- I had access to several datasets
- Master crab and env spreadsheet
- Temporal data spreadsheet
- jho correlation data spreadsheet
- anova spreadsheets sent to Beth
- crab size distribution
- Small differences in the various sources complicated reproducing the exact results in the original draft paper. So that results are consistent, I started with the Master spreadsheet, pulled those data into R and cleaned that dataset
- Need to:
- move master spreadsheet to data/raw.
- move temporal data spreadhseet to data/raw
- Data cleaning is in R/data_prep_master.R, R/data_prep_temporal.R, and R/data_prep_size.R
- need to update Readme with this.
- Cleaned output csv that is basis for all analysis is data/crab_data.csv
- burrows mp in jho correlations, and mp only in master have messed up burrow counts.
- Given issues above with data, correlations re-done with master data
- slight differences in original source data for anova vs corr
- Also, focus on signficance dropped and all correlations reported in figure.
- correlations are calculated in R/crab_calc_correlation.R
- correlation, p, and n are included in results/crab_correlations.csv
- Correlation figure calced in R/corr_fig.R
- I checked results in crab_correlations against what was reported in Table 4.
All check out, except burrow_density, shear_strength, mp.
- burrow counts messed up for burrow density in mp in the jho correlation data and in the master mp only tab. Looks good in master data and in R version of master data. Value recorded in Table 4 is incorrect. It is not 0.49, should be -0.088.
- Need to work on figure: Color scheme, sizes aren't cutting it.
- Filtered out pairs with less than 10 samples
- Keep main anovas
- was able to reproduce Table 2. with exception of carcinus. Slight diferences in the F statistic. Got this with master spreadsheet as source and also with anova spreadsheet as source. Need to update values in Table 2.
- Drop multiple comparisons and Table 3
- small sample size for each comparison (only 10) and within habitats are pseudo-replicates.
- Not sure what it tells us
- yep, lots of differences between/within marsh and habitats, but I don't find that very interesting. The big picture diff's are more interesting.
- anovas re-run in R/anovas.R
- anova results output in results/anova_results.csv
- Temporal data was reorganized by hand and is in sheet 2 in data/raw/jho_temporal_data_summarized.xls
- Data read in an prepped in R/data_prep_temporal.R
- Temporal figures built in R/temporal_fig.R
- Temporal anlaysis in R/temporal_analysis.R
- I would like to drop the water temperature plot. It is flat, currently on a plot with two y-axis, and doesn't add much to the story (IMO).
- t-tests and values in burrow_density bar plots are not the same as what I get. Need to figure out why the difference.
- All regressions match up
- output in
- Raw data in data/raw/species size histograms.xls and brrow data for histrograms.xls
- data read in and prepped in R/data_prep_size.R
- Size distribution figure in R/size_fig.R