the backup for this as I get better at build gitbooks using RStudio and bookdown. This is currently only accessible if you have the private link that I will have sent through email. | Dropbox link here |
| [Abstract] | Always last..ish a overview is online here | additional resources for collaborators here |
| [Style sheet] | A way of recording semantic choices for this research project. | Dropbox Link here |
| [Introduction] | Currently within the draft manuscript | Dropbox Link here; Online link here |
| [Methods] | manuscript methods can be found here and other extensions below | Online link here |
| | This report takes the raw CR data and generates simple average plots of beech seed, mice and rat abundances | Model wrangling |
| | To estimate the differences between Prediction A and B | Simple ANOVAs |
| | To estimate the differences between Prediction C, D, and E | Model outputs |
| | Simulation model | Full simulation document here |
| [Results] | The figures can be found here | Online link here |
| [Discussion] | | Online link here |
| Bayesian methods | | Dropbox |
| Figures | | Dropbox |
| Functional response | | Dropbox |
| Mapping | coming online soon | Dropbox |
| [References] | | Dropbox |
| [Appendix] | | Dropbox |
| Extra resources | | Dropbox |
| | | |
| | | |
{%- assign gh-user = "davan690" -%}
{%- assign gh-project = "davan690/beech-forest-dynamics" -%}
{{- gh-project -}}
The beginnings of a interactive PhD thesis using Markdown.
My notes
Follow up on these comments:
#We did this by selecting only non-mast years over the duration of our study.
#---------------
# You have a before-after design (ANCOVA?)
# how did your analysis account for this.
# And what about rats?
seed estimation
# This needs a clearer explanation to step the reader through what you did.
And posts so far to help with development below:
davan690/beech-publication-wr documentation built on March 29, 2020, 11:09 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Status {#status}
TO do
Points to check
Change food avalability where approarate: - available seed is raw data collected from seedtraps - Seedfall $(Seed_{j,t})$ = accumulative seedfall. - intake rate to $(S_{j,t})$ = seedfall converted to a rate conversion
Results section
- MAKE plots and figures DYNAMIC
-
[ ] This is dynamic nowish (Feb2020)
-
Wrong numbers... in anovas..
- [ ] Different numbers to wendy?? Check why?
Seed - [x] Split this by valley because stoats dont effect seedfall so doesnt matter about control was comment.
References?
Sorting references has been much hard than I expected when there are multiple types of software to use and different ways to link them.
The core problems I have needed to solve are:
-
Storing pdfs locally and working on them.
-
Mendeley works well for looking and searching through pdfs and was the reason I switched from EndNote (that my supervisors were using at the time) to Mendeley.
-
Convert references attached to pdfs in reference manager into a
bibtexfile so thatcitrandrefmanageRcan read these. -
Zotero because it has good extentions that can turn bib references into bibtex structure for R packages that use a variation on the
.bibstructure in R. -
Convert stable referencing in
.Rmdto other document types and structures. -
This has now become hard to understand how this is all working so I have had to layout a software path (and maybe future Docker image) to ensure that the refences converge and the errors are solvable (or at least I can work out where they come from)
Editor??
To work with .bib files (to find errors to begin with) it is much nice to have some code snippit support (highlighting syntax). These are the options for .bib file editors:
- [ ]
> Sys.getenv() ALLUSERSPROFILE C:\ProgramData APPDATA C:\Users\s435389\AppData\Roaming CLICOLOR_FORCE 1 CommonProgramFiles C:\Program Files\Common Files CommonProgramFiles(x86) C:\Program Files (x86)\Common Files CommonProgramW6432 C:\Program Files\Common Files COMPUTERNAME 6MLNYY2 ComSpec C:\WINDOWS\system32\cmd.exe DISPLAY :0 DriverData C:\Windows\System32\Drivers\DriverData FPS_BROWSER_APP_PROFILE_STRING Internet Explorer FPS_BROWSER_USER_PROFILE_STRING Default GFORTRAN_STDERR_UNIT -1 GFORTRAN_STDOUT_UNIT -1 HOME \\Stafffiles.win.canberra.edu.au\Homes$\s435389\My Documents HOMEDRIVE H: HOMEPATH \ HOMESHARE \\Stafffiles.win.canberra.edu.au\Homes$\s435389 LOCALAPPDATA C:\Users\s435389\AppData\Local LOGONSERVER \\KAYSERI MPLENGINE tkAgg MSYS2_ENV_CONV_EXCL R_ARCH NUMBER_OF_PROCESSORS 8 OneDrive C:\Users\s435389\OneDrive - University of Canberra OneDriveCommercial C:\Users\s435389\OneDrive - University of Canberra OS Windows_NT PATH \\Stafffiles.win.canberra.edu.au\Homes$\s435389\My Documents\R\R-3.6.2\bin\x64;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Users\s435389\AppData\Local\Microsoft\WindowsApps;C:\Users\s435389\AppData\Local\Programs\Microsoft VS Code\bin;C:\Users\s435389\AppData\Local\Programs\Git\cmd;C:\Users\s435389\AppData\Local\Pandoc\ PATHEXT .