to-do list - Githubissues

martinig commented 6 months ago

@martinig

[x] finalize ISBE abstract
[x] submit ISBE travel grant
[x] create taxonomic tree with phylopic images
[x] save the images for attribution
[x] add GPS points to each paper
[x] check five of each confirmation bias types for agreement
[x] make country map with points at each location

[x] check for mistakes in species columns

df %>% as_tibble() %>% count(speciesID) %>% nrow() #148 species     
df %>% as_tibble() %>% count(common_name) %>% nrow() #150 species       
df %>% as_tibble() %>% count(species) %>% nrow() #147 species       
df %>% as_tibble() %>% count(species_cleaned) %>% nrow() #144 species

[ ] export rayyan included/excluded full-texts and clean CSV
[x] supplemental materials (methods section)
[ ] methods: Literature searches and study selection
[ ] methods: Eligibility criteria
[ ] methods: Data extraction and effect size calculations
[ ] methods: Meta-analysis and meta-regressions
[ ] methods: Sensitivity analyses and publication bias
[ ] methods: Deviations from registration
[ ] introduction
[ ] results: data summary
[ ] results: meta-analysis
[ ] results: meta-regression
[ ] results: publication bias
[ ] figures
[ ] tables
[ ] discussion
[ ] abstract
[x] keywords

martinig commented 2 months ago

@Spenser

[x] author emails for: Spatial organization and recruitment of lynx (Lynx lynx) in a re-introduced population in the Swiss Jura Mountains
[x] author emails for: Dispersal movements and survival rates of juvenile Mexican Spotted Owls in Northern Arizona
[x] author emails for: Proximate and ultimate causes of dispersal in the Iberian lynx Lynx pardinus
[x] author emails for: Emigration to new habitats by voles: The cost of dispersal paradox
[ ] add column for whether paper stated dispersal was costly in abstract/introduction (confirmation bias)
[x] score rows 1-100
[x] score rows 101-200
[ ] score rows 201-300
[ ] score rows 301-400
[ ] score rows 401-500
[ ] score rows 501-600
[ ] score rows 601-692
[x] flag which studies might be repeats of each other (e.g., Germain et al. 2017a and 2017b) - this is also included in Rayyan under "exclusion" reasons
[ ] flag studies that use mark recapture methods (i.e., possible apparent survival)
[ ] add papers in github for april to check
[ ] also flag in rayyan
[x] cross-checking records L316-328
[x] cross-checking records L446-449
[x] cross-checking records L458-459
[x] cross-checking records L463-464
[x] cross-checking records L484-489
[x] cross-checking records L555-557
[x] Aim 1 in rayyan mark "Correlates and consequences of breeding dispersal in a migratory songbird" as excluded
[x] add "label" for "overlapping population [species]" to studies that are using datasets that are have some degree of overlap for included studies only
[x] cross check Greenwood et al. 1979 and fill in red blanks
[x] cross check Pusey & Packer 1987 and fill in red blanks
[x] fill in red blanks for Hines 1986

martinig commented 2 months ago

@itchyshin

[x] cross-checking records (to be assigned)
[x] quarto - table
[x] quarto - uni-mod
[x] quarto - mulit-mod
[x] quarto - run
[x] interactions - sex * species_class
[x] interactions -sex * fitness_higher_level
[x] interactions - sex * whose_fitness
[x] interactions - sex * dispersal_type
[x] how to do sanity checks for proportion_method2 and percent_method2 (with SD)
sanity checks - d/mean
[x] #Krohne & Burgin 1987 (line 41) -> had to convert SE to SD using an estimated n -> we concluded this is likely SD
[x] #Engh et al. 2002 (line 242) -> had to convert SE to SD -> we concluded this is OK
[x] #Pärn et al. 2009 (line 301-302) -> had to convert SE to SD -> we fixed the typo (on our end)
[x] #Cotto et al. 2015 (line 383-384) -> They measured fitness as reproductive effort (realized value relative to what would be expected given body size). -> we concluded this is okay because of how they measure fitness
[x] #Green & Hatchwell 2018 (line 465) -> authors calculated this and sent us the mean and SD, all other calculations aren't flagged. Note this is indirect fitness, so this spread isn't crazy. -> we concluded this is okay
[x] #Qu et al. 2018 (line 458-459) -> extracted from figure using an estimated n -> we concluded this is okay
[x] #Spence-Jones et al. 2021 (line 662-663) -> data extracted from figure -> we concluded this is ok
sanity checks - sd/proportion or sd/percentage below 0.05 or above 4
[x] #Small et al. 1993 (line 141-144) -> estimated n and converted 95% CIs to SD (table 2 page 2023) -> keep the composite because sample size overall is
[x] #Orell et al. 1999 (line 544 & 549) -> converted SE to SD (text page 290) -> we concluded this is okay
[x] #Spence-Jones et al. 2021 (line 661) -> converted SE to SD (text page 241) -> we concluded this is okay
[x] #Brown et al. 2008 (line 293-294) -> extracted from figure (figure 1 page 8) -> we concluded this is okay
[x] #Devillard & Bray 2009 (line 308-309) -> extracted from figure (figure 1 page 2908) -> we concluded this is okay
[x] figure out why code won't run in analysis.qmd (line 573)
[x] fix effect size function needs mending - it is causing errors and problems are now coming up

martinig commented 2 months ago

@mlagisz

[x] cross check records that are marked as "yes" in the "needs_another_opinion" column (link to dataset)

martinig / Fitness-and-dispersal-MA

to-do list #16