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC PROCESSOR_ARCHITECTURE AMD64 PROCESSOR_IDENTIFIER Intel64 Family 6 Model 142 Stepping 12, GenuineIntel PROCESSOR_LEVEL 6 PROCESSOR_REVISION 8e0c ProgramData C:\ProgramData ProgramFiles C:\Program Files ProgramFiles(x86) C:\Program Files (x86) ProgramW6432 C:\Program Files PSModulePath C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules PUBLIC C:\Users\Public QT_D3DCREATE_MULTITHREADED 1 R_ARCH /x64 R_COMPILED_BY gcc 4.9.3 R_DOC_DIR //Stafffiles.win.canberra.edu.au/Homes$/s435389/My Documents/R/R-3.6.2/doc R_HOME //Stafffiles.win.canberra.edu.au/Homes$/s435389/My Documents/R/R-3.6.2 R_LIBS_USER //Stafffiles.win.canberra.edu.au/Homes$/s435389/My Documents/R/win-library/3.6 R_USER //Stafffiles.win.canberra.edu.au/Homes$/s435389/My Documents RMARKDOWN_MATHJAX_PATH C:/Program Files/RStudio/resources/mathjax-26 RS_LOCAL_PEER \\.\pipe\25236-rsession RS_RPOSTBACK_PATH C:/Program Files/RStudio/bin/rpostback RS_SHARED_SECRET 63341846741 RSTUDIO 1 RSTUDIO_CONSOLE_COLOR 256 RSTUDIO_CONSOLE_WIDTH 80 RSTUDIO_MSYS_SSH C:/Program Files/RStudio/bin/msys-ssh-1000-18 RSTUDIO_PANDOC //Stafffiles.win.canberra.edu.au/Homes$/s435389/My Documents/rstudio-pandoc RSTUDIO_SESSION_PORT 25236 RSTUDIO_USER_IDENTITY s435389 RSTUDIO_WINUTILS C:/Program Files/RStudio/bin/winutils SESSIONNAME Console SystemDrive C: SystemRoot C:\WINDOWS TEMP C:\Users\s435389\AppData\Local\Temp TERM xterm-256color TMP C:\Users\s435389\AppData\Local\Temp UATDATA C:\WINDOWS\CCM\UATData\D9F8C395-CAB8-491d-B8AC-179A1FE1BE77 USERDNSDOMAIN UCSTAFF.WIN.CANBERRA.EDU.AU USERDOMAIN UCSTAFF USERDOMAIN_ROAMINGPROFILE UCSTAFF USERNAME s435389 USERPROFILE C:\Users\s435389 windir C:\WINDOWS
if(!knitr:::is_html_output()) { options("width"=56) knitr::opts_chunk$set(tidy.opts=list(width.cutoff=56, indent = 2), tidy = TRUE) knitr::opts_chunk$set(fig.pos = 'H') }
All other data and resources to render project from raw data (copied from my private GIT repository) can be found on dropbox and online here and are currently at a draft quality as I build my phd thesis.
| GIThub Document | Overview | Status |
| ------------------------------------------------------------ | ------------------------------------------------------------ | ------------------------------------------------------------ |
| Pre-registration | not needed | NA |
| [Current draft] | As I am developing this approach to reproducible research this draft will look better and better. | Online here |
| Online link here | Dropbox is currently the backup for this as I get better at build gitbooks using RStudio and bookdown. This is currently only accessible if you have the private link that I will have sent through email. | Dropbox link here |
| [Abstract] | Always last..ish a overview is online here | additional resources for collaborators here |
| [Style sheet] | A way of recording semantic choices for this research project. | Dropbox Link here |
| [Introduction] | Currently within the draft manuscript | Dropbox Link here; Online link here |
| [Methods] | manuscript methods can be found here and other extensions below | Online link here |
| | This report takes the raw CR data and generates simple average plots of beech seed, mice and rat abundances | Model wrangling |
| | To estimate the differences between Prediction A and B | Simple ANOVAs |
| | To estimate the differences between Prediction C, D, and E | Model outputs |
| | Simulation model | Full simulation document here |
| [Results] | The figures can be found here | Online link here |
| [Discussion] | | Online link here |
| Bayesian methods | | Dropbox |
| Figures | | Dropbox |
| Functional response | | Dropbox |
| Mapping | coming online soon | Dropbox |
| [References] | | Dropbox |
| [Appendix] | | Dropbox |
| Extra resources | | Dropbox |
| | | |
| | | |
{%- assign gh-user = "davan690" -%}
{%- assign gh-project = "davan690/beech-forest-dynamics" -%}
{{- gh-project -}}
The beginnings of a interactive PhD thesis using Markdown.
My notes
Follow up on these comments:
#We did this by selecting only non-mast years over the duration of our study. #--------------- # You have a before-after design (ANCOVA?) # how did your analysis account for this. # And what about rats?
seed estimation
# This needs a clearer explanation to step the reader through what you did.
And posts so far to help with development below:
{{ post.description }} {% endfor %}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